From e849fb1b1ca6a242b7ce54659b98884062bee11b Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 14 Jun 2021 14:48:38 +0200 Subject: [PATCH 001/120] Minor PEP8 cleanup --- c3d.py | 2 +- test/base.py | 1 + test/zipload.py | 4 ++-- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/c3d.py b/c3d.py index 61dac5d..11b17b9 100644 --- a/c3d.py +++ b/c3d.py @@ -1367,7 +1367,7 @@ def proc_type(self): Get the processory type associated with the data format in the file. """ processor_type = ['PROCESSOR_INTEL', 'PROCESSOR_DEC', 'PROCESSOR_MIPS'] - return processor_type[self.processor-PROCESSOR_INTEL] + return processor_type[self.processor - PROCESSOR_INTEL] class Writer(Manager): diff --git a/test/base.py b/test/base.py index b409c22..afc3ab5 100644 --- a/test/base.py +++ b/test/base.py @@ -4,6 +4,7 @@ VERBOSE = False + class Base(unittest.TestCase): def setUp(self): Zipload.download() diff --git a/test/zipload.py b/test/zipload.py index 0bf5482..3e32f00 100644 --- a/test/zipload.py +++ b/test/zipload.py @@ -37,10 +37,10 @@ def extract(zf): out_path = os.path.join(TEMP, os.path.basename(zf)[:-4]) zip = zipfile.ZipFile(os.path.join(TEMP, zf)) + # Loop equivalent to zip.extractall(out_path) but avoids overwriting files for zf in zip.namelist(): - #zip.extractall(out_path) but avoids overwriting files fpath = os.path.join(out_path, zf) - # If file already exist, don' extract + # If file already exist, don't extract if not os.path.isfile(fpath) and not os.path.isdir(fpath): print('Extracted:', fpath) zip.extract(zf, path=out_path) From 33539ecf1dc28de05d52a9b3260d39793bb6694d Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 17:51:54 +0200 Subject: [PATCH 002/120] check_metadata() -> _check_metadata() processor_convert() -> _processor_convert() --- c3d.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/c3d.py b/c3d.py index 11b17b9..d813887 100644 --- a/c3d.py +++ b/c3d.py @@ -342,7 +342,7 @@ def read(self, handle, fmt=BINARY_FORMAT_READ): # Check long event key self.long_event_labels = self.long_event_labels == 0x3039 - def processor_convert(self, dtypes, handle): + def _processor_convert(self, dtypes, handle): ''' Function interpreting the header once processor type has been determined. ''' @@ -825,7 +825,7 @@ def __init__(self, header=None): self.header = header or Header() self.groups = {} - def check_metadata(self): + def _check_metadata(self): '''Ensure that the metadata in our file is self-consistent.''' assert self.header.point_count == self.point_used, ( 'inconsistent point count! {} header != {} POINT:USED'.format( @@ -1137,7 +1137,7 @@ def seek_param_section_header(): _, _, parameter_blocks, self.processor = struct.unpack('BBBB', buf) self.dtypes = DataTypes(self.processor) # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) - self.header.processor_convert(self.dtypes, handle) + self.header._processor_convert(self.dtypes, handle) # Restart reading the parameter header after parsing processor type buf = seek_param_section_header() @@ -1184,7 +1184,7 @@ def seek_param_section_header(): else: self.add_group(group_id, name, desc) - self.check_metadata() + self._check_metadata() def read_frames(self, copy=True): '''Iterate over the data frames from our C3D file handle. @@ -1440,7 +1440,7 @@ def _write_metadata(self, handle): Write metadata and C3D motion frames to the given file handle. The writer does not close the handle. ''' - self.check_metadata() + self._check_metadata() # header self.header.write(handle) From 23e9f76d262ddfb35735ebb08bacb9d61eadfde2 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 17:52:53 +0200 Subject: [PATCH 003/120] Reader.dtype -> Reader._dtype --- c3d.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/c3d.py b/c3d.py index d813887..54ce83e 100644 --- a/c3d.py +++ b/c3d.py @@ -1135,9 +1135,9 @@ def seek_param_section_header(): # Begin by reading the processor type: buf = seek_param_section_header() _, _, parameter_blocks, self.processor = struct.unpack('BBBB', buf) - self.dtypes = DataTypes(self.processor) + self._dtypes = DataTypes(self.processor) # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) - self.header._processor_convert(self.dtypes, handle) + self.header._processor_convert(self._dtypes, handle) # Restart reading the parameter header after parsing processor type buf = seek_param_section_header() @@ -1150,7 +1150,7 @@ def seek_param_section_header(): if group_id == 0 or chars_in_name == 0: # we've reached the end of the parameter section. break - name = self.dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper() + name = self._dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper() # Read the byte segment associated with the parameter and create a # separate binary stream object from the data. @@ -1167,7 +1167,7 @@ def seek_param_section_header(): # we've just started reading a parameter. if its group doesn't # exist, create a blank one. add the parameter to the group. self.groups.setdefault( - group_id, Group()).add_param(name, self.dtypes, handle=buf) + group_id, Group()).add_param(name, self._dtypes, handle=buf) else: # we've just started reading a group. if a group with the # appropriate id exists already (because we've already created @@ -1223,28 +1223,28 @@ def read_frames(self, copy=True): if is_float: point_word_bytes = 4 - point_dtype = self.dtypes.uint32 + point_dtype = self._dtypes.uint32 else: point_word_bytes = 2 - point_dtype = self.dtypes.int16 + point_dtype = self._dtypes.int16 points = np.zeros((self.point_used, 5), np.float32) # TODO: handle ANALOG:BITS parameter here! p = self.get('ANALOG:FORMAT') analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED' if is_float: - analog_dtype = self.dtypes.float32 + analog_dtype = self._dtypes.float32 analog_word_bytes = 4 elif analog_unsigned: # Note*: Floating point is 'always' defined for both analog and point data, according to the standard. - analog_dtype = self.dtypes.uint16 + analog_dtype = self._dtypes.uint16 analog_word_bytes = 2 # Verify BITS parameter for analog p = self.get('ANALOG:BITS') if p and p._as_integer_value / 8 != analog_word_bytes: raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value)) else: - analog_dtype = self.dtypes.int16 + analog_dtype = self._dtypes.int16 analog_word_bytes = 2 analog = np.array([], float) @@ -1295,7 +1295,7 @@ def read_frames(self, copy=True): else: # If IEEE or MIPS: # Re-read the raw byte representation directly points[:, :4] = np.frombuffer(raw_bytes, - dtype=self.dtypes.float32, + dtype=self._dtypes.float32, count=N_point).reshape((int(self.point_used), 4)) # Parse the camera-observed bits and residuals. @@ -1322,7 +1322,7 @@ def read_frames(self, copy=True): # Parse last 16-bit word as two 8-bit words valid = raw[:, 3] > -1 points[~valid, 3:5] = -1 - c = raw[valid, 3].astype(self.dtypes.uint16) + c = raw[valid, 3].astype(self._dtypes.uint16) # Convert coordinate data # fourth value is floating-point (scaled) error estimate (residual) From 1cf5b503eef2a8cd1aabad0833c58f548a5eba67 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 17:59:33 +0200 Subject: [PATCH 004/120] Manager.header -> Manager._header + @property Manager.header --- c3d.py | 65 +++++++++++++++++++++++++++++++--------------------------- 1 file changed, 35 insertions(+), 30 deletions(-) diff --git a/c3d.py b/c3d.py index 54ce83e..e03cb9a 100644 --- a/c3d.py +++ b/c3d.py @@ -822,26 +822,31 @@ class Manager(object): def __init__(self, header=None): '''Set up a new Manager with a Header.''' - self.header = header or Header() + self._header = header or Header() self.groups = {} + + @property + def header(self): + return self._header + def _check_metadata(self): '''Ensure that the metadata in our file is self-consistent.''' - assert self.header.point_count == self.point_used, ( + assert self._header.point_count == self.point_used, ( 'inconsistent point count! {} header != {} POINT:USED'.format( - self.header.point_count, + self._header.point_count, self.point_used, )) - assert self.header.scale_factor == self.point_scale, ( + assert self._header.scale_factor == self.point_scale, ( 'inconsistent scale factor! {} header != {} POINT:SCALE'.format( - self.header.scale_factor, + self._header.scale_factor, self.point_scale, )) - assert self.header.frame_rate == self.point_rate, ( + assert self._header.frame_rate == self.point_rate, ( 'inconsistent frame rate! {} header != {} POINT:RATE'.format( - self.header.frame_rate, + self._header.frame_rate, self.point_rate, )) @@ -849,26 +854,26 @@ def _check_metadata(self): ratio = self.analog_rate / self.point_rate else: ratio = 0 - assert self.header.analog_per_frame == ratio, ( + assert self._header.analog_per_frame == ratio, ( 'inconsistent analog rate! {} header != {} analog-fps / {} point-fps'.format( - self.header.analog_per_frame, + self._header.analog_per_frame, self.analog_rate, self.point_rate, )) - count = self.analog_used * self.header.analog_per_frame - assert self.header.analog_count == count, ( + count = self.analog_used * self._header.analog_per_frame + assert self._header.analog_count == count, ( 'inconsistent analog count! {} header != {} analog used * {} per-frame'.format( - self.header.analog_count, + self._header.analog_count, self.analog_used, - self.header.analog_per_frame, + self._header.analog_per_frame, )) try: start = self.get_uint16('POINT:DATA_START') - if self.header.data_block != start: + if self._header.data_block != start: warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( - self.header.data_block, start)) + self._header.data_block, start)) except AttributeError: warnings.warn('''no pointer available in POINT:DATA_START indicating the start of the data block, using header pointer as fallback''') @@ -1128,7 +1133,7 @@ def __init__(self, handle): def seek_param_section_header(): ''' Seek to and read the first 4 byte of the parameter header section ''' - self._handle.seek((self.header.parameter_block - 1) * 512) + self._handle.seek((self._header.parameter_block - 1) * 512) # metadata header return self._handle.read(4) @@ -1137,7 +1142,7 @@ def seek_param_section_header(): _, _, parameter_blocks, self.processor = struct.unpack('BBBB', buf) self._dtypes = DataTypes(self.processor) # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) - self.header._processor_convert(self._dtypes, handle) + self._header._processor_convert(self._dtypes, handle) # Restart reading the parameter header after parsing processor type buf = seek_param_section_header() @@ -1264,7 +1269,7 @@ def read_frames(self, copy=True): gen_scale = param.float_value # Seek to the start point of the data blocks - self._handle.seek((self.header.data_block - 1) * 512) + self._handle.seek((self._header.data_block - 1) * 512) # Number of values (words) read in regard to POINT/ANALOG data N_point = 4 * self.point_used N_analog = self.analog_used * self.analog_per_frame @@ -1442,12 +1447,12 @@ def _write_metadata(self, handle): ''' self._check_metadata() - # header - self.header.write(handle) + # Header + self._header.write(handle) self._pad_block(handle) assert handle.tell() == 512 - # groups + # Groups handle.write(struct.pack( 'BBBB', 0, 0, self.parameter_blocks(), PROCESSOR_INTEL)) id_groups = sorted( @@ -1455,7 +1460,7 @@ def _write_metadata(self, handle): for group_id, group in id_groups: group.write(group_id, handle) - # padding + # Padding self._pad_block(handle) while handle.tell() != 512 * (self.header.data_block - 1): handle.write(b'\x00' * 512) @@ -1469,7 +1474,7 @@ def _write_frames(self, handle): Write metadata and C3D motion frames to the given file handle. The writer does not close the handle. ''' - assert handle.tell() == 512 * (self.header.data_block - 1) + assert handle.tell() == 512 * (self._header.data_block - 1) scale = abs(self.point_scale) is_float = self.point_scale < 0 if is_float: @@ -1573,13 +1578,13 @@ def add_empty_array(name, desc, bpe): blocks = self.parameter_blocks() self.get('POINT:DATA_START').bytes = struct.pack(' Date: Sun, 27 Jun 2021 18:02:46 +0200 Subject: [PATCH 005/120] Header property descriptor --- c3d.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/c3d.py b/c3d.py index e03cb9a..ca2bd37 100644 --- a/c3d.py +++ b/c3d.py @@ -824,12 +824,12 @@ def __init__(self, header=None): '''Set up a new Manager with a Header.''' self._header = header or Header() self.groups = {} - + @property def header(self): + ''' Access the parsed c3d header. ''' return self._header - def _check_metadata(self): '''Ensure that the metadata in our file is self-consistent.''' assert self._header.point_count == self.point_used, ( From 5f43a05023ed790fb51bccc6f5c35d5e580e9763 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 19:43:13 +0200 Subject: [PATCH 006/120] Manager.group -> Manager._group + Manager.group_items + Manager.group_listed --- c3d.py | 46 +++++++++++++++++++++++++++++++------------- scripts/c3d-metadata | 9 ++++----- 2 files changed, 37 insertions(+), 18 deletions(-) diff --git a/c3d.py b/c3d.py index ca2bd37..51eb2d3 100644 --- a/c3d.py +++ b/c3d.py @@ -823,13 +823,35 @@ class Manager(object): def __init__(self, header=None): '''Set up a new Manager with a Header.''' self._header = header or Header() - self.groups = {} + self._groups = {} @property def header(self): ''' Access the parsed c3d header. ''' return self._header + def group(self, key): + ''' Access a paramater group from a group key. + + Attributes + ---------- + key : int or str + Index or name for the parameter group. + ''' + return self._groups[key] + + @property + def group_items(self): + ''' Acquire iterable over group parameter pairs (str key, group). + ''' + return ((k, v) for k, v in self._groups if isinstance(k, str)) + + @property + def group_listed(self): + ''' Acquire iterable over sorted group parameter pairs (int key, group). + ''' + return sorted((i, g) for i, g in self._groups if isinstance(i, int)) + def _check_metadata(self): '''Ensure that the metadata in our file is self-consistent.''' assert self._header.point_count == self.point_used, ( @@ -914,12 +936,12 @@ def add_group(self, group_id, name, desc): KeyError If a group with a duplicate ID or name already exists. ''' - if group_id in self.groups: + if group_id in self._groups: raise KeyError(group_id) name = name.upper() - if name in self.groups: + if name in self._groups: raise KeyError(name) - group = self.groups[name] = self.groups[group_id] = Group(name, desc) + group = self._groups[name] = self._groups[group_id] = Group(name, desc) return group def get(self, group, default=None): @@ -943,16 +965,16 @@ def get(self, group, default=None): is found, returns the default value. ''' if isinstance(group, int): - return self.groups.get(group, default) + return self._groups.get(group, default) group = group.upper() param = None if '.' in group: group, param = group.split('.', 1) if ':' in group: group, param = group.split(':', 1) - if group not in self.groups: + if group not in self._groups: return default - group = self.groups[group] + group = self._groups[group] if param is not None: return group.get(param, default) return group @@ -995,7 +1017,7 @@ def get_string(self, key): def parameter_blocks(self): '''Compute the size (in 512B blocks) of the parameter section.''' - bytes = 4. + sum(g.binary_size() for g in self.groups.values()) + bytes = 4. + sum(g.binary_size() for g in self._groups.values()) return int(np.ceil(bytes / 512)) @property @@ -1171,7 +1193,7 @@ def seek_param_section_header(): if group_id > 0: # we've just started reading a parameter. if its group doesn't # exist, create a blank one. add the parameter to the group. - self.groups.setdefault( + self._groups.setdefault( group_id, Group()).add_param(name, self._dtypes, handle=buf) else: # we've just started reading a group. if a group with the @@ -1185,7 +1207,7 @@ def seek_param_section_header(): if group is not None: group.name = name group.desc = desc - self.groups[name] = group + self._groups[name] = group else: self.add_group(group_id, name, desc) @@ -1455,9 +1477,7 @@ def _write_metadata(self, handle): # Groups handle.write(struct.pack( 'BBBB', 0, 0, self.parameter_blocks(), PROCESSOR_INTEL)) - id_groups = sorted( - (i, g) for i, g in self.groups.items() if isinstance(i, int)) - for group_id, group in id_groups: + for group_id, group in self.group_listed(): group.write(group_id, handle) # Padding diff --git a/scripts/c3d-metadata b/scripts/c3d-metadata index 2cec59b..14d4c88 100755 --- a/scripts/c3d-metadata +++ b/scripts/c3d-metadata @@ -15,12 +15,11 @@ parser.add_argument('input', default='-', metavar='FILE', nargs='+', def print_metadata(reader): print('Header information:\n{}'.format(reader.header)) - groups = ((k, v) for k, v in reader.groups.items() if isinstance(k, str)) + groups = reader.group_items() for key, g in sorted(groups): - if not isinstance(key, int): - print('') - for key, p in sorted(g.params.items()): - print_param(g, p) + print('') + for key, p in sorted(g.params.items()): + print_param(g, p) def print_param(g, p): From 437de96ccc1e6859d2e161c1d4c2f29aae933776 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 19:51:53 +0200 Subject: [PATCH 007/120] Replaced Reader.processor to use DataTypes.proc_type instead. --- c3d.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/c3d.py b/c3d.py index 51eb2d3..3b16379 100644 --- a/c3d.py +++ b/c3d.py @@ -1161,14 +1161,13 @@ def seek_param_section_header(): # Begin by reading the processor type: buf = seek_param_section_header() - _, _, parameter_blocks, self.processor = struct.unpack('BBBB', buf) - self._dtypes = DataTypes(self.processor) + _, _, parameter_blocks, processor = struct.unpack('BBBB', buf) + self._dtypes = DataTypes(processor) # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) self._header._processor_convert(self._dtypes, handle) # Restart reading the parameter header after parsing processor type buf = seek_param_section_header() - is_mips = self.processor == PROCESSOR_MIPS start_byte = self._handle.tell() endbyte = start_byte + 512 * parameter_blocks - 4 @@ -1181,7 +1180,7 @@ def seek_param_section_header(): # Read the byte segment associated with the parameter and create a # separate binary stream object from the data. - offset_to_next, = struct.unpack(['h'][is_mips], self._handle.read(2)) + offset_to_next, = struct.unpack(['h'][self._dtypes.is_mips], self._handle.read(2)) if offset_to_next == 0: # Last parameter, as number of bytes are unknown, # read the remaining bytes in the parameter section. @@ -1316,7 +1315,7 @@ def read_frames(self, copy=True): if is_float: # Convert every 4 byte words to a float-32 reprensentation # (the fourth column is still not a float32 representation) - if self.processor == PROCESSOR_DEC: + if self._dtypes.is_dec: # Convert each of the first 6 16-bit words from DEC to IEEE float points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4)) else: # If IEEE or MIPS: @@ -1361,7 +1360,7 @@ def read_frames(self, copy=True): # Check if analog data exist, and parse if so if N_analog > 0: - if is_float and self.processor == PROCESSOR_DEC: + if is_float and self._dtypes.is_dec: # Convert each of the 16-bit words from DEC to IEEE float analog = DEC_to_IEEE_BYTES(raw_analog) else: @@ -1394,7 +1393,7 @@ def proc_type(self): Get the processory type associated with the data format in the file. """ processor_type = ['PROCESSOR_INTEL', 'PROCESSOR_DEC', 'PROCESSOR_MIPS'] - return processor_type[self.processor - PROCESSOR_INTEL] + return processor_type[self._dtypes.proc_type - PROCESSOR_INTEL] class Writer(Manager): From 18315669f0fa12612b2895df419bebcc40cc4c84 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 20:13:55 +0200 Subject: [PATCH 008/120] Header.interpret_events() -> Header._parse_events() --- c3d.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/c3d.py b/c3d.py index 3b16379..eb8bcde 100644 --- a/c3d.py +++ b/c3d.py @@ -362,10 +362,10 @@ def _processor_convert(self, dtypes, handle): self.frame_rate = UNPACK_FLOAT_IEEE(self.frame_rate) float_unpack = UNPACK_FLOAT_IEEE - self.interpret_events(dtypes, float_unpack) + self._parse_events(dtypes, float_unpack) - def interpret_events(self, dtypes, float_unpack): - ''' Function interpreting the event section of the header. + def _parse_events(self, dtypes, float_unpack): + ''' Parse the event section of the header. ''' # Event section byte blocks From ca797297f237b43396870800912afe5baa02ec20 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 21:12:14 +0200 Subject: [PATCH 009/120] Added Param properties for: + int_array, uint_array, int64_array, uint64_array float32_array, float64_array +- float_array now returns either float32 or float64 arrays. + int_array/uint_array return either 1/2/4/8 bit integer arrays. --- c3d.py | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 65 insertions(+), 2 deletions(-) diff --git a/c3d.py b/c3d.py index eb8bcde..723e8b8 100644 --- a/c3d.py +++ b/c3d.py @@ -336,7 +336,7 @@ def read(self, handle, fmt=BINARY_FORMAT_READ): self.event_block, _) = struct.unpack(fmt, raw) - # Check magic number if reading in little endian + # Check magic number assert magic == 80, 'C3D magic {} != 80 !'.format(magic) # Check long event key @@ -638,7 +638,17 @@ def uint32_array(self): return self._as_array(self.dtype.uint32) @property - def float_array(self): + def int64_array(self): + '''Get the param as an array of 32-bit signed integers.''' + return self._as_array(self.dtype.int64) + + @property + def uint64_array(self): + '''Get the param as an array of 32-bit unsigned integers.''' + return self._as_array(self.dtype.uint64) + + @property + def float32_array(self): '''Get the param as an array of 32-bit floats.''' # Convert float data if not IEEE processor if self.dtype.is_dec: @@ -649,6 +659,59 @@ def float_array(self): else: # is_ieee or is_mips return self._as_array(self.dtype.float32) + @property + def float64_array(self): + '''Get the param as an array of 64-bit floats.''' + # Convert float data if not IEEE processor + if self.dtype.is_dec: + raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.') + else: # is_ieee or is_mips + return self._as_array(self.dtype.float64) + + @property + def float_array(self): + '''Get the param as an array of 32 or 64 bit floats.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 4: + return self.float32_array + elif self.bytes_per_element == 8: + return self.float64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element + + "floating-point precission is not unsupported." %) + + @property + def int_array(self): + '''Get the param as an array of integer values.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 1: + return self.int8_array + elif self.bytes_per_element == 2: + return self.int16_array + elif self.bytes_per_element == 4: + return self.int32_array + elif self.bytes_per_element == 8: + return self.int64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % + self.bytes_per_element) + + @property + def uint_array(self): + '''Get the param as an array of integer values.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 1: + return self.uint8_array + elif self.bytes_per_element == 2: + return self.uint16_array + elif self.bytes_per_element == 4: + return self.uint32_array + elif self.bytes_per_element == 8: + return self.uint64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % + self.bytes_per_element) + @property def bytes_array(self): '''Get the param as an array of raw byte strings.''' From 1c41d8bb720b0e1685afcab55b2cb091977e2853 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 21:12:45 +0200 Subject: [PATCH 010/120] Tailing % --- c3d.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/c3d.py b/c3d.py index 723e8b8..dbd0f4a 100644 --- a/c3d.py +++ b/c3d.py @@ -678,7 +678,7 @@ def float_array(self): return self.float64_array else: raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element + - "floating-point precission is not unsupported." %) + "floating-point precission is not unsupported.") @property def int_array(self): From 73ef1c65ac5f69f389f35f880c70325867171987 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 22:08:06 +0200 Subject: [PATCH 011/120] - Manager.group(), Manager.get() should be used. --- c3d.py | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/c3d.py b/c3d.py index dbd0f4a..891277a 100644 --- a/c3d.py +++ b/c3d.py @@ -893,30 +893,18 @@ def header(self): ''' Access the parsed c3d header. ''' return self._header - def group(self, key): - ''' Access a paramater group from a group key. - - Attributes - ---------- - key : int or str - Index or name for the parameter group. - ''' - return self._groups[key] - @property def group_items(self): - ''' Acquire iterable over group parameter pairs (str key, group). - ''' + ''' Acquire iterable over group parameter pairs (str key, group). ''' return ((k, v) for k, v in self._groups if isinstance(k, str)) @property def group_listed(self): - ''' Acquire iterable over sorted group parameter pairs (int key, group). - ''' + ''' Acquire iterable over sorted group parameter pairs (int key, group). ''' return sorted((i, g) for i, g in self._groups if isinstance(i, int)) def _check_metadata(self): - '''Ensure that the metadata in our file is self-consistent.''' + ''' Ensure that the metadata in our file is self-consistent. ''' assert self._header.point_count == self.point_used, ( 'inconsistent point count! {} header != {} POINT:USED'.format( self._header.point_count, From dbd962c8f06c95ed3d2c6fd226132b6b15da335f Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 23:51:36 +0200 Subject: [PATCH 012/120] Changes ---- Param.dtype -> Param._dtypes Group.name, Group.desc -> Group._name, Group._desc Additions ---- + Group._dtypes + rename_group(), rename_param(), remove_group(), remove_param() --- c3d.py | 221 ++++++++++++++++++++++++++++++++----------- scripts/c3d-metadata | 5 +- 2 files changed, 170 insertions(+), 56 deletions(-) diff --git a/c3d.py b/c3d.py index 891277a..62acbd7 100644 --- a/c3d.py +++ b/c3d.py @@ -435,7 +435,7 @@ def __init__(self, handle=None): '''Set up a new parameter, only the name is required.''' self.name = name - self.dtype = dtype + self._dtypes = dtype self.desc = desc self.bytes_per_element = bytes_per_element self.dimensions = dimensions or [] @@ -509,7 +509,7 @@ def read(self, handle): if self.total_bytes: self.bytes = handle.read(self.total_bytes) desc_size, = struct.unpack('B', handle.read(1)) - self.desc = desc_size and self.dtype.decode_string(handle.read(desc_size)) or '' + self.desc = desc_size and self._dtypes.decode_string(handle.read(desc_size)) or '' def _as(self, dtype): '''Unpack the raw bytes of this param using the given struct format.''' @@ -562,40 +562,40 @@ def _as_integer_value(self): @property def int8_value(self): '''Get the param as an 8-bit signed integer.''' - return self._as(self.dtype.int8) + return self._as(self._dtypes.int8) @property def uint8_value(self): '''Get the param as an 8-bit unsigned integer.''' - return self._as(self.dtype.uint8) + return self._as(self._dtypes.uint8) @property def int16_value(self): '''Get the param as a 16-bit signed integer.''' - return self._as(self.dtype.int16) + return self._as(self._dtypes.int16) @property def uint16_value(self): '''Get the param as a 16-bit unsigned integer.''' - return self._as(self.dtype.uint16) + return self._as(self._dtypes.uint16) @property def int32_value(self): '''Get the param as a 32-bit signed integer.''' - return self._as(self.dtype.int32) + return self._as(self._dtypes.int32) @property def uint32_value(self): '''Get the param as a 32-bit unsigned integer.''' - return self._as(self.dtype.uint32) + return self._as(self._dtypes.uint32) @property def float_value(self): '''Get the param as a 32-bit float.''' - if self.dtype.is_dec: + if self._dtypes.is_dec: return DEC_to_IEEE(self._as(np.uint32)) else: # is_mips or is_ieee - return self._as(self.dtype.float32) + return self._as(self._dtypes.float32) @property def bytes_value(self): @@ -605,68 +605,68 @@ def bytes_value(self): @property def string_value(self): '''Get the param as a unicode string.''' - return self.dtype.decode_string(self.bytes) + return self._dtypes.decode_string(self.bytes) @property def int8_array(self): '''Get the param as an array of 8-bit signed integers.''' - return self._as_array(self.dtype.int8) + return self._as_array(self._dtypes.int8) @property def uint8_array(self): '''Get the param as an array of 8-bit unsigned integers.''' - return self._as_array(self.dtype.uint8) + return self._as_array(self._dtypes.uint8) @property def int16_array(self): '''Get the param as an array of 16-bit signed integers.''' - return self._as_array(self.dtype.int16) + return self._as_array(self._dtypes.int16) @property def uint16_array(self): '''Get the param as an array of 16-bit unsigned integers.''' - return self._as_array(self.dtype.uint16) + return self._as_array(self._dtypes.uint16) @property def int32_array(self): '''Get the param as an array of 32-bit signed integers.''' - return self._as_array(self.dtype.int32) + return self._as_array(self._dtypes.int32) @property def uint32_array(self): '''Get the param as an array of 32-bit unsigned integers.''' - return self._as_array(self.dtype.uint32) + return self._as_array(self._dtypes.uint32) @property def int64_array(self): '''Get the param as an array of 32-bit signed integers.''' - return self._as_array(self.dtype.int64) + return self._as_array(self._dtypes.int64) @property def uint64_array(self): '''Get the param as an array of 32-bit unsigned integers.''' - return self._as_array(self.dtype.uint64) + return self._as_array(self._dtypes.uint64) @property def float32_array(self): '''Get the param as an array of 32-bit floats.''' # Convert float data if not IEEE processor - if self.dtype.is_dec: + if self._dtypes.is_dec: # _as_array but for DEC assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, self.dtype.float32) + '{}: cannot get value as {} array!'.format(self.name, self._dtypes.float32) return DEC_to_IEEE_BYTES(self.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format else: # is_ieee or is_mips - return self._as_array(self.dtype.float32) + return self._as_array(self._dtypes.float32) @property def float64_array(self): '''Get the param as an array of 64-bit floats.''' # Convert float data if not IEEE processor - if self.dtype.is_dec: + if self._dtypes.is_dec: raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.') else: # is_ieee or is_mips - return self._as_array(self.dtype.float64) + return self._as_array(self._dtypes.float64) @property def float_array(self): @@ -746,7 +746,7 @@ def string_array(self): byte_arr = self.bytes_array # Decode sequences for i in np.ndindex(byte_arr.shape): - byte_arr[i] = self.dtype.decode_string(byte_arr[i]) + byte_arr[i] = self._dtypes.decode_string(byte_arr[i]) return byte_arr @@ -758,20 +758,67 @@ class Group(object): Attributes ---------- + dtypes : 'DataTypes' + Data types object used for parsing. name : str Name of this parameter group. desc : str Description for this parameter group. ''' - def __init__(self, name=None, desc=None): + def __init__(self, dtypes, name=None, desc=None): + self._params = {} + self._dtypes = dtypes self.name = name self.desc = desc - self.params = {} def __repr__(self): return ''.format(self.desc) + @property + def name(self): + ''' Group name. ''' + return self._name + + @name.setter + def name(self, value): + ''' Group name string. + + Parameters + ---------- + value : str + New name for the group. + ''' + if value is None or isinstance(value, str): + self._name = value + else: + raise TypeError('Expected group name to be string, was %s.' % type(value)) + + @property + def desc(self): + ''' Group descriptor. ''' + if isinstance(self._desc, bytes): + self._dtypes.decode_string(self._desc) + return self._desc + + @desc.setter + def desc(self, value): + ''' Group descriptor. + + Parameters + ---------- + value : str, or bytes + New description for this parameter group. + ''' + if value is not None and not isinstance(value, (str, bytes)): + raise TypeError('Expected descriptor to be byte string or python string, was %s.' % type(value)) + self._desc = value + + @property + def param_items(self): + ''' Acquie group parameter iterator for key-value pairs. ''' + return params.items() + def get(self, key, default=None): '''Get a parameter by key. @@ -787,7 +834,7 @@ def get(self, key, default=None): param : :class:`Param` A parameter from the current group. ''' - return self.params.get(key, default) + return self._params.get(key, default) def add_param(self, name, dtypes, **kwargs): '''Add a parameter to this group. @@ -802,16 +849,46 @@ def add_param(self, name, dtypes, **kwargs): Additional keyword arguments will be passed to the `Param` constructor. ''' - self.params[name.upper()] = Param(name.upper(), dtypes, **kwargs) + self._params[name.upper()] = Param(name.upper(), dtypes, **kwargs) + + def remove_param(self, name): + '''Remove the specified parameter. + + Parameters + ---------- + name : str + Name for the parameter to remove. + ''' + del self._params[group_id] + + def rename_param(self, name, new_name): + ''' Rename a specified parameter group. + + Parameters + ---------- + name : str, or 'Param' + Parameter instance, or name. + new_name : str + New name for the parameter. + ''' + if isinstance(name, Param): + param = name + else: + # Aquire instance using id + param = self._params.get(name, None) + if param is None: + raise ValueError('No parameter found matching the identifier: %s' % str(name)) + del self._params[name] + self._params[new_name] = param def binary_size(self): '''Return the number of bytes to store this group and its parameters.''' return ( 1 + # group_id - 1 + len(self.name.encode('utf-8')) + # size of name and name bytes + 1 + len(self._name.encode('utf-8')) + # size of name and name bytes 2 + # next offset marker - 1 + len(self.desc.encode('utf-8')) + # size of desc and desc bytes - sum(p.binary_size() for p in self.params.values())) + 1 + len(self._desc.encode('utf-8')) + # size of desc and desc bytes + sum(p.binary_size() for p in self._params.values())) def write(self, group_id, handle): '''Write this parameter group, with parameters, to a file handle. @@ -823,51 +900,51 @@ def write(self, group_id, handle): handle : file handle An open, writable, binary file handle. ''' - name = self.name.encode('utf-8') - desc = self.desc.encode('utf-8') + name = self._name.encode('utf-8') + desc = self._desc.encode('utf-8') handle.write(struct.pack('bb', len(name), -group_id)) handle.write(name) handle.write(struct.pack(' 0: - # we've just started reading a parameter. if its group doesn't + # We've just started reading a parameter. If its group doesn't # exist, create a blank one. add the parameter to the group. self._groups.setdefault( - group_id, Group()).add_param(name, self._dtypes, handle=buf) + group_id, Group(self._dtypes)).add_param(name, self._dtypes, handle=buf) else: - # we've just started reading a group. if a group with the - # appropriate id exists already (because we've already created - # it for a parameter), just set the name of the group. - # otherwise, add a new group. + # We've just started reading a group. If a group with the + # appropriate numerical id exists already (because we've + # already created it for a parameter), just set the name of + # the group. Otherwise, add a new group. group_id = abs(group_id) size, = struct.unpack('B', buf.read(1)) desc = size and buf.read(size) or '' group = self.get(group_id) if group is not None: - group.name = name + self.rename_group(group, name) group.desc = desc - self._groups[name] = group else: self.add_group(group_id, name, desc) diff --git a/scripts/c3d-metadata b/scripts/c3d-metadata index 14d4c88..5b25eac 100755 --- a/scripts/c3d-metadata +++ b/scripts/c3d-metadata @@ -15,10 +15,9 @@ parser.add_argument('input', default='-', metavar='FILE', nargs='+', def print_metadata(reader): print('Header information:\n{}'.format(reader.header)) - groups = reader.group_items() - for key, g in sorted(groups): + for key, g in sorted(reader.group_items()): print('') - for key, p in sorted(g.params.items()): + for key, p in sorted(g.param_items()): print_param(g, p) From 67ea346fac4d12b0c360225d39ca21bfb064ea1f Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 27 Jun 2021 23:54:40 +0200 Subject: [PATCH 013/120] Decode when setting descriptor. --- c3d.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/c3d.py b/c3d.py index 62acbd7..88b37ee 100644 --- a/c3d.py +++ b/c3d.py @@ -769,6 +769,7 @@ class Group(object): def __init__(self, dtypes, name=None, desc=None): self._params = {} self._dtypes = dtypes + # Assign through property setters self.name = name self.desc = desc @@ -797,8 +798,6 @@ def name(self, value): @property def desc(self): ''' Group descriptor. ''' - if isinstance(self._desc, bytes): - self._dtypes.decode_string(self._desc) return self._desc @desc.setter @@ -810,7 +809,9 @@ def desc(self, value): value : str, or bytes New description for this parameter group. ''' - if value is not None and not isinstance(value, (str, bytes)): + if isinstance(value, bytes): + self._desc = self._dtypes.decode_string(value) + elif value is not None and not isinstance(value, str): raise TypeError('Expected descriptor to be byte string or python string, was %s.' % type(value)) self._desc = value From f33c720e78c4eb393224ae7f062dec2c46bf67b7 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 00:04:33 +0200 Subject: [PATCH 014/120] Assert numeric group id replacement doesnt exist --- c3d.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/c3d.py b/c3d.py index 88b37ee..0c63bad 100644 --- a/c3d.py +++ b/c3d.py @@ -1090,7 +1090,7 @@ def rename_group(self, group_id, new_group_id): ---------- group_id : int, str, or 'Group' Group instance, name, or numerical identifier for the group. - name : str, or int + new_group_id : str, or int If string, it is the new name for the group. If integer, it will replace its numerical group id. ''' if isinstance(group_id, Group): @@ -1100,6 +1100,11 @@ def rename_group(self, group_id, new_group_id): grp = self._groups.get(group_id, None) if grp is None: raise ValueError('No group found matching the identifier: %s' % str(group_id)) + if isinstance(new_group_id, int) and new_group_id in self._groups: + if new_group_id == group_id: + return + raise ValueError('New numeric group identifier %i for group %s already exist.' % (new_group_id, grp.name)) + # Clear old id if isinstance(new_group_id, str): if grp.name in _groups: From 16398154589bad5cc2ccc7cbdd51c8e489840bb5 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 16:56:00 +0200 Subject: [PATCH 015/120] + is_integer() + Comments + Code corrections --- c3d.py | 67 ++++++++++++++++++++++++++++++++++++++++++---------------- 1 file changed, 49 insertions(+), 18 deletions(-) diff --git a/c3d.py b/c3d.py index 0c63bad..d1c09a7 100644 --- a/c3d.py +++ b/c3d.py @@ -164,6 +164,9 @@ def DEC_to_IEEE_BYTES(bytes): dtype=np.float32, count=int(len(bytes) / 4)) +def is_integer(value): + '''Check if value input is integer.''' + return isinstance(value, (int, np.int32, np.int64)) class Header(object): '''Header information from a C3D file. @@ -973,13 +976,25 @@ def header(self): @property def group_items(self): - ''' Acquire iterable over group parameter pairs (str key, group). ''' - return ((k, v) for k, v in self._groups if isinstance(k, str)) + ''' Acquire iterable over parameter group pairs. + + Returns + ------- + items : Touple of ((str, :class:`Group`), ...) + Python touple containing pairs of name keys and parameter group entries. + ''' + return ((k, v) for k, v in self._groups.items() if isinstance(k, str)) @property def group_listed(self): - ''' Acquire iterable over sorted group parameter pairs (int key, group). ''' - return sorted((i, g) for i, g in self._groups if isinstance(i, int)) + ''' Acquire iterable over sorted numerical parameter group pairs. + + Returns + ------- + items : Touple of ((int, :class:`Group`), ...) + Sorted python touple containing pairs of numerical keys and parameter group entries. + ''' + return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int)) def _check_metadata(self): ''' Ensure that the metadata in our file is self-consistent. ''' @@ -1062,9 +1077,14 @@ def add_group(self, group_id, name, desc): Raises ------ - KeyError - If a group with a duplicate ID or name already exists. + TypeError + Input arguments are of the wrong type. ''' + if not is_integer(group_id): + raise ValueError('Expected Group numerical key to be integer, was %s.' % type(group_id)) + if not isinstance(name, str): + raise ValueError('Expected Group name key to be string, was %s.' % type(name) + group_id = int(group_id) # Assert python int if group_id in self._groups: raise KeyError(group_id) name = name.upper() @@ -1079,9 +1099,14 @@ def remove_group(self, group_id): Parameters ---------- group_id : int, or str - The numeric or name ID for a group to remove. + The numeric or name ID key for a group to remove all entries for. ''' - del self._groups[group_id] + grp = self._groups.get(group_id, None) + if grp is None: + return + gkeys = [k for (k, v) in self._groups.items() if v == grp] + for k in gkeys: + del self._groups[k] def rename_group(self, group_id, new_group_id): ''' Rename a specified parameter group. @@ -1092,6 +1117,11 @@ def rename_group(self, group_id, new_group_id): Group instance, name, or numerical identifier for the group. new_group_id : str, or int If string, it is the new name for the group. If integer, it will replace its numerical group id. + + Raises + ------ + KeyError + If a group with a duplicate ID or name already exists. ''' if isinstance(group_id, Group): grp = group_id @@ -1099,21 +1129,22 @@ def rename_group(self, group_id, new_group_id): # Aquire instance using id grp = self._groups.get(group_id, None) if grp is None: - raise ValueError('No group found matching the identifier: %s' % str(group_id)) - if isinstance(new_group_id, int) and new_group_id in self._groups: + raise KeyError('No group found matching the identifier: %s' % str(group_id)) + if new_group_id in self._groups: if new_group_id == group_id: return - raise ValueError('New numeric group identifier %i for group %s already exist.' % (new_group_id, grp.name)) + raise KeyError('New group identifier %s for group %s already exist.' % (str(new_group_id), grp.name)) # Clear old id - if isinstance(new_group_id, str): - if grp.name in _groups: + if isinstance(new_group_id, (str, bytes)): + if grp.name in self._groups: del self._groups[grp.name] - grp.name = new_group_id - elif isinstance(new_group_id, int): + grp._name = new_group_id + elif is_integer(new_group_id): + new_group_id = int(new_group_id) # Ensure python int del self._groups[group_id] else: - raise ValueError('Invalid group identifier of type: %s' % str(type(new_group_id))) + raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id))) # Update self._groups[new_group_id] = grp @@ -1137,8 +1168,8 @@ def get(self, group, default=None): Either a group or parameter with the specified name(s). If neither is found, returns the default value. ''' - if isinstance(group, int): - return self._groups.get(group, default) + if is_integer(group): + return self._groups.get(int(group), default) group = group.upper() param = None if '.' in group: From 2a46ef6ee498f950da67f9daf9e762722aeed623 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 16:57:29 +0200 Subject: [PATCH 016/120] Tests for managing Group functions --- test/test_group_functionality.py | 129 +++++++++++++++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 test/test_group_functionality.py diff --git a/test/test_group_functionality.py b/test/test_group_functionality.py new file mode 100644 index 0000000..fb4d46f --- /dev/null +++ b/test/test_group_functionality.py @@ -0,0 +1,129 @@ +import unittest +import c3d +import numpy as np +import test.verify as verify +from test.zipload import Zipload +from test.base import Base + +class GroupSample(): + ''' Verify groups persist. ''' + def __init__(self, manager): + self.manager = manager + self.sample() + + @property + def group_items(self): + '''Helper to access group items. ''' + return [(k, g) for (k, g) in self.manager.group_items] + + @property + def group_list(self): + '''Helper to access group numerical key-value pairs. ''' + return [(k, g) for (k, g) in self.manager.group_listed] + + @property + def fetch_groups(self): + return self.group_items, self.group_list + + def sample(self): + '''Call before applying changes. ''' + self.s_grp_items, self.s_grp_list = self.fetch_groups + + def assert_entry_count(self): + '''Assert all values in group still exist. ''' + grp_items, grp_list = self.fetch_groups + + assert len(self.s_grp_items) == len(grp_items),\ + 'Rename added item entry. Had %i entries, now has %i.' % (len(self.s_grp_items), len(grp_items)) + assert len(self.s_grp_list) == len(grp_list),\ + 'Rename added list entry. Had %i entries, now has %i.' % (len(self.s_grp_list), len(grp_list)) + assert len(grp_items) == len(grp_list),\ + 'Mismatch in the number of numerical and name keys. Had %i entries, now has %i.' %\ + (len(grp_items), len(grp_list)) + + def assert_group_items(self): + '''Assert all named (str, Group) pairs persisted after change.''' + enumerator = range(len(self.s_grp_items)) + for i, (n, g), (n2, g2) in zip(enumerator, sorted(self.s_grp_items), sorted(self.group_items)): + assert n == n2, 'Group numeric id missmatch after changes for entry %i. ' % i +\ + 'Initially %i, after change entry was %i' % (n, n2) + assert g == g2, 'Group listed order changed for entry %i.' % i + + def assert_group_list(self): + '''Assert all numerical (int, Group) pairs persisted after change.''' + enumerator = range(len(self.s_grp_list)) + for i, (n, g), (n2, g2) in zip(enumerator, self.s_grp_list, self.group_list): + assert n == n2, 'Group string id missmatch after changes for entry %i. ' % i +\ + 'Initially %i, after change entry was %i' % (n, n2) + assert g == g2, 'Group listed order changed for entry %i.' % i + + +class Sample00(Base): + ZIP = 'sample01.zip' + INTEL_INT = 'Eb015pi.c3d' + INTEL_REAL = 'Eb015pr.c3d' + + def test_Group_group_items(self): + '''Test Group.group_items''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + grp_keys = [k for (k, g) in reader.group_items] + assert len(grp_keys) > 0, 'No group items in file or Group.group_items failed' + + def test_Group_group_listed(self): + '''Test Group.group_listed''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + grp_list = [k for (k, g) in reader.group_listed] + assert len(grp_list) > 0, 'No group items in file or Group.group_listed failed' + + def test_Group_rename_group(self): + '''Test if renaming groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + grp_keys = [k for (k, g) in reader.group_items] + ref = GroupSample(reader) + + for i, key in enumerate(grp_keys): + test_name = 'TEST_NAME' + str(i) + + grp = reader.get(key) + reader.rename_group(key, test_name) + grp2 = reader.get(test_name) + + assert grp2 is not None, "Rename failed, group with name '%s' does not exist." + assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' + + ref.assert_entry_count() + ref.assert_group_list() + + def test_Group_renumber_group(self): + '''Test if renaming (renumbering) groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + grp_ids = [k for (k, g) in reader.group_listed] + ref = GroupSample(reader) + + max_key = np.max(grp_ids) + + for i, key in enumerate(grp_ids): + test_num = max_key + i + 1 + + grp = reader.get(key) + reader.rename_group(key, test_num) + grp2 = reader.get(test_num) + + assert grp2 is not None, "Rename failed, group with name '%s' does not exist." + assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' + + ref.assert_entry_count() + ref.assert_group_items() + + try: + reader.rename_group(max_key + 1, max_key + 2) + raise RuntimeError('Overwriting existing numerical ID should raise a ValueError.') + except KeyError as e: + pass # Correct + + + + + +if __name__ == '__main__': + unittest.main() From 3fcc9e46d5197814ece7e3e215b12ba627a5e8a6 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 17:09:45 +0200 Subject: [PATCH 017/120] Type + added test to verify renaming string key throws if it exists. --- c3d.py | 2 +- test/test_group_functionality.py | 44 ++++++++++++++++++++++---------- 2 files changed, 31 insertions(+), 15 deletions(-) diff --git a/c3d.py b/c3d.py index d1c09a7..3b6924b 100644 --- a/c3d.py +++ b/c3d.py @@ -1083,7 +1083,7 @@ def add_group(self, group_id, name, desc): if not is_integer(group_id): raise ValueError('Expected Group numerical key to be integer, was %s.' % type(group_id)) if not isinstance(name, str): - raise ValueError('Expected Group name key to be string, was %s.' % type(name) + raise ValueError('Expected Group name key to be string, was %s.' % type(name)) group_id = int(group_id) # Assert python int if group_id in self._groups: raise KeyError(group_id) diff --git a/test/test_group_functionality.py b/test/test_group_functionality.py index fb4d46f..81e0430 100644 --- a/test/test_group_functionality.py +++ b/test/test_group_functionality.py @@ -6,7 +6,7 @@ from test.base import Base class GroupSample(): - ''' Verify groups persist. ''' + ''' Helper object to verify groups entries persist. ''' def __init__(self, manager): self.manager = manager self.sample() @@ -23,22 +23,30 @@ def group_list(self): @property def fetch_groups(self): + '''Acquire both group sets. ''' return self.group_items, self.group_list def sample(self): '''Call before applying changes. ''' self.s_grp_items, self.s_grp_list = self.fetch_groups - def assert_entry_count(self): - '''Assert all values in group still exist. ''' + def assert_entry_count(self, delta=0): + '''Assert all values in group still exist. + + Arguments + --------- + delta: Number of entries added (+) or removed (-) since last sample. + ''' grp_items, grp_list = self.fetch_groups - assert len(self.s_grp_items) == len(grp_items),\ - 'Rename added item entry. Had %i entries, now has %i.' % (len(self.s_grp_items), len(grp_items)) - assert len(self.s_grp_list) == len(grp_list),\ - 'Rename added list entry. Had %i entries, now has %i.' % (len(self.s_grp_list), len(grp_list)) + assert len(self.s_grp_items) + delta == len(grp_items),\ + 'Rename added item entry. Expected %i entries, now has %i.' %\ + (len(self.s_grp_items), len(grp_items)) + assert len(self.s_grp_list) + delta == len(grp_list),\ + 'Rename added list entry. Expected %i entries, now has %i.' %\ + (len(self.s_grp_list) + delta, len(grp_list)) assert len(grp_items) == len(grp_list),\ - 'Mismatch in the number of numerical and name keys. Had %i entries, now has %i.' %\ + 'Mismatch in the number of numerical and name keys. Has %i numerical entries and %i name entries.' %\ (len(grp_items), len(grp_list)) def assert_group_items(self): @@ -58,19 +66,21 @@ def assert_group_list(self): assert g == g2, 'Group listed order changed for entry %i.' % i -class Sample00(Base): +class ManagerGroupTests(Base): + ''' Tests functionality associated with editing Group entries in the Manager class. + ''' ZIP = 'sample01.zip' INTEL_INT = 'Eb015pi.c3d' INTEL_REAL = 'Eb015pr.c3d' def test_Group_group_items(self): - '''Test Group.group_items''' + '''Test Manager.group_items''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_keys = [k for (k, g) in reader.group_items] assert len(grp_keys) > 0, 'No group items in file or Group.group_items failed' def test_Group_group_listed(self): - '''Test Group.group_listed''' + '''Test Manager.group_listed''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_list = [k for (k, g) in reader.group_listed] assert len(grp_list) > 0, 'No group items in file or Group.group_listed failed' @@ -81,9 +91,9 @@ def test_Group_rename_group(self): grp_keys = [k for (k, g) in reader.group_items] ref = GroupSample(reader) - for i, key in enumerate(grp_keys): - test_name = 'TEST_NAME' + str(i) + new_names = ['TEST_NAME' + str(i) for i in range(len(grp_keys))] + for key, test_name in zip(grp_keys, new_names): grp = reader.get(key) reader.rename_group(key, test_name) grp2 = reader.get(test_name) @@ -94,6 +104,12 @@ def test_Group_rename_group(self): ref.assert_entry_count() ref.assert_group_list() + try: + reader.rename_group(new_names[0], new_names[1]) + raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') + except KeyError as e: + pass # Correct + def test_Group_renumber_group(self): '''Test if renaming (renumbering) groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) @@ -117,7 +133,7 @@ def test_Group_renumber_group(self): try: reader.rename_group(max_key + 1, max_key + 2) - raise RuntimeError('Overwriting existing numerical ID should raise a ValueError.') + raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') except KeyError as e: pass # Correct From 36d24485d4e112e50a14319e009ad4de8835afcb Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 17:39:56 +0200 Subject: [PATCH 018/120] Added tests: ManagerGroupTests.test_Manager_add_group ManagerGroupTests.test_Manager_remove_group_from_numeric ManagerGroupTests.test_Manager_remove_group_from_name --- c3d.py | 2 +- test/test_group_functionality.py | 75 +++++++++++++++++++++++++++++--- 2 files changed, 70 insertions(+), 7 deletions(-) diff --git a/c3d.py b/c3d.py index 3b6924b..01e1634 100644 --- a/c3d.py +++ b/c3d.py @@ -1082,7 +1082,7 @@ def add_group(self, group_id, name, desc): ''' if not is_integer(group_id): raise ValueError('Expected Group numerical key to be integer, was %s.' % type(group_id)) - if not isinstance(name, str): + if not (isinstance(name, str) or name is None): raise ValueError('Expected Group name key to be string, was %s.' % type(name)) group_id = int(group_id) # Assert python int if group_id in self._groups: diff --git a/test/test_group_functionality.py b/test/test_group_functionality.py index 81e0430..8472a5c 100644 --- a/test/test_group_functionality.py +++ b/test/test_group_functionality.py @@ -17,19 +17,26 @@ def group_items(self): return [(k, g) for (k, g) in self.manager.group_items] @property - def group_list(self): + def group_listed(self): '''Helper to access group numerical key-value pairs. ''' return [(k, g) for (k, g) in self.manager.group_listed] @property def fetch_groups(self): '''Acquire both group sets. ''' - return self.group_items, self.group_list + return self.group_items, self.group_listed + + @property + def max_key(self): + if len(self.group_items) > 0: + return np.max([k for (k, g) in self.group_listed]) + return 0 def sample(self): '''Call before applying changes. ''' self.s_grp_items, self.s_grp_list = self.fetch_groups + def assert_entry_count(self, delta=0): '''Assert all values in group still exist. @@ -60,11 +67,45 @@ def assert_group_items(self): def assert_group_list(self): '''Assert all numerical (int, Group) pairs persisted after change.''' enumerator = range(len(self.s_grp_list)) - for i, (n, g), (n2, g2) in zip(enumerator, self.s_grp_list, self.group_list): + for i, (n, g), (n2, g2) in zip(enumerator, self.s_grp_list, self.group_listed): assert n == n2, 'Group string id missmatch after changes for entry %i. ' % i +\ 'Initially %i, after change entry was %i' % (n, n2) assert g == g2, 'Group listed order changed for entry %i.' % i + def verify_add_groups(self, N): + '''Add N groups and verify count at each iteration.''' + self.sample() + max_key = self.max_key + for i in range(1, N): + test_name = 'TEST_ADD_GROUP_%i' % i + self.manager.add_group(max_key + i, test_name, '') + assert self.manager.get(test_name) is not None, 'Added group does not exist.' + self.assert_entry_count(delta=i) + + def verify_remove_all_using_numeric(self): + '''Remove all groups using numeric key and verify count at each iteration.''' + self.sample() + keys = [k for (k, g) in self.group_listed] + for i, key in enumerate(keys): + grp = self.manager.get(key) + assert grp is not None, 'Expected group to exist.' + self.manager.remove_group(key) + assert self.manager.get(key) is None, 'Removed group persisted.' + assert self.manager.get(grp.name) is None, 'Removed group persisted.' + self.assert_entry_count(delta=-1 - i) + + def verify_remove_all_using_name(self): + '''Remove all groups using name key and verify count at each iteration.''' + self.sample() + keys = [k for (k, g) in self.group_items] + for i, key in enumerate(keys): + grp = self.manager.get(key) + assert grp is not None, 'Expected group to exist.' + self.manager.remove_group(key) + assert self.manager.get(key) is None, 'Removed group persisted.' + assert self.manager.get(grp.name) is None, 'Removed group persisted.' + self.assert_entry_count(delta=-1 - i) + class ManagerGroupTests(Base): ''' Tests functionality associated with editing Group entries in the Manager class. @@ -85,7 +126,29 @@ def test_Group_group_listed(self): grp_list = [k for (k, g) in reader.group_listed] assert len(grp_list) > 0, 'No group items in file or Group.group_listed failed' - def test_Group_rename_group(self): + + def test_Manager_add_group(self): + '''Test if renaming groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + ref = GroupSample(reader) + ref.verify_add_groups(100) + ref.verify_remove_all_using_numeric() + + def test_Manager_removing_group_from_numeric(self): + '''Test if removing groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + ref = GroupSample(reader) + ref.verify_remove_all_using_numeric() + ref.verify_add_groups(100) + + def test_Manager_removing_group_from_name(self): + '''Test if removing groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + ref = GroupSample(reader) + ref.verify_remove_all_using_name() + ref.verify_add_groups(100) + + def test_Manager_rename_group(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_keys = [k for (k, g) in reader.group_items] @@ -110,13 +173,13 @@ def test_Group_rename_group(self): except KeyError as e: pass # Correct - def test_Group_renumber_group(self): + def test_Manager_renumber_group(self): '''Test if renaming (renumbering) groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_ids = [k for (k, g) in reader.group_listed] ref = GroupSample(reader) - max_key = np.max(grp_ids) + max_key = ref.max_key for i, key in enumerate(grp_ids): test_num = max_key + i + 1 From 538506d85e2edb7da376dbfcde30a7c31c000756 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 17:44:38 +0200 Subject: [PATCH 019/120] test_group_functionality -> test_manager_group_functions --- ...est_group_functionality.py => test_manager_group_functions.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename test/{test_group_functionality.py => test_manager_group_functions.py} (100%) diff --git a/test/test_group_functionality.py b/test/test_manager_group_functions.py similarity index 100% rename from test/test_group_functionality.py rename to test/test_manager_group_functions.py From c351882662abb9c9a1ccf5681418b975fb878c7a Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 18:33:54 +0200 Subject: [PATCH 020/120] + Removed property tag from Manager._groups accessors + Added Group.values() accessor + Writer._dtypes --- c3d.py | 41 ++++++++++++++++------------ test/test_c3d.py | 4 +-- test/test_manager_group_functions.py | 16 ++++++----- 3 files changed, 35 insertions(+), 26 deletions(-) diff --git a/c3d.py b/c3d.py index 01e1634..9cd52c2 100644 --- a/c3d.py +++ b/c3d.py @@ -346,7 +346,7 @@ def read(self, handle, fmt=BINARY_FORMAT_READ): self.long_event_labels = self.long_event_labels == 0x3039 def _processor_convert(self, dtypes, handle): - ''' Function interpreting the header once processor type has been determined. + ''' Function interpreting the header once a processor type has been determined. ''' if dtypes.is_dec: @@ -818,10 +818,13 @@ def desc(self, value): raise TypeError('Expected descriptor to be byte string or python string, was %s.' % type(value)) self._desc = value - @property - def param_items(self): - ''' Acquie group parameter iterator for key-value pairs. ''' - return params.items() + def items(self): + ''' Acquire iterator for paramater key-entry pairs. ''' + return self._params.items() + + def values(self): + ''' Acquire iterator for parameter entries. ''' + return self._params.values() def get(self, key, default=None): '''Get a parameter by key. @@ -840,7 +843,7 @@ def get(self, key, default=None): ''' return self._params.get(key, default) - def add_param(self, name, dtypes, **kwargs): + def add_param(self, name, **kwargs): '''Add a parameter to this group. Parameters @@ -848,12 +851,10 @@ def add_param(self, name, dtypes, **kwargs): name : str Name of the parameter to add to this group. The name will automatically be case-normalized. - dtypes : DataTypes - Object struct containing the data types used for reading parameter data. Additional keyword arguments will be passed to the `Param` constructor. ''' - self._params[name.upper()] = Param(name.upper(), dtypes, **kwargs) + self._params[name.upper()] = Param(name.upper(), self._dtypes, **kwargs) def remove_param(self, name): '''Remove the specified parameter. @@ -974,7 +975,6 @@ def header(self): ''' Access the parsed c3d header. ''' return self._header - @property def group_items(self): ''' Acquire iterable over parameter group pairs. @@ -985,7 +985,16 @@ def group_items(self): ''' return ((k, v) for k, v in self._groups.items() if isinstance(k, str)) - @property + def group_values(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + values : Touple of (:class:`Group`, ...) + Python touple containing unique parameter group entries. + ''' + return (v for k, v in self._groups.items() if isinstance(k, str)) + def group_listed(self): ''' Acquire iterable over sorted numerical parameter group pairs. @@ -1397,7 +1406,7 @@ def seek_param_section_header(): # We've just started reading a parameter. If its group doesn't # exist, create a blank one. add the parameter to the group. self._groups.setdefault( - group_id, Group(self._dtypes)).add_param(name, self._dtypes, handle=buf) + group_id, Group(self._dtypes)).add_param(name, handle=buf) else: # We've just started reading a group. If a group with the # appropriate numerical id exists already (because we've @@ -1635,6 +1644,8 @@ def __init__(self, '''Set metadata for this writer. ''' + # Always write INTEL format + self._dtypes = DataTypes(PROCESSOR_INTEL) super(Writer, self).__init__() self._point_rate = point_rate self._analog_rate = analog_rate @@ -1736,11 +1747,8 @@ def write(self, handle, labels): if not self._frames: return - dtypes = DataTypes(PROCESSOR_INTEL) - def add(name, desc, bpe, format, bytes, *dimensions): group.add_param(name, - dtypes, desc=desc, bytes_per_element=bpe, bytes=struct.pack(format, bytes), @@ -1748,14 +1756,13 @@ def add(name, desc, bpe, format, bytes, *dimensions): def add_str(name, desc, bytes, *dimensions): group.add_param(name, - dtypes, desc=desc, bytes_per_element=-1, bytes=bytes.encode('utf-8'), dimensions=list(dimensions)) def add_empty_array(name, desc, bpe): - group.add_param(name, dtypes, desc=desc, + group.add_param(name, desc=desc, bytes_per_element=bpe, dimensions=[0]) points, analog = self._frames[0] diff --git a/test/test_c3d.py b/test/test_c3d.py index 119e650..5738bb0 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -36,8 +36,8 @@ def test_paramsa(self): def test_paramsb(self): r = c3d.Reader(Zipload._get('sample08.zip', 'TESTBPI.c3d')) self._log(r) - for g in r.groups.values(): - for p in g.params.values(): + for g in r.group_values(): + for p in g.values(): if len(p.dimensions) == 0: val = None width = len(p.bytes) diff --git a/test/test_manager_group_functions.py b/test/test_manager_group_functions.py index 8472a5c..539df3e 100644 --- a/test/test_manager_group_functions.py +++ b/test/test_manager_group_functions.py @@ -1,3 +1,5 @@ +''' Purpose for this file is to verify functions associated with Manager._groups dictionary. +''' import unittest import c3d import numpy as np @@ -6,7 +8,7 @@ from test.base import Base class GroupSample(): - ''' Helper object to verify groups entries persist. ''' + ''' Helper object to verify group entries persist or terminate properly. ''' def __init__(self, manager): self.manager = manager self.sample() @@ -14,12 +16,12 @@ def __init__(self, manager): @property def group_items(self): '''Helper to access group items. ''' - return [(k, g) for (k, g) in self.manager.group_items] + return [(k, g) for (k, g) in self.manager.group_items()] @property def group_listed(self): '''Helper to access group numerical key-value pairs. ''' - return [(k, g) for (k, g) in self.manager.group_listed] + return [(k, g) for (k, g) in self.manager.group_listed()] @property def fetch_groups(self): @@ -117,13 +119,13 @@ class ManagerGroupTests(Base): def test_Group_group_items(self): '''Test Manager.group_items''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - grp_keys = [k for (k, g) in reader.group_items] + grp_keys = [k for (k, g) in reader.group_items()] assert len(grp_keys) > 0, 'No group items in file or Group.group_items failed' def test_Group_group_listed(self): '''Test Manager.group_listed''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - grp_list = [k for (k, g) in reader.group_listed] + grp_list = [k for (k, g) in reader.group_listed()] assert len(grp_list) > 0, 'No group items in file or Group.group_listed failed' @@ -151,8 +153,8 @@ def test_Manager_removing_group_from_name(self): def test_Manager_rename_group(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - grp_keys = [k for (k, g) in reader.group_items] ref = GroupSample(reader) + grp_keys = [k for (k, g) in ref.group_items] new_names = ['TEST_NAME' + str(i) for i in range(len(grp_keys))] @@ -176,8 +178,8 @@ def test_Manager_rename_group(self): def test_Manager_renumber_group(self): '''Test if renaming (renumbering) groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - grp_ids = [k for (k, g) in reader.group_listed] ref = GroupSample(reader) + grp_ids = [k for (k, g) in ref.group_listed] max_key = ref.max_key From f286bcadfb3d254352a9902d168d45df23ae2f5a Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 28 Jun 2021 18:34:16 +0200 Subject: [PATCH 021/120] Rename of parameter test file --- ....py => test_parameter_bytes_conversion.py} | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) rename test/{test_parameter_functions.py => test_parameter_bytes_conversion.py} (93%) diff --git a/test/test_parameter_functions.py b/test/test_parameter_bytes_conversion.py similarity index 93% rename from test/test_parameter_functions.py rename to test/test_parameter_bytes_conversion.py index 18fc76b..14d02c4 100644 --- a/test/test_parameter_functions.py +++ b/test/test_parameter_bytes_conversion.py @@ -144,11 +144,23 @@ def test_a_parse_float32_array(self): for shape in ParameterArrayTest.SHAPES: arr = self.rnd.uniform(flt_range[0], flt_range[1], size=shape).astype(np.float32) P = c3d.Param('FLOAT_TEST', self.dtypes, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes()) - arr_out = P.float_array + arr_out = P.float32_array assert arr.T.shape == arr_out.shape, "Mismatch in 'float_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading float array' - def test_b_parse_int32_array(self): + def test_b_parse_float64_array(self): + ''' Verify array of 64 bit floating point values are parsed correctly + ''' + flt_range = (-1e6, 1e6) + + for shape in ParameterArrayTest.SHAPES: + arr = self.rnd.uniform(flt_range[0], flt_range[1], size=shape).astype(np.float64) + P = c3d.Param('FLOAT_TEST', self.dtypes, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes()) + arr_out = P.float64_array + assert arr.T.shape == arr_out.shape, "Mismatch in 'float_array' converted shape" + assert np.all(arr.T == arr_out), 'Value mismatch when reading float array' + + def test_c_parse_int32_array(self): ''' Verify array of 32 bit integer values are parsed correctly ''' flt_range = (-1e6, 1e6) @@ -160,7 +172,7 @@ def test_b_parse_int32_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'int32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array' - def test_c_parse_uint32_array(self): + def test_d_parse_uint32_array(self): ''' Verify array of 32 bit unsigned integer values are parsed correctly ''' flt_range = (0, 1e6) @@ -172,7 +184,7 @@ def test_c_parse_uint32_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'uint32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array' - def test_d_parse_int16_array(self): + def test_e_parse_int16_array(self): ''' Verify array of 16 bit integer values are parsed correctly ''' flt_range = (-1e4, 1e4) @@ -184,7 +196,7 @@ def test_d_parse_int16_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'int32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array' - def test_e_parse_uint16_array(self): + def test_f_parse_uint16_array(self): ''' Verify array of 16 bit unsigned integer values are parsed correctly ''' flt_range = (0, 1e4) @@ -196,7 +208,7 @@ def test_e_parse_uint16_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'uint32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array' - def test_e_parse_int8_array(self): + def test_g_parse_int8_array(self): ''' Verify array of 8 bit integer values are parsed correctly ''' flt_range = (-127, 127) @@ -208,7 +220,7 @@ def test_e_parse_int8_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'int32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array' - def test_f_parse_uint8_array(self): + def test_h_parse_uint8_array(self): ''' Verify array of 8 bit unsigned integer values are parsed correctly ''' flt_range = (0, 255) @@ -220,7 +232,7 @@ def test_f_parse_uint8_array(self): assert arr.T.shape == arr_out.shape, "Mismatch in 'uint32_array' converted shape" assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array' - def test_g_parse_byte_array(self): + def test_i_parse_byte_array(self): ''' Verify byte arrays are parsed correctly ''' word = b'WRIST' @@ -252,7 +264,7 @@ def test_g_parse_byte_array(self): for i in np.ndindex(arr_out.shape): assert np.all(arr[i[::-1]] == arr_out[i]), "Mismatch in 'bytes_array' converted value at index %s" % str(i) - def test_h_parse_string_array(self): + def test_j_parse_string_array(self): ''' Verify repeated word arrays are parsed correctly ''' word = b'ANCLE' @@ -290,7 +302,7 @@ def test_h_parse_string_array(self): assert self.dtypes.decode_string(arr[i[::-1]]) == arr_out[i],\ "Mismatch in 'string_array' converted value at index %s" % str(i) - def test_i_parse_random_string_array(self): + def test_k_parse_random_string_array(self): ''' Verify random word arrays are parsed correctly ''' ## From 9e0dcb9ce785f40e79a3fc53ea9387e762845fc1 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Tue, 29 Jun 2021 00:44:32 +0200 Subject: [PATCH 022/120] Added --- + Group.param_keys() + Manager.group_keys() Changed ---- Group.values() -> Group.param_values() Group.items() -> Group.param_items() KeyError -> ValueError for existing keys --- c3d.py | 25 +++- test/test_c3d.py | 2 +- ...p_functions.py => test_group_accessors.py} | 22 +-- test/test_parameter_accessors.py | 139 ++++++++++++++++++ 4 files changed, 172 insertions(+), 16 deletions(-) rename test/{test_manager_group_functions.py => test_group_accessors.py} (94%) create mode 100644 test/test_parameter_accessors.py diff --git a/c3d.py b/c3d.py index 9cd52c2..d359216 100644 --- a/c3d.py +++ b/c3d.py @@ -818,14 +818,18 @@ def desc(self, value): raise TypeError('Expected descriptor to be byte string or python string, was %s.' % type(value)) self._desc = value - def items(self): + def param_items(self): ''' Acquire iterator for paramater key-entry pairs. ''' return self._params.items() - def values(self): + def param_values(self): ''' Acquire iterator for parameter entries. ''' return self._params.values() + def param_keys(self): + ''' Acquire iterator for parameter entry keys. ''' + return self._params.keys() + def get(self, key, default=None): '''Get a parameter by key. @@ -864,7 +868,7 @@ def remove_param(self, name): name : str Name for the parameter to remove. ''' - del self._params[group_id] + del self._params[name] def rename_param(self, name, new_name): ''' Rename a specified parameter group. @@ -876,8 +880,11 @@ def rename_param(self, name, new_name): new_name : str New name for the parameter. ''' + if new_name in self._params: + raise ValueError("Key %s already exist." % new_name) if isinstance(name, Param): param = name + name = param.name else: # Aquire instance using id param = self._params.get(name, None) @@ -995,6 +1002,16 @@ def group_values(self): ''' return (v for k, v in self._groups.items() if isinstance(k, str)) + def group_keys(self): + ''' Acquire iterable over parameter group entry string keys. + + Returns + ------- + keys : Touple of (str, ...) + Python touple containing keys for the parameter group entries. + ''' + return (k for k in self._groups.keys() if isinstance(k, str)) + def group_listed(self): ''' Acquire iterable over sorted numerical parameter group pairs. @@ -1142,7 +1159,7 @@ def rename_group(self, group_id, new_group_id): if new_group_id in self._groups: if new_group_id == group_id: return - raise KeyError('New group identifier %s for group %s already exist.' % (str(new_group_id), grp.name)) + raise ValueError('Key %s for group %s already exist.' % (str(new_group_id), grp.name)) # Clear old id if isinstance(new_group_id, (str, bytes)): diff --git a/test/test_c3d.py b/test/test_c3d.py index 5738bb0..cd34f2d 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -37,7 +37,7 @@ def test_paramsb(self): r = c3d.Reader(Zipload._get('sample08.zip', 'TESTBPI.c3d')) self._log(r) for g in r.group_values(): - for p in g.values(): + for p in g.param_values(): if len(p.dimensions) == 0: val = None width = len(p.bytes) diff --git a/test/test_manager_group_functions.py b/test/test_group_accessors.py similarity index 94% rename from test/test_manager_group_functions.py rename to test/test_group_accessors.py index 539df3e..eaf1722 100644 --- a/test/test_manager_group_functions.py +++ b/test/test_group_accessors.py @@ -74,7 +74,7 @@ def assert_group_list(self): 'Initially %i, after change entry was %i' % (n, n2) assert g == g2, 'Group listed order changed for entry %i.' % i - def verify_add_groups(self, N): + def verify_add_group(self, N): '''Add N groups and verify count at each iteration.''' self.sample() max_key = self.max_key @@ -109,31 +109,31 @@ def verify_remove_all_using_name(self): self.assert_entry_count(delta=-1 - i) -class ManagerGroupTests(Base): +class TestGroupAccessors(Base): ''' Tests functionality associated with editing Group entries in the Manager class. ''' ZIP = 'sample01.zip' INTEL_INT = 'Eb015pi.c3d' INTEL_REAL = 'Eb015pr.c3d' - def test_Group_group_items(self): + def test_Manager_group_items(self): '''Test Manager.group_items''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_keys = [k for (k, g) in reader.group_items()] - assert len(grp_keys) > 0, 'No group items in file or Group.group_items failed' + assert len(grp_keys) > 0, 'No group items in file or Manager.group_items failed' - def test_Group_group_listed(self): + def test_Manager_group_listed(self): '''Test Manager.group_listed''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) grp_list = [k for (k, g) in reader.group_listed()] - assert len(grp_list) > 0, 'No group items in file or Group.group_listed failed' + assert len(grp_list) > 0, 'No group items in file or Manager.group_listed failed' def test_Manager_add_group(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) ref = GroupSample(reader) - ref.verify_add_groups(100) + ref.verify_add_group(100) ref.verify_remove_all_using_numeric() def test_Manager_removing_group_from_numeric(self): @@ -141,14 +141,14 @@ def test_Manager_removing_group_from_numeric(self): reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) ref = GroupSample(reader) ref.verify_remove_all_using_numeric() - ref.verify_add_groups(100) + ref.verify_add_group(100) def test_Manager_removing_group_from_name(self): '''Test if removing groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) ref = GroupSample(reader) ref.verify_remove_all_using_name() - ref.verify_add_groups(100) + ref.verify_add_group(100) def test_Manager_rename_group(self): '''Test if renaming groups acts as intended.''' @@ -172,7 +172,7 @@ def test_Manager_rename_group(self): try: reader.rename_group(new_names[0], new_names[1]) raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') - except KeyError as e: + except ValueError as e: pass # Correct def test_Manager_renumber_group(self): @@ -199,7 +199,7 @@ def test_Manager_renumber_group(self): try: reader.rename_group(max_key + 1, max_key + 2) raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') - except KeyError as e: + except ValueError as e: pass # Correct diff --git a/test/test_parameter_accessors.py b/test/test_parameter_accessors.py new file mode 100644 index 0000000..5238b83 --- /dev/null +++ b/test/test_parameter_accessors.py @@ -0,0 +1,139 @@ +''' Purpose for this file is to verify functions associated with Groups._params dictionary. +''' +import unittest +import c3d +import numpy as np +import test.verify as verify +from test.zipload import Zipload +from test.base import Base + +class ParamSample(): + ''' Helper object to verify parameter entries persist or terminate properly. ''' + def __init__(self, group): + assert isinstance(group, c3d.Group), 'Must pass group to ParamSample instance.' + self.flt_range = (-1e6, 1e6) + self.shape = (10, 2) + self.group = group + self.rnd = np.random.default_rng() + self.sample() + + @property + def items(self): + '''Helper to access group items. ''' + return [(k, g) for (k, g) in self.group.param_items()] + + @property + def keys(self): + '''Helper to access group items. ''' + return [k for (k, g) in self.group.param_items()] + + def sample(self): + '''Call before applying changes. ''' + self.s_items = self.items + self.s_keys = self.keys + + def assert_entry_count(self, delta=0): + '''Assert entry count. + + Arguments + --------- + delta: Number of entries added (+) or removed (-) since last sample. + ''' + items = self.items + assert len(self.s_items) + delta == len(items),\ + 'Rename added item entry. Expected %i entries, now has %i.' %\ + (len(self.s_items), len(items)) + + def assert_group_items(self, ignore=None): + '''Assert all named (str, Group) pairs persisted after change.''' + enumerator = range(len(self.s_items)) + for i, (n, g) in enumerate(self.s_items): + if n == ignore: + continue + g2 = self.group.get(n) + assert g == g2, 'Group listed order changed for entry %i.' % i + + def verify_add_parameter(self, N): + '''Add N parameters and verify count at each iteration.''' + self.sample() + for i in range(1, N): + test_name = 'TEST_ADD_PARAM_%i' % i + arr = self.rnd.uniform(*self.flt_range, size=self.shape).astype(np.float32) + self.group.add_param(test_name, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes()) + assert self.group.get(test_name) is not None, 'Added group does not exist.' + self.assert_group_items() + + def verify_remove_all(self): + '''Remove all groups using name key and verify count at each iteration.''' + self.sample() + keys = [k for (k, g) in self.items] + for i, key in enumerate(keys): + grp = self.group.get(key) + assert grp is not None, 'Expected group to exist.' + self.group.remove_param(key) + assert self.group.get(key) is None, 'Removed param persisted.' + self.assert_entry_count(delta=-1 - i) + + +class TestParameterAccessors(Base): + ''' Tests functionality associated with accessing and editing Paramater entries in Group objects. + ''' + ZIP = 'sample01.zip' + INTEL_INT = 'Eb015pi.c3d' + INTEL_REAL = 'Eb015pr.c3d' + + def test_Group_values(self): + '''Test Group.values()''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + for g in reader.group_values(): + assert len(g.param_values()) > 0, 'No group values in file or Group.param_values() failed' + + def test_Group_items(self): + '''Test Group.items()''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + for g in reader.group_values(): + assert len(g.param_items()) > 0, 'No group items in file or Group.param_items() failed' + + def test_Group_add_param(self): + '''Test if adding and groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + for g in reader.group_values(): + ref = ParamSample(g) + ref.verify_add_parameter(100) + ref.verify_remove_all() + + def test_Group_remove_param(self): + '''Test if removing groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + for g in reader.group_values(): + ref = ParamSample(g) + ref.verify_remove_all() + ref.verify_add_parameter(100) + + def test_Group_rename_param(self): + '''Test if renaming groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + + for g in reader.group_values(): + ref = ParamSample(g) + prm_keys = ref.keys + new_names = ['TEST_NAME' + str(i) for i in range(len(prm_keys))] + for key, nname in zip(prm_keys, new_names): + prm = g.get(key) + g.rename_param(key, nname) + prm2 = g.get(nname) + assert prm2 is not None, "Rename failed, renamed param does not exist." + assert prm == prm2, 'Rename failed, param acquired from new name is not identical.' + + ref.assert_entry_count() + try: + g.rename_param(new_names[0], new_names[1]) + raise RuntimeError('Overwriting existing numerical ID should raise a ValueError.') + except ValueError as e: + pass # Correct + + + + +if __name__ == '__main__': + unittest.main() From b0e25ea8f72c6b53e6ef697ff5ea2c76a895bbd8 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Tue, 29 Jun 2021 16:24:43 +0200 Subject: [PATCH 023/120] Moved custom writer properties to the header where possible --- c3d.py | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/c3d.py b/c3d.py index d359216..36887fd 100644 --- a/c3d.py +++ b/c3d.py @@ -189,8 +189,8 @@ class Header(object): Index of the last frame of data. analog_per_frame : int Number of analog frames per frame of 3D point data. The analog frame - rate (ANALOG:RATE) apparently equals the point frame rate (POINT:RATE) - times this value. + rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE) + times the analog per frame value. frame_rate : float The frame rate of the recording, in frames per second. scale_factor : float @@ -1649,7 +1649,7 @@ class Writer(Manager): point_units : str, optional The units that the point numbers represent. Defaults to ``'mm '``. gen_scale : float, optional - General scaling factor for data. Defaults to 1. + General scaling factor for analog data. Defaults to 1. ''' def __init__(self, @@ -1661,17 +1661,25 @@ def __init__(self, '''Set metadata for this writer. ''' - # Always write INTEL format - self._dtypes = DataTypes(PROCESSOR_INTEL) + self._dtypes = DataTypes(PROCESSOR_INTEL) # Always write INTEL format super(Writer, self).__init__() - self._point_rate = point_rate - self._analog_rate = analog_rate - self._analog_per_frame = analog_rate / point_rate - self._point_scale = point_scale + + # Custom properties self._point_units = point_units self._gen_scale = gen_scale + + # Header properties + self._header.frame_rate = np.float32(point_rate) + self._header.scale_factor = np.float32(self._point_scale) + self.analog_rate = analog_rate self._frames = [] + @analog_rate.setter + def analog_rate(self, value): + per_frame_rate = value / self.frame_rate + assert per_frame_rate.is_integer(), "Analog rate must be a multiple of the point rate." + return self._header.analog_per_frame = np.uint16(per_frame_rate) + def add_frames(self, frames): '''Add frames to this writer instance. @@ -1796,8 +1804,8 @@ def add_empty_array(name, desc, bpe): add('USED', 'Number of 3d markers', 2, ' Date: Tue, 29 Jun 2021 18:12:15 +0200 Subject: [PATCH 024/120] DataTypes.proc_type -> DataTypes._proc_type --- c3d.py | 50 ++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 40 insertions(+), 10 deletions(-) diff --git a/c3d.py b/c3d.py index 36887fd..3ac1df4 100644 --- a/c3d.py +++ b/c3d.py @@ -4,6 +4,7 @@ import array import io +import copy import numpy as np import struct import warnings @@ -19,8 +20,8 @@ class DataTypes(object): Data types depend on the processor format the file is stored in. ''' def __init__(self, proc_type): - self.proc_type = proc_type - if proc_type == PROCESSOR_MIPS: + self._proc_type = proc_type + if self._proc_type == PROCESSOR_MIPS: # Big-Endian (SGI/MIPS format) self.float32 = np.dtype(np.float32).newbyteorder('>') self.float64 = np.dtype(np.float64).newbyteorder('>') @@ -49,19 +50,26 @@ def __init__(self, proc_type): def is_ieee(self): ''' True if the associated file is in the Intel format. ''' - return self.proc_type == PROCESSOR_INTEL + return self._proc_type == PROCESSOR_INTEL @property def is_dec(self): ''' True if the associated file is in the DEC format. ''' - return self.proc_type == PROCESSOR_DEC + return self._proc_type == PROCESSOR_DEC @property def is_mips(self): ''' True if the associated file is in the SGI/MIPS format. ''' - return self.proc_type == PROCESSOR_MIPS + return self._proc_type == PROCESSOR_MIPS + + @property + def proc_type(self): + ''' Get the processory type associated with the data format in the file. + ''' + processor_type = ['INTEL', 'DEC', 'MIPS'] + return processor_type[self._proc_type - PROCESSOR_INTEL] def decode_string(self, bytes): ''' Decode a byte array to a string. @@ -1618,11 +1626,9 @@ def read_frames(self, copy=True): @property def proc_type(self): - """ - Get the processory type associated with the data format in the file. - """ - processor_type = ['PROCESSOR_INTEL', 'PROCESSOR_DEC', 'PROCESSOR_MIPS'] - return processor_type[self._dtypes.proc_type - PROCESSOR_INTEL] + '''Get the processory type associated with the data format in the file. + ''' + return self._dtypes.proc_type class Writer(Manager): @@ -1680,6 +1686,30 @@ def analog_rate(self, value): assert per_frame_rate.is_integer(), "Analog rate must be a multiple of the point rate." return self._header.analog_per_frame = np.uint16(per_frame_rate) + @staticmethod + def from_reader(reader, conversion='consume'): + ''' + source : 'class' Manager + Source to copy. + conversion : str + Conversion mode, supported modes are: + 'consume' - (Default) Reader object will be consumed and explicitly deleted. + 'copy' - Reader objects will be deep copied. + 'shallow_copy' - No group parameters are copied. + ''' + writer = Writer() + if not reader._dtypes.is_intel: + warnings.warn('File was read in !'.format( + self._handle.tell() - final_byte_index)) + if consume == False: + + if consume: + writer._header = copy.deepcopy(reader._header) + else: + # Consume + writer._header = reader._header + reader._header = None + def add_frames(self, frames): '''Add frames to this writer instance. From e4a5e009cf7b40a39e8b8e7e044651fbf4e10321 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Tue, 29 Jun 2021 20:34:47 +0200 Subject: [PATCH 025/120] Correction for existing tests, updated readme, comments --- README.rst | 3 ++ c3d.py | 77 ++++++++++++++++++++++++++-------- test/test_software_examples.py | 5 +++ 3 files changed, 67 insertions(+), 18 deletions(-) diff --git a/README.rst b/README.rst index 11242de..aefb9c6 100644 --- a/README.rst +++ b/README.rst @@ -56,6 +56,9 @@ To run tests available in the test folder, following command can be run from the python -m unittest discover . +Test scripts will automatically download test files from `c3d.org`_. + +.. _c3d.org: https://www.c3d.org/sampledata.html Caveats ------- diff --git a/c3d.py b/c3d.py index 3ac1df4..266f846 100644 --- a/c3d.py +++ b/c3d.py @@ -1630,6 +1630,12 @@ def proc_type(self): ''' return self._dtypes.proc_type + def as_writer(self, conversion): + ''' Convert to writer using the conversion mode. + See Writer.from_reader() for supported converstion modes. + ''' + return Writer.from_reader(self, conversion=mode) + class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -1676,39 +1682,74 @@ def __init__(self, # Header properties self._header.frame_rate = np.float32(point_rate) - self._header.scale_factor = np.float32(self._point_scale) + self._header.scale_factor = np.float32(point_scale) self.analog_rate = analog_rate self._frames = [] + @property + def analog_rate(self): + return super(Writer, self).analog_rate + @analog_rate.setter def analog_rate(self, value): - per_frame_rate = value / self.frame_rate - assert per_frame_rate.is_integer(), "Analog rate must be a multiple of the point rate." - return self._header.analog_per_frame = np.uint16(per_frame_rate) + per_frame_rate = value / self.point_rate + assert float(per_frame_rate).is_integer(), "Analog rate must be a multiple of the point rate." + self._header.analog_per_frame = np.uint16(per_frame_rate) @staticmethod - def from_reader(reader, conversion='consume'): + def from_reader(reader, conversion=None): ''' source : 'class' Manager Source to copy. conversion : str - Conversion mode, supported modes are: + Conversion mode, None is equivalent to the default mode. Supported modes are: 'consume' - (Default) Reader object will be consumed and explicitly deleted. 'copy' - Reader objects will be deep copied. - 'shallow_copy' - No group parameters are copied. + 'shallow_copy' - Similar to 'copy' but group parameters are not copied. + + Returns + ------- + param : :class:`Param` + A parameter from the current group. + + Raises + ------ + ValueError + If mode string is not equivalent to one of the supported modes. + If attempting to convert non-Intel files using mode other than 'shallow_copy'. ''' writer = Writer() - if not reader._dtypes.is_intel: - warnings.warn('File was read in !'.format( - self._handle.tell() - final_byte_index)) - if consume == False: - - if consume: - writer._header = copy.deepcopy(reader._header) - else: - # Consume + # Modes + is_consume = conversion == 'consume' or conversion is None + is_shallow_copy = conversion == 'shallow_copy' + is_deep_copy = conversion == 'copy' + # Verify mode + if not (is_consume or is_shallow_copy or is_deep_copy): + raise ValueError( + "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(mode)) + if not reader._dtypes.is_intel and not is_shallow_copy: + # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. + raise ValueError( + "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( + reader.proc_format)) + + if is_consume: writer._header = reader._header reader._header = None + writer._groups = reader._groups + reader._groups = None + del reader + elif is_deep_copy: + writer._header = copy.deepcopy(reader._header) + writer._groups = copy.deepcopy(reader._groups) + elif is_shallow_copy: + # Only copy header (no groups) + writer._header = copy.deepcopy(reader._header) + + # Copy frames + for i, frame in enumerate(reader.read_frames(copy=True)): + self.add_frames(frame) + def add_frames(self, frames): '''Add frames to this writer instance. @@ -1834,8 +1875,8 @@ def add_empty_array(name, desc, bpe): add('USED', 'Number of 3d markers', 2, ' Date: Thu, 1 Jul 2021 12:08:59 +0200 Subject: [PATCH 026/120] Working WriteRead --- c3d.py | 633 ++++++++++++++++------ test/test_c3d.py | 5 +- test/test_software_examples_write_read.py | 66 +++ test/verify.py | 75 ++- 4 files changed, 593 insertions(+), 186 deletions(-) create mode 100644 test/test_software_examples_write_read.py diff --git a/c3d.py b/c3d.py index 266f846..5501804 100644 --- a/c3d.py +++ b/c3d.py @@ -2,7 +2,6 @@ from __future__ import unicode_literals -import array import io import copy import numpy as np @@ -14,6 +13,7 @@ PROCESSOR_DEC = 85 PROCESSOR_MIPS = 86 +INVALID_FLAG = -100000 class DataTypes(object): ''' Container defining different data types used for reading file data. @@ -84,6 +84,13 @@ def decode_string(self, bytes): # Revert to using default decoder but replace characters return codecs.decode(bytes, decoders[0], 'replace') +class Decorator(object): + '''Base class for extending (decotrating) a python object. + ''' + def __init__(self, decoratee): + self._decoratee = decoratee + def __getattr__(self, name): + return getattr(self._decoratee, name) def UNPACK_FLOAT_IEEE(uint_32): '''Unpacks a single 32 bit unsigned int to a IEEE float representation @@ -176,6 +183,10 @@ def is_integer(value): '''Check if value input is integer.''' return isinstance(value, (int, np.int32, np.int64)) +def is_iterable(value): + '''Check if value is iterable.''' + return hasattr(value, '__iter__') + class Header(object): '''Header information from a C3D file. @@ -787,6 +798,9 @@ def __init__(self, dtypes, name=None, desc=None): def __repr__(self): return ''.format(self.desc) + def __contains__(self, key): + return key in self._params + @property def name(self): ''' Group name. ''' @@ -822,9 +836,10 @@ def desc(self, value): ''' if isinstance(value, bytes): self._desc = self._dtypes.decode_string(value) - elif value is not None and not isinstance(value, str): - raise TypeError('Expected descriptor to be byte string or python string, was %s.' % type(value)) - self._desc = value + elif isinstance(value, str) or value is None: + self._desc = value + else: + raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(value)) def param_items(self): ''' Acquire iterator for paramater key-entry pairs. ''' @@ -865,8 +880,20 @@ def add_param(self, name, **kwargs): automatically be case-normalized. Additional keyword arguments will be passed to the `Param` constructor. + + Raises + ------ + TypeError + Input arguments are of the wrong type. + KeyError + Name or numerical key already exist (attempt to overwrite existing data). ''' - self._params[name.upper()] = Param(name.upper(), self._dtypes, **kwargs) + if not isinstance(name, str): + raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name))) + name = name.upper() + if name in self._params: + raise KeyError('Parameter already exists with key {}'.format(name)) + self._params[name] = Param(name, self._dtypes, **kwargs) def remove_param(self, name): '''Remove the specified parameter. @@ -887,9 +914,16 @@ def rename_param(self, name, new_name): Parameter instance, or name. new_name : str New name for the parameter. + + Raises + ------ + KeyError + If no parameter with the original name exists. + ValueError + If the new name already exist (attempt to overwrite existing data). ''' if new_name in self._params: - raise ValueError("Key %s already exist." % new_name) + raise ValueError("Key {} already exist.".format(new_name)) if isinstance(name, Param): param = name name = param.name @@ -897,7 +931,7 @@ def rename_param(self, name, new_name): # Aquire instance using id param = self._params.get(name, None) if param is None: - raise ValueError('No parameter found matching the identifier: %s' % str(name)) + raise KeyError('No parameter found matching the identifier: {}'.format(str(name))) del self._params[name] self._params[new_name] = param @@ -985,6 +1019,9 @@ def __init__(self, header=None): self._header = header or Header() self._groups = {} + def __contains__(self, key): + return key in self._groups + @property def header(self): ''' Access the parsed c3d header. ''' @@ -1113,17 +1150,19 @@ def add_group(self, group_id, name, desc): ------ TypeError Input arguments are of the wrong type. + KeyError + Name or numerical key already exist (attempt to overwrite existing data). ''' if not is_integer(group_id): - raise ValueError('Expected Group numerical key to be integer, was %s.' % type(group_id)) + raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id)) if not (isinstance(name, str) or name is None): - raise ValueError('Expected Group name key to be string, was %s.' % type(name)) - group_id = int(group_id) # Assert python int + raise TypeError('Expected Group name key to be string, was %s.' % type(name)) + group_id = int(group_id) # Asserts python int if group_id in self._groups: - raise KeyError(group_id) + raise KeyError('Group with numerical key {} already exists'.format(group_id)) name = name.upper() if name in self._groups: - raise KeyError(name) + raise KeyError('No group matched name key {}'.format(name)) group = self._groups[name] = self._groups[group_id] = Group(self._dtypes, name, desc) return group @@ -1356,6 +1395,29 @@ def last_frame(self): # Return the largest of the all (queue bad reading...) return int(np.max(end_frame)) + def _get_analog_transform(self): + ''' Parse analog data transform parameters. + ''' + # Offsets + analog_offsets = np.zeros((self.analog_used, 1), int) + param = self.get('ANALOG:OFFSET') + if param is not None and param.num_elements > 0: + analog_offsets[:, 0] = param.int16_array[:self.analog_used] + + # Scale factors + analog_scales = np.ones((self.analog_used, 1), float) + gen_scale = 1. + param = self.get('ANALOG:GEN_SCALE') + if param is not None: + gen_scale = param.float_value + param = self.get('ANALOG:SCALE') + if param is not None and param.num_elements > 0: + analog_scales[:, 0] = param.float_array[:self.analog_used] + analog_scales *= gen_scale + + analog_scales = np.broadcast_to(analog_scales, (self.analog_used, self.analog_per_frame)) + analog_offsets = np.broadcast_to(analog_offsets, (self.analog_used, self.analog_per_frame)) + return analog_scales, analog_offsets class Reader(Manager): '''This class provides methods for reading the data in a C3D file. @@ -1430,8 +1492,8 @@ def seek_param_section_header(): if group_id > 0: # We've just started reading a parameter. If its group doesn't # exist, create a blank one. add the parameter to the group. - self._groups.setdefault( - group_id, Group(self._dtypes)).add_param(name, handle=buf) + group = self._groups.setdefault(group_id, Group(self._dtypes)) + group.add_param(name, handle=buf) else: # We've just started reading a group. If a group with the # appropriate numerical id exists already (because we've @@ -1442,14 +1504,14 @@ def seek_param_section_header(): desc = size and buf.read(size) or '' group = self.get(group_id) if group is not None: - self.rename_group(group, name) + self.rename_group(group, name) # Inserts name key group.desc = desc else: self.add_group(group_id, name, desc) self._check_metadata() - def read_frames(self, copy=True): + def read_frames(self, copy=True, analog_transform=True, camera_sum=False): '''Iterate over the data frames from our C3D file handle. Parameters @@ -1511,26 +1573,14 @@ def read_frames(self, copy=True): analog_word_bytes = 2 analog = np.array([], float) - offsets = np.zeros((self.analog_used, 1), int) - param = self.get('ANALOG:OFFSET') - if param is not None: - offsets = param.int16_array[:self.analog_used, None] - - analog_scales = np.ones((self.analog_used, 1), float) - param = self.get('ANALOG:SCALE') - if param is not None: - analog_scales[:, :] = param.float_array[:self.analog_used, None] - - gen_scale = 1. - param = self.get('ANALOG:GEN_SCALE') - if param is not None: - gen_scale = param.float_value + analog_scales, analog_offsets = self._get_analog_transform() # Seek to the start point of the data blocks self._handle.seek((self._header.data_block - 1) * 512) # Number of values (words) read in regard to POINT/ANALOG data N_point = 4 * self.point_used N_analog = self.analog_used * self.analog_per_frame + # Total bytes per frame point_bytes = N_point * point_word_bytes analog_bytes = N_analog * analog_word_bytes @@ -1559,7 +1609,7 @@ def read_frames(self, copy=True): # Re-read the raw byte representation directly points[:, :4] = np.frombuffer(raw_bytes, dtype=self._dtypes.float32, - count=N_point).reshape((int(self.point_used), 4)) + count=N_point).reshape((self.point_used, 4)) # Parse the camera-observed bits and residuals. # Notes: @@ -1570,8 +1620,13 @@ def read_frames(self, copy=True): # - While words are 16 bit, residual and camera mask is always interpreted as 8 packed in a single word! # - 16 or 32 bit may represent a sign (indication that certain files write a -1 floating point only) last_word = points[:, 3].astype(np.int32) - valid = (last_word & 0x80008000) == 0 - points[~valid, 3:5] = -1.0 + valid = last_word > -1 # (last_word & 0x80008000) == 0 + # Lookup other + #if np.sum(~valid) > 0: + #print(np.sum(~valid)) + #print(points[~valid, :3]) + #print(last_word[~valid]) + points[~valid, 3:5] = INVALID_FLAG c = last_word[valid] else: @@ -1584,16 +1639,18 @@ def read_frames(self, copy=True): # Parse last 16-bit word as two 8-bit words valid = raw[:, 3] > -1 - points[~valid, 3:5] = -1 + points[~valid, 3:5] = INVALID_FLAG c = raw[valid, 3].astype(self._dtypes.uint16) # Convert coordinate data # fourth value is floating-point (scaled) error estimate (residual) - points[valid, 3] = (c & 0xff).astype(np.float32) * scale_mag + points[valid, 3] = (c & 0x00ff).astype(np.float32) * scale_mag # fifth value is number of bits set in camera-observation byte - points[valid, 4] = sum((c & (1 << k)) >> k for k in range(8, 15)) - # Get value as is: points[valid, 4] = (c >> 8) + if camera_sum: + points[valid, 4] = sum((c & (1 << k)) >> k for k in range(8, 15)) + else: + points[valid, 4] = (c & 0xff00 >> 8) # Check if analog data exist, and parse if so if N_analog > 0: @@ -1608,7 +1665,7 @@ def read_frames(self, copy=True): analog = analog.reshape((-1, self.analog_used)).T analog = analog.astype(float) # Convert analog - analog = (analog - offsets) * analog_scales * gen_scale + analog = (analog - analog_offsets) * analog_scales # Output buffers if copy: @@ -1630,11 +1687,131 @@ def proc_type(self): ''' return self._dtypes.proc_type - def as_writer(self, conversion): - ''' Convert to writer using the conversion mode. - See Writer.from_reader() for supported converstion modes. + def to_writer(self, conversion): + ''' Convert to 'Writer' using the conversion mode. + See Writer.from_reader() for supported conversion modes and possible exceptions. + ''' + return Writer.from_reader(self, conversion=conversion) + + +class GroupEditable(Decorator): + ''' Group instance decorator providing convenience functions for Writer editing. + ''' + def __init__(self, group): + super(GroupEditable, self).__init__(group) + + def __contains__(self, key): + return key in self._decoratee + # + # Add decorator functions (throws on overwrite) + # + def add(self, name, desc, bpe, format, data, *dimensions): + ''' Add a parameter with 'data' package formated in accordance with 'format'. + ''' + if isinstance(data, bytes): + pass + else: + data = struct.pack(format, data) + + self.add_param(name, + desc=desc, + bytes_per_element=bpe, + bytes=data, + dimensions=list(dimensions)) + + def add_array(self, name, desc, data, dtype=None): + '''Add a parameter with the 'data' package. + + Arguments + --------- + data : Numpy array, or python iterable. + dtype : Numpy dtype to encode the array (Optional if data is numpy type). + ''' + if not isinstance(data, np.ndarray): + if dtype is not None: + raise ValueError('Must specify dtype when passning non-numpy array type.') + data = np.array(data, dtype=dtype) + elif dtype is None: + dtype = data.dtype + + self.add_param(name, + desc=desc, + bytes_per_element=dtype.itemsize, + bytes=data, + dimensions=data.shape) + + def add_str(self, name, desc, data, *dimensions): + ''' Add a string parameter. + ''' + self.add_param(name, + desc=desc, + bytes_per_element=-1, + bytes=data.encode('utf-8'), + dimensions=list(dimensions)) + + def add_empty_array(self, name, desc, bpe): + ''' Add an empty parameter block. + ''' + self.add_param(name, desc=desc, + bytes_per_element=bpe, dimensions=[0]) + + # + # Set decorator functions (overwrites) + # + def set(self, name, *args, **kwargs): + ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'. + ''' + try: + self.remove_param(name) + except KeyError as e: + pass + self.add(name, *args, **kwargs) + + def set_str(self, name, *args, **kwargs): + ''' Add a string parameter. ''' - return Writer.from_reader(self, conversion=mode) + try: + self.remove_param(name) + except KeyError as e: + pass + self.add_str(name, *args, **kwargs) + + def set_array(self, name, *args, **kwargs): + ''' Add a string parameter. + ''' + try: + self.remove_param(name) + except KeyError as e: + pass + self.add_array(name, *args, **kwargs) + + def set_empty_array(self, name, *args, **kwargs): + ''' Add an empty parameter block. + ''' + try: + self.remove_param(name) + except KeyError as e: + pass + self.add_empty_array(name, *args, **kwargs) + + # + # Try add decorator functions (catches KeyError) + # + def try_add(self, name, *args, **kwargs): + ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'. + ''' + try: + self.add(name, *args, **kwargs) + except KeyError as e: + pass + + def try_add_str(self, name, *args, **kwargs): + ''' Add a string parameter. + ''' + try: + self.add_str(name, *args, **kwargs) + except KeyError as e: + pass class Writer(Manager): @@ -1678,7 +1855,6 @@ def __init__(self, # Custom properties self._point_units = point_units - self._gen_scale = gen_scale # Header properties self._header.frame_rate = np.float32(point_rate) @@ -1686,16 +1862,6 @@ def __init__(self, self.analog_rate = analog_rate self._frames = [] - @property - def analog_rate(self): - return super(Writer, self).analog_rate - - @analog_rate.setter - def analog_rate(self, value): - per_frame_rate = value / self.point_rate - assert float(per_frame_rate).is_integer(), "Analog rate must be a multiple of the point rate." - self._header.analog_per_frame = np.uint16(per_frame_rate) - @staticmethod def from_reader(reader, conversion=None): ''' @@ -1705,12 +1871,14 @@ def from_reader(reader, conversion=None): Conversion mode, None is equivalent to the default mode. Supported modes are: 'consume' - (Default) Reader object will be consumed and explicitly deleted. 'copy' - Reader objects will be deep copied. - 'shallow_copy' - Similar to 'copy' but group parameters are not copied. + 'copy_metadata' - Similar to 'copy' but only copies metadata and not point and analog frame data. + 'copy_shallow' - Similar to 'copy' but group parameters are not copied. + 'copy_header' - Similar to 'copy_shallow' but only the header is copied (frame data is not copied). Returns ------- - param : :class:`Param` - A parameter from the current group. + param : :class:`Writer` + A writeable and persistent representation of the 'Reader' object. Raises ------ @@ -1720,14 +1888,18 @@ def from_reader(reader, conversion=None): ''' writer = Writer() # Modes + is_header_only = conversion == 'copy_header' + is_meta_copy = conversion == 'copy_metadata' + is_meta_only = is_header_only or is_meta_copy is_consume = conversion == 'consume' or conversion is None - is_shallow_copy = conversion == 'shallow_copy' - is_deep_copy = conversion == 'copy' + is_shallow_copy = conversion == 'shallow_copy' or is_header_only + is_deep_copy = conversion == 'copy' or is_meta_copy # Verify mode if not (is_consume or is_shallow_copy or is_deep_copy): raise ValueError( - "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(mode)) - if not reader._dtypes.is_intel and not is_shallow_copy: + "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format( + conversion)) + if not reader._dtypes.is_ieee and not is_shallow_copy: # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. raise ValueError( "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( @@ -1746,21 +1918,231 @@ def from_reader(reader, conversion=None): # Only copy header (no groups) writer._header = copy.deepcopy(reader._header) - # Copy frames - for i, frame in enumerate(reader.read_frames(copy=True)): - self.add_frames(frame) + if not is_meta_only: + # Copy frames + for (i, point, analog) in reader.read_frames(copy=True, camera_sum=False): + writer.add_frames((point, analog)) + return writer + + @property + def analog_rate(self): + return super(Writer, self).analog_rate + + @analog_rate.setter + def analog_rate(self, value): + per_frame_rate = value / self.point_rate + assert float(per_frame_rate).is_integer(), "Analog rate must be a multiple of the point rate." + self._header.analog_per_frame = np.uint16(per_frame_rate) + + @property + def numeric_key_max(self): + ''' Get the largest numeric key. + ''' + num = 0 + if len(self._groups) > 0: + for i in self._groups.keys(): + if isinstance(i, int): + num = max(i, num) + return num + + @property + def numeric_key_next(self): + ''' Get a new unique numeric group key. + ''' + return self.numeric_key_max + 1 + + def get_create(self, label): + ''' Get or create the specified parameter group.''' + label = label.upper() + group = self.get(label) + if group is None: + group = self.add_group(self.numeric_key_next, label, label + ' group') + return group + + @property + def point_group(self): + ''' Get or create the POINT parameter group.''' + return self.get_create('POINT') + + @property + def analog_group(self): + ''' Get or create the ANALOG parameter group.''' + return self.get_create('ANALOG') + + @property + def trial_group(self): + ''' Get or create the TRIAL parameter group.''' + return self.get_create('TRIAL') + + def get(self, group, default=None): + '''Get a GroupEditable decorator for keyed group instance, or a parameter instance. + + Parameters + ---------- + group : str + Key, see Manager.get() for valid key formats. + default : any + Return this value if the named group and parameter are not found. + Returns + ------- + value : :class:`GroupEditable` or :class:`Param` + Either a decorated group instance or parameter with the specified name(s). If neither + is found, the default value is returned. + ''' + val = super(Writer, self).get(group, default) + if isinstance(val, Group): + return GroupEditable(val) + return val # Parameter + + def add_group(self, *args, **kwargs): + '''Add a new parameter group. See Manager.add_group() for more information. + + Returns + ------- + group : :class:`Group` + An editable group instance. + ''' + return GroupEditable(super(Writer, self).add_group(*args, **kwargs)) def add_frames(self, frames): '''Add frames to this writer instance. Parameters ---------- - frames : sequence of (point, analog) tuples - A sequence of frame data to add to the writer. + frames : single or sequence of (point, analog) pairs + A sequence or frame of frame data to add to the writer. ''' + sh = np.shape(frames) + # Single frame + if len(sh) != 2: + frames = [frames] + sh = np.shape(frames) + # Sequence of invalid shape + if sh[1] != 2: + raise ValueError( + 'Expected frame input to be sequence of point and analog pairs on form (-1, 2). ' + + '\Input was of shape {}.'.format(str(sh))) self._frames.extend(frames) + def set_point_labels(self, labels): + group = self.point_group + labels = np.ravel(labels) + # Get longest label name + label_max_size = 0 + label_max_size = max(label_max_size, np.max([len(label) for label in labels])) + + label_str = ''.join(label.ljust(label_max_size) for label in labels) + group.add_str('LABELS', 'labels', label_str, label_max_size, len(labels)) + + def set_analog_general_scale(self, value): + ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor). + ''' + self.analog_group.set('GEN_SCALE', 'Analog general scale factor', 4, '= UINT16_MAX: + # Should be floating point + group.set('LONG_FRAMES', 'Total frame count', 4, ' -1 - raw[~valid, 3] = -1 + raw[~valid, 3] = INVALID_FLAG raw[valid, :3] = points[valid, :3] / point_scale - raw[valid, 3] = ( - ((points[valid, 4]).astype(np.uint8) << 8) | - (points[valid, 3] / scale).astype(np.uint16) - ) - point = array.array(point_format) - point.extend(raw.flatten()) - point.tofile(handle) - analog = array.array(point_format) - analog.extend(analog) - analog.tofile(handle) + raw[valid, 3] = np.bitwise_or(np.rint(points[valid, 3] / scale_mag).astype(np.uint8), + (points[valid, 4].astype(np.uint16) << 8), + dtype=np.uint16) + + # Transform analog data + analog = analog * analog_scales_inv + analog_offsets + analog = analog.T + + # Write + analog = analog.astype(point_dtype) + handle.write(raw.tobytes()) + handle.write(analog.tobytes()) self._pad_block(handle) - - def write(self, handle, labels): - '''Write metadata and point + analog frames to a file handle. - - Parameters - ---------- - handle : file - Write metadata and C3D motion frames to the given file handle. The - writer does not close the handle. - ''' - if not self._frames: - return - - def add(name, desc, bpe, format, bytes, *dimensions): - group.add_param(name, - desc=desc, - bytes_per_element=bpe, - bytes=struct.pack(format, bytes), - dimensions=list(dimensions)) - - def add_str(name, desc, bytes, *dimensions): - group.add_param(name, - desc=desc, - bytes_per_element=-1, - bytes=bytes.encode('utf-8'), - dimensions=list(dimensions)) - - def add_empty_array(name, desc, bpe): - group.add_param(name, desc=desc, - bytes_per_element=bpe, dimensions=[0]) - - points, analog = self._frames[0] - ppf = len(points) - labels = np.ravel(labels) - - # POINT group - - # Get longest label name - label_max_size = 0 - label_max_size = max(label_max_size, np.max([len(label) for label in labels])) - - group = self.add_group(1, 'POINT', 'POINT group') - add('USED', 'Number of 3d markers', 2, ' -1.0 + bvalid = bpoint[:, 3] > -1.0 + valid_diff = np.sum(np.logical_xor(avalid, bvalid)) + if valid_diff > 0: + diff = np.logical_xor(avalid, bvalid) + print('A', apoint[diff, 3]) + print('B', bpoint[diff, 3]) + assert valid_diff == 0, '\n' +\ + 'Error in number of valid samples between {} and {}.\n'.format(alabel, blabel) +\ + 'Total number of validation mismatches: {} of {}'.format(valid_diff, len(avalid)) + + # Only compare valid point data + valid = avalid + apoint = apoint[valid] + bpoint = bpoint[valid] + + tot_points = len(apoint) + tot_analog = areader.analog_used * analog_count # Compare point data (coordinates) c = ['X', 'Y', 'Z'] + atol = equal_scale_fac * abs(areader.point_scale) for i in range(3): - axis_diff = nsampled_coordinates - np.sum(np.isclose(apoint[:, :, i], bpoint[:, :, i], - atol=equal_scale_fac*abs(areader.point_scale))) - assert axis_diff == 0, \ - 'Mismatched coordinates on {} axis for {} and {}, number of sampled diff: {} of {}'.format( - c[i], alabel, blabel, axis_diff, nsampled_coordinates) + was_close = np.isclose(apoint[:, i], bpoint[:, i], atol=atol) + axis_notclose = tot_points - np.sum(was_close) + assert axis_notclose == 0, '\n' +\ + 'Mismatched coordinates on {} axis between {} and {}.\n'.format(c[i], alabel, blabel) +\ + 'Samples with absolute difference larger then {:0.4f}: {} of {}.\n'.format( + atol, axis_notclose, tot_points) +\ + 'Maximum difference: {}'.format(np.max(np.abs(apoint[:, i] - bpoint[:, i]))) # Word 4 (residual + camera bits) - residual_diff = nsampled_coordinates - np.sum(np.isclose(apoint[:, :, 3], bpoint[:, :, 3])) - cam_diff = nsampled_coordinates - np.sum(np.isclose(apoint[:, :, 4], bpoint[:, :, 4], atol=1.001)) - cam_diff_non_equal = nsampled_coordinates - np.sum(np.isclose(apoint[:, :, 4], bpoint[:, :, 4])) + residual_diff = tot_points - np.sum(np.isclose(apoint[:, 3], bpoint[:, 3])) + cam_close = np.isclose(apoint[:, 4], bpoint[:, 4], atol=1.001) + cam_diff = tot_points - np.sum(cam_close) + cam_diff_non_equal = tot_points - np.sum(np.isclose(apoint[:, 4], bpoint[:, 4])) # Camera bit errors (warn if non identical, allow 1 cam bit diff, might be bad DEC implementation, or bad data) if cam_diff_non_equal > 0: - assert cam_diff == 0, 'Mismatch error in camera bit flags for {} and {}, number of samples with flag diff:\ - {} of {}'.format(alabel, blabel, cam_diff, nsampled_coordinates) - err_str = 'Mismatch in camera bit flags between {} and {}, number of samples with flag diff:\ - {} of {}'.format(alabel, blabel, cam_diff_non_equal, nsampled_coordinates) + print(apoint[~cam_close, 4]) + print(bpoint[~cam_close, 4]) + assert cam_diff == 0, \ + 'Mismatch error in camera bit flags for {} and {}, number of samples with flag diff: {} of {}'.format( + alabel, blabel, cam_diff, tot_points) + err_str =\ + 'Mismatch in camera bit flags between {} and {}, number of samples with flag diff: {} of {}'.format( + alabel, blabel, cam_diff_non_equal, tot_points) warnings.warn(err_str, RuntimeWarning) # Residual assert - assert residual_diff == 0, \ - 'Error in sample residuals between {} and {}, number of residual diff: {} of {}'.format( - alabel, blabel, residual_diff, nsampled_coordinates) + assert residual_diff == 0, '\n' +\ + 'Error in sample residuals between {} and {}.\n'.format(alabel, blabel) +\ + 'Total number of failed samples: {} of {}'.format(residual_diff, tot_points) # Compare analog - analog_diff = nsampled_analog - np.sum(np.isclose(aanalog, banalog)) - assert analog_diff == 0, \ - 'Mismatched analog samples between {} and {}, number of sampled diff: {} of {}'.format( - alabel, blabel, analog_diff, nsampled_analog) + was_close = np.isclose(aanalog, banalog) + analog_notclose = tot_analog - np.sum(was_close) + assert analog_notclose == 0, '\n' + \ + 'Mismatched analog samples between {} and {}.\n'.format(alabel, blabel) +\ + 'Total number of failed samples: {} of {}.\n'.format(analog_notclose, tot_analog) +\ + 'Largest absolute difference: {}.'.format(np.max(np.abs(aanalog - banalog))) From 1a8f678e1dc316d6f876d3a3755bacc3f0b55897 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Thu, 1 Jul 2021 20:18:20 +0200 Subject: [PATCH 027/120] Added nan-check, cleaned up + corrected read_frames, added big-endian system warning --- c3d.py | 132 ++++++++++++++-------- test/test_software_examples.py | 5 +- test/test_software_examples_write_read.py | 19 ++-- test/verify.py | 44 ++++---- 4 files changed, 122 insertions(+), 78 deletions(-) diff --git a/c3d.py b/c3d.py index 5501804..172b757 100644 --- a/c3d.py +++ b/c3d.py @@ -2,6 +2,7 @@ from __future__ import unicode_literals +import sys import io import copy import numpy as np @@ -21,6 +22,12 @@ class DataTypes(object): ''' def __init__(self, proc_type): self._proc_type = proc_type + self._little_endian_sys = sys.byteorder == 'little' + self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \ + (self.is_mips and self.big_endian_sys) + if self.big_endian_sys: + warnings.warn('Systems with native byte order of big-endian are not supported.') + if self._proc_type == PROCESSOR_MIPS: # Big-Endian (SGI/MIPS format) self.float32 = np.dtype(np.float32).newbyteorder('>') @@ -46,6 +53,24 @@ def __init__(self, proc_type): self.int32 = np.int32 self.int64 = np.int64 + @property + def native(self): + ''' True if the native (system) byte order matches the file byte order. + ''' + return self._native + + @property + def little_endian_sys(self): + ''' True if native byte order is little-endian. + ''' + return self._little_endian_sys + + @property + def big_endian_sys(self): + ''' True if native byte order is big-endian. + ''' + return not self._little_endian_sys + @property def is_ieee(self): ''' True if the associated file is in the Intel format. @@ -158,12 +183,13 @@ def DEC_to_IEEE_BYTES(bytes): # See comments in DEC_to_IEEE() for DEC format definition # Reshuffle - bytes = np.frombuffer(bytes, dtype=np.dtype('B')) + bytes = memoryview(bytes) reshuffled = np.empty(len(bytes), dtype=np.dtype('B')) - reshuffled[0::4] = bytes[2::4] + reshuffled[::4] = bytes[2::4] reshuffled[1::4] = bytes[3::4] - reshuffled[2::4] = bytes[0::4] - reshuffled[3::4] = bytes[1::4] + ((bytes[1::4] & 0x7f == 0) - 1) # Decrement exponent by 2, if exp. > 1 + reshuffled[2::4] = bytes[::4] + # Decrement exponent by 2, if exp. > 1 + reshuffled[3::4] = bytes[1::4] + (np.bitwise_and(bytes[1::4], 0x7f) == 0) - 1 # There are different ways to adjust for differences in DEC/IEEE representation # after reshuffle. Two simple methods are: @@ -187,6 +213,11 @@ def is_iterable(value): '''Check if value is iterable.''' return hasattr(value, '__iter__') +def type_npy2struct(dtype): + ''' Convert numpy dtype format to a struct package format string. + ''' + return dtype.byteorder + dtype.char + class Header(object): '''Header information from a C3D file. @@ -1511,7 +1542,7 @@ def seek_param_section_header(): self._check_metadata() - def read_frames(self, copy=True, analog_transform=True, camera_sum=False): + def read_frames(self, copy=True, analog_transform=True, camera_sum=False, check_nan=True): '''Iterate over the data frames from our C3D file handle. Parameters @@ -1548,10 +1579,8 @@ def read_frames(self, copy=True, analog_transform=True, camera_sum=False): if is_float: point_word_bytes = 4 - point_dtype = self._dtypes.uint32 else: point_word_bytes = 2 - point_dtype = self._dtypes.int16 points = np.zeros((self.point_used, 5), np.float32) # TODO: handle ANALOG:BITS parameter here! @@ -1606,51 +1635,55 @@ def read_frames(self, copy=True, analog_transform=True, camera_sum=False): # Convert each of the first 6 16-bit words from DEC to IEEE float points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4)) else: # If IEEE or MIPS: - # Re-read the raw byte representation directly + # Convert each of the first 6 16-bit words to native float points[:, :4] = np.frombuffer(raw_bytes, dtype=self._dtypes.float32, count=N_point).reshape((self.point_used, 4)) - # Parse the camera-observed bits and residuals. - # Notes: - # - Invalid sample if residual is equal to -1. - # - A residual of 0.0 represent modeled data (filtered or interpolated). - # - The same format should be used internally when a float or integer representation is used, - # with the difference that the words are 16 and 8 bit respectively (see the MLS guide). - # - While words are 16 bit, residual and camera mask is always interpreted as 8 packed in a single word! - # - 16 or 32 bit may represent a sign (indication that certain files write a -1 floating point only) + # Cast last word to signed integer in system endian format last_word = points[:, 3].astype(np.int32) - valid = last_word > -1 # (last_word & 0x80008000) == 0 - # Lookup other - #if np.sum(~valid) > 0: - #print(np.sum(~valid)) - #print(points[~valid, :3]) - #print(last_word[~valid]) - points[~valid, 3:5] = INVALID_FLAG - c = last_word[valid] else: - # Convert the bytes to a unsigned 32 bit or signed 16 bit representation + # View the bytes as signed 16-bit integers raw = np.frombuffer(raw_bytes, - dtype=point_dtype, + dtype=self._dtypes.int16, count=N_point).reshape((self.point_used, 4)) - # Read point 2 byte words in int-16 format + # Read the first six 16-bit words as x, y, z coordinates points[:, :3] = raw[:, :3] * scale_mag - - # Parse last 16-bit word as two 8-bit words - valid = raw[:, 3] > -1 - points[~valid, 3:5] = INVALID_FLAG - c = raw[valid, 3].astype(self._dtypes.uint16) - - # Convert coordinate data - # fourth value is floating-point (scaled) error estimate (residual) - points[valid, 3] = (c & 0x00ff).astype(np.float32) * scale_mag - - # fifth value is number of bits set in camera-observation byte + # Cast last word to signed integer in system endian format + last_word = raw[:, 3].astype(np.int16) + + # Parse camera-observed bits and residuals. + # Notes: + # - Invalid sample if residual is equal to -1 (check if word < 0). + # - A residual of 0.0 represent modeled data (filtered or interpolated). + # - Camera and residual words are always 8-bit (1 byte), never 16-bit. + # - If floating point, the byte words are encoded in an integer cast to a float, + # and are written directly in byte form (see the MLS guide). + ## + # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded). + residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8 + #if self._dtypes.big_endian_sys -> swap words? + + # Fourth value is floating-point (scaled) error estimate (residual) + points[:, 3] = residual_byte * scale_mag + + # Determine invalid samples + invalid = last_word < 0 + if check_nan: + is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) + points[is_nan, :3] = 0.0 + invalid &= is_nan + # Update discarded - sign + points[invalid, 3] = -1 + + + # Fifth value is the camera-observation byte if camera_sum: - points[valid, 4] = sum((c & (1 << k)) >> k for k in range(8, 15)) + # Convert to observation sum + points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(8)) else: - points[valid, 4] = (c & 0xff00 >> 8) + points[:, 4] = camera_byte #.astype(np.float32) # Check if analog data exist, and parse if so if N_analog > 0: @@ -2087,7 +2120,13 @@ def write(self, handle): points, analog = self._frames[0] ppf = len(points) apf = len(analog) + + + first_frame = self.first_frame + if first_frame <= 0: # Bad value + first_frame = 1 nframes = len(self._frames) + last_frame = first_frame + nframes - 1 UINT16_MAX = 65535 @@ -2128,15 +2167,18 @@ def write(self, handle): # TRIAL group group = self.trial_group - group.set('ACTUAL_START_FIELD', 'actual start frame', 2, '= 65535: + first_frame = 1 + self._header.first_frame = np.uint16(first_frame) + self._header.last_frame = np.uint16(min(last_frame, 65535)) self._header.point_count = np.uint16(ppf) self._header.analog_count = np.uint16(np.prod(analog.shape)) @@ -2201,8 +2243,8 @@ def _write_frames(self, handle): for points, analog in self._frames: # Transform point data - valid = points[:, 3] > -1 - raw[~valid, 3] = INVALID_FLAG + valid = points[:, 3] >= 0.0 + raw[~valid, 3] = -1 raw[valid, :3] = points[valid, :3] / point_scale raw[valid, 3] = np.bitwise_or(np.rint(points[valid, 3] / scale_mag).astype(np.uint8), (points[valid, 4].astype(np.uint16) << 8), diff --git a/test/test_software_examples.py b/test/test_software_examples.py index 6d98c0c..0310f25 100644 --- a/test/test_software_examples.py +++ b/test/test_software_examples.py @@ -20,9 +20,8 @@ class Sample00(verify.WithinRangeTest, Base): ('Innovative Sports Training', ['Gait with EMG.c3d', 'Static Pose.c3d']), ('Motion Analysis Corporation', ['Sample_Jump2.c3d', 'Walk1.c3d']), ('NexGen Ergonomics', ['test1.c3d']), - ('Vicon Motion Systems', ['TableTennis.c3d']), - # Vicon files are weird, uses non-standard encodings. Walking01.c3d contain nan values and is not tested. - # ('Vicon Motion Systems', ['pyCGM2 lower limb CGM24 Walking01.c3d', 'TableTennis.c3d']), + # Vicon files are weird, uses non-standard encodings. Walking01.c3d contain nan values. + ('Vicon Motion Systems', ['pyCGM2 lower limb CGM24 Walking01.c3d', 'TableTennis.c3d']), ] diff --git a/test/test_software_examples_write_read.py b/test/test_software_examples_write_read.py index 94bc65b..981bffa 100644 --- a/test/test_software_examples_write_read.py +++ b/test/test_software_examples_write_read.py @@ -8,21 +8,20 @@ from test.base import Base from test.zipload import Zipload, TEMP -class WriteRead_SoftwareExamples(Base): +class Sample00(Base): ZIP = 'sample00.zip' DATA_RANGE = (-1e6, 1e6) zip_files = \ [ - #('Advanced Realtime Tracking GmbH', ['arthuman-sample.c3d', 'arthuman-sample-fingers.c3d']), - #('Codamotion', ['codamotion_gaitwands_19970212.c3d', 'codamotion_gaitwands_20150204.c3d']), - #('Cometa Systems', ['EMG Data Cometa.c3d']), - #('Innovative Sports Training', ['Gait with EMG.c3d', 'Static Pose.c3d']), - #('Motion Analysis Corporation', ['Sample_Jump2.c3d', 'Walk1.c3d']), - #('NexGen Ergonomics', ['test1.c3d']), - ('Vicon Motion Systems', ['TableTennis.c3d']), - # Vicon files are weird, uses non-standard encodings. Walking01.c3d contain nan values and is not tested. - # ('Vicon Motion Systems', ['pyCGM2 lower limb CGM24 Walking01.c3d', 'TableTennis.c3d']), + ('Advanced Realtime Tracking GmbH', ['arthuman-sample.c3d', 'arthuman-sample-fingers.c3d']), + ('Codamotion', ['codamotion_gaitwands_19970212.c3d', 'codamotion_gaitwands_20150204.c3d']), + ('Cometa Systems', ['EMG Data Cometa.c3d']), + ('Innovative Sports Training', ['Gait with EMG.c3d', 'Static Pose.c3d']), + ('Motion Analysis Corporation', ['Sample_Jump2.c3d', 'Walk1.c3d']), + ('NexGen Ergonomics', ['test1.c3d']), + # Vicon files are weird, uses non-standard encodings. Walking01.c3d contain nan values. + ('Vicon Motion Systems', ['pyCGM2 lower limb CGM24 Walking01.c3d', 'TableTennis.c3d']), ] def verify_read_write(self, file_path): diff --git a/test/verify.py b/test/verify.py index 43ba142..4551262 100644 --- a/test/verify.py +++ b/test/verify.py @@ -110,15 +110,17 @@ def check_zipfile(file_path): analog_min = np.min(analog) analog_max = np.max(analog) - assert np.all(npoint == reader.frame_count),\ - """Failed verifying POINT data in range ({}, {}), found {} number of mismatches in each axis - for all samples. Range for data was ({}, {})."""\ - .format(min_range, max_range, np.sum(np.abs(npoint - reader.frame_count), axis=0), - point_min, point_max) - assert np.all(nanalog == reader.analog_sample_count),\ - """Failed verifying ANALOG data in range ({}, {}), found {} number of mismatches for each channel - for all samples. Range for data was ({}, {})."""\ - .format(min_range, max_range, np.abs(nanalog - reader.analog_sample_count), analog_min, analog_max) + assert np.all(npoint == reader.frame_count), '\n' + \ + 'Failed verifying POINT data in range ({}, {}).\n'.format(min_range, max_range) +\ + 'Found a total of {} values outside plausible range.\n'.format( + np.sum(np.abs(npoint - reader.frame_count), axis=0)) +\ + 'Range for data was ({}, {})'.format(point_min, point_max) + + assert np.all(nanalog == reader.analog_sample_count),'\n' + \ + 'Failed verifying ANALOG data in range ({}, {}).\n'.format(min_range, max_range) +\ + 'Found a total of {} values outside plausible range.\n'.format( + np.abs(nanalog - reader.analog_sample_count)) +\ + 'Range for data was ({}, {})'.format(analog_min, analog_max) print('{} | READ: OK'.format(file)) @@ -284,8 +286,8 @@ def data_is_equal(areader, breader, alabel, blabel): apoint = np.reshape(apoint, (-1, 5)) bpoint = np.reshape(bpoint, (-1, 5)) - avalid = apoint[:, 3] > -1.0 - bvalid = bpoint[:, 3] > -1.0 + avalid = apoint[:, 3] >= 0 + bvalid = bpoint[:, 3] >= 0 valid_diff = np.sum(np.logical_xor(avalid, bvalid)) if valid_diff > 0: diff = np.logical_xor(avalid, bvalid) @@ -305,6 +307,7 @@ def data_is_equal(areader, breader, alabel, blabel): # Compare point data (coordinates) c = ['X', 'Y', 'Z'] + # Tolerance (allow scale x integer rounding error) atol = equal_scale_fac * abs(areader.point_scale) for i in range(3): was_close = np.isclose(apoint[:, i], bpoint[:, i], atol=atol) @@ -317,20 +320,21 @@ def data_is_equal(areader, breader, alabel, blabel): # Word 4 (residual + camera bits) residual_diff = tot_points - np.sum(np.isclose(apoint[:, 3], bpoint[:, 3])) - cam_close = np.isclose(apoint[:, 4], bpoint[:, 4], atol=1.001) - cam_diff = tot_points - np.sum(cam_close) - cam_diff_non_equal = tot_points - np.sum(np.isclose(apoint[:, 4], bpoint[:, 4])) + cam_close = np.isclose(apoint[:, 4], bpoint[:, 4]) + cam_diff_non_equal = tot_points - np.sum(cam_close) # Camera bit errors (warn if non identical, allow 1 cam bit diff, might be bad DEC implementation, or bad data) if cam_diff_non_equal > 0: print(apoint[~cam_close, 4]) print(bpoint[~cam_close, 4]) - assert cam_diff == 0, \ - 'Mismatch error in camera bit flags for {} and {}, number of samples with flag diff: {} of {}'.format( - alabel, blabel, cam_diff, tot_points) - err_str =\ - 'Mismatch in camera bit flags between {} and {}, number of samples with flag diff: {} of {}'.format( - alabel, blabel, cam_diff_non_equal, tot_points) + cam_close = np.isclose(apoint[:, 4], bpoint[:, 4], atol=1.001) + cam_diff = tot_points - np.sum(cam_close) + assert cam_diff == 0, '\n' + \ + 'Mismatch in camera bit flags between {} and {}.\n'.format(alabel, blabel) +\ + 'Number of samples with flag differences larger then 1 bit: {} of {}'.format(cam_diff, tot_points) + err_str = '\n' + \ + 'Mismatch in camera bit flags between {} and {}.\n'.format(alabel, blabel) +\ + 'Number of samples with flag difference of 1 bit: {} of {}'.format(cam_diff_non_equal, tot_points) warnings.warn(err_str, RuntimeWarning) # Residual assert assert residual_diff == 0, '\n' +\ From 09d2657fb38c510b4fd2051f798ce8d6199285aa Mon Sep 17 00:00:00 2001 From: MattiasF Date: Thu, 1 Jul 2021 20:20:20 +0200 Subject: [PATCH 028/120] Cleaned up verify --- test/verify.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/test/verify.py b/test/verify.py index 4551262..17e6d05 100644 --- a/test/verify.py +++ b/test/verify.py @@ -289,10 +289,6 @@ def data_is_equal(areader, breader, alabel, blabel): avalid = apoint[:, 3] >= 0 bvalid = bpoint[:, 3] >= 0 valid_diff = np.sum(np.logical_xor(avalid, bvalid)) - if valid_diff > 0: - diff = np.logical_xor(avalid, bvalid) - print('A', apoint[diff, 3]) - print('B', bpoint[diff, 3]) assert valid_diff == 0, '\n' +\ 'Error in number of valid samples between {} and {}.\n'.format(alabel, blabel) +\ 'Total number of validation mismatches: {} of {}'.format(valid_diff, len(avalid)) @@ -325,8 +321,8 @@ def data_is_equal(areader, breader, alabel, blabel): # Camera bit errors (warn if non identical, allow 1 cam bit diff, might be bad DEC implementation, or bad data) if cam_diff_non_equal > 0: - print(apoint[~cam_close, 4]) - print(bpoint[~cam_close, 4]) + #print(apoint[~cam_close, 4]) + #print(bpoint[~cam_close, 4]) cam_close = np.isclose(apoint[:, 4], bpoint[:, 4], atol=1.001) cam_diff = tot_points - np.sum(cam_close) assert cam_diff == 0, '\n' + \ From 813a3bf7dd367129548f6594d9ec0f50db319ecf Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 02:04:06 +0200 Subject: [PATCH 029/120] Event encodings in header, Support for Writer.from_reader('shallow_copy') + more Corrections: ---- Read TRIAL:ACTUAL_END_FIELD as 2 16 bit words in accordance with docs Read POINT:LONG_FRAMES as float in accordance with docs Set parameters helpers: --- analog labels point labels analog transform analog offset start/end frame +? --- c3d.py | 247 ++++++++++++++++------ test/test_software_examples_write_read.py | 78 ++++--- 2 files changed, 231 insertions(+), 94 deletions(-) diff --git a/c3d.py b/c3d.py index 172b757..edf14d3 100644 --- a/c3d.py +++ b/c3d.py @@ -53,24 +53,6 @@ def __init__(self, proc_type): self.int32 = np.int32 self.int64 = np.int64 - @property - def native(self): - ''' True if the native (system) byte order matches the file byte order. - ''' - return self._native - - @property - def little_endian_sys(self): - ''' True if native byte order is little-endian. - ''' - return self._little_endian_sys - - @property - def big_endian_sys(self): - ''' True if native byte order is big-endian. - ''' - return not self._little_endian_sys - @property def is_ieee(self): ''' True if the associated file is in the Intel format. @@ -96,6 +78,24 @@ def proc_type(self): processor_type = ['INTEL', 'DEC', 'MIPS'] return processor_type[self._proc_type - PROCESSOR_INTEL] + @property + def native(self): + ''' True if the native (system) byte order matches the file byte order. + ''' + return self._native + + @property + def little_endian_sys(self): + ''' True if native byte order is little-endian. + ''' + return self._little_endian_sys + + @property + def big_endian_sys(self): + ''' True if native byte order is big-endian. + ''' + return not self._little_endian_sys + def decode_string(self, bytes): ''' Decode a byte array to a string. ''' @@ -335,18 +335,18 @@ def write(self, handle): def __str__(self): '''Return a string representation of this Header's attributes.''' return '''\ - parameter_block: {0.parameter_block} - point_count: {0.point_count} - analog_count: {0.analog_count} - first_frame: {0.first_frame} - last_frame: {0.last_frame} - max_gap: {0.max_gap} - scale_factor: {0.scale_factor} - data_block: {0.data_block} - analog_per_frame: {0.analog_per_frame} - frame_rate: {0.frame_rate} -long_event_labels: {0.long_event_labels} - event_block: {0.event_block}'''.format(self) + parameter_block: {0.parameter_block} + point_count: {0.point_count} + analog_count: {0.analog_count} + first_frame: {0.first_frame} + last_frame: {0.last_frame} + max_gap: {0.max_gap} + scale_factor: {0.scale_factor} + data_block: {0.data_block} + analog_per_frame: {0.analog_per_frame} + frame_rate: {0.frame_rate} + long_event_labels: {0.long_event_labels} + event_block: {0.event_block}'''.format(self) def read(self, handle, fmt=BINARY_FORMAT_READ): '''Read and parse binary header data from a file handle. @@ -436,11 +436,11 @@ def _parse_events(self, dtypes, float_unpack): self.event_disp_flags = np.zeros(read_count, dtype=np.bool) self.event_labels = np.empty(read_count, dtype=object) for i in range(read_count): - ilong = i*4 + ilong = i * 4 # Unpack self.event_disp_flags[i] = disp_bytes[i] > 0 - self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong+4])[0]) - self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong+4]) + self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong + 4])[0]) + self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong + 4]) @property def events(self): @@ -452,6 +452,59 @@ def events(self): ''' return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags]) + def encode_events(self, events): + ''' Encode event data in the event block. + + Parameters + ---------- + events : [(float, str), ...] + Event data, iterable of touples containing the event timing and a 4 character label string. + Event timings should be calculated relative to sample 1 with the timing 0.0s, and should + not be relative to the first_frame header parameter. + ''' + endian = '<' + if sys.byteorder == 'big': + endian = '>' + + # Event block format + fmt = '{}{}{}{}{}'.format(endian, + str(18 * 4) + 's', # Timings + str(18) + 's', # Flags + 'H', # __ + str(18 * 4) + 's' # Labels + ) + # Pack bytes + event_timings = np.zeros(18, dtype=np.float32) + event_disp_flags = np.zeros(18, dtype=np.uint8) + event_labels = np.empty(18, dtype=object) + label_bytes = bytearray(18 * 4) + for i, (time, label) in enumerate(events): + if i > 17: + # Don't raise Error, header events are rarely used. + warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.') + break + + event_timings[i] = time + event_labels[i] = label + label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8') + + write_count = min(i + 1, 18) + event_disp_flags[:write_count] = 1 + + # Update event headers in self + self.long_event_labels = 0x3039 # Magic number + self.event_count = write_count + # Update event block + self.event_timings = event_timings[:write_count] + self.event_disp_flags = np.ones(write_count, dtype=np.bool) + self.event_labels = event_labels[:write_count] + self.event_block = struct.pack(fmt, + event_timings.tobytes(), + event_disp_flags.tobytes(), + 0, + label_bytes + ) + class Param(object): '''A class representing a single named parameter from a C3D file. @@ -542,7 +595,7 @@ def write(self, group_id, handle): handle.write(struct.pack('b', self.bytes_per_element)) handle.write(struct.pack('B', len(self.dimensions))) handle.write(struct.pack('B' * len(self.dimensions), *self.dimensions)) - if self.bytes: + if self.bytes is not None and len(self.bytes) > 0: handle.write(self.bytes) desc = self.desc.encode('utf-8') handle.write(struct.pack('B', len(desc))) @@ -568,13 +621,16 @@ def _as(self, dtype): '''Unpack the raw bytes of this param using the given struct format.''' return np.frombuffer(self.bytes, count=1, dtype=dtype)[0] - def _as_array(self, dtype): + def _as_array(self, dtype, copy=True): '''Unpack the raw bytes of this param using the given data format.''' assert self.dimensions, \ '{}: cannot get value as {} array!'.format(self.name, dtype) elems = np.frombuffer(self.bytes, dtype=dtype) # Reverse shape as the shape is defined in fortran format - return elems.reshape(self.dimensions[::-1]) + view = elems.reshape(self.dimensions[::-1]) + if copy: + return view.copy() + return view def _as_any(self, dtype): '''Unpack the raw bytes of this param as either array or single value.''' @@ -1402,7 +1458,9 @@ def first_frame(self): # this is a hack for phasespace files ... should put it in a subclass. param = self.get('TRIAL:ACTUAL_START_FIELD') if param is not None: - return param.uint32_value + # ACTUAL_START_FIELD is encoded in two 16 byte words... + words = param.uint16_array + return words[0] + words[1] * 65535 return self.header.first_frame @property @@ -1415,10 +1473,14 @@ def last_frame(self): end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: - end_frame[1] = param._as_integer_value + # Encoded as 2 16 bit words (rather then 1 32 bit word) + words = param.uint16_array + end_frame[1] = words[0] + words[1] * 65536 + #end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: - end_frame[2] = param._as_integer_value + # Encoded as float + end_frame[2] = int(param.float_value) param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint @@ -1426,28 +1488,34 @@ def last_frame(self): # Return the largest of the all (queue bad reading...) return int(np.max(end_frame)) - def _get_analog_transform(self): + def get_analog_transform_parameters(self): ''' Parse analog data transform parameters. ''' # Offsets - analog_offsets = np.zeros((self.analog_used, 1), int) + analog_offsets = np.zeros((self.analog_used), int) param = self.get('ANALOG:OFFSET') if param is not None and param.num_elements > 0: - analog_offsets[:, 0] = param.int16_array[:self.analog_used] + analog_offsets[:] = param.int16_array[:self.analog_used] # Scale factors - analog_scales = np.ones((self.analog_used, 1), float) + analog_scales = np.ones((self.analog_used), float) gen_scale = 1. param = self.get('ANALOG:GEN_SCALE') if param is not None: gen_scale = param.float_value param = self.get('ANALOG:SCALE') if param is not None and param.num_elements > 0: - analog_scales[:, 0] = param.float_array[:self.analog_used] - analog_scales *= gen_scale + analog_scales[:] = param.float_array[:self.analog_used] - analog_scales = np.broadcast_to(analog_scales, (self.analog_used, self.analog_per_frame)) - analog_offsets = np.broadcast_to(analog_offsets, (self.analog_used, self.analog_per_frame)) + return gen_scale, analog_scales, analog_offsets + + def get_analog_transform(self): + ''' Get broadcastable analog transformation parameters. + ''' + gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters() + analog_scales *= gen_scale + analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) + analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) return analog_scales, analog_offsets class Reader(Manager): @@ -1602,7 +1670,7 @@ def read_frames(self, copy=True, analog_transform=True, camera_sum=False, check_ analog_word_bytes = 2 analog = np.array([], float) - analog_scales, analog_offsets = self._get_analog_transform() + analog_scales, analog_offsets = self.get_analog_transform() # Seek to the start point of the data blocks self._handle.seek((self._header.data_block - 1) * 512) @@ -1936,7 +2004,7 @@ def from_reader(reader, conversion=None): # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. raise ValueError( "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( - reader.proc_format)) + reader._dtypes.proc_type)) if is_consume: writer._header = reader._header @@ -1950,6 +2018,18 @@ def from_reader(reader, conversion=None): elif is_shallow_copy: # Only copy header (no groups) writer._header = copy.deepcopy(reader._header) + # Reformat header events + writer._header.encode_events(writer._header.events) + + # Transfer a minimal set parameters + writer.set_start_frame(reader.first_frame) + writer.set_point_labels(reader.point_labels) + writer.set_analog_labels(reader.analog_labels) + + gen_scale, analog_scales, analog_offsets = reader.get_analog_transform_parameters() + writer.set_analog_general_scale(gen_scale) + writer.set_analog_scales(analog_scales) + writer.set_analog_offsets(analog_offsets) if not is_meta_only: # Copy frames @@ -2058,20 +2138,31 @@ def add_frames(self, frames): '\Input was of shape {}.'.format(str(sh))) self._frames.extend(frames) - def set_point_labels(self, labels): - group = self.point_group + @staticmethod + def pack_labels(labels): labels = np.ravel(labels) # Get longest label name label_max_size = 0 label_max_size = max(label_max_size, np.max([len(label) for label in labels])) - label_str = ''.join(label.ljust(label_max_size) for label in labels) - group.add_str('LABELS', 'labels', label_str, label_max_size, len(labels)) + return label_str, label_max_size + + def set_point_labels(self, labels): + ''' Set point data labels. + ''' + label_str, label_max_size = Writer.pack_labels(labels) + self.point_group.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) + + def set_analog_labels(self, labels): + ''' Set analog data labels. + ''' + label_str, label_max_size = Writer.pack_labels(labels) + self.analog_group.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) def set_analog_general_scale(self, value): ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor). ''' - self.analog_group.set('GEN_SCALE', 'Analog general scale factor', 4, '= 65535: - first_frame = 1 - self._header.first_frame = np.uint16(first_frame) - self._header.last_frame = np.uint16(min(last_frame, 65535)) self._header.point_count = np.uint16(ppf) self._header.analog_count = np.uint16(np.prod(analog.shape)) @@ -2238,7 +2345,7 @@ def _write_frames(self, handle): point_scale = scale_mag raw = np.zeros((self.point_used, 4), point_dtype) - analog_scales, analog_offsets = self._get_analog_transform() + analog_scales, analog_offsets = self.get_analog_transform() analog_scales_inv = 1.0 / analog_scales for points, analog in self._frames: diff --git a/test/test_software_examples_write_read.py b/test/test_software_examples_write_read.py index 981bffa..2d924f3 100644 --- a/test/test_software_examples_write_read.py +++ b/test/test_software_examples_write_read.py @@ -8,10 +8,34 @@ from test.base import Base from test.zipload import Zipload, TEMP + +def verify_read_write(zip, file_path, proc_type='INTEL', real=True): + ''' Compare read write ouput to original read file. + ''' + A = c3d.Reader(Zipload._get(zip, file_path)) + + cpy_mode = 'copy' + if proc_type != 'INTEL': + cpy_mode = 'shallow_copy' + writer = A.to_writer(cpy_mode) + + tmp_path = os.path.join(TEMP, 'write_test.c3d') + with open(tmp_path, 'wb') as handle: + writer.write(handle) + + aname = 'Original' + bname = 'WriteRead' + test_id = '{} write read test'.format(proc_type) + + with open(tmp_path, 'rb') as handle: + B = c3d.Reader(handle) + verify.equal_headers(test_id, A, B, aname, bname, real, real) + verify.data_is_equal(A, B, aname, bname) + + class Sample00(Base): - ZIP = 'sample00.zip' - DATA_RANGE = (-1e6, 1e6) + ZIP = 'sample00.zip' zip_files = \ [ ('Advanced Realtime Tracking GmbH', ['arthuman-sample.c3d', 'arthuman-sample-fingers.c3d']), @@ -24,41 +48,47 @@ class Sample00(Base): ('Vicon Motion Systems', ['pyCGM2 lower limb CGM24 Walking01.c3d', 'TableTennis.c3d']), ] - def verify_read_write(self, file_path): - ''' Compare read write ouput to original read file. + def test_read_write_examples(self): + return + ''' Compare write ouput to original read ''' - A = c3d.Reader(Zipload._get(self.ZIP, file_path)) - writer = A.to_writer('copy') - - tmp_path = os.path.join(TEMP, 'write_test.c3d') - with open(tmp_path, 'wb') as handle: - writer.write(handle) - proc_type = 'INTEL' - aname = 'Original' - bname = 'WriteRead' - test_id = '{} write read test'.format(proc_type) + print('----------------------------') + print(type(self)) + print('----------------------------') + for folder, files in self.zip_files: + print('{} | Validating...'.format(folder)) + for file in files: + verify_read_write(self.ZIP, '{}/{}'.format(folder, file)) + print('... OK') + print('DONE') - with open(tmp_path, 'rb') as handle: - B = c3d.Reader(handle) - verify.equal_headers(test_id, A, B, aname, bname, True, True) - verify.data_is_equal(A, B, aname, bname) +class Sample01(Base): + ZIP = 'sample01.zip' + zip_files = \ + [ + ('Eb015pi.c3d', 'INTEL', False), + ('Eb015pr.c3d', 'INTEL', True), + ('Eb015vi.c3d', 'DEC', False), + ('Eb015vr.c3d', 'DEC', True), + ('Eb015si.c3d', 'SGI', False), + ('Eb015sr.c3d', 'SGI', True), + ] def test_read_write_examples(self): ''' Compare write ouput to original read ''' - print('----------------------------') print(type(self)) print('----------------------------') - for folder, files in self.zip_files: - print('{} | Validating...'.format(folder)) - for file in files: - self.verify_read_write('{}/{}'.format(folder, file)) + for (file, proc, is_real) in self.zip_files: + print('{} | Validating...'.format(file)) + verify_read_write(self.ZIP, file, proc, is_real) print('... OK') - print('DONE') + print('Done.') + if __name__ == '__main__': From 3925edfd0a9792ccd7f6e1db165d68a531927e72 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:03:22 +0200 Subject: [PATCH 030/120] set_screen_axis --- c3d.py | 37 ++++++++++++++++--------------------- 1 file changed, 16 insertions(+), 21 deletions(-) diff --git a/c3d.py b/c3d.py index edf14d3..9e1954a 100644 --- a/c3d.py +++ b/c3d.py @@ -1895,25 +1895,6 @@ def set_empty_array(self, name, *args, **kwargs): pass self.add_empty_array(name, *args, **kwargs) - # - # Try add decorator functions (catches KeyError) - # - def try_add(self, name, *args, **kwargs): - ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'. - ''' - try: - self.add(name, *args, **kwargs) - except KeyError as e: - pass - - def try_add_str(self, name, *args, **kwargs): - ''' Add a string parameter. - ''' - try: - self.add_str(name, *args, **kwargs) - except KeyError as e: - pass - class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -2217,6 +2198,22 @@ def _set_last_frame(self, frame): self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, ' Date: Fri, 2 Jul 2021 11:04:33 +0200 Subject: [PATCH 031/120] set_screen_axis, default values + actual set --- c3d.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/c3d.py b/c3d.py index 9e1954a..1ec869c 100644 --- a/c3d.py +++ b/c3d.py @@ -2199,7 +2199,7 @@ def _set_last_frame(self, frame): self._header.last_frame = np.uint16(min(frame, 65535)) - def set_screen_axis(self, X, Y): + def set_screen_axis(self, X='+X', Y='+Y'): ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. Parameter @@ -2211,8 +2211,8 @@ def set_screen_axis(self, X, Y): Second axis string with same format as Y. Determines the second Y screen axis. ''' group = self.point_group - group.set_str('X_SCREEN', 'X_SCREEN parameter', '+X', 2) - group.set_str('Y_SCREEN', 'Y_SCREEN parameter', '+Y', 2) + group.set_str('X_SCREEN', 'X_SCREEN parameter', X, 2) + group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y, 2) def write(self, handle): '''Write metadata and point + analog frames to a file handle. From 187e0fe24ecdee0f8b81f3723f180b6d24f7db20 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:06:50 +0200 Subject: [PATCH 032/120] assert input values --- c3d.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/c3d.py b/c3d.py index 1ec869c..4624773 100644 --- a/c3d.py +++ b/c3d.py @@ -2210,6 +2210,10 @@ def set_screen_axis(self, X='+X', Y='+Y'): Y : str Second axis string with same format as Y. Determines the second Y screen axis. ''' + if len(X) != 2: + raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter'. + if len(Y) != 2: + raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter'. group = self.point_group group.set_str('X_SCREEN', 'X_SCREEN parameter', X, 2) group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y, 2) From 235920a153a845b644c756f5b8189669e8711cbc Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:07:42 +0200 Subject: [PATCH 033/120] Missing bracket --- c3d.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/c3d.py b/c3d.py index 4624773..bd34fb5 100644 --- a/c3d.py +++ b/c3d.py @@ -2211,9 +2211,9 @@ def set_screen_axis(self, X='+X', Y='+Y'): Second axis string with same format as Y. Determines the second Y screen axis. ''' if len(X) != 2: - raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter'. + raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter.') if len(Y) != 2: - raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter'. + raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter.') group = self.point_group group.set_str('X_SCREEN', 'X_SCREEN parameter', X, 2) group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y, 2) From 42d39777e45e1ffd76f8f9dc5414e6d70b1dd471 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:29:48 +0200 Subject: [PATCH 034/120] Added insert option to Writer.add_frames Added some simple Writer tests for add_frames and set_xxx --- c3d.py | 13 ++++++++++--- test/test_c3d.py | 22 +++++++++++++++++++++- 2 files changed, 31 insertions(+), 4 deletions(-) diff --git a/c3d.py b/c3d.py index bd34fb5..74ae354 100644 --- a/c3d.py +++ b/c3d.py @@ -2099,13 +2099,16 @@ def add_group(self, *args, **kwargs): ''' return GroupEditable(super(Writer, self).add_group(*args, **kwargs)) - def add_frames(self, frames): + def add_frames(self, frames, index=None): '''Add frames to this writer instance. Parameters ---------- - frames : single or sequence of (point, analog) pairs + frames : Single or sequence of (point, analog) pairs A sequence or frame of frame data to add to the writer. + index : int or None + Insert the frame or sequence at the index (the first sequence frame will be inserted at give index). + Note that the index should be relative to 0 rather then the frame number provided by read_frames()! ''' sh = np.shape(frames) # Single frame @@ -2117,7 +2120,11 @@ def add_frames(self, frames): raise ValueError( 'Expected frame input to be sequence of point and analog pairs on form (-1, 2). ' + '\Input was of shape {}.'.format(str(sh))) - self._frames.extend(frames) + + if index is not None: + self._frames[index:index] = frames + else: + self._frames.extend(frames) @staticmethod def pack_labels(labels): diff --git a/test/test_c3d.py b/test/test_c3d.py index a8ebf0f..7883b2e 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -82,7 +82,7 @@ def test_frames(self): class WriterTest(Base): - def test_paramsd(self): + def test_add_frames(self): r = c3d.Reader(Zipload._get('sample08.zip', 'TESTDPI.c3d')) w = c3d.Writer( point_rate=r.point_rate, @@ -91,11 +91,31 @@ def test_paramsd(self): gen_scale=r.get_float('ANALOG:GEN_SCALE'), ) w.add_frames([(p, a) for _, p, a in r.read_frames()]) + w.add_frames([(p, a) for _, p, a in r.read_frames()], index=5) h = io.BytesIO() w.set_point_labels(r.point_labels) + w.set_analog_labels(r.analog_labels) w.write(h) + def test_set_params(self): + r = c3d.Reader(Zipload._get('sample08.zip', 'TESTDPI.c3d')) + w = c3d.Writer( + point_rate=r.point_rate, + analog_rate=r.analog_rate, + point_scale=r.point_scale, + gen_scale=r.get_float('ANALOG:GEN_SCALE'), + ) + w.add_frames([(p, a) for _, p, a in r.read_frames()]) + + h = io.BytesIO() + w.set_start_frame(255) + w.set_screen_axis() + w.set_screen_axis('-Y', '+Z') + w.set_point_labels(r.point_labels) + w.set_analog_labels(r.analog_labels) + + w.write(h) if __name__ == '__main__': unittest.main() From 8b0ab99777c3b0a09a62e366643c05d2f8d65cec Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:30:39 +0200 Subject: [PATCH 035/120] Comments --- test/test_c3d.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/test/test_c3d.py b/test/test_c3d.py index 7883b2e..7793d0f 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -1,4 +1,7 @@ -import c3d +''' Basic Reader and Writer tests. +''' + +'import c3d import importlib import io import unittest @@ -15,6 +18,8 @@ class ReaderTest(Base): + ''' Test basic Reader functionality + ''' def test_format_pi(self): r = c3d.Reader(Zipload._get('sample01.zip', 'Eb015pi.c3d')) self._log(r) @@ -82,6 +87,8 @@ def test_frames(self): class WriterTest(Base): + ''' Test basic writer functionality + ''' def test_add_frames(self): r = c3d.Reader(Zipload._get('sample08.zip', 'TESTDPI.c3d')) w = c3d.Writer( From 649cd68bd6c966f96846a3d6c96eb9bb8323552e Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:40:10 +0200 Subject: [PATCH 036/120] get_screen_axis() --- c3d.py | 14 ++++++++++++++ test/test_c3d.py | 15 +++++++++++---- 2 files changed, 25 insertions(+), 4 deletions(-) diff --git a/c3d.py b/c3d.py index 74ae354..9490484 100644 --- a/c3d.py +++ b/c3d.py @@ -1488,6 +1488,20 @@ def last_frame(self): # Return the largest of the all (queue bad reading...) return int(np.max(end_frame)) + def get_screen_axis(self): + ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. + + Returns + ------- + value : Touple on form (str, str) or None + Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. + ''' + X = self.get('POINT:X_SCREEN') + Y = self.get('POINT:Y_SCREEN') + if X and Y: + return (X.string_value, Y.string_value) + return None + def get_analog_transform_parameters(self): ''' Parse analog data transform parameters. ''' diff --git a/test/test_c3d.py b/test/test_c3d.py index 7793d0f..1ae41e3 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -1,10 +1,10 @@ ''' Basic Reader and Writer tests. ''' - -'import c3d +import c3d import importlib import io import unittest +import numpy as np from test.base import Base from test.zipload import Zipload climate_spec = importlib.util.find_spec("climate") @@ -117,11 +117,18 @@ def test_set_params(self): h = io.BytesIO() w.set_start_frame(255) - w.set_screen_axis() - w.set_screen_axis('-Y', '+Z') w.set_point_labels(r.point_labels) w.set_analog_labels(r.analog_labels) + # Screen axis + X, Y = '-Y', '+Z' + w.set_screen_axis() + w.set_screen_axis(X, Y) + X_v, Y_v = w.get_screen_axis() + assert X_v == X and Y == Y_v, 'Mismatch between set & get screen axis.' + + assert np.all(np.equal(r.point_labels, w.point_labels)), 'Expected labels to be equal.' + w.write(h) if __name__ == '__main__': From 2b8abd7ca9c41142920d09134d7307df203871ca Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 11:52:29 +0200 Subject: [PATCH 037/120] default proc_type --- c3d.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/c3d.py b/c3d.py index 9490484..f119a85 100644 --- a/c3d.py +++ b/c3d.py @@ -14,13 +14,11 @@ PROCESSOR_DEC = 85 PROCESSOR_MIPS = 86 -INVALID_FLAG = -100000 - class DataTypes(object): ''' Container defining different data types used for reading file data. Data types depend on the processor format the file is stored in. ''' - def __init__(self, proc_type): + def __init__(self, proc_type=PROCESSOR_INTEL): self._proc_type = proc_type self._little_endian_sys = sys.byteorder == 'little' self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \ From 02e4490b0337ca6e5d85c0787aa985cd8171d205 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 12:08:55 +0200 Subject: [PATCH 038/120] Moved trailing functions --- c3d.py | 213 +--------------------- src/dtypes.py | 106 +++++++++++ src/utils.py | 109 +++++++++++ test/test_software_examples_write_read.py | 1 - 4 files changed, 219 insertions(+), 210 deletions(-) create mode 100644 src/dtypes.py create mode 100644 src/utils.py diff --git a/c3d.py b/c3d.py index f119a85..ffa05eb 100644 --- a/c3d.py +++ b/c3d.py @@ -8,213 +8,9 @@ import numpy as np import struct import warnings -import codecs +from src.dtypes import DataTypes +from src.utils import is_integer, is_iterable, DEC_to_IEEE, DEC_to_IEEE_BYTES, UNPACK_FLOAT_IEEE, Decorator -PROCESSOR_INTEL = 84 -PROCESSOR_DEC = 85 -PROCESSOR_MIPS = 86 - -class DataTypes(object): - ''' Container defining different data types used for reading file data. - Data types depend on the processor format the file is stored in. - ''' - def __init__(self, proc_type=PROCESSOR_INTEL): - self._proc_type = proc_type - self._little_endian_sys = sys.byteorder == 'little' - self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \ - (self.is_mips and self.big_endian_sys) - if self.big_endian_sys: - warnings.warn('Systems with native byte order of big-endian are not supported.') - - if self._proc_type == PROCESSOR_MIPS: - # Big-Endian (SGI/MIPS format) - self.float32 = np.dtype(np.float32).newbyteorder('>') - self.float64 = np.dtype(np.float64).newbyteorder('>') - self.uint8 = np.uint8 - self.uint16 = np.dtype(np.uint16).newbyteorder('>') - self.uint32 = np.dtype(np.uint32).newbyteorder('>') - self.uint64 = np.dtype(np.uint64).newbyteorder('>') - self.int8 = np.int8 - self.int16 = np.dtype(np.int16).newbyteorder('>') - self.int32 = np.dtype(np.int32).newbyteorder('>') - self.int64 = np.dtype(np.int64).newbyteorder('>') - else: - # Little-Endian format (Intel or DEC format) - self.float32 = np.float32 - self.float64 = np.float64 - self.uint8 = np.uint8 - self.uint16 = np.uint16 - self.uint32 = np.uint32 - self.uint64 = np.uint64 - self.int8 = np.int8 - self.int16 = np.int16 - self.int32 = np.int32 - self.int64 = np.int64 - - @property - def is_ieee(self): - ''' True if the associated file is in the Intel format. - ''' - return self._proc_type == PROCESSOR_INTEL - - @property - def is_dec(self): - ''' True if the associated file is in the DEC format. - ''' - return self._proc_type == PROCESSOR_DEC - - @property - def is_mips(self): - ''' True if the associated file is in the SGI/MIPS format. - ''' - return self._proc_type == PROCESSOR_MIPS - - @property - def proc_type(self): - ''' Get the processory type associated with the data format in the file. - ''' - processor_type = ['INTEL', 'DEC', 'MIPS'] - return processor_type[self._proc_type - PROCESSOR_INTEL] - - @property - def native(self): - ''' True if the native (system) byte order matches the file byte order. - ''' - return self._native - - @property - def little_endian_sys(self): - ''' True if native byte order is little-endian. - ''' - return self._little_endian_sys - - @property - def big_endian_sys(self): - ''' True if native byte order is big-endian. - ''' - return not self._little_endian_sys - - def decode_string(self, bytes): - ''' Decode a byte array to a string. - ''' - # Attempt to decode using different decoders - decoders = ['utf-8', 'latin-1'] - for dec in decoders: - try: - return codecs.decode(bytes, dec) - except UnicodeDecodeError: - continue - # Revert to using default decoder but replace characters - return codecs.decode(bytes, decoders[0], 'replace') - -class Decorator(object): - '''Base class for extending (decotrating) a python object. - ''' - def __init__(self, decoratee): - self._decoratee = decoratee - def __getattr__(self, name): - return getattr(self._decoratee, name) - -def UNPACK_FLOAT_IEEE(uint_32): - '''Unpacks a single 32 bit unsigned int to a IEEE float representation - ''' - return struct.unpack('f', struct.pack("I", uint_32))[0] - - -def DEC_to_IEEE(uint_32): - '''Convert the 32 bit representation of a DEC float to IEEE format. - - Params: - ---- - uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits. - Returns : IEEE formated floating point of the same shape as the input. - ''' - # Follows the bit pattern found: - # http://home.fnal.gov/~yang/Notes/ieee_vs_dec_float.txt - # Further formating descriptions can be found: - # http://www.irig106.org/docs/106-07/appendixO.pdf - # In accodance with the first ref. first & second 16 bit words are placed - # in a big endian 16 bit word representation, and needs to be inverted. - # Second reference describe the DEC->IEEE conversion. - - # Warning! Unsure if NaN numbers are managed appropriately. - - # Shuffle the first two bit words from DEC bit representation to an ordered representation. - # Note that the most significant fraction bits are placed in the first 7 bits. - # - # Below are the DEC layout in accordance with the references: - # ___________________________________________________________________________________ - # | Mantissa (16:0) | SIGN | Exponent (8:0) | Mantissa (23:17) | - # ___________________________________________________________________________________ - # |32- -16| 15 |14- -7|6- -0| - # - # Legend: - # _______________________________________________________ - # | Part (left bit of segment : right bit) | Part | .. - # _______________________________________________________ - # |Bit adress - .. - Bit adress | Bit adress - .. - #### - - # Swap the first and last 16 bits for a consistent alignment of the fraction - reshuffled = ((uint_32 & 0xFFFF0000) >> 16) | ((uint_32 & 0x0000FFFF) << 16) - # After the shuffle each part are in little-endian and ordered as: SIGN-Exponent-Fraction - exp_bits = ((reshuffled & 0xFF000000) - 1) & 0xFF000000 - reshuffled = (reshuffled & 0x00FFFFFF) | exp_bits - return UNPACK_FLOAT_IEEE(reshuffled) - - -def DEC_to_IEEE_BYTES(bytes): - '''Convert byte array containing 32 bit DEC floats to IEEE format. - - Params: - ---- - bytes : Byte array where every 4 bytes represent a single precision DEC float. - Returns : IEEE formated floating point of the same shape as the input. - ''' - - # See comments in DEC_to_IEEE() for DEC format definition - - # Reshuffle - bytes = memoryview(bytes) - reshuffled = np.empty(len(bytes), dtype=np.dtype('B')) - reshuffled[::4] = bytes[2::4] - reshuffled[1::4] = bytes[3::4] - reshuffled[2::4] = bytes[::4] - # Decrement exponent by 2, if exp. > 1 - reshuffled[3::4] = bytes[1::4] + (np.bitwise_and(bytes[1::4], 0x7f) == 0) - 1 - - # There are different ways to adjust for differences in DEC/IEEE representation - # after reshuffle. Two simple methods are: - # 1) Decrement exponent bits by 2, then convert to IEEE. - # 2) Convert to IEEE directly and divide by four. - # 3) Handle edge cases, expensive in python... - # However these are simple methods, and do not accurately convert when: - # 1) Exponent < 2 (without bias), impossible to decrement exponent without adjusting fraction/mantissa. - # 2) Exponent == 0, DEC numbers are then 0 or undefined while IEEE is not. NaN are produced when exponent == 255. - # Here method 1) is used, which mean that only small numbers will be represented incorrectly. - - return np.frombuffer(reshuffled.tobytes(), - dtype=np.float32, - count=int(len(bytes) / 4)) - -def is_integer(value): - '''Check if value input is integer.''' - return isinstance(value, (int, np.int32, np.int64)) - -def is_iterable(value): - '''Check if value is iterable.''' - return hasattr(value, '__iter__') - -def type_npy2struct(dtype): - ''' Convert numpy dtype format to a struct package format string. - ''' - return dtype.byteorder + dtype.char class Header(object): '''Header information from a C3D file. @@ -1743,7 +1539,6 @@ def read_frames(self, copy=True, analog_transform=True, camera_sum=False, check_ ## # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded). residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8 - #if self._dtypes.big_endian_sys -> swap words? # Fourth value is floating-point (scaled) error estimate (residual) points[:, 3] = residual_byte * scale_mag @@ -1944,7 +1739,7 @@ def __init__(self, '''Set metadata for this writer. ''' - self._dtypes = DataTypes(PROCESSOR_INTEL) # Always write INTEL format + self._dtypes = DataTypes() # Only support INTEL format from writing super(Writer, self).__init__() # Custom properties @@ -2334,7 +2129,7 @@ def _write_metadata(self, handle): # Groups handle.write(struct.pack( - 'BBBB', 0, 0, self.parameter_blocks(), PROCESSOR_INTEL)) + 'BBBB', 0, 0, self.parameter_blocks(), self._dtypes.processor)) for group_id, group in self.group_listed(): group.write(group_id, handle) diff --git a/src/dtypes.py b/src/dtypes.py new file mode 100644 index 0000000..e327b27 --- /dev/null +++ b/src/dtypes.py @@ -0,0 +1,106 @@ +import sys +import codecs +import numpy as np + +PROCESSOR_INTEL = 84 +PROCESSOR_DEC = 85 +PROCESSOR_MIPS = 86 + +class DataTypes(object): + ''' Container defining different data types used for reading file data. + Data types depend on the processor format the file is stored in. + ''' + def __init__(self, proc_type=PROCESSOR_INTEL): + self._proc_type = proc_type + self._little_endian_sys = sys.byteorder == 'little' + self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \ + (self.is_mips and self.big_endian_sys) + if self.big_endian_sys: + warnings.warn('Systems with native byte order of big-endian are not supported.') + + if self._proc_type == PROCESSOR_MIPS: + # Big-Endian (SGI/MIPS format) + self.float32 = np.dtype(np.float32).newbyteorder('>') + self.float64 = np.dtype(np.float64).newbyteorder('>') + self.uint8 = np.uint8 + self.uint16 = np.dtype(np.uint16).newbyteorder('>') + self.uint32 = np.dtype(np.uint32).newbyteorder('>') + self.uint64 = np.dtype(np.uint64).newbyteorder('>') + self.int8 = np.int8 + self.int16 = np.dtype(np.int16).newbyteorder('>') + self.int32 = np.dtype(np.int32).newbyteorder('>') + self.int64 = np.dtype(np.int64).newbyteorder('>') + else: + # Little-Endian format (Intel or DEC format) + self.float32 = np.float32 + self.float64 = np.float64 + self.uint8 = np.uint8 + self.uint16 = np.uint16 + self.uint32 = np.uint32 + self.uint64 = np.uint64 + self.int8 = np.int8 + self.int16 = np.int16 + self.int32 = np.int32 + self.int64 = np.int64 + + @property + def is_ieee(self): + ''' True if the associated file is in the Intel format. + ''' + return self._proc_type == PROCESSOR_INTEL + + @property + def is_dec(self): + ''' True if the associated file is in the DEC format. + ''' + return self._proc_type == PROCESSOR_DEC + + @property + def is_mips(self): + ''' True if the associated file is in the SGI/MIPS format. + ''' + return self._proc_type == PROCESSOR_MIPS + + @property + def proc_type(self): + ''' Get the processory type associated with the data format in the file. + ''' + processor_type = ['INTEL', 'DEC', 'MIPS'] + return processor_type[self._proc_type - PROCESSOR_INTEL] + + @property + def processor(self): + ''' Get the processor number encoded in the .c3d file. + ''' + return self._proc_type + + @property + def native(self): + ''' True if the native (system) byte order matches the file byte order. + ''' + return self._native + + @property + def little_endian_sys(self): + ''' True if native byte order is little-endian. + ''' + return self._little_endian_sys + + @property + def big_endian_sys(self): + ''' True if native byte order is big-endian. + ''' + return not self._little_endian_sys + + def decode_string(self, bytes): + ''' Decode a byte array to a string. + ''' + # Attempt to decode using different decoders + decoders = ['utf-8', 'latin-1'] + for dec in decoders: + try: + return codecs.decode(bytes, dec) + except UnicodeDecodeError: + continue + # Revert to using default decoder but replace characters + return codecs.decode(bytes, decoders[0], 'replace') diff --git a/src/utils.py b/src/utils.py new file mode 100644 index 0000000..5d4c8c3 --- /dev/null +++ b/src/utils.py @@ -0,0 +1,109 @@ +import numpy as np +import struct + +def is_integer(value): + '''Check if value input is integer.''' + return isinstance(value, (int, np.int32, np.int64)) + +def is_iterable(value): + '''Check if value is iterable.''' + return hasattr(value, '__iter__') + +def type_npy2struct(dtype): + ''' Convert numpy dtype format to a struct package format string. + ''' + return dtype.byteorder + dtype.char + +class Decorator(object): + '''Base class for extending (decorating) a python object. + ''' + def __init__(self, decoratee): + self._decoratee = decoratee + def __getattr__(self, name): + return getattr(self._decoratee, name) + +def UNPACK_FLOAT_IEEE(uint_32): + '''Unpacks a single 32 bit unsigned int to a IEEE float representation + ''' + return struct.unpack('f', struct.pack("I", uint_32))[0] + +def DEC_to_IEEE(uint_32): + '''Convert the 32 bit representation of a DEC float to IEEE format. + + Params: + ---- + uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits. + Returns : IEEE formated floating point of the same shape as the input. + ''' + # Follows the bit pattern found: + # http://home.fnal.gov/~yang/Notes/ieee_vs_dec_float.txt + # Further formating descriptions can be found: + # http://www.irig106.org/docs/106-07/appendixO.pdf + # In accodance with the first ref. first & second 16 bit words are placed + # in a big endian 16 bit word representation, and needs to be inverted. + # Second reference describe the DEC->IEEE conversion. + + # Warning! Unsure if NaN numbers are managed appropriately. + + # Shuffle the first two bit words from DEC bit representation to an ordered representation. + # Note that the most significant fraction bits are placed in the first 7 bits. + # + # Below are the DEC layout in accordance with the references: + # ___________________________________________________________________________________ + # | Mantissa (16:0) | SIGN | Exponent (8:0) | Mantissa (23:17) | + # ___________________________________________________________________________________ + # |32- -16| 15 |14- -7|6- -0| + # + # Legend: + # _______________________________________________________ + # | Part (left bit of segment : right bit) | Part | .. + # _______________________________________________________ + # |Bit adress - .. - Bit adress | Bit adress - .. + #### + + # Swap the first and last 16 bits for a consistent alignment of the fraction + reshuffled = ((uint_32 & 0xFFFF0000) >> 16) | ((uint_32 & 0x0000FFFF) << 16) + # After the shuffle each part are in little-endian and ordered as: SIGN-Exponent-Fraction + exp_bits = ((reshuffled & 0xFF000000) - 1) & 0xFF000000 + reshuffled = (reshuffled & 0x00FFFFFF) | exp_bits + return UNPACK_FLOAT_IEEE(reshuffled) + + +def DEC_to_IEEE_BYTES(bytes): + '''Convert byte array containing 32 bit DEC floats to IEEE format. + + Params: + ---- + bytes : Byte array where every 4 bytes represent a single precision DEC float. + Returns : IEEE formated floating point of the same shape as the input. + ''' + + # See comments in DEC_to_IEEE() for DEC format definition + + # Reshuffle + bytes = memoryview(bytes) + reshuffled = np.empty(len(bytes), dtype=np.dtype('B')) + reshuffled[::4] = bytes[2::4] + reshuffled[1::4] = bytes[3::4] + reshuffled[2::4] = bytes[::4] + # Decrement exponent by 2, if exp. > 1 + reshuffled[3::4] = bytes[1::4] + (np.bitwise_and(bytes[1::4], 0x7f) == 0) - 1 + + # There are different ways to adjust for differences in DEC/IEEE representation + # after reshuffle. Two simple methods are: + # 1) Decrement exponent bits by 2, then convert to IEEE. + # 2) Convert to IEEE directly and divide by four. + # 3) Handle edge cases, expensive in python... + # However these are simple methods, and do not accurately convert when: + # 1) Exponent < 2 (without bias), impossible to decrement exponent without adjusting fraction/mantissa. + # 2) Exponent == 0, DEC numbers are then 0 or undefined while IEEE is not. NaN are produced when exponent == 255. + # Here method 1) is used, which mean that only small numbers will be represented incorrectly. + + return np.frombuffer(reshuffled.tobytes(), + dtype=np.float32, + count=int(len(bytes) / 4)) diff --git a/test/test_software_examples_write_read.py b/test/test_software_examples_write_read.py index 2d924f3..3f02ae9 100644 --- a/test/test_software_examples_write_read.py +++ b/test/test_software_examples_write_read.py @@ -49,7 +49,6 @@ class Sample00(Base): ] def test_read_write_examples(self): - return ''' Compare write ouput to original read ''' From 6eece5953bcc5ebd82929cbf57c1a79120c7fab6 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 13:05:44 +0200 Subject: [PATCH 039/120] group.py, parameter.py --- c3d.py | 876 +---------------------------------------------- src/group.py | 231 +++++++++++++ src/parameter.py | 355 +++++++++++++++++++ 3 files changed, 590 insertions(+), 872 deletions(-) create mode 100644 src/group.py create mode 100644 src/parameter.py diff --git a/c3d.py b/c3d.py index ffa05eb..fc4a201 100644 --- a/c3d.py +++ b/c3d.py @@ -8,878 +8,10 @@ import numpy as np import struct import warnings +from src.header import Header +from src.group import Group from src.dtypes import DataTypes -from src.utils import is_integer, is_iterable, DEC_to_IEEE, DEC_to_IEEE_BYTES, UNPACK_FLOAT_IEEE, Decorator - - -class Header(object): - '''Header information from a C3D file. - - Attributes - ---------- - event_block : int - Index of the 512-byte block where labels (metadata) are found. - parameter_block : int - Index of the 512-byte block where parameters (metadata) are found. - data_block : int - Index of the 512-byte block where data starts. - point_count : int - Number of motion capture channels recorded in this file. - analog_count : int - Number of analog values recorded per frame of 3D point data. - first_frame : int - Index of the first frame of data. - last_frame : int - Index of the last frame of data. - analog_per_frame : int - Number of analog frames per frame of 3D point data. The analog frame - rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE) - times the analog per frame value. - frame_rate : float - The frame rate of the recording, in frames per second. - scale_factor : float - Multiply values in the file by this scale parameter. - long_event_labels : bool - max_gap : int - - .. note:: - The ``scale_factor`` attribute is not used in Phasespace C3D files; - instead, use the POINT.SCALE parameter. - - .. note:: - The ``first_frame`` and ``last_frame`` header attributes are not used in - C3D files generated by Phasespace. Instead, the first and last - frame numbers are stored in the POINTS:ACTUAL_START_FIELD and - POINTS:ACTUAL_END_FIELD parameters. - ''' - - # Read/Write header formats, read values as unsigned ints rather then floats. - BINARY_FORMAT_WRITE = ' 0 - self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong + 4])[0]) - self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong + 4]) - - @property - def events(self): - ''' Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label). - - Note*: - Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter. - Frame 1 therefor has the time 0.0 in relation to the event timing. - ''' - return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags]) - - def encode_events(self, events): - ''' Encode event data in the event block. - - Parameters - ---------- - events : [(float, str), ...] - Event data, iterable of touples containing the event timing and a 4 character label string. - Event timings should be calculated relative to sample 1 with the timing 0.0s, and should - not be relative to the first_frame header parameter. - ''' - endian = '<' - if sys.byteorder == 'big': - endian = '>' - - # Event block format - fmt = '{}{}{}{}{}'.format(endian, - str(18 * 4) + 's', # Timings - str(18) + 's', # Flags - 'H', # __ - str(18 * 4) + 's' # Labels - ) - # Pack bytes - event_timings = np.zeros(18, dtype=np.float32) - event_disp_flags = np.zeros(18, dtype=np.uint8) - event_labels = np.empty(18, dtype=object) - label_bytes = bytearray(18 * 4) - for i, (time, label) in enumerate(events): - if i > 17: - # Don't raise Error, header events are rarely used. - warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.') - break - - event_timings[i] = time - event_labels[i] = label - label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8') - - write_count = min(i + 1, 18) - event_disp_flags[:write_count] = 1 - - # Update event headers in self - self.long_event_labels = 0x3039 # Magic number - self.event_count = write_count - # Update event block - self.event_timings = event_timings[:write_count] - self.event_disp_flags = np.ones(write_count, dtype=np.bool) - self.event_labels = event_labels[:write_count] - self.event_block = struct.pack(fmt, - event_timings.tobytes(), - event_disp_flags.tobytes(), - 0, - label_bytes - ) - - -class Param(object): - '''A class representing a single named parameter from a C3D file. - - Attributes - ---------- - name : str - Name of this parameter. - dtype: DataTypes - Reference to the DataTypes object associated with the file. - desc : str - Brief description of this parameter. - bytes_per_element : int, optional - For array data, this describes the size of each element of data. For - string data (including arrays of strings), this should be -1. - dimensions : list of int - For array data, this describes the dimensions of the array, stored in - column-major order. For arrays of strings, the dimensions here will be - the number of columns (length of each string) followed by the number of - rows (number of strings). - bytes : str - Raw data for this parameter. - handle : - File handle positioned at the first byte of a .c3d parameter description. - ''' - - def __init__(self, - name, - dtype, - desc='', - bytes_per_element=1, - dimensions=None, - bytes=b'', - handle=None): - '''Set up a new parameter, only the name is required.''' - self.name = name - self._dtypes = dtype - self.desc = desc - self.bytes_per_element = bytes_per_element - self.dimensions = dimensions or [] - self.bytes = bytes - if handle: - self.read(handle) - - def __repr__(self): - return ''.format(self.desc) - - @property - def num_elements(self): - '''Return the number of elements in this parameter's array value.''' - e = 1 - for d in self.dimensions: - e *= d - return e - - @property - def total_bytes(self): - '''Return the number of bytes used for storing this parameter's data.''' - return self.num_elements * abs(self.bytes_per_element) - - def binary_size(self): - '''Return the number of bytes needed to store this parameter.''' - return ( - 1 + # group_id - 2 + # next offset marker - 1 + len(self.name.encode('utf-8')) + # size of name and name bytes - 1 + # data size - # size of dimensions and dimension bytes - 1 + len(self.dimensions) + - self.total_bytes + # data - 1 + len(self.desc.encode('utf-8')) # size of desc and desc bytes - ) - - def write(self, group_id, handle): - '''Write binary data for this parameter to a file handle. - - Parameters - ---------- - group_id : int - The numerical ID of the group that holds this parameter. - handle : file handle - An open, writable, binary file handle. - ''' - name = self.name.encode('utf-8') - handle.write(struct.pack('bb', len(name), group_id)) - handle.write(name) - handle.write(struct.pack(' 0: - handle.write(self.bytes) - desc = self.desc.encode('utf-8') - handle.write(struct.pack('B', len(desc))) - handle.write(desc) - - def read(self, handle): - '''Read binary data for this parameter from a file handle. - - This reads exactly enough data from the current position in the file to - initialize the parameter. - ''' - self.bytes_per_element, = struct.unpack('b', handle.read(1)) - dims, = struct.unpack('B', handle.read(1)) - self.dimensions = [struct.unpack('B', handle.read(1))[ - 0] for _ in range(dims)] - self.bytes = b'' - if self.total_bytes: - self.bytes = handle.read(self.total_bytes) - desc_size, = struct.unpack('B', handle.read(1)) - self.desc = desc_size and self._dtypes.decode_string(handle.read(desc_size)) or '' - - def _as(self, dtype): - '''Unpack the raw bytes of this param using the given struct format.''' - return np.frombuffer(self.bytes, count=1, dtype=dtype)[0] - - def _as_array(self, dtype, copy=True): - '''Unpack the raw bytes of this param using the given data format.''' - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, dtype) - elems = np.frombuffer(self.bytes, dtype=dtype) - # Reverse shape as the shape is defined in fortran format - view = elems.reshape(self.dimensions[::-1]) - if copy: - return view.copy() - return view - - def _as_any(self, dtype): - '''Unpack the raw bytes of this param as either array or single value.''' - if 0 in self.dimensions[:]: # Check if any dimension is 0 (empty buffer) - return [] # Buffer is empty - - if len(self.dimensions) == 0: # Parse data as a single value - if dtype == np.float32: # Floats need to be parsed separately! - return self.float_value - return self._as(dtype) - else: # Parse data as array - if dtype == np.float32: - data = self.float_array - else: - data = self._as_array(dtype) - if len(self.dimensions) < 2: # Check if data is contained in a single dimension - return data.flatten() - return data - - @property - def _as_integer_value(self): - ''' Get the param as either 32 bit float or unsigned integer. - Evaluates if an integer is stored as a floating point representation. - - Note: This is implemented purely for parsing start/end frames. - ''' - if self.total_bytes >= 4: - # Check if float value representation is an integer - value = self.float_value - if int(value) == value: - return value - return self.uint32_value - elif self.total_bytes >= 2: - return self.uint16_value - else: - return self.uint8_value - - @property - def int8_value(self): - '''Get the param as an 8-bit signed integer.''' - return self._as(self._dtypes.int8) - - @property - def uint8_value(self): - '''Get the param as an 8-bit unsigned integer.''' - return self._as(self._dtypes.uint8) - - @property - def int16_value(self): - '''Get the param as a 16-bit signed integer.''' - return self._as(self._dtypes.int16) - - @property - def uint16_value(self): - '''Get the param as a 16-bit unsigned integer.''' - return self._as(self._dtypes.uint16) - - @property - def int32_value(self): - '''Get the param as a 32-bit signed integer.''' - return self._as(self._dtypes.int32) - - @property - def uint32_value(self): - '''Get the param as a 32-bit unsigned integer.''' - return self._as(self._dtypes.uint32) - - @property - def float_value(self): - '''Get the param as a 32-bit float.''' - if self._dtypes.is_dec: - return DEC_to_IEEE(self._as(np.uint32)) - else: # is_mips or is_ieee - return self._as(self._dtypes.float32) - - @property - def bytes_value(self): - '''Get the param as a raw byte string.''' - return self.bytes - - @property - def string_value(self): - '''Get the param as a unicode string.''' - return self._dtypes.decode_string(self.bytes) - - @property - def int8_array(self): - '''Get the param as an array of 8-bit signed integers.''' - return self._as_array(self._dtypes.int8) - - @property - def uint8_array(self): - '''Get the param as an array of 8-bit unsigned integers.''' - return self._as_array(self._dtypes.uint8) - - @property - def int16_array(self): - '''Get the param as an array of 16-bit signed integers.''' - return self._as_array(self._dtypes.int16) - - @property - def uint16_array(self): - '''Get the param as an array of 16-bit unsigned integers.''' - return self._as_array(self._dtypes.uint16) - - @property - def int32_array(self): - '''Get the param as an array of 32-bit signed integers.''' - return self._as_array(self._dtypes.int32) - - @property - def uint32_array(self): - '''Get the param as an array of 32-bit unsigned integers.''' - return self._as_array(self._dtypes.uint32) - - @property - def int64_array(self): - '''Get the param as an array of 32-bit signed integers.''' - return self._as_array(self._dtypes.int64) - - @property - def uint64_array(self): - '''Get the param as an array of 32-bit unsigned integers.''' - return self._as_array(self._dtypes.uint64) - - @property - def float32_array(self): - '''Get the param as an array of 32-bit floats.''' - # Convert float data if not IEEE processor - if self._dtypes.is_dec: - # _as_array but for DEC - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, self._dtypes.float32) - return DEC_to_IEEE_BYTES(self.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format - else: # is_ieee or is_mips - return self._as_array(self._dtypes.float32) - - @property - def float64_array(self): - '''Get the param as an array of 64-bit floats.''' - # Convert float data if not IEEE processor - if self._dtypes.is_dec: - raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.') - else: # is_ieee or is_mips - return self._as_array(self._dtypes.float64) - - @property - def float_array(self): - '''Get the param as an array of 32 or 64 bit floats.''' - # Convert float data if not IEEE processor - if self.bytes_per_element == 4: - return self.float32_array - elif self.bytes_per_element == 8: - return self.float64_array - else: - raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element + - "floating-point precission is not unsupported.") - - @property - def int_array(self): - '''Get the param as an array of integer values.''' - # Convert float data if not IEEE processor - if self.bytes_per_element == 1: - return self.int8_array - elif self.bytes_per_element == 2: - return self.int16_array - elif self.bytes_per_element == 4: - return self.int32_array - elif self.bytes_per_element == 8: - return self.int64_array - else: - raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % - self.bytes_per_element) - - @property - def uint_array(self): - '''Get the param as an array of integer values.''' - # Convert float data if not IEEE processor - if self.bytes_per_element == 1: - return self.uint8_array - elif self.bytes_per_element == 2: - return self.uint16_array - elif self.bytes_per_element == 4: - return self.uint32_array - elif self.bytes_per_element == 8: - return self.uint64_array - else: - raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % - self.bytes_per_element) - - @property - def bytes_array(self): - '''Get the param as an array of raw byte strings.''' - # Decode different dimensions - if len(self.dimensions) == 0: - return np.array([]) - elif len(self.dimensions) == 1: - return np.array(self.bytes) - else: - # Convert Fortran shape (data in memory is identical, shape is transposed) - word_len = self.dimensions[0] - dims = self.dimensions[1:][::-1] # Identical to: [:0:-1] - byte_steps = np.cumprod(self.dimensions[:-1])[::-1] - # Generate mult-dimensional array and parse byte words - byte_arr = np.empty(dims, dtype=object) - for i in np.ndindex(*dims): - # Calculate byte offset as sum of each array index times the byte step of each dimension. - off = np.sum(np.multiply(i, byte_steps)) - byte_arr[i] = self.bytes[off:off+word_len] - return byte_arr - - @property - def string_array(self): - '''Get the param as a python array of unicode strings.''' - # Decode different dimensions - if len(self.dimensions) == 0: - return np.array([]) - elif len(self.dimensions) == 1: - return np.array([self.string_value]) - else: - # Parse byte sequences - byte_arr = self.bytes_array - # Decode sequences - for i in np.ndindex(byte_arr.shape): - byte_arr[i] = self._dtypes.decode_string(byte_arr[i]) - return byte_arr - - -class Group(object): - '''A group of parameters from a C3D file. - - In C3D files, parameters are organized in groups. Each group has a name, a - description, and a set of named parameters. - - Attributes - ---------- - dtypes : 'DataTypes' - Data types object used for parsing. - name : str - Name of this parameter group. - desc : str - Description for this parameter group. - ''' - - def __init__(self, dtypes, name=None, desc=None): - self._params = {} - self._dtypes = dtypes - # Assign through property setters - self.name = name - self.desc = desc - - def __repr__(self): - return ''.format(self.desc) - - def __contains__(self, key): - return key in self._params - - @property - def name(self): - ''' Group name. ''' - return self._name - - @name.setter - def name(self, value): - ''' Group name string. - - Parameters - ---------- - value : str - New name for the group. - ''' - if value is None or isinstance(value, str): - self._name = value - else: - raise TypeError('Expected group name to be string, was %s.' % type(value)) - - @property - def desc(self): - ''' Group descriptor. ''' - return self._desc - - @desc.setter - def desc(self, value): - ''' Group descriptor. - - Parameters - ---------- - value : str, or bytes - New description for this parameter group. - ''' - if isinstance(value, bytes): - self._desc = self._dtypes.decode_string(value) - elif isinstance(value, str) or value is None: - self._desc = value - else: - raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(value)) - - def param_items(self): - ''' Acquire iterator for paramater key-entry pairs. ''' - return self._params.items() - - def param_values(self): - ''' Acquire iterator for parameter entries. ''' - return self._params.values() - - def param_keys(self): - ''' Acquire iterator for parameter entry keys. ''' - return self._params.keys() - - def get(self, key, default=None): - '''Get a parameter by key. - - Parameters - ---------- - key : any - Parameter key to look up in this group. - default : any, optional - Value to return if the key is not found. Defaults to None. - - Returns - ------- - param : :class:`Param` - A parameter from the current group. - ''' - return self._params.get(key, default) - - def add_param(self, name, **kwargs): - '''Add a parameter to this group. - - Parameters - ---------- - name : str - Name of the parameter to add to this group. The name will - automatically be case-normalized. - - Additional keyword arguments will be passed to the `Param` constructor. - - Raises - ------ - TypeError - Input arguments are of the wrong type. - KeyError - Name or numerical key already exist (attempt to overwrite existing data). - ''' - if not isinstance(name, str): - raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name))) - name = name.upper() - if name in self._params: - raise KeyError('Parameter already exists with key {}'.format(name)) - self._params[name] = Param(name, self._dtypes, **kwargs) - - def remove_param(self, name): - '''Remove the specified parameter. - - Parameters - ---------- - name : str - Name for the parameter to remove. - ''' - del self._params[name] - - def rename_param(self, name, new_name): - ''' Rename a specified parameter group. - - Parameters - ---------- - name : str, or 'Param' - Parameter instance, or name. - new_name : str - New name for the parameter. - - Raises - ------ - KeyError - If no parameter with the original name exists. - ValueError - If the new name already exist (attempt to overwrite existing data). - ''' - if new_name in self._params: - raise ValueError("Key {} already exist.".format(new_name)) - if isinstance(name, Param): - param = name - name = param.name - else: - # Aquire instance using id - param = self._params.get(name, None) - if param is None: - raise KeyError('No parameter found matching the identifier: {}'.format(str(name))) - del self._params[name] - self._params[new_name] = param - - def binary_size(self): - '''Return the number of bytes to store this group and its parameters.''' - return ( - 1 + # group_id - 1 + len(self._name.encode('utf-8')) + # size of name and name bytes - 2 + # next offset marker - 1 + len(self._desc.encode('utf-8')) + # size of desc and desc bytes - sum(p.binary_size() for p in self._params.values())) - - def write(self, group_id, handle): - '''Write this parameter group, with parameters, to a file handle. - - Parameters - ---------- - group_id : int - The numerical ID of the group. - handle : file handle - An open, writable, binary file handle. - ''' - name = self._name.encode('utf-8') - desc = self._desc.encode('utf-8') - handle.write(struct.pack('bb', len(name), -group_id)) - handle.write(name) - handle.write(struct.pack(''.format(self.desc) + + def __contains__(self, key): + return key in self._params + + @property + def name(self): + ''' Group name. ''' + return self._name + + @name.setter + def name(self, value): + ''' Group name string. + + Parameters + ---------- + value : str + New name for the group. + ''' + if value is None or isinstance(value, str): + self._name = value + else: + raise TypeError('Expected group name to be string, was %s.' % type(value)) + + @property + def desc(self): + ''' Group descriptor. ''' + return self._desc + + @desc.setter + def desc(self, value): + ''' Group descriptor. + + Parameters + ---------- + value : str, or bytes + New description for this parameter group. + ''' + if isinstance(value, bytes): + self._desc = self._dtypes.decode_string(value) + elif isinstance(value, str) or value is None: + self._desc = value + else: + raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(value)) + + def param_items(self): + ''' Acquire iterator for paramater key-entry pairs. ''' + return self._params.items() + + def param_values(self): + ''' Acquire iterator for parameter entries. ''' + return self._params.values() + + def param_keys(self): + ''' Acquire iterator for parameter entry keys. ''' + return self._params.keys() + + def get(self, key, default=None): + '''Get a parameter by key. + + Parameters + ---------- + key : any + Parameter key to look up in this group. + default : any, optional + Value to return if the key is not found. Defaults to None. + + Returns + ------- + param : :class:`Param` + A parameter from the current group. + ''' + return self._params.get(key, default) + + def add_param(self, name, **kwargs): + '''Add a parameter to this group. + + Parameters + ---------- + name : str + Name of the parameter to add to this group. The name will + automatically be case-normalized. + + Additional keyword arguments will be passed to the `Param` constructor. + + Raises + ------ + TypeError + Input arguments are of the wrong type. + KeyError + Name or numerical key already exist (attempt to overwrite existing data). + ''' + if not isinstance(name, str): + raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name))) + name = name.upper() + if name in self._params: + raise KeyError('Parameter already exists with key {}'.format(name)) + self._params[name] = Param(name, self._dtypes, **kwargs) + + def remove_param(self, name): + '''Remove the specified parameter. + + Parameters + ---------- + name : str + Name for the parameter to remove. + ''' + del self._params[name] + + def rename_param(self, name, new_name): + ''' Rename a specified parameter group. + + Parameters + ---------- + name : str, or 'Param' + Parameter instance, or name. + new_name : str + New name for the parameter. + + Raises + ------ + KeyError + If no parameter with the original name exists. + ValueError + If the new name already exist (attempt to overwrite existing data). + ''' + if new_name in self._params: + raise ValueError("Key {} already exist.".format(new_name)) + if isinstance(name, Param): + param = name + name = param.name + else: + # Aquire instance using id + param = self._params.get(name, None) + if param is None: + raise KeyError('No parameter found matching the identifier: {}'.format(str(name))) + del self._params[name] + self._params[new_name] = param + + def binary_size(self): + '''Return the number of bytes to store this group and its parameters.''' + return ( + 1 + # group_id + 1 + len(self._name.encode('utf-8')) + # size of name and name bytes + 2 + # next offset marker + 1 + len(self._desc.encode('utf-8')) + # size of desc and desc bytes + sum(p.binary_size() for p in self._params.values())) + + def write(self, group_id, handle): + '''Write this parameter group, with parameters, to a file handle. + + Parameters + ---------- + group_id : int + The numerical ID of the group. + handle : file handle + An open, writable, binary file handle. + ''' + name = self._name.encode('utf-8') + desc = self._desc.encode('utf-8') + handle.write(struct.pack('bb', len(name), -group_id)) + handle.write(name) + handle.write(struct.pack(''.format(self.desc) + + @property + def num_elements(self): + '''Return the number of elements in this parameter's array value.''' + e = 1 + for d in self.dimensions: + e *= d + return e + + @property + def total_bytes(self): + '''Return the number of bytes used for storing this parameter's data.''' + return self.num_elements * abs(self.bytes_per_element) + + def binary_size(self): + '''Return the number of bytes needed to store this parameter.''' + return ( + 1 + # group_id + 2 + # next offset marker + 1 + len(self.name.encode('utf-8')) + # size of name and name bytes + 1 + # data size + # size of dimensions and dimension bytes + 1 + len(self.dimensions) + + self.total_bytes + # data + 1 + len(self.desc.encode('utf-8')) # size of desc and desc bytes + ) + + def write(self, group_id, handle): + '''Write binary data for this parameter to a file handle. + + Parameters + ---------- + group_id : int + The numerical ID of the group that holds this parameter. + handle : file handle + An open, writable, binary file handle. + ''' + name = self.name.encode('utf-8') + handle.write(struct.pack('bb', len(name), group_id)) + handle.write(name) + handle.write(struct.pack(' 0: + handle.write(self.bytes) + desc = self.desc.encode('utf-8') + handle.write(struct.pack('B', len(desc))) + handle.write(desc) + + def read(self, handle): + '''Read binary data for this parameter from a file handle. + + This reads exactly enough data from the current position in the file to + initialize the parameter. + ''' + self.bytes_per_element, = struct.unpack('b', handle.read(1)) + dims, = struct.unpack('B', handle.read(1)) + self.dimensions = [struct.unpack('B', handle.read(1))[ + 0] for _ in range(dims)] + self.bytes = b'' + if self.total_bytes: + self.bytes = handle.read(self.total_bytes) + desc_size, = struct.unpack('B', handle.read(1)) + self.desc = desc_size and self._dtypes.decode_string(handle.read(desc_size)) or '' + + def _as(self, dtype): + '''Unpack the raw bytes of this param using the given struct format.''' + return np.frombuffer(self.bytes, count=1, dtype=dtype)[0] + + def _as_array(self, dtype, copy=True): + '''Unpack the raw bytes of this param using the given data format.''' + assert self.dimensions, \ + '{}: cannot get value as {} array!'.format(self.name, dtype) + elems = np.frombuffer(self.bytes, dtype=dtype) + # Reverse shape as the shape is defined in fortran format + view = elems.reshape(self.dimensions[::-1]) + if copy: + return view.copy() + return view + + def _as_any(self, dtype): + '''Unpack the raw bytes of this param as either array or single value.''' + if 0 in self.dimensions[:]: # Check if any dimension is 0 (empty buffer) + return [] # Buffer is empty + + if len(self.dimensions) == 0: # Parse data as a single value + if dtype == np.float32: # Floats need to be parsed separately! + return self.float_value + return self._as(dtype) + else: # Parse data as array + if dtype == np.float32: + data = self.float_array + else: + data = self._as_array(dtype) + if len(self.dimensions) < 2: # Check if data is contained in a single dimension + return data.flatten() + return data + + @property + def _as_integer_value(self): + ''' Get the param as either 32 bit float or unsigned integer. + Evaluates if an integer is stored as a floating point representation. + + Note: This is implemented purely for parsing start/end frames. + ''' + if self.total_bytes >= 4: + # Check if float value representation is an integer + value = self.float_value + if int(value) == value: + return value + return self.uint32_value + elif self.total_bytes >= 2: + return self.uint16_value + else: + return self.uint8_value + + @property + def int8_value(self): + '''Get the param as an 8-bit signed integer.''' + return self._as(self._dtypes.int8) + + @property + def uint8_value(self): + '''Get the param as an 8-bit unsigned integer.''' + return self._as(self._dtypes.uint8) + + @property + def int16_value(self): + '''Get the param as a 16-bit signed integer.''' + return self._as(self._dtypes.int16) + + @property + def uint16_value(self): + '''Get the param as a 16-bit unsigned integer.''' + return self._as(self._dtypes.uint16) + + @property + def int32_value(self): + '''Get the param as a 32-bit signed integer.''' + return self._as(self._dtypes.int32) + + @property + def uint32_value(self): + '''Get the param as a 32-bit unsigned integer.''' + return self._as(self._dtypes.uint32) + + @property + def float_value(self): + '''Get the param as a 32-bit float.''' + if self._dtypes.is_dec: + return DEC_to_IEEE(self._as(np.uint32)) + else: # is_mips or is_ieee + return self._as(self._dtypes.float32) + + @property + def bytes_value(self): + '''Get the param as a raw byte string.''' + return self.bytes + + @property + def string_value(self): + '''Get the param as a unicode string.''' + return self._dtypes.decode_string(self.bytes) + + @property + def int8_array(self): + '''Get the param as an array of 8-bit signed integers.''' + return self._as_array(self._dtypes.int8) + + @property + def uint8_array(self): + '''Get the param as an array of 8-bit unsigned integers.''' + return self._as_array(self._dtypes.uint8) + + @property + def int16_array(self): + '''Get the param as an array of 16-bit signed integers.''' + return self._as_array(self._dtypes.int16) + + @property + def uint16_array(self): + '''Get the param as an array of 16-bit unsigned integers.''' + return self._as_array(self._dtypes.uint16) + + @property + def int32_array(self): + '''Get the param as an array of 32-bit signed integers.''' + return self._as_array(self._dtypes.int32) + + @property + def uint32_array(self): + '''Get the param as an array of 32-bit unsigned integers.''' + return self._as_array(self._dtypes.uint32) + + @property + def int64_array(self): + '''Get the param as an array of 32-bit signed integers.''' + return self._as_array(self._dtypes.int64) + + @property + def uint64_array(self): + '''Get the param as an array of 32-bit unsigned integers.''' + return self._as_array(self._dtypes.uint64) + + @property + def float32_array(self): + '''Get the param as an array of 32-bit floats.''' + # Convert float data if not IEEE processor + if self._dtypes.is_dec: + # _as_array but for DEC + assert self.dimensions, \ + '{}: cannot get value as {} array!'.format(self.name, self._dtypes.float32) + return DEC_to_IEEE_BYTES(self.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format + else: # is_ieee or is_mips + return self._as_array(self._dtypes.float32) + + @property + def float64_array(self): + '''Get the param as an array of 64-bit floats.''' + # Convert float data if not IEEE processor + if self._dtypes.is_dec: + raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.') + else: # is_ieee or is_mips + return self._as_array(self._dtypes.float64) + + @property + def float_array(self): + '''Get the param as an array of 32 or 64 bit floats.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 4: + return self.float32_array + elif self.bytes_per_element == 8: + return self.float64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element + + "floating-point precission is not unsupported.") + + @property + def int_array(self): + '''Get the param as an array of integer values.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 1: + return self.int8_array + elif self.bytes_per_element == 2: + return self.int16_array + elif self.bytes_per_element == 4: + return self.int32_array + elif self.bytes_per_element == 8: + return self.int64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % + self.bytes_per_element) + + @property + def uint_array(self): + '''Get the param as an array of integer values.''' + # Convert float data if not IEEE processor + if self.bytes_per_element == 1: + return self.uint8_array + elif self.bytes_per_element == 2: + return self.uint16_array + elif self.bytes_per_element == 4: + return self.uint32_array + elif self.bytes_per_element == 8: + return self.uint64_array + else: + raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." % + self.bytes_per_element) + + @property + def bytes_array(self): + '''Get the param as an array of raw byte strings.''' + # Decode different dimensions + if len(self.dimensions) == 0: + return np.array([]) + elif len(self.dimensions) == 1: + return np.array(self.bytes) + else: + # Convert Fortran shape (data in memory is identical, shape is transposed) + word_len = self.dimensions[0] + dims = self.dimensions[1:][::-1] # Identical to: [:0:-1] + byte_steps = np.cumprod(self.dimensions[:-1])[::-1] + # Generate mult-dimensional array and parse byte words + byte_arr = np.empty(dims, dtype=object) + for i in np.ndindex(*dims): + # Calculate byte offset as sum of each array index times the byte step of each dimension. + off = np.sum(np.multiply(i, byte_steps)) + byte_arr[i] = self.bytes[off:off+word_len] + return byte_arr + + @property + def string_array(self): + '''Get the param as a python array of unicode strings.''' + # Decode different dimensions + if len(self.dimensions) == 0: + return np.array([]) + elif len(self.dimensions) == 1: + return np.array([self.string_value]) + else: + # Parse byte sequences + byte_arr = self.bytes_array + # Decode sequences + for i in np.ndindex(byte_arr.shape): + byte_arr[i] = self._dtypes.decode_string(byte_arr[i]) + return byte_arr From b7482721491236ed61407538a6512d7f2027479e Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 13:06:00 +0200 Subject: [PATCH 040/120] header.py --- src/header.py | 291 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 291 insertions(+) create mode 100644 src/header.py diff --git a/src/header.py b/src/header.py new file mode 100644 index 0000000..1024bcd --- /dev/null +++ b/src/header.py @@ -0,0 +1,291 @@ +import sys +import struct +import numpy as np +from .utils import UNPACK_FLOAT_IEEE, DEC_to_IEEE + +class Header(object): + '''Header information from a C3D file. + + Attributes + ---------- + event_block : int + Index of the 512-byte block where labels (metadata) are found. + parameter_block : int + Index of the 512-byte block where parameters (metadata) are found. + data_block : int + Index of the 512-byte block where data starts. + point_count : int + Number of motion capture channels recorded in this file. + analog_count : int + Number of analog values recorded per frame of 3D point data. + first_frame : int + Index of the first frame of data. + last_frame : int + Index of the last frame of data. + analog_per_frame : int + Number of analog frames per frame of 3D point data. The analog frame + rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE) + times the analog per frame value. + frame_rate : float + The frame rate of the recording, in frames per second. + scale_factor : float + Multiply values in the file by this scale parameter. + long_event_labels : bool + max_gap : int + + .. note:: + The ``scale_factor`` attribute is not used in Phasespace C3D files; + instead, use the POINT.SCALE parameter. + + .. note:: + The ``first_frame`` and ``last_frame`` header attributes are not used in + C3D files generated by Phasespace. Instead, the first and last + frame numbers are stored in the POINTS:ACTUAL_START_FIELD and + POINTS:ACTUAL_END_FIELD parameters. + ''' + + # Read/Write header formats, read values as unsigned ints rather then floats. + BINARY_FORMAT_WRITE = ' 0 + self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong + 4])[0]) + self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong + 4]) + + @property + def events(self): + ''' Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label). + + Note*: + Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter. + Frame 1 therefor has the time 0.0 in relation to the event timing. + ''' + return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags]) + + def encode_events(self, events): + ''' Encode event data in the event block. + + Parameters + ---------- + events : [(float, str), ...] + Event data, iterable of touples containing the event timing and a 4 character label string. + Event timings should be calculated relative to sample 1 with the timing 0.0s, and should + not be relative to the first_frame header parameter. + ''' + endian = '<' + if sys.byteorder == 'big': + endian = '>' + + # Event block format + fmt = '{}{}{}{}{}'.format(endian, + str(18 * 4) + 's', # Timings + str(18) + 's', # Flags + 'H', # __ + str(18 * 4) + 's' # Labels + ) + # Pack bytes + event_timings = np.zeros(18, dtype=np.float32) + event_disp_flags = np.zeros(18, dtype=np.uint8) + event_labels = np.empty(18, dtype=object) + label_bytes = bytearray(18 * 4) + for i, (time, label) in enumerate(events): + if i > 17: + # Don't raise Error, header events are rarely used. + warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.') + break + + event_timings[i] = time + event_labels[i] = label + label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8') + + write_count = min(i + 1, 18) + event_disp_flags[:write_count] = 1 + + # Update event headers in self + self.long_event_labels = 0x3039 # Magic number + self.event_count = write_count + # Update event block + self.event_timings = event_timings[:write_count] + self.event_disp_flags = np.ones(write_count, dtype=np.bool) + self.event_labels = event_labels[:write_count] + self.event_block = struct.pack(fmt, + event_timings.tobytes(), + event_disp_flags.tobytes(), + 0, + label_bytes + ) From a8622292312c92aa94c1b79d2afaf139750b8a54 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 13:40:56 +0200 Subject: [PATCH 041/120] manager.py + working tests --- c3d.py | 446 +---------------------- src/__init__.py | 0 src/manager.py | 450 ++++++++++++++++++++++++ test/test_parameter_bytes_conversion.py | 54 +-- 4 files changed, 479 insertions(+), 471 deletions(-) create mode 100644 src/__init__.py create mode 100644 src/manager.py diff --git a/c3d.py b/c3d.py index fc4a201..e67bf09 100644 --- a/c3d.py +++ b/c3d.py @@ -1,5 +1,4 @@ '''A Python module for reading and writing C3D files.''' - from __future__ import unicode_literals import sys @@ -8,456 +7,13 @@ import numpy as np import struct import warnings +from src.manager import Manager from src.header import Header from src.group import Group from src.dtypes import DataTypes from src.utils import is_integer, is_iterable, DEC_to_IEEE_BYTES, Decorator -class Manager(object): - '''A base class for managing C3D file metadata. - - This class manages a C3D header (which contains some stock metadata fields) - as well as a set of parameter groups. Each group is accessible using its - name. - - Attributes - ---------- - header : `Header` - Header information for the C3D file. - ''' - - def __init__(self, header=None): - '''Set up a new Manager with a Header.''' - self._header = header or Header() - self._groups = {} - - def __contains__(self, key): - return key in self._groups - - @property - def header(self): - ''' Access to .c3d header data. ''' - return self._header - - def group_items(self): - ''' Acquire iterable over parameter group pairs. - - Returns - ------- - items : Touple of ((str, :class:`Group`), ...) - Python touple containing pairs of name keys and parameter group entries. - ''' - return ((k, v) for k, v in self._groups.items() if isinstance(k, str)) - - def group_values(self): - ''' Acquire iterable over parameter group entries. - - Returns - ------- - values : Touple of (:class:`Group`, ...) - Python touple containing unique parameter group entries. - ''' - return (v for k, v in self._groups.items() if isinstance(k, str)) - - def group_keys(self): - ''' Acquire iterable over parameter group entry string keys. - - Returns - ------- - keys : Touple of (str, ...) - Python touple containing keys for the parameter group entries. - ''' - return (k for k in self._groups.keys() if isinstance(k, str)) - - def group_listed(self): - ''' Acquire iterable over sorted numerical parameter group pairs. - - Returns - ------- - items : Touple of ((int, :class:`Group`), ...) - Sorted python touple containing pairs of numerical keys and parameter group entries. - ''' - return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int)) - - def _check_metadata(self): - ''' Ensure that the metadata in our file is self-consistent. ''' - assert self._header.point_count == self.point_used, ( - 'inconsistent point count! {} header != {} POINT:USED'.format( - self._header.point_count, - self.point_used, - )) - - assert self._header.scale_factor == self.point_scale, ( - 'inconsistent scale factor! {} header != {} POINT:SCALE'.format( - self._header.scale_factor, - self.point_scale, - )) - - assert self._header.frame_rate == self.point_rate, ( - 'inconsistent frame rate! {} header != {} POINT:RATE'.format( - self._header.frame_rate, - self.point_rate, - )) - - if self.point_rate: - ratio = self.analog_rate / self.point_rate - else: - ratio = 0 - assert self._header.analog_per_frame == ratio, ( - 'inconsistent analog rate! {} header != {} analog-fps / {} point-fps'.format( - self._header.analog_per_frame, - self.analog_rate, - self.point_rate, - )) - - count = self.analog_used * self._header.analog_per_frame - assert self._header.analog_count == count, ( - 'inconsistent analog count! {} header != {} analog used * {} per-frame'.format( - self._header.analog_count, - self.analog_used, - self._header.analog_per_frame, - )) - - try: - start = self.get_uint16('POINT:DATA_START') - if self._header.data_block != start: - warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( - self._header.data_block, start)) - except AttributeError: - warnings.warn('''no pointer available in POINT:DATA_START indicating the start of the data block, using - header pointer as fallback''') - - def check_parameters(params): - for name in params: - if self.get(name) is None: - warnings.warn('missing parameter {}'.format(name)) - - if self.point_used > 0: - check_parameters(('POINT:LABELS', 'POINT:DESCRIPTIONS')) - else: - warnings.warn('No point data found in file.') - if self.analog_used > 0: - check_parameters(('ANALOG:LABELS', 'ANALOG:DESCRIPTIONS')) - else: - warnings.warn('No analog data found in file.') - - def add_group(self, group_id, name, desc): - '''Add a new parameter group. - - Parameters - ---------- - group_id : int - The numeric ID for a group to check or create. - name : str, optional - If a group is created, assign this name to the group. - desc : str, optional - If a group is created, assign this description to the group. - - Returns - ------- - group : :class:`Group` - A group with the given ID, name, and description. - - Raises - ------ - TypeError - Input arguments are of the wrong type. - KeyError - Name or numerical key already exist (attempt to overwrite existing data). - ''' - if not is_integer(group_id): - raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id)) - if not (isinstance(name, str) or name is None): - raise TypeError('Expected Group name key to be string, was %s.' % type(name)) - group_id = int(group_id) # Asserts python int - if group_id in self._groups: - raise KeyError('Group with numerical key {} already exists'.format(group_id)) - name = name.upper() - if name in self._groups: - raise KeyError('No group matched name key {}'.format(name)) - group = self._groups[name] = self._groups[group_id] = Group(self._dtypes, name, desc) - return group - - def remove_group(self, group_id): - '''Remove the parameter group. - - Parameters - ---------- - group_id : int, or str - The numeric or name ID key for a group to remove all entries for. - ''' - grp = self._groups.get(group_id, None) - if grp is None: - return - gkeys = [k for (k, v) in self._groups.items() if v == grp] - for k in gkeys: - del self._groups[k] - - def rename_group(self, group_id, new_group_id): - ''' Rename a specified parameter group. - - Parameters - ---------- - group_id : int, str, or 'Group' - Group instance, name, or numerical identifier for the group. - new_group_id : str, or int - If string, it is the new name for the group. If integer, it will replace its numerical group id. - - Raises - ------ - KeyError - If a group with a duplicate ID or name already exists. - ''' - if isinstance(group_id, Group): - grp = group_id - else: - # Aquire instance using id - grp = self._groups.get(group_id, None) - if grp is None: - raise KeyError('No group found matching the identifier: %s' % str(group_id)) - if new_group_id in self._groups: - if new_group_id == group_id: - return - raise ValueError('Key %s for group %s already exist.' % (str(new_group_id), grp.name)) - - # Clear old id - if isinstance(new_group_id, (str, bytes)): - if grp.name in self._groups: - del self._groups[grp.name] - grp._name = new_group_id - elif is_integer(new_group_id): - new_group_id = int(new_group_id) # Ensure python int - del self._groups[group_id] - else: - raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id))) - # Update - self._groups[new_group_id] = grp - - def get(self, group, default=None): - '''Get a group or parameter. - - Parameters - ---------- - group : str - If this string contains a period (.), then the part before the - period will be used to retrieve a group, and the part after the - period will be used to retrieve a parameter from that group. If this - string does not contain a period, then just a group will be - returned. - default : any - Return this value if the named group and parameter are not found. - - Returns - ------- - value : :class:`Group` or :class:`Param` - Either a group or parameter with the specified name(s). If neither - is found, returns the default value. - ''' - if is_integer(group): - return self._groups.get(int(group), default) - group = group.upper() - param = None - if '.' in group: - group, param = group.split('.', 1) - if ':' in group: - group, param = group.split(':', 1) - if group not in self._groups: - return default - group = self._groups[group] - if param is not None: - return group.get(param, default) - return group - - def get_int8(self, key): - '''Get a parameter value as an 8-bit signed integer.''' - return self.get(key).int8_value - - def get_uint8(self, key): - '''Get a parameter value as an 8-bit unsigned integer.''' - return self.get(key).uint8_value - - def get_int16(self, key): - '''Get a parameter value as a 16-bit signed integer.''' - return self.get(key).int16_value - - def get_uint16(self, key): - '''Get a parameter value as a 16-bit unsigned integer.''' - return self.get(key).uint16_value - - def get_int32(self, key): - '''Get a parameter value as a 32-bit signed integer.''' - return self.get(key).int32_value - - def get_uint32(self, key): - '''Get a parameter value as a 32-bit unsigned integer.''' - return self.get(key).uint32_value - - def get_float(self, key): - '''Get a parameter value as a 32-bit float.''' - return self.get(key).float_value - - def get_bytes(self, key): - '''Get a parameter value as a byte string.''' - return self.get(key).bytes_value - - def get_string(self, key): - '''Get a parameter value as a string.''' - return self.get(key).string_value - - def parameter_blocks(self): - '''Compute the size (in 512B blocks) of the parameter section.''' - bytes = 4. + sum(g.binary_size() for g in self._groups.values()) - return int(np.ceil(bytes / 512)) - - @property - def point_rate(self): - ''' Number of sampled 3D coordinates per second. - ''' - try: - return self.get_float('POINT:RATE') - except AttributeError: - return self.header.frame_rate - - @property - def point_scale(self): - try: - return self.get_float('POINT:SCALE') - except AttributeError: - return self.header.scale_factor - - @property - def point_used(self): - ''' Number of sampled 3D point coordinates per frame. - ''' - try: - return self.get_uint16('POINT:USED') - except AttributeError: - return self.header.point_count - - @property - def analog_used(self): - ''' Number of analog measurements, or channels, for each analog data sample. - ''' - try: - return self.get_uint16('ANALOG:USED') - except AttributeError: - return self.header.analog_count - - @property - def analog_rate(self): - ''' Number of analog data samples per second. - ''' - try: - return self.get_float('ANALOG:RATE') - except AttributeError: - return self.header.analog_per_frame * self.point_rate - - @property - def analog_per_frame(self): - ''' Number of analog samples per 3D frame (point sample). - ''' - return int(self.analog_rate / self.point_rate) - - @property - def analog_sample_count(self): - ''' Number of analog samples per channel. - ''' - has_analog = self.analog_used > 0 - return int(self.frame_count * self.analog_per_frame) * has_analog - - @property - def point_labels(self): - return self.get('POINT:LABELS').string_array - - @property - def analog_labels(self): - return self.get('ANALOG:LABELS').string_array - - @property - def frame_count(self): - return self.last_frame - self.first_frame + 1 # Add 1 since range is inclusive [first, last] - - @property - def first_frame(self): - # Start frame seems to be less of an issue to determine. - # this is a hack for phasespace files ... should put it in a subclass. - param = self.get('TRIAL:ACTUAL_START_FIELD') - if param is not None: - # ACTUAL_START_FIELD is encoded in two 16 byte words... - words = param.uint16_array - return words[0] + words[1] * 65535 - return self.header.first_frame - - @property - def last_frame(self): - # Number of frames can be represented in many formats, first check if valid header values - if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: - return self.header.last_frame - - # Check different parameter options where the frame can be encoded - end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] - param = self.get('TRIAL:ACTUAL_END_FIELD') - if param is not None: - # Encoded as 2 16 bit words (rather then 1 32 bit word) - words = param.uint16_array - end_frame[1] = words[0] + words[1] * 65536 - #end_frame[1] = param.uint32_value - param = self.get('POINT:LONG_FRAMES') - if param is not None: - # Encoded as float - end_frame[2] = int(param.float_value) - param = self.get('POINT:FRAMES') - if param is not None: - # Can be encoded either as 32 bit float or 16 bit uint - end_frame[3] = param._as_integer_value - # Return the largest of the all (queue bad reading...) - return int(np.max(end_frame)) - - def get_screen_axis(self): - ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. - - Returns - ------- - value : Touple on form (str, str) or None - Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. - ''' - X = self.get('POINT:X_SCREEN') - Y = self.get('POINT:Y_SCREEN') - if X and Y: - return (X.string_value, Y.string_value) - return None - - def get_analog_transform_parameters(self): - ''' Parse analog data transform parameters. - ''' - # Offsets - analog_offsets = np.zeros((self.analog_used), int) - param = self.get('ANALOG:OFFSET') - if param is not None and param.num_elements > 0: - analog_offsets[:] = param.int16_array[:self.analog_used] - - # Scale factors - analog_scales = np.ones((self.analog_used), float) - gen_scale = 1. - param = self.get('ANALOG:GEN_SCALE') - if param is not None: - gen_scale = param.float_value - param = self.get('ANALOG:SCALE') - if param is not None and param.num_elements > 0: - analog_scales[:] = param.float_array[:self.analog_used] - - return gen_scale, analog_scales, analog_offsets - - def get_analog_transform(self): - ''' Get broadcastable analog transformation parameters. - ''' - gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters() - analog_scales *= gen_scale - analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) - analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) - return analog_scales, analog_offsets - class Reader(Manager): '''This class provides methods for reading the data in a C3D file. diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/manager.py b/src/manager.py new file mode 100644 index 0000000..1e0bcdc --- /dev/null +++ b/src/manager.py @@ -0,0 +1,450 @@ +import numpy as np +import warnings +from src.header import Header +from src.group import Group +from src.utils import is_integer, is_iterable + + +class Manager(object): + '''A base class for managing C3D file metadata. + + This class manages a C3D header (which contains some stock metadata fields) + as well as a set of parameter groups. Each group is accessible using its + name. + + Attributes + ---------- + header : `Header` + Header information for the C3D file. + ''' + + def __init__(self, header=None): + '''Set up a new Manager with a Header.''' + self._header = header or Header() + self._groups = {} + + def __contains__(self, key): + return key in self._groups + + @property + def header(self): + ''' Access to .c3d header data. ''' + return self._header + + def group_items(self): + ''' Acquire iterable over parameter group pairs. + + Returns + ------- + items : Touple of ((str, :class:`Group`), ...) + Python touple containing pairs of name keys and parameter group entries. + ''' + return ((k, v) for k, v in self._groups.items() if isinstance(k, str)) + + def group_values(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + values : Touple of (:class:`Group`, ...) + Python touple containing unique parameter group entries. + ''' + return (v for k, v in self._groups.items() if isinstance(k, str)) + + def group_keys(self): + ''' Acquire iterable over parameter group entry string keys. + + Returns + ------- + keys : Touple of (str, ...) + Python touple containing keys for the parameter group entries. + ''' + return (k for k in self._groups.keys() if isinstance(k, str)) + + def group_listed(self): + ''' Acquire iterable over sorted numerical parameter group pairs. + + Returns + ------- + items : Touple of ((int, :class:`Group`), ...) + Sorted python touple containing pairs of numerical keys and parameter group entries. + ''' + return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int)) + + def _check_metadata(self): + ''' Ensure that the metadata in our file is self-consistent. ''' + assert self._header.point_count == self.point_used, ( + 'inconsistent point count! {} header != {} POINT:USED'.format( + self._header.point_count, + self.point_used, + )) + + assert self._header.scale_factor == self.point_scale, ( + 'inconsistent scale factor! {} header != {} POINT:SCALE'.format( + self._header.scale_factor, + self.point_scale, + )) + + assert self._header.frame_rate == self.point_rate, ( + 'inconsistent frame rate! {} header != {} POINT:RATE'.format( + self._header.frame_rate, + self.point_rate, + )) + + if self.point_rate: + ratio = self.analog_rate / self.point_rate + else: + ratio = 0 + assert self._header.analog_per_frame == ratio, ( + 'inconsistent analog rate! {} header != {} analog-fps / {} point-fps'.format( + self._header.analog_per_frame, + self.analog_rate, + self.point_rate, + )) + + count = self.analog_used * self._header.analog_per_frame + assert self._header.analog_count == count, ( + 'inconsistent analog count! {} header != {} analog used * {} per-frame'.format( + self._header.analog_count, + self.analog_used, + self._header.analog_per_frame, + )) + + try: + start = self.get_uint16('POINT:DATA_START') + if self._header.data_block != start: + warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( + self._header.data_block, start)) + except AttributeError: + warnings.warn('''no pointer available in POINT:DATA_START indicating the start of the data block, using + header pointer as fallback''') + + def check_parameters(params): + for name in params: + if self.get(name) is None: + warnings.warn('missing parameter {}'.format(name)) + + if self.point_used > 0: + check_parameters(('POINT:LABELS', 'POINT:DESCRIPTIONS')) + else: + warnings.warn('No point data found in file.') + if self.analog_used > 0: + check_parameters(('ANALOG:LABELS', 'ANALOG:DESCRIPTIONS')) + else: + warnings.warn('No analog data found in file.') + + def add_group(self, group_id, name, desc): + '''Add a new parameter group. + + Parameters + ---------- + group_id : int + The numeric ID for a group to check or create. + name : str, optional + If a group is created, assign this name to the group. + desc : str, optional + If a group is created, assign this description to the group. + + Returns + ------- + group : :class:`Group` + A group with the given ID, name, and description. + + Raises + ------ + TypeError + Input arguments are of the wrong type. + KeyError + Name or numerical key already exist (attempt to overwrite existing data). + ''' + if not is_integer(group_id): + raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id)) + if not (isinstance(name, str) or name is None): + raise TypeError('Expected Group name key to be string, was %s.' % type(name)) + group_id = int(group_id) # Asserts python int + if group_id in self._groups: + raise KeyError('Group with numerical key {} already exists'.format(group_id)) + name = name.upper() + if name in self._groups: + raise KeyError('No group matched name key {}'.format(name)) + group = self._groups[name] = self._groups[group_id] = Group(self._dtypes, name, desc) + return group + + def remove_group(self, group_id): + '''Remove the parameter group. + + Parameters + ---------- + group_id : int, or str + The numeric or name ID key for a group to remove all entries for. + ''' + grp = self._groups.get(group_id, None) + if grp is None: + return + gkeys = [k for (k, v) in self._groups.items() if v == grp] + for k in gkeys: + del self._groups[k] + + def rename_group(self, group_id, new_group_id): + ''' Rename a specified parameter group. + + Parameters + ---------- + group_id : int, str, or 'Group' + Group instance, name, or numerical identifier for the group. + new_group_id : str, or int + If string, it is the new name for the group. If integer, it will replace its numerical group id. + + Raises + ------ + KeyError + If a group with a duplicate ID or name already exists. + ''' + if isinstance(group_id, Group): + grp = group_id + else: + # Aquire instance using id + grp = self._groups.get(group_id, None) + if grp is None: + raise KeyError('No group found matching the identifier: %s' % str(group_id)) + if new_group_id in self._groups: + if new_group_id == group_id: + return + raise ValueError('Key %s for group %s already exist.' % (str(new_group_id), grp.name)) + + # Clear old id + if isinstance(new_group_id, (str, bytes)): + if grp.name in self._groups: + del self._groups[grp.name] + grp._name = new_group_id + elif is_integer(new_group_id): + new_group_id = int(new_group_id) # Ensure python int + del self._groups[group_id] + else: + raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id))) + # Update + self._groups[new_group_id] = grp + + def get(self, group, default=None): + '''Get a group or parameter. + + Parameters + ---------- + group : str + If this string contains a period (.), then the part before the + period will be used to retrieve a group, and the part after the + period will be used to retrieve a parameter from that group. If this + string does not contain a period, then just a group will be + returned. + default : any + Return this value if the named group and parameter are not found. + + Returns + ------- + value : :class:`Group` or :class:`Param` + Either a group or parameter with the specified name(s). If neither + is found, returns the default value. + ''' + if is_integer(group): + return self._groups.get(int(group), default) + group = group.upper() + param = None + if '.' in group: + group, param = group.split('.', 1) + if ':' in group: + group, param = group.split(':', 1) + if group not in self._groups: + return default + group = self._groups[group] + if param is not None: + return group.get(param, default) + return group + + def get_int8(self, key): + '''Get a parameter value as an 8-bit signed integer.''' + return self.get(key).int8_value + + def get_uint8(self, key): + '''Get a parameter value as an 8-bit unsigned integer.''' + return self.get(key).uint8_value + + def get_int16(self, key): + '''Get a parameter value as a 16-bit signed integer.''' + return self.get(key).int16_value + + def get_uint16(self, key): + '''Get a parameter value as a 16-bit unsigned integer.''' + return self.get(key).uint16_value + + def get_int32(self, key): + '''Get a parameter value as a 32-bit signed integer.''' + return self.get(key).int32_value + + def get_uint32(self, key): + '''Get a parameter value as a 32-bit unsigned integer.''' + return self.get(key).uint32_value + + def get_float(self, key): + '''Get a parameter value as a 32-bit float.''' + return self.get(key).float_value + + def get_bytes(self, key): + '''Get a parameter value as a byte string.''' + return self.get(key).bytes_value + + def get_string(self, key): + '''Get a parameter value as a string.''' + return self.get(key).string_value + + def parameter_blocks(self): + '''Compute the size (in 512B blocks) of the parameter section.''' + bytes = 4. + sum(g.binary_size() for g in self._groups.values()) + return int(np.ceil(bytes / 512)) + + @property + def point_rate(self): + ''' Number of sampled 3D coordinates per second. + ''' + try: + return self.get_float('POINT:RATE') + except AttributeError: + return self.header.frame_rate + + @property + def point_scale(self): + try: + return self.get_float('POINT:SCALE') + except AttributeError: + return self.header.scale_factor + + @property + def point_used(self): + ''' Number of sampled 3D point coordinates per frame. + ''' + try: + return self.get_uint16('POINT:USED') + except AttributeError: + return self.header.point_count + + @property + def analog_used(self): + ''' Number of analog measurements, or channels, for each analog data sample. + ''' + try: + return self.get_uint16('ANALOG:USED') + except AttributeError: + return self.header.analog_count + + @property + def analog_rate(self): + ''' Number of analog data samples per second. + ''' + try: + return self.get_float('ANALOG:RATE') + except AttributeError: + return self.header.analog_per_frame * self.point_rate + + @property + def analog_per_frame(self): + ''' Number of analog samples per 3D frame (point sample). + ''' + return int(self.analog_rate / self.point_rate) + + @property + def analog_sample_count(self): + ''' Number of analog samples per channel. + ''' + has_analog = self.analog_used > 0 + return int(self.frame_count * self.analog_per_frame) * has_analog + + @property + def point_labels(self): + return self.get('POINT:LABELS').string_array + + @property + def analog_labels(self): + return self.get('ANALOG:LABELS').string_array + + @property + def frame_count(self): + return self.last_frame - self.first_frame + 1 # Add 1 since range is inclusive [first, last] + + @property + def first_frame(self): + # Start frame seems to be less of an issue to determine. + # this is a hack for phasespace files ... should put it in a subclass. + param = self.get('TRIAL:ACTUAL_START_FIELD') + if param is not None: + # ACTUAL_START_FIELD is encoded in two 16 byte words... + words = param.uint16_array + return words[0] + words[1] * 65535 + return self.header.first_frame + + @property + def last_frame(self): + # Number of frames can be represented in many formats, first check if valid header values + if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: + return self.header.last_frame + + # Check different parameter options where the frame can be encoded + end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] + param = self.get('TRIAL:ACTUAL_END_FIELD') + if param is not None: + # Encoded as 2 16 bit words (rather then 1 32 bit word) + words = param.uint16_array + end_frame[1] = words[0] + words[1] * 65536 + #end_frame[1] = param.uint32_value + param = self.get('POINT:LONG_FRAMES') + if param is not None: + # Encoded as float + end_frame[2] = int(param.float_value) + param = self.get('POINT:FRAMES') + if param is not None: + # Can be encoded either as 32 bit float or 16 bit uint + end_frame[3] = param._as_integer_value + # Return the largest of the all (queue bad reading...) + return int(np.max(end_frame)) + + def get_screen_axis(self): + ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. + + Returns + ------- + value : Touple on form (str, str) or None + Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. + ''' + X = self.get('POINT:X_SCREEN') + Y = self.get('POINT:Y_SCREEN') + if X and Y: + return (X.string_value, Y.string_value) + return None + + def get_analog_transform_parameters(self): + ''' Parse analog data transform parameters. + ''' + # Offsets + analog_offsets = np.zeros((self.analog_used), int) + param = self.get('ANALOG:OFFSET') + if param is not None and param.num_elements > 0: + analog_offsets[:] = param.int16_array[:self.analog_used] + + # Scale factors + analog_scales = np.ones((self.analog_used), float) + gen_scale = 1. + param = self.get('ANALOG:GEN_SCALE') + if param is not None: + gen_scale = param.float_value + param = self.get('ANALOG:SCALE') + if param is not None and param.num_elements > 0: + analog_scales[:] = param.float_array[:self.analog_used] + + return gen_scale, analog_scales, analog_offsets + + def get_analog_transform(self): + ''' Get broadcastable analog transformation parameters. + ''' + gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters() + analog_scales *= gen_scale + analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) + analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) + return analog_scales, analog_offsets diff --git a/test/test_parameter_bytes_conversion.py b/test/test_parameter_bytes_conversion.py index 14d02c4..03d8827 100644 --- a/test/test_parameter_bytes_conversion.py +++ b/test/test_parameter_bytes_conversion.py @@ -2,6 +2,8 @@ import struct import unittest import numpy as np +from src.dtypes import DataTypes, PROCESSOR_INTEL +from src.parameter import Param def genByteWordArr(word, shape): @@ -46,7 +48,7 @@ class ParameterValueTest(unittest.TestCase): def setUp(self): self.rnd = np.random.default_rng() - self.dtypes = c3d.DataTypes(c3d.PROCESSOR_INTEL) + self.dtypes = DataTypes(PROCESSOR_INTEL) def test_a_param_float32(self): ''' Verify a single 32 bit floating point value is parsed correctly @@ -54,7 +56,7 @@ def test_a_param_float32(self): for i in range(ParameterValueTest.TEST_ITERATIONS): value = np.float32(self.rnd.uniform(*ParameterValueTest.RANGE_32_BIT)) bytes = struct.pack(' 5) - P = c3d.Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ @@ -323,7 +325,7 @@ def test_k_parse_random_string_array(self): # 4 dims for wlen in range(10): arr, shape = genRndByteArr(wlen, [7, 5, 3], wlen > 5) - P = c3d.Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ @@ -335,7 +337,7 @@ def test_k_parse_random_string_array(self): # 5 dims for wlen in range(10): arr, shape = genRndByteArr(wlen, [7, 6, 5, 3], wlen > 5) - P = c3d.Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ From 2f34fc17849bfddfcefcdf94859e0fb7e95dc8f9 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 23:35:13 +0200 Subject: [PATCH 042/120] Step in the 'right' direction --- c3d.py | 204 +++++-------- src/group.py | 389 ++++++++++++++++++------ src/manager.py | 178 +++++------ src/parameter.py | 132 +++++--- test/test_c3d.py | 10 +- test/test_group_accessors.py | 63 ++-- test/test_parameter_accessors.py | 53 ++-- test/test_parameter_bytes_conversion.py | 54 ++-- 8 files changed, 679 insertions(+), 404 deletions(-) diff --git a/c3d.py b/c3d.py index e67bf09..414789d 100644 --- a/c3d.py +++ b/c3d.py @@ -9,9 +9,9 @@ import warnings from src.manager import Manager from src.header import Header -from src.group import Group +from src.group import GroupData, GroupWritable, GroupReadonly from src.dtypes import DataTypes -from src.utils import is_integer, is_iterable, DEC_to_IEEE_BYTES, Decorator +from src.utils import is_integer, is_iterable, DEC_to_IEEE_BYTES class Reader(Manager): @@ -87,7 +87,7 @@ def seek_param_section_header(): if group_id > 0: # We've just started reading a parameter. If its group doesn't # exist, create a blank one. add the parameter to the group. - group = self._groups.setdefault(group_id, Group(self._dtypes)) + group = self._groups.setdefault(group_id, GroupData(self._dtypes)) group.add_param(name, handle=buf) else: # We've just started reading a group. If a group with the @@ -97,16 +97,16 @@ def seek_param_section_header(): group_id = abs(group_id) size, = struct.unpack('B', buf.read(1)) desc = size and buf.read(size) or '' - group = self.get(group_id) + group = self._get(group_id) if group is not None: - self.rename_group(group, name) # Inserts name key + self._rename_group(group, name) # Inserts name key group.desc = desc else: - self.add_group(group_id, name, desc) + self._add_group(group_id, name, desc) self._check_metadata() - def read_frames(self, copy=True, analog_transform=True, camera_sum=False, check_nan=True): + def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False): '''Iterate over the data frames from our C3D file handle. Parameters @@ -283,113 +283,56 @@ def proc_type(self): ''' return self._dtypes.proc_type - def to_writer(self, conversion): + def to_writer(self, conversion=None): ''' Convert to 'Writer' using the conversion mode. See Writer.from_reader() for supported conversion modes and possible exceptions. ''' return Writer.from_reader(self, conversion=conversion) + def get(self, key, default=None): + '''Get a readonly group or parameter. -class GroupEditable(Decorator): - ''' Group instance decorator providing convenience functions for Writer editing. - ''' - def __init__(self, group): - super(GroupEditable, self).__init__(group) - - def __contains__(self, key): - return key in self._decoratee - # - # Add decorator functions (throws on overwrite) - # - def add(self, name, desc, bpe, format, data, *dimensions): - ''' Add a parameter with 'data' package formated in accordance with 'format'. - ''' - if isinstance(data, bytes): - pass - else: - data = struct.pack(format, data) + Parameters + ---------- + key : str + If this string contains a period (.), then the part before the + period will be used to retrieve a group, and the part after the + period will be used to retrieve a parameter from that group. If this + string does not contain a period, then just a group will be + returned. + default : any + Return this value if the named group and parameter are not found. - self.add_param(name, - desc=desc, - bytes_per_element=bpe, - bytes=data, - dimensions=list(dimensions)) + Returns + ------- + value : :class:`GroupReadonly` or :class:`Param` + Either a group or parameter with the specified name(s). If neither + is found, returns the default value. + ''' + val = self._get(key) + if val is None: + return default + return val.readonly() - def add_array(self, name, desc, data, dtype=None): - '''Add a parameter with the 'data' package. + def items(self): + ''' Acquire iterable over parameter group pairs. - Arguments - --------- - data : Numpy array, or python iterable. - dtype : Numpy dtype to encode the array (Optional if data is numpy type). - ''' - if not isinstance(data, np.ndarray): - if dtype is not None: - raise ValueError('Must specify dtype when passning non-numpy array type.') - data = np.array(data, dtype=dtype) - elif dtype is None: - dtype = data.dtype - - self.add_param(name, - desc=desc, - bytes_per_element=dtype.itemsize, - bytes=data, - dimensions=data.shape) - - def add_str(self, name, desc, data, *dimensions): - ''' Add a string parameter. - ''' - self.add_param(name, - desc=desc, - bytes_per_element=-1, - bytes=data.encode('utf-8'), - dimensions=list(dimensions)) - - def add_empty_array(self, name, desc, bpe): - ''' Add an empty parameter block. - ''' - self.add_param(name, desc=desc, - bytes_per_element=bpe, dimensions=[0]) - - # - # Set decorator functions (overwrites) - # - def set(self, name, *args, **kwargs): - ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'. - ''' - try: - self.remove_param(name) - except KeyError as e: - pass - self.add(name, *args, **kwargs) - - def set_str(self, name, *args, **kwargs): - ''' Add a string parameter. - ''' - try: - self.remove_param(name) - except KeyError as e: - pass - self.add_str(name, *args, **kwargs) - - def set_array(self, name, *args, **kwargs): - ''' Add a string parameter. - ''' - try: - self.remove_param(name) - except KeyError as e: - pass - self.add_array(name, *args, **kwargs) - - def set_empty_array(self, name, *args, **kwargs): - ''' Add an empty parameter block. + Returns + ------- + items : Touple of ((str, :class:`Group`), ...) + Python touple containing pairs of name keys and parameter group entries. ''' - try: - self.remove_param(name) - except KeyError as e: - pass - self.add_empty_array(name, *args, **kwargs) + return ((k, GroupReadonly(v)) for k, v in self._groups.items() if isinstance(k, str)) + def values(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + values : Touple of (:class:`Group`, ...) + Python touple containing unique parameter group entries. + ''' + return (GroupReadonly(v) for k, v in self._groups.items() if isinstance(k, str)) class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -421,18 +364,13 @@ class Writer(Manager): def __init__(self, point_rate=480., analog_rate=0., - point_scale=-1., - point_units='mm ', - gen_scale=1.): + point_scale=-1.): '''Set metadata for this writer. ''' self._dtypes = DataTypes() # Only support INTEL format from writing super(Writer, self).__init__() - # Custom properties - self._point_units = point_units - # Header properties self._header.frame_rate = np.float32(point_rate) self._header.scale_factor = np.float32(point_scale) @@ -484,10 +422,7 @@ def from_reader(reader, conversion=None): if is_consume: writer._header = reader._header - reader._header = None writer._groups = reader._groups - reader._groups = None - del reader elif is_deep_copy: writer._header = copy.deepcopy(reader._header) writer._groups = copy.deepcopy(reader._groups) @@ -511,6 +446,11 @@ def from_reader(reader, conversion=None): # Copy frames for (i, point, analog) in reader.read_frames(copy=True, camera_sum=False): writer.add_frames((point, analog)) + if is_consume: + # Cleanup + reader._header = None + reader._groups = None + del reader return writer @property @@ -564,35 +504,32 @@ def trial_group(self): return self.get_create('TRIAL') def get(self, group, default=None): - '''Get a GroupEditable decorator for keyed group instance, or a parameter instance. + '''Get a writable group or a parameter instance. Parameters ---------- - group : str + key : str Key, see Manager.get() for valid key formats. default : any Return this value if the named group and parameter are not found. Returns ------- - value : :class:`GroupEditable` or :class:`Param` + value : :class:`GroupWritable` or :class:`ParamWritable` Either a decorated group instance or parameter with the specified name(s). If neither is found, the default value is returned. ''' - val = super(Writer, self).get(group, default) - if isinstance(val, Group): - return GroupEditable(val) - return val # Parameter + return super(Writer, self)._get(group, default) def add_group(self, *args, **kwargs): '''Add a new parameter group. See Manager.add_group() for more information. Returns ------- - group : :class:`Group` + group : :class:`GroupWritable` An editable group instance. ''' - return GroupEditable(super(Writer, self).add_group(*args, **kwargs)) + return GroupWritable(super(Writer, self)._add_group(*args, **kwargs)) def add_frames(self, frames, index=None): '''Add frames to this writer instance. @@ -630,6 +567,18 @@ def pack_labels(labels): label_str = ''.join(label.ljust(label_max_size) for label in labels) return label_str, label_max_size + def add_group(self, *args): + ''' Add a new parameter group (see Manager._rename_group for args). ''' + return self._add_group(*args) + + def rename_group(self, *args): + ''' Rename a specified parameter group (see Manager._rename_group for args). ''' + self._rename_group(*args) + + def remove_group(self, *args): + '''Remove the parameter group. (see Manager._rename_group for args). ''' + self._remove_group(*args) + def set_point_labels(self, labels): ''' Set point data labels. ''' @@ -760,8 +709,7 @@ def write(self, handle): group.set('RATE', 'Point data sample rate', 4, ''.format(self.desc) @@ -31,75 +32,36 @@ def __repr__(self): def __contains__(self, key): return key in self._params - @property - def name(self): - ''' Group name. ''' - return self._name + def __getitem__(self, key): + return self._params[key] - @name.setter - def name(self, value): - ''' Group name string. + @property + def binary_size(self): + '''Return the number of bytes to store this group and its parameters.''' + return ( + 1 + # group_id + 1 + len(self.name.encode('utf-8')) + # size of name and name bytes + 2 + # next offset marker + 1 + len(self.desc.encode('utf-8')) + # size of desc and desc bytes + sum(p.binary_size for p in self._params.values())) - Parameters - ---------- - value : str - New name for the group. - ''' + def set_name(self, value): + ''' Set the group name string. ''' if value is None or isinstance(value, str): - self._name = value + self.name = value else: raise TypeError('Expected group name to be string, was %s.' % type(value)) - @property - def desc(self): - ''' Group descriptor. ''' - return self._desc - - @desc.setter - def desc(self, value): - ''' Group descriptor. - - Parameters - ---------- - value : str, or bytes - New description for this parameter group. + def set_desc(self, value): + ''' Set the Group descriptor. ''' if isinstance(value, bytes): - self._desc = self._dtypes.decode_string(value) + self.desc = self._dtypes.decode_string(value) elif isinstance(value, str) or value is None: - self._desc = value + self.desc = value else: raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(value)) - def param_items(self): - ''' Acquire iterator for paramater key-entry pairs. ''' - return self._params.items() - - def param_values(self): - ''' Acquire iterator for parameter entries. ''' - return self._params.values() - - def param_keys(self): - ''' Acquire iterator for parameter entry keys. ''' - return self._params.keys() - - def get(self, key, default=None): - '''Get a parameter by key. - - Parameters - ---------- - key : any - Parameter key to look up in this group. - default : any, optional - Value to return if the key is not found. Defaults to None. - - Returns - ------- - param : :class:`Param` - A parameter from the current group. - ''' - return self._params.get(key, default) - def add_param(self, name, **kwargs): '''Add a parameter to this group. @@ -109,7 +71,7 @@ def add_param(self, name, **kwargs): Name of the parameter to add to this group. The name will automatically be case-normalized. - Additional keyword arguments will be passed to the `Param` constructor. + Additional keyword arguments will be passed to the `ParamData` constructor. Raises ------ @@ -123,7 +85,7 @@ def add_param(self, name, **kwargs): name = name.upper() if name in self._params: raise KeyError('Parameter already exists with key {}'.format(name)) - self._params[name] = Param(name, self._dtypes, **kwargs) + self._params[name] = ParamData(name, self._dtypes, **kwargs) def remove_param(self, name): '''Remove the specified parameter. @@ -140,7 +102,7 @@ def rename_param(self, name, new_name): Parameters ---------- - name : str, or 'Param' + name : str, or 'ParamData' Parameter instance, or name. new_name : str New name for the parameter. @@ -154,7 +116,7 @@ def rename_param(self, name, new_name): ''' if new_name in self._params: raise ValueError("Key {} already exist.".format(new_name)) - if isinstance(name, Param): + if isinstance(name, ParamData): param = name name = param.name else: @@ -165,15 +127,6 @@ def rename_param(self, name, new_name): del self._params[name] self._params[new_name] = param - def binary_size(self): - '''Return the number of bytes to store this group and its parameters.''' - return ( - 1 + # group_id - 1 + len(self._name.encode('utf-8')) + # size of name and name bytes - 2 + # next offset marker - 1 + len(self._desc.encode('utf-8')) + # size of desc and desc bytes - sum(p.binary_size() for p in self._params.values())) - def write(self, group_id, handle): '''Write this parameter group, with parameters, to a file handle. @@ -184,8 +137,8 @@ def write(self, group_id, handle): handle : file handle An open, writable, binary file handle. ''' - name = self._name.encode('utf-8') - desc = self._desc.encode('utf-8') + name = self.name.encode('utf-8') + desc = self.desc.encode('utf-8') handle.write(struct.pack('bb', len(name), -group_id)) handle.write(name) handle.write(struct.pack(' 0: @@ -133,7 +129,7 @@ def check_parameters(params): else: warnings.warn('No analog data found in file.') - def add_group(self, group_id, name, desc): + def _add_group(self, group_id, name, desc): '''Add a new parameter group. Parameters @@ -167,10 +163,10 @@ def add_group(self, group_id, name, desc): name = name.upper() if name in self._groups: raise KeyError('No group matched name key {}'.format(name)) - group = self._groups[name] = self._groups[group_id] = Group(self._dtypes, name, desc) + group = self._groups[name] = self._groups[group_id] = GroupData(self._dtypes, name, desc) return group - def remove_group(self, group_id): + def _remove_group(self, group_id): '''Remove the parameter group. Parameters @@ -185,7 +181,7 @@ def remove_group(self, group_id): for k in gkeys: del self._groups[k] - def rename_group(self, group_id, new_group_id): + def _rename_group(self, group_id, new_group_id): ''' Rename a specified parameter group. Parameters @@ -200,8 +196,8 @@ def rename_group(self, group_id, new_group_id): KeyError If a group with a duplicate ID or name already exists. ''' - if isinstance(group_id, Group): - grp = group_id + if isinstance(group_id, GroupReadonly): + grp = group_id._data else: # Aquire instance using id grp = self._groups.get(group_id, None) @@ -216,7 +212,7 @@ def rename_group(self, group_id, new_group_id): if isinstance(new_group_id, (str, bytes)): if grp.name in self._groups: del self._groups[grp.name] - grp._name = new_group_id + grp.name = new_group_id elif is_integer(new_group_id): new_group_id = int(new_group_id) # Ensure python int del self._groups[group_id] @@ -225,7 +221,7 @@ def rename_group(self, group_id, new_group_id): # Update self._groups[new_group_id] = grp - def get(self, group, default=None): + def _get(self, group, default=None): '''Get a group or parameter. Parameters @@ -246,7 +242,10 @@ def get(self, group, default=None): is found, returns the default value. ''' if is_integer(group): - return self._groups.get(int(group), default) + group = self._groups.get(int(group)) + if group is None: + return default + return GroupWritable(group) group = group.upper() param = None if '.' in group: @@ -255,56 +254,24 @@ def get(self, group, default=None): group, param = group.split(':', 1) if group not in self._groups: return default - group = self._groups[group] + group = GroupWritable(self._groups[group]) if param is not None: return group.get(param, default) return group - def get_int8(self, key): - '''Get a parameter value as an 8-bit signed integer.''' - return self.get(key).int8_value - - def get_uint8(self, key): - '''Get a parameter value as an 8-bit unsigned integer.''' - return self.get(key).uint8_value - - def get_int16(self, key): - '''Get a parameter value as a 16-bit signed integer.''' - return self.get(key).int16_value - - def get_uint16(self, key): - '''Get a parameter value as a 16-bit unsigned integer.''' - return self.get(key).uint16_value - - def get_int32(self, key): - '''Get a parameter value as a 32-bit signed integer.''' - return self.get(key).int32_value - - def get_uint32(self, key): - '''Get a parameter value as a 32-bit unsigned integer.''' - return self.get(key).uint32_value - - def get_float(self, key): - '''Get a parameter value as a 32-bit float.''' - return self.get(key).float_value - - def get_bytes(self, key): - '''Get a parameter value as a byte string.''' - return self.get(key).bytes_value - - def get_string(self, key): - '''Get a parameter value as a string.''' - return self.get(key).string_value + @property + def header(self): + ''' Access to .c3d header data. ''' + return self._header def parameter_blocks(self): '''Compute the size (in 512B blocks) of the parameter section.''' - bytes = 4. + sum(g.binary_size() for g in self._groups.values()) + bytes = 4. + sum(g.binary_size for g in self._groups.values()) return int(np.ceil(bytes / 512)) @property def point_rate(self): - ''' Number of sampled 3D coordinates per second. - ''' + ''' Number of sampled 3D coordinates per second. ''' try: return self.get_float('POINT:RATE') except AttributeError: @@ -312,6 +279,7 @@ def point_rate(self): @property def point_scale(self): + ''' Scaling applied to non-float data. ''' try: return self.get_float('POINT:SCALE') except AttributeError: @@ -319,8 +287,7 @@ def point_scale(self): @property def point_used(self): - ''' Number of sampled 3D point coordinates per frame. - ''' + ''' Number of sampled 3D point coordinates per frame. ''' try: return self.get_uint16('POINT:USED') except AttributeError: @@ -328,17 +295,18 @@ def point_used(self): @property def analog_used(self): - ''' Number of analog measurements, or channels, for each analog data sample. - ''' + ''' Number of analog measurements, or channels, for each analog data sample. ''' try: return self.get_uint16('ANALOG:USED') except AttributeError: - return self.header.analog_count + per_frame = self.header.analog_per_frame + if per_frame > 0: + return int(self.header.analog_count / per_frame) + return 0 @property def analog_rate(self): - ''' Number of analog data samples per second. - ''' + ''' Number of analog data samples per second. ''' try: return self.get_float('ANALOG:RATE') except AttributeError: @@ -346,34 +314,36 @@ def analog_rate(self): @property def analog_per_frame(self): - ''' Number of analog samples per 3D frame (point sample). - ''' + ''' Number of analog frames per 3D frame (point sample). ''' return int(self.analog_rate / self.point_rate) @property def analog_sample_count(self): - ''' Number of analog samples per channel. - ''' + ''' Number of analog samples per channel. ''' has_analog = self.analog_used > 0 return int(self.frame_count * self.analog_per_frame) * has_analog @property def point_labels(self): - return self.get('POINT:LABELS').string_array + ''' Labels for each POINT data channel. ''' + return self._get('POINT:LABELS').string_array @property def analog_labels(self): + ''' Labels for each ANALOG data channel. ''' return self.get('ANALOG:LABELS').string_array @property def frame_count(self): + ''' Number of frames recorded in the data. ''' return self.last_frame - self.first_frame + 1 # Add 1 since range is inclusive [first, last] @property def first_frame(self): + ''' Trial frame corresponding to the first frame recorded in the data. ''' # Start frame seems to be less of an issue to determine. # this is a hack for phasespace files ... should put it in a subclass. - param = self.get('TRIAL:ACTUAL_START_FIELD') + param = self._get('TRIAL:ACTUAL_START_FIELD') if param is not None: # ACTUAL_START_FIELD is encoded in two 16 byte words... words = param.uint16_array @@ -382,23 +352,24 @@ def first_frame(self): @property def last_frame(self): + ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: return self.header.last_frame # Check different parameter options where the frame can be encoded end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] - param = self.get('TRIAL:ACTUAL_END_FIELD') + param = self._get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) words = param.uint16_array end_frame[1] = words[0] + words[1] * 65536 #end_frame[1] = param.uint32_value - param = self.get('POINT:LONG_FRAMES') + param = self._get('POINT:LONG_FRAMES') if param is not None: # Encoded as float end_frame[2] = int(param.float_value) - param = self.get('POINT:FRAMES') + param = self._get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint end_frame[3] = param._as_integer_value @@ -406,35 +377,34 @@ def last_frame(self): return int(np.max(end_frame)) def get_screen_axis(self): - ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. + ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group. Returns ------- value : Touple on form (str, str) or None Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. ''' - X = self.get('POINT:X_SCREEN') - Y = self.get('POINT:Y_SCREEN') + X = self._get('POINT:X_SCREEN') + Y = self._get('POINT:Y_SCREEN') if X and Y: return (X.string_value, Y.string_value) return None def get_analog_transform_parameters(self): - ''' Parse analog data transform parameters. - ''' + ''' Parse analog data transform parameters. ''' # Offsets analog_offsets = np.zeros((self.analog_used), int) - param = self.get('ANALOG:OFFSET') + param = self._get('ANALOG:OFFSET') if param is not None and param.num_elements > 0: analog_offsets[:] = param.int16_array[:self.analog_used] # Scale factors analog_scales = np.ones((self.analog_used), float) gen_scale = 1. - param = self.get('ANALOG:GEN_SCALE') + param = self._get('ANALOG:GEN_SCALE') if param is not None: gen_scale = param.float_value - param = self.get('ANALOG:SCALE') + param = self._get('ANALOG:SCALE') if param is not None and param.num_elements > 0: analog_scales[:] = param.float_array[:self.analog_used] @@ -448,3 +418,39 @@ def get_analog_transform(self): analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) return analog_scales, analog_offsets + + def get_int8(self, key): + '''Get a parameter value as an 8-bit signed integer.''' + return self._get(key).int8_value + + def get_uint8(self, key): + '''Get a parameter value as an 8-bit unsigned integer.''' + return self._get(key).uint8_value + + def get_int16(self, key): + '''Get a parameter value as a 16-bit signed integer.''' + return self._get(key).int16_value + + def get_uint16(self, key): + '''Get a parameter value as a 16-bit unsigned integer.''' + return self._get(key).uint16_value + + def get_int32(self, key): + '''Get a parameter value as a 32-bit signed integer.''' + return self._get(key).int32_value + + def get_uint32(self, key): + '''Get a parameter value as a 32-bit unsigned integer.''' + return self._get(key).uint32_value + + def get_float(self, key): + '''Get a parameter value as a 32-bit float.''' + return self._get(key).float_value + + def get_bytes(self, key): + '''Get a parameter value as a byte string.''' + return self._get(key).bytes_value + + def get_string(self, key): + '''Get a parameter value as a string.''' + return self._get(key).string_value diff --git a/src/parameter.py b/src/parameter.py index 1bab30e..3a8b570 100644 --- a/src/parameter.py +++ b/src/parameter.py @@ -2,7 +2,7 @@ import numpy as np from .utils import DEC_to_IEEE, DEC_to_IEEE_BYTES -class Param(object): +class ParamData(object): '''A class representing a single named parameter from a C3D file. Attributes @@ -23,8 +23,6 @@ class Param(object): rows (number of strings). bytes : str Raw data for this parameter. - handle : - File handle positioned at the first byte of a .c3d parameter description. ''' def __init__(self, @@ -37,7 +35,7 @@ def __init__(self, handle=None): '''Set up a new parameter, only the name is required.''' self.name = name - self._dtypes = dtype + self.dtypes = dtype self.desc = desc self.bytes_per_element = bytes_per_element self.dimensions = dimensions or [] @@ -61,6 +59,7 @@ def total_bytes(self): '''Return the number of bytes used for storing this parameter's data.''' return self.num_elements * abs(self.bytes_per_element) + @property def binary_size(self): '''Return the number of bytes needed to store this parameter.''' return ( @@ -87,7 +86,7 @@ def write(self, group_id, handle): name = self.name.encode('utf-8') handle.write(struct.pack('bb', len(name), group_id)) handle.write(name) - handle.write(struct.pack(' 0, 'No group items in file or Manager.group_items failed' def test_Manager_group_listed(self): '''Test Manager.group_listed''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - grp_list = [k for (k, g) in reader.group_listed()] + grp_list = [k for (k, g) in reader.listed()] assert len(grp_list) > 0, 'No group items in file or Manager.group_listed failed' + def test_Manager_add_group(self): + '''Test if renaming groups acts as intended.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + keys = reader.keys() + try: + reader.add_group(0) + raise ValueError('Reader should not allow adding groups.') + except AttributeError: + pass + try: + reader.remove_group(keys[0]) + raise ValueError('Reader should not allow removing groups.') + except AttributeError: + pass + try: + reader.rename_group(keys[0], 'TEST_NAME') + raise ValueError('Reader should not allow renaming groups.') + except AttributeError: + pass def test_Manager_add_group(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - ref = GroupSample(reader) + ref = GroupSample(reader.to_writer()) ref.verify_add_group(100) ref.verify_remove_all_using_numeric() def test_Manager_removing_group_from_numeric(self): '''Test if removing groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - ref = GroupSample(reader) + ref = GroupSample(reader.to_writer()) ref.verify_remove_all_using_numeric() ref.verify_add_group(100) def test_Manager_removing_group_from_name(self): '''Test if removing groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - ref = GroupSample(reader) + ref = GroupSample(reader.to_writer()) ref.verify_remove_all_using_name() ref.verify_add_group(100) def test_Manager_rename_group(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - ref = GroupSample(reader) + writer = reader.to_writer() + ref = GroupSample(writer) grp_keys = [k for (k, g) in ref.group_items] new_names = ['TEST_NAME' + str(i) for i in range(len(grp_keys))] for key, test_name in zip(grp_keys, new_names): - grp = reader.get(key) - reader.rename_group(key, test_name) - grp2 = reader.get(test_name) + grp = writer.get(key) + writer.rename_group(key, test_name) + grp2 = writer.get(test_name) assert grp2 is not None, "Rename failed, group with name '%s' does not exist." - assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' + assert grp._data == grp2._data, 'Rename failed, group acquired from new name is not identical.' ref.assert_entry_count() ref.assert_group_list() try: - reader.rename_group(new_names[0], new_names[1]) + writer.rename_group(new_names[0], new_names[1]) raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') except ValueError as e: pass # Correct @@ -178,7 +198,8 @@ def test_Manager_rename_group(self): def test_Manager_renumber_group(self): '''Test if renaming (renumbering) groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - ref = GroupSample(reader) + writer = reader.to_writer() + ref = GroupSample(writer) grp_ids = [k for (k, g) in ref.group_listed] max_key = ref.max_key @@ -186,18 +207,18 @@ def test_Manager_renumber_group(self): for i, key in enumerate(grp_ids): test_num = max_key + i + 1 - grp = reader.get(key) - reader.rename_group(key, test_num) - grp2 = reader.get(test_num) + grp = writer.get(key) + writer.rename_group(key, test_num) + grp2 = writer.get(test_num) assert grp2 is not None, "Rename failed, group with name '%s' does not exist." - assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' + assert grp._data == grp2._data, 'Rename failed, group acquired from new name is not identical.' ref.assert_entry_count() ref.assert_group_items() try: - reader.rename_group(max_key + 1, max_key + 2) + writer.rename_group(max_key + 1, max_key + 2) raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.') except ValueError as e: pass # Correct diff --git a/test/test_parameter_accessors.py b/test/test_parameter_accessors.py index 5238b83..dedd16a 100644 --- a/test/test_parameter_accessors.py +++ b/test/test_parameter_accessors.py @@ -2,30 +2,35 @@ ''' import unittest import c3d +from src.group import GroupReadonly, GroupWritable import numpy as np import test.verify as verify from test.zipload import Zipload from test.base import Base +rnd = np.random.default_rng() + +def add_dummy_param(group, name='TEST_NAME', shape=(10, 2), flt_range=(-1e6, 1e6)): + arr = rnd.uniform(*flt_range, size=shape).astype(np.float32) + group.add_param(name, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes()) + class ParamSample(): ''' Helper object to verify parameter entries persist or terminate properly. ''' def __init__(self, group): - assert isinstance(group, c3d.Group), 'Must pass group to ParamSample instance.' - self.flt_range = (-1e6, 1e6) - self.shape = (10, 2) + assert isinstance(group, GroupWritable), \ + 'Must pass GroupWritable to ParamSample instance, was %s' % type(group) self.group = group - self.rnd = np.random.default_rng() self.sample() @property def items(self): '''Helper to access group items. ''' - return [(k, g) for (k, g) in self.group.param_items()] + return [(k, g) for (k, g) in self.group.items()] @property def keys(self): '''Helper to access group items. ''' - return [k for (k, g) in self.group.param_items()] + return [k for (k, g) in self.group.items()] def sample(self): '''Call before applying changes. ''' @@ -51,15 +56,14 @@ def assert_group_items(self, ignore=None): if n == ignore: continue g2 = self.group.get(n) - assert g == g2, 'Group listed order changed for entry %i.' % i + assert g._data == g2._data, 'Group listed order changed for entry %i.' % i def verify_add_parameter(self, N): '''Add N parameters and verify count at each iteration.''' self.sample() for i in range(1, N): test_name = 'TEST_ADD_PARAM_%i' % i - arr = self.rnd.uniform(*self.flt_range, size=self.shape).astype(np.float32) - self.group.add_param(test_name, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes()) + add_dummy_param(self.group, test_name) assert self.group.get(test_name) is not None, 'Added group does not exist.' self.assert_group_items() @@ -85,19 +89,32 @@ class TestParameterAccessors(Base): def test_Group_values(self): '''Test Group.values()''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - for g in reader.group_values(): - assert len(g.param_values()) > 0, 'No group values in file or Group.param_values() failed' + for g in reader.values(): + N = len([v for v in g.values()]) + assert N > 0, 'No group values in file or GroupReadonly.values() failed' def test_Group_items(self): '''Test Group.items()''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - for g in reader.group_values(): - assert len(g.param_items()) > 0, 'No group items in file or Group.param_items() failed' + for g in reader.values(): + N = len([kv for kv in g.items()]) + assert N > 0, 'No group items in file or GroupReadonly.items() failed' + + def test_Group_readonly_add_param(self): + '''Test if adding parameter to a readonly group fails.''' + reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) + for g in reader.values(): + try: + add_dummy_param(g) + raise RuntimeError('Adding to readonly should not be possible.') + except AttributeError: + pass def test_Group_add_param(self): '''Test if adding and groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - for g in reader.group_values(): + writer = reader.to_writer() + for g in writer.values(): ref = ParamSample(g) ref.verify_add_parameter(100) ref.verify_remove_all() @@ -105,7 +122,8 @@ def test_Group_add_param(self): def test_Group_remove_param(self): '''Test if removing groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - for g in reader.group_values(): + writer = reader.to_writer() + for g in writer.values(): ref = ParamSample(g) ref.verify_remove_all() ref.verify_add_parameter(100) @@ -114,7 +132,8 @@ def test_Group_rename_param(self): '''Test if renaming groups acts as intended.''' reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL)) - for g in reader.group_values(): + writer = reader.to_writer() + for g in writer.values(): ref = ParamSample(g) prm_keys = ref.keys new_names = ['TEST_NAME' + str(i) for i in range(len(prm_keys))] @@ -123,7 +142,7 @@ def test_Group_rename_param(self): g.rename_param(key, nname) prm2 = g.get(nname) assert prm2 is not None, "Rename failed, renamed param does not exist." - assert prm == prm2, 'Rename failed, param acquired from new name is not identical.' + assert prm._data == prm2._data, 'Rename failed, param acquired from new name is not identical.' ref.assert_entry_count() try: diff --git a/test/test_parameter_bytes_conversion.py b/test/test_parameter_bytes_conversion.py index 03d8827..db3466e 100644 --- a/test/test_parameter_bytes_conversion.py +++ b/test/test_parameter_bytes_conversion.py @@ -1,9 +1,8 @@ -import c3d import struct import unittest import numpy as np from src.dtypes import DataTypes, PROCESSOR_INTEL -from src.parameter import Param +from src.parameter import ParamData, ParamReadonly def genByteWordArr(word, shape): @@ -33,6 +32,9 @@ def genRndFloatArr(shape, rnd, range=(-1e6, 1e6)): ''' return rnd.uniform(range[0], range[1], shape) +def make_param(*args, **kwargs): + return ParamReadonly(ParamData(*args, **kwargs)) + class ParameterValueTest(unittest.TestCase): ''' Test read Parameter arrays @@ -56,7 +58,7 @@ def test_a_param_float32(self): for i in range(ParameterValueTest.TEST_ITERATIONS): value = np.float32(self.rnd.uniform(*ParameterValueTest.RANGE_32_BIT)) bytes = struct.pack(' 5) - P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = make_param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ @@ -325,7 +327,7 @@ def test_k_parse_random_string_array(self): # 4 dims for wlen in range(10): arr, shape = genRndByteArr(wlen, [7, 5, 3], wlen > 5) - P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = make_param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ @@ -337,7 +339,7 @@ def test_k_parse_random_string_array(self): # 5 dims for wlen in range(10): arr, shape = genRndByteArr(wlen, [7, 6, 5, 3], wlen > 5) - P = Param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) + P = make_param('STRING_TEST', self.dtypes, bytes_per_element=-1, dimensions=shape, bytes=arr.T.tobytes()) arr_out = P.string_array assert arr.T.shape == arr_out.shape, "Mismatch in 'string_array' converted shape. Was %s, expected %s" %\ From 89ad991b30581be6a8955c414c657c2eb13b6b12 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Fri, 2 Jul 2021 23:47:14 +0200 Subject: [PATCH 043/120] Restructure + unittests working --- c3d.py | 22 +++++++++------------- src/manager.py | 5 ++++- src/parameter.py | 36 ++++++++++++++++++------------------ test/verify.py | 4 ++-- 4 files changed, 33 insertions(+), 34 deletions(-) diff --git a/c3d.py b/c3d.py index 414789d..8286223 100644 --- a/c3d.py +++ b/c3d.py @@ -531,6 +531,14 @@ def add_group(self, *args, **kwargs): ''' return GroupWritable(super(Writer, self)._add_group(*args, **kwargs)) + def rename_group(self, *args): + ''' Rename a specified parameter group (see Manager._rename_group for args). ''' + self._rename_group(*args) + + def remove_group(self, *args): + '''Remove the parameter group. (see Manager._rename_group for args). ''' + self._remove_group(*args) + def add_frames(self, frames, index=None): '''Add frames to this writer instance. @@ -567,18 +575,6 @@ def pack_labels(labels): label_str = ''.join(label.ljust(label_max_size) for label in labels) return label_str, label_max_size - def add_group(self, *args): - ''' Add a new parameter group (see Manager._rename_group for args). ''' - return self._add_group(*args) - - def rename_group(self, *args): - ''' Rename a specified parameter group (see Manager._rename_group for args). ''' - self._rename_group(*args) - - def remove_group(self, *args): - '''Remove the parameter group. (see Manager._rename_group for args). ''' - self._remove_group(*args) - def set_point_labels(self, labels): ''' Set point data labels. ''' @@ -766,7 +762,7 @@ def _write_metadata(self, handle): # Groups handle.write(struct.pack( 'BBBB', 0, 0, self.parameter_blocks(), self._dtypes.processor)) - for group_id, group in self._listed(): + for group_id, group in self.listed(): group._data.write(group_id, handle) # Padding diff --git a/src/manager.py b/src/manager.py index 20130d0..dd8eefc 100644 --- a/src/manager.py +++ b/src/manager.py @@ -372,7 +372,10 @@ def last_frame(self): param = self._get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint - end_frame[3] = param._as_integer_value + if param.bytes_per_element == 2: + end_frame[3] = param.uint16_value + else: + end_frame[3] = int(param.float_value) # Return the largest of the all (queue bad reading...) return int(np.max(end_frame)) diff --git a/src/parameter.py b/src/parameter.py index 3a8b570..aba932e 100644 --- a/src/parameter.py +++ b/src/parameter.py @@ -145,24 +145,6 @@ def _as_any(self, dtype): return data.flatten() return data - @property - def _as_integer_value(self): - ''' Get the param as either 32 bit float or unsigned integer. - Evaluates if an integer is stored as a floating point representation. - - Note: This is implemented purely for parsing start/end frames. - ''' - if self.total_bytes >= 4: - # Check if float value representation is an integer - value = self.float_value - if int(value) == value: - return value - return self.uint32_value - elif self.total_bytes >= 2: - return self.uint16_value - else: - return self.uint8_value - class ParamReadonly(object): def __init__(self, data): @@ -396,6 +378,24 @@ def string_array(self): byte_arr[i] = self.dtypes.decode_string(byte_arr[i]) return byte_arr + @property + def _as_integer_value(self): + ''' Get the param as either 32 bit float or unsigned integer. + Evaluates if an integer is stored as a floating point representation. + + Note: This is implemented purely for parsing start/end frames. + ''' + if self.total_bytes >= 4: + # Check if float value representation is an integer + value = self.float_value + if int(value) == value: + return value + return self.uint32_value + elif self.total_bytes >= 2: + return self.uint16_value + else: + return self.uint8_value + class ParamWritable(ParamReadonly): def __init__(self, data): super(ParamWritable, self).__init__(data) diff --git a/test/verify.py b/test/verify.py index 17e6d05..807ee80 100644 --- a/test/verify.py +++ b/test/verify.py @@ -327,10 +327,10 @@ def data_is_equal(areader, breader, alabel, blabel): cam_diff = tot_points - np.sum(cam_close) assert cam_diff == 0, '\n' + \ 'Mismatch in camera bit flags between {} and {}.\n'.format(alabel, blabel) +\ - 'Number of samples with flag differences larger then 1 bit: {} of {}'.format(cam_diff, tot_points) + 'Number of samples with flag differences larger then 1: {} of {}'.format(cam_diff, tot_points) err_str = '\n' + \ 'Mismatch in camera bit flags between {} and {}.\n'.format(alabel, blabel) +\ - 'Number of samples with flag difference of 1 bit: {} of {}'.format(cam_diff_non_equal, tot_points) + 'Number of samples with flag difference of 1: {} of {}'.format(cam_diff_non_equal, tot_points) warnings.warn(err_str, RuntimeWarning) # Residual assert assert residual_diff == 0, '\n' +\ From 3bcf57b4e8b280d27bfb12347e299ebf20efd3e0 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 11:33:27 +0200 Subject: [PATCH 044/120] GroupWritable -> Group ParamWritable -> Param Group.__eq__ Param.__eq__ --- c3d.py | 61 +++++++++++++--------------- src/group.py | 40 +++++++++---------- src/manager.py | 68 ++++++++++++++++---------------- src/parameter.py | 9 +++-- test/test_group_accessors.py | 8 ++-- test/test_parameter_accessors.py | 10 ++--- 6 files changed, 96 insertions(+), 100 deletions(-) diff --git a/c3d.py b/c3d.py index 8286223..b5d721e 100644 --- a/c3d.py +++ b/c3d.py @@ -9,7 +9,6 @@ import warnings from src.manager import Manager from src.header import Header -from src.group import GroupData, GroupWritable, GroupReadonly from src.dtypes import DataTypes from src.utils import is_integer, is_iterable, DEC_to_IEEE_BYTES @@ -87,7 +86,9 @@ def seek_param_section_header(): if group_id > 0: # We've just started reading a parameter. If its group doesn't # exist, create a blank one. add the parameter to the group. - group = self._groups.setdefault(group_id, GroupData(self._dtypes)) + group = super(Reader, self).get(group_id) + if group is None: + group = self._add_group(group_id) group.add_param(name, handle=buf) else: # We've just started reading a group. If a group with the @@ -97,7 +98,7 @@ def seek_param_section_header(): group_id = abs(group_id) size, = struct.unpack('B', buf.read(1)) desc = size and buf.read(size) or '' - group = self._get(group_id) + group = super(Reader, self).get(group_id) if group is not None: self._rename_group(group, name) # Inserts name key group.desc = desc @@ -309,30 +310,40 @@ def get(self, key, default=None): Either a group or parameter with the specified name(s). If neither is found, returns the default value. ''' - val = self._get(key) - if val is None: - return default - return val.readonly() + val = super(Reader, self).get(key) + if val: + return val.readonly() + return default def items(self): ''' Acquire iterable over parameter group pairs. Returns ------- - items : Touple of ((str, :class:`Group`), ...) + items : Touple of ((str, :class:`GroupReadonly`), ...) Python touple containing pairs of name keys and parameter group entries. ''' - return ((k, GroupReadonly(v)) for k, v in self._groups.items() if isinstance(k, str)) + return ((k, v.readonly()) for k, v in super(Reader, self).items()) def values(self): ''' Acquire iterable over parameter group entries. Returns ------- - values : Touple of (:class:`Group`, ...) + values : Touple of (:class:`GroupReadonly`, ...) Python touple containing unique parameter group entries. ''' - return (GroupReadonly(v) for k, v in self._groups.items() if isinstance(k, str)) + return (v.readonly() for k, v in super(Reader, self).items()) + + def listed(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + items : Touple of ((int, :class:`GroupReadonly`), ...) + Python touple containing unique parameter group entries. + ''' + return ((k, v.readonly()) for k, v in super(Reader, self).listed()) class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -503,41 +514,23 @@ def trial_group(self): ''' Get or create the TRIAL parameter group.''' return self.get_create('TRIAL') - def get(self, group, default=None): - '''Get a writable group or a parameter instance. - - Parameters - ---------- - key : str - Key, see Manager.get() for valid key formats. - default : any - Return this value if the named group and parameter are not found. - - Returns - ------- - value : :class:`GroupWritable` or :class:`ParamWritable` - Either a decorated group instance or parameter with the specified name(s). If neither - is found, the default value is returned. - ''' - return super(Writer, self)._get(group, default) - - def add_group(self, *args, **kwargs): + def add_group(self, group_id, name, desc): '''Add a new parameter group. See Manager.add_group() for more information. Returns ------- - group : :class:`GroupWritable` + group : :class:`Group` An editable group instance. ''' - return GroupWritable(super(Writer, self)._add_group(*args, **kwargs)) + return super(Writer, self)._add_group(group_id, name, desc) def rename_group(self, *args): ''' Rename a specified parameter group (see Manager._rename_group for args). ''' - self._rename_group(*args) + super(Writer, self)._rename_group(*args) def remove_group(self, *args): '''Remove the parameter group. (see Manager._rename_group for args). ''' - self._remove_group(*args) + super(Writer, self)._remove_group(*args) def add_frames(self, frames, index=None): '''Add frames to this writer instance. diff --git a/src/group.py b/src/group.py index a732adf..53726f8 100644 --- a/src/group.py +++ b/src/group.py @@ -1,6 +1,6 @@ import struct import numpy as np -from .parameter import ParamData, ParamReadonly, ParamWritable +from .parameter import ParamData, Param from .utils import Decorator class GroupData(object): @@ -85,7 +85,7 @@ def add_param(self, name, **kwargs): name = name.upper() if name in self._params: raise KeyError('Parameter already exists with key {}'.format(name)) - self._params[name] = ParamData(name, self._dtypes, **kwargs) + self._params[name] = Param(ParamData(name, self._dtypes, **kwargs)) def remove_param(self, name): '''Remove the specified parameter. @@ -102,7 +102,7 @@ def rename_param(self, name, new_name): Parameters ---------- - name : str, or 'ParamData' + name : str, or 'Param' Parameter instance, or name. new_name : str New name for the parameter. @@ -116,14 +116,12 @@ def rename_param(self, name, new_name): ''' if new_name in self._params: raise ValueError("Key {} already exist.".format(new_name)) - if isinstance(name, ParamData): + if isinstance(name, Param): param = name name = param.name else: # Aquire instance using id - param = self._params.get(name, None) - if param is None: - raise KeyError('No parameter found matching the identifier: {}'.format(str(name))) + param = self._params[name] del self._params[name] self._params[new_name] = param @@ -145,7 +143,7 @@ def write(self, group_id, handle): handle.write(struct.pack('B', len(desc))) handle.write(desc) for param in self._params.values(): - param.write(group_id, handle) + param._data.write(group_id, handle) class GroupReadonly(object): ''' Handle exposing readable attributes of a GroupData entry. @@ -156,6 +154,9 @@ def __init__(self, data): def __contains__(self, key): return key in self._data._params + def __eq__(self, other): + return self._data is other._data + @property def name(self): ''' Group name. ''' @@ -168,11 +169,11 @@ def desc(self): def items(self): ''' Acquire iterator for paramater key-entry pairs. ''' - return ((k, ParamReadonly(v)) for k, v in self._data._params.items()) + return ((k, v.readonly()) for k, v in self._data._params.items()) def values(self): ''' Acquire iterator for parameter entries. ''' - return (ParamReadonly(v) for v in self._data._params.values()) + return (v.readonly() for v in self._data._params.values()) def keys(self): ''' Acquire iterator for parameter entry keys. ''' @@ -193,9 +194,9 @@ def get(self, key, default=None): param : :class:`ParamReadable` A parameter from the current group. ''' - val = self._data._params.get(key) + val = self._data._params.get(key, default) if val: - return ParamReadonly(val) + return val.readonly() return default def get_int8(self, key): @@ -234,13 +235,13 @@ def get_string(self, key): '''Get the value of the given parameter as a string.''' return self._data[key.upper()].string_value -class GroupWritable(GroupReadonly): +class Group(GroupReadonly): ''' Handle exposing readable and writeable attributes of a GroupData entry. Group instance decorator providing convenience functions for Writer editing. ''' def __init__(self, data): - super(GroupWritable, self).__init__(data) + super(Group, self).__init__(data) def readonly(self): ''' Make access readonly. ''' @@ -280,11 +281,11 @@ def desc(self, value): def items(self): ''' Acquire iterator for paramater key-entry pairs. ''' - return ((k, ParamWritable(v)) for k, v in self._data._params.items()) + return ((k, v) for k, v in self._data._params.items()) def values(self): ''' Acquire iterator for parameter entries. ''' - return (ParamWritable(v) for v in self._data._params.values()) + return (v for v in self._data._params.values()) def get(self, key, default=None): '''Get a parameter by key. @@ -301,10 +302,7 @@ def get(self, key, default=None): param : :class:`ParamReadable` A parameter from the current group. ''' - val = self._data._params.get(key) - if val: - return ParamWritable(val) - return default + return self._data._params.get(key, default) # # Forward param editing # @@ -343,7 +341,7 @@ def rename_param(self, name, new_name): Parameters ---------- - name : str, or 'ParamData' + name : str, or 'Param' Parameter instance, or name. new_name : str New name for the parameter. diff --git a/src/manager.py b/src/manager.py index dd8eefc..2a7f742 100644 --- a/src/manager.py +++ b/src/manager.py @@ -1,7 +1,7 @@ import numpy as np import warnings from src.header import Header -from src.group import GroupData, GroupReadonly, GroupWritable +from src.group import GroupData, GroupReadonly, Group from src.utils import is_integer, is_iterable @@ -34,7 +34,7 @@ def items(self): items : Touple of ((str, :class:`Group`), ...) Python touple containing pairs of name keys and parameter group entries. ''' - return ((k, GroupWritable(v)) for k, v in self._groups.items() if isinstance(k, str)) + return ((k, v) for k, v in self._groups.items() if isinstance(k, str)) def values(self): ''' Acquire iterable over parameter group entries. @@ -44,7 +44,7 @@ def values(self): values : Touple of (:class:`Group`, ...) Python touple containing unique parameter group entries. ''' - return (GroupWritable(v) for k, v in self._groups.items() if isinstance(k, str)) + return (v for k, v in self._groups.items() if isinstance(k, str)) def keys(self): ''' Acquire iterable over parameter group entry string keys. @@ -64,7 +64,7 @@ def listed(self): items : Touple of ((int, :class:`Group`), ...) Sorted python touple containing pairs of numerical keys and parameter group entries. ''' - return sorted((i, GroupWritable(g)) for i, g in self._groups.items() if isinstance(i, int)) + return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int)) def _check_metadata(self): ''' Ensure that the metadata in our file is self-consistent. ''' @@ -117,7 +117,7 @@ def _check_metadata(self): def check_parameters(params): for name in params: - if self._get(name) is None: + if self.get(name) is None: warnings.warn('missing parameter {}'.format(name)) if self.point_used > 0: @@ -129,7 +129,7 @@ def check_parameters(params): else: warnings.warn('No analog data found in file.') - def _add_group(self, group_id, name, desc): + def _add_group(self, group_id, name=None, desc=None): '''Add a new parameter group. Parameters @@ -155,15 +155,17 @@ def _add_group(self, group_id, name, desc): ''' if not is_integer(group_id): raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id)) - if not (isinstance(name, str) or name is None): - raise TypeError('Expected Group name key to be string, was %s.' % type(name)) + if not isinstance(name, str): + if name is not None: + raise TypeError('Expected Group name key to be string, was %s.' % type(name)) + else: + name = name.upper() group_id = int(group_id) # Asserts python int if group_id in self._groups: raise KeyError('Group with numerical key {} already exists'.format(group_id)) - name = name.upper() if name in self._groups: raise KeyError('No group matched name key {}'.format(name)) - group = self._groups[name] = self._groups[group_id] = GroupData(self._dtypes, name, desc) + group = self._groups[name] = self._groups[group_id] = Group(GroupData(self._dtypes, name, desc)) return group def _remove_group(self, group_id): @@ -221,7 +223,7 @@ def _rename_group(self, group_id, new_group_id): # Update self._groups[new_group_id] = grp - def _get(self, group, default=None): + def get(self, group, default=None): '''Get a group or parameter. Parameters @@ -245,7 +247,7 @@ def _get(self, group, default=None): group = self._groups.get(int(group)) if group is None: return default - return GroupWritable(group) + return group group = group.upper() param = None if '.' in group: @@ -254,7 +256,7 @@ def _get(self, group, default=None): group, param = group.split(':', 1) if group not in self._groups: return default - group = GroupWritable(self._groups[group]) + group = self._groups[group] if param is not None: return group.get(param, default) return group @@ -266,7 +268,7 @@ def header(self): def parameter_blocks(self): '''Compute the size (in 512B blocks) of the parameter section.''' - bytes = 4. + sum(g.binary_size for g in self._groups.values()) + bytes = 4. + sum(g._data.binary_size for g in self._groups.values()) return int(np.ceil(bytes / 512)) @property @@ -326,7 +328,7 @@ def analog_sample_count(self): @property def point_labels(self): ''' Labels for each POINT data channel. ''' - return self._get('POINT:LABELS').string_array + return self.get('POINT:LABELS').string_array @property def analog_labels(self): @@ -343,7 +345,7 @@ def first_frame(self): ''' Trial frame corresponding to the first frame recorded in the data. ''' # Start frame seems to be less of an issue to determine. # this is a hack for phasespace files ... should put it in a subclass. - param = self._get('TRIAL:ACTUAL_START_FIELD') + param = self.get('TRIAL:ACTUAL_START_FIELD') if param is not None: # ACTUAL_START_FIELD is encoded in two 16 byte words... words = param.uint16_array @@ -359,17 +361,17 @@ def last_frame(self): # Check different parameter options where the frame can be encoded end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] - param = self._get('TRIAL:ACTUAL_END_FIELD') + param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) words = param.uint16_array end_frame[1] = words[0] + words[1] * 65536 #end_frame[1] = param.uint32_value - param = self._get('POINT:LONG_FRAMES') + param = self.get('POINT:LONG_FRAMES') if param is not None: # Encoded as float end_frame[2] = int(param.float_value) - param = self._get('POINT:FRAMES') + param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint if param.bytes_per_element == 2: @@ -387,8 +389,8 @@ def get_screen_axis(self): value : Touple on form (str, str) or None Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. ''' - X = self._get('POINT:X_SCREEN') - Y = self._get('POINT:Y_SCREEN') + X = self.get('POINT:X_SCREEN') + Y = self.get('POINT:Y_SCREEN') if X and Y: return (X.string_value, Y.string_value) return None @@ -397,17 +399,17 @@ def get_analog_transform_parameters(self): ''' Parse analog data transform parameters. ''' # Offsets analog_offsets = np.zeros((self.analog_used), int) - param = self._get('ANALOG:OFFSET') + param = self.get('ANALOG:OFFSET') if param is not None and param.num_elements > 0: analog_offsets[:] = param.int16_array[:self.analog_used] # Scale factors analog_scales = np.ones((self.analog_used), float) gen_scale = 1. - param = self._get('ANALOG:GEN_SCALE') + param = self.get('ANALOG:GEN_SCALE') if param is not None: gen_scale = param.float_value - param = self._get('ANALOG:SCALE') + param = self.get('ANALOG:SCALE') if param is not None and param.num_elements > 0: analog_scales[:] = param.float_array[:self.analog_used] @@ -424,36 +426,36 @@ def get_analog_transform(self): def get_int8(self, key): '''Get a parameter value as an 8-bit signed integer.''' - return self._get(key).int8_value + return self.get(key).int8_value def get_uint8(self, key): '''Get a parameter value as an 8-bit unsigned integer.''' - return self._get(key).uint8_value + return self.get(key).uint8_value def get_int16(self, key): '''Get a parameter value as a 16-bit signed integer.''' - return self._get(key).int16_value + return self.get(key).int16_value def get_uint16(self, key): '''Get a parameter value as a 16-bit unsigned integer.''' - return self._get(key).uint16_value + return self.get(key).uint16_value def get_int32(self, key): '''Get a parameter value as a 32-bit signed integer.''' - return self._get(key).int32_value + return self.get(key).int32_value def get_uint32(self, key): '''Get a parameter value as a 32-bit unsigned integer.''' - return self._get(key).uint32_value + return self.get(key).uint32_value def get_float(self, key): '''Get a parameter value as a 32-bit float.''' - return self._get(key).float_value + return self.get(key).float_value def get_bytes(self, key): '''Get a parameter value as a byte string.''' - return self._get(key).bytes_value + return self.get(key).bytes_value def get_string(self, key): '''Get a parameter value as a string.''' - return self._get(key).string_value + return self.get(key).string_value diff --git a/src/parameter.py b/src/parameter.py index aba932e..30ffa34 100644 --- a/src/parameter.py +++ b/src/parameter.py @@ -150,6 +150,9 @@ class ParamReadonly(object): def __init__(self, data): self._data = data + def __eq__(self, other): + return self._data is other._data + @property def name(self): ''' Name string. ''' @@ -395,10 +398,10 @@ def _as_integer_value(self): return self.uint16_value else: return self.uint8_value - -class ParamWritable(ParamReadonly): + +class Param(ParamReadonly): def __init__(self, data): - super(ParamWritable, self).__init__(data) + super(Param, self).__init__(data) def readonly(self): ''' Readonly ''' diff --git a/test/test_group_accessors.py b/test/test_group_accessors.py index b4a49cd..8d92531 100644 --- a/test/test_group_accessors.py +++ b/test/test_group_accessors.py @@ -64,7 +64,7 @@ def assert_group_items(self): for i, (n, g), (n2, g2) in zip(enumerator, sorted(self.s_grp_items), sorted(self.group_items)): assert n == n2, 'Group numeric id missmatch after changes for entry %i. ' % i +\ 'Initially %i, after change entry was %i' % (n, n2) - assert g._data == g2._data, 'Group listed order changed for entry %i.' % i + assert g == g2, 'Group listed order changed for entry %i.' % i def assert_group_list(self): '''Assert all numerical (int, Group) pairs persisted after change.''' @@ -72,7 +72,7 @@ def assert_group_list(self): for i, (n, g), (n2, g2) in zip(enumerator, self.s_grp_list, self.group_listed): assert n == n2, 'Group string id missmatch after changes for entry %i. ' % i +\ 'Initially %i, after change entry was %i' % (n, n2) - assert g._data == g2._data, 'Group listed order changed for entry %i.' % i + assert g == g2, 'Group listed order changed for entry %i.' % i def verify_add_group(self, N): '''Add N groups and verify count at each iteration.''' @@ -184,7 +184,7 @@ def test_Manager_rename_group(self): grp2 = writer.get(test_name) assert grp2 is not None, "Rename failed, group with name '%s' does not exist." - assert grp._data == grp2._data, 'Rename failed, group acquired from new name is not identical.' + assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' ref.assert_entry_count() ref.assert_group_list() @@ -212,7 +212,7 @@ def test_Manager_renumber_group(self): grp2 = writer.get(test_num) assert grp2 is not None, "Rename failed, group with name '%s' does not exist." - assert grp._data == grp2._data, 'Rename failed, group acquired from new name is not identical.' + assert grp == grp2, 'Rename failed, group acquired from new name is not identical.' ref.assert_entry_count() ref.assert_group_items() diff --git a/test/test_parameter_accessors.py b/test/test_parameter_accessors.py index dedd16a..c6ff0fb 100644 --- a/test/test_parameter_accessors.py +++ b/test/test_parameter_accessors.py @@ -2,7 +2,7 @@ ''' import unittest import c3d -from src.group import GroupReadonly, GroupWritable +from src.group import Group import numpy as np import test.verify as verify from test.zipload import Zipload @@ -17,8 +17,8 @@ def add_dummy_param(group, name='TEST_NAME', shape=(10, 2), flt_range=(-1e6, 1e6 class ParamSample(): ''' Helper object to verify parameter entries persist or terminate properly. ''' def __init__(self, group): - assert isinstance(group, GroupWritable), \ - 'Must pass GroupWritable to ParamSample instance, was %s' % type(group) + assert isinstance(group, Group), \ + 'Must pass Group to ParamSample instance, was %s' % type(group) self.group = group self.sample() @@ -56,7 +56,7 @@ def assert_group_items(self, ignore=None): if n == ignore: continue g2 = self.group.get(n) - assert g._data == g2._data, 'Group listed order changed for entry %i.' % i + assert g == g2, 'Group listed order changed for entry %i.' % i def verify_add_parameter(self, N): '''Add N parameters and verify count at each iteration.''' @@ -142,7 +142,7 @@ def test_Group_rename_param(self): g.rename_param(key, nname) prm2 = g.get(nname) assert prm2 is not None, "Rename failed, renamed param does not exist." - assert prm._data == prm2._data, 'Rename failed, param acquired from new name is not identical.' + assert prm == prm2, 'Rename failed, param acquired from new name is not identical.' ref.assert_entry_count() try: From c2779f467deb388bb1445745a2350169319ded50 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 11:54:29 +0200 Subject: [PATCH 045/120] Parameter.uint_value, Parameter.int_value --- src/group.py | 4 ++-- src/parameter.py | 44 ++++++++++++++++++++++++++++++++++++-------- 2 files changed, 38 insertions(+), 10 deletions(-) diff --git a/src/group.py b/src/group.py index 53726f8..ec975b5 100644 --- a/src/group.py +++ b/src/group.py @@ -356,7 +356,7 @@ def rename_param(self, name, new_name): self._data.rename_param(name, new_name) # - # Add decorator functions (throws on overwrite) + # Add convenience functions (throws on overwrite) # def add(self, name, desc, bpe, format, data, *dimensions): ''' Add a parameter with 'data' package formated in accordance with 'format'. @@ -409,7 +409,7 @@ def add_empty_array(self, name, desc, bpe): bytes_per_element=bpe, dimensions=[0]) # - # Set decorator functions (overwrite) + # Set convenience functions (overwrite) # def set(self, name, *args, **kwargs): ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'. diff --git a/src/parameter.py b/src/parameter.py index 30ffa34..d66ab23 100644 --- a/src/parameter.py +++ b/src/parameter.py @@ -221,13 +221,43 @@ def uint32_value(self): '''Get the param as a 32-bit unsigned integer.''' return self._data._as(self.dtypes.uint32) + @property + def uint_value(self): + ''' Get the param as a unsigned integer of appropriate type. + ''' + if self.total_bytes >= 4: + return self.uint32_value + elif self.total_bytes >= 2: + return self.uint16_value + else: + return self.uint8_value + + @property + def int_value(self): + ''' Get the param as a signed integer of appropriate type. + ''' + if self.total_bytes >= 4: + return self.int32_value + elif self.total_bytes >= 2: + return self.int16_value + else: + return self.int8_value + @property def float_value(self): - '''Get the param as a 32-bit float.''' - if self.dtypes.is_dec: - return DEC_to_IEEE(self._data._as(np.uint32)) - else: # is_mips or is_ieee - return self._data._as(self.dtypes.float32) + '''Get the param as a floating point value of appropriate type.''' + if self.total_bytes > 4: + if self.dtypes.is_dec: + raise AttributeError("64 bit DEC floating point is not supported.") + # 64-bit floating point is not a standard + return self._data._as(self.dtypes.float64) + elif self.total_bytes == 4: + if self.dtypes.is_dec: + return DEC_to_IEEE(self._data._as(np.uint32)) + else: # is_mips or is_ieee + return self._data._as(self.dtypes.float32) + else: + raise AttributeError("Only 32 and 64 bit floating point is supported.") @property def bytes_value(self): @@ -382,11 +412,9 @@ def string_array(self): return byte_arr @property - def _as_integer_value(self): + def _as_integer_or_float_value(self): ''' Get the param as either 32 bit float or unsigned integer. Evaluates if an integer is stored as a floating point representation. - - Note: This is implemented purely for parsing start/end frames. ''' if self.total_bytes >= 4: # Check if float value representation is an integer From 64c1947675d34ce83714adbaec3033345fb815d7 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 11:57:05 +0200 Subject: [PATCH 046/120] .py --- scripts/{c3d-metadata => c3d-metadata.py} | 0 scripts/{c3d-viewer => c3d-viewer.py} | 0 scripts/{c3d2npz => c3d2npz.py} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename scripts/{c3d-metadata => c3d-metadata.py} (100%) mode change 100755 => 100644 rename scripts/{c3d-viewer => c3d-viewer.py} (100%) mode change 100755 => 100644 rename scripts/{c3d2npz => c3d2npz.py} (100%) mode change 100755 => 100644 diff --git a/scripts/c3d-metadata b/scripts/c3d-metadata.py old mode 100755 new mode 100644 similarity index 100% rename from scripts/c3d-metadata rename to scripts/c3d-metadata.py diff --git a/scripts/c3d-viewer b/scripts/c3d-viewer.py old mode 100755 new mode 100644 similarity index 100% rename from scripts/c3d-viewer rename to scripts/c3d-viewer.py diff --git a/scripts/c3d2npz b/scripts/c3d2npz.py old mode 100755 new mode 100644 similarity index 100% rename from scripts/c3d2npz rename to scripts/c3d2npz.py From 3839ad6003497dd5ede4c49a4fc8c8daa25da56a Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 12:17:48 +0200 Subject: [PATCH 047/120] Looped viewer --- scripts/c3d-viewer.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/scripts/c3d-viewer.py b/scripts/c3d-viewer.py index 5be64b1..b215e36 100644 --- a/scripts/c3d-viewer.py +++ b/scripts/c3d-viewer.py @@ -1,8 +1,13 @@ #!/usr/bin/env python '''A simple OpenGL viewer for C3D files.''' - -import c3d +try: + import c3d +except ModuleNotFoundError: + import sys + import os + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d import argparse import collections import contextlib @@ -90,7 +95,8 @@ def __init__(self, c3d_reader, trace=None, paused=False): super(Viewer, self).__init__( width=800, height=450, resizable=True, vsync=False, config=config) - self._frames = c3d_reader.read_frames(copy=False) + self.c3d_reader = c3d_reader + self._frames = iter(()) self._frame_rate = c3d_reader.header.frame_rate self._maxlen = 16 @@ -221,6 +227,8 @@ def _next_frame(self): try: return next(self._frames) except StopIteration: + self._frames = self.c3d_reader.read_frames(copy=False) + return self._next_frame() pyglet.app.exit() def update(self, dt): From 2ce5afaf85cd2ce8a2a73404d559e4c597516e7c Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 12:24:17 +0200 Subject: [PATCH 048/120] Script readme --- scripts/README.rst | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 scripts/README.rst diff --git a/scripts/README.rst b/scripts/README.rst new file mode 100644 index 0000000..c693686 --- /dev/null +++ b/scripts/README.rst @@ -0,0 +1,18 @@ +Viewer +~~~~~ + +A + +Requirements :: + + pip install pyglet + +Run (from script directory) :: + + py .\c3d-viewer.py 'path-to-c3d-file' + +Commands + + Esc - Terminate + Space - Pause + Mouse - Orientate view From 1426b6f2bb702ddec45e64f581a0ac23396f6f21 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 12:25:56 +0200 Subject: [PATCH 049/120] readme --- scripts/README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/README.rst b/scripts/README.rst index c693686..1aaed4a 100644 --- a/scripts/README.rst +++ b/scripts/README.rst @@ -1,7 +1,7 @@ Viewer ~~~~~ -A +Simple 3D-viewer for .c3d data. Requirements :: @@ -13,6 +13,6 @@ Run (from script directory) :: Commands - Esc - Terminate - Space - Pause - Mouse - Orientate view + Esc : Terminate + Space : Pause + Mouse : Orientate view From 7be54d3c0a7328b1b613c8942257631bf19804d5 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sat, 3 Jul 2021 15:52:31 +0200 Subject: [PATCH 050/120] Update README.rst --- scripts/README.rst | 61 +++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 55 insertions(+), 6 deletions(-) diff --git a/scripts/README.rst b/scripts/README.rst index 1aaed4a..5236271 100644 --- a/scripts/README.rst +++ b/scripts/README.rst @@ -1,18 +1,67 @@ -Viewer +Scripts are installed with the package and can be executed from a suitable command prompt by:: + + script-name.py 'path-to-c3d-file' + +or from the script directory:: + + py .\script-name.py 'path-to-c3d-file' -options + +The first option only works on Windows if .py files are associated with the python executable (`this answer`_ might help if its not working). + +.. _this answer: https://stackoverflow.com/questions/1934675/how-to-execute-python-scripts-in-windows + + +CSV converter +~~~~~ + +Generate a .csv file from frame data contained in a .c3d file. + +Invoke as:: + + c3d2csv.py 'path-to-c3d-file' -options + +Commandline options + + -r : Output column with residual values after point x,y,z coordinate columns. + -c : Output column with camera counts as the last point coordinate column. + -a : Output analog channel values after point coordinates. + -e : Endline string appended after each record (defaults to '\n'). + -s : Separator string inserted between records (defaults to ','). + + +NPZ converter +~~~~~ + +Generate a .npz file from frame data (point and analog) contained in a .c3d file. + +Invoke as:: + + c3d2npz.py 'path-to-c3d-file' + +C3D Viewer ~~~~~ -Simple 3D-viewer for .c3d data. +Simple 3D-viewer for displaying .c3d data. Requirements :: pip install pyglet -Run (from script directory) :: +Invoke as:: - py .\c3d-viewer.py 'path-to-c3d-file' + c3d-viewer.py 'path-to-c3d-file' -Commands +Interaction commands :: - Esc : Terminate + Esc : Terminate Space : Pause Mouse : Orientate view + +Metadata viewer +~~~~~ + +Prints metadata for a .c3d file to console. + +Invoke as:: + + c3d-metadata.py 'path-to-c3d-file' From dbacfffd42d9a270d004b556a8ff61be026a8553 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sat, 3 Jul 2021 15:53:34 +0200 Subject: [PATCH 051/120] Update README.rst --- scripts/README.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/README.rst b/scripts/README.rst index 5236271..7bfe662 100644 --- a/scripts/README.rst +++ b/scripts/README.rst @@ -20,13 +20,13 @@ Invoke as:: c3d2csv.py 'path-to-c3d-file' -options -Commandline options +Commandline options :: -r : Output column with residual values after point x,y,z coordinate columns. -c : Output column with camera counts as the last point coordinate column. -a : Output analog channel values after point coordinates. - -e : Endline string appended after each record (defaults to '\n'). - -s : Separator string inserted between records (defaults to ','). + -e : Endline string appended after each record (defaults to '\n'). + -s : Separator string inserted between records (defaults to ','). NPZ converter From 0043b42bc68b47c6bd8cddb8fa19e1b124259045 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 15:54:42 +0200 Subject: [PATCH 052/120] Package re-organization for setup.py --- __init__.py | 0 c3d/__init__.py | 8 + {src => c3d}/dtypes.py | 0 {src => c3d}/group.py | 0 {src => c3d}/header.py | 0 {src => c3d}/manager.py | 6 +- {src => c3d}/parameter.py | 2 +- c3d/reader.py | 344 ++++++++++++++++++++++++ {src => c3d}/utils.py | 0 c3d.py => c3d/writer.py | 344 +----------------------- scripts/c3d-metadata.py | 15 +- scripts/c3d2csv.py | 16 +- scripts/c3d2npz.py | 13 +- setup.py | 4 +- src/__init__.py | 0 test/test_parameter_accessors.py | 2 +- test/test_parameter_bytes_conversion.py | 4 +- 17 files changed, 395 insertions(+), 363 deletions(-) delete mode 100644 __init__.py create mode 100644 c3d/__init__.py rename {src => c3d}/dtypes.py (100%) rename {src => c3d}/group.py (100%) rename {src => c3d}/header.py (100%) rename {src => c3d}/manager.py (99%) rename {src => c3d}/parameter.py (99%) create mode 100644 c3d/reader.py rename {src => c3d}/utils.py (100%) rename c3d.py => c3d/writer.py (53%) delete mode 100644 src/__init__.py diff --git a/__init__.py b/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/c3d/__init__.py b/c3d/__init__.py new file mode 100644 index 0000000..3a4dfbc --- /dev/null +++ b/c3d/__init__.py @@ -0,0 +1,8 @@ +from . import dtypes +from . import group +from . import header +from . import manager +from . import parameter +from . import utils +from .reader import Reader +from .writer import Writer diff --git a/src/dtypes.py b/c3d/dtypes.py similarity index 100% rename from src/dtypes.py rename to c3d/dtypes.py diff --git a/src/group.py b/c3d/group.py similarity index 100% rename from src/group.py rename to c3d/group.py diff --git a/src/header.py b/c3d/header.py similarity index 100% rename from src/header.py rename to c3d/header.py diff --git a/src/manager.py b/c3d/manager.py similarity index 99% rename from src/manager.py rename to c3d/manager.py index 2a7f742..74ce113 100644 --- a/src/manager.py +++ b/c3d/manager.py @@ -1,8 +1,8 @@ import numpy as np import warnings -from src.header import Header -from src.group import GroupData, GroupReadonly, Group -from src.utils import is_integer, is_iterable +from .header import Header +from .group import GroupData, GroupReadonly, Group +from .utils import is_integer, is_iterable class Manager(object): diff --git a/src/parameter.py b/c3d/parameter.py similarity index 99% rename from src/parameter.py rename to c3d/parameter.py index d66ab23..6a65da5 100644 --- a/src/parameter.py +++ b/c3d/parameter.py @@ -262,7 +262,7 @@ def float_value(self): @property def bytes_value(self): '''Get the param as a raw byte string.''' - return self._data.bytes.copy() + return self._data.bytes @property def string_value(self): diff --git a/c3d/reader.py b/c3d/reader.py new file mode 100644 index 0000000..26b8335 --- /dev/null +++ b/c3d/reader.py @@ -0,0 +1,344 @@ +'''A Python module for reading and writing C3D files.''' + +import io +import numpy as np +import struct +import warnings +from .manager import Manager +from .header import Header +from .dtypes import DataTypes +from .utils import DEC_to_IEEE_BYTES + + +class Reader(Manager): + '''This class provides methods for reading the data in a C3D file. + + A C3D file contains metadata and frame-based data describing 3D motion. + + You can iterate over the frames in the file by calling `read_frames()` after + construction: + + >>> r = c3d.Reader(open('capture.c3d', 'rb')) + >>> for frame_no, points, analog in r.read_frames(): + ... print('{0.shape} points in this frame'.format(points)) + ''' + + def __init__(self, handle): + '''Initialize this C3D file by reading header and parameter data. + + Parameters + ---------- + handle : file handle + Read metadata and C3D motion frames from the given file handle. This + handle is assumed to be `seek`-able and `read`-able. The handle must + remain open for the life of the `Reader` instance. The `Reader` does + not `close` the handle. + + Raises + ------ + ValueError + If the processor metadata in the C3D file is anything other than 84 + (Intel format). + ''' + super(Reader, self).__init__(Header(handle)) + + self._handle = handle + + def seek_param_section_header(): + ''' Seek to and read the first 4 byte of the parameter header section ''' + self._handle.seek((self._header.parameter_block - 1) * 512) + # metadata header + return self._handle.read(4) + + # Begin by reading the processor type: + buf = seek_param_section_header() + _, _, parameter_blocks, processor = struct.unpack('BBBB', buf) + self._dtypes = DataTypes(processor) + # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) + self._header._processor_convert(self._dtypes, handle) + + # Restart reading the parameter header after parsing processor type + buf = seek_param_section_header() + + start_byte = self._handle.tell() + endbyte = start_byte + 512 * parameter_blocks - 4 + while self._handle.tell() < endbyte: + chars_in_name, group_id = struct.unpack('bb', self._handle.read(2)) + if group_id == 0 or chars_in_name == 0: + # we've reached the end of the parameter section. + break + name = self._dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper() + + # Read the byte segment associated with the parameter and create a + # separate binary stream object from the data. + offset_to_next, = struct.unpack(['h'][self._dtypes.is_mips], self._handle.read(2)) + if offset_to_next == 0: + # Last parameter, as number of bytes are unknown, + # read the remaining bytes in the parameter section. + bytes = self._handle.read(endbyte - self._handle.tell()) + else: + bytes = self._handle.read(offset_to_next - 2) + buf = io.BytesIO(bytes) + + if group_id > 0: + # We've just started reading a parameter. If its group doesn't + # exist, create a blank one. add the parameter to the group. + group = super(Reader, self).get(group_id) + if group is None: + group = self._add_group(group_id) + group.add_param(name, handle=buf) + else: + # We've just started reading a group. If a group with the + # appropriate numerical id exists already (because we've + # already created it for a parameter), just set the name of + # the group. Otherwise, add a new group. + group_id = abs(group_id) + size, = struct.unpack('B', buf.read(1)) + desc = size and buf.read(size) or '' + group = super(Reader, self).get(group_id) + if group is not None: + self._rename_group(group, name) # Inserts name key + group.desc = desc + else: + self._add_group(group_id, name, desc) + + self._check_metadata() + + def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False): + '''Iterate over the data frames from our C3D file handle. + + Parameters + ---------- + copy : bool + If False, the reader returns a reference to the same data buffers + for every frame. The default is True, which causes the reader to + return a unique data buffer for each frame. Set this to False if you + consume frames as you iterate over them, or True if you store them + for later. + + Returns + ------- + frames : sequence of (frame number, points, analog) + This method generates a sequence of (frame number, points, analog) + tuples, one tuple per frame. The first element of each tuple is the + frame number. The second is a numpy array of parsed, 5D point data + and the third element of each tuple is a numpy array of analog + values that were recorded during the frame. (Often the analog data + are sampled at a higher frequency than the 3D point data, resulting + in multiple analog frames per frame of point data.) + + The first three columns in the returned point data are the (x, y, z) + coordinates of the observed motion capture point. The fourth column + is an estimate of the error for this particular point, and the fifth + column is the number of cameras that observed the point in question. + Both the fourth and fifth values are -1 if the point is considered + to be invalid. + ''' + # Point magnitude scalar, if scale parameter is < 0 data is floating point + # (in which case the magnitude is the absolute value) + scale_mag = abs(self.point_scale) + is_float = self.point_scale < 0 + + if is_float: + point_word_bytes = 4 + else: + point_word_bytes = 2 + points = np.zeros((self.point_used, 5), np.float32) + + # TODO: handle ANALOG:BITS parameter here! + p = self.get('ANALOG:FORMAT') + analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED' + if is_float: + analog_dtype = self._dtypes.float32 + analog_word_bytes = 4 + elif analog_unsigned: + # Note*: Floating point is 'always' defined for both analog and point data, according to the standard. + analog_dtype = self._dtypes.uint16 + analog_word_bytes = 2 + # Verify BITS parameter for analog + p = self.get('ANALOG:BITS') + if p and p._as_integer_value / 8 != analog_word_bytes: + raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value)) + else: + analog_dtype = self._dtypes.int16 + analog_word_bytes = 2 + + analog = np.array([], float) + analog_scales, analog_offsets = self.get_analog_transform() + + # Seek to the start point of the data blocks + self._handle.seek((self._header.data_block - 1) * 512) + # Number of values (words) read in regard to POINT/ANALOG data + N_point = 4 * self.point_used + N_analog = self.analog_used * self.analog_per_frame + + # Total bytes per frame + point_bytes = N_point * point_word_bytes + analog_bytes = N_analog * analog_word_bytes + # Parse the data blocks + for frame_no in range(self.first_frame, self.last_frame + 1): + # Read the byte data (used) for the block + raw_bytes = self._handle.read(N_point * point_word_bytes) + raw_analog = self._handle.read(N_analog * analog_word_bytes) + # Verify read pointers (any of the two can be assumed to be 0) + if len(raw_bytes) < point_bytes: + warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {} + and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell())) + return + if len(raw_analog) < analog_bytes: + warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {} + and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell())) + return + + if is_float: + # Convert every 4 byte words to a float-32 reprensentation + # (the fourth column is still not a float32 representation) + if self._dtypes.is_dec: + # Convert each of the first 6 16-bit words from DEC to IEEE float + points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4)) + else: # If IEEE or MIPS: + # Convert each of the first 6 16-bit words to native float + points[:, :4] = np.frombuffer(raw_bytes, + dtype=self._dtypes.float32, + count=N_point).reshape((self.point_used, 4)) + + # Cast last word to signed integer in system endian format + last_word = points[:, 3].astype(np.int32) + + else: + # View the bytes as signed 16-bit integers + raw = np.frombuffer(raw_bytes, + dtype=self._dtypes.int16, + count=N_point).reshape((self.point_used, 4)) + # Read the first six 16-bit words as x, y, z coordinates + points[:, :3] = raw[:, :3] * scale_mag + # Cast last word to signed integer in system endian format + last_word = raw[:, 3].astype(np.int16) + + # Parse camera-observed bits and residuals. + # Notes: + # - Invalid sample if residual is equal to -1 (check if word < 0). + # - A residual of 0.0 represent modeled data (filtered or interpolated). + # - Camera and residual words are always 8-bit (1 byte), never 16-bit. + # - If floating point, the byte words are encoded in an integer cast to a float, + # and are written directly in byte form (see the MLS guide). + ## + # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded). + residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8 + + # Fourth value is floating-point (scaled) error estimate (residual) + points[:, 3] = residual_byte * scale_mag + + # Determine invalid samples + invalid = last_word < 0 + if check_nan: + is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) + points[is_nan, :3] = 0.0 + invalid &= is_nan + # Update discarded - sign + points[invalid, 3] = -1 + + + # Fifth value is the camera-observation byte + if camera_sum: + # Convert to observation sum + points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(8)) + else: + points[:, 4] = camera_byte #.astype(np.float32) + + # Check if analog data exist, and parse if so + if N_analog > 0: + if is_float and self._dtypes.is_dec: + # Convert each of the 16-bit words from DEC to IEEE float + analog = DEC_to_IEEE_BYTES(raw_analog) + else: + # Integer or INTEL/MIPS floating point data can be parsed directly + analog = np.frombuffer(raw_analog, dtype=analog_dtype, count=N_analog) + + # Reformat and convert + analog = analog.reshape((-1, self.analog_used)).T + analog = analog.astype(float) + # Convert analog + analog = (analog - analog_offsets) * analog_scales + + # Output buffers + if copy: + yield frame_no, points.copy(), analog # .copy(), a new array is generated per frame for analog data. + else: + yield frame_no, points, analog + + # Function evaluating EOF, note that data section is written in blocks of 512 + final_byte_index = self._handle.tell() + self._handle.seek(0, 2) # os.SEEK_END) + # Check if more then 1 block remain + if self._handle.tell() - final_byte_index >= 512: + warnings.warn('incomplete reading of data blocks. {} bytes remained after all datablocks were read!'.format( + self._handle.tell() - final_byte_index)) + + @property + def proc_type(self): + '''Get the processory type associated with the data format in the file. + ''' + return self._dtypes.proc_type + + def to_writer(self, conversion=None): + ''' Convert to 'Writer' using the conversion mode. + See Writer.from_reader() for supported conversion modes and possible exceptions. + ''' + from .writer import Writer + return Writer.from_reader(self, conversion=conversion) + + def get(self, key, default=None): + '''Get a readonly group or parameter. + + Parameters + ---------- + key : str + If this string contains a period (.), then the part before the + period will be used to retrieve a group, and the part after the + period will be used to retrieve a parameter from that group. If this + string does not contain a period, then just a group will be + returned. + default : any + Return this value if the named group and parameter are not found. + + Returns + ------- + value : :class:`GroupReadonly` or :class:`Param` + Either a group or parameter with the specified name(s). If neither + is found, returns the default value. + ''' + val = super(Reader, self).get(key) + if val: + return val.readonly() + return default + + def items(self): + ''' Acquire iterable over parameter group pairs. + + Returns + ------- + items : Touple of ((str, :class:`GroupReadonly`), ...) + Python touple containing pairs of name keys and parameter group entries. + ''' + return ((k, v.readonly()) for k, v in super(Reader, self).items()) + + def values(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + values : Touple of (:class:`GroupReadonly`, ...) + Python touple containing unique parameter group entries. + ''' + return (v.readonly() for k, v in super(Reader, self).items()) + + def listed(self): + ''' Acquire iterable over parameter group entries. + + Returns + ------- + items : Touple of ((int, :class:`GroupReadonly`), ...) + Python touple containing unique parameter group entries. + ''' + return ((k, v.readonly()) for k, v in super(Reader, self).listed()) diff --git a/src/utils.py b/c3d/utils.py similarity index 100% rename from src/utils.py rename to c3d/utils.py diff --git a/c3d.py b/c3d/writer.py similarity index 53% rename from c3d.py rename to c3d/writer.py index b5d721e..bb0c173 100644 --- a/c3d.py +++ b/c3d/writer.py @@ -1,350 +1,14 @@ '''A Python module for reading and writing C3D files.''' -from __future__ import unicode_literals -import sys -import io import copy import numpy as np import struct -import warnings -from src.manager import Manager -from src.header import Header -from src.dtypes import DataTypes -from src.utils import is_integer, is_iterable, DEC_to_IEEE_BYTES +#import warnings +from .manager import Manager +from .dtypes import DataTypes +from .utils import is_integer, is_iterable -class Reader(Manager): - '''This class provides methods for reading the data in a C3D file. - - A C3D file contains metadata and frame-based data describing 3D motion. - - You can iterate over the frames in the file by calling `read_frames()` after - construction: - - >>> r = c3d.Reader(open('capture.c3d', 'rb')) - >>> for frame_no, points, analog in r.read_frames(): - ... print('{0.shape} points in this frame'.format(points)) - ''' - - def __init__(self, handle): - '''Initialize this C3D file by reading header and parameter data. - - Parameters - ---------- - handle : file handle - Read metadata and C3D motion frames from the given file handle. This - handle is assumed to be `seek`-able and `read`-able. The handle must - remain open for the life of the `Reader` instance. The `Reader` does - not `close` the handle. - - Raises - ------ - ValueError - If the processor metadata in the C3D file is anything other than 84 - (Intel format). - ''' - super(Reader, self).__init__(Header(handle)) - - self._handle = handle - - def seek_param_section_header(): - ''' Seek to and read the first 4 byte of the parameter header section ''' - self._handle.seek((self._header.parameter_block - 1) * 512) - # metadata header - return self._handle.read(4) - - # Begin by reading the processor type: - buf = seek_param_section_header() - _, _, parameter_blocks, processor = struct.unpack('BBBB', buf) - self._dtypes = DataTypes(processor) - # Convert header parameters in accordance with the processor type (MIPS format re-reads the header) - self._header._processor_convert(self._dtypes, handle) - - # Restart reading the parameter header after parsing processor type - buf = seek_param_section_header() - - start_byte = self._handle.tell() - endbyte = start_byte + 512 * parameter_blocks - 4 - while self._handle.tell() < endbyte: - chars_in_name, group_id = struct.unpack('bb', self._handle.read(2)) - if group_id == 0 or chars_in_name == 0: - # we've reached the end of the parameter section. - break - name = self._dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper() - - # Read the byte segment associated with the parameter and create a - # separate binary stream object from the data. - offset_to_next, = struct.unpack(['h'][self._dtypes.is_mips], self._handle.read(2)) - if offset_to_next == 0: - # Last parameter, as number of bytes are unknown, - # read the remaining bytes in the parameter section. - bytes = self._handle.read(endbyte - self._handle.tell()) - else: - bytes = self._handle.read(offset_to_next - 2) - buf = io.BytesIO(bytes) - - if group_id > 0: - # We've just started reading a parameter. If its group doesn't - # exist, create a blank one. add the parameter to the group. - group = super(Reader, self).get(group_id) - if group is None: - group = self._add_group(group_id) - group.add_param(name, handle=buf) - else: - # We've just started reading a group. If a group with the - # appropriate numerical id exists already (because we've - # already created it for a parameter), just set the name of - # the group. Otherwise, add a new group. - group_id = abs(group_id) - size, = struct.unpack('B', buf.read(1)) - desc = size and buf.read(size) or '' - group = super(Reader, self).get(group_id) - if group is not None: - self._rename_group(group, name) # Inserts name key - group.desc = desc - else: - self._add_group(group_id, name, desc) - - self._check_metadata() - - def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False): - '''Iterate over the data frames from our C3D file handle. - - Parameters - ---------- - copy : bool - If False, the reader returns a reference to the same data buffers - for every frame. The default is True, which causes the reader to - return a unique data buffer for each frame. Set this to False if you - consume frames as you iterate over them, or True if you store them - for later. - - Returns - ------- - frames : sequence of (frame number, points, analog) - This method generates a sequence of (frame number, points, analog) - tuples, one tuple per frame. The first element of each tuple is the - frame number. The second is a numpy array of parsed, 5D point data - and the third element of each tuple is a numpy array of analog - values that were recorded during the frame. (Often the analog data - are sampled at a higher frequency than the 3D point data, resulting - in multiple analog frames per frame of point data.) - - The first three columns in the returned point data are the (x, y, z) - coordinates of the observed motion capture point. The fourth column - is an estimate of the error for this particular point, and the fifth - column is the number of cameras that observed the point in question. - Both the fourth and fifth values are -1 if the point is considered - to be invalid. - ''' - # Point magnitude scalar, if scale parameter is < 0 data is floating point - # (in which case the magnitude is the absolute value) - scale_mag = abs(self.point_scale) - is_float = self.point_scale < 0 - - if is_float: - point_word_bytes = 4 - else: - point_word_bytes = 2 - points = np.zeros((self.point_used, 5), np.float32) - - # TODO: handle ANALOG:BITS parameter here! - p = self.get('ANALOG:FORMAT') - analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED' - if is_float: - analog_dtype = self._dtypes.float32 - analog_word_bytes = 4 - elif analog_unsigned: - # Note*: Floating point is 'always' defined for both analog and point data, according to the standard. - analog_dtype = self._dtypes.uint16 - analog_word_bytes = 2 - # Verify BITS parameter for analog - p = self.get('ANALOG:BITS') - if p and p._as_integer_value / 8 != analog_word_bytes: - raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value)) - else: - analog_dtype = self._dtypes.int16 - analog_word_bytes = 2 - - analog = np.array([], float) - analog_scales, analog_offsets = self.get_analog_transform() - - # Seek to the start point of the data blocks - self._handle.seek((self._header.data_block - 1) * 512) - # Number of values (words) read in regard to POINT/ANALOG data - N_point = 4 * self.point_used - N_analog = self.analog_used * self.analog_per_frame - - # Total bytes per frame - point_bytes = N_point * point_word_bytes - analog_bytes = N_analog * analog_word_bytes - # Parse the data blocks - for frame_no in range(self.first_frame, self.last_frame + 1): - # Read the byte data (used) for the block - raw_bytes = self._handle.read(N_point * point_word_bytes) - raw_analog = self._handle.read(N_analog * analog_word_bytes) - # Verify read pointers (any of the two can be assumed to be 0) - if len(raw_bytes) < point_bytes: - warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {} - and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell())) - return - if len(raw_analog) < analog_bytes: - warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {} - and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell())) - return - - if is_float: - # Convert every 4 byte words to a float-32 reprensentation - # (the fourth column is still not a float32 representation) - if self._dtypes.is_dec: - # Convert each of the first 6 16-bit words from DEC to IEEE float - points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4)) - else: # If IEEE or MIPS: - # Convert each of the first 6 16-bit words to native float - points[:, :4] = np.frombuffer(raw_bytes, - dtype=self._dtypes.float32, - count=N_point).reshape((self.point_used, 4)) - - # Cast last word to signed integer in system endian format - last_word = points[:, 3].astype(np.int32) - - else: - # View the bytes as signed 16-bit integers - raw = np.frombuffer(raw_bytes, - dtype=self._dtypes.int16, - count=N_point).reshape((self.point_used, 4)) - # Read the first six 16-bit words as x, y, z coordinates - points[:, :3] = raw[:, :3] * scale_mag - # Cast last word to signed integer in system endian format - last_word = raw[:, 3].astype(np.int16) - - # Parse camera-observed bits and residuals. - # Notes: - # - Invalid sample if residual is equal to -1 (check if word < 0). - # - A residual of 0.0 represent modeled data (filtered or interpolated). - # - Camera and residual words are always 8-bit (1 byte), never 16-bit. - # - If floating point, the byte words are encoded in an integer cast to a float, - # and are written directly in byte form (see the MLS guide). - ## - # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded). - residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8 - - # Fourth value is floating-point (scaled) error estimate (residual) - points[:, 3] = residual_byte * scale_mag - - # Determine invalid samples - invalid = last_word < 0 - if check_nan: - is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) - points[is_nan, :3] = 0.0 - invalid &= is_nan - # Update discarded - sign - points[invalid, 3] = -1 - - - # Fifth value is the camera-observation byte - if camera_sum: - # Convert to observation sum - points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(8)) - else: - points[:, 4] = camera_byte #.astype(np.float32) - - # Check if analog data exist, and parse if so - if N_analog > 0: - if is_float and self._dtypes.is_dec: - # Convert each of the 16-bit words from DEC to IEEE float - analog = DEC_to_IEEE_BYTES(raw_analog) - else: - # Integer or INTEL/MIPS floating point data can be parsed directly - analog = np.frombuffer(raw_analog, dtype=analog_dtype, count=N_analog) - - # Reformat and convert - analog = analog.reshape((-1, self.analog_used)).T - analog = analog.astype(float) - # Convert analog - analog = (analog - analog_offsets) * analog_scales - - # Output buffers - if copy: - yield frame_no, points.copy(), analog # .copy(), a new array is generated per frame for analog data. - else: - yield frame_no, points, analog - - # Function evaluating EOF, note that data section is written in blocks of 512 - final_byte_index = self._handle.tell() - self._handle.seek(0, 2) # os.SEEK_END) - # Check if more then 1 block remain - if self._handle.tell() - final_byte_index >= 512: - warnings.warn('incomplete reading of data blocks. {} bytes remained after all datablocks were read!'.format( - self._handle.tell() - final_byte_index)) - - @property - def proc_type(self): - '''Get the processory type associated with the data format in the file. - ''' - return self._dtypes.proc_type - - def to_writer(self, conversion=None): - ''' Convert to 'Writer' using the conversion mode. - See Writer.from_reader() for supported conversion modes and possible exceptions. - ''' - return Writer.from_reader(self, conversion=conversion) - - def get(self, key, default=None): - '''Get a readonly group or parameter. - - Parameters - ---------- - key : str - If this string contains a period (.), then the part before the - period will be used to retrieve a group, and the part after the - period will be used to retrieve a parameter from that group. If this - string does not contain a period, then just a group will be - returned. - default : any - Return this value if the named group and parameter are not found. - - Returns - ------- - value : :class:`GroupReadonly` or :class:`Param` - Either a group or parameter with the specified name(s). If neither - is found, returns the default value. - ''' - val = super(Reader, self).get(key) - if val: - return val.readonly() - return default - - def items(self): - ''' Acquire iterable over parameter group pairs. - - Returns - ------- - items : Touple of ((str, :class:`GroupReadonly`), ...) - Python touple containing pairs of name keys and parameter group entries. - ''' - return ((k, v.readonly()) for k, v in super(Reader, self).items()) - - def values(self): - ''' Acquire iterable over parameter group entries. - - Returns - ------- - values : Touple of (:class:`GroupReadonly`, ...) - Python touple containing unique parameter group entries. - ''' - return (v.readonly() for k, v in super(Reader, self).items()) - - def listed(self): - ''' Acquire iterable over parameter group entries. - - Returns - ------- - items : Touple of ((int, :class:`GroupReadonly`), ...) - Python touple containing unique parameter group entries. - ''' - return ((k, v.readonly()) for k, v in super(Reader, self).listed()) - class Writer(Manager): '''This class writes metadata and frames to a C3D file. diff --git a/scripts/c3d-metadata.py b/scripts/c3d-metadata.py index 5b25eac..cb054f6 100644 --- a/scripts/c3d-metadata.py +++ b/scripts/c3d-metadata.py @@ -4,9 +4,14 @@ from __future__ import print_function -import c3d import argparse import sys +try: + import c3d +except ModuleNotFoundError: + import os + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d parser = argparse.ArgumentParser(description='Display C3D group and parameter information.') parser.add_argument('input', default='-', metavar='FILE', nargs='+', @@ -15,9 +20,9 @@ def print_metadata(reader): print('Header information:\n{}'.format(reader.header)) - for key, g in sorted(reader.group_items()): + for key, g in sorted(reader.items()): print('') - for key, p in sorted(g.param_items()): + for key, p in sorted(g.items()): print_param(g, p) @@ -26,7 +31,7 @@ def print_param(g, p): if len(p.dimensions) == 0: val = None - width = len(p.bytes) + width = p.total_bytes if width == 2: val = p.int16_value elif width == 4: @@ -51,7 +56,7 @@ def print_param(g, p): C, R = p.dimensions for r in range(R): print('{0.name}.{1.name}[{2}] = {3}'.format( - g, p, r, repr(p.bytes[r * C:(r+1) * C]))) + g, p, r, repr(p.bytes_value[r * C:(r+1) * C]))) def main(args): diff --git a/scripts/c3d2csv.py b/scripts/c3d2csv.py index 128b01a..b15966f 100644 --- a/scripts/c3d2csv.py +++ b/scripts/c3d2csv.py @@ -4,14 +4,19 @@ from __future__ import print_function -import c3d import sys import argparse +try: + import c3d +except ModuleNotFoundError: + import os + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d parser = argparse.ArgumentParser(description='Convert a C3D file to CSV (text) format.') -parser.add_argument('-a', '--include-analog', action='store_true', help='output analog values after point positions') -parser.add_argument('-c', '--include-camera', action='store_true', help='output camera count with each point position') -parser.add_argument('-r', '--include-error', action='store_true', help='output error value with each point position') +parser.add_argument('-a', '--include-analog', action='store_true', help='Output analog channel values after point coordinates.') +parser.add_argument('-c', '--include-camera', action='store_true', help='Output column with camera counts as the last point coordinate column.') +parser.add_argument('-r', '--include-error', action='store_true', help='Output column with residual values after point x,y,z coordinate columns.') parser.add_argument('-e', '--end', default='\\n', metavar='K', help='write K between records') parser.add_argument('-s', '--sep', default=',', metavar='C', help='write C between fields in a record') parser.add_argument('input', default='-', metavar='FILE', nargs='+', help='process data from this input FILE') @@ -24,8 +29,9 @@ def convert(filename, args, sep, end): if open_file_streams: input = open(filename, 'rb') output = open(filename.replace('.c3d', '.csv'), 'w') + try: - for frame_no, points, analog in c3d.Reader(input).read_frames(copy=False): + for frame_no, points, analog in c3d.Reader(input).read_frames(copy=False, camera_sum=True): fields = [frame_no] for x, y, z, err, cam in points: fields.append(str(x)) diff --git a/scripts/c3d2npz.py b/scripts/c3d2npz.py index d2a7e79..4629b3c 100644 --- a/scripts/c3d2npz.py +++ b/scripts/c3d2npz.py @@ -9,8 +9,13 @@ import logging import gzip import numpy as np -import sys from tempfile import TemporaryFile +try: + import c3d +except ModuleNotFoundError: + import os + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d parser = argparse.ArgumentParser(description='Convert a C3D file to NPZ (numpy binary) format.') parser.add_argument('input', default='-', metavar='FILE', nargs='+', help='process data from this input FILE') @@ -22,7 +27,7 @@ def convert(filename, args): if filename != '-': input = open(filename, 'rb') outname = filename.replace('.c3d', '.npz') - + points = [] analog = [] for i, (_, p, a) in enumerate(c3d.Reader(input).read_frames()): @@ -32,10 +37,10 @@ def convert(filename, args): logging.debug('%s: extracted %d point frames', outname, len(points)) np.savez(outname, points=points, analog=analog) - print(outname + ': saved', len(points), "x", str(points[0].shape), "points,", + print(outname + ': saved', len(points), "x", str(points[0].shape), "points,", len(analog), analog[0].shape, 'analog' if len(analog) else () ) - + if filename != '-': input.close() diff --git a/setup.py b/setup.py index 5f847ab..3e19414 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ setuptools.setup( name='c3d', version='0.3.0', - py_modules=['c3d'], + py_modules=['c3d.dtypes', 'c3d.group', 'c3d.header', 'c3d.manager', 'c3d.reader', 'c3d.writer', 'c3d.parameter', 'c3d.utils', 'scripts.c3d-viewer'], author='UT Vision, Cognition, and Action Lab', author_email='leif@cs.utexas.edu', description='A library for manipulating C3D binary files', @@ -13,7 +13,7 @@ url='http://github.com/EmbodiedCognition/py-c3d', keywords=('c3d motion-capture'), install_requires=['numpy'], - scripts=['scripts/c3d{}'.format(s) for s in '-metadata -viewer 2csv 2npz'.split()], + scripts=['scripts/c3d{}.py'.format(s) for s in '-metadata -viewer 2csv 2npz'.split()], classifiers=[ 'Development Status :: 4 - Beta', 'Intended Audience :: Science/Research', diff --git a/src/__init__.py b/src/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/test/test_parameter_accessors.py b/test/test_parameter_accessors.py index c6ff0fb..1be26ae 100644 --- a/test/test_parameter_accessors.py +++ b/test/test_parameter_accessors.py @@ -2,7 +2,7 @@ ''' import unittest import c3d -from src.group import Group +from c3d.group import Group import numpy as np import test.verify as verify from test.zipload import Zipload diff --git a/test/test_parameter_bytes_conversion.py b/test/test_parameter_bytes_conversion.py index db3466e..3525ccf 100644 --- a/test/test_parameter_bytes_conversion.py +++ b/test/test_parameter_bytes_conversion.py @@ -1,8 +1,8 @@ import struct import unittest import numpy as np -from src.dtypes import DataTypes, PROCESSOR_INTEL -from src.parameter import ParamData, ParamReadonly +from c3d.dtypes import DataTypes, PROCESSOR_INTEL +from c3d.parameter import ParamData, ParamReadonly def genByteWordArr(word, shape): From 5ccf0b8bc3721af24b30a4014d4701cf83f2f967 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sat, 3 Jul 2021 16:00:16 +0200 Subject: [PATCH 053/120] Update README.rst script link --- README.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index aefb9c6..b836757 100644 --- a/README.rst +++ b/README.rst @@ -25,10 +25,13 @@ Usage Tools ~~~~~ -This package includes a script for converting C3D motion data to CSV format +This package includes scripts_ for converting C3D motion data to CSV format (``c3d2csv``) and an OpenGL-based visualization tool for observing the motion described by a C3D file (``c3d-viewer``). +.. _package documentation: http://c3d.readthedocs.org +.. _scripts: ./scripts + Library ~~~~~~~ From 8c07bf762ba047f1b28f1946b2f50217fed3c2ad Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 16:01:22 +0200 Subject: [PATCH 054/120] New version number --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3e19414..42bae93 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ setuptools.setup( name='c3d', - version='0.3.0', + version='0.5.0', py_modules=['c3d.dtypes', 'c3d.group', 'c3d.header', 'c3d.manager', 'c3d.reader', 'c3d.writer', 'c3d.parameter', 'c3d.utils', 'scripts.c3d-viewer'], author='UT Vision, Cognition, and Action Lab', author_email='leif@cs.utexas.edu', From bdbbe0496e501cb66f4486b85bf55f6d8a56785c Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 21:16:22 +0200 Subject: [PATCH 055/120] =?UTF-8?q?Improved=20mod=C3=BAle,=20class,=20and?= =?UTF-8?q?=20function=20documentation?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- c3d/dtypes.py | 24 +++--- c3d/group.py | 200 +++++++++++++++++++++++++---------------------- c3d/header.py | 3 + c3d/manager.py | 65 ++++++--------- c3d/parameter.py | 47 ++++++----- c3d/reader.py | 35 +++------ c3d/utils.py | 2 + c3d/writer.py | 50 +++++++++--- test/test_c3d.py | 9 ++- 9 files changed, 231 insertions(+), 204 deletions(-) diff --git a/c3d/dtypes.py b/c3d/dtypes.py index e327b27..9071d0d 100644 --- a/c3d/dtypes.py +++ b/c3d/dtypes.py @@ -1,3 +1,7 @@ +''' +State object defining the data types associated with a given .c3d processor format. +''' + import sys import codecs import numpy as np @@ -7,7 +11,7 @@ PROCESSOR_MIPS = 86 class DataTypes(object): - ''' Container defining different data types used for reading file data. + ''' Container defining the data types used when parsing byte data. Data types depend on the processor format the file is stored in. ''' def __init__(self, proc_type=PROCESSOR_INTEL): @@ -44,55 +48,55 @@ def __init__(self, proc_type=PROCESSOR_INTEL): self.int64 = np.int64 @property - def is_ieee(self): + def is_ieee(self) -> bool: ''' True if the associated file is in the Intel format. ''' return self._proc_type == PROCESSOR_INTEL @property - def is_dec(self): + def is_dec(self) -> bool: ''' True if the associated file is in the DEC format. ''' return self._proc_type == PROCESSOR_DEC @property - def is_mips(self): + def is_mips(self) -> bool: ''' True if the associated file is in the SGI/MIPS format. ''' return self._proc_type == PROCESSOR_MIPS @property - def proc_type(self): + def proc_type(self) -> str: ''' Get the processory type associated with the data format in the file. ''' processor_type = ['INTEL', 'DEC', 'MIPS'] return processor_type[self._proc_type - PROCESSOR_INTEL] @property - def processor(self): + def processor(self) -> int: ''' Get the processor number encoded in the .c3d file. ''' return self._proc_type @property - def native(self): + def native(self) -> bool: ''' True if the native (system) byte order matches the file byte order. ''' return self._native @property - def little_endian_sys(self): + def little_endian_sys(self) -> bool: ''' True if native byte order is little-endian. ''' return self._little_endian_sys @property - def big_endian_sys(self): + def big_endian_sys(self) -> bool: ''' True if native byte order is big-endian. ''' return not self._little_endian_sys - def decode_string(self, bytes): + def decode_string(self, bytes) -> str: ''' Decode a byte array to a string. ''' # Attempt to decode using different decoders diff --git a/c3d/group.py b/c3d/group.py index ec975b5..46b539f 100644 --- a/c3d/group.py +++ b/c3d/group.py @@ -1,17 +1,20 @@ +''' Classes used to represent the concept of parameter groups in a .c3d file. +''' import struct import numpy as np from .parameter import ParamData, Param from .utils import Decorator class GroupData(object): - '''A group of parameters from a C3D file. + '''A group of parameters stored in a C3D file. - In C3D files, parameters are organized in groups. Each group has a name, a - description, and a set of named parameters. + In C3D files, parameters are organized in groups. Each group has a name (key), a + description, and a set of named parameters. Each group is also internally associated + with a numeric key. Attributes ---------- - dtypes : 'DataTypes' + dtypes : `c3d.dtypes.DataTypes` Data types object used for parsing. name : str Name of this parameter group. @@ -36,7 +39,7 @@ def __getitem__(self, key): return self._params[key] @property - def binary_size(self): + def binary_size(self) -> int: '''Return the number of bytes to store this group and its parameters.''' return ( 1 + # group_id @@ -45,22 +48,22 @@ def binary_size(self): 1 + len(self.desc.encode('utf-8')) + # size of desc and desc bytes sum(p.binary_size for p in self._params.values())) - def set_name(self, value): + def set_name(self, name): ''' Set the group name string. ''' - if value is None or isinstance(value, str): - self.name = value + if name is None or isinstance(name, str): + self.name = name else: - raise TypeError('Expected group name to be string, was %s.' % type(value)) + raise TypeError('Expected group name to be string, was %s.' % type(name)) - def set_desc(self, value): + def set_desc(self, desc): ''' Set the Group descriptor. ''' - if isinstance(value, bytes): - self.desc = self._dtypes.decode_string(value) - elif isinstance(value, str) or value is None: - self.desc = value + if isinstance(desc, bytes): + self.desc = self._dtypes.decode_string(desc) + elif isinstance(desc, str) or desc is None: + self.desc = desc else: - raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(value)) + raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(desc)) def add_param(self, name, **kwargs): '''Add a parameter to this group. @@ -71,7 +74,7 @@ def add_param(self, name, **kwargs): Name of the parameter to add to this group. The name will automatically be case-normalized. - Additional keyword arguments will be passed to the `ParamData` constructor. + See constructor of `c3d.parameter.ParamData` for additional keyword arguments. Raises ------ @@ -102,11 +105,10 @@ def rename_param(self, name, new_name): Parameters ---------- - name : str, or 'Param' + name : str, or `c3d.group.GroupReadonly` Parameter instance, or name. new_name : str New name for the parameter. - Raises ------ KeyError @@ -146,7 +148,7 @@ def write(self, group_id, handle): param._data.write(group_id, handle) class GroupReadonly(object): - ''' Handle exposing readable attributes of a GroupData entry. + ''' Wrapper exposing readonly attributes of a `c3d.group.GroupData` entry. ''' def __init__(self, data): self._data = data @@ -158,25 +160,25 @@ def __eq__(self, other): return self._data is other._data @property - def name(self): - ''' Group name. ''' + def name(self) -> str: + ''' Access group name. ''' return self._data.name @property - def desc(self): - ''' Group descriptor. ''' + def desc(self) -> str: + '''Access group descriptor. ''' return self._data.desc def items(self): - ''' Acquire iterator for paramater key-entry pairs. ''' + ''' Get iterator for paramater key-entry pairs. ''' return ((k, v.readonly()) for k, v in self._data._params.items()) def values(self): - ''' Acquire iterator for parameter entries. ''' + ''' Get iterator for parameter entries. ''' return (v.readonly() for v in self._data._params.values()) def keys(self): - ''' Acquire iterator for parameter entry keys. ''' + ''' Get iterator for parameter entry keys. ''' return self._data._params.keys() def get(self, key, default=None): @@ -236,55 +238,39 @@ def get_string(self, key): return self._data[key.upper()].string_value class Group(GroupReadonly): - ''' Handle exposing readable and writeable attributes of a GroupData entry. - - Group instance decorator providing convenience functions for Writer editing. + ''' Wrapper exposing readable and writeable attributes of a `c3d.group.GroupData` entry. ''' def __init__(self, data): super(Group, self).__init__(data) def readonly(self): - ''' Make access readonly. ''' + ''' Returns a `c3d.group.GroupReadonly` instance with readonly access. ''' return GroupReadonly(self._data) @property - def name(self): - ''' Group name. ''' + def name(self) -> str: + ''' Get or set name. ''' return self._data.name @name.setter - def name(self, value): - ''' Group name string. - - Parameters - ---------- - value : str - New name for the group. - ''' + def name(self, value) -> str: self._data.set_name(value) @property - def desc(self): - ''' Group descriptor. ''' + def desc(self) -> str: + ''' Get or set descriptor. ''' return self._data.desc @desc.setter - def desc(self, value): - ''' Group descriptor. - - Parameters - ---------- - value : str, or bytes - New description for this parameter group. - ''' + def desc(self, value) -> str: self._data.set_desc(value) def items(self): - ''' Acquire iterator for paramater key-entry pairs. ''' + ''' Iterator for paramater key-entry pairs. ''' return ((k, v) for k, v in self._data._params.items()) def values(self): - ''' Acquire iterator for parameter entries. ''' + ''' Iterator iterator for parameter entries. ''' return (v for v in self._data._params.values()) def get(self, key, default=None): @@ -309,20 +295,7 @@ def get(self, key, default=None): def add_param(self, name, **kwargs): '''Add a parameter to this group. - Parameters - ---------- - name : str - Name of the parameter to add to this group. The name will - automatically be case-normalized. - - Additional keyword arguments will be passed to the `ParamData` constructor. - - Raises - ------ - TypeError - Input arguments are of the wrong type. - KeyError - Name or numerical key already exist (attempt to overwrite existing data). + See constructor of `c3d.parameter.ParamData` for additional keyword arguments. ''' self._data.add_param(name, **kwargs) @@ -341,25 +314,35 @@ def rename_param(self, name, new_name): Parameters ---------- - name : str, or 'Param' - Parameter instance, or name. - new_name : str - New name for the parameter. - - Raises - ------ - KeyError - If no parameter with the original name exists. - ValueError - If the new name already exist (attempt to overwrite existing data). + See arguments in `c3d.group.GroupData.rename_param`. ''' self._data.rename_param(name, new_name) # - # Add convenience functions (throws on overwrite) + # Convenience functions for adding parameters. # def add(self, name, desc, bpe, format, data, *dimensions): - ''' Add a parameter with 'data' package formated in accordance with 'format'. + ''' Add a parameter with `data` package formated in accordance with `format`. + + Convenience function for `c3d.group.GroupData.add_param` calling struct.pack() on `data`. + + Example: + + >>> group.set('RATE', 'Point data sample rate', 4, ' '`c3d.header.Header`': ''' Access to .c3d header data. ''' return self._header - def parameter_blocks(self): + def parameter_blocks(self) -> int: '''Compute the size (in 512B blocks) of the parameter section.''' bytes = 4. + sum(g._data.binary_size for g in self._groups.values()) return int(np.ceil(bytes / 512)) @property - def point_rate(self): + def point_rate(self) -> float: ''' Number of sampled 3D coordinates per second. ''' try: return self.get_float('POINT:RATE') @@ -280,7 +261,7 @@ def point_rate(self): return self.header.frame_rate @property - def point_scale(self): + def point_scale(self) -> float: ''' Scaling applied to non-float data. ''' try: return self.get_float('POINT:SCALE') @@ -288,7 +269,7 @@ def point_scale(self): return self.header.scale_factor @property - def point_used(self): + def point_used(self) -> int: ''' Number of sampled 3D point coordinates per frame. ''' try: return self.get_uint16('POINT:USED') @@ -296,7 +277,7 @@ def point_used(self): return self.header.point_count @property - def analog_used(self): + def analog_used(self) -> int: ''' Number of analog measurements, or channels, for each analog data sample. ''' try: return self.get_uint16('ANALOG:USED') @@ -307,7 +288,7 @@ def analog_used(self): return 0 @property - def analog_rate(self): + def analog_rate(self) -> float: ''' Number of analog data samples per second. ''' try: return self.get_float('ANALOG:RATE') @@ -315,33 +296,33 @@ def analog_rate(self): return self.header.analog_per_frame * self.point_rate @property - def analog_per_frame(self): + def analog_per_frame(self) -> int: ''' Number of analog frames per 3D frame (point sample). ''' return int(self.analog_rate / self.point_rate) @property - def analog_sample_count(self): + def analog_sample_count(self) -> int: ''' Number of analog samples per channel. ''' has_analog = self.analog_used > 0 return int(self.frame_count * self.analog_per_frame) * has_analog @property - def point_labels(self): + def point_labels(self) -> list: ''' Labels for each POINT data channel. ''' return self.get('POINT:LABELS').string_array @property - def analog_labels(self): + def analog_labels(self) -> list: ''' Labels for each ANALOG data channel. ''' return self.get('ANALOG:LABELS').string_array @property - def frame_count(self): + def frame_count(self) -> int: ''' Number of frames recorded in the data. ''' return self.last_frame - self.first_frame + 1 # Add 1 since range is inclusive [first, last] @property - def first_frame(self): + def first_frame(self) -> int: ''' Trial frame corresponding to the first frame recorded in the data. ''' # Start frame seems to be less of an issue to determine. # this is a hack for phasespace files ... should put it in a subclass. @@ -353,7 +334,7 @@ def first_frame(self): return self.header.first_frame @property - def last_frame(self): + def last_frame(self) -> int: ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: @@ -386,7 +367,7 @@ def get_screen_axis(self): Returns ------- - value : Touple on form (str, str) or None + value : (str, str) or None Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found. ''' X = self.get('POINT:X_SCREEN') diff --git a/c3d/parameter.py b/c3d/parameter.py index 6a65da5..542d6c6 100644 --- a/c3d/parameter.py +++ b/c3d/parameter.py @@ -1,3 +1,5 @@ +''' Classes used to represent the concept of a parameter in a .c3d file. +''' import struct import numpy as np from .utils import DEC_to_IEEE, DEC_to_IEEE_BYTES @@ -18,7 +20,7 @@ class ParamData(object): string data (including arrays of strings), this should be -1. dimensions : list of int For array data, this describes the dimensions of the array, stored in - column-major order. For arrays of strings, the dimensions here will be + column-major (Fortran) order. For arrays of strings, the dimensions here will be the number of columns (length of each string) followed by the number of rows (number of strings). bytes : str @@ -47,7 +49,7 @@ def __repr__(self): return ''.format(self.desc) @property - def num_elements(self): + def num_elements(self) -> int: '''Return the number of elements in this parameter's array value.''' e = 1 for d in self.dimensions: @@ -55,12 +57,12 @@ def num_elements(self): return e @property - def total_bytes(self): + def total_bytes(self) -> int: '''Return the number of bytes used for storing this parameter's data.''' return self.num_elements * abs(self.bytes_per_element) @property - def binary_size(self): + def binary_size(self) -> int: '''Return the number of bytes needed to store this parameter.''' return ( 1 + # group_id @@ -146,6 +148,8 @@ def _as_any(self, dtype): return data class ParamReadonly(object): + ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry. + ''' def __init__(self, data): self._data = data @@ -154,40 +158,42 @@ def __eq__(self, other): return self._data is other._data @property - def name(self): - ''' Name string. ''' + def name(self) -> str: + ''' Get the parameter name. ''' return self._data.name @property - def desc(self): - ''' Descriptor string. ''' + def desc(self) -> str: + ''' Get the parameter descriptor. ''' return self._data.desc @property def dtypes(self): + ''' Convenience accessor to the `c3d.dtypes.DataTypes` instance associated with the parameter. ''' return self._data.dtypes @property - def dimensions(self): + def dimensions(self) -> (int, ...): + ''' Shape of the parameter data (Fortran shape). ''' return self._data.dimensions @property - def num_elements(self): + def num_elements(self) -> int: '''Return the number of elements in this parameter's array value.''' return self._data.num_elements @property - def bytes_per_element(self): + def bytes_per_element(self) -> int: '''Return the number of bytes used to store each data element.''' return self._data.bytes_per_element @property - def total_bytes(self): + def total_bytes(self) -> int: '''Return the number of bytes used for storing this parameter's data.''' return self._data.total_bytes @property - def binary_size(self): + def binary_size(self) -> int: '''Return the number of bytes needed to store this parameter.''' return self._data.binary_size @@ -223,8 +229,7 @@ def uint32_value(self): @property def uint_value(self): - ''' Get the param as a unsigned integer of appropriate type. - ''' + ''' Get the param as a unsigned integer of appropriate type. ''' if self.total_bytes >= 4: return self.uint32_value elif self.total_bytes >= 2: @@ -234,8 +239,7 @@ def uint_value(self): @property def int_value(self): - ''' Get the param as a signed integer of appropriate type. - ''' + ''' Get the param as a signed integer of appropriate type. ''' if self.total_bytes >= 4: return self.int32_value elif self.total_bytes >= 2: @@ -428,19 +432,20 @@ def _as_integer_or_float_value(self): return self.uint8_value class Param(ParamReadonly): + ''' Wrapper exposing both readable and writable attributes of a `c3d.parameter.ParamData` entry. + ''' def __init__(self, data): super(Param, self).__init__(data) def readonly(self): - ''' Readonly ''' + ''' Returns a readonly `c3d.parameter.ParamReadonly` instance. ''' return ParamReadonly(self._data) @property - def bytes(self): - ''' Raw access to parameter bytes. ''' + def bytes(self) -> bytes: + ''' Get or set the parameter bytes. ''' return self._data.bytes @bytes.setter def bytes(self, value): - ''' Set parameter bytes. ''' self._data.bytes = value diff --git a/c3d/reader.py b/c3d/reader.py index 26b8335..d5abca4 100644 --- a/c3d/reader.py +++ b/c3d/reader.py @@ -36,9 +36,8 @@ def __init__(self, handle): Raises ------ - ValueError - If the processor metadata in the C3D file is anything other than 84 - (Intel format). + AssertionError + If the metadata in the C3D file is inconsistent. ''' super(Reader, self).__init__(Header(handle)) @@ -276,14 +275,15 @@ def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_s self._handle.tell() - final_byte_index)) @property - def proc_type(self): + def proc_type(self) -> int: '''Get the processory type associated with the data format in the file. ''' return self._dtypes.proc_type def to_writer(self, conversion=None): - ''' Convert to 'Writer' using the conversion mode. - See Writer.from_reader() for supported conversion modes and possible exceptions. + ''' Converts the reader to a `c3d.writer.Writer` instance using the conversion mode. + + See `c3d.writer.Writer.from_reader()` for supported conversion modes. ''' from .writer import Writer return Writer.from_reader(self, conversion=conversion) @@ -304,7 +304,7 @@ def get(self, key, default=None): Returns ------- - value : :class:`GroupReadonly` or :class:`Param` + value : `c3d.group.GroupReadonly` or `c3d.parameter.ParamReadonly` Either a group or parameter with the specified name(s). If neither is found, returns the default value. ''' @@ -314,31 +314,16 @@ def get(self, key, default=None): return default def items(self): - ''' Acquire iterable over parameter group pairs. - - Returns - ------- - items : Touple of ((str, :class:`GroupReadonly`), ...) - Python touple containing pairs of name keys and parameter group entries. + ''' Get iterable over pairs of (str, `c3d.group.GroupReadonly`) entries. ''' return ((k, v.readonly()) for k, v in super(Reader, self).items()) def values(self): - ''' Acquire iterable over parameter group entries. - - Returns - ------- - values : Touple of (:class:`GroupReadonly`, ...) - Python touple containing unique parameter group entries. + ''' Get iterable over `c3d.group.GroupReadonly` entries. ''' return (v.readonly() for k, v in super(Reader, self).items()) def listed(self): - ''' Acquire iterable over parameter group entries. - - Returns - ------- - items : Touple of ((int, :class:`GroupReadonly`), ...) - Python touple containing unique parameter group entries. + ''' Get iterable over pairs of (int, `c3d.group.GroupReadonly`) entries. ''' return ((k, v.readonly()) for k, v in super(Reader, self).listed()) diff --git a/c3d/utils.py b/c3d/utils.py index 5d4c8c3..0c28231 100644 --- a/c3d/utils.py +++ b/c3d/utils.py @@ -1,3 +1,5 @@ +''' Trailing utility functions. +''' import numpy as np import struct diff --git a/c3d/writer.py b/c3d/writer.py index bb0c173..2029f1e 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -40,7 +40,7 @@ def __init__(self, point_rate=480., analog_rate=0., point_scale=-1.): - '''Set metadata for this writer. + '''Set minimal metadata for this writer. ''' self._dtypes = DataTypes() # Only support INTEL format from writing @@ -55,7 +55,7 @@ def __init__(self, @staticmethod def from_reader(reader, conversion=None): ''' - source : 'class' Manager + source : `c3d.manager.Manager` Source to copy. conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: @@ -216,7 +216,7 @@ def add_frames(self, frames, index=None): if sh[1] != 2: raise ValueError( 'Expected frame input to be sequence of point and analog pairs on form (-1, 2). ' + - '\Input was of shape {}.'.format(str(sh))) + 'Input was of shape {}.'.format(str(sh))) if index is not None: self._frames[index:index] = frames @@ -225,6 +225,32 @@ def add_frames(self, frames, index=None): @staticmethod def pack_labels(labels): + ''' Static method used to pack and pad the set of `labels` strings before + passing the output into a `c3d.group.Group.add_str`. + + Parameters + ---------- + labels : iterable + List of strings to pack and pad into a single string suitable for encoding in a Parameter entry. + + Example + ------- + >>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3'] + >>> param_str, label_max_size = Writer.pack_labels(labels) + >>> writer.point_group.add_str('LABELS', + 'Point labels.', + label_str, + label_max_size, + len(labels)) + + Returns + ------- + param_str : str + String containing `labels` packed into a single variable where + each string is padded to match the longest `labels` string. + label_max_size : int + Number of bytes associated with the longest `label` string, all strings are padded to this length. + ''' labels = np.ravel(labels) # Get longest label name label_max_size = 0 @@ -319,8 +345,8 @@ def set_screen_axis(self, X='+X', Y='+Y'): if len(Y) != 2: raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter.') group = self.point_group - group.set_str('X_SCREEN', 'X_SCREEN parameter', X, 2) - group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y, 2) + group.set_str('X_SCREEN', 'X_SCREEN parameter', X) + group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y) def write(self, handle): '''Write metadata and point + analog frames to a file handle. @@ -353,23 +379,23 @@ def write(self, handle): group.set('FRAMES', 'Total frame count', 2, '= UINT16_MAX: # Should be floating point - group.set('LONG_FRAMES', 'Total frame count', 4, ' Date: Sat, 3 Jul 2021 21:45:56 +0200 Subject: [PATCH 056/120] Module documentation edit --- c3d/header.py | 2 +- c3d/manager.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/c3d/header.py b/c3d/header.py index 2f1df87..25a3718 100644 --- a/c3d/header.py +++ b/c3d/header.py @@ -1,5 +1,5 @@ ''' -Defines the header class used for reading, writing and tracking the metadata in the header of a .c3d file. +Defines the header class used for reading, writing and tracking metadata in the .c3d header. ''' import sys import struct diff --git a/c3d/manager.py b/c3d/manager.py index 3779f34..13ebb16 100644 --- a/c3d/manager.py +++ b/c3d/manager.py @@ -1,4 +1,4 @@ -''' Defines the base class containing common attributes for both the Reader and Writer instances. +''' Manager base class defining common attributes for both the Reader and Writer instances. ''' import numpy as np import warnings From c0ec8d67dbcf127045dad56063bbb27bce66c756 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 21:46:33 +0200 Subject: [PATCH 057/120] Removed the sphinx-better-theme documentation --- docs/Makefile | 153 -------------------------------- docs/_static/style-tweaks.css | 1 - docs/_templates/gitwidgets.html | 4 - docs/conf.py | 62 ------------- docs/index.rst | 66 -------------- docs/reference.rst | 13 --- docs/requirements.txt | 2 - 7 files changed, 301 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/_static/style-tweaks.css delete mode 100644 docs/_templates/gitwidgets.html delete mode 100644 docs/conf.py delete mode 100644 docs/index.rst delete mode 100644 docs/reference.rst delete mode 100644 docs/requirements.txt diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 7a05fd9..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,153 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - -rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/c3d.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/c3d.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/c3d" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/c3d" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. 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The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/_static/style-tweaks.css b/docs/_static/style-tweaks.css deleted file mode 100644 index 825e6f1..0000000 --- a/docs/_static/style-tweaks.css +++ /dev/null @@ -1 +0,0 @@ -a tt, a:visited tt, a:active tt { color: #369; } diff --git a/docs/_templates/gitwidgets.html b/docs/_templates/gitwidgets.html deleted file mode 100644 index ccc4c9d..0000000 --- a/docs/_templates/gitwidgets.html +++ /dev/null @@ -1,4 +0,0 @@ -
- - -
diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 9d308c6..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,62 +0,0 @@ -import better - -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.autosummary', - # 'sphinx.ext.doctest', - 'sphinx.ext.intersphinx', - 'sphinx.ext.mathjax', - # 'sphinx.ext.pngmath', - 'sphinx.ext.viewcode', - 'numpydoc', - ] -autosummary_generate = True -autodoc_default_flags = ['members'] -numpydoc_show_class_members = False -numpydoc_show_inherited_class_members = True -source_suffix = '.rst' -source_encoding = 'utf-8-sig' -master_doc = 'index' -project = u'C3D' -copyright = u'2015, Leif Johnson' -version = '0.3' -release = '0.3.1pre' -exclude_patterns = ['_build'] -templates_path = ['_templates'] -pygments_style = 'tango' - -html_theme = 'better' -html_theme_path = [better.better_theme_path] -html_theme_options = dict( - rightsidebar=False, - inlinecss='', - cssfiles=['_static/style-tweaks.css'], - showheader=True, - showrelbartop=True, - showrelbarbottom=True, - linktotheme=True, - sidebarwidth='15rem', - textcolor='#111', - headtextcolor='#333', - footertextcolor='#333', - ga_ua='', - ga_domain='', -) -html_short_title = 'Home' -html_static_path = ['_static'] - - -def h(xs): - return ['{}.html'.format(x) for x in xs.split()] - - -html_sidebars = { - 'index': h('gitwidgets globaltoc sourcelink searchbox'), - '**': h('gitwidgets localtoc sourcelink searchbox'), -} - -intersphinx_mapping = { - 'python': ('http://docs.python.org/', None), - 'numpy': ('http://docs.scipy.org/doc/numpy/', None), - 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), -} diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index d8cd9dc..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,66 +0,0 @@ -===================== -Python C3D Processing -===================== - -This package provides a single Python module for reading and writing binary -motion-capture files in the `C3D file format`_. - -.. _C3D file format: https://www.c3d.org/HTML/default.htm - -Examples -======== - -Reading -------- - -To read the frames of a C3D file, use a :class:`Reader ` instance:: - - import c3d - - reader = c3d.Reader(open('my-motion.c3d', 'rb')) - for i, points, analog in reader.read_frames(): - print('frame {}: point {}, analog {}'.format( - i, points.shape, analog.shape) - -The :func:`read_frames ` method generates tuples -containing the frame index, a ``numpy`` array of point data, and a ``numpy`` -array of analog data. - -Writing -------- - -To write data frames to a C3D file, use a :class:`Writer ` -instance:: - - import c3d - import numpy as np - - writer = c3d.Writer() - for _ in range(100): - writer.add_frame(np.random.randn(30, 5)) - with open('random-points.c3d', 'wb') as h: - writer.write(h) - -The :func:`add_frame ` method takes a ``numpy`` array of -point data---and, optionally, a ``numpy`` array of analog data---and adds it to -an internal data buffer. The :func:`write ` method serializes -all of the frame data to a C3D binary file. - -Command-Line Scripts -==================== - -The ``c3d`` package also contains several command-line scripts. - -Two of these scripts convert C3D binary data to other formats: -- ``c3d2csv``: Converts C3D data to comma-separated values. -- ``c3d2npz``: Converts C3D data to serialized ``numpy`` arrays. - -The ``c3d-metadata`` script simply prints out the metadata from a C3D file. - -Finally, the ``c3d-viewer`` script provides a basic OpenGL viewer for C3D data. -This script depends on ``pyglet``. - -.. toctree:: - :maxdepth: 2 - - reference diff --git a/docs/reference.rst b/docs/reference.rst deleted file mode 100644 index bfbb4e5..0000000 --- a/docs/reference.rst +++ /dev/null @@ -1,13 +0,0 @@ -========= -Reference -========= - -.. automodule:: c3d - :no-members: - :no-inherited-members: - -.. autosummary:: - :toctree: generated/ - - Reader - Writer diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index e10c929..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -numpydoc -sphinx-better-theme From 9f2728de8763b0e325cdedbe0f66ddca2215c618 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sat, 3 Jul 2021 23:09:03 +0200 Subject: [PATCH 058/120] examples.md --- c3d/__init__.py | 13 +++++++++++++ c3d/writer.py | 2 +- docs/examples.md | 43 +++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 57 insertions(+), 1 deletion(-) create mode 100644 docs/examples.md diff --git a/c3d/__init__.py b/c3d/__init__.py index 3a4dfbc..e6ed081 100644 --- a/c3d/__init__.py +++ b/c3d/__init__.py @@ -1,3 +1,16 @@ +""" +===================== +Python C3D Processing +===================== + +This package provides a single Python module for reading and writing binary +motion-capture files in the [C3D file format]. + +[C3D file format]: https://www.c3d.org/HTML/default.htm + +.. include:: ../docs/examples.md + +""" from . import dtypes from . import group from . import header diff --git a/c3d/writer.py b/c3d/writer.py index 2029f1e..289ddb6 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -204,7 +204,7 @@ def add_frames(self, frames, index=None): frames : Single or sequence of (point, analog) pairs A sequence or frame of frame data to add to the writer. index : int or None - Insert the frame or sequence at the index (the first sequence frame will be inserted at give index). + Insert the frame or sequence at the index (the first sequence frame will be inserted at the given `index`). Note that the index should be relative to 0 rather then the frame number provided by read_frames()! ''' sh = np.shape(frames) diff --git a/docs/examples.md b/docs/examples.md new file mode 100644 index 0000000..7b23cd3 --- /dev/null +++ b/docs/examples.md @@ -0,0 +1,43 @@ + + +Examples +======== + +Reading +------- + +To read the frames from a C3D file, use a `c3d.reader.Reader` instance: + +>>> import c3d +>>> +>>> reader = c3d.Reader(open('my-motion.c3d', 'rb')) +>>> for i, points, analog in reader.read_frames(): +>>> print('frame {}: point {}, analog {}'.format( +>>> i, points.shape, analog.shape) + +The method `c3d.reader.Reader.read_frames` generates tuples +containing the trial frame index, a ``numpy`` array of point data, +and a ``numpy`` array of analog data. + +Writing +------- + +To write data frames to a C3D file, use a `c3d.writer.Writer` +instance: + +>>> import c3d +>>> import numpy as np +>>> +>>> writer = c3d.Writer() +>>> for _ in range(100): +>>> writer.add_frame(np.random.randn(30, 5)) +>>> with open('random-points.c3d', 'wb') as h: +>>> writer.write(h) + +The function `c3d.writer.Writer.add_frames` takes ``numpy`` array of +point data---and, optionally, a ``numpy`` array of analog data---and adds it to +an internal data buffer. The :func:`write ` method serializes +all of the frame data to a C3D binary file. + +Editing +------- From eb875c260d277b89447fa770715a72e710e71ef8 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 12:40:47 +0200 Subject: [PATCH 059/120] Moved pack_labels() -> utils Added check for frame shape in Writer.add_frames() Documentation --- c3d/utils.py | 37 +++++++++++++++++ c3d/writer.py | 109 ++++++++++++++++++++++++-------------------------- 2 files changed, 90 insertions(+), 56 deletions(-) diff --git a/c3d/utils.py b/c3d/utils.py index 0c28231..8f81e9a 100644 --- a/c3d/utils.py +++ b/c3d/utils.py @@ -7,15 +7,52 @@ def is_integer(value): '''Check if value input is integer.''' return isinstance(value, (int, np.int32, np.int64)) + def is_iterable(value): '''Check if value is iterable.''' return hasattr(value, '__iter__') + def type_npy2struct(dtype): ''' Convert numpy dtype format to a struct package format string. ''' return dtype.byteorder + dtype.char + +def pack_labels(labels): + ''' Static method used to pack and pad the set of `labels` strings before + passing the output into a `c3d.group.Group.add_str`. + + Parameters + ---------- + labels : iterable + List of strings to pack and pad into a single string suitable for encoding in a Parameter entry. + + Example + ------- + >>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3'] + >>> param_str, label_max_size = Writer.pack_labels(labels) + >>> writer.point_group.add_str('LABELS', + 'Point labels.', + label_str, + label_max_size, + len(labels)) + + Returns + ------- + param_str : str + String containing `labels` packed into a single variable where + each string is padded to match the longest `labels` string. + label_max_size : int + Number of bytes associated with the longest `label` string, all strings are padded to this length. + ''' + labels = np.ravel(labels) + # Get longest label name + label_max_size = 0 + label_max_size = max(label_max_size, np.max([len(label) for label in labels])) + label_str = ''.join(label.ljust(label_max_size) for label in labels) + return label_str, label_max_size + class Decorator(object): '''Base class for extending (decorating) a python object. ''' diff --git a/c3d/writer.py b/c3d/writer.py index 289ddb6..2a272d9 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -4,10 +4,9 @@ import numpy as np import struct #import warnings +from . import utils from .manager import Manager from .dtypes import DataTypes -from .utils import is_integer, is_iterable - class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -55,15 +54,27 @@ def __init__(self, @staticmethod def from_reader(reader, conversion=None): ''' + + Parameters + ---------- source : `c3d.manager.Manager` Source to copy. conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: - 'consume' - (Default) Reader object will be consumed and explicitly deleted. + + 'consume' - (Default) Reader object will be + consumed and explicitly deleted. + 'copy' - Reader objects will be deep copied. - 'copy_metadata' - Similar to 'copy' but only copies metadata and not point and analog frame data. - 'copy_shallow' - Similar to 'copy' but group parameters are not copied. - 'copy_header' - Similar to 'copy_shallow' but only the header is copied (frame data is not copied). + + 'copy_metadata' - Similar to 'copy' but only copies metadata and + not point and analog frame data. + + 'copy_shallow' - Similar to 'copy' but group parameters are + not copied. + + 'copy_header' - Similar to 'copy_shallow' but only the + header is copied (frame data is not copied). Returns ------- @@ -209,13 +220,30 @@ def add_frames(self, frames, index=None): ''' sh = np.shape(frames) # Single frame - if len(sh) != 2: + if len(sh) < 2: frames = [frames] sh = np.shape(frames) + + # Check data shapes match + if len(self._frames) > 0: + point0, analog0 = self._frames[0] + psh, ash = np.shape(point0), np.shape(analog0) + for f in frames: + if np.shape(f[0]) != psh: + raise ValueError( + 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( + str(psh), str(np.shape(f[0])) + )) + if np.shape(f[1]) != ash: + raise ValueError( + 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( + str(ash), str(np.shape(f[1])) + )) + # Sequence of invalid shape if sh[1] != 2: raise ValueError( - 'Expected frame input to be sequence of point and analog pairs on form (-1, 2). ' + + 'Expected frame input to be sequence of point and analog pairs on form (None, 2). ' + 'Input was of shape {}.'.format(str(sh))) if index is not None: @@ -223,52 +251,21 @@ def add_frames(self, frames, index=None): else: self._frames.extend(frames) - @staticmethod - def pack_labels(labels): - ''' Static method used to pack and pad the set of `labels` strings before - passing the output into a `c3d.group.Group.add_str`. - - Parameters - ---------- - labels : iterable - List of strings to pack and pad into a single string suitable for encoding in a Parameter entry. - - Example - ------- - >>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3'] - >>> param_str, label_max_size = Writer.pack_labels(labels) - >>> writer.point_group.add_str('LABELS', - 'Point labels.', - label_str, - label_max_size, - len(labels)) - - Returns - ------- - param_str : str - String containing `labels` packed into a single variable where - each string is padded to match the longest `labels` string. - label_max_size : int - Number of bytes associated with the longest `label` string, all strings are padded to this length. - ''' - labels = np.ravel(labels) - # Get longest label name - label_max_size = 0 - label_max_size = max(label_max_size, np.max([len(label) for label in labels])) - label_str = ''.join(label.ljust(label_max_size) for label in labels) - return label_str, label_max_size - def set_point_labels(self, labels): ''' Set point data labels. ''' - label_str, label_max_size = Writer.pack_labels(labels) + label_str, label_max_size = utils.pack_labels(labels) self.point_group.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) def set_analog_labels(self, labels): ''' Set analog data labels. ''' - label_str, label_max_size = Writer.pack_labels(labels) - self.analog_group.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) + grp = self.analog_group + if labels is None: + grp.add_empty_array('LABELS', 'Analog labels.', -1) + else: + label_str, label_max_size = utils.pack_labels(labels) + grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) def set_analog_general_scale(self, value): ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor). @@ -283,7 +280,7 @@ def set_analog_scales(self, values): values : iterable or None Iterable containing individual scale factors for encoding analog channel data. ''' - if is_iterable(values): + if utils.is_iterable(values): data = np.array([v for v in values], dtype=np.float32) self.analog_group.set_array('SCALE', 'Analog channel scale factors', data) elif values is None: @@ -299,7 +296,7 @@ def set_analog_offsets(self, values): values : iterable or None Iterable containing individual offsets for encoding analog channel data. ''' - if is_iterable(values): + if utils.is_iterable(values): data = np.array([v for v in values], dtype=np.int16) self.analog_group.set_array('OFFSET', 'Analog channel offsets', data) elif values is None: @@ -310,8 +307,8 @@ def set_analog_offsets(self, values): def set_start_frame(self, frame=1): ''' Set the 'TRIAL:ACTUAL_START_FIELD' parameter and header.first_frame entry. - Parameter - --------- + Parameters + ---------- frame : int Number for the first frame recorded in the file. Frame counter for a trial recording always start at 1 for the first frame. @@ -332,11 +329,11 @@ def _set_last_frame(self, frame): def set_screen_axis(self, X='+X', Y='+Y'): ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. - Parameter - --------- + Parameters + ---------- X : str - 2 character string with first character indicating positive or negative axis (+/-), - and the second axis (X/Y/Z). Examples: '+X' or '-Y' + Two byte string with first character indicating positive or negative axis (+/-), + and the second axis (X/Y/Z). Example strings '+X' or '-Y' Y : str Second axis string with same format as Y. Determines the second Y screen axis. ''' @@ -349,7 +346,7 @@ def set_screen_axis(self, X='+X', Y='+Y'): group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y) def write(self, handle): - '''Write metadata and point + analog frames to a file handle. + '''Write metadata, point and analog frames to a file handle. Parameters ---------- @@ -415,7 +412,7 @@ def write(self, handle): self.get('POINT:DATA_START').bytes = struct.pack(' Date: Sun, 4 Jul 2021 12:42:55 +0200 Subject: [PATCH 060/120] Changed metadata warning for existence of POINT/ANALOG data to not consider cases when respective LABEL entry exists but is empty. --- c3d/manager.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/c3d/manager.py b/c3d/manager.py index 13ebb16..eb858a3 100644 --- a/c3d/manager.py +++ b/c3d/manager.py @@ -104,11 +104,20 @@ def check_parameters(params): if self.point_used > 0: check_parameters(('POINT:LABELS', 'POINT:DESCRIPTIONS')) else: - warnings.warn('No point data found in file.') + lab = self.get('POINT:LABELS') + if lab is None: + warnings.warn('No point data found in file.') + elif lab.num_elements > 0: + warnings.warn('No point data found in file, but file contains POINT:LABELS entries') if self.analog_used > 0: check_parameters(('ANALOG:LABELS', 'ANALOG:DESCRIPTIONS')) else: - warnings.warn('No analog data found in file.') + lab = self.get('ANALOG:LABELS') + if lab is None: + warnings.warn('No analog data found in file.') + elif lab.num_elements > 0: + warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries') + def _add_group(self, group_id, name=None, desc=None): '''Add a new parameter group. From 1f9860a683499ee83dd6bacfb112a10b6bb060da Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 12:57:17 +0200 Subject: [PATCH 061/120] Allow None to be passed to set_xxx_labels --- c3d/writer.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/c3d/writer.py b/c3d/writer.py index 2a272d9..bd6dbe9 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -253,12 +253,26 @@ def add_frames(self, frames, index=None): def set_point_labels(self, labels): ''' Set point data labels. + + Parameters + ---------- + labels : iterable + Set POINT:LABELS parameter entry from a set of string labels. ''' - label_str, label_max_size = utils.pack_labels(labels) - self.point_group.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) + grp = self.point_group + if labels is None: + grp.add_empty_array('LABELS', 'Point labels.', -1) + else: + label_str, label_max_size = utils.pack_labels(labels) + grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) def set_analog_labels(self, labels): ''' Set analog data labels. + + Parameters + ---------- + labels : iterable + Set ANALOG:LABELS parameter entry from a set of string labels. ''' grp = self.analog_group if labels is None: From cebf825e1de6a2a1147868515c3681dbc1078ccb Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 12:57:46 +0200 Subject: [PATCH 062/120] Examples --- docs/examples.md | 2 +- examples/write.py | 17 +++++++++++++++++ test/test_examples.py | 24 ++++++++++++++++++++++++ 3 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 examples/write.py create mode 100644 test/test_examples.py diff --git a/docs/examples.md b/docs/examples.md index 7b23cd3..0e52b22 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -36,7 +36,7 @@ instance: The function `c3d.writer.Writer.add_frames` takes ``numpy`` array of point data---and, optionally, a ``numpy`` array of analog data---and adds it to -an internal data buffer. The :func:`write ` method serializes +an internal data buffer. The function `c3d.writer.Writer.write` serializes all of the frame data to a C3D binary file. Editing diff --git a/examples/write.py b/examples/write.py new file mode 100644 index 0000000..10dcd8e --- /dev/null +++ b/examples/write.py @@ -0,0 +1,17 @@ +import numpy as np +try: + import c3d +except ModuleNotFoundError: + import sys + import os + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d + + +writer = c3d.Writer() +for _ in range(100): + writer.add_frames((np.random.randn(30, 5), ())) +writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2']) +writer.set_analog_labels(None) +with open('random-points.c3d', 'wb') as h: + writer.write(h) diff --git a/test/test_examples.py b/test/test_examples.py new file mode 100644 index 0000000..5d274d7 --- /dev/null +++ b/test/test_examples.py @@ -0,0 +1,24 @@ +''' Tests for the documentation examples +''' +import c3d +import io +import unittest +import numpy as np +from test.base import Base + +import sys +import os +sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\examples')) + + +class Examples(Base): + ''' Test basic writer functionality + ''' + def test_write(self): + import write + # Raises 'FileNotFound' if the file was not generated + os.remove('..\\random-points.c3d') + + +if __name__ == '__main__': + unittest.main() From 146ab40fa223866d7be56e0047aa4fee49d2fccc Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 13:55:21 +0200 Subject: [PATCH 063/120] Writing example --- docs/examples.md | 39 ++++++++++++++++++++++++++------------- examples/write.py | 14 ++++++++++---- test/test_examples.py | 10 +++++++++- 3 files changed, 45 insertions(+), 18 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index 0e52b22..b63b734 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -25,19 +25,32 @@ Writing To write data frames to a C3D file, use a `c3d.writer.Writer` instance: ->>> import c3d ->>> import numpy as np ->>> ->>> writer = c3d.Writer() ->>> for _ in range(100): ->>> writer.add_frame(np.random.randn(30, 5)) ->>> with open('random-points.c3d', 'wb') as h: ->>> writer.write(h) - -The function `c3d.writer.Writer.add_frames` takes ``numpy`` array of -point data---and, optionally, a ``numpy`` array of analog data---and adds it to -an internal data buffer. The function `c3d.writer.Writer.write` serializes -all of the frame data to a C3D binary file. + import c3d + import numpy as np + + # Writes 100 frames recorded at 200 Hz. + # Each frame contains recordings for 24 coordinate markers. + writer = c3d.Writer(point_rate=200) + for _ in range(100): + writer.add_frames((np.random.randn(24, 5), ())) + + writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'RFT4', + 'LFT1', 'LFT2', 'LFT3', 'LFT4', + 'RSK1', 'RSK2', 'RSK3', 'RSK4', + 'LSK1', 'LSK2', 'LSK3', 'LSK4', + 'RTH1', 'RTH2', 'RTH3', 'RTH4', + 'LTH1', 'LTH2', 'LTH3', 'LTH4' + ]) + writer.set_analog_labels(None) + + with open('random-points.c3d', 'wb') as h: + writer.write(h) + +The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` +or python arrays. First array in each frame tuple contains the point +data and the second analog data for the frame. References of the data +are tracked until `c3d.writer.Writer.write` is called, serializing all +data frames to a C3D binary file. Editing ------- diff --git a/examples/write.py b/examples/write.py index 10dcd8e..6d0b83c 100644 --- a/examples/write.py +++ b/examples/write.py @@ -7,11 +7,17 @@ sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) import c3d - -writer = c3d.Writer() +# Writes 100 frames recorded at 200 Hz. +# Each frame contains recordings for 24 coordinate markers. +writer = c3d.Writer(point_rate=200) for _ in range(100): - writer.add_frames((np.random.randn(30, 5), ())) -writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2']) + writer.add_frames((np.random.randn(24, 5), ())) + +writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'RFT4', 'LFT1', 'LFT2', 'LFT3', 'LFT4', + 'RSK1', 'RSK2', 'RSK3', 'RSK4', 'LSK1', 'LSK2', 'LSK3', 'LSK4', + 'RTH1', 'RTH2', 'RTH3', 'RTH4', 'LTH1', 'LTH2', 'LTH3', 'LTH4' + ]) writer.set_analog_labels(None) + with open('random-points.c3d', 'wb') as h: writer.write(h) diff --git a/test/test_examples.py b/test/test_examples.py index 5d274d7..0d3d2a7 100644 --- a/test/test_examples.py +++ b/test/test_examples.py @@ -16,8 +16,16 @@ class Examples(Base): ''' def test_write(self): import write + path = 'random-points.c3d' + + with open(path, 'rb') as f: + reader = c3d.Reader(f) + assert reader.frame_count == 100, \ + 'Expected 30 point frames in write.py test, was {}'.format(reader.frame_count) + assert reader.point_used == 24, \ + 'Expected 5 point samples in write.py test, was {}'.format(reader.point_used) # Raises 'FileNotFound' if the file was not generated - os.remove('..\\random-points.c3d') + os.remove(path) if __name__ == '__main__': From aeaebd066f5896a70c67e0d04445a19b100c0a7c Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 14:04:51 +0200 Subject: [PATCH 064/120] Reading example --- docs/examples.md | 12 ++++++------ test/test_examples.py | 3 +++ 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index b63b734..830c239 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -8,12 +8,12 @@ Reading To read the frames from a C3D file, use a `c3d.reader.Reader` instance: ->>> import c3d ->>> ->>> reader = c3d.Reader(open('my-motion.c3d', 'rb')) ->>> for i, points, analog in reader.read_frames(): ->>> print('frame {}: point {}, analog {}'.format( ->>> i, points.shape, analog.shape) + import c3d + + reader = c3d.Reader(open('my-motion.c3d', 'rb')) + for i, points, analog in reader.read_frames(): + print('frame {}: point {}, analog {}'.format( + i, points.shape, analog.shape) The method `c3d.reader.Reader.read_frames` generates tuples containing the trial frame index, a ``numpy`` array of point data, diff --git a/test/test_examples.py b/test/test_examples.py index 0d3d2a7..aad4f8c 100644 --- a/test/test_examples.py +++ b/test/test_examples.py @@ -14,6 +14,9 @@ class Examples(Base): ''' Test basic writer functionality ''' + def test_read(self): + import read + def test_write(self): import write path = 'random-points.c3d' From 0a99ed6d9da801d84eabf099e90fd0ca11447c04 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 14:22:14 +0200 Subject: [PATCH 065/120] Example documentation --- docs/examples.md | 24 +++++++++++++----------- examples/write.py | 1 + 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index 830c239..54cdc77 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -10,14 +10,15 @@ To read the frames from a C3D file, use a `c3d.reader.Reader` instance: import c3d - reader = c3d.Reader(open('my-motion.c3d', 'rb')) - for i, points, analog in reader.read_frames(): - print('frame {}: point {}, analog {}'.format( - i, points.shape, analog.shape) + with open(file_path, 'rb') as file: + reader = c3d.Reader(file) + for i, points, analog in reader.read_frames(): + print('frame {}: point {}, analog {}'.format( + i, points.shape, analog.shape)) The method `c3d.reader.Reader.read_frames` generates tuples -containing the trial frame index, a ``numpy`` array of point data, -and a ``numpy`` array of analog data. +containing the trial frame number, a ``numpy`` array of point +data, and a ``numpy`` array of analog data. Writing ------- @@ -46,11 +47,12 @@ instance: with open('random-points.c3d', 'wb') as h: writer.write(h) -The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` -or python arrays. First array in each frame tuple contains the point -data and the second analog data for the frame. References of the data -are tracked until `c3d.writer.Writer.write` is called, serializing all -data frames to a C3D binary file. +The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` or python +arrays. First array in each frame tuple contains the point data and the second +contains analog data for the frame, leaving one of the arrays empty indicates +no analog --- or point data--- should be included in the file. References of the +data arrays are tracked until `c3d.writer.Writer.write` is called, serializing +metadata and data frames to a C3D binary file. Editing ------- diff --git a/examples/write.py b/examples/write.py index 6d0b83c..6a05b73 100644 --- a/examples/write.py +++ b/examples/write.py @@ -2,6 +2,7 @@ try: import c3d except ModuleNotFoundError: + # Force load package with no instalation import sys import os sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) From 9bef84129a858cb9dc1215135f69d9c6c89a6de8 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 15:03:53 +0200 Subject: [PATCH 066/120] Documentation --- c3d/__init__.py | 6 +++--- c3d/reader.py | 10 +++++++++- docs/examples.md | 14 ++++++++------ 3 files changed, 20 insertions(+), 10 deletions(-) diff --git a/c3d/__init__.py b/c3d/__init__.py index e6ed081..b985753 100644 --- a/c3d/__init__.py +++ b/c3d/__init__.py @@ -1,9 +1,9 @@ """ -===================== +--------------------- Python C3D Processing -===================== +--------------------- -This package provides a single Python module for reading and writing binary +This package provides pure Python modules for reading, writing, and editing binary motion-capture files in the [C3D file format]. [C3D file format]: https://www.c3d.org/HTML/default.htm diff --git a/c3d/reader.py b/c3d/reader.py index d5abca4..2e0d4cf 100644 --- a/c3d/reader.py +++ b/c3d/reader.py @@ -114,6 +114,14 @@ def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_s return a unique data buffer for each frame. Set this to False if you consume frames as you iterate over them, or True if you store them for later. + analog_transform : bool, default=True + If True, ANALOG:SCALE, ANALOG:GEN_SCALE, and ANALOG:OFFSET transforms + available in the file are applied to the analog channels. + check_nan : bool, default=True + If True, point x,y,z coordinates with nan values will be marked invalidated + and residuals will be set to -1. + camera_sum : bool, default=False + Camera flag bits will be summed, converting the fifth column to a camera visibility counter. Returns ------- @@ -241,7 +249,7 @@ def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_s # Fifth value is the camera-observation byte if camera_sum: # Convert to observation sum - points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(8)) + points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7)) else: points[:, 4] = camera_byte #.astype(np.float32) diff --git a/docs/examples.md b/docs/examples.md index 54cdc77..4b4f336 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -3,6 +3,8 @@ Examples ======== +Access to data blocks in a .c3d file is provided through the `c3d.reader.Reader` and `c3d.writer.Writer` classes. + Reading ------- @@ -47,12 +49,12 @@ instance: with open('random-points.c3d', 'wb') as h: writer.write(h) -The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` or python -arrays. First array in each frame tuple contains the point data and the second -contains analog data for the frame, leaving one of the arrays empty indicates -no analog --- or point data--- should be included in the file. References of the -data arrays are tracked until `c3d.writer.Writer.write` is called, serializing -metadata and data frames to a C3D binary file. +The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` or ``python +arrays``, with the first array in each tuple defining point data and the second +defining the analog data for the frame. Leaving one of the arrays empty indicates +to the writer that no analog --- or point data--- should be included in the file. +References of the data arrays are tracked until `c3d.writer.Writer.write` +is called, which serializes metadata and data frames into a C3D binary file stream. Editing ------- From 56a5d8f42a9d64aa92b687736fb3b475ceb1c566 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 15:36:11 +0200 Subject: [PATCH 067/120] Edit example --- docs/examples.md | 19 ++++++++++++++++++- examples/edit.py | 21 +++++++++++++++++++++ examples/my-looped-motion.c3d | Bin 0 -> 311808 bytes examples/my-motion.c3d | Bin 0 -> 156672 bytes examples/read.py | 18 ++++++++++++++++++ test/test_examples.py | 10 ++++++++++ 6 files changed, 67 insertions(+), 1 deletion(-) create mode 100644 examples/edit.py create mode 100644 examples/my-looped-motion.c3d create mode 100644 examples/my-motion.c3d create mode 100644 examples/read.py diff --git a/docs/examples.md b/docs/examples.md index 4b4f336..6917c66 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -12,7 +12,7 @@ To read the frames from a C3D file, use a `c3d.reader.Reader` instance: import c3d - with open(file_path, 'rb') as file: + with open('my-motion.c3d', 'rb') as file: reader = c3d.Reader(file) for i, points, analog in reader.read_frames(): print('frame {}: point {}, analog {}'.format( @@ -58,3 +58,20 @@ is called, which serializes metadata and data frames into a C3D binary file stre Editing ------- + +Editing c3d files is possible by combining the use of `c3d.reader.Reader` and `c3d.writer.Writer` +instances through the use of `c3d.reader.Reader.to_writer`. By opening a .c3d file stream through +a reader instance, `c3d.reader.Reader.to_writer` can be used to create an independent Writer instance +copying the file contents onto the heap. Rereading the `reader` frame data from the file +and inserting the frames in reverse, a looped version of the .c3d file can be created! + + import c3d + + with open('my-motion.c3d', 'rb') as file: + reader = c3d.Reader(file) + writer = reader.to_writer('copy') + for i, points, analog in reader.read_frames(): + writer.add_frames((points, analog), index=reader.frame_count) + + with open('my-looped-motion.c3d', 'wb') as h: + writer.write(h) diff --git a/examples/edit.py b/examples/edit.py new file mode 100644 index 0000000..c1c9444 --- /dev/null +++ b/examples/edit.py @@ -0,0 +1,21 @@ +import numpy as np +import os +try: + import c3d +except ModuleNotFoundError: + # Force load package with no instalation + import sys + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d + +# My motion == Sample01.Eb015pi.c3d +file_path = os.path.join(os.path.dirname(__file__), 'my-motion.c3d') + +with open(file_path, 'rb') as file: + reader = c3d.Reader(file) + writer = reader.to_writer('copy') + for i, points, analog in reader.read_frames(): + writer.add_frames((points, analog), index=reader.frame_count) + +with open('my-looped-motion.c3d', 'wb') as h: + writer.write(h) diff --git a/examples/my-looped-motion.c3d b/examples/my-looped-motion.c3d new file mode 100644 index 0000000000000000000000000000000000000000..428d5b1d59f917c921d677692ba36aa9cbc77d85 GIT binary patch literal 311808 zcmeFad3+P~`Zhe7Nivh!6VimHO`8Crl$N!$>@5Y#zS#l-F33_8*=a!**->!=K~Mn& z_XR{nSyU8MHbn&y1l&*rcac@#keTGYzWH|Aa6ISvz3=mWp1&SBpB!3dk~UYa`@XJw znUU=mU^*~1W+5js>({MoUyHFb4AZS6{_meZ*C5ckDTnW8dK-86^plr6OltpIhieZ1 zfBeQ~v;FNErQJJ)O1qVXO8fT>{q5lYv43#)cf|Yk?cS%qpYi53>KvLlVf6UQ(8OVr zhm9+*ET3E<+d7w&bt>)NuYdQxeacp|aW>@b+`X)SlU~LBLtXmz?H~I4pYDCi`j_<|-Y?M+L&^lyeob3F2T;cGmaO1t52JWBiZ z3-!XIv<%H|6ZxN)ISdMMO+bVcQ`@gvGZ`IVy&Yn>e<-!fESLTHL#& ztTxVC$hrGZs2nynG>RmZ(1;0B##f5A&c*$Uhayf&`!~ZmwU~xoMo+G&42>LCIV?1M z?1T|xaN_vNVWY>7#s^2AS@qhD9k#Mg#l1@EK&*&prB;!FJhNiNu(63J3>#57VY1y; 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+
+
+

Module c3d.dtypes

+
+
+

State object defining the data types associated with a given .c3d processor format.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class DataTypes +(proc_type=84) +
+
+

Container defining the data types used when parsing byte data. +Data types depend on the processor format the file is stored in.

+

Instance variables

+
+
var big_endian_sys : bool
+
+

True if native byte order is big-endian.

+
+
var is_dec : bool
+
+

True if the associated file is in the DEC format.

+
+
var is_ieee : bool
+
+

True if the associated file is in the Intel format.

+
+
var is_mips : bool
+
+

True if the associated file is in the SGI/MIPS format.

+
+
var little_endian_sys : bool
+
+

True if native byte order is little-endian.

+
+
var native : bool
+
+

True if the native (system) byte order matches the file byte order.

+
+
var proc_type : str
+
+

Get the processory type associated with the data format in the file.

+
+
var processor : int
+
+

Get the processor number encoded in the .c3d file.

+
+
+

Methods

+
+
+def decode_string(self, bytes) ‑> str +
+
+

Decode a byte array to a string.

+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/group.html b/docs/c3d/group.html new file mode 100644 index 0000000..15d8f73 --- /dev/null +++ b/docs/c3d/group.html @@ -0,0 +1,536 @@ + + + + + + +c3d.group API documentation + + + + + + + + + + + +
+
+
+

Module c3d.group

+
+
+

Classes used to represent the concept of parameter groups in a .c3d file.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Group +(data) +
+
+

Wrapper exposing readable and writeable attributes of a GroupData entry.

+

Ancestors

+ +

Instance variables

+
+
var desc : str
+
+

Get or set descriptor.

+
+
var name : str
+
+

Get or set name.

+
+
+

Methods

+
+
+def add(self, name, desc, bpe, format, data, *dimensions) +
+
+

Add a parameter with data package formated in accordance with format.

+

Convenience function for GroupData.add_param() calling struct.pack() on data.

+

Example:

+
>>> group.set('RATE', 'Point data sample rate', 4, '<f', 100)
+
+

Parameters

+
+
name : str
+
Parameter name.
+
desc : str
+
Parameter descriptor.
+
bpe : int
+
Number of bytes for each atomic element.
+
format : str or None
+
struct.format() compatible format string see: +https://docs.python.org/3/library/struct.html#format-characters
+
*dimensions : int, optional
+
Shape associated with the data (if the data argument represents multiple elements).
+
+
+
+def add_array(self, name, desc, data, dtype=None) +
+
+

Add a parameter with the data package.

+

Parameters

+
+
name : str
+
Parameter name.
+
desc : str
+
Parameter descriptor.
+
data : np.ndarray, or iterable
+
Data array to encode in the parameter.
+
dtype : np.dtype, optional
+
Numpy data type used to encode the array (optional only if data.dtype returns a numpy type).
+
+
+
+def add_empty_array(self, name, desc='', bpe=1) +
+
+

Add an empty parameter block.

+

Parameters

+
+
name : str
+
Parameter name.
+
+
+
+def add_param(self, name, **kwargs) +
+
+

Add a parameter to this group.

+

See constructor of ParamData for additional keyword arguments.

+
+
+def add_str(self, name, desc, data, *dimensions) +
+
+

Add a string parameter.

+

Parameters

+
+
name : str
+
Parameter name.
+
desc : str
+
Parameter descriptor.
+
data : str
+
String to encode in the parameter.
+
*dimensions : int, optional
+
Shape associated with the string (if the string represents multiple elements).
+
+
+
+def get(self, key, default=None) +
+
+

Get a parameter by key.

+

Parameters

+
+
key : any
+
Parameter key to look up in this group.
+
default : any, optional
+
Value to return if the key is not found. Defaults to None.
+
+

Returns

+
+
param : :class:ParamReadable``
+
A parameter from the current group.
+
+
+
+def items(self) +
+
+

Iterator for paramater key-entry pairs.

+
+
+def readonly(self) +
+
+

Returns a GroupReadonly instance with readonly access.

+
+
+def remove_param(self, name) +
+
+

Remove the specified parameter.

+

Parameters

+
+
name : str
+
Name for the parameter to remove.
+
+
+
+def rename_param(self, name, new_name) +
+
+

Rename a specified parameter group.

+

Parameters

+

See arguments in GroupData.rename_param().

+
+
+def set(self, name, *args, **kwargs) +
+
+

Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'.

+

See arguments in Group.add().

+
+
+def set_array(self, name, *args, **kwargs) +
+
+

Add or overwrite a parameter with the data package.

+

See arguments in Group.add_array().

+
+
+def set_empty_array(self, name, *args, **kwargs) +
+
+

Add an empty parameter block.

+

See arguments in Group.add_empty_array().

+
+
+def set_str(self, name, *args, **kwargs) +
+
+

Add or overwrite a string parameter.

+

See arguments in Group.add_str().

+
+
+def values(self) +
+
+

Iterator iterator for parameter entries.

+
+
+

Inherited members

+ +
+
+class GroupData +(dtypes, name=None, desc=None) +
+
+

A group of parameters stored in a C3D file.

+

In C3D files, parameters are organized in groups. Each group has a name (key), a +description, and a set of named parameters. Each group is also internally associated +with a numeric key.

+

Attributes

+
+
dtypes : DataTypes
+
Data types object used for parsing.
+
name : str
+
Name of this parameter group.
+
desc : str
+
Description for this parameter group.
+
+

Instance variables

+
+
var binary_size : int
+
+

Return the number of bytes to store this group and its parameters.

+
+
+

Methods

+
+
+def add_param(self, name, **kwargs) +
+
+

Add a parameter to this group.

+

Parameters

+
+
name : str
+
Name of the parameter to add to this group. The name will +automatically be case-normalized.
+
+

See constructor of ParamData for additional keyword arguments.

+

Raises

+
+
TypeError
+
Input arguments are of the wrong type.
+
KeyError
+
Name or numerical key already exist (attempt to overwrite existing data).
+
+
+
+def remove_param(self, name) +
+
+

Remove the specified parameter.

+

Parameters

+
+
name : str
+
Name for the parameter to remove.
+
+
+
+def rename_param(self, name, new_name) +
+
+

Rename a specified parameter group.

+

Parameters

+
+
name : str, or GroupReadonly
+
Parameter instance, or name.
+
new_name : str
+
New name for the parameter.
+
+

Raises

+
+
KeyError
+
If no parameter with the original name exists.
+
ValueError
+
If the new name already exist (attempt to overwrite existing data).
+
+
+
+def set_desc(self, desc) +
+
+

Set the Group descriptor.

+
+
+def set_name(self, name) +
+
+

Set the group name string.

+
+
+def write(self, group_id, handle) +
+
+

Write this parameter group, with parameters, to a file handle.

+

Parameters

+
+
group_id : int
+
The numerical ID of the group.
+
handle : file handle
+
An open, writable, binary file handle.
+
+
+
+
+
+class GroupReadonly +(data) +
+
+

Wrapper exposing readonly attributes of a GroupData entry.

+

Subclasses

+ +

Instance variables

+
+
var desc : str
+
+

Access group descriptor.

+
+
var name : str
+
+

Access group name.

+
+
+

Methods

+
+
+def get(self, key, default=None) +
+
+

Get a readonly parameter by key.

+

Parameters

+
+
key : any
+
Parameter key to look up in this group.
+
default : any, optional
+
Value to return if the key is not found. Defaults to None.
+
+

Returns

+
+
param : :class:ParamReadable``
+
A parameter from the current group.
+
+
+
+def get_bytes(self, key) +
+
+

Get the value of the given parameter as a byte array.

+
+
+def get_float(self, key) +
+
+

Get the value of the given parameter as a 32-bit float.

+
+
+def get_int16(self, key) +
+
+

Get the value of the given parameter as a 16-bit signed integer.

+
+
+def get_int32(self, key) +
+
+

Get the value of the given parameter as a 32-bit signed integer.

+
+
+def get_int8(self, key) +
+
+

Get the value of the given parameter as an 8-bit signed integer.

+
+
+def get_string(self, key) +
+
+

Get the value of the given parameter as a string.

+
+
+def get_uint16(self, key) +
+
+

Get the value of the given parameter as a 16-bit unsigned integer.

+
+
+def get_uint32(self, key) +
+
+

Get the value of the given parameter as a 32-bit unsigned integer.

+
+
+def get_uint8(self, key) +
+
+

Get the value of the given parameter as an 8-bit unsigned integer.

+
+
+def items(self) +
+
+

Get iterator for paramater key-entry pairs.

+
+
+def keys(self) +
+
+

Get iterator for parameter entry keys.

+
+
+def values(self) +
+
+

Get iterator for parameter entries.

+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/header.html b/docs/c3d/header.html new file mode 100644 index 0000000..e29382b --- /dev/null +++ b/docs/c3d/header.html @@ -0,0 +1,206 @@ + + + + + + +c3d.header API documentation + + + + + + + + + + + +
+
+
+

Module c3d.header

+
+
+

Defines the header class used for reading, writing and tracking metadata in the .c3d header.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Header +(handle=None) +
+
+

Header information from a C3D file.

+

Attributes

+
+
event_block : int
+
Index of the 512-byte block where labels (metadata) are found.
+
parameter_block : int
+
Index of the 512-byte block where parameters (metadata) are found.
+
data_block : int
+
Index of the 512-byte block where data starts.
+
point_count : int
+
Number of motion capture channels recorded in this file.
+
analog_count : int
+
Number of analog values recorded per frame of 3D point data.
+
first_frame : int
+
Index of the first frame of data.
+
last_frame : int
+
Index of the last frame of data.
+
analog_per_frame : int
+
Number of analog frames per frame of 3D point data. The analog frame +rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE) +times the analog per frame value.
+
frame_rate : float
+
The frame rate of the recording, in frames per second.
+
scale_factor : float
+
Multiply values in the file by this scale parameter.
+
long_event_labels : bool
+
 
+
max_gap : int
+
 
+
+
+

Note

+

The scale_factor attribute is not used in Phasespace C3D files; +instead, use the POINT.SCALE parameter.

+
+
+

Note

+

The first_frame and last_frame header attributes are not used in +C3D files generated by Phasespace. Instead, the first and last +frame numbers are stored in the POINTS:ACTUAL_START_FIELD and +POINTS:ACTUAL_END_FIELD parameters.

+
+

Create a new Header object.

+

Parameters

+
+
handle : file handle, optional
+
If given, initialize attributes for the Header from this file +handle. The handle must be seek-able and readable. If handle is +not given, Header attributes are initialized with default values.
+
+

Class variables

+
+
var BINARY_FORMAT_READ
+
+
+
+
var BINARY_FORMAT_READ_BIG_ENDIAN
+
+
+
+
var BINARY_FORMAT_WRITE
+
+
+
+
+

Instance variables

+
+
var events
+
+

Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label).

+

Note*: +Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter. +Frame 1 therefor has the time 0.0 in relation to the event timing.

+
+
+

Methods

+
+
+def encode_events(self, events) +
+
+

Encode event data in the event block.

+

Parameters

+
+
events : [(float, str), …]
+
Event data, iterable of touples containing the event timing and a 4 character label string. +Event timings should be calculated relative to sample 1 with the timing 0.0s, and should +not be relative to the first_frame header parameter.
+
+
+
+def read(self, handle, fmt='<BBHHHHHIHHI274sHHH164s44s') +
+
+

Read and parse binary header data from a file handle.

+

This method reads exactly 512 bytes from the beginning of the given file +handle.

+

Parameters

+
+
handle : file handle
+
The given handle will be reset to 0 using seek and then 512 bytes +will be read to initialize the attributes in this Header. The handle +must be readable.
+
+

fmt : Formating string used to read the header.

+

Raises

+
+
AssertionError
+
If the magic byte from the header is not 80 (the C3D magic value).
+
+
+
+def write(self, handle) +
+
+

Write binary header data to a file handle.

+

This method writes exactly 512 bytes to the beginning of the given file +handle.

+

Parameters

+
+
handle : file handle
+
The given handle will be reset to 0 using seek and then 512 bytes +will be written to describe the parameters in this Header. The +handle must be writeable.
+
+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/index.html b/docs/c3d/index.html new file mode 100644 index 0000000..cac4396 --- /dev/null +++ b/docs/c3d/index.html @@ -0,0 +1,176 @@ + + + + + + +c3d API documentation + + + + + + + + + + + +
+
+
+

Package c3d

+
+
+
+

Python C3D Processing

+

This package provides pure Python modules for reading, writing, and editing binary +motion-capture files in the C3D file format.

+

Scripts

+

The package installation comes with some pre-packaged scripts for +viewing, and converting .c3d files to .csv and .npz formats. +See the script directory on github for more information.

+

Examples

+

Access to data blocks in a .c3d file is provided through the Reader and Writer classes. +Runnable implementation of the examples are provided in the examples/ directory in the github repository.

+

Reading

+

To read the frames from a C3D file, use a Reader instance:

+
import c3d
+
+with open('my-motion.c3d', 'rb') as file:
+    reader = c3d.Reader(file)
+    for i, points, analog in reader.read_frames():
+        print('frame {}: point {}, analog {}'.format(
+              i, points.shape, analog.shape))
+
+

The method Reader.read_frames() generates tuples +containing the trial frame number, a numpy array of point +data, and a numpy array of analog data.

+

Writing

+

To write data frames to a C3D file, use a Writer +instance:

+
import c3d
+import numpy as np
+
+# Writes 100 frames recorded at 200 Hz.
+# Each frame contains recordings for 24 coordinate markers.
+writer = c3d.Writer(point_rate=200)
+for _ in range(100):
+    writer.add_frames((np.random.randn(24, 5), ()))
+
+writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'RFT4',
+                         'LFT1', 'LFT2', 'LFT3', 'LFT4',
+                         'RSK1', 'RSK2', 'RSK3', 'RSK4',
+                         'LSK1', 'LSK2', 'LSK3', 'LSK4',
+                         'RTH1', 'RTH2', 'RTH3', 'RTH4',
+                         'LTH1', 'LTH2', 'LTH3', 'LTH4'
+                        ])
+writer.set_analog_labels(None)
+
+with open('random-points.c3d', 'wb') as h:
+    writer.write(h)
+
+

The function Writer.add_frames() take pairs of numpy or python +arrays, with the first array in each tuple defining point data and the second +defining the analog data for the frame. Leaving one of the arrays empty indicates +to the writer that no analog — or point data— should be included in the file. +References of the data arrays are tracked until Writer.write() +is called, which serializes metadata and data frames into a C3D binary file stream.

+

Editing

+

Editing c3d files is possible by combining the use of Reader and Writer +instances through the use of Reader.to_writer(). By opening a .c3d file stream through +a reader instance, Reader.to_writer() can be used to create an independent Writer instance +copying the file contents onto the heap. Rereading the c3d.reader frame data from the file +and inserting the frames in reverse, a looped version of the .c3d file can be created!

+
import c3d
+
+with open('my-motion.c3d', 'rb') as file:
+    reader = c3d.Reader(file)
+    writer = reader.to_writer('copy')
+    for i, points, analog in reader.read_frames():
+        writer.add_frames((points, analog), index=reader.frame_count)
+
+with open('my-looped-motion.c3d', 'wb') as h:
+    writer.write(h)
+
+
+
+

Sub-modules

+
+
c3d.dtypes
+
+

State object defining the data types associated with a given .c3d processor format.

+
+
c3d.group
+
+

Classes used to represent the concept of parameter groups in a .c3d file.

+
+
c3d.header
+
+

Defines the header class used for reading, writing and tracking metadata in the .c3d header.

+
+
c3d.manager
+
+

Manager base class defining common attributes for both the Reader and Writer instances.

+
+
c3d.parameter
+
+

Classes used to represent the concept of a parameter in a .c3d file.

+
+
c3d.reader
+
+

A Python module for reading and writing C3D files.

+
+
c3d.utils
+
+

Trailing utility functions.

+
+
c3d.writer
+
+

A Python module for reading and writing C3D files.

+
+
+
+
+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html new file mode 100644 index 0000000..f0ce4b0 --- /dev/null +++ b/docs/c3d/manager.html @@ -0,0 +1,306 @@ + + + + + + +c3d.manager API documentation + + + + + + + + + + + +
+
+
+

Module c3d.manager

+
+
+

Manager base class defining common attributes for both the Reader and Writer instances.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Manager +(header=None) +
+
+

A base class for managing C3D file metadata.

+

This class manages a C3D header (which contains some stock metadata fields) +as well as a set of parameter groups. Each group is accessible using its +name.

+

Attributes

+
+
header : Header
+
Header information for the C3D file.
+
+

Set up a new Manager with a Header.

+

Subclasses

+ +

Instance variables

+
+
var analog_labels : list
+
+

Labels for each ANALOG data channel.

+
+
var analog_per_frame : int
+
+

Number of analog frames per 3D frame (point sample).

+
+
var analog_rate : float
+
+

Number of analog data samples per second.

+
+
var analog_sample_count : int
+
+

Number of analog samples per channel.

+
+
var analog_used : int
+
+

Number of analog measurements, or channels, for each analog data sample.

+
+
var first_frame : int
+
+

Trial frame corresponding to the first frame recorded in the data.

+
+
var frame_count : int
+
+

Number of frames recorded in the data.

+
+
var header : `Header`
+
+

Access to .c3d header data.

+
+
var last_frame : int
+
+

Trial frame corresponding to the last frame recorded in the data (inclusive).

+
+
var point_labels : list
+
+

Labels for each POINT data channel.

+
+
var point_rate : float
+
+

Number of sampled 3D coordinates per second.

+
+
var point_scale : float
+
+

Scaling applied to non-float data.

+
+
var point_used : int
+
+

Number of sampled 3D point coordinates per frame.

+
+
+

Methods

+
+
+def get(self, group, default=None) +
+
+

Get a group or parameter.

+

Parameters

+
+
group : str
+
If this string contains a period (.), then the part before the +period will be used to retrieve a group, and the part after the +period will be used to retrieve a parameter from that group. If this +string does not contain a period, then just a group will be +returned.
+
default : any
+
Return this value if the named group and parameter are not found.
+
+

Returns

+
+
value : Group or Param
+
Either a group or parameter with the specified name(s). If neither +is found, returns the default value.
+
+
+
+def get_analog_transform(self) +
+
+

Get broadcastable analog transformation parameters.

+
+
+def get_analog_transform_parameters(self) +
+
+

Parse analog data transform parameters.

+
+
+def get_bytes(self, key) +
+
+

Get a parameter value as a byte string.

+
+
+def get_float(self, key) +
+
+

Get a parameter value as a 32-bit float.

+
+
+def get_int16(self, key) +
+
+

Get a parameter value as a 16-bit signed integer.

+
+
+def get_int32(self, key) +
+
+

Get a parameter value as a 32-bit signed integer.

+
+
+def get_int8(self, key) +
+
+

Get a parameter value as an 8-bit signed integer.

+
+
+def get_screen_axis(self) +
+
+

Get the X_SCREEN and Y_SCREEN parameters in the POINT group.

+

Returns

+
+
value : (str, str) or None
+
Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+
+
+
+def get_string(self, key) +
+
+

Get a parameter value as a string.

+
+
+def get_uint16(self, key) +
+
+

Get a parameter value as a 16-bit unsigned integer.

+
+
+def get_uint32(self, key) +
+
+

Get a parameter value as a 32-bit unsigned integer.

+
+
+def get_uint8(self, key) +
+
+

Get a parameter value as an 8-bit unsigned integer.

+
+
+def items(self) +
+
+

Get iterable over pairs of (str, Group) entries.

+
+
+def keys(self) +
+
+

Get iterable over parameter name keys.

+
+
+def listed(self) +
+
+

Get iterable over pairs of (int, Group) entries.

+
+
+def parameter_blocks(self) ‑> int +
+
+

Compute the size (in 512B blocks) of the parameter section.

+
+
+def values(self) +
+
+

Get iterable over Group entries.

+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/parameter.html b/docs/c3d/parameter.html new file mode 100644 index 0000000..1d62160 --- /dev/null +++ b/docs/c3d/parameter.html @@ -0,0 +1,401 @@ + + + + + + +c3d.parameter API documentation + + + + + + + + + + + +
+
+
+

Module c3d.parameter

+
+
+

Classes used to represent the concept of a parameter in a .c3d file.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Param +(data) +
+
+

Wrapper exposing both readable and writable attributes of a ParamData entry.

+

Ancestors

+ +

Instance variables

+
+
var bytes : bytes
+
+

Get or set the parameter bytes.

+
+
+

Methods

+
+
+def readonly(self) +
+
+

Returns a readonly ParamReadonly instance.

+
+
+

Inherited members

+ +
+
+class ParamData +(name, dtype, desc='', bytes_per_element=1, dimensions=None, bytes=b'', handle=None) +
+
+

A class representing a single named parameter from a C3D file.

+

Attributes

+
+
name : str
+
Name of this parameter.
+
dtype : DataTypes
+
Reference to the DataTypes object associated with the file.
+
desc : str
+
Brief description of this parameter.
+
bytes_per_element : int, optional
+
For array data, this describes the size of each element of data. For +string data (including arrays of strings), this should be -1.
+
dimensions : list of int
+
For array data, this describes the dimensions of the array, stored in +column-major (Fortran) order. For arrays of strings, the dimensions here will be +the number of columns (length of each string) followed by the number of +rows (number of strings).
+
bytes : str
+
Raw data for this parameter.
+
+

Set up a new parameter, only the name is required.

+

Instance variables

+
+
var binary_size : int
+
+

Return the number of bytes needed to store this parameter.

+
+
var num_elements : int
+
+

Return the number of elements in this parameter's array value.

+
+
var total_bytes : int
+
+

Return the number of bytes used for storing this parameter's data.

+
+
+

Methods

+
+
+def read(self, handle) +
+
+

Read binary data for this parameter from a file handle.

+

This reads exactly enough data from the current position in the file to +initialize the parameter.

+
+
+def write(self, group_id, handle) +
+
+

Write binary data for this parameter to a file handle.

+

Parameters

+
+
group_id : int
+
The numerical ID of the group that holds this parameter.
+
handle : file handle
+
An open, writable, binary file handle.
+
+
+
+
+
+class ParamReadonly +(data) +
+
+

Wrapper exposing readonly attributes of a ParamData entry.

+

Subclasses

+ +

Instance variables

+
+
var binary_size : int
+
+

Return the number of bytes needed to store this parameter.

+
+
var bytes_array
+
+

Get the param as an array of raw byte strings.

+
+
var bytes_per_element : int
+
+

Return the number of bytes used to store each data element.

+
+
var bytes_value
+
+

Get the param as a raw byte string.

+
+
var desc : str
+
+

Get the parameter descriptor.

+
+
var dimensions : (, Ellipsis)
+
+

Shape of the parameter data (Fortran shape).

+
+
var dtypes
+
+

Convenience accessor to the DataTypes instance associated with the parameter.

+
+
var float32_array
+
+

Get the param as an array of 32-bit floats.

+
+
var float64_array
+
+

Get the param as an array of 64-bit floats.

+
+
var float_array
+
+

Get the param as an array of 32 or 64 bit floats.

+
+
var float_value
+
+

Get the param as a floating point value of appropriate type.

+
+
var int16_array
+
+

Get the param as an array of 16-bit signed integers.

+
+
var int16_value
+
+

Get the param as a 16-bit signed integer.

+
+
var int32_array
+
+

Get the param as an array of 32-bit signed integers.

+
+
var int32_value
+
+

Get the param as a 32-bit signed integer.

+
+
var int64_array
+
+

Get the param as an array of 32-bit signed integers.

+
+
var int8_array
+
+

Get the param as an array of 8-bit signed integers.

+
+
var int8_value
+
+

Get the param as an 8-bit signed integer.

+
+
var int_array
+
+

Get the param as an array of integer values.

+
+
var int_value
+
+

Get the param as a signed integer of appropriate type.

+
+
var name : str
+
+

Get the parameter name.

+
+
var num_elements : int
+
+

Return the number of elements in this parameter's array value.

+
+
var string_array
+
+

Get the param as a python array of unicode strings.

+
+
var string_value
+
+

Get the param as a unicode string.

+
+
var total_bytes : int
+
+

Return the number of bytes used for storing this parameter's data.

+
+
var uint16_array
+
+

Get the param as an array of 16-bit unsigned integers.

+
+
var uint16_value
+
+

Get the param as a 16-bit unsigned integer.

+
+
var uint32_array
+
+

Get the param as an array of 32-bit unsigned integers.

+
+
var uint32_value
+
+

Get the param as a 32-bit unsigned integer.

+
+
var uint64_array
+
+

Get the param as an array of 32-bit unsigned integers.

+
+
var uint8_array
+
+

Get the param as an array of 8-bit unsigned integers.

+
+
var uint8_value
+
+

Get the param as an 8-bit unsigned integer.

+
+
var uint_array
+
+

Get the param as an array of integer values.

+
+
var uint_value
+
+

Get the param as a unsigned integer of appropriate type.

+
+
+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html new file mode 100644 index 0000000..a9eac9d --- /dev/null +++ b/docs/c3d/reader.html @@ -0,0 +1,239 @@ + + + + + + +c3d.reader API documentation + + + + + + + + + + + +
+
+
+

Module c3d.reader

+
+
+

A Python module for reading and writing C3D files.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Reader +(handle) +
+
+

This class provides methods for reading the data in a C3D file.

+

A C3D file contains metadata and frame-based data describing 3D motion.

+

You can iterate over the frames in the file by calling read_frames() after +construction:

+
>>> r = c3d.Reader(open('capture.c3d', 'rb'))
+>>> for frame_no, points, analog in r.read_frames():
+...     print('{0.shape} points in this frame'.format(points))
+
+

Initialize this C3D file by reading header and parameter data.

+

Parameters

+
+
handle : file handle
+
Read metadata and C3D motion frames from the given file handle. This +handle is assumed to be seek-able and read-able. The handle must +remain open for the life of the Reader instance. The Reader does +not close the handle.
+
+

Raises

+
+
AssertionError
+
If the metadata in the C3D file is inconsistent.
+
+

Ancestors

+ +

Instance variables

+
+
var proc_type : int
+
+

Get the processory type associated with the data format in the file.

+
+
+

Methods

+
+
+def get(self, key, default=None) +
+
+

Get a readonly group or parameter.

+

Parameters

+
+
key : str
+
If this string contains a period (.), then the part before the +period will be used to retrieve a group, and the part after the +period will be used to retrieve a parameter from that group. If this +string does not contain a period, then just a group will be +returned.
+
default : any
+
Return this value if the named group and parameter are not found.
+
+

Returns

+
+
value : GroupReadonly or ParamReadonly
+
Either a group or parameter with the specified name(s). If neither +is found, returns the default value.
+
+
+
+def items(self) +
+
+

Get iterable over pairs of (str, GroupReadonly) entries.

+
+
+def listed(self) +
+
+

Get iterable over pairs of (int, GroupReadonly) entries.

+
+
+def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False) +
+
+

Iterate over the data frames from our C3D file handle.

+

Parameters

+
+
copy : bool
+
If False, the reader returns a reference to the same data buffers +for every frame. The default is True, which causes the reader to +return a unique data buffer for each frame. Set this to False if you +consume frames as you iterate over them, or True if you store them +for later.
+
analog_transform : bool, default=True
+
If True, ANALOG:SCALE, ANALOG:GEN_SCALE, and ANALOG:OFFSET transforms +available in the file are applied to the analog channels.
+
check_nan : bool, default=True
+
If True, point x,y,z coordinates with nan values will be marked invalidated +and residuals will be set to -1.
+
camera_sum : bool, default=False
+
Camera flag bits will be summed, converting the fifth column to a camera visibility counter.
+
+

Returns

+
+
frames : sequence of (frame number, points, analog)
+
+

This method generates a sequence of (frame number, points, analog) +tuples, one tuple per frame. The first element of each tuple is the +frame number. The second is a numpy array of parsed, 5D point data +and the third element of each tuple is a numpy array of analog +values that were recorded during the frame. (Often the analog data +are sampled at a higher frequency than the 3D point data, resulting +in multiple analog frames per frame of point data.)

+

The first three columns in the returned point data are the (x, y, z) +coordinates of the observed motion capture point. The fourth column +is an estimate of the error for this particular point, and the fifth +column is the number of cameras that observed the point in question. +Both the fourth and fifth values are -1 if the point is considered +to be invalid.

+
+
+
+
+def to_writer(self, conversion=None) +
+
+

Converts the reader to a Writer instance using the conversion mode.

+

See Writer.from_reader() for supported conversion modes.

+
+
+def values(self) +
+
+

Get iterable over GroupReadonly entries.

+
+
+

Inherited members

+ +
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/utils.html b/docs/c3d/utils.html new file mode 100644 index 0000000..9560227 --- /dev/null +++ b/docs/c3d/utils.html @@ -0,0 +1,163 @@ + + + + + + +c3d.utils API documentation + + + + + + + + + + + +
+
+
+

Module c3d.utils

+
+
+

Trailing utility functions.

+
+
+
+
+
+
+

Functions

+
+
+def DEC_to_IEEE(uint_32) +
+
+

Convert the 32 bit representation of a DEC float to IEEE format.

+

Params:

+

uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits. +Returns : IEEE formated floating point of the same shape as the input.

+
+
+def DEC_to_IEEE_BYTES(bytes) +
+
+

Convert byte array containing 32 bit DEC floats to IEEE format.

+

Params:

+

bytes : Byte array where every 4 bytes represent a single precision DEC float. +Returns : IEEE formated floating point of the same shape as the input.

+
+
+def UNPACK_FLOAT_IEEE(uint_32) +
+
+

Unpacks a single 32 bit unsigned int to a IEEE float representation

+
+
+def UNPACK_FLOAT_MIPS(uint_32) +
+
+

Unpacks a single 32 bit unsigned int to a IEEE float representation

+
+
+def is_integer(value) +
+
+

Check if value input is integer.

+
+
+def is_iterable(value) +
+
+

Check if value is iterable.

+
+
+def pack_labels(labels) +
+
+

Static method used to pack and pad the set of labels strings before +passing the output into a Group.add_str().

+

Parameters

+
+
labels : iterable
+
List of strings to pack and pad into a single string suitable for encoding in a Parameter entry.
+
+

Example

+
>>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3']
+>>> param_str, label_max_size = Writer.pack_labels(labels)
+>>> writer.point_group.add_str('LABELS',
+                               'Point labels.',
+                               label_str,
+                               label_max_size,
+                               len(labels))
+
+

Returns

+
+
param_str : str
+
String containing labels packed into a single variable where +each string is padded to match the longest labels string.
+
label_max_size : int
+
Number of bytes associated with the longest label string, all strings are padded to this length.
+
+
+
+def type_npy2struct(dtype) +
+
+

Convert numpy dtype format to a struct package format string.

+
+
+
+
+

Classes

+
+
+class Decorator +(decoratee) +
+
+

Base class for extending (decorating) a python object.

+
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html new file mode 100644 index 0000000..2ba71a3 --- /dev/null +++ b/docs/c3d/writer.html @@ -0,0 +1,355 @@ + + + + + + +c3d.writer API documentation + + + + + + + + + + + +
+
+
+

Module c3d.writer

+
+
+

A Python module for reading and writing C3D files.

+
+
+
+
+
+
+
+
+

Classes

+
+
+class Writer +(point_rate=480.0, analog_rate=0.0, point_scale=-1.0) +
+
+

This class writes metadata and frames to a C3D file.

+

For example, to read an existing C3D file, apply some sort of data +processing to the frames, and write out another C3D file::

+
>>> r = c3d.Reader(open('data.c3d', 'rb'))
+>>> w = c3d.Writer()
+>>> w.add_frames(process_frames_somehow(r.read_frames()))
+>>> with open('smoothed.c3d', 'wb') as handle:
+>>>     w.write(handle)
+
+

Parameters

+
+
point_rate : float, optional
+
The frame rate of the data. Defaults to 480.
+
analog_rate : float, optional
+
The number of analog samples per frame. Defaults to 0.
+
point_scale : float, optional
+
The scale factor for point data. Defaults to -1 (i.e., "check the +POINT:SCALE parameter").
+
point_units : str, optional
+
The units that the point numbers represent. Defaults to 'mm +'.
+
gen_scale : float, optional
+
General scaling factor for analog data. Defaults to 1.
+
+

Set minimal metadata for this writer.

+

Ancestors

+ +

Static methods

+
+
+def from_reader(reader, conversion=None) +
+
+

Parameters

+
+
source : Manager
+
Source to copy.
+
conversion : str
+
Conversion mode, None is equivalent to the default mode. Supported modes are:
'consume'       - (Default) Reader object will be
+                  consumed and explicitly deleted.
+
+'copy'          - Reader objects will be deep copied.
+
+'copy_metadata' - Similar to 'copy' but only copies metadata and
+                  not point and analog frame data.
+
+'copy_shallow'  - Similar to 'copy' but group parameters are
+                  not copied.
+
+'copy_header'   - Similar to 'copy_shallow' but only the
+                  header is copied (frame data is not copied).
+
+
+
+

Returns

+
+
param : :class:Writer``
+
A writeable and persistent representation of the 'Reader' object.
+
+

Raises

+
+
ValueError
+
If mode string is not equivalent to one of the supported modes. +If attempting to convert non-Intel files using mode other than 'shallow_copy'.
+
+
+
+

Instance variables

+
+
var analog_group
+
+

Get or create the ANALOG parameter group.

+
+
var numeric_key_max
+
+

Get the largest numeric key.

+
+
var numeric_key_next
+
+

Get a new unique numeric group key.

+
+
var point_group
+
+

Get or create the POINT parameter group.

+
+
var trial_group
+
+

Get or create the TRIAL parameter group.

+
+
+

Methods

+
+
+def add_frames(self, frames, index=None) +
+
+

Add frames to this writer instance.

+

Parameters

+
+
frames : Single or sequence of (point, analog) pairs
+
A sequence or frame of frame data to add to the writer.
+
index : int or None
+
Insert the frame or sequence at the index (the first sequence frame will be inserted at the given index). +Note that the index should be relative to 0 rather then the frame number provided by read_frames()!
+
+
+
+def add_group(self, group_id, name, desc) +
+
+

Add a new parameter group. See Manager.add_group() for more information.

+

Returns

+
+
group : :class:Group``
+
An editable group instance.
+
+
+
+def get_create(self, label) +
+
+

Get or create the specified parameter group.

+
+
+def remove_group(self, *args) +
+
+

Remove the parameter group. (see Manager._rename_group for args).

+
+
+def rename_group(self, *args) +
+
+

Rename a specified parameter group (see Manager._rename_group for args).

+
+
+def set_analog_general_scale(self, value) +
+
+

Set ANALOG:GEN_SCALE factor (uniform analog scale factor).

+
+
+def set_analog_labels(self, labels) +
+
+

Set analog data labels.

+

Parameters

+
+
labels : iterable
+
Set ANALOG:LABELS parameter entry from a set of string labels.
+
+
+
+def set_analog_offsets(self, values) +
+
+

Set ANALOG:OFFSET offsets (per channel offset).

+

Parameters

+
+
values : iterable or None
+
Iterable containing individual offsets for encoding analog channel data.
+
+
+
+def set_analog_scales(self, values) +
+
+

Set ANALOG:SCALE factors (per channel scale factor).

+

Parameters

+
+
values : iterable or None
+
Iterable containing individual scale factors for encoding analog channel data.
+
+
+
+def set_point_labels(self, labels) +
+
+

Set point data labels.

+

Parameters

+
+
labels : iterable
+
Set POINT:LABELS parameter entry from a set of string labels.
+
+
+
+def set_screen_axis(self, X='+X', Y='+Y') +
+
+

Set the X_SCREEN and Y_SCREEN parameters in the POINT group.

+

Parameters

+
+
X : str
+
Two byte string with first character indicating positive or negative axis (+/-), +and the second axis (X/Y/Z). Example strings '+X' or '-Y'
+
Y : str
+
Second axis string with same format as Y. Determines the second Y screen axis.
+
+
+
+def set_start_frame(self, frame=1) +
+
+

Set the 'TRIAL:ACTUAL_START_FIELD' parameter and header.first_frame entry.

+

Parameters

+
+
frame : int
+
Number for the first frame recorded in the file. +Frame counter for a trial recording always start at 1 for the first frame.
+
+
+
+def write(self, handle) +
+
+

Write metadata, point and analog frames to a file handle.

+

Parameters

+
+
handle : file
+
Write metadata and C3D motion frames to the given file handle. The +writer does not close the handle.
+
+
+
+

Inherited members

+ +
+
+
+
+ +
+ + + \ No newline at end of file diff --git a/docs/examples.md b/docs/examples.md index 4c77c3a..69f396d 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -1,10 +1,17 @@ +Scripts +======== + +The package installation comes with some pre-packaged scripts for +viewing, and converting .c3d files to .csv and .npz formats. +See the [script directory] on github for more information. +[script directory]: ../scripts Examples ======== Access to data blocks in a .c3d file is provided through the `c3d.reader.Reader` and `c3d.writer.Writer` classes. -Implementation of the examples are provided in the `example/` in the github repository. +Runnable implementation of the examples are provided in the `examples/` directory in the github repository. Reading ------- From 7350a83bf0bfb40dcda30cb534e364ea16769b8b Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 16:52:26 +0200 Subject: [PATCH 071/120] Set theme jekyll-theme-cayman --- docs/_config.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/_config.yml diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..c419263 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1 @@ +theme: jekyll-theme-cayman \ No newline at end of file From 06517464466e232117f50907c7bf5ed0effc5226 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 16:56:02 +0200 Subject: [PATCH 072/120] Links --- docs/examples.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index 69f396d..d07e75a 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -3,15 +3,17 @@ Scripts The package installation comes with some pre-packaged scripts for viewing, and converting .c3d files to .csv and .npz formats. -See the [script directory] on github for more information. +See the [scripts/] directory on github for more information. -[script directory]: ../scripts +[scripts/]: https://github.com/EmbodiedCognition/py-c3d/tree/master/scripts Examples ======== Access to data blocks in a .c3d file is provided through the `c3d.reader.Reader` and `c3d.writer.Writer` classes. -Runnable implementation of the examples are provided in the `examples/` directory in the github repository. +Runnable implementation of the examples are provided in the [examples/] directory in the github repository. + +[examples/]: https://github.com/EmbodiedCognition/py-c3d/tree/master/examples Reading ------- From 277ecd39f32826bd25d2fd10b5fdfa8e407362e1 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 16:59:58 +0200 Subject: [PATCH 073/120] index.md --- docs/index.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 docs/index.md diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..78faf4e --- /dev/null +++ b/docs/index.md @@ -0,0 +1,3 @@ +{{ define "html" }} +{{ with .GetPage "/c3d" }}{{.Render}}{{end}} +{{ end }} From 9567309ddc45feef2000648b747cbf85e2173457 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 17:05:15 +0200 Subject: [PATCH 074/120] Test readme --- docs/README.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 docs/README.md diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..78faf4e --- /dev/null +++ b/docs/README.md @@ -0,0 +1,3 @@ +{{ define "html" }} +{{ with .GetPage "/c3d" }}{{.Render}}{{end}} +{{ end }} From 3df5e624fac1f089313bc690d13ad1bb0906ca95 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 17:19:16 +0200 Subject: [PATCH 075/120] rst --- docs/README.md | 3 --- docs/README.rst | 11 +++++++++++ docs/index.md | 24 +++++++++++++++++++++--- 3 files changed, 32 insertions(+), 6 deletions(-) delete mode 100644 docs/README.md create mode 100644 docs/README.rst diff --git a/docs/README.md b/docs/README.md deleted file mode 100644 index 78faf4e..0000000 --- a/docs/README.md +++ /dev/null @@ -1,3 +0,0 @@ -{{ define "html" }} -{{ with .GetPage "/c3d" }}{{.Render}}{{end}} -{{ end }} diff --git a/docs/README.rst b/docs/README.rst new file mode 100644 index 0000000..1ae953a --- /dev/null +++ b/docs/README.rst @@ -0,0 +1,11 @@ +Building the docs +----------------- + + +Requirement for building the documentation is the pdoc3 package:: + + pip install pdoc3 + +and once installed the package can be built from the root directory with the command:: + + pdoc --html c3d --force --config show_source_code=False --output-dir docs diff --git a/docs/index.md b/docs/index.md index 78faf4e..f89b494 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,3 +1,21 @@ -{{ define "html" }} -{{ with .GetPage "/c3d" }}{{.Render}}{{end}} -{{ end }} + +Documentation +---------- + +https://mattiasfredriksson.github.io/py-c3d/c3d/ + + +Installing +---------- + +Currently pip installation is outdate, installation requires cloning the github +repository and build and install using the normal Python setup process:: + + git clone https://github.com/EmbodiedCognition/py-c3d + cd py-c3d + python setup.py install + + +or install the outdated version with pip:: + + pip install c3d From 7817533af3799b1c22f29611dd43e6dbc9df84f7 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 17:26:46 +0200 Subject: [PATCH 076/120] Links --- docs/README.rst | 7 ++++++- docs/index.md | 10 ++++++---- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/docs/README.rst b/docs/README.rst index 1ae953a..97630cd 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -1,3 +1,8 @@ +Reading the docs +----------------- + +Documentation is available at: https://mattiasfredriksson.github.io/py-c3d/c3d/ + Building the docs ----------------- @@ -6,6 +11,6 @@ Requirement for building the documentation is the pdoc3 package:: pip install pdoc3 -and once installed the package can be built from the root directory with the command:: +Once installed, documentation can be updated from the root directory with the command:: pdoc --html c3d --force --config show_source_code=False --output-dir docs diff --git a/docs/index.md b/docs/index.md index f89b494..2c99bf6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,15 +1,17 @@ -Documentation ----------- +* [Documentation] + +* [Scripts] -https://mattiasfredriksson.github.io/py-c3d/c3d/ +[Documentation]: https://mattiasfredriksson.github.io/py-c3d/c3d/ +[Scripts]: ../scripts Installing ---------- Currently pip installation is outdate, installation requires cloning the github -repository and build and install using the normal Python setup process:: +repository and installing using the Python setup process:: git clone https://github.com/EmbodiedCognition/py-c3d cd py-c3d From c02fd0821a1312668ece0aa0e31492dbef073281 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 18:41:03 +0200 Subject: [PATCH 077/120] doc main page update --- docs/README.rst | 6 +++++- docs/index.md | 8 ++++---- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/README.rst b/docs/README.rst index 97630cd..67926b7 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -7,10 +7,14 @@ Building the docs ----------------- -Requirement for building the documentation is the pdoc3 package:: +Building the docs requires the pdoc3 package:: pip install pdoc3 Once installed, documentation can be updated from the root directory with the command:: pdoc --html c3d --force --config show_source_code=False --output-dir docs + +Once updated you can access the documentation in the `docs/c3d/`_ folder. + +.. _docs/c3d/: docs/c3d/index.html diff --git a/docs/index.md b/docs/index.md index 2c99bf6..0828fc1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,20 +4,20 @@ * [Scripts] -[Documentation]: https://mattiasfredriksson.github.io/py-c3d/c3d/ -[Scripts]: ../scripts +[Documentation]: ./c3d/ +[Scripts]: https://github.com/EmbodiedCognition/py-c3d/tree/master/scripts Installing ---------- Currently pip installation is outdate, installation requires cloning the github -repository and installing using the Python setup process:: +repository and installing using the Python setup process: git clone https://github.com/EmbodiedCognition/py-c3d cd py-c3d python setup.py install -or install the outdated version with pip:: +or install the outdated version with pip: pip install c3d From c101962721ca74c5312f2215c283aac05859bc91 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 18:42:25 +0200 Subject: [PATCH 078/120] Docs --- docs/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/README.rst b/docs/README.rst index 67926b7..9fa877f 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -17,4 +17,4 @@ Once installed, documentation can be updated from the root directory with the co Once updated you can access the documentation in the `docs/c3d/`_ folder. -.. _docs/c3d/: docs/c3d/index.html +.. _docs/c3d/: ./c3d/index.html From 1c6fbced08a00b04cb4c9fa47d6a991f9994cc9b Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 18:44:26 +0200 Subject: [PATCH 079/120] Update README.rst Folder not index --- docs/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/README.rst b/docs/README.rst index 9fa877f..2003a97 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -17,4 +17,4 @@ Once installed, documentation can be updated from the root directory with the co Once updated you can access the documentation in the `docs/c3d/`_ folder. -.. _docs/c3d/: ./c3d/index.html +.. _docs/c3d/: ./c3d From d76722aec5ad2b70667500e811a2242765b4b016 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 19:02:33 +0200 Subject: [PATCH 080/120] Updated docs --- README.rst | 13 +------------ c3d/__init__.py | 7 +++++++ docs/c3d/index.html | 10 ++++------ docs/examples.md | 9 --------- test/README.rst | 10 ++++++++++ 5 files changed, 22 insertions(+), 27 deletions(-) create mode 100644 test/README.rst diff --git a/README.rst b/README.rst index b836757..751d6a9 100644 --- a/README.rst +++ b/README.rst @@ -29,7 +29,6 @@ This package includes scripts_ for converting C3D motion data to CSV format (``c3d2csv``) and an OpenGL-based visualization tool for observing the motion described by a C3D file (``c3d-viewer``). -.. _package documentation: http://c3d.readthedocs.org .. _scripts: ./scripts Library @@ -50,18 +49,8 @@ To use the C3D library, just import the package and create a ``Reader`` or You can also get and set metadata fields using the library; see the `package documentation`_ for more details. -.. _package documentation: http://c3d.readthedocs.org +.. _package documentation: https://mattiasfredriksson.github.io/py-c3d/c3d/ -Tests -~~~~~ - -To run tests available in the test folder, following command can be run from the root of the package directory:: - - python -m unittest discover . - -Test scripts will automatically download test files from `c3d.org`_. - -.. _c3d.org: https://www.c3d.org/sampledata.html Caveats ------- diff --git a/c3d/__init__.py b/c3d/__init__.py index b985753..5731759 100644 --- a/c3d/__init__.py +++ b/c3d/__init__.py @@ -8,6 +8,13 @@ [C3D file format]: https://www.c3d.org/HTML/default.htm +Installing +---------- + +See the [main page] https://mattiasfredriksson.github.io/py-c3d/ + +[C3D file format]: https://www.c3d.org/HTML/default.htm + .. include:: ../docs/examples.md """ diff --git a/docs/c3d/index.html b/docs/c3d/index.html index cac4396..158a29d 100644 --- a/docs/c3d/index.html +++ b/docs/c3d/index.html @@ -27,13 +27,11 @@

Package c3d

Python C3D Processing

This package provides pure Python modules for reading, writing, and editing binary motion-capture files in the C3D file format.

-

Scripts

-

The package installation comes with some pre-packaged scripts for -viewing, and converting .c3d files to .csv and .npz formats. -See the script directory on github for more information.

+

Installing

+

See the [main page] https://mattiasfredriksson.github.io/py-c3d/

Examples

Access to data blocks in a .c3d file is provided through the Reader and Writer classes. -Runnable implementation of the examples are provided in the examples/ directory in the github repository.

+Runnable implementation of the examples are provided in the examples/ directory in the github repository.

Reading

To read the frames from a C3D file, use a Reader instance:

import c3d
@@ -144,7 +142,7 @@ 
Index

 

 
    
 
  • Python C3D Processing
    • 
-
  • Scripts
    • 
+
  • Installing
    • 
 
  • Examples
      
 
    • Reading
      • 
 
    • Writing
      • 
diff --git a/docs/examples.md b/docs/examples.md
index d07e75a..27f0b05 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -1,12 +1,3 @@
-Scripts
-========
-
-The package installation comes with some pre-packaged scripts for
-viewing, and converting .c3d files to .csv and .npz formats.
-See the [scripts/] directory on github for more information.
-
-[scripts/]: https://github.com/EmbodiedCognition/py-c3d/tree/master/scripts
-
 Examples
 ========
 
diff --git a/test/README.rst b/test/README.rst
new file mode 100644
index 0000000..bf286c0
--- /dev/null
+++ b/test/README.rst
@@ -0,0 +1,10 @@
+Tests
+~~~~~
+
+To run tests, use the following command from the root of the package directory::
+
+    python -m unittest discover .
+
+Test scripts will automatically download test files from `c3d.org`_.
+
+.. _c3d.org: https://www.c3d.org/sampledata.html

From 58fe5422a97f1c9063489802f9d9023fe73eb596 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 19:13:48 +0200
Subject: [PATCH 081/120] corrected main page link

---
 README.rst          | 4 ++--
 c3d/__init__.py     | 4 ++--
 docs/c3d/index.html | 2 +-
 docs/index.md       | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index 751d6a9..b93d717 100644
--- a/README.rst
+++ b/README.rst
@@ -8,7 +8,7 @@ data recorded by a 3D motion tracking apparatus.
 Installing
 ----------
 
-Install with pip::
+Install with pip (currently outdated, download package from github instead)::
 
     pip install c3d
 
@@ -34,7 +34,7 @@ described by a C3D file (``c3d-viewer``).
 Library
 ~~~~~~~
 
-To use the C3D library, just import the package and create a ``Reader`` or
+To use the C3D library, just import the package and create a ``Reader`` and/or
 ``Writer`` depending on your intended usage
 
 .. code-block:: python
diff --git a/c3d/__init__.py b/c3d/__init__.py
index 5731759..be4619e 100644
--- a/c3d/__init__.py
+++ b/c3d/__init__.py
@@ -11,9 +11,9 @@
 Installing
 ----------
 
-See the [main page] https://mattiasfredriksson.github.io/py-c3d/
+See the [main page].
 
-[C3D file format]: https://www.c3d.org/HTML/default.htm
+[main page]: https://mattiasfredriksson.github.io/py-c3d/
 
 .. include:: ../docs/examples.md
 
diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index 158a29d..0474685 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -28,7 +28,7 @@ 
      Python C3D Processing
      
 
      This package provides pure Python modules for reading, writing, and editing binary
 motion-capture files in the C3D file format.
      
 
      Installing
      
-
      See the [main page] https://mattiasfredriksson.github.io/py-c3d/
      
+
      See the main page.
      
 
      Examples
      
 
      Access to data blocks in a .c3d file is provided through the Reader and Writer classes.
 Runnable implementation of the examples are provided in the examples/ directory in the github repository.
      
diff --git a/docs/index.md b/docs/index.md
index 0828fc1..5535bfa 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,7 +1,7 @@
 
 * [Documentation]
 
-* [Scripts]
+* [Tool scripts]
 
 
 [Documentation]: ./c3d/

From 647e06a9235a939f3daa67c18c19e05fa6d56b6e Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 4 Jul 2021 20:04:54 +0200
Subject: [PATCH 082/120] Update README.rst

---
 README.rst | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/README.rst b/README.rst
index b93d717..0af68d9 100644
--- a/README.rst
+++ b/README.rst
@@ -22,6 +22,8 @@ repository and build and install using the normal Python setup process::
 Usage
 -----
 
+Documentation and examples are available in the `package documentation`_.
+
 Tools
 ~~~~~
 
@@ -41,29 +43,32 @@ To use the C3D library, just import the package and create a ``Reader`` and/or
 
     import c3d
 
-    with open('data.c3d', 'rb') as handle:
-        reader = c3d.Reader(handle)
-        for i, (points, analog) in enumerate(reader.read_frames()):
-            print('Frame {}: {}'.format(i, points.round(2)))
+    with open('my-motion.c3d', 'rb') as file:
+        reader = c3d.Reader(file)
+        for i, points, analog in reader.read_frames():
+            print('frame {}: point {}, analog {}'.format(
+                  i, points.shape, analog.shape))
 
 You can also get and set metadata fields using the library; see the `package
 documentation`_ for more details.
 
 .. _package documentation: https://mattiasfredriksson.github.io/py-c3d/c3d/
 
-
 Caveats
 -------
 
-This library is minimally effective, in the sense that the only motion tracking
-system I have access to (for testing) is a Phasespace system. If you try out the
-library and find that it doesn't work with your motion tracking system, let me
-know. Pull requests are also welcome!
+The package is tested against the `software examples`_ but may still not support
+every possible format. For example, parameters serialized in multiple parameters 
+are not handled automatically (such as POINT:LABELS and POINT:LABELS2). Reading and 
+writing files from a big-endian system is also not supported. 
+
+Tests are currently only run on Windows, which means that Linux and Mac users may 
+experience some issues. If you experience issues with a file or feature, feel free 
+to post an issue (preferably by including example file/code/python exception) 
+or make a pull request!
+
+The package is also Python only, for other languages there are other packages such as `ezc3d`_.
 
-Also, if you're looking for more functionality than just reading and writing C3D
-files, there are a lot of better toolkits out there that support a lot more file
-formats and provide more functionality, perhaps at the cost of increased
-complexity. The `biomechanical toolkit`_ is a good package for analyzing motion
-data.
+.. _software examples: https://www.c3d.org/sampledata.html
+.. _ezc3d: https://github.com/pyomeca/ezc3d
 
-.. _biomechanical toolkit: http://code.google.com/p/b-tk/

From ec4883102fa1dfd3015ece234522697c5bc1d855 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 20:06:04 +0200
Subject: [PATCH 083/120] Scripts listing

---
 docs/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/index.md b/docs/index.md
index 5535bfa..0828fc1 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,7 +1,7 @@
 
 * [Documentation]
 
-* [Tool scripts]
+* [Scripts]
 
 
 [Documentation]: ./c3d/

From 77048d5b7f84ac6a58e70aeaddc1304934076302 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 20:09:04 +0200
Subject: [PATCH 084/120] Version 0.6.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 42bae93..d795261 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 
 setuptools.setup(
     name='c3d',
-    version='0.5.0',
+    version='0.6.0',
     py_modules=['c3d.dtypes', 'c3d.group', 'c3d.header', 'c3d.manager', 'c3d.reader', 'c3d.writer', 'c3d.parameter', 'c3d.utils', 'scripts.c3d-viewer'],
     author='UT Vision, Cognition, and Action Lab',
     author_email='leif@cs.utexas.edu',

From 35e25cb8c7d2ec490b72c634f944ee656f8c36d5 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 20:33:00 +0200
Subject: [PATCH 085/120] Updated docs

---
 c3d/__init__.py     |  3 ++-
 docs/c3d/index.html | 12 ++++++------
 docs/examples.md    | 10 +++++-----
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/c3d/__init__.py b/c3d/__init__.py
index be4619e..cb3c41e 100644
--- a/c3d/__init__.py
+++ b/c3d/__init__.py
@@ -11,9 +11,10 @@
 Installing
 ----------
 
-See the [main page].
+See the [main page] or [github page].
 
 [main page]: https://mattiasfredriksson.github.io/py-c3d/
+[github page]: https://github.com/EmbodiedCognition/py-c3d
 
 .. include:: ../docs/examples.md
 
diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index 0474685..774bb4e 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -28,7 +28,7 @@ 
      Python C3D Processing
      
 
      This package provides pure Python modules for reading, writing, and editing binary
 motion-capture files in the C3D file format.
      
 
      Installing
      
-
      See the main page.
      
+
      See the main page or github page.
      
 
      Examples
      
 
      Access to data blocks in a .c3d file is provided through the Reader and Writer classes.
 Runnable implementation of the examples are provided in the examples/ directory in the github repository.
      
@@ -71,16 +71,16 @@ 
      Writing

The function Writer.add_frames() take pairs of numpy or python arrays, with the first array in each tuple defining point data and the second -defining the analog data for the frame. Leaving one of the arrays empty indicates +analog data for the frame. Leaving one of the arrays empty indicates to the writer that no analog — or point data— should be included in the file. References of the data arrays are tracked until Writer.write() -is called, which serializes metadata and data frames into a C3D binary file stream.

+is called, which serializes the metadata and data frames into a C3D binary file stream.

Editing

Editing c3d files is possible by combining the use of Reader and Writer -instances through the use of Reader.to_writer(). By opening a .c3d file stream through +instances through the use of Reader.to_writer(). Opening a .c3d file stream through a reader instance, Reader.to_writer() can be used to create an independent Writer instance -copying the file contents onto the heap. Rereading the c3d.reader frame data from the file -and inserting the frames in reverse, a looped version of the .c3d file can be created!

+containing a heap copy of the file contents. Rereading the data frames from the file +and inserting into the writer in reverse, a looped version of the .c3d file can be created!

import c3d
 
 with open('my-motion.c3d', 'rb') as file:
diff --git a/docs/examples.md b/docs/examples.md
index 27f0b05..d9d63e4 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -52,19 +52,19 @@ instance:
 
 The function `c3d.writer.Writer.add_frames` take pairs of ``numpy`` or ``python
 arrays``, with the first array in each tuple defining point data and the second
-defining the analog data for the frame. Leaving one of the arrays empty indicates
+analog data for the frame. Leaving one of the arrays empty indicates
 to the writer that no analog --- or point data--- should be included in the file.
 References of the data arrays are tracked until `c3d.writer.Writer.write`
-is called, which serializes metadata and data frames into a C3D binary file stream.
+is called, which serializes the metadata and data frames into a C3D binary file stream.
 
 Editing
 -------
 
 Editing c3d files is possible by combining the use of `c3d.reader.Reader` and `c3d.writer.Writer`
-instances through the use of `c3d.reader.Reader.to_writer`. By opening a .c3d file stream through
+instances through the use of `c3d.reader.Reader.to_writer`. Opening a .c3d file stream through
 a reader instance, `c3d.reader.Reader.to_writer` can be used to create an independent Writer instance
-copying the file contents onto the heap. Rereading the `reader` frame data from the file
-and inserting the frames in reverse, a looped version of the .c3d file can be created!
+containing a heap copy of the file contents. Rereading the data frames from the file
+and inserting into the writer in reverse, a looped version of the .c3d file can be created!
 
     import c3d
 

From bcba72564c9925401f3b2573c2e0d28d7f878b37 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 21:56:33 +0200
Subject: [PATCH 086/120] Updated docs

---
 c3d/reader.py           |    2 +-
 c3d/writer.py           |   10 +-
 docs/c3d/dtypes.html    |  316 +++++++++
 docs/c3d/group.html     | 1480 +++++++++++++++++++++++++++++++++++++++
 docs/c3d/header.html    |  750 ++++++++++++++++++++
 docs/c3d/index.html     |   82 ++-
 docs/c3d/manager.html   | 1284 +++++++++++++++++++++++++++++++++
 docs/c3d/parameter.html | 1411 +++++++++++++++++++++++++++++++++++++
 docs/c3d/reader.html    |  937 ++++++++++++++++++++++++-
 docs/c3d/utils.html     |  329 +++++++++
 docs/c3d/writer.html    | 1465 +++++++++++++++++++++++++++++++++++++-
 docs/examples.md        |   56 +-
 test/test_examples.py   |    7 +-
 13 files changed, 8102 insertions(+), 27 deletions(-)

diff --git a/c3d/reader.py b/c3d/reader.py
index 2e0d4cf..5a94992 100644
--- a/c3d/reader.py
+++ b/c3d/reader.py
@@ -1,4 +1,4 @@
-'''A Python module for reading and writing C3D files.'''
+'''Contains the Reader class for reading C3D files.'''
 
 import io
 import numpy as np
diff --git a/c3d/writer.py b/c3d/writer.py
index bd6dbe9..3a76a22 100644
--- a/c3d/writer.py
+++ b/c3d/writer.py
@@ -1,4 +1,4 @@
-'''A Python module for reading and writing C3D files.'''
+'''Contains the Writer class for writing C3D files.'''
 
 import copy
 import numpy as np
@@ -167,7 +167,7 @@ def numeric_key_next(self):
         return self.numeric_key_max + 1
 
     def get_create(self, label):
-        ''' Get or create the specified parameter group.'''
+        ''' Get or create a parameter `c3d.group.Group`.'''
         label = label.upper()
         group = self.get(label)
         if group is None:
@@ -194,7 +194,7 @@ def add_group(self, group_id, name, desc):
 
         Returns
         -------
-        group : :class:`Group`
+        group : `c3d.group.Group`
             An editable group instance.
         '''
         return super(Writer, self)._add_group(group_id, name, desc)
@@ -292,7 +292,7 @@ def set_analog_scales(self, values):
         Parameters
         ----------
         values : iterable or None
-            Iterable containing individual scale factors for encoding analog channel data.
+            Iterable containing individual scale factors (float32) for scaling analog channel data.
         '''
         if utils.is_iterable(values):
             data = np.array([v for v in values], dtype=np.float32)
@@ -308,7 +308,7 @@ def set_analog_offsets(self, values):
         Parameters
         ----------
         values : iterable or None
-            Iterable containing individual offsets for encoding analog channel data.
+            Iterable containing individual offsets (int16) for encoding analog channel data.
         '''
         if utils.is_iterable(values):
             data = np.array([v for v in values], dtype=np.int16)
diff --git a/docs/c3d/dtypes.html b/docs/c3d/dtypes.html
index 729ad33..81ca407 100644
--- a/docs/c3d/dtypes.html
+++ b/docs/c3d/dtypes.html
@@ -23,6 +23,121 @@ 
Module c3d.dtypes

 
 

 
State object defining the data types associated with a given .c3d processor format.

+

+
+Expand source code
+
+
'''
+State object defining the data types associated with a given .c3d processor format.
+'''
+
+import sys
+import codecs
+import numpy as np
+
+PROCESSOR_INTEL = 84
+PROCESSOR_DEC = 85
+PROCESSOR_MIPS = 86
+
+class DataTypes(object):
+    ''' Container defining the data types used when parsing byte data.
+        Data types depend on the processor format the file is stored in.
+    '''
+    def __init__(self, proc_type=PROCESSOR_INTEL):
+        self._proc_type = proc_type
+        self._little_endian_sys = sys.byteorder == 'little'
+        self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \
+                       (self.is_mips and self.big_endian_sys)
+        if self.big_endian_sys:
+            warnings.warn('Systems with native byte order of big-endian are not supported.')
+
+        if self._proc_type == PROCESSOR_MIPS:
+            # Big-Endian (SGI/MIPS format)
+            self.float32 = np.dtype(np.float32).newbyteorder('>')
+            self.float64 = np.dtype(np.float64).newbyteorder('>')
+            self.uint8 = np.uint8
+            self.uint16 = np.dtype(np.uint16).newbyteorder('>')
+            self.uint32 = np.dtype(np.uint32).newbyteorder('>')
+            self.uint64 = np.dtype(np.uint64).newbyteorder('>')
+            self.int8 = np.int8
+            self.int16 = np.dtype(np.int16).newbyteorder('>')
+            self.int32 = np.dtype(np.int32).newbyteorder('>')
+            self.int64 = np.dtype(np.int64).newbyteorder('>')
+        else:
+            # Little-Endian format (Intel or DEC format)
+            self.float32 = np.float32
+            self.float64 = np.float64
+            self.uint8 = np.uint8
+            self.uint16 = np.uint16
+            self.uint32 = np.uint32
+            self.uint64 = np.uint64
+            self.int8 = np.int8
+            self.int16 = np.int16
+            self.int32 = np.int32
+            self.int64 = np.int64
+
+    @property
+    def is_ieee(self) -> bool:
+        ''' True if the associated file is in the Intel format.
+        '''
+        return self._proc_type == PROCESSOR_INTEL
+
+    @property
+    def is_dec(self) -> bool:
+        ''' True if the associated file is in the DEC format.
+        '''
+        return self._proc_type == PROCESSOR_DEC
+
+    @property
+    def is_mips(self) -> bool:
+        ''' True if the associated file is in the SGI/MIPS format.
+        '''
+        return self._proc_type == PROCESSOR_MIPS
+
+    @property
+    def proc_type(self) -> str:
+        ''' Get the processory type associated with the data format in the file.
+        '''
+        processor_type = ['INTEL', 'DEC', 'MIPS']
+        return processor_type[self._proc_type - PROCESSOR_INTEL]
+
+    @property
+    def processor(self) -> int:
+        ''' Get the processor number encoded in the .c3d file.
+        '''
+        return self._proc_type
+
+    @property
+    def native(self) -> bool:
+        ''' True if the native (system) byte order matches the file byte order.
+        '''
+        return self._native
+
+    @property
+    def little_endian_sys(self) -> bool:
+        ''' True if native byte order is little-endian.
+        '''
+        return self._little_endian_sys
+
+    @property
+    def big_endian_sys(self) -> bool:
+        ''' True if native byte order is big-endian.
+        '''
+        return not self._little_endian_sys
+
+    def decode_string(self, bytes) -> str:
+        ''' Decode a byte array to a string.
+        '''
+        # Attempt to decode using different decoders
+        decoders = ['utf-8', 'latin-1']
+        for dec in decoders:
+            try:
+                return codecs.decode(bytes, dec)
+            except UnicodeDecodeError:
+                continue
+        # Revert to using default decoder but replace characters
+        return codecs.decode(bytes, decoders[0], 'replace')

+

 

 

 

@@ -40,39 +155,223 @@ 
Classes

 

 
Container defining the data types used when parsing byte data.
 Data types depend on the processor format the file is stored in.

+

+
+Expand source code
+
+
class DataTypes(object):
+    ''' Container defining the data types used when parsing byte data.
+        Data types depend on the processor format the file is stored in.
+    '''
+    def __init__(self, proc_type=PROCESSOR_INTEL):
+        self._proc_type = proc_type
+        self._little_endian_sys = sys.byteorder == 'little'
+        self._native = ((self.is_ieee or self.is_dec) and self.little_endian_sys) or \
+                       (self.is_mips and self.big_endian_sys)
+        if self.big_endian_sys:
+            warnings.warn('Systems with native byte order of big-endian are not supported.')
+
+        if self._proc_type == PROCESSOR_MIPS:
+            # Big-Endian (SGI/MIPS format)
+            self.float32 = np.dtype(np.float32).newbyteorder('>')
+            self.float64 = np.dtype(np.float64).newbyteorder('>')
+            self.uint8 = np.uint8
+            self.uint16 = np.dtype(np.uint16).newbyteorder('>')
+            self.uint32 = np.dtype(np.uint32).newbyteorder('>')
+            self.uint64 = np.dtype(np.uint64).newbyteorder('>')
+            self.int8 = np.int8
+            self.int16 = np.dtype(np.int16).newbyteorder('>')
+            self.int32 = np.dtype(np.int32).newbyteorder('>')
+            self.int64 = np.dtype(np.int64).newbyteorder('>')
+        else:
+            # Little-Endian format (Intel or DEC format)
+            self.float32 = np.float32
+            self.float64 = np.float64
+            self.uint8 = np.uint8
+            self.uint16 = np.uint16
+            self.uint32 = np.uint32
+            self.uint64 = np.uint64
+            self.int8 = np.int8
+            self.int16 = np.int16
+            self.int32 = np.int32
+            self.int64 = np.int64
+
+    @property
+    def is_ieee(self) -> bool:
+        ''' True if the associated file is in the Intel format.
+        '''
+        return self._proc_type == PROCESSOR_INTEL
+
+    @property
+    def is_dec(self) -> bool:
+        ''' True if the associated file is in the DEC format.
+        '''
+        return self._proc_type == PROCESSOR_DEC
+
+    @property
+    def is_mips(self) -> bool:
+        ''' True if the associated file is in the SGI/MIPS format.
+        '''
+        return self._proc_type == PROCESSOR_MIPS
+
+    @property
+    def proc_type(self) -> str:
+        ''' Get the processory type associated with the data format in the file.
+        '''
+        processor_type = ['INTEL', 'DEC', 'MIPS']
+        return processor_type[self._proc_type - PROCESSOR_INTEL]
+
+    @property
+    def processor(self) -> int:
+        ''' Get the processor number encoded in the .c3d file.
+        '''
+        return self._proc_type
+
+    @property
+    def native(self) -> bool:
+        ''' True if the native (system) byte order matches the file byte order.
+        '''
+        return self._native
+
+    @property
+    def little_endian_sys(self) -> bool:
+        ''' True if native byte order is little-endian.
+        '''
+        return self._little_endian_sys
+
+    @property
+    def big_endian_sys(self) -> bool:
+        ''' True if native byte order is big-endian.
+        '''
+        return not self._little_endian_sys
+
+    def decode_string(self, bytes) -> str:
+        ''' Decode a byte array to a string.
+        '''
+        # Attempt to decode using different decoders
+        decoders = ['utf-8', 'latin-1']
+        for dec in decoders:
+            try:
+                return codecs.decode(bytes, dec)
+            except UnicodeDecodeError:
+                continue
+        # Revert to using default decoder but replace characters
+        return codecs.decode(bytes, decoders[0], 'replace')

+

 
Instance variables

 

 
var big_endian_sys : bool

 

 
True if native byte order is big-endian.

+

+
+Expand source code
+
+
@property
+def big_endian_sys(self) -> bool:
+    ''' True if native byte order is big-endian.
+    '''
+    return not self._little_endian_sys

+

 

 
var is_dec : bool

 

 
True if the associated file is in the DEC format.

+

+
+Expand source code
+
+
@property
+def is_dec(self) -> bool:
+    ''' True if the associated file is in the DEC format.
+    '''
+    return self._proc_type == PROCESSOR_DEC

+

 

 
var is_ieee : bool

 

 
True if the associated file is in the Intel format.

+

+
+Expand source code
+
+
@property
+def is_ieee(self) -> bool:
+    ''' True if the associated file is in the Intel format.
+    '''
+    return self._proc_type == PROCESSOR_INTEL

+

 

 
var is_mips : bool

 

 
True if the associated file is in the SGI/MIPS format.

+

+
+Expand source code
+
+
@property
+def is_mips(self) -> bool:
+    ''' True if the associated file is in the SGI/MIPS format.
+    '''
+    return self._proc_type == PROCESSOR_MIPS

+

 

 
var little_endian_sys : bool

 

 
True if native byte order is little-endian.

+

+
+Expand source code
+
+
@property
+def little_endian_sys(self) -> bool:
+    ''' True if native byte order is little-endian.
+    '''
+    return self._little_endian_sys

+

 

 
var native : bool

 

 
True if the native (system) byte order matches the file byte order.

+

+
+Expand source code
+
+
@property
+def native(self) -> bool:
+    ''' True if the native (system) byte order matches the file byte order.
+    '''
+    return self._native

+

 

 
var proc_type : str

 

 
Get the processory type associated with the data format in the file.

+

+
+Expand source code
+
+
@property
+def proc_type(self) -> str:
+    ''' Get the processory type associated with the data format in the file.
+    '''
+    processor_type = ['INTEL', 'DEC', 'MIPS']
+    return processor_type[self._proc_type - PROCESSOR_INTEL]

+

 

 
var processor : int

 

 
Get the processor number encoded in the .c3d file.

+

+
+Expand source code
+
+
@property
+def processor(self) -> int:
+    ''' Get the processor number encoded in the .c3d file.
+    '''
+    return self._proc_type

+

 

 

 
Methods

@@ -82,6 +381,23 @@ 
Methods

 
 

 
Decode a byte array to a string.

+

+
+Expand source code
+
+
def decode_string(self, bytes) -> str:
+    ''' Decode a byte array to a string.
+    '''
+    # Attempt to decode using different decoders
+    decoders = ['utf-8', 'latin-1']
+    for dec in decoders:
+        try:
+            return codecs.decode(bytes, dec)
+        except UnicodeDecodeError:
+            continue
+    # Revert to using default decoder but replace characters
+    return codecs.decode(bytes, decoders[0], 'replace')

+

 

 
 
diff --git a/docs/c3d/group.html b/docs/c3d/group.html
index 15d8f73..833dd60 100644
--- a/docs/c3d/group.html
+++ b/docs/c3d/group.html
@@ -23,6 +23,473 @@ 
Module c3d.group

 
 

 
Classes used to represent the concept of parameter groups in a .c3d file.

+

+
+Expand source code
+
+
''' Classes used to represent the concept of parameter groups in a .c3d file.
+'''
+import struct
+import numpy as np
+from .parameter import ParamData, Param
+from .utils import Decorator
+
+class GroupData(object):
+    '''A group of parameters stored in a C3D file.
+
+    In C3D files, parameters are organized in groups. Each group has a name (key), a
+    description, and a set of named parameters. Each group is also internally associated
+    with a numeric key.
+
+    Attributes
+    ----------
+    dtypes : `c3d.dtypes.DataTypes`
+        Data types object used for parsing.
+    name : str
+        Name of this parameter group.
+    desc : str
+        Description for this parameter group.
+    '''
+
+    def __init__(self, dtypes, name=None, desc=None):
+        self._params = {}
+        self._dtypes = dtypes
+        # Assign through property setters
+        self.set_name(name)
+        self.set_desc(desc)
+
+    def __repr__(self):
+        return '<Group: {}>'.format(self.desc)
+
+    def __contains__(self, key):
+        return key in self._params
+
+    def __getitem__(self, key):
+        return self._params[key]
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes to store this group and its parameters.'''
+        return (
+            1 +  # group_id
+            1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+            2 +  # next offset marker
+            1 + len(self.desc.encode('utf-8')) +  # size of desc and desc bytes
+            sum(p.binary_size for p in self._params.values()))
+
+    def set_name(self, name):
+        ''' Set the group name string. '''
+        if name is None or isinstance(name, str):
+            self.name = name
+        else:
+            raise TypeError('Expected group name to be string, was %s.' % type(name))
+
+    def set_desc(self, desc):
+        ''' Set the Group descriptor.
+        '''
+        if isinstance(desc, bytes):
+            self.desc = self._dtypes.decode_string(desc)
+        elif isinstance(desc, str) or desc is None:
+            self.desc = desc
+        else:
+            raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(desc))
+
+    def add_param(self, name, **kwargs):
+        '''Add a parameter to this group.
+
+        Parameters
+        ----------
+        name : str
+            Name of the parameter to add to this group. The name will
+            automatically be case-normalized.
+
+        See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+
+        Raises
+        ------
+        TypeError
+            Input arguments are of the wrong type.
+        KeyError
+            Name or numerical key already exist (attempt to overwrite existing data).
+        '''
+        if not isinstance(name, str):
+            raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name)))
+        name = name.upper()
+        if name in self._params:
+            raise KeyError('Parameter already exists with key {}'.format(name))
+        self._params[name] = Param(ParamData(name, self._dtypes, **kwargs))
+
+    def remove_param(self, name):
+        '''Remove the specified parameter.
+
+        Parameters
+        ----------
+        name : str
+            Name for the parameter to remove.
+        '''
+        del self._params[name]
+
+    def rename_param(self, name, new_name):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        name : str, or `c3d.group.GroupReadonly`
+            Parameter instance, or name.
+        new_name : str
+            New name for the parameter.
+        Raises
+        ------
+        KeyError
+            If no parameter with the original name exists.
+        ValueError
+            If the new name already exist (attempt to overwrite existing data).
+        '''
+        if new_name in self._params:
+            raise ValueError("Key {} already exist.".format(new_name))
+        if isinstance(name, Param):
+            param = name
+            name = param.name
+        else:
+            # Aquire instance using id
+            param = self._params[name]
+        del self._params[name]
+        self._params[new_name] = param
+
+    def write(self, group_id, handle):
+        '''Write this parameter group, with parameters, to a file handle.
+
+        Parameters
+        ----------
+        group_id : int
+            The numerical ID of the group.
+        handle : file handle
+            An open, writable, binary file handle.
+        '''
+        name = self.name.encode('utf-8')
+        desc = self.desc.encode('utf-8')
+        handle.write(struct.pack('bb', len(name), -group_id))
+        handle.write(name)
+        handle.write(struct.pack('<h', 3 + len(desc)))
+        handle.write(struct.pack('B', len(desc)))
+        handle.write(desc)
+        for param in self._params.values():
+            param._data.write(group_id, handle)
+
+class GroupReadonly(object):
+    ''' Wrapper exposing readonly attributes of a `c3d.group.GroupData` entry.
+    '''
+    def __init__(self, data):
+        self._data = data
+
+    def __contains__(self, key):
+        return key in self._data._params
+
+    def __eq__(self, other):
+        return self._data is other._data
+
+    @property
+    def name(self) -> str:
+        ''' Access group name. '''
+        return self._data.name
+
+    @property
+    def desc(self) -> str:
+        '''Access group descriptor. '''
+        return self._data.desc
+
+    def items(self):
+        ''' Get iterator for paramater key-entry pairs. '''
+        return ((k, v.readonly()) for k, v in self._data._params.items())
+
+    def values(self):
+        ''' Get iterator for parameter entries. '''
+        return (v.readonly() for v in self._data._params.values())
+
+    def keys(self):
+        ''' Get iterator for parameter entry keys. '''
+        return self._data._params.keys()
+
+    def get(self, key, default=None):
+        '''Get a readonly parameter by key.
+
+        Parameters
+        ----------
+        key : any
+            Parameter key to look up in this group.
+        default : any, optional
+            Value to return if the key is not found. Defaults to None.
+
+        Returns
+        -------
+        param : :class:`ParamReadable`
+            A parameter from the current group.
+        '''
+        val = self._data._params.get(key, default)
+        if val:
+            return val.readonly()
+        return default
+
+    def get_int8(self, key):
+        '''Get the value of the given parameter as an 8-bit signed integer.'''
+        return self._data[key.upper()].int8_value
+
+    def get_uint8(self, key):
+        '''Get the value of the given parameter as an 8-bit unsigned integer.'''
+        return self._data[key.upper()].uint8_value
+
+    def get_int16(self, key):
+        '''Get the value of the given parameter as a 16-bit signed integer.'''
+        return self._data[key.upper()].int16_value
+
+    def get_uint16(self, key):
+        '''Get the value of the given parameter as a 16-bit unsigned integer.'''
+        return self._data[key.upper()].uint16_value
+
+    def get_int32(self, key):
+        '''Get the value of the given parameter as a 32-bit signed integer.'''
+        return self._data[key.upper()].int32_value
+
+    def get_uint32(self, key):
+        '''Get the value of the given parameter as a 32-bit unsigned integer.'''
+        return self._data[key.upper()].uint32_value
+
+    def get_float(self, key):
+        '''Get the value of the given parameter as a 32-bit float.'''
+        return self._data[key.upper()].float_value
+
+    def get_bytes(self, key):
+        '''Get the value of the given parameter as a byte array.'''
+        return self._data[key.upper()].bytes_value
+
+    def get_string(self, key):
+        '''Get the value of the given parameter as a string.'''
+        return self._data[key.upper()].string_value
+
+class Group(GroupReadonly):
+    ''' Wrapper exposing readable and writeable attributes of a `c3d.group.GroupData` entry.
+    '''
+    def __init__(self, data):
+        super(Group, self).__init__(data)
+
+    def readonly(self):
+        ''' Returns a `c3d.group.GroupReadonly` instance with readonly access. '''
+        return GroupReadonly(self._data)
+
+    @property
+    def name(self) -> str:
+        ''' Get or set name. '''
+        return self._data.name
+
+    @name.setter
+    def name(self, value) -> str:
+        self._data.set_name(value)
+
+    @property
+    def desc(self) -> str:
+        ''' Get or set descriptor. '''
+        return self._data.desc
+
+    @desc.setter
+    def desc(self, value) -> str:
+        self._data.set_desc(value)
+
+    def items(self):
+        ''' Iterator for paramater key-entry pairs. '''
+        return ((k, v) for k, v in self._data._params.items())
+
+    def values(self):
+        ''' Iterator iterator for parameter entries. '''
+        return (v for v in self._data._params.values())
+
+    def get(self, key, default=None):
+        '''Get a parameter by key.
+
+        Parameters
+        ----------
+        key : any
+            Parameter key to look up in this group.
+        default : any, optional
+            Value to return if the key is not found. Defaults to None.
+
+        Returns
+        -------
+        param : :class:`ParamReadable`
+            A parameter from the current group.
+        '''
+        return self._data._params.get(key, default)
+    #
+    #  Forward param editing
+    #
+    def add_param(self, name, **kwargs):
+        '''Add a parameter to this group.
+
+        See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+        '''
+        self._data.add_param(name, **kwargs)
+
+    def remove_param(self, name):
+        '''Remove the specified parameter.
+
+        Parameters
+        ----------
+        name : str
+            Name for the parameter to remove.
+        '''
+        self._data.remove_param(name)
+
+    def rename_param(self, name, new_name):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        See arguments in `c3d.group.GroupData.rename_param`.
+        '''
+        self._data.rename_param(name, new_name)
+
+    #
+    #   Convenience functions for adding parameters.
+    #
+    def add(self, name, desc, bpe, format, data, *dimensions):
+        ''' Add a parameter with `data` package formated in accordance with `format`.
+
+        Convenience function for `c3d.group.GroupData.add_param` calling struct.pack() on `data`.
+
+        Example:
+
+        >>> group.set('RATE', 'Point data sample rate', 4, '<f', 100)
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        bpe : int
+            Number of bytes for each atomic element.
+        format : str or None
+            `struct.format()` compatible format string see:
+            https://docs.python.org/3/library/struct.html#format-characters
+        *dimensions : int, optional
+            Shape associated with the data (if the data argument represents multiple elements).
+        '''
+        if isinstance(data, bytes):
+            pass
+        else:
+            data = struct.pack(format, data)
+
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=bpe,
+                       bytes=data,
+                       dimensions=list(dimensions))
+
+    def add_array(self, name, desc, data, dtype=None):
+        '''Add a parameter with the `data` package.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        data : np.ndarray, or iterable
+            Data array to encode in the parameter.
+        dtype : np.dtype, optional
+            Numpy data type used to encode the array (optional only if `data.dtype` returns a numpy type).
+        '''
+        if not isinstance(data, np.ndarray):
+            if dtype is None:
+                dtype = data.dtype
+            data = np.array(data, dtype=dtype)
+        elif dtype is None:
+            dtype = data.dtype
+
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=dtype.itemsize,
+                       bytes=data.tobytes(),
+                       dimensions=data.shape[::-1])
+
+    def add_str(self, name, desc, data, *dimensions):
+        ''' Add a string parameter.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        data : str
+            String to encode in the parameter.
+        *dimensions : int, optional
+            Shape associated with the string (if the string represents multiple elements).
+        '''
+        shape = list(dimensions)
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=-1,
+                       bytes=data.encode('utf-8'),
+                       dimensions=shape or [len(data)])
+
+    def add_empty_array(self, name, desc='', bpe=1):
+        ''' Add an empty parameter block.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        '''
+        self.add_param(name, desc=desc,
+                       bytes_per_element=bpe, dimensions=[0])
+
+    #
+    #   Convenience functions for adding or overwriting parameters.
+    #
+    def set(self, name, *args, **kwargs):
+        ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'.
+
+        See arguments in `c3d.group.Group.add`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add(name, *args, **kwargs)
+
+    def set_str(self, name, *args, **kwargs):
+        ''' Add or overwrite a string parameter.
+
+        See arguments in `c3d.group.Group.add_str`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_str(name, *args, **kwargs)
+
+    def set_array(self, name, *args, **kwargs):
+        ''' Add or overwrite a parameter with the `data` package.
+
+        See arguments in `c3d.group.Group.add_array`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_array(name, *args, **kwargs)
+
+    def set_empty_array(self, name, *args, **kwargs):
+        ''' Add an empty parameter block.
+
+        See arguments in `c3d.group.Group.add_empty_array`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_empty_array(name, *args, **kwargs)

+

 

 

 

@@ -39,6 +506,234 @@ 
Classes

 
 

 
Wrapper exposing readable and writeable attributes of a GroupData entry.

+

+
+Expand source code
+
+
class Group(GroupReadonly):
+    ''' Wrapper exposing readable and writeable attributes of a `c3d.group.GroupData` entry.
+    '''
+    def __init__(self, data):
+        super(Group, self).__init__(data)
+
+    def readonly(self):
+        ''' Returns a `c3d.group.GroupReadonly` instance with readonly access. '''
+        return GroupReadonly(self._data)
+
+    @property
+    def name(self) -> str:
+        ''' Get or set name. '''
+        return self._data.name
+
+    @name.setter
+    def name(self, value) -> str:
+        self._data.set_name(value)
+
+    @property
+    def desc(self) -> str:
+        ''' Get or set descriptor. '''
+        return self._data.desc
+
+    @desc.setter
+    def desc(self, value) -> str:
+        self._data.set_desc(value)
+
+    def items(self):
+        ''' Iterator for paramater key-entry pairs. '''
+        return ((k, v) for k, v in self._data._params.items())
+
+    def values(self):
+        ''' Iterator iterator for parameter entries. '''
+        return (v for v in self._data._params.values())
+
+    def get(self, key, default=None):
+        '''Get a parameter by key.
+
+        Parameters
+        ----------
+        key : any
+            Parameter key to look up in this group.
+        default : any, optional
+            Value to return if the key is not found. Defaults to None.
+
+        Returns
+        -------
+        param : :class:`ParamReadable`
+            A parameter from the current group.
+        '''
+        return self._data._params.get(key, default)
+    #
+    #  Forward param editing
+    #
+    def add_param(self, name, **kwargs):
+        '''Add a parameter to this group.
+
+        See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+        '''
+        self._data.add_param(name, **kwargs)
+
+    def remove_param(self, name):
+        '''Remove the specified parameter.
+
+        Parameters
+        ----------
+        name : str
+            Name for the parameter to remove.
+        '''
+        self._data.remove_param(name)
+
+    def rename_param(self, name, new_name):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        See arguments in `c3d.group.GroupData.rename_param`.
+        '''
+        self._data.rename_param(name, new_name)
+
+    #
+    #   Convenience functions for adding parameters.
+    #
+    def add(self, name, desc, bpe, format, data, *dimensions):
+        ''' Add a parameter with `data` package formated in accordance with `format`.
+
+        Convenience function for `c3d.group.GroupData.add_param` calling struct.pack() on `data`.
+
+        Example:
+
+        >>> group.set('RATE', 'Point data sample rate', 4, '<f', 100)
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        bpe : int
+            Number of bytes for each atomic element.
+        format : str or None
+            `struct.format()` compatible format string see:
+            https://docs.python.org/3/library/struct.html#format-characters
+        *dimensions : int, optional
+            Shape associated with the data (if the data argument represents multiple elements).
+        '''
+        if isinstance(data, bytes):
+            pass
+        else:
+            data = struct.pack(format, data)
+
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=bpe,
+                       bytes=data,
+                       dimensions=list(dimensions))
+
+    def add_array(self, name, desc, data, dtype=None):
+        '''Add a parameter with the `data` package.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        data : np.ndarray, or iterable
+            Data array to encode in the parameter.
+        dtype : np.dtype, optional
+            Numpy data type used to encode the array (optional only if `data.dtype` returns a numpy type).
+        '''
+        if not isinstance(data, np.ndarray):
+            if dtype is None:
+                dtype = data.dtype
+            data = np.array(data, dtype=dtype)
+        elif dtype is None:
+            dtype = data.dtype
+
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=dtype.itemsize,
+                       bytes=data.tobytes(),
+                       dimensions=data.shape[::-1])
+
+    def add_str(self, name, desc, data, *dimensions):
+        ''' Add a string parameter.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        desc : str
+            Parameter descriptor.
+        data : str
+            String to encode in the parameter.
+        *dimensions : int, optional
+            Shape associated with the string (if the string represents multiple elements).
+        '''
+        shape = list(dimensions)
+        self.add_param(name,
+                       desc=desc,
+                       bytes_per_element=-1,
+                       bytes=data.encode('utf-8'),
+                       dimensions=shape or [len(data)])
+
+    def add_empty_array(self, name, desc='', bpe=1):
+        ''' Add an empty parameter block.
+
+        Parameters
+        ----------
+        name : str
+            Parameter name.
+        '''
+        self.add_param(name, desc=desc,
+                       bytes_per_element=bpe, dimensions=[0])
+
+    #
+    #   Convenience functions for adding or overwriting parameters.
+    #
+    def set(self, name, *args, **kwargs):
+        ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'.
+
+        See arguments in `c3d.group.Group.add`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add(name, *args, **kwargs)
+
+    def set_str(self, name, *args, **kwargs):
+        ''' Add or overwrite a string parameter.
+
+        See arguments in `c3d.group.Group.add_str`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_str(name, *args, **kwargs)
+
+    def set_array(self, name, *args, **kwargs):
+        ''' Add or overwrite a parameter with the `data` package.
+
+        See arguments in `c3d.group.Group.add_array`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_array(name, *args, **kwargs)
+
+    def set_empty_array(self, name, *args, **kwargs):
+        ''' Add an empty parameter block.
+
+        See arguments in `c3d.group.Group.add_empty_array`.
+        '''
+        try:
+            self.remove_param(name)
+        except KeyError as e:
+            pass
+        self.add_empty_array(name, *args, **kwargs)

+

 
Ancestors

 
    
 
  • GroupReadonly
    • 
@@ -48,10 +743,28 @@ 
    Instance variables
    
 
    var desc : str
    
 
    
 
    Get or set descriptor.
    
+
    
+
+Expand source code
+
+
    @property
+def desc(self) -> str:
+    ''' Get or set descriptor. '''
+    return self._data.desc
    
+
    
 
    
 
    var name : str
    
 
    
 
    Get or set name.
    
+
    
+
+Expand source code
+
+
    @property
+def name(self) -> str:
+    ''' Get or set name. '''
+    return self._data.name
    
+
    
 
    
 
 
    Methods
    
@@ -79,6 +792,44 @@ 
    Parameters
    
 
    *dimensions : int, optional
    
 
    Shape associated with the data (if the data argument represents multiple elements).
    
 
+
    
+
+Expand source code
+
+
    def add(self, name, desc, bpe, format, data, *dimensions):
+    ''' Add a parameter with `data` package formated in accordance with `format`.
+
+    Convenience function for `c3d.group.GroupData.add_param` calling struct.pack() on `data`.
+
+    Example:
+
+    >>> group.set('RATE', 'Point data sample rate', 4, '<f', 100)
+
+    Parameters
+    ----------
+    name : str
+        Parameter name.
+    desc : str
+        Parameter descriptor.
+    bpe : int
+        Number of bytes for each atomic element.
+    format : str or None
+        `struct.format()` compatible format string see:
+        https://docs.python.org/3/library/struct.html#format-characters
+    *dimensions : int, optional
+        Shape associated with the data (if the data argument represents multiple elements).
+    '''
+    if isinstance(data, bytes):
+        pass
+    else:
+        data = struct.pack(format, data)
+
+    self.add_param(name,
+                   desc=desc,
+                   bytes_per_element=bpe,
+                   bytes=data,
+                   dimensions=list(dimensions))
    
+
    
 

 

 def add_array(self, name, desc, data, dtype=None)
@@ -96,6 +847,37 @@ 
Parameters

 
dtype : np.dtype, optional

 
Numpy data type used to encode the array (optional only if data.dtype returns a numpy type).

 
+

+
+Expand source code
+
+
def add_array(self, name, desc, data, dtype=None):
+    '''Add a parameter with the `data` package.
+
+    Parameters
+    ----------
+    name : str
+        Parameter name.
+    desc : str
+        Parameter descriptor.
+    data : np.ndarray, or iterable
+        Data array to encode in the parameter.
+    dtype : np.dtype, optional
+        Numpy data type used to encode the array (optional only if `data.dtype` returns a numpy type).
+    '''
+    if not isinstance(data, np.ndarray):
+        if dtype is None:
+            dtype = data.dtype
+        data = np.array(data, dtype=dtype)
+    elif dtype is None:
+        dtype = data.dtype
+
+    self.add_param(name,
+                   desc=desc,
+                   bytes_per_element=dtype.itemsize,
+                   bytes=data.tobytes(),
+                   dimensions=data.shape[::-1])

+

 
 

 def add_empty_array(self, name, desc='', bpe=1)
@@ -107,6 +889,21 @@ 
Parameters

 
name : str

 
Parameter name.

 
+

+
+Expand source code
+
+
def add_empty_array(self, name, desc='', bpe=1):
+    ''' Add an empty parameter block.
+
+    Parameters
+    ----------
+    name : str
+        Parameter name.
+    '''
+    self.add_param(name, desc=desc,
+                   bytes_per_element=bpe, dimensions=[0])

+

 
 

 def add_param(self, name, **kwargs)
@@ -114,6 +911,17 @@ 
Parameters

 

 
Add a parameter to this group.

 
See constructor of ParamData for additional keyword arguments.

+

+
+Expand source code
+
+
def add_param(self, name, **kwargs):
+    '''Add a parameter to this group.
+
+    See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+    '''
+    self._data.add_param(name, **kwargs)

+

 

 

 def add_str(self, name, desc, data, *dimensions)
@@ -131,6 +939,31 @@ 
Parameters

 
*dimensions : int, optional

 
Shape associated with the string (if the string represents multiple elements).

 
+

+
+Expand source code
+
+
def add_str(self, name, desc, data, *dimensions):
+    ''' Add a string parameter.
+
+    Parameters
+    ----------
+    name : str
+        Parameter name.
+    desc : str
+        Parameter descriptor.
+    data : str
+        String to encode in the parameter.
+    *dimensions : int, optional
+        Shape associated with the string (if the string represents multiple elements).
+    '''
+    shape = list(dimensions)
+    self.add_param(name,
+                   desc=desc,
+                   bytes_per_element=-1,
+                   bytes=data.encode('utf-8'),
+                   dimensions=shape or [len(data)])

+

 
 

 def get(self, key, default=None)
@@ -149,18 +982,55 @@ 
Returns

 
param : :class:ParamReadable``

 
A parameter from the current group.

 
+

+
+Expand source code
+
+
def get(self, key, default=None):
+    '''Get a parameter by key.
+
+    Parameters
+    ----------
+    key : any
+        Parameter key to look up in this group.
+    default : any, optional
+        Value to return if the key is not found. Defaults to None.
+
+    Returns
+    -------
+    param : :class:`ParamReadable`
+        A parameter from the current group.
+    '''
+    return self._data._params.get(key, default)

+

 
 

 def items(self)
 

 

 
Iterator for paramater key-entry pairs.

+

+
+Expand source code
+
+
def items(self):
+    ''' Iterator for paramater key-entry pairs. '''
+    return ((k, v) for k, v in self._data._params.items())

+

 

 

 def readonly(self)
 

 

 
Returns a GroupReadonly instance with readonly access.

+

+
+Expand source code
+
+
def readonly(self):
+    ''' Returns a `c3d.group.GroupReadonly` instance with readonly access. '''
+    return GroupReadonly(self._data)

+

 

 

 def remove_param(self, name)
@@ -172,6 +1042,20 @@ 
Parameters

 
name : str

 
Name for the parameter to remove.

 
+

+
+Expand source code
+
+
def remove_param(self, name):
+    '''Remove the specified parameter.
+
+    Parameters
+    ----------
+    name : str
+        Name for the parameter to remove.
+    '''
+    self._data.remove_param(name)

+

 
 

 def rename_param(self, name, new_name)
@@ -180,6 +1064,19 @@ 
Parameters

 
Rename a specified parameter group.

 
Parameters

 
See arguments in GroupData.rename_param().

+

+
+Expand source code
+
+
def rename_param(self, name, new_name):
+    ''' Rename a specified parameter group.
+
+    Parameters
+    ----------
+    See arguments in `c3d.group.GroupData.rename_param`.
+    '''
+    self._data.rename_param(name, new_name)

+

 
 

 def set(self, name, *args, **kwargs)
@@ -187,6 +1084,21 @@ 
Parameters

 

 
Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'.

 
See arguments in Group.add().

+

+
+Expand source code
+
+
def set(self, name, *args, **kwargs):
+    ''' Add or overwrite a parameter with 'bytes' package formated in accordance with 'format'.
+
+    See arguments in `c3d.group.Group.add`.
+    '''
+    try:
+        self.remove_param(name)
+    except KeyError as e:
+        pass
+    self.add(name, *args, **kwargs)

+

 

 

 def set_array(self, name, *args, **kwargs)
@@ -194,6 +1106,21 @@ 
Parameters

 

 
Add or overwrite a parameter with the data package.

 
See arguments in Group.add_array().

+

+
+Expand source code
+
+
def set_array(self, name, *args, **kwargs):
+    ''' Add or overwrite a parameter with the `data` package.
+
+    See arguments in `c3d.group.Group.add_array`.
+    '''
+    try:
+        self.remove_param(name)
+    except KeyError as e:
+        pass
+    self.add_array(name, *args, **kwargs)

+

 

 

 def set_empty_array(self, name, *args, **kwargs)
@@ -201,6 +1128,21 @@ 
Parameters

 

 
Add an empty parameter block.

 
See arguments in Group.add_empty_array().

+

+
+Expand source code
+
+
def set_empty_array(self, name, *args, **kwargs):
+    ''' Add an empty parameter block.
+
+    See arguments in `c3d.group.Group.add_empty_array`.
+    '''
+    try:
+        self.remove_param(name)
+    except KeyError as e:
+        pass
+    self.add_empty_array(name, *args, **kwargs)

+

 

 

 def set_str(self, name, *args, **kwargs)
@@ -208,12 +1150,35 @@ 
Parameters

 

 
Add or overwrite a string parameter.

 
See arguments in Group.add_str().

+

+
+Expand source code
+
+
def set_str(self, name, *args, **kwargs):
+    ''' Add or overwrite a string parameter.
+
+    See arguments in `c3d.group.Group.add_str`.
+    '''
+    try:
+        self.remove_param(name)
+    except KeyError as e:
+        pass
+    self.add_str(name, *args, **kwargs)

+

 

 

 def values(self)
 

 

 
Iterator iterator for parameter entries.

+

+
+Expand source code
+
+
def values(self):
+    ''' Iterator iterator for parameter entries. '''
+    return (v for v in self._data._params.values())

+

 

 
 
Inherited members

@@ -252,11 +1217,171 @@ 
Attributes

 
desc : str

 
Description for this parameter group.

 
+

+
+Expand source code
+
+
class GroupData(object):
+    '''A group of parameters stored in a C3D file.
+
+    In C3D files, parameters are organized in groups. Each group has a name (key), a
+    description, and a set of named parameters. Each group is also internally associated
+    with a numeric key.
+
+    Attributes
+    ----------
+    dtypes : `c3d.dtypes.DataTypes`
+        Data types object used for parsing.
+    name : str
+        Name of this parameter group.
+    desc : str
+        Description for this parameter group.
+    '''
+
+    def __init__(self, dtypes, name=None, desc=None):
+        self._params = {}
+        self._dtypes = dtypes
+        # Assign through property setters
+        self.set_name(name)
+        self.set_desc(desc)
+
+    def __repr__(self):
+        return '<Group: {}>'.format(self.desc)
+
+    def __contains__(self, key):
+        return key in self._params
+
+    def __getitem__(self, key):
+        return self._params[key]
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes to store this group and its parameters.'''
+        return (
+            1 +  # group_id
+            1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+            2 +  # next offset marker
+            1 + len(self.desc.encode('utf-8')) +  # size of desc and desc bytes
+            sum(p.binary_size for p in self._params.values()))
+
+    def set_name(self, name):
+        ''' Set the group name string. '''
+        if name is None or isinstance(name, str):
+            self.name = name
+        else:
+            raise TypeError('Expected group name to be string, was %s.' % type(name))
+
+    def set_desc(self, desc):
+        ''' Set the Group descriptor.
+        '''
+        if isinstance(desc, bytes):
+            self.desc = self._dtypes.decode_string(desc)
+        elif isinstance(desc, str) or desc is None:
+            self.desc = desc
+        else:
+            raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(desc))
+
+    def add_param(self, name, **kwargs):
+        '''Add a parameter to this group.
+
+        Parameters
+        ----------
+        name : str
+            Name of the parameter to add to this group. The name will
+            automatically be case-normalized.
+
+        See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+
+        Raises
+        ------
+        TypeError
+            Input arguments are of the wrong type.
+        KeyError
+            Name or numerical key already exist (attempt to overwrite existing data).
+        '''
+        if not isinstance(name, str):
+            raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name)))
+        name = name.upper()
+        if name in self._params:
+            raise KeyError('Parameter already exists with key {}'.format(name))
+        self._params[name] = Param(ParamData(name, self._dtypes, **kwargs))
+
+    def remove_param(self, name):
+        '''Remove the specified parameter.
+
+        Parameters
+        ----------
+        name : str
+            Name for the parameter to remove.
+        '''
+        del self._params[name]
+
+    def rename_param(self, name, new_name):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        name : str, or `c3d.group.GroupReadonly`
+            Parameter instance, or name.
+        new_name : str
+            New name for the parameter.
+        Raises
+        ------
+        KeyError
+            If no parameter with the original name exists.
+        ValueError
+            If the new name already exist (attempt to overwrite existing data).
+        '''
+        if new_name in self._params:
+            raise ValueError("Key {} already exist.".format(new_name))
+        if isinstance(name, Param):
+            param = name
+            name = param.name
+        else:
+            # Aquire instance using id
+            param = self._params[name]
+        del self._params[name]
+        self._params[new_name] = param
+
+    def write(self, group_id, handle):
+        '''Write this parameter group, with parameters, to a file handle.
+
+        Parameters
+        ----------
+        group_id : int
+            The numerical ID of the group.
+        handle : file handle
+            An open, writable, binary file handle.
+        '''
+        name = self.name.encode('utf-8')
+        desc = self.desc.encode('utf-8')
+        handle.write(struct.pack('bb', len(name), -group_id))
+        handle.write(name)
+        handle.write(struct.pack('<h', 3 + len(desc)))
+        handle.write(struct.pack('B', len(desc)))
+        handle.write(desc)
+        for param in self._params.values():
+            param._data.write(group_id, handle)

+

 
Instance variables

 

 
var binary_size : int

 

 
Return the number of bytes to store this group and its parameters.

+

+
+Expand source code
+
+
@property
+def binary_size(self) -> int:
+    '''Return the number of bytes to store this group and its parameters.'''
+    return (
+        1 +  # group_id
+        1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+        2 +  # next offset marker
+        1 + len(self.desc.encode('utf-8')) +  # size of desc and desc bytes
+        sum(p.binary_size for p in self._params.values()))

+

 

 

 
Methods

@@ -280,6 +1405,35 @@ 
Raises

 
KeyError

 
Name or numerical key already exist (attempt to overwrite existing data).

 
+

+
+Expand source code
+
+
def add_param(self, name, **kwargs):
+    '''Add a parameter to this group.
+
+    Parameters
+    ----------
+    name : str
+        Name of the parameter to add to this group. The name will
+        automatically be case-normalized.
+
+    See constructor of `c3d.parameter.ParamData` for additional keyword arguments.
+
+    Raises
+    ------
+    TypeError
+        Input arguments are of the wrong type.
+    KeyError
+        Name or numerical key already exist (attempt to overwrite existing data).
+    '''
+    if not isinstance(name, str):
+        raise TypeError("Expected 'name' argument to be a string, was of type {}".format(type(name)))
+    name = name.upper()
+    if name in self._params:
+        raise KeyError('Parameter already exists with key {}'.format(name))
+    self._params[name] = Param(ParamData(name, self._dtypes, **kwargs))

+

 
 

 def remove_param(self, name)
@@ -291,6 +1445,20 @@ 
Parameters

 
name : str

 
Name for the parameter to remove.

 
+

+
+Expand source code
+
+
def remove_param(self, name):
+    '''Remove the specified parameter.
+
+    Parameters
+    ----------
+    name : str
+        Name for the parameter to remove.
+    '''
+    del self._params[name]

+

 
 

 def rename_param(self, name, new_name)
@@ -311,18 +1479,74 @@ 
Raises

 
ValueError

 
If the new name already exist (attempt to overwrite existing data).

 
+

+
+Expand source code
+
+
def rename_param(self, name, new_name):
+    ''' Rename a specified parameter group.
+
+    Parameters
+    ----------
+    name : str, or `c3d.group.GroupReadonly`
+        Parameter instance, or name.
+    new_name : str
+        New name for the parameter.
+    Raises
+    ------
+    KeyError
+        If no parameter with the original name exists.
+    ValueError
+        If the new name already exist (attempt to overwrite existing data).
+    '''
+    if new_name in self._params:
+        raise ValueError("Key {} already exist.".format(new_name))
+    if isinstance(name, Param):
+        param = name
+        name = param.name
+    else:
+        # Aquire instance using id
+        param = self._params[name]
+    del self._params[name]
+    self._params[new_name] = param

+

 
 

 def set_desc(self, desc)
 

 

 
Set the Group descriptor.

+

+
+Expand source code
+
+
def set_desc(self, desc):
+    ''' Set the Group descriptor.
+    '''
+    if isinstance(desc, bytes):
+        self.desc = self._dtypes.decode_string(desc)
+    elif isinstance(desc, str) or desc is None:
+        self.desc = desc
+    else:
+        raise TypeError('Expected descriptor to be python string, bytes or None, was %s.' % type(desc))

+

 

 

 def set_name(self, name)
 

 

 
Set the group name string.

+

+
+Expand source code
+
+
def set_name(self, name):
+    ''' Set the group name string. '''
+    if name is None or isinstance(name, str):
+        self.name = name
+    else:
+        raise TypeError('Expected group name to be string, was %s.' % type(name))

+

 

 

 def write(self, group_id, handle)
@@ -336,6 +1560,30 @@ 
Parameters

 
handle : file handle

 
An open, writable, binary file handle.

 
+

+
+Expand source code
+
+
def write(self, group_id, handle):
+    '''Write this parameter group, with parameters, to a file handle.
+
+    Parameters
+    ----------
+    group_id : int
+        The numerical ID of the group.
+    handle : file handle
+        An open, writable, binary file handle.
+    '''
+    name = self.name.encode('utf-8')
+    desc = self.desc.encode('utf-8')
+    handle.write(struct.pack('bb', len(name), -group_id))
+    handle.write(name)
+    handle.write(struct.pack('<h', 3 + len(desc)))
+    handle.write(struct.pack('B', len(desc)))
+    handle.write(desc)
+    for param in self._params.values():
+        param._data.write(group_id, handle)

+

 
 
 
@@ -345,6 +1593,100 @@ 
Parameters

 
 

 
Wrapper exposing readonly attributes of a GroupData entry.

+

+
+Expand source code
+
+
class GroupReadonly(object):
+    ''' Wrapper exposing readonly attributes of a `c3d.group.GroupData` entry.
+    '''
+    def __init__(self, data):
+        self._data = data
+
+    def __contains__(self, key):
+        return key in self._data._params
+
+    def __eq__(self, other):
+        return self._data is other._data
+
+    @property
+    def name(self) -> str:
+        ''' Access group name. '''
+        return self._data.name
+
+    @property
+    def desc(self) -> str:
+        '''Access group descriptor. '''
+        return self._data.desc
+
+    def items(self):
+        ''' Get iterator for paramater key-entry pairs. '''
+        return ((k, v.readonly()) for k, v in self._data._params.items())
+
+    def values(self):
+        ''' Get iterator for parameter entries. '''
+        return (v.readonly() for v in self._data._params.values())
+
+    def keys(self):
+        ''' Get iterator for parameter entry keys. '''
+        return self._data._params.keys()
+
+    def get(self, key, default=None):
+        '''Get a readonly parameter by key.
+
+        Parameters
+        ----------
+        key : any
+            Parameter key to look up in this group.
+        default : any, optional
+            Value to return if the key is not found. Defaults to None.
+
+        Returns
+        -------
+        param : :class:`ParamReadable`
+            A parameter from the current group.
+        '''
+        val = self._data._params.get(key, default)
+        if val:
+            return val.readonly()
+        return default
+
+    def get_int8(self, key):
+        '''Get the value of the given parameter as an 8-bit signed integer.'''
+        return self._data[key.upper()].int8_value
+
+    def get_uint8(self, key):
+        '''Get the value of the given parameter as an 8-bit unsigned integer.'''
+        return self._data[key.upper()].uint8_value
+
+    def get_int16(self, key):
+        '''Get the value of the given parameter as a 16-bit signed integer.'''
+        return self._data[key.upper()].int16_value
+
+    def get_uint16(self, key):
+        '''Get the value of the given parameter as a 16-bit unsigned integer.'''
+        return self._data[key.upper()].uint16_value
+
+    def get_int32(self, key):
+        '''Get the value of the given parameter as a 32-bit signed integer.'''
+        return self._data[key.upper()].int32_value
+
+    def get_uint32(self, key):
+        '''Get the value of the given parameter as a 32-bit unsigned integer.'''
+        return self._data[key.upper()].uint32_value
+
+    def get_float(self, key):
+        '''Get the value of the given parameter as a 32-bit float.'''
+        return self._data[key.upper()].float_value
+
+    def get_bytes(self, key):
+        '''Get the value of the given parameter as a byte array.'''
+        return self._data[key.upper()].bytes_value
+
+    def get_string(self, key):
+        '''Get the value of the given parameter as a string.'''
+        return self._data[key.upper()].string_value

+

 
Subclasses

 
    
 
  • Group
    • 
@@ -354,10 +1696,28 @@ 
    Instance variables
    
 
    var desc : str
    
 
    
 
    Access group descriptor.
    
+
    
+
+Expand source code
+
+
    @property
+def desc(self) -> str:
+    '''Access group descriptor. '''
+    return self._data.desc
    
+
    
 
    
 
    var name : str
    
 
    
 
    Access group name.
    
+
    
+
+Expand source code
+
+
    @property
+def name(self) -> str:
+    ''' Access group name. '''
+    return self._data.name
    
+
    
 
    
 
 
    Methods
    
@@ -379,78 +1739,198 @@ 
    Returns
    
 
    param : :class:ParamReadable``
    
 
    A parameter from the current group.
    
 
+
    
+
+Expand source code
+
+
    def get(self, key, default=None):
+    '''Get a readonly parameter by key.
+
+    Parameters
+    ----------
+    key : any
+        Parameter key to look up in this group.
+    default : any, optional
+        Value to return if the key is not found. Defaults to None.
+
+    Returns
+    -------
+    param : :class:`ParamReadable`
+        A parameter from the current group.
+    '''
+    val = self._data._params.get(key, default)
+    if val:
+        return val.readonly()
+    return default
    
+
    
 

 

 def get_bytes(self, key)
 

 

 
Get the value of the given parameter as a byte array.

+

+
+Expand source code
+
+
def get_bytes(self, key):
+    '''Get the value of the given parameter as a byte array.'''
+    return self._data[key.upper()].bytes_value

+

 

 

 def get_float(self, key)
 

 

 
Get the value of the given parameter as a 32-bit float.

+

+
+Expand source code
+
+
def get_float(self, key):
+    '''Get the value of the given parameter as a 32-bit float.'''
+    return self._data[key.upper()].float_value

+

 

 

 def get_int16(self, key)
 

 

 
Get the value of the given parameter as a 16-bit signed integer.

+

+
+Expand source code
+
+
def get_int16(self, key):
+    '''Get the value of the given parameter as a 16-bit signed integer.'''
+    return self._data[key.upper()].int16_value

+

 

 

 def get_int32(self, key)
 

 

 
Get the value of the given parameter as a 32-bit signed integer.

+

+
+Expand source code
+
+
def get_int32(self, key):
+    '''Get the value of the given parameter as a 32-bit signed integer.'''
+    return self._data[key.upper()].int32_value

+

 

 

 def get_int8(self, key)
 

 

 
Get the value of the given parameter as an 8-bit signed integer.

+

+
+Expand source code
+
+
def get_int8(self, key):
+    '''Get the value of the given parameter as an 8-bit signed integer.'''
+    return self._data[key.upper()].int8_value

+

 

 

 def get_string(self, key)
 

 

 
Get the value of the given parameter as a string.

+

+
+Expand source code
+
+
def get_string(self, key):
+    '''Get the value of the given parameter as a string.'''
+    return self._data[key.upper()].string_value

+

 

 

 def get_uint16(self, key)
 

 

 
Get the value of the given parameter as a 16-bit unsigned integer.

+

+
+Expand source code
+
+
def get_uint16(self, key):
+    '''Get the value of the given parameter as a 16-bit unsigned integer.'''
+    return self._data[key.upper()].uint16_value

+

 

 

 def get_uint32(self, key)
 

 

 
Get the value of the given parameter as a 32-bit unsigned integer.

+

+
+Expand source code
+
+
def get_uint32(self, key):
+    '''Get the value of the given parameter as a 32-bit unsigned integer.'''
+    return self._data[key.upper()].uint32_value

+

 

 

 def get_uint8(self, key)
 

 

 
Get the value of the given parameter as an 8-bit unsigned integer.

+

+
+Expand source code
+
+
def get_uint8(self, key):
+    '''Get the value of the given parameter as an 8-bit unsigned integer.'''
+    return self._data[key.upper()].uint8_value

+

 

 

 def items(self)
 

 

 
Get iterator for paramater key-entry pairs.

+

+
+Expand source code
+
+
def items(self):
+    ''' Get iterator for paramater key-entry pairs. '''
+    return ((k, v.readonly()) for k, v in self._data._params.items())

+

 

 

 def keys(self)
 

 

 
Get iterator for parameter entry keys.

+

+
+Expand source code
+
+
def keys(self):
+    ''' Get iterator for parameter entry keys. '''
+    return self._data._params.keys()

+

 

 

 def values(self)
 

 

 
Get iterator for parameter entries.

+

+
+Expand source code
+
+
def values(self):
+    ''' Get iterator for parameter entries. '''
+    return (v.readonly() for v in self._data._params.values())

+

 

 
 
diff --git a/docs/c3d/header.html b/docs/c3d/header.html
index e29382b..dd42c47 100644
--- a/docs/c3d/header.html
+++ b/docs/c3d/header.html
@@ -23,6 +23,305 @@ 
Module c3d.header

 
 

 
Defines the header class used for reading, writing and tracking metadata in the .c3d header.

+

+
+Expand source code
+
+
'''
+Defines the header class used for reading, writing and tracking metadata in the .c3d header.
+'''
+import sys
+import struct
+import numpy as np
+from .utils import UNPACK_FLOAT_IEEE, DEC_to_IEEE
+
+class Header(object):
+    '''Header information from a C3D file.
+
+    Attributes
+    ----------
+    event_block : int
+        Index of the 512-byte block where labels (metadata) are found.
+    parameter_block : int
+        Index of the 512-byte block where parameters (metadata) are found.
+    data_block : int
+        Index of the 512-byte block where data starts.
+    point_count : int
+        Number of motion capture channels recorded in this file.
+    analog_count : int
+        Number of analog values recorded per frame of 3D point data.
+    first_frame : int
+        Index of the first frame of data.
+    last_frame : int
+        Index of the last frame of data.
+    analog_per_frame : int
+        Number of analog frames per frame of 3D point data. The analog frame
+        rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE)
+        times the analog per frame value.
+    frame_rate : float
+        The frame rate of the recording, in frames per second.
+    scale_factor : float
+        Multiply values in the file by this scale parameter.
+    long_event_labels : bool
+    max_gap : int
+
+    .. note::
+        The ``scale_factor`` attribute is not used in Phasespace C3D files;
+        instead, use the POINT.SCALE parameter.
+
+    .. note::
+        The ``first_frame`` and ``last_frame`` header attributes are not used in
+        C3D files generated by Phasespace. Instead, the first and last
+        frame numbers are stored in the POINTS:ACTUAL_START_FIELD and
+        POINTS:ACTUAL_END_FIELD parameters.
+    '''
+
+    # Read/Write header formats, read values as unsigned ints rather then floats.
+    BINARY_FORMAT_WRITE = '<BBHHHHHfHHf274sHHH164s44s'
+    BINARY_FORMAT_READ = '<BBHHHHHIHHI274sHHH164s44s'
+    BINARY_FORMAT_READ_BIG_ENDIAN = '>BBHHHHHIHHI274sHHH164s44s'
+
+    def __init__(self, handle=None):
+        '''Create a new Header object.
+
+        Parameters
+        ----------
+        handle : file handle, optional
+            If given, initialize attributes for the Header from this file
+            handle. The handle must be seek-able and readable. If `handle` is
+            not given, Header attributes are initialized with default values.
+        '''
+        self.parameter_block = 2
+        self.data_block = 3
+
+        self.point_count = 50
+        self.analog_count = 0
+
+        self.first_frame = 1
+        self.last_frame = 1
+        self.analog_per_frame = 0
+        self.frame_rate = 60.0
+
+        self.max_gap = 0
+        self.scale_factor = -1.0
+        self.long_event_labels = False
+        self.event_count = 0
+
+        self.event_block = b''
+        self.event_timings = np.zeros(0, dtype=np.float32)
+        self.event_disp_flags = np.zeros(0, dtype=np.bool)
+        self.event_labels = []
+
+        if handle:
+            self.read(handle)
+
+    def write(self, handle):
+        '''Write binary header data to a file handle.
+
+        This method writes exactly 512 bytes to the beginning of the given file
+        handle.
+
+        Parameters
+        ----------
+        handle : file handle
+            The given handle will be reset to 0 using `seek` and then 512 bytes
+            will be written to describe the parameters in this Header. The
+            handle must be writeable.
+        '''
+        handle.seek(0)
+        handle.write(struct.pack(self.BINARY_FORMAT_WRITE,
+                                 # Pack vars:
+                                 self.parameter_block,
+                                 0x50,
+                                 self.point_count,
+                                 self.analog_count,
+                                 self.first_frame,
+                                 self.last_frame,
+                                 self.max_gap,
+                                 self.scale_factor,
+                                 self.data_block,
+                                 self.analog_per_frame,
+                                 self.frame_rate,
+                                 b'',
+                                 self.long_event_labels and 0x3039 or 0x0,  # If True write long_event_key else 0
+                                 self.event_count,
+                                 0x0,
+                                 self.event_block,
+                                 b''))
+
+    def __str__(self):
+        '''Return a string representation of this Header's attributes.'''
+        return '''\
+                  parameter_block: {0.parameter_block}
+                      point_count: {0.point_count}
+                     analog_count: {0.analog_count}
+                      first_frame: {0.first_frame}
+                       last_frame: {0.last_frame}
+                          max_gap: {0.max_gap}
+                     scale_factor: {0.scale_factor}
+                       data_block: {0.data_block}
+                 analog_per_frame: {0.analog_per_frame}
+                       frame_rate: {0.frame_rate}
+                long_event_labels: {0.long_event_labels}
+                      event_block: {0.event_block}'''.format(self)
+
+    def read(self, handle, fmt=BINARY_FORMAT_READ):
+        '''Read and parse binary header data from a file handle.
+
+        This method reads exactly 512 bytes from the beginning of the given file
+        handle.
+
+        Parameters
+        ----------
+        handle : file handle
+            The given handle will be reset to 0 using `seek` and then 512 bytes
+            will be read to initialize the attributes in this Header. The handle
+            must be readable.
+
+        fmt : Formating string used to read the header.
+
+        Raises
+        ------
+        AssertionError
+            If the magic byte from the header is not 80 (the C3D magic value).
+        '''
+        handle.seek(0)
+        raw = handle.read(512)
+
+        (self.parameter_block,
+         magic,
+         self.point_count,
+         self.analog_count,
+         self.first_frame,
+         self.last_frame,
+         self.max_gap,
+         self.scale_factor,
+         self.data_block,
+         self.analog_per_frame,
+         self.frame_rate,
+         _,
+         self.long_event_labels,
+         self.event_count,
+         __,
+         self.event_block,
+         _) = struct.unpack(fmt, raw)
+
+        # Check magic number
+        assert magic == 80, 'C3D magic {} != 80 !'.format(magic)
+
+        # Check long event key
+        self.long_event_labels = self.long_event_labels == 0x3039
+
+    def _processor_convert(self, dtypes, handle):
+        ''' Function interpreting the header once a processor type has been determined.
+        '''
+
+        if dtypes.is_dec:
+            self.scale_factor = DEC_to_IEEE(self.scale_factor)
+            self.frame_rate = DEC_to_IEEE(self.frame_rate)
+            float_unpack = DEC_to_IEEE
+        elif dtypes.is_ieee:
+            self.scale_factor = UNPACK_FLOAT_IEEE(self.scale_factor)
+            self.frame_rate = UNPACK_FLOAT_IEEE(self.frame_rate)
+            float_unpack = UNPACK_FLOAT_IEEE
+        elif dtypes.is_mips:
+            # Re-read header in big-endian
+            self.read(handle, Header.BINARY_FORMAT_READ_BIG_ENDIAN)
+            # Then unpack
+            self.scale_factor = UNPACK_FLOAT_IEEE(self.scale_factor)
+            self.frame_rate = UNPACK_FLOAT_IEEE(self.frame_rate)
+            float_unpack = UNPACK_FLOAT_IEEE
+
+        self._parse_events(dtypes, float_unpack)
+
+    def _parse_events(self, dtypes, float_unpack):
+        ''' Parse the event section of the header.
+        '''
+
+        # Event section byte blocks
+        time_bytes = self.event_block[:72]
+        disp_bytes = self.event_block[72:90]
+        label_bytes = self.event_block[92:]
+
+        if dtypes.is_mips:
+            unpack_fmt = '>I'
+        else:
+            unpack_fmt = '<I'
+
+        read_count = self.event_count
+        self.event_timings = np.zeros(read_count, dtype=np.float32)
+        self.event_disp_flags = np.zeros(read_count, dtype=np.bool)
+        self.event_labels = np.empty(read_count, dtype=object)
+        for i in range(read_count):
+            ilong = i * 4
+            # Unpack
+            self.event_disp_flags[i] = disp_bytes[i] > 0
+            self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong + 4])[0])
+            self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong + 4])
+
+    @property
+    def events(self):
+        ''' Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label).
+
+            Note*:
+            Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter.
+            Frame 1 therefor has the time 0.0 in relation to the event timing.
+        '''
+        return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags])
+
+    def encode_events(self, events):
+        ''' Encode event data in the event block.
+
+        Parameters
+        ----------
+        events : [(float, str), ...]
+            Event data, iterable of touples containing the event timing and a 4 character label string.
+             Event timings should be calculated relative to sample 1 with the timing 0.0s, and should
+             not be relative to the first_frame header parameter.
+        '''
+        endian = '<'
+        if sys.byteorder == 'big':
+            endian = '>'
+
+        # Event block format
+        fmt = '{}{}{}{}{}'.format(endian,
+                                  str(18 * 4) + 's',  # Timings
+                                  str(18) + 's',      # Flags
+                                  'H',                # __
+                                  str(18 * 4) + 's'   # Labels
+                                 )
+        # Pack bytes
+        event_timings = np.zeros(18, dtype=np.float32)
+        event_disp_flags = np.zeros(18, dtype=np.uint8)
+        event_labels = np.empty(18, dtype=object)
+        label_bytes = bytearray(18 * 4)
+        for i, (time, label) in enumerate(events):
+            if i > 17:
+                # Don't raise Error, header events are rarely used.
+                warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.')
+                break
+
+            event_timings[i] = time
+            event_labels[i] = label
+            label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8')
+
+        write_count = min(i + 1, 18)
+        event_disp_flags[:write_count] = 1
+
+        # Update event headers in self
+        self.long_event_labels = 0x3039 # Magic number
+        self.event_count = write_count
+        # Update event block
+        self.event_timings = event_timings[:write_count]
+        self.event_disp_flags = np.ones(write_count, dtype=np.bool)
+        self.event_labels = event_labels[:write_count]
+        self.event_block = struct.pack(fmt,
+                                       event_timings.tobytes(),
+                                       event_disp_flags.tobytes(),
+                                       0,
+                                       label_bytes
+                                      )

+

 

 

 

@@ -88,6 +387,297 @@ 
Parameters

 handle. The handle must be seek-able and readable. If handle is
 not given, Header attributes are initialized with default values.
 
+

+
+Expand source code
+
+
class Header(object):
+    '''Header information from a C3D file.
+
+    Attributes
+    ----------
+    event_block : int
+        Index of the 512-byte block where labels (metadata) are found.
+    parameter_block : int
+        Index of the 512-byte block where parameters (metadata) are found.
+    data_block : int
+        Index of the 512-byte block where data starts.
+    point_count : int
+        Number of motion capture channels recorded in this file.
+    analog_count : int
+        Number of analog values recorded per frame of 3D point data.
+    first_frame : int
+        Index of the first frame of data.
+    last_frame : int
+        Index of the last frame of data.
+    analog_per_frame : int
+        Number of analog frames per frame of 3D point data. The analog frame
+        rate (ANALOG:RATE) is equivalent to the point frame rate (POINT:RATE)
+        times the analog per frame value.
+    frame_rate : float
+        The frame rate of the recording, in frames per second.
+    scale_factor : float
+        Multiply values in the file by this scale parameter.
+    long_event_labels : bool
+    max_gap : int
+
+    .. note::
+        The ``scale_factor`` attribute is not used in Phasespace C3D files;
+        instead, use the POINT.SCALE parameter.
+
+    .. note::
+        The ``first_frame`` and ``last_frame`` header attributes are not used in
+        C3D files generated by Phasespace. Instead, the first and last
+        frame numbers are stored in the POINTS:ACTUAL_START_FIELD and
+        POINTS:ACTUAL_END_FIELD parameters.
+    '''
+
+    # Read/Write header formats, read values as unsigned ints rather then floats.
+    BINARY_FORMAT_WRITE = '<BBHHHHHfHHf274sHHH164s44s'
+    BINARY_FORMAT_READ = '<BBHHHHHIHHI274sHHH164s44s'
+    BINARY_FORMAT_READ_BIG_ENDIAN = '>BBHHHHHIHHI274sHHH164s44s'
+
+    def __init__(self, handle=None):
+        '''Create a new Header object.
+
+        Parameters
+        ----------
+        handle : file handle, optional
+            If given, initialize attributes for the Header from this file
+            handle. The handle must be seek-able and readable. If `handle` is
+            not given, Header attributes are initialized with default values.
+        '''
+        self.parameter_block = 2
+        self.data_block = 3
+
+        self.point_count = 50
+        self.analog_count = 0
+
+        self.first_frame = 1
+        self.last_frame = 1
+        self.analog_per_frame = 0
+        self.frame_rate = 60.0
+
+        self.max_gap = 0
+        self.scale_factor = -1.0
+        self.long_event_labels = False
+        self.event_count = 0
+
+        self.event_block = b''
+        self.event_timings = np.zeros(0, dtype=np.float32)
+        self.event_disp_flags = np.zeros(0, dtype=np.bool)
+        self.event_labels = []
+
+        if handle:
+            self.read(handle)
+
+    def write(self, handle):
+        '''Write binary header data to a file handle.
+
+        This method writes exactly 512 bytes to the beginning of the given file
+        handle.
+
+        Parameters
+        ----------
+        handle : file handle
+            The given handle will be reset to 0 using `seek` and then 512 bytes
+            will be written to describe the parameters in this Header. The
+            handle must be writeable.
+        '''
+        handle.seek(0)
+        handle.write(struct.pack(self.BINARY_FORMAT_WRITE,
+                                 # Pack vars:
+                                 self.parameter_block,
+                                 0x50,
+                                 self.point_count,
+                                 self.analog_count,
+                                 self.first_frame,
+                                 self.last_frame,
+                                 self.max_gap,
+                                 self.scale_factor,
+                                 self.data_block,
+                                 self.analog_per_frame,
+                                 self.frame_rate,
+                                 b'',
+                                 self.long_event_labels and 0x3039 or 0x0,  # If True write long_event_key else 0
+                                 self.event_count,
+                                 0x0,
+                                 self.event_block,
+                                 b''))
+
+    def __str__(self):
+        '''Return a string representation of this Header's attributes.'''
+        return '''\
+                  parameter_block: {0.parameter_block}
+                      point_count: {0.point_count}
+                     analog_count: {0.analog_count}
+                      first_frame: {0.first_frame}
+                       last_frame: {0.last_frame}
+                          max_gap: {0.max_gap}
+                     scale_factor: {0.scale_factor}
+                       data_block: {0.data_block}
+                 analog_per_frame: {0.analog_per_frame}
+                       frame_rate: {0.frame_rate}
+                long_event_labels: {0.long_event_labels}
+                      event_block: {0.event_block}'''.format(self)
+
+    def read(self, handle, fmt=BINARY_FORMAT_READ):
+        '''Read and parse binary header data from a file handle.
+
+        This method reads exactly 512 bytes from the beginning of the given file
+        handle.
+
+        Parameters
+        ----------
+        handle : file handle
+            The given handle will be reset to 0 using `seek` and then 512 bytes
+            will be read to initialize the attributes in this Header. The handle
+            must be readable.
+
+        fmt : Formating string used to read the header.
+
+        Raises
+        ------
+        AssertionError
+            If the magic byte from the header is not 80 (the C3D magic value).
+        '''
+        handle.seek(0)
+        raw = handle.read(512)
+
+        (self.parameter_block,
+         magic,
+         self.point_count,
+         self.analog_count,
+         self.first_frame,
+         self.last_frame,
+         self.max_gap,
+         self.scale_factor,
+         self.data_block,
+         self.analog_per_frame,
+         self.frame_rate,
+         _,
+         self.long_event_labels,
+         self.event_count,
+         __,
+         self.event_block,
+         _) = struct.unpack(fmt, raw)
+
+        # Check magic number
+        assert magic == 80, 'C3D magic {} != 80 !'.format(magic)
+
+        # Check long event key
+        self.long_event_labels = self.long_event_labels == 0x3039
+
+    def _processor_convert(self, dtypes, handle):
+        ''' Function interpreting the header once a processor type has been determined.
+        '''
+
+        if dtypes.is_dec:
+            self.scale_factor = DEC_to_IEEE(self.scale_factor)
+            self.frame_rate = DEC_to_IEEE(self.frame_rate)
+            float_unpack = DEC_to_IEEE
+        elif dtypes.is_ieee:
+            self.scale_factor = UNPACK_FLOAT_IEEE(self.scale_factor)
+            self.frame_rate = UNPACK_FLOAT_IEEE(self.frame_rate)
+            float_unpack = UNPACK_FLOAT_IEEE
+        elif dtypes.is_mips:
+            # Re-read header in big-endian
+            self.read(handle, Header.BINARY_FORMAT_READ_BIG_ENDIAN)
+            # Then unpack
+            self.scale_factor = UNPACK_FLOAT_IEEE(self.scale_factor)
+            self.frame_rate = UNPACK_FLOAT_IEEE(self.frame_rate)
+            float_unpack = UNPACK_FLOAT_IEEE
+
+        self._parse_events(dtypes, float_unpack)
+
+    def _parse_events(self, dtypes, float_unpack):
+        ''' Parse the event section of the header.
+        '''
+
+        # Event section byte blocks
+        time_bytes = self.event_block[:72]
+        disp_bytes = self.event_block[72:90]
+        label_bytes = self.event_block[92:]
+
+        if dtypes.is_mips:
+            unpack_fmt = '>I'
+        else:
+            unpack_fmt = '<I'
+
+        read_count = self.event_count
+        self.event_timings = np.zeros(read_count, dtype=np.float32)
+        self.event_disp_flags = np.zeros(read_count, dtype=np.bool)
+        self.event_labels = np.empty(read_count, dtype=object)
+        for i in range(read_count):
+            ilong = i * 4
+            # Unpack
+            self.event_disp_flags[i] = disp_bytes[i] > 0
+            self.event_timings[i] = float_unpack(struct.unpack(unpack_fmt, time_bytes[ilong:ilong + 4])[0])
+            self.event_labels[i] = dtypes.decode_string(label_bytes[ilong:ilong + 4])
+
+    @property
+    def events(self):
+        ''' Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label).
+
+            Note*:
+            Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter.
+            Frame 1 therefor has the time 0.0 in relation to the event timing.
+        '''
+        return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags])
+
+    def encode_events(self, events):
+        ''' Encode event data in the event block.
+
+        Parameters
+        ----------
+        events : [(float, str), ...]
+            Event data, iterable of touples containing the event timing and a 4 character label string.
+             Event timings should be calculated relative to sample 1 with the timing 0.0s, and should
+             not be relative to the first_frame header parameter.
+        '''
+        endian = '<'
+        if sys.byteorder == 'big':
+            endian = '>'
+
+        # Event block format
+        fmt = '{}{}{}{}{}'.format(endian,
+                                  str(18 * 4) + 's',  # Timings
+                                  str(18) + 's',      # Flags
+                                  'H',                # __
+                                  str(18 * 4) + 's'   # Labels
+                                 )
+        # Pack bytes
+        event_timings = np.zeros(18, dtype=np.float32)
+        event_disp_flags = np.zeros(18, dtype=np.uint8)
+        event_labels = np.empty(18, dtype=object)
+        label_bytes = bytearray(18 * 4)
+        for i, (time, label) in enumerate(events):
+            if i > 17:
+                # Don't raise Error, header events are rarely used.
+                warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.')
+                break
+
+            event_timings[i] = time
+            event_labels[i] = label
+            label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8')
+
+        write_count = min(i + 1, 18)
+        event_disp_flags[:write_count] = 1
+
+        # Update event headers in self
+        self.long_event_labels = 0x3039 # Magic number
+        self.event_count = write_count
+        # Update event block
+        self.event_timings = event_timings[:write_count]
+        self.event_disp_flags = np.ones(write_count, dtype=np.bool)
+        self.event_labels = event_labels[:write_count]
+        self.event_block = struct.pack(fmt,
+                                       event_timings.tobytes(),
+                                       event_disp_flags.tobytes(),
+                                       0,
+                                       label_bytes
+                                      )

+

 
Class variables

 

 
var BINARY_FORMAT_READ

@@ -111,6 +701,20 @@ 
Instance variables

 
Note*:
 Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter.
 Frame 1 therefor has the time 0.0 in relation to the event timing.

+

+
+Expand source code
+
+
@property
+def events(self):
+    ''' Get an iterable over displayed events defined in the header. Iterable items are on form (timing, label).
+
+        Note*:
+        Time as defined by the 'timing' is relative to frame 1 and not the 'first_frame' parameter.
+        Frame 1 therefor has the time 0.0 in relation to the event timing.
+    '''
+    return zip(self.event_timings[self.event_disp_flags], self.event_labels[self.event_disp_flags])

+

 
 

 
Methods

@@ -127,6 +731,63 @@ 
Parameters

 Event timings should be calculated relative to sample 1 with the timing 0.0s, and should
 not be relative to the first_frame header parameter.
 
+

+
+Expand source code
+
+
def encode_events(self, events):
+    ''' Encode event data in the event block.
+
+    Parameters
+    ----------
+    events : [(float, str), ...]
+        Event data, iterable of touples containing the event timing and a 4 character label string.
+         Event timings should be calculated relative to sample 1 with the timing 0.0s, and should
+         not be relative to the first_frame header parameter.
+    '''
+    endian = '<'
+    if sys.byteorder == 'big':
+        endian = '>'
+
+    # Event block format
+    fmt = '{}{}{}{}{}'.format(endian,
+                              str(18 * 4) + 's',  # Timings
+                              str(18) + 's',      # Flags
+                              'H',                # __
+                              str(18 * 4) + 's'   # Labels
+                             )
+    # Pack bytes
+    event_timings = np.zeros(18, dtype=np.float32)
+    event_disp_flags = np.zeros(18, dtype=np.uint8)
+    event_labels = np.empty(18, dtype=object)
+    label_bytes = bytearray(18 * 4)
+    for i, (time, label) in enumerate(events):
+        if i > 17:
+            # Don't raise Error, header events are rarely used.
+            warnings.warn('Maximum of 18 events can be encoded in the header, skipping remaining events.')
+            break
+
+        event_timings[i] = time
+        event_labels[i] = label
+        label_bytes[i * 4:(i + 1) * 4] = label.encode('utf-8')
+
+    write_count = min(i + 1, 18)
+    event_disp_flags[:write_count] = 1
+
+    # Update event headers in self
+    self.long_event_labels = 0x3039 # Magic number
+    self.event_count = write_count
+    # Update event block
+    self.event_timings = event_timings[:write_count]
+    self.event_disp_flags = np.ones(write_count, dtype=np.bool)
+    self.event_labels = event_labels[:write_count]
+    self.event_block = struct.pack(fmt,
+                                   event_timings.tobytes(),
+                                   event_disp_flags.tobytes(),
+                                   0,
+                                   label_bytes
+                                  )

+

 
 

 def read(self, handle, fmt='<BBHHHHHIHHI274sHHH164s44s')
@@ -148,6 +809,57 @@ 
Raises

 
AssertionError

 
If the magic byte from the header is not 80 (the C3D magic value).

 
+

+
+Expand source code
+
+
def read(self, handle, fmt=BINARY_FORMAT_READ):
+    '''Read and parse binary header data from a file handle.
+
+    This method reads exactly 512 bytes from the beginning of the given file
+    handle.
+
+    Parameters
+    ----------
+    handle : file handle
+        The given handle will be reset to 0 using `seek` and then 512 bytes
+        will be read to initialize the attributes in this Header. The handle
+        must be readable.
+
+    fmt : Formating string used to read the header.
+
+    Raises
+    ------
+    AssertionError
+        If the magic byte from the header is not 80 (the C3D magic value).
+    '''
+    handle.seek(0)
+    raw = handle.read(512)
+
+    (self.parameter_block,
+     magic,
+     self.point_count,
+     self.analog_count,
+     self.first_frame,
+     self.last_frame,
+     self.max_gap,
+     self.scale_factor,
+     self.data_block,
+     self.analog_per_frame,
+     self.frame_rate,
+     _,
+     self.long_event_labels,
+     self.event_count,
+     __,
+     self.event_block,
+     _) = struct.unpack(fmt, raw)
+
+    # Check magic number
+    assert magic == 80, 'C3D magic {} != 80 !'.format(magic)
+
+    # Check long event key
+    self.long_event_labels = self.long_event_labels == 0x3039

+

 
 

 def write(self, handle)
@@ -163,6 +875,44 @@ 
Parameters

 will be written to describe the parameters in this Header. The
 handle must be writeable.
 
+

+
+Expand source code
+
+
def write(self, handle):
+    '''Write binary header data to a file handle.
+
+    This method writes exactly 512 bytes to the beginning of the given file
+    handle.
+
+    Parameters
+    ----------
+    handle : file handle
+        The given handle will be reset to 0 using `seek` and then 512 bytes
+        will be written to describe the parameters in this Header. The
+        handle must be writeable.
+    '''
+    handle.seek(0)
+    handle.write(struct.pack(self.BINARY_FORMAT_WRITE,
+                             # Pack vars:
+                             self.parameter_block,
+                             0x50,
+                             self.point_count,
+                             self.analog_count,
+                             self.first_frame,
+                             self.last_frame,
+                             self.max_gap,
+                             self.scale_factor,
+                             self.data_block,
+                             self.analog_per_frame,
+                             self.frame_rate,
+                             b'',
+                             self.long_event_labels and 0x3039 or 0x0,  # If True write long_event_key else 0
+                             self.event_count,
+                             0x0,
+                             self.event_block,
+                             b''))

+

 
 
 
diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index 774bb4e..1b42573 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -31,7 +31,7 @@ 
Installing

 
See the main page or github page.

 
Examples

 
Access to data blocks in a .c3d file is provided through the Reader and Writer classes.
-Runnable implementation of the examples are provided in the examples/ directory in the github repository.

+Implementation of the examples below are provided in the examples/ directory in the github repository.

 
Reading

 
To read the frames from a C3D file, use a Reader instance:

 
import c3d
@@ -77,10 +77,11 @@ 
Writing

 is called, which serializes the metadata and data frames into a C3D binary file stream.

 
Editing

 
Editing c3d files is possible by combining the use of Reader and Writer
-instances through the use of Reader.to_writer(). Opening a .c3d file stream through
-a reader instance, Reader.to_writer() can be used to create an independent Writer instance
-containing a heap copy of the file contents. Rereading the data frames from the file
-and inserting into the writer in reverse, a looped version of the .c3d file can be created!

+instances through the Reader.to_writer() method. To edit a file, open a file stream and pass
+it to a Reader instance. Convert it using the Reader.to_writer() method to create
+an independent Writer instance containing a heap copy of the file contents.
+Rereading the data frames from the reader and inserting them in reverse into
+the writer will then create a looped version of the .c3d file!

 
import c3d
 
 with open('my-motion.c3d', 'rb') as file:
@@ -92,6 +93,71 @@ 
Editing

 with open('my-looped-motion.c3d', 'wb') as h:
     writer.write(h)
 

+
Accessing Metadata

+
Metadata in a .c3d file exists in two forms, a Header and ParamData.
+Reading metadata fields can be done though the Reader but editing requires a
+Writer instance.

+
Header fields can be accessed from the common Manager.header attribute.
+Parameters are available through a parameter Group, and can be accessed
+through the Manager.get() method:

+
group = reader.get('POINT')
+param = group.get('LABELS')
+

+
or use the simpler method

+
param = reader.get('POINT:LABELS')
+

+
Note that for accessing parameters in the Reader, Reader.get()
+returns a GroupReadonly instance. Convenience functions are provided
+for some of the common metadata fields
+such as Manager.frame_count. In the case you require specific
+metadata fields, consider visiting the documentation for the C3D format and/or inspect
+the file using the c3d-metadata script.

+
Writing Metadata

+
Once a Writer instance is created, to edit
+parameter data Writer.get_create() a group:

+
group = writer.get_create('ANALOG')
+

+
and to write a float32 entry, use the Group.add() or Group.set() functions

+
group.set('GEN_SCALE', 'Analog general scale factor', 4, '<f', value)
+

+
In this case, one can use the Writer.set_analog_general_scale() method instead.
+For serializing other types, see the source code for some of the convenience functions such as
+Writer.set_point_labels() (2D string array) or
+Writer.set_analog_scales() (1D float array).

+

+
+Expand source code
+
+
"""
+---------------------
+Python C3D Processing
+---------------------
+
+This package provides pure Python modules for reading, writing, and editing binary
+motion-capture files in the [C3D file format].
+
+[C3D file format]: https://www.c3d.org/HTML/default.htm
+
+Installing
+----------
+
+See the [main page] or [github page].
+
+[main page]: https://mattiasfredriksson.github.io/py-c3d/
+[github page]: https://github.com/EmbodiedCognition/py-c3d
+
+.. include:: ../docs/examples.md
+
+"""
+from . import dtypes
+from . import group
+from . import header
+from . import manager
+from . import parameter
+from . import utils
+from .reader import Reader
+from .writer import Writer

+

 
 

 
Sub-modules

@@ -118,7 +184,7 @@ 
Sub-modules

 
 
c3d.reader

 

-
A Python module for reading and writing C3D files.

+
Contains the Reader class for reading C3D files.

 

 
c3d.utils

 

@@ -126,7 +192,7 @@ 
Sub-modules

 

 
c3d.writer

 

-
A Python module for reading and writing C3D files.

+
Contains the Writer class for writing C3D files.

 

 
 

@@ -147,6 +213,8 @@ 
Index

 
  • Reading
    • 
 
  • Writing
    • 
 
  • Editing
    • 
+
  • Accessing metadata
    • 
+
  • Writing metadata
    • 
 
 
 
diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html
index f0ce4b0..41cfcbe 100644
--- a/docs/c3d/manager.html
+++ b/docs/c3d/manager.html
@@ -23,6 +23,462 @@ 
    Module c3d.manager
    
 
 
    
 
    Manager base class defining common attributes for both the Reader and Writer instances.
    
+
    
+
+Expand source code
+
+
    ''' Manager base class defining common attributes for both the Reader and Writer instances.
+'''
+import numpy as np
+import warnings
+from .header import Header
+from .group import GroupData, GroupReadonly, Group
+from .utils import is_integer, is_iterable
+
+
+class Manager(object):
+    '''A base class for managing C3D file metadata.
+
+    This class manages a C3D header (which contains some stock metadata fields)
+    as well as a set of parameter groups. Each group is accessible using its
+    name.
+
+    Attributes
+    ----------
+    header : `c3d.header.Header`
+        Header information for the C3D file.
+    '''
+
+    def __init__(self, header=None):
+        '''Set up a new Manager with a Header.'''
+        self._header = header or Header()
+        self._groups = {}
+
+    def __contains__(self, key):
+        return key in self._groups
+
+    def items(self):
+        ''' Get iterable over pairs of (str, `c3d.group.Group`) entries.
+        '''
+        return ((k, v) for k, v in self._groups.items() if isinstance(k, str))
+
+    def values(self):
+        ''' Get iterable over `c3d.group.Group` entries.
+        '''
+        return (v for k, v in self._groups.items() if isinstance(k, str))
+
+    def keys(self):
+        ''' Get iterable over parameter name keys.
+        '''
+        return (k for k in self._groups.keys() if isinstance(k, str))
+
+    def listed(self):
+        ''' Get iterable over pairs of (int, `c3d.group.Group`) entries.
+        '''
+        return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int))
+
+    def _check_metadata(self):
+        ''' Ensure that the metadata in our file is self-consistent. '''
+        assert self._header.point_count == self.point_used, (
+            'inconsistent point count! {} header != {} POINT:USED'.format(
+                self._header.point_count,
+                self.point_used,
+            ))
+
+        assert self._header.scale_factor == self.point_scale, (
+            'inconsistent scale factor! {} header != {} POINT:SCALE'.format(
+                self._header.scale_factor,
+                self.point_scale,
+            ))
+
+        assert self._header.frame_rate == self.point_rate, (
+            'inconsistent frame rate! {} header != {} POINT:RATE'.format(
+                self._header.frame_rate,
+                self.point_rate,
+            ))
+
+        if self.point_rate:
+            ratio = self.analog_rate / self.point_rate
+        else:
+            ratio = 0
+        assert self._header.analog_per_frame == ratio, (
+            'inconsistent analog rate! {} header != {} analog-fps / {} point-fps'.format(
+                self._header.analog_per_frame,
+                self.analog_rate,
+                self.point_rate,
+            ))
+
+        count = self.analog_used * self._header.analog_per_frame
+        assert self._header.analog_count == count, (
+            'inconsistent analog count! {} header != {} analog used * {} per-frame'.format(
+                self._header.analog_count,
+                self.analog_used,
+                self._header.analog_per_frame,
+            ))
+
+        try:
+            start = self.get_uint16('POINT:DATA_START')
+            if self._header.data_block != start:
+                warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format(
+                    self._header.data_block, start))
+        except AttributeError:
+            warnings.warn('''no pointer available in POINT:DATA_START indicating the start of the data block, using
+                             header pointer as fallback''')
+
+        def check_parameters(params):
+            for name in params:
+                if self.get(name) is None:
+                    warnings.warn('missing parameter {}'.format(name))
+
+        if self.point_used > 0:
+            check_parameters(('POINT:LABELS', 'POINT:DESCRIPTIONS'))
+        else:
+            lab = self.get('POINT:LABELS')
+            if lab is None:
+                warnings.warn('No point data found in file.')
+            elif lab.num_elements > 0:
+                warnings.warn('No point data found in file, but file contains POINT:LABELS entries')
+        if self.analog_used > 0:
+            check_parameters(('ANALOG:LABELS', 'ANALOG:DESCRIPTIONS'))
+        else:
+            lab = self.get('ANALOG:LABELS')
+            if lab is None:
+                warnings.warn('No analog data found in file.')
+            elif lab.num_elements > 0:
+                warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries')
+
+
+    def _add_group(self, group_id, name=None, desc=None):
+        '''Add a new parameter group.
+
+        Parameters
+        ----------
+        group_id : int
+            The numeric ID for a group to check or create.
+        name : str, optional
+            If a group is created, assign this name to the group.
+        desc : str, optional
+            If a group is created, assign this description to the group.
+
+        Returns
+        -------
+        group : :class:`Group`
+            A group with the given ID, name, and description.
+
+        Raises
+        ------
+        TypeError
+            Input arguments are of the wrong type.
+        KeyError
+            Name or numerical key already exist (attempt to overwrite existing data).
+        '''
+        if not is_integer(group_id):
+            raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id))
+        if not isinstance(name, str):
+            if name is not None:
+                raise TypeError('Expected Group name key to be string, was %s.' % type(name))
+        else:
+            name = name.upper()
+        group_id = int(group_id) # Asserts python int
+        if group_id in self._groups:
+            raise KeyError('Group with numerical key {} already exists'.format(group_id))
+        if name in self._groups:
+            raise KeyError('No group matched name key {}'.format(name))
+        group = self._groups[name] = self._groups[group_id] = Group(GroupData(self._dtypes, name, desc))
+        return group
+
+    def _remove_group(self, group_id):
+        '''Remove the parameter group.
+
+        Parameters
+        ----------
+        group_id : int, or str
+            The numeric or name ID key for a group to remove all entries for.
+        '''
+        grp = self._groups.get(group_id, None)
+        if grp is None:
+            return
+        gkeys = [k for (k, v) in self._groups.items() if v == grp]
+        for k in gkeys:
+            del self._groups[k]
+
+    def _rename_group(self, group_id, new_group_id):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        group_id : int, str, or 'Group'
+            Group instance, name, or numerical identifier for the group.
+        new_group_id : str, or int
+            If string, it is the new name for the group. If integer, it will replace its numerical group id.
+
+        Raises
+        ------
+        KeyError
+            If a group with a duplicate ID or name already exists.
+        '''
+        if isinstance(group_id, GroupReadonly):
+            grp = group_id._data
+        else:
+            # Aquire instance using id
+            grp = self._groups.get(group_id, None)
+            if grp is None:
+                raise KeyError('No group found matching the identifier: %s' % str(group_id))
+        if new_group_id in self._groups:
+            if new_group_id == group_id:
+                return
+            raise ValueError('Key %s for group %s already exist.' % (str(new_group_id), grp.name))
+
+        # Clear old id
+        if isinstance(new_group_id, (str, bytes)):
+            if grp.name in self._groups:
+                del self._groups[grp.name]
+            grp.name = new_group_id
+        elif is_integer(new_group_id):
+            new_group_id = int(new_group_id) # Ensure python int
+            del self._groups[group_id]
+        else:
+            raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id)))
+        # Update
+        self._groups[new_group_id] = grp
+
+    def get(self, group, default=None):
+        '''Get a group or parameter.
+
+        Parameters
+        ----------
+        group : str
+            If this string contains a period (.), then the part before the
+            period will be used to retrieve a group, and the part after the
+            period will be used to retrieve a parameter from that group. If this
+            string does not contain a period, then just a group will be
+            returned.
+        default : any
+            Return this value if the named group and parameter are not found.
+
+        Returns
+        -------
+        value : `c3d.group.Group` or `c3d.parameter.Param`
+            Either a group or parameter with the specified name(s). If neither
+            is found, returns the default value.
+        '''
+        if is_integer(group):
+            group = self._groups.get(int(group))
+            if group is None:
+                return default
+            return group
+        group = group.upper()
+        param = None
+        if '.' in group:
+            group, param = group.split('.', 1)
+        if ':' in group:
+            group, param = group.split(':', 1)
+        if group not in self._groups:
+            return default
+        group = self._groups[group]
+        if param is not None:
+            return group.get(param, default)
+        return group
+
+    @property
+    def header(self) -> '`c3d.header.Header`':
+        ''' Access to .c3d header data. '''
+        return self._header
+
+    def parameter_blocks(self) -> int:
+        '''Compute the size (in 512B blocks) of the parameter section.'''
+        bytes = 4. + sum(g._data.binary_size for g in self._groups.values())
+        return int(np.ceil(bytes / 512))
+
+    @property
+    def point_rate(self) -> float:
+        ''' Number of sampled 3D coordinates per second. '''
+        try:
+            return self.get_float('POINT:RATE')
+        except AttributeError:
+            return self.header.frame_rate
+
+    @property
+    def point_scale(self) -> float:
+        ''' Scaling applied to non-float data. '''
+        try:
+            return self.get_float('POINT:SCALE')
+        except AttributeError:
+            return self.header.scale_factor
+
+    @property
+    def point_used(self) -> int:
+        ''' Number of sampled 3D point coordinates per frame. '''
+        try:
+            return self.get_uint16('POINT:USED')
+        except AttributeError:
+            return self.header.point_count
+
+    @property
+    def analog_used(self) -> int:
+        ''' Number of analog measurements, or channels, for each analog data sample. '''
+        try:
+            return self.get_uint16('ANALOG:USED')
+        except AttributeError:
+            per_frame = self.header.analog_per_frame
+            if per_frame > 0:
+                return int(self.header.analog_count / per_frame)
+            return 0
+
+    @property
+    def analog_rate(self) -> float:
+        '''  Number of analog data samples per second. '''
+        try:
+            return self.get_float('ANALOG:RATE')
+        except AttributeError:
+            return self.header.analog_per_frame * self.point_rate
+
+    @property
+    def analog_per_frame(self) -> int:
+        '''  Number of analog frames per 3D frame (point sample). '''
+        return int(self.analog_rate / self.point_rate)
+
+    @property
+    def analog_sample_count(self) -> int:
+        ''' Number of analog samples per channel. '''
+        has_analog = self.analog_used > 0
+        return int(self.frame_count * self.analog_per_frame) * has_analog
+
+    @property
+    def point_labels(self) -> list:
+        ''' Labels for each POINT data channel. '''
+        return self.get('POINT:LABELS').string_array
+
+    @property
+    def analog_labels(self) -> list:
+        ''' Labels for each ANALOG data channel. '''
+        return self.get('ANALOG:LABELS').string_array
+
+    @property
+    def frame_count(self) -> int:
+        ''' Number of frames recorded in the data. '''
+        return self.last_frame - self.first_frame + 1  # Add 1 since range is inclusive [first, last]
+
+    @property
+    def first_frame(self) -> int:
+        ''' Trial frame corresponding to the first frame recorded in the data. '''
+        # Start frame seems to be less of an issue to determine.
+        # this is a hack for phasespace files ... should put it in a subclass.
+        param = self.get('TRIAL:ACTUAL_START_FIELD')
+        if param is not None:
+            # ACTUAL_START_FIELD is encoded in two 16 byte words...
+            words = param.uint16_array
+            return words[0] + words[1] * 65535
+        return self.header.first_frame
+
+    @property
+    def last_frame(self) -> int:
+        ''' Trial frame corresponding to the last frame recorded in the data (inclusive). '''
+        # Number of frames can be represented in many formats, first check if valid header values
+        if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535:
+            return self.header.last_frame
+
+        # Check different parameter options where the frame can be encoded
+        end_frame = [self.header.last_frame, 0.0, 0.0, 0.0]
+        param = self.get('TRIAL:ACTUAL_END_FIELD')
+        if param is not None:
+            # Encoded as 2 16 bit words (rather then 1 32 bit word)
+            words = param.uint16_array
+            end_frame[1] = words[0] + words[1] * 65536
+            #end_frame[1] = param.uint32_value
+        param = self.get('POINT:LONG_FRAMES')
+        if param is not None:
+            # Encoded as float
+            end_frame[2] = int(param.float_value)
+        param = self.get('POINT:FRAMES')
+        if param is not None:
+            # Can be encoded either as 32 bit float or 16 bit uint
+            if param.bytes_per_element == 2:
+                end_frame[3] = param.uint16_value
+            else:
+                end_frame[3] = int(param.float_value)
+        # Return the largest of the all (queue bad reading...)
+        return int(np.max(end_frame))
+
+    def get_screen_axis(self):
+        ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+        Returns
+        -------
+        value : (str, str) or None
+            Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+        '''
+        X = self.get('POINT:X_SCREEN')
+        Y = self.get('POINT:Y_SCREEN')
+        if X and Y:
+            return (X.string_value, Y.string_value)
+        return None
+
+    def get_analog_transform_parameters(self):
+        ''' Parse analog data transform parameters. '''
+        # Offsets
+        analog_offsets = np.zeros((self.analog_used), int)
+        param = self.get('ANALOG:OFFSET')
+        if param is not None and param.num_elements > 0:
+            analog_offsets[:] = param.int16_array[:self.analog_used]
+
+        # Scale factors
+        analog_scales = np.ones((self.analog_used), float)
+        gen_scale = 1.
+        param = self.get('ANALOG:GEN_SCALE')
+        if param is not None:
+            gen_scale = param.float_value
+        param = self.get('ANALOG:SCALE')
+        if param is not None and param.num_elements > 0:
+            analog_scales[:] = param.float_array[:self.analog_used]
+
+        return gen_scale, analog_scales, analog_offsets
+
+    def get_analog_transform(self):
+        ''' Get broadcastable analog transformation parameters.
+        '''
+        gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters()
+        analog_scales *= gen_scale
+        analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+        analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+        return analog_scales, analog_offsets
+
+    def get_int8(self, key):
+        '''Get a parameter value as an 8-bit signed integer.'''
+        return self.get(key).int8_value
+
+    def get_uint8(self, key):
+        '''Get a parameter value as an 8-bit unsigned integer.'''
+        return self.get(key).uint8_value
+
+    def get_int16(self, key):
+        '''Get a parameter value as a 16-bit signed integer.'''
+        return self.get(key).int16_value
+
+    def get_uint16(self, key):
+        '''Get a parameter value as a 16-bit unsigned integer.'''
+        return self.get(key).uint16_value
+
+    def get_int32(self, key):
+        '''Get a parameter value as a 32-bit signed integer.'''
+        return self.get(key).int32_value
+
+    def get_uint32(self, key):
+        '''Get a parameter value as a 32-bit unsigned integer.'''
+        return self.get(key).uint32_value
+
+    def get_float(self, key):
+        '''Get a parameter value as a 32-bit float.'''
+        return self.get(key).float_value
+
+    def get_bytes(self, key):
+        '''Get a parameter value as a byte string.'''
+        return self.get(key).bytes_value
+
+    def get_string(self, key):
+        '''Get a parameter value as a string.'''
+        return self.get(key).string_value
    
+
    
 
    
 
    
 
    
@@ -48,6 +504,453 @@ 
    Attributes
    
 
    Header information for the C3D file.
    
 
 
    Set up a new Manager with a Header.
    
+
    
+
+Expand source code
+
+
    class Manager(object):
+    '''A base class for managing C3D file metadata.
+
+    This class manages a C3D header (which contains some stock metadata fields)
+    as well as a set of parameter groups. Each group is accessible using its
+    name.
+
+    Attributes
+    ----------
+    header : `c3d.header.Header`
+        Header information for the C3D file.
+    '''
+
+    def __init__(self, header=None):
+        '''Set up a new Manager with a Header.'''
+        self._header = header or Header()
+        self._groups = {}
+
+    def __contains__(self, key):
+        return key in self._groups
+
+    def items(self):
+        ''' Get iterable over pairs of (str, `c3d.group.Group`) entries.
+        '''
+        return ((k, v) for k, v in self._groups.items() if isinstance(k, str))
+
+    def values(self):
+        ''' Get iterable over `c3d.group.Group` entries.
+        '''
+        return (v for k, v in self._groups.items() if isinstance(k, str))
+
+    def keys(self):
+        ''' Get iterable over parameter name keys.
+        '''
+        return (k for k in self._groups.keys() if isinstance(k, str))
+
+    def listed(self):
+        ''' Get iterable over pairs of (int, `c3d.group.Group`) entries.
+        '''
+        return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int))
+
+    def _check_metadata(self):
+        ''' Ensure that the metadata in our file is self-consistent. '''
+        assert self._header.point_count == self.point_used, (
+            'inconsistent point count! {} header != {} POINT:USED'.format(
+                self._header.point_count,
+                self.point_used,
+            ))
+
+        assert self._header.scale_factor == self.point_scale, (
+            'inconsistent scale factor! {} header != {} POINT:SCALE'.format(
+                self._header.scale_factor,
+                self.point_scale,
+            ))
+
+        assert self._header.frame_rate == self.point_rate, (
+            'inconsistent frame rate! {} header != {} POINT:RATE'.format(
+                self._header.frame_rate,
+                self.point_rate,
+            ))
+
+        if self.point_rate:
+            ratio = self.analog_rate / self.point_rate
+        else:
+            ratio = 0
+        assert self._header.analog_per_frame == ratio, (
+            'inconsistent analog rate! {} header != {} analog-fps / {} point-fps'.format(
+                self._header.analog_per_frame,
+                self.analog_rate,
+                self.point_rate,
+            ))
+
+        count = self.analog_used * self._header.analog_per_frame
+        assert self._header.analog_count == count, (
+            'inconsistent analog count! {} header != {} analog used * {} per-frame'.format(
+                self._header.analog_count,
+                self.analog_used,
+                self._header.analog_per_frame,
+            ))
+
+        try:
+            start = self.get_uint16('POINT:DATA_START')
+            if self._header.data_block != start:
+                warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format(
+                    self._header.data_block, start))
+        except AttributeError:
+            warnings.warn('''no pointer available in POINT:DATA_START indicating the start of the data block, using
+                             header pointer as fallback''')
+
+        def check_parameters(params):
+            for name in params:
+                if self.get(name) is None:
+                    warnings.warn('missing parameter {}'.format(name))
+
+        if self.point_used > 0:
+            check_parameters(('POINT:LABELS', 'POINT:DESCRIPTIONS'))
+        else:
+            lab = self.get('POINT:LABELS')
+            if lab is None:
+                warnings.warn('No point data found in file.')
+            elif lab.num_elements > 0:
+                warnings.warn('No point data found in file, but file contains POINT:LABELS entries')
+        if self.analog_used > 0:
+            check_parameters(('ANALOG:LABELS', 'ANALOG:DESCRIPTIONS'))
+        else:
+            lab = self.get('ANALOG:LABELS')
+            if lab is None:
+                warnings.warn('No analog data found in file.')
+            elif lab.num_elements > 0:
+                warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries')
+
+
+    def _add_group(self, group_id, name=None, desc=None):
+        '''Add a new parameter group.
+
+        Parameters
+        ----------
+        group_id : int
+            The numeric ID for a group to check or create.
+        name : str, optional
+            If a group is created, assign this name to the group.
+        desc : str, optional
+            If a group is created, assign this description to the group.
+
+        Returns
+        -------
+        group : :class:`Group`
+            A group with the given ID, name, and description.
+
+        Raises
+        ------
+        TypeError
+            Input arguments are of the wrong type.
+        KeyError
+            Name or numerical key already exist (attempt to overwrite existing data).
+        '''
+        if not is_integer(group_id):
+            raise TypeError('Expected Group numerical key to be integer, was %s.' % type(group_id))
+        if not isinstance(name, str):
+            if name is not None:
+                raise TypeError('Expected Group name key to be string, was %s.' % type(name))
+        else:
+            name = name.upper()
+        group_id = int(group_id) # Asserts python int
+        if group_id in self._groups:
+            raise KeyError('Group with numerical key {} already exists'.format(group_id))
+        if name in self._groups:
+            raise KeyError('No group matched name key {}'.format(name))
+        group = self._groups[name] = self._groups[group_id] = Group(GroupData(self._dtypes, name, desc))
+        return group
+
+    def _remove_group(self, group_id):
+        '''Remove the parameter group.
+
+        Parameters
+        ----------
+        group_id : int, or str
+            The numeric or name ID key for a group to remove all entries for.
+        '''
+        grp = self._groups.get(group_id, None)
+        if grp is None:
+            return
+        gkeys = [k for (k, v) in self._groups.items() if v == grp]
+        for k in gkeys:
+            del self._groups[k]
+
+    def _rename_group(self, group_id, new_group_id):
+        ''' Rename a specified parameter group.
+
+        Parameters
+        ----------
+        group_id : int, str, or 'Group'
+            Group instance, name, or numerical identifier for the group.
+        new_group_id : str, or int
+            If string, it is the new name for the group. If integer, it will replace its numerical group id.
+
+        Raises
+        ------
+        KeyError
+            If a group with a duplicate ID or name already exists.
+        '''
+        if isinstance(group_id, GroupReadonly):
+            grp = group_id._data
+        else:
+            # Aquire instance using id
+            grp = self._groups.get(group_id, None)
+            if grp is None:
+                raise KeyError('No group found matching the identifier: %s' % str(group_id))
+        if new_group_id in self._groups:
+            if new_group_id == group_id:
+                return
+            raise ValueError('Key %s for group %s already exist.' % (str(new_group_id), grp.name))
+
+        # Clear old id
+        if isinstance(new_group_id, (str, bytes)):
+            if grp.name in self._groups:
+                del self._groups[grp.name]
+            grp.name = new_group_id
+        elif is_integer(new_group_id):
+            new_group_id = int(new_group_id) # Ensure python int
+            del self._groups[group_id]
+        else:
+            raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id)))
+        # Update
+        self._groups[new_group_id] = grp
+
+    def get(self, group, default=None):
+        '''Get a group or parameter.
+
+        Parameters
+        ----------
+        group : str
+            If this string contains a period (.), then the part before the
+            period will be used to retrieve a group, and the part after the
+            period will be used to retrieve a parameter from that group. If this
+            string does not contain a period, then just a group will be
+            returned.
+        default : any
+            Return this value if the named group and parameter are not found.
+
+        Returns
+        -------
+        value : `c3d.group.Group` or `c3d.parameter.Param`
+            Either a group or parameter with the specified name(s). If neither
+            is found, returns the default value.
+        '''
+        if is_integer(group):
+            group = self._groups.get(int(group))
+            if group is None:
+                return default
+            return group
+        group = group.upper()
+        param = None
+        if '.' in group:
+            group, param = group.split('.', 1)
+        if ':' in group:
+            group, param = group.split(':', 1)
+        if group not in self._groups:
+            return default
+        group = self._groups[group]
+        if param is not None:
+            return group.get(param, default)
+        return group
+
+    @property
+    def header(self) -> '`c3d.header.Header`':
+        ''' Access to .c3d header data. '''
+        return self._header
+
+    def parameter_blocks(self) -> int:
+        '''Compute the size (in 512B blocks) of the parameter section.'''
+        bytes = 4. + sum(g._data.binary_size for g in self._groups.values())
+        return int(np.ceil(bytes / 512))
+
+    @property
+    def point_rate(self) -> float:
+        ''' Number of sampled 3D coordinates per second. '''
+        try:
+            return self.get_float('POINT:RATE')
+        except AttributeError:
+            return self.header.frame_rate
+
+    @property
+    def point_scale(self) -> float:
+        ''' Scaling applied to non-float data. '''
+        try:
+            return self.get_float('POINT:SCALE')
+        except AttributeError:
+            return self.header.scale_factor
+
+    @property
+    def point_used(self) -> int:
+        ''' Number of sampled 3D point coordinates per frame. '''
+        try:
+            return self.get_uint16('POINT:USED')
+        except AttributeError:
+            return self.header.point_count
+
+    @property
+    def analog_used(self) -> int:
+        ''' Number of analog measurements, or channels, for each analog data sample. '''
+        try:
+            return self.get_uint16('ANALOG:USED')
+        except AttributeError:
+            per_frame = self.header.analog_per_frame
+            if per_frame > 0:
+                return int(self.header.analog_count / per_frame)
+            return 0
+
+    @property
+    def analog_rate(self) -> float:
+        '''  Number of analog data samples per second. '''
+        try:
+            return self.get_float('ANALOG:RATE')
+        except AttributeError:
+            return self.header.analog_per_frame * self.point_rate
+
+    @property
+    def analog_per_frame(self) -> int:
+        '''  Number of analog frames per 3D frame (point sample). '''
+        return int(self.analog_rate / self.point_rate)
+
+    @property
+    def analog_sample_count(self) -> int:
+        ''' Number of analog samples per channel. '''
+        has_analog = self.analog_used > 0
+        return int(self.frame_count * self.analog_per_frame) * has_analog
+
+    @property
+    def point_labels(self) -> list:
+        ''' Labels for each POINT data channel. '''
+        return self.get('POINT:LABELS').string_array
+
+    @property
+    def analog_labels(self) -> list:
+        ''' Labels for each ANALOG data channel. '''
+        return self.get('ANALOG:LABELS').string_array
+
+    @property
+    def frame_count(self) -> int:
+        ''' Number of frames recorded in the data. '''
+        return self.last_frame - self.first_frame + 1  # Add 1 since range is inclusive [first, last]
+
+    @property
+    def first_frame(self) -> int:
+        ''' Trial frame corresponding to the first frame recorded in the data. '''
+        # Start frame seems to be less of an issue to determine.
+        # this is a hack for phasespace files ... should put it in a subclass.
+        param = self.get('TRIAL:ACTUAL_START_FIELD')
+        if param is not None:
+            # ACTUAL_START_FIELD is encoded in two 16 byte words...
+            words = param.uint16_array
+            return words[0] + words[1] * 65535
+        return self.header.first_frame
+
+    @property
+    def last_frame(self) -> int:
+        ''' Trial frame corresponding to the last frame recorded in the data (inclusive). '''
+        # Number of frames can be represented in many formats, first check if valid header values
+        if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535:
+            return self.header.last_frame
+
+        # Check different parameter options where the frame can be encoded
+        end_frame = [self.header.last_frame, 0.0, 0.0, 0.0]
+        param = self.get('TRIAL:ACTUAL_END_FIELD')
+        if param is not None:
+            # Encoded as 2 16 bit words (rather then 1 32 bit word)
+            words = param.uint16_array
+            end_frame[1] = words[0] + words[1] * 65536
+            #end_frame[1] = param.uint32_value
+        param = self.get('POINT:LONG_FRAMES')
+        if param is not None:
+            # Encoded as float
+            end_frame[2] = int(param.float_value)
+        param = self.get('POINT:FRAMES')
+        if param is not None:
+            # Can be encoded either as 32 bit float or 16 bit uint
+            if param.bytes_per_element == 2:
+                end_frame[3] = param.uint16_value
+            else:
+                end_frame[3] = int(param.float_value)
+        # Return the largest of the all (queue bad reading...)
+        return int(np.max(end_frame))
+
+    def get_screen_axis(self):
+        ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+        Returns
+        -------
+        value : (str, str) or None
+            Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+        '''
+        X = self.get('POINT:X_SCREEN')
+        Y = self.get('POINT:Y_SCREEN')
+        if X and Y:
+            return (X.string_value, Y.string_value)
+        return None
+
+    def get_analog_transform_parameters(self):
+        ''' Parse analog data transform parameters. '''
+        # Offsets
+        analog_offsets = np.zeros((self.analog_used), int)
+        param = self.get('ANALOG:OFFSET')
+        if param is not None and param.num_elements > 0:
+            analog_offsets[:] = param.int16_array[:self.analog_used]
+
+        # Scale factors
+        analog_scales = np.ones((self.analog_used), float)
+        gen_scale = 1.
+        param = self.get('ANALOG:GEN_SCALE')
+        if param is not None:
+            gen_scale = param.float_value
+        param = self.get('ANALOG:SCALE')
+        if param is not None and param.num_elements > 0:
+            analog_scales[:] = param.float_array[:self.analog_used]
+
+        return gen_scale, analog_scales, analog_offsets
+
+    def get_analog_transform(self):
+        ''' Get broadcastable analog transformation parameters.
+        '''
+        gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters()
+        analog_scales *= gen_scale
+        analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+        analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+        return analog_scales, analog_offsets
+
+    def get_int8(self, key):
+        '''Get a parameter value as an 8-bit signed integer.'''
+        return self.get(key).int8_value
+
+    def get_uint8(self, key):
+        '''Get a parameter value as an 8-bit unsigned integer.'''
+        return self.get(key).uint8_value
+
+    def get_int16(self, key):
+        '''Get a parameter value as a 16-bit signed integer.'''
+        return self.get(key).int16_value
+
+    def get_uint16(self, key):
+        '''Get a parameter value as a 16-bit unsigned integer.'''
+        return self.get(key).uint16_value
+
+    def get_int32(self, key):
+        '''Get a parameter value as a 32-bit signed integer.'''
+        return self.get(key).int32_value
+
+    def get_uint32(self, key):
+        '''Get a parameter value as a 32-bit unsigned integer.'''
+        return self.get(key).uint32_value
+
+    def get_float(self, key):
+        '''Get a parameter value as a 32-bit float.'''
+        return self.get(key).float_value
+
+    def get_bytes(self, key):
+        '''Get a parameter value as a byte string.'''
+        return self.get(key).bytes_value
+
+    def get_string(self, key):
+        '''Get a parameter value as a string.'''
+        return self.get(key).string_value
    
+
    
 
    Subclasses
    
 
      
 
    • Reader
      • 
@@ -58,54 +961,221 @@ 
      Instance variables
      
 
      var analog_labels : list
      
 
      
 
      Labels for each ANALOG data channel.
      
+
      
+
+Expand source code
+
+
      @property
+def analog_labels(self) -> list:
+    ''' Labels for each ANALOG data channel. '''
+    return self.get('ANALOG:LABELS').string_array
      
+
      
 
      
 
      var analog_per_frame : int
      
 
      
 
      Number of analog frames per 3D frame (point sample).
      
+
      
+
+Expand source code
+
+
      @property
+def analog_per_frame(self) -> int:
+    '''  Number of analog frames per 3D frame (point sample). '''
+    return int(self.analog_rate / self.point_rate)
      
+
      
 
      
 
      var analog_rate : float
      
 
      
 
      Number of analog data samples per second.
      
+
      
+
+Expand source code
+
+
      @property
+def analog_rate(self) -> float:
+    '''  Number of analog data samples per second. '''
+    try:
+        return self.get_float('ANALOG:RATE')
+    except AttributeError:
+        return self.header.analog_per_frame * self.point_rate
      
+
      
 
      
 
      var analog_sample_count : int
      
 
      
 
      Number of analog samples per channel.
      
+
      
+
+Expand source code
+
+
      @property
+def analog_sample_count(self) -> int:
+    ''' Number of analog samples per channel. '''
+    has_analog = self.analog_used > 0
+    return int(self.frame_count * self.analog_per_frame) * has_analog
      
+
      
 
      
 
      var analog_used : int
      
 
      
 
      Number of analog measurements, or channels, for each analog data sample.
      
+
      
+
+Expand source code
+
+
      @property
+def analog_used(self) -> int:
+    ''' Number of analog measurements, or channels, for each analog data sample. '''
+    try:
+        return self.get_uint16('ANALOG:USED')
+    except AttributeError:
+        per_frame = self.header.analog_per_frame
+        if per_frame > 0:
+            return int(self.header.analog_count / per_frame)
+        return 0
      
+
      
 
      
 
      var first_frame : int
      
 
      
 
      Trial frame corresponding to the first frame recorded in the data.
      
+
      
+
+Expand source code
+
+
      @property
+def first_frame(self) -> int:
+    ''' Trial frame corresponding to the first frame recorded in the data. '''
+    # Start frame seems to be less of an issue to determine.
+    # this is a hack for phasespace files ... should put it in a subclass.
+    param = self.get('TRIAL:ACTUAL_START_FIELD')
+    if param is not None:
+        # ACTUAL_START_FIELD is encoded in two 16 byte words...
+        words = param.uint16_array
+        return words[0] + words[1] * 65535
+    return self.header.first_frame
      
+
      
 
      
 
      var frame_count : int
      
 
      
 
      Number of frames recorded in the data.
      
+
      
+
+Expand source code
+
+
      @property
+def frame_count(self) -> int:
+    ''' Number of frames recorded in the data. '''
+    return self.last_frame - self.first_frame + 1  # Add 1 since range is inclusive [first, last]
      
+
      
 
      
 
      var header : `Header`
      
 
      
 
      Access to .c3d header data.
      
+
      
+
+Expand source code
+
+
      @property
+def header(self) -> '`c3d.header.Header`':
+    ''' Access to .c3d header data. '''
+    return self._header
      
+
      
 
      
 
      var last_frame : int
      
 
      
 
      Trial frame corresponding to the last frame recorded in the data (inclusive).
      
+
      
+
+Expand source code
+
+
      @property
+def last_frame(self) -> int:
+    ''' Trial frame corresponding to the last frame recorded in the data (inclusive). '''
+    # Number of frames can be represented in many formats, first check if valid header values
+    if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535:
+        return self.header.last_frame
+
+    # Check different parameter options where the frame can be encoded
+    end_frame = [self.header.last_frame, 0.0, 0.0, 0.0]
+    param = self.get('TRIAL:ACTUAL_END_FIELD')
+    if param is not None:
+        # Encoded as 2 16 bit words (rather then 1 32 bit word)
+        words = param.uint16_array
+        end_frame[1] = words[0] + words[1] * 65536
+        #end_frame[1] = param.uint32_value
+    param = self.get('POINT:LONG_FRAMES')
+    if param is not None:
+        # Encoded as float
+        end_frame[2] = int(param.float_value)
+    param = self.get('POINT:FRAMES')
+    if param is not None:
+        # Can be encoded either as 32 bit float or 16 bit uint
+        if param.bytes_per_element == 2:
+            end_frame[3] = param.uint16_value
+        else:
+            end_frame[3] = int(param.float_value)
+    # Return the largest of the all (queue bad reading...)
+    return int(np.max(end_frame))
      
+
      
 
      
 
      var point_labels : list
      
 
      
 
      Labels for each POINT data channel.
      
+
      
+
+Expand source code
+
+
      @property
+def point_labels(self) -> list:
+    ''' Labels for each POINT data channel. '''
+    return self.get('POINT:LABELS').string_array
      
+
      
 
      
 
      var point_rate : float
      
 
      
 
      Number of sampled 3D coordinates per second.
      
+
      
+
+Expand source code
+
+
      @property
+def point_rate(self) -> float:
+    ''' Number of sampled 3D coordinates per second. '''
+    try:
+        return self.get_float('POINT:RATE')
+    except AttributeError:
+        return self.header.frame_rate
      
+
      
 
      
 
      var point_scale : float
      
 
      
 
      Scaling applied to non-float data.
      
+
      
+
+Expand source code
+
+
      @property
+def point_scale(self) -> float:
+    ''' Scaling applied to non-float data. '''
+    try:
+        return self.get_float('POINT:SCALE')
+    except AttributeError:
+        return self.header.scale_factor
      
+
      
 
      
 
      var point_used : int
      
 
      
 
      Number of sampled 3D point coordinates per frame.
      
+
      
+
+Expand source code
+
+
      @property
+def point_used(self) -> int:
+    ''' Number of sampled 3D point coordinates per frame. '''
+    try:
+        return self.get_uint16('POINT:USED')
+    except AttributeError:
+        return self.header.point_count
      
+
      
 
      
 
 
      Methods
      
@@ -132,48 +1202,167 @@ 
      Returns
      
 
      Either a group or parameter with the specified name(s). If neither
 is found, returns the default value.
      
 
+
      
+
+Expand source code
+
+
      def get(self, group, default=None):
+    '''Get a group or parameter.
+
+    Parameters
+    ----------
+    group : str
+        If this string contains a period (.), then the part before the
+        period will be used to retrieve a group, and the part after the
+        period will be used to retrieve a parameter from that group. If this
+        string does not contain a period, then just a group will be
+        returned.
+    default : any
+        Return this value if the named group and parameter are not found.
+
+    Returns
+    -------
+    value : `c3d.group.Group` or `c3d.parameter.Param`
+        Either a group or parameter with the specified name(s). If neither
+        is found, returns the default value.
+    '''
+    if is_integer(group):
+        group = self._groups.get(int(group))
+        if group is None:
+            return default
+        return group
+    group = group.upper()
+    param = None
+    if '.' in group:
+        group, param = group.split('.', 1)
+    if ':' in group:
+        group, param = group.split(':', 1)
+    if group not in self._groups:
+        return default
+    group = self._groups[group]
+    if param is not None:
+        return group.get(param, default)
+    return group
      
+
      
 
 
      
 def get_analog_transform(self)
 
      
 
      
 
      Get broadcastable analog transformation parameters.
      
+
      
+
+Expand source code
+
+
      def get_analog_transform(self):
+    ''' Get broadcastable analog transformation parameters.
+    '''
+    gen_scale, analog_scales, analog_offsets = self.get_analog_transform_parameters()
+    analog_scales *= gen_scale
+    analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+    analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame))
+    return analog_scales, analog_offsets
      
+
      
 
      
 
      
 def get_analog_transform_parameters(self)
 
      
 
      
 
      Parse analog data transform parameters.
      
+
      
+
+Expand source code
+
+
      def get_analog_transform_parameters(self):
+    ''' Parse analog data transform parameters. '''
+    # Offsets
+    analog_offsets = np.zeros((self.analog_used), int)
+    param = self.get('ANALOG:OFFSET')
+    if param is not None and param.num_elements > 0:
+        analog_offsets[:] = param.int16_array[:self.analog_used]
+
+    # Scale factors
+    analog_scales = np.ones((self.analog_used), float)
+    gen_scale = 1.
+    param = self.get('ANALOG:GEN_SCALE')
+    if param is not None:
+        gen_scale = param.float_value
+    param = self.get('ANALOG:SCALE')
+    if param is not None and param.num_elements > 0:
+        analog_scales[:] = param.float_array[:self.analog_used]
+
+    return gen_scale, analog_scales, analog_offsets
      
+
      
 
      
 
      
 def get_bytes(self, key)
 
      
 
      
 
      Get a parameter value as a byte string.
      
+
      
+
+Expand source code
+
+
      def get_bytes(self, key):
+    '''Get a parameter value as a byte string.'''
+    return self.get(key).bytes_value
      
+
      
 
      
 
      
 def get_float(self, key)
 
      
 
      
 
      Get a parameter value as a 32-bit float.
      
+
      
+
+Expand source code
+
+
      def get_float(self, key):
+    '''Get a parameter value as a 32-bit float.'''
+    return self.get(key).float_value
      
+
      
 
      
 
      
 def get_int16(self, key)
 
      
 
      
 
      Get a parameter value as a 16-bit signed integer.
      
+
      
+
+Expand source code
+
+
      def get_int16(self, key):
+    '''Get a parameter value as a 16-bit signed integer.'''
+    return self.get(key).int16_value
      
+
      
 
      
 
      
 def get_int32(self, key)
 
      
 
      
 
      Get a parameter value as a 32-bit signed integer.
      
+
      
+
+Expand source code
+
+
      def get_int32(self, key):
+    '''Get a parameter value as a 32-bit signed integer.'''
+    return self.get(key).int32_value
      
+
      
 
      
 
      
 def get_int8(self, key)
 
      
 
      
 
      Get a parameter value as an 8-bit signed integer.
      
+
      
+
+Expand source code
+
+
      def get_int8(self, key):
+    '''Get a parameter value as an 8-bit signed integer.'''
+    return self.get(key).int8_value
      
+
      
 
      
 
      
 def get_screen_axis(self)
@@ -185,60 +1374,155 @@ 
      Returns
      
 
      value : (str, str) or None
      
 
      Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
      
 
+
      
+
+Expand source code
+
+
      def get_screen_axis(self):
+    ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+    Returns
+    -------
+    value : (str, str) or None
+        Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+    '''
+    X = self.get('POINT:X_SCREEN')
+    Y = self.get('POINT:Y_SCREEN')
+    if X and Y:
+        return (X.string_value, Y.string_value)
+    return None
      
+
      
 
 
      
 def get_string(self, key)
 
      
 
      
 
      Get a parameter value as a string.
      
+
      
+
+Expand source code
+
+
      def get_string(self, key):
+    '''Get a parameter value as a string.'''
+    return self.get(key).string_value
      
+
      
 
      
 
      
 def get_uint16(self, key)
 
      
 
      
 
      Get a parameter value as a 16-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      def get_uint16(self, key):
+    '''Get a parameter value as a 16-bit unsigned integer.'''
+    return self.get(key).uint16_value
      
+
      
 
      
 
      
 def get_uint32(self, key)
 
      
 
      
 
      Get a parameter value as a 32-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      def get_uint32(self, key):
+    '''Get a parameter value as a 32-bit unsigned integer.'''
+    return self.get(key).uint32_value
      
+
      
 
      
 
      
 def get_uint8(self, key)
 
      
 
      
 
      Get a parameter value as an 8-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      def get_uint8(self, key):
+    '''Get a parameter value as an 8-bit unsigned integer.'''
+    return self.get(key).uint8_value
      
+
      
 
      
 
      
 def items(self)
 
      
 
      
 
      Get iterable over pairs of (str, Group) entries.
      
+
      
+
+Expand source code
+
+
      def items(self):
+    ''' Get iterable over pairs of (str, `c3d.group.Group`) entries.
+    '''
+    return ((k, v) for k, v in self._groups.items() if isinstance(k, str))
      
+
      
 
      
 
      
 def keys(self)
 
      
 
      
 
      Get iterable over parameter name keys.
      
+
      
+
+Expand source code
+
+
      def keys(self):
+    ''' Get iterable over parameter name keys.
+    '''
+    return (k for k in self._groups.keys() if isinstance(k, str))
      
+
      
 
      
 
      
 def listed(self)
 
      
 
      
 
      Get iterable over pairs of (int, Group) entries.
      
+
      
+
+Expand source code
+
+
      def listed(self):
+    ''' Get iterable over pairs of (int, `c3d.group.Group`) entries.
+    '''
+    return sorted((i, g) for i, g in self._groups.items() if isinstance(i, int))
      
+
      
 
      
 
      
 def parameter_blocks(self) ‑> int
 
      
 
      
 
      Compute the size (in 512B blocks) of the parameter section.
      
+
      
+
+Expand source code
+
+
      def parameter_blocks(self) -> int:
+    '''Compute the size (in 512B blocks) of the parameter section.'''
+    bytes = 4. + sum(g._data.binary_size for g in self._groups.values())
+    return int(np.ceil(bytes / 512))
      
+
      
 
      
 
      
 def values(self)
 
      
 
      
 
      Get iterable over Group entries.
      
+
      
+
+Expand source code
+
+
      def values(self):
+    ''' Get iterable over `c3d.group.Group` entries.
+    '''
+    return (v for k, v in self._groups.items() if isinstance(k, str))
      
+
      
 
      
 
 
diff --git a/docs/c3d/parameter.html b/docs/c3d/parameter.html
index 1d62160..f32c8ab 100644
--- a/docs/c3d/parameter.html
+++ b/docs/c3d/parameter.html
@@ -23,6 +23,462 @@ 
      Module c3d.parameter
      
 
 
      
 
      Classes used to represent the concept of a parameter in a .c3d file.
      
+
      
+
+Expand source code
+
+
      ''' Classes used to represent the concept of a parameter in a .c3d file.
+'''
+import struct
+import numpy as np
+from .utils import DEC_to_IEEE, DEC_to_IEEE_BYTES
+
+class ParamData(object):
+    '''A class representing a single named parameter from a C3D file.
+
+    Attributes
+    ----------
+    name : str
+        Name of this parameter.
+    dtype: DataTypes
+        Reference to the DataTypes object associated with the file.
+    desc : str
+        Brief description of this parameter.
+    bytes_per_element : int, optional
+        For array data, this describes the size of each element of data. For
+        string data (including arrays of strings), this should be -1.
+    dimensions : list of int
+        For array data, this describes the dimensions of the array, stored in
+        column-major (Fortran) order. For arrays of strings, the dimensions here will be
+        the number of columns (length of each string) followed by the number of
+        rows (number of strings).
+    bytes : str
+        Raw data for this parameter.
+    '''
+
+    def __init__(self,
+                 name,
+                 dtype,
+                 desc='',
+                 bytes_per_element=1,
+                 dimensions=None,
+                 bytes=b'',
+                 handle=None):
+        '''Set up a new parameter, only the name is required.'''
+        self.name = name
+        self.dtypes = dtype
+        self.desc = desc
+        self.bytes_per_element = bytes_per_element
+        self.dimensions = dimensions or []
+        self.bytes = bytes
+        if handle:
+            self.read(handle)
+
+    def __repr__(self):
+        return '<Param: {}>'.format(self.desc)
+
+    @property
+    def num_elements(self) -> int:
+        '''Return the number of elements in this parameter's array value.'''
+        e = 1
+        for d in self.dimensions:
+            e *= d
+        return e
+
+    @property
+    def total_bytes(self) -> int:
+        '''Return the number of bytes used for storing this parameter's data.'''
+        return self.num_elements * abs(self.bytes_per_element)
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes needed to store this parameter.'''
+        return (
+            1 +  # group_id
+            2 +  # next offset marker
+            1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+            1 +  # data size
+            # size of dimensions and dimension bytes
+            1 + len(self.dimensions) +
+            self.total_bytes +  # data
+            1 + len(self.desc.encode('utf-8'))  # size of desc and desc bytes
+        )
+
+    def write(self, group_id, handle):
+        '''Write binary data for this parameter to a file handle.
+
+        Parameters
+        ----------
+        group_id : int
+            The numerical ID of the group that holds this parameter.
+        handle : file handle
+            An open, writable, binary file handle.
+        '''
+        name = self.name.encode('utf-8')
+        handle.write(struct.pack('bb', len(name), group_id))
+        handle.write(name)
+        handle.write(struct.pack('<h', self.binary_size - 2 - len(name)))
+        handle.write(struct.pack('b', self.bytes_per_element))
+        handle.write(struct.pack('B', len(self.dimensions)))
+        handle.write(struct.pack('B' * len(self.dimensions), *self.dimensions))
+        if self.bytes is not None and len(self.bytes) > 0:
+            handle.write(self.bytes)
+        desc = self.desc.encode('utf-8')
+        handle.write(struct.pack('B', len(desc)))
+        handle.write(desc)
+
+    def read(self, handle):
+        '''Read binary data for this parameter from a file handle.
+
+        This reads exactly enough data from the current position in the file to
+        initialize the parameter.
+        '''
+        self.bytes_per_element, = struct.unpack('b', handle.read(1))
+        dims, = struct.unpack('B', handle.read(1))
+        self.dimensions = [struct.unpack('B', handle.read(1))[
+            0] for _ in range(dims)]
+        self.bytes = b''
+        if self.total_bytes:
+            self.bytes = handle.read(self.total_bytes)
+        desc_size, = struct.unpack('B', handle.read(1))
+        self.desc = desc_size and self.dtypes.decode_string(handle.read(desc_size)) or ''
+
+    def _as(self, dtype):
+        '''Unpack the raw bytes of this param using the given struct format.'''
+        return np.frombuffer(self.bytes, count=1, dtype=dtype)[0]
+
+    def _as_array(self, dtype, copy=True):
+        '''Unpack the raw bytes of this param using the given data format.'''
+        assert self.dimensions, \
+            '{}: cannot get value as {} array!'.format(self.name, dtype)
+        elems = np.frombuffer(self.bytes, dtype=dtype)
+        # Reverse shape as the shape is defined in fortran format
+        view = elems.reshape(self.dimensions[::-1])
+        if copy:
+            return view.copy()
+        return view
+
+    def _as_any(self, dtype):
+        '''Unpack the raw bytes of this param as either array or single value.'''
+        if 0 in self.dimensions[:]:             # Check if any dimension is 0 (empty buffer)
+            return []                                           # Buffer is empty
+
+        if len(self.dimensions) == 0:           # Parse data as a single value
+            if dtype == np.float32:                     # Floats need to be parsed separately!
+                return self.float_value
+            return self._data._as(dtype)
+        else:                                                           # Parse data as array
+            if dtype == np.float32:
+                data = self.float_array
+            else:
+                data = self._data._as_array(dtype)
+            if len(self.dimensions) < 2:    # Check if data is contained in a single dimension
+                return data.flatten()
+            return data
+
+class ParamReadonly(object):
+    ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry.
+    '''
+
+    def __init__(self, data):
+        self._data = data
+
+    def __eq__(self, other):
+        return self._data is other._data
+
+    @property
+    def name(self) -> str:
+        ''' Get the parameter name. '''
+        return self._data.name
+
+    @property
+    def desc(self) -> str:
+        ''' Get the parameter descriptor. '''
+        return self._data.desc
+
+    @property
+    def dtypes(self):
+        ''' Convenience accessor to the `c3d.dtypes.DataTypes` instance associated with the parameter. '''
+        return self._data.dtypes
+
+    @property
+    def dimensions(self) -> (int, ...):
+        ''' Shape of the parameter data (Fortran shape). '''
+        return self._data.dimensions
+
+    @property
+    def num_elements(self) -> int:
+        '''Return the number of elements in this parameter's array value.'''
+        return self._data.num_elements
+
+    @property
+    def bytes_per_element(self) -> int:
+        '''Return the number of bytes used to store each data element.'''
+        return self._data.bytes_per_element
+
+    @property
+    def total_bytes(self) -> int:
+        '''Return the number of bytes used for storing this parameter's data.'''
+        return self._data.total_bytes
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes needed to store this parameter.'''
+        return self._data.binary_size
+
+    @property
+    def int8_value(self):
+        '''Get the param as an 8-bit signed integer.'''
+        return self._data._as(self.dtypes.int8)
+
+    @property
+    def uint8_value(self):
+        '''Get the param as an 8-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint8)
+
+    @property
+    def int16_value(self):
+        '''Get the param as a 16-bit signed integer.'''
+        return self._data._as(self.dtypes.int16)
+
+    @property
+    def uint16_value(self):
+        '''Get the param as a 16-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint16)
+
+    @property
+    def int32_value(self):
+        '''Get the param as a 32-bit signed integer.'''
+        return self._data._as(self.dtypes.int32)
+
+    @property
+    def uint32_value(self):
+        '''Get the param as a 32-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint32)
+
+    @property
+    def uint_value(self):
+        ''' Get the param as a unsigned integer of appropriate type. '''
+        if self.total_bytes >= 4:
+            return self.uint32_value
+        elif self.total_bytes >= 2:
+            return self.uint16_value
+        else:
+            return self.uint8_value
+
+    @property
+    def int_value(self):
+        ''' Get the param as a signed integer of appropriate type. '''
+        if self.total_bytes >= 4:
+            return self.int32_value
+        elif self.total_bytes >= 2:
+            return self.int16_value
+        else:
+            return self.int8_value
+
+    @property
+    def float_value(self):
+        '''Get the param as a floating point value of appropriate type.'''
+        if self.total_bytes > 4:
+            if self.dtypes.is_dec:
+                raise AttributeError("64 bit DEC floating point is not supported.")
+            # 64-bit floating point is not a standard
+            return self._data._as(self.dtypes.float64)
+        elif self.total_bytes == 4:
+            if self.dtypes.is_dec:
+                return DEC_to_IEEE(self._data._as(np.uint32))
+            else:  # is_mips or is_ieee
+                return self._data._as(self.dtypes.float32)
+        else:
+            raise AttributeError("Only 32 and 64 bit floating point is supported.")
+
+    @property
+    def bytes_value(self):
+        '''Get the param as a raw byte string.'''
+        return self._data.bytes
+
+    @property
+    def string_value(self):
+        '''Get the param as a unicode string.'''
+        return self.dtypes.decode_string(self._data.bytes)
+
+    @property
+    def int8_array(self):
+        '''Get the param as an array of 8-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int8)
+
+    @property
+    def uint8_array(self):
+        '''Get the param as an array of 8-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint8)
+
+    @property
+    def int16_array(self):
+        '''Get the param as an array of 16-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int16)
+
+    @property
+    def uint16_array(self):
+        '''Get the param as an array of 16-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint16)
+
+    @property
+    def int32_array(self):
+        '''Get the param as an array of 32-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int32)
+
+    @property
+    def uint32_array(self):
+        '''Get the param as an array of 32-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint32)
+
+    @property
+    def int64_array(self):
+        '''Get the param as an array of 32-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int64)
+
+    @property
+    def uint64_array(self):
+        '''Get the param as an array of 32-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint64)
+
+    @property
+    def float32_array(self):
+        '''Get the param as an array of 32-bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.dtypes.is_dec:
+            # _as_array but for DEC
+            assert self.dimensions, \
+                '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32)
+            return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1])  # Reverse fortran format
+        else:  # is_ieee or is_mips
+            return self._data._as_array(self.dtypes.float32)
+
+    @property
+    def float64_array(self):
+        '''Get the param as an array of 64-bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.dtypes.is_dec:
+            raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
+        else:  # is_ieee or is_mips
+            return self._data._as_array(self.dtypes.float64)
+
+    @property
+    def float_array(self):
+        '''Get the param as an array of 32 or 64 bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 4:
+            return self.float32_array
+        elif self.bytes_per_element == 8:
+            return self.float64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element +
+                            "floating-point precission is not unsupported.")
+
+    @property
+    def int_array(self):
+        '''Get the param as an array of integer values.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 1:
+            return self.int8_array
+        elif self.bytes_per_element == 2:
+            return self.int16_array
+        elif self.bytes_per_element == 4:
+            return self.int32_array
+        elif self.bytes_per_element == 8:
+            return self.int64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                            self.bytes_per_element)
+
+    @property
+    def uint_array(self):
+        '''Get the param as an array of integer values.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 1:
+            return self.uint8_array
+        elif self.bytes_per_element == 2:
+            return self.uint16_array
+        elif self.bytes_per_element == 4:
+            return self.uint32_array
+        elif self.bytes_per_element == 8:
+            return self.uint64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                            self.bytes_per_element)
+
+    @property
+    def bytes_array(self):
+        '''Get the param as an array of raw byte strings.'''
+        # Decode different dimensions
+        if len(self.dimensions) == 0:
+            return np.array([])
+        elif len(self.dimensions) == 1:
+            return np.array(self._data.bytes)
+        else:
+            # Convert Fortran shape (data in memory is identical, shape is transposed)
+            word_len = self.dimensions[0]
+            dims = self.dimensions[1:][::-1]  # Identical to: [:0:-1]
+            byte_steps = np.cumprod(self.dimensions[:-1])[::-1]
+            # Generate mult-dimensional array and parse byte words
+            byte_arr = np.empty(dims, dtype=object)
+            for i in np.ndindex(*dims):
+                # Calculate byte offset as sum of each array index times the byte step of each dimension.
+                off = np.sum(np.multiply(i, byte_steps))
+                byte_arr[i] = self._data.bytes[off:off+word_len]
+            return byte_arr
+
+    @property
+    def string_array(self):
+        '''Get the param as a python array of unicode strings.'''
+        # Decode different dimensions
+        if len(self.dimensions) == 0:
+            return np.array([])
+        elif len(self.dimensions) == 1:
+            return np.array([self.string_value])
+        else:
+            # Parse byte sequences
+            byte_arr = self.bytes_array
+            # Decode sequences
+            for i in np.ndindex(byte_arr.shape):
+                byte_arr[i] = self.dtypes.decode_string(byte_arr[i])
+            return byte_arr
+
+    @property
+    def _as_integer_or_float_value(self):
+        ''' Get the param as either 32 bit float or unsigned integer.
+            Evaluates if an integer is stored as a floating point representation.
+        '''
+        if self.total_bytes >= 4:
+            # Check if float value representation is an integer
+            value = self.float_value
+            if int(value) == value:
+                return value
+            return self.uint32_value
+        elif self.total_bytes >= 2:
+            return self.uint16_value
+        else:
+            return self.uint8_value
+
+class Param(ParamReadonly):
+    ''' Wrapper exposing both readable and writable attributes of a `c3d.parameter.ParamData` entry.
+    '''
+    def __init__(self, data):
+        super(Param, self).__init__(data)
+
+    def readonly(self):
+        ''' Returns a readonly `c3d.parameter.ParamReadonly` instance. '''
+        return ParamReadonly(self._data)
+
+    @property
+    def bytes(self) -> bytes:
+        ''' Get or set the parameter bytes. '''
+        return self._data.bytes
+
+    @bytes.setter
+    def bytes(self, value):
+        self._data.bytes = value
      
+
      
 
      
 
      
 
      
@@ -39,6 +495,29 @@ 
      Classes
      
 
    
 
    
 
    Wrapper exposing both readable and writable attributes of a ParamData entry.
    
+
    
+
+Expand source code
+
+
    class Param(ParamReadonly):
+    ''' Wrapper exposing both readable and writable attributes of a `c3d.parameter.ParamData` entry.
+    '''
+    def __init__(self, data):
+        super(Param, self).__init__(data)
+
+    def readonly(self):
+        ''' Returns a readonly `c3d.parameter.ParamReadonly` instance. '''
+        return ParamReadonly(self._data)
+
+    @property
+    def bytes(self) -> bytes:
+        ''' Get or set the parameter bytes. '''
+        return self._data.bytes
+
+    @bytes.setter
+    def bytes(self, value):
+        self._data.bytes = value
    
+
    
 
    Ancestors
    
 
      
 
    • ParamReadonly
      • 
@@ -48,6 +527,15 @@ 
      Instance variables
      
 
      var bytes : bytes
      
 
      
 
      Get or set the parameter bytes.
      
+
      
+
+Expand source code
+
+
      @property
+def bytes(self) -> bytes:
+    ''' Get or set the parameter bytes. '''
+    return self._data.bytes
      
+
      
 
      
 
 
      Methods
      
@@ -57,6 +545,14 @@ 
      Methods
      
       
 
      
 
      Returns a readonly ParamReadonly instance.
      
+
      
+
+Expand source code
+
+
      def readonly(self):
+    ''' Returns a readonly `c3d.parameter.ParamReadonly` instance. '''
+    return ParamReadonly(self._data)
      
+
      
 
      
 
 
      Inherited members
      
@@ -127,19 +623,205 @@ 
      Attributes
      
 
      Raw data for this parameter.
      
 
 
      Set up a new parameter, only the name is required.
      
+
      
+
+Expand source code
+
+
      class ParamData(object):
+    '''A class representing a single named parameter from a C3D file.
+
+    Attributes
+    ----------
+    name : str
+        Name of this parameter.
+    dtype: DataTypes
+        Reference to the DataTypes object associated with the file.
+    desc : str
+        Brief description of this parameter.
+    bytes_per_element : int, optional
+        For array data, this describes the size of each element of data. For
+        string data (including arrays of strings), this should be -1.
+    dimensions : list of int
+        For array data, this describes the dimensions of the array, stored in
+        column-major (Fortran) order. For arrays of strings, the dimensions here will be
+        the number of columns (length of each string) followed by the number of
+        rows (number of strings).
+    bytes : str
+        Raw data for this parameter.
+    '''
+
+    def __init__(self,
+                 name,
+                 dtype,
+                 desc='',
+                 bytes_per_element=1,
+                 dimensions=None,
+                 bytes=b'',
+                 handle=None):
+        '''Set up a new parameter, only the name is required.'''
+        self.name = name
+        self.dtypes = dtype
+        self.desc = desc
+        self.bytes_per_element = bytes_per_element
+        self.dimensions = dimensions or []
+        self.bytes = bytes
+        if handle:
+            self.read(handle)
+
+    def __repr__(self):
+        return '<Param: {}>'.format(self.desc)
+
+    @property
+    def num_elements(self) -> int:
+        '''Return the number of elements in this parameter's array value.'''
+        e = 1
+        for d in self.dimensions:
+            e *= d
+        return e
+
+    @property
+    def total_bytes(self) -> int:
+        '''Return the number of bytes used for storing this parameter's data.'''
+        return self.num_elements * abs(self.bytes_per_element)
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes needed to store this parameter.'''
+        return (
+            1 +  # group_id
+            2 +  # next offset marker
+            1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+            1 +  # data size
+            # size of dimensions and dimension bytes
+            1 + len(self.dimensions) +
+            self.total_bytes +  # data
+            1 + len(self.desc.encode('utf-8'))  # size of desc and desc bytes
+        )
+
+    def write(self, group_id, handle):
+        '''Write binary data for this parameter to a file handle.
+
+        Parameters
+        ----------
+        group_id : int
+            The numerical ID of the group that holds this parameter.
+        handle : file handle
+            An open, writable, binary file handle.
+        '''
+        name = self.name.encode('utf-8')
+        handle.write(struct.pack('bb', len(name), group_id))
+        handle.write(name)
+        handle.write(struct.pack('<h', self.binary_size - 2 - len(name)))
+        handle.write(struct.pack('b', self.bytes_per_element))
+        handle.write(struct.pack('B', len(self.dimensions)))
+        handle.write(struct.pack('B' * len(self.dimensions), *self.dimensions))
+        if self.bytes is not None and len(self.bytes) > 0:
+            handle.write(self.bytes)
+        desc = self.desc.encode('utf-8')
+        handle.write(struct.pack('B', len(desc)))
+        handle.write(desc)
+
+    def read(self, handle):
+        '''Read binary data for this parameter from a file handle.
+
+        This reads exactly enough data from the current position in the file to
+        initialize the parameter.
+        '''
+        self.bytes_per_element, = struct.unpack('b', handle.read(1))
+        dims, = struct.unpack('B', handle.read(1))
+        self.dimensions = [struct.unpack('B', handle.read(1))[
+            0] for _ in range(dims)]
+        self.bytes = b''
+        if self.total_bytes:
+            self.bytes = handle.read(self.total_bytes)
+        desc_size, = struct.unpack('B', handle.read(1))
+        self.desc = desc_size and self.dtypes.decode_string(handle.read(desc_size)) or ''
+
+    def _as(self, dtype):
+        '''Unpack the raw bytes of this param using the given struct format.'''
+        return np.frombuffer(self.bytes, count=1, dtype=dtype)[0]
+
+    def _as_array(self, dtype, copy=True):
+        '''Unpack the raw bytes of this param using the given data format.'''
+        assert self.dimensions, \
+            '{}: cannot get value as {} array!'.format(self.name, dtype)
+        elems = np.frombuffer(self.bytes, dtype=dtype)
+        # Reverse shape as the shape is defined in fortran format
+        view = elems.reshape(self.dimensions[::-1])
+        if copy:
+            return view.copy()
+        return view
+
+    def _as_any(self, dtype):
+        '''Unpack the raw bytes of this param as either array or single value.'''
+        if 0 in self.dimensions[:]:             # Check if any dimension is 0 (empty buffer)
+            return []                                           # Buffer is empty
+
+        if len(self.dimensions) == 0:           # Parse data as a single value
+            if dtype == np.float32:                     # Floats need to be parsed separately!
+                return self.float_value
+            return self._data._as(dtype)
+        else:                                                           # Parse data as array
+            if dtype == np.float32:
+                data = self.float_array
+            else:
+                data = self._data._as_array(dtype)
+            if len(self.dimensions) < 2:    # Check if data is contained in a single dimension
+                return data.flatten()
+            return data
      
+
      
 
      Instance variables
      
 
      
 
      var binary_size : int
      
 
      
 
      Return the number of bytes needed to store this parameter.
      
+
      
+
+Expand source code
+
+
      @property
+def binary_size(self) -> int:
+    '''Return the number of bytes needed to store this parameter.'''
+    return (
+        1 +  # group_id
+        2 +  # next offset marker
+        1 + len(self.name.encode('utf-8')) +  # size of name and name bytes
+        1 +  # data size
+        # size of dimensions and dimension bytes
+        1 + len(self.dimensions) +
+        self.total_bytes +  # data
+        1 + len(self.desc.encode('utf-8'))  # size of desc and desc bytes
+    )
      
+
      
 
      
 
      var num_elements : int
      
 
      
 
      Return the number of elements in this parameter's array value.
      
+
      
+
+Expand source code
+
+
      @property
+def num_elements(self) -> int:
+    '''Return the number of elements in this parameter's array value.'''
+    e = 1
+    for d in self.dimensions:
+        e *= d
+    return e
      
+
      
 
      
 
      var total_bytes : int
      
 
      
 
      Return the number of bytes used for storing this parameter's data.
      
+
      
+
+Expand source code
+
+
      @property
+def total_bytes(self) -> int:
+    '''Return the number of bytes used for storing this parameter's data.'''
+    return self.num_elements * abs(self.bytes_per_element)
      
+
      
 
      
 
      
 
      Methods
      
@@ -151,6 +833,26 @@ 
      Methods
      
 
      Read binary data for this parameter from a file handle.
      
 
      This reads exactly enough data from the current position in the file to
 initialize the parameter.
      
+
      
+
+Expand source code
+
+
      def read(self, handle):
+    '''Read binary data for this parameter from a file handle.
+
+    This reads exactly enough data from the current position in the file to
+    initialize the parameter.
+    '''
+    self.bytes_per_element, = struct.unpack('b', handle.read(1))
+    dims, = struct.unpack('B', handle.read(1))
+    self.dimensions = [struct.unpack('B', handle.read(1))[
+        0] for _ in range(dims)]
+    self.bytes = b''
+    if self.total_bytes:
+        self.bytes = handle.read(self.total_bytes)
+    desc_size, = struct.unpack('B', handle.read(1))
+    self.desc = desc_size and self.dtypes.decode_string(handle.read(desc_size)) or ''
      
+
      
 
    
 
    
 def write(self, group_id, handle)
@@ -164,6 +866,33 @@ 
    Parameters
    
 
    handle : file handle
    
 
    An open, writable, binary file handle.
    
 
+
    
+
+Expand source code
+
+
    def write(self, group_id, handle):
+    '''Write binary data for this parameter to a file handle.
+
+    Parameters
+    ----------
+    group_id : int
+        The numerical ID of the group that holds this parameter.
+    handle : file handle
+        An open, writable, binary file handle.
+    '''
+    name = self.name.encode('utf-8')
+    handle.write(struct.pack('bb', len(name), group_id))
+    handle.write(name)
+    handle.write(struct.pack('<h', self.binary_size - 2 - len(name)))
+    handle.write(struct.pack('b', self.bytes_per_element))
+    handle.write(struct.pack('B', len(self.dimensions)))
+    handle.write(struct.pack('B' * len(self.dimensions), *self.dimensions))
+    if self.bytes is not None and len(self.bytes) > 0:
+        handle.write(self.bytes)
+    desc = self.desc.encode('utf-8')
+    handle.write(struct.pack('B', len(desc)))
+    handle.write(desc)
    
+
    
 
 
 
@@ -173,6 +902,294 @@ 
    Parameters
    
     
 
    
 
    Wrapper exposing readonly attributes of a ParamData entry.
    
+
    
+
+Expand source code
+
+
    class ParamReadonly(object):
+    ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry.
+    '''
+
+    def __init__(self, data):
+        self._data = data
+
+    def __eq__(self, other):
+        return self._data is other._data
+
+    @property
+    def name(self) -> str:
+        ''' Get the parameter name. '''
+        return self._data.name
+
+    @property
+    def desc(self) -> str:
+        ''' Get the parameter descriptor. '''
+        return self._data.desc
+
+    @property
+    def dtypes(self):
+        ''' Convenience accessor to the `c3d.dtypes.DataTypes` instance associated with the parameter. '''
+        return self._data.dtypes
+
+    @property
+    def dimensions(self) -> (int, ...):
+        ''' Shape of the parameter data (Fortran shape). '''
+        return self._data.dimensions
+
+    @property
+    def num_elements(self) -> int:
+        '''Return the number of elements in this parameter's array value.'''
+        return self._data.num_elements
+
+    @property
+    def bytes_per_element(self) -> int:
+        '''Return the number of bytes used to store each data element.'''
+        return self._data.bytes_per_element
+
+    @property
+    def total_bytes(self) -> int:
+        '''Return the number of bytes used for storing this parameter's data.'''
+        return self._data.total_bytes
+
+    @property
+    def binary_size(self) -> int:
+        '''Return the number of bytes needed to store this parameter.'''
+        return self._data.binary_size
+
+    @property
+    def int8_value(self):
+        '''Get the param as an 8-bit signed integer.'''
+        return self._data._as(self.dtypes.int8)
+
+    @property
+    def uint8_value(self):
+        '''Get the param as an 8-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint8)
+
+    @property
+    def int16_value(self):
+        '''Get the param as a 16-bit signed integer.'''
+        return self._data._as(self.dtypes.int16)
+
+    @property
+    def uint16_value(self):
+        '''Get the param as a 16-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint16)
+
+    @property
+    def int32_value(self):
+        '''Get the param as a 32-bit signed integer.'''
+        return self._data._as(self.dtypes.int32)
+
+    @property
+    def uint32_value(self):
+        '''Get the param as a 32-bit unsigned integer.'''
+        return self._data._as(self.dtypes.uint32)
+
+    @property
+    def uint_value(self):
+        ''' Get the param as a unsigned integer of appropriate type. '''
+        if self.total_bytes >= 4:
+            return self.uint32_value
+        elif self.total_bytes >= 2:
+            return self.uint16_value
+        else:
+            return self.uint8_value
+
+    @property
+    def int_value(self):
+        ''' Get the param as a signed integer of appropriate type. '''
+        if self.total_bytes >= 4:
+            return self.int32_value
+        elif self.total_bytes >= 2:
+            return self.int16_value
+        else:
+            return self.int8_value
+
+    @property
+    def float_value(self):
+        '''Get the param as a floating point value of appropriate type.'''
+        if self.total_bytes > 4:
+            if self.dtypes.is_dec:
+                raise AttributeError("64 bit DEC floating point is not supported.")
+            # 64-bit floating point is not a standard
+            return self._data._as(self.dtypes.float64)
+        elif self.total_bytes == 4:
+            if self.dtypes.is_dec:
+                return DEC_to_IEEE(self._data._as(np.uint32))
+            else:  # is_mips or is_ieee
+                return self._data._as(self.dtypes.float32)
+        else:
+            raise AttributeError("Only 32 and 64 bit floating point is supported.")
+
+    @property
+    def bytes_value(self):
+        '''Get the param as a raw byte string.'''
+        return self._data.bytes
+
+    @property
+    def string_value(self):
+        '''Get the param as a unicode string.'''
+        return self.dtypes.decode_string(self._data.bytes)
+
+    @property
+    def int8_array(self):
+        '''Get the param as an array of 8-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int8)
+
+    @property
+    def uint8_array(self):
+        '''Get the param as an array of 8-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint8)
+
+    @property
+    def int16_array(self):
+        '''Get the param as an array of 16-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int16)
+
+    @property
+    def uint16_array(self):
+        '''Get the param as an array of 16-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint16)
+
+    @property
+    def int32_array(self):
+        '''Get the param as an array of 32-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int32)
+
+    @property
+    def uint32_array(self):
+        '''Get the param as an array of 32-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint32)
+
+    @property
+    def int64_array(self):
+        '''Get the param as an array of 32-bit signed integers.'''
+        return self._data._as_array(self.dtypes.int64)
+
+    @property
+    def uint64_array(self):
+        '''Get the param as an array of 32-bit unsigned integers.'''
+        return self._data._as_array(self.dtypes.uint64)
+
+    @property
+    def float32_array(self):
+        '''Get the param as an array of 32-bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.dtypes.is_dec:
+            # _as_array but for DEC
+            assert self.dimensions, \
+                '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32)
+            return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1])  # Reverse fortran format
+        else:  # is_ieee or is_mips
+            return self._data._as_array(self.dtypes.float32)
+
+    @property
+    def float64_array(self):
+        '''Get the param as an array of 64-bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.dtypes.is_dec:
+            raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
+        else:  # is_ieee or is_mips
+            return self._data._as_array(self.dtypes.float64)
+
+    @property
+    def float_array(self):
+        '''Get the param as an array of 32 or 64 bit floats.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 4:
+            return self.float32_array
+        elif self.bytes_per_element == 8:
+            return self.float64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element +
+                            "floating-point precission is not unsupported.")
+
+    @property
+    def int_array(self):
+        '''Get the param as an array of integer values.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 1:
+            return self.int8_array
+        elif self.bytes_per_element == 2:
+            return self.int16_array
+        elif self.bytes_per_element == 4:
+            return self.int32_array
+        elif self.bytes_per_element == 8:
+            return self.int64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                            self.bytes_per_element)
+
+    @property
+    def uint_array(self):
+        '''Get the param as an array of integer values.'''
+        # Convert float data if not IEEE processor
+        if self.bytes_per_element == 1:
+            return self.uint8_array
+        elif self.bytes_per_element == 2:
+            return self.uint16_array
+        elif self.bytes_per_element == 4:
+            return self.uint32_array
+        elif self.bytes_per_element == 8:
+            return self.uint64_array
+        else:
+            raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                            self.bytes_per_element)
+
+    @property
+    def bytes_array(self):
+        '''Get the param as an array of raw byte strings.'''
+        # Decode different dimensions
+        if len(self.dimensions) == 0:
+            return np.array([])
+        elif len(self.dimensions) == 1:
+            return np.array(self._data.bytes)
+        else:
+            # Convert Fortran shape (data in memory is identical, shape is transposed)
+            word_len = self.dimensions[0]
+            dims = self.dimensions[1:][::-1]  # Identical to: [:0:-1]
+            byte_steps = np.cumprod(self.dimensions[:-1])[::-1]
+            # Generate mult-dimensional array and parse byte words
+            byte_arr = np.empty(dims, dtype=object)
+            for i in np.ndindex(*dims):
+                # Calculate byte offset as sum of each array index times the byte step of each dimension.
+                off = np.sum(np.multiply(i, byte_steps))
+                byte_arr[i] = self._data.bytes[off:off+word_len]
+            return byte_arr
+
+    @property
+    def string_array(self):
+        '''Get the param as a python array of unicode strings.'''
+        # Decode different dimensions
+        if len(self.dimensions) == 0:
+            return np.array([])
+        elif len(self.dimensions) == 1:
+            return np.array([self.string_value])
+        else:
+            # Parse byte sequences
+            byte_arr = self.bytes_array
+            # Decode sequences
+            for i in np.ndindex(byte_arr.shape):
+                byte_arr[i] = self.dtypes.decode_string(byte_arr[i])
+            return byte_arr
+
+    @property
+    def _as_integer_or_float_value(self):
+        ''' Get the param as either 32 bit float or unsigned integer.
+            Evaluates if an integer is stored as a floating point representation.
+        '''
+        if self.total_bytes >= 4:
+            # Check if float value representation is an integer
+            value = self.float_value
+            if int(value) == value:
+                return value
+            return self.uint32_value
+        elif self.total_bytes >= 2:
+            return self.uint16_value
+        else:
+            return self.uint8_value
    
+
    
 
    Subclasses
    
 
      
 
    • Param
      • 
@@ -182,138 +1199,532 @@ 
      Instance variables
      
 
      var binary_size : int
      
 
      
 
      Return the number of bytes needed to store this parameter.
      
+
      
+
+Expand source code
+
+
      @property
+def binary_size(self) -> int:
+    '''Return the number of bytes needed to store this parameter.'''
+    return self._data.binary_size
      
+
      
 
      
 
      var bytes_array
      
 
      
 
      Get the param as an array of raw byte strings.
      
+
      
+
+Expand source code
+
+
      @property
+def bytes_array(self):
+    '''Get the param as an array of raw byte strings.'''
+    # Decode different dimensions
+    if len(self.dimensions) == 0:
+        return np.array([])
+    elif len(self.dimensions) == 1:
+        return np.array(self._data.bytes)
+    else:
+        # Convert Fortran shape (data in memory is identical, shape is transposed)
+        word_len = self.dimensions[0]
+        dims = self.dimensions[1:][::-1]  # Identical to: [:0:-1]
+        byte_steps = np.cumprod(self.dimensions[:-1])[::-1]
+        # Generate mult-dimensional array and parse byte words
+        byte_arr = np.empty(dims, dtype=object)
+        for i in np.ndindex(*dims):
+            # Calculate byte offset as sum of each array index times the byte step of each dimension.
+            off = np.sum(np.multiply(i, byte_steps))
+            byte_arr[i] = self._data.bytes[off:off+word_len]
+        return byte_arr
      
+
      
 
      
 
      var bytes_per_element : int
      
 
      
 
      Return the number of bytes used to store each data element.
      
+
      
+
+Expand source code
+
+
      @property
+def bytes_per_element(self) -> int:
+    '''Return the number of bytes used to store each data element.'''
+    return self._data.bytes_per_element
      
+
      
 
      
 
      var bytes_value
      
 
      
 
      Get the param as a raw byte string.
      
+
      
+
+Expand source code
+
+
      @property
+def bytes_value(self):
+    '''Get the param as a raw byte string.'''
+    return self._data.bytes
      
+
      
 
      
 
      var desc : str
      
 
      
 
      Get the parameter descriptor.
      
+
      
+
+Expand source code
+
+
      @property
+def desc(self) -> str:
+    ''' Get the parameter descriptor. '''
+    return self._data.desc
      
+
      
 
      
 
      var dimensions : (, Ellipsis)
      
 
      
 
      Shape of the parameter data (Fortran shape).
      
+
      
+
+Expand source code
+
+
      @property
+def dimensions(self) -> (int, ...):
+    ''' Shape of the parameter data (Fortran shape). '''
+    return self._data.dimensions
      
+
      
 
      
 
      var dtypes
      
 
      
 
      Convenience accessor to the DataTypes instance associated with the parameter.
      
+
      
+
+Expand source code
+
+
      @property
+def dtypes(self):
+    ''' Convenience accessor to the `c3d.dtypes.DataTypes` instance associated with the parameter. '''
+    return self._data.dtypes
      
+
      
 
      
 
      var float32_array
      
 
      
 
      Get the param as an array of 32-bit floats.
      
+
      
+
+Expand source code
+
+
      @property
+def float32_array(self):
+    '''Get the param as an array of 32-bit floats.'''
+    # Convert float data if not IEEE processor
+    if self.dtypes.is_dec:
+        # _as_array but for DEC
+        assert self.dimensions, \
+            '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32)
+        return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1])  # Reverse fortran format
+    else:  # is_ieee or is_mips
+        return self._data._as_array(self.dtypes.float32)
      
+
      
 
      
 
      var float64_array
      
 
      
 
      Get the param as an array of 64-bit floats.
      
+
      
+
+Expand source code
+
+
      @property
+def float64_array(self):
+    '''Get the param as an array of 64-bit floats.'''
+    # Convert float data if not IEEE processor
+    if self.dtypes.is_dec:
+        raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
+    else:  # is_ieee or is_mips
+        return self._data._as_array(self.dtypes.float64)
      
+
      
 
      
 
      var float_array
      
 
      
 
      Get the param as an array of 32 or 64 bit floats.
      
+
      
+
+Expand source code
+
+
      @property
+def float_array(self):
+    '''Get the param as an array of 32 or 64 bit floats.'''
+    # Convert float data if not IEEE processor
+    if self.bytes_per_element == 4:
+        return self.float32_array
+    elif self.bytes_per_element == 8:
+        return self.float64_array
+    else:
+        raise TypeError("Parsing parameter bytes to an array with %i bit " % self.bytes_per_element +
+                        "floating-point precission is not unsupported.")
      
+
      
 
      
 
      var float_value
      
 
      
 
      Get the param as a floating point value of appropriate type.
      
+
      
+
+Expand source code
+
+
      @property
+def float_value(self):
+    '''Get the param as a floating point value of appropriate type.'''
+    if self.total_bytes > 4:
+        if self.dtypes.is_dec:
+            raise AttributeError("64 bit DEC floating point is not supported.")
+        # 64-bit floating point is not a standard
+        return self._data._as(self.dtypes.float64)
+    elif self.total_bytes == 4:
+        if self.dtypes.is_dec:
+            return DEC_to_IEEE(self._data._as(np.uint32))
+        else:  # is_mips or is_ieee
+            return self._data._as(self.dtypes.float32)
+    else:
+        raise AttributeError("Only 32 and 64 bit floating point is supported.")
      
+
      
 
      
 
      var int16_array
      
 
      
 
      Get the param as an array of 16-bit signed integers.
      
+
      
+
+Expand source code
+
+
      @property
+def int16_array(self):
+    '''Get the param as an array of 16-bit signed integers.'''
+    return self._data._as_array(self.dtypes.int16)
      
+
      
 
      
 
      var int16_value
      
 
      
 
      Get the param as a 16-bit signed integer.
      
+
      
+
+Expand source code
+
+
      @property
+def int16_value(self):
+    '''Get the param as a 16-bit signed integer.'''
+    return self._data._as(self.dtypes.int16)
      
+
      
 
      
 
      var int32_array
      
 
      
 
      Get the param as an array of 32-bit signed integers.
      
+
      
+
+Expand source code
+
+
      @property
+def int32_array(self):
+    '''Get the param as an array of 32-bit signed integers.'''
+    return self._data._as_array(self.dtypes.int32)
      
+
      
 
      
 
      var int32_value
      
 
      
 
      Get the param as a 32-bit signed integer.
      
+
      
+
+Expand source code
+
+
      @property
+def int32_value(self):
+    '''Get the param as a 32-bit signed integer.'''
+    return self._data._as(self.dtypes.int32)
      
+
      
 
      
 
      var int64_array
      
 
      
 
      Get the param as an array of 32-bit signed integers.
      
+
      
+
+Expand source code
+
+
      @property
+def int64_array(self):
+    '''Get the param as an array of 32-bit signed integers.'''
+    return self._data._as_array(self.dtypes.int64)
      
+
      
 
      
 
      var int8_array
      
 
      
 
      Get the param as an array of 8-bit signed integers.
      
+
      
+
+Expand source code
+
+
      @property
+def int8_array(self):
+    '''Get the param as an array of 8-bit signed integers.'''
+    return self._data._as_array(self.dtypes.int8)
      
+
      
 
      
 
      var int8_value
      
 
      
 
      Get the param as an 8-bit signed integer.
      
+
      
+
+Expand source code
+
+
      @property
+def int8_value(self):
+    '''Get the param as an 8-bit signed integer.'''
+    return self._data._as(self.dtypes.int8)
      
+
      
 
      
 
      var int_array
      
 
      
 
      Get the param as an array of integer values.
      
+
      
+
+Expand source code
+
+
      @property
+def int_array(self):
+    '''Get the param as an array of integer values.'''
+    # Convert float data if not IEEE processor
+    if self.bytes_per_element == 1:
+        return self.int8_array
+    elif self.bytes_per_element == 2:
+        return self.int16_array
+    elif self.bytes_per_element == 4:
+        return self.int32_array
+    elif self.bytes_per_element == 8:
+        return self.int64_array
+    else:
+        raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                        self.bytes_per_element)
      
+
      
 
      
 
      var int_value
      
 
      
 
      Get the param as a signed integer of appropriate type.
      
+
      
+
+Expand source code
+
+
      @property
+def int_value(self):
+    ''' Get the param as a signed integer of appropriate type. '''
+    if self.total_bytes >= 4:
+        return self.int32_value
+    elif self.total_bytes >= 2:
+        return self.int16_value
+    else:
+        return self.int8_value
      
+
      
 
      
 
      var name : str
      
 
      
 
      Get the parameter name.
      
+
      
+
+Expand source code
+
+
      @property
+def name(self) -> str:
+    ''' Get the parameter name. '''
+    return self._data.name
      
+
      
 
      
 
      var num_elements : int
      
 
      
 
      Return the number of elements in this parameter's array value.
      
+
      
+
+Expand source code
+
+
      @property
+def num_elements(self) -> int:
+    '''Return the number of elements in this parameter's array value.'''
+    return self._data.num_elements
      
+
      
 
      
 
      var string_array
      
 
      
 
      Get the param as a python array of unicode strings.
      
+
      
+
+Expand source code
+
+
      @property
+def string_array(self):
+    '''Get the param as a python array of unicode strings.'''
+    # Decode different dimensions
+    if len(self.dimensions) == 0:
+        return np.array([])
+    elif len(self.dimensions) == 1:
+        return np.array([self.string_value])
+    else:
+        # Parse byte sequences
+        byte_arr = self.bytes_array
+        # Decode sequences
+        for i in np.ndindex(byte_arr.shape):
+            byte_arr[i] = self.dtypes.decode_string(byte_arr[i])
+        return byte_arr
      
+
      
 
      
 
      var string_value
      
 
      
 
      Get the param as a unicode string.
      
+
      
+
+Expand source code
+
+
      @property
+def string_value(self):
+    '''Get the param as a unicode string.'''
+    return self.dtypes.decode_string(self._data.bytes)
      
+
      
 
      
 
      var total_bytes : int
      
 
      
 
      Return the number of bytes used for storing this parameter's data.
      
+
      
+
+Expand source code
+
+
      @property
+def total_bytes(self) -> int:
+    '''Return the number of bytes used for storing this parameter's data.'''
+    return self._data.total_bytes
      
+
      
 
      
 
      var uint16_array
      
 
      
 
      Get the param as an array of 16-bit unsigned integers.
      
+
      
+
+Expand source code
+
+
      @property
+def uint16_array(self):
+    '''Get the param as an array of 16-bit unsigned integers.'''
+    return self._data._as_array(self.dtypes.uint16)
      
+
      
 
      
 
      var uint16_value
      
 
      
 
      Get the param as a 16-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      @property
+def uint16_value(self):
+    '''Get the param as a 16-bit unsigned integer.'''
+    return self._data._as(self.dtypes.uint16)
      
+
      
 
      
 
      var uint32_array
      
 
      
 
      Get the param as an array of 32-bit unsigned integers.
      
+
      
+
+Expand source code
+
+
      @property
+def uint32_array(self):
+    '''Get the param as an array of 32-bit unsigned integers.'''
+    return self._data._as_array(self.dtypes.uint32)
      
+
      
 
      
 
      var uint32_value
      
 
      
 
      Get the param as a 32-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      @property
+def uint32_value(self):
+    '''Get the param as a 32-bit unsigned integer.'''
+    return self._data._as(self.dtypes.uint32)
      
+
      
 
      
 
      var uint64_array
      
 
      
 
      Get the param as an array of 32-bit unsigned integers.
      
+
      
+
+Expand source code
+
+
      @property
+def uint64_array(self):
+    '''Get the param as an array of 32-bit unsigned integers.'''
+    return self._data._as_array(self.dtypes.uint64)
      
+
      
 
      
 
      var uint8_array
      
 
      
 
      Get the param as an array of 8-bit unsigned integers.
      
+
      
+
+Expand source code
+
+
      @property
+def uint8_array(self):
+    '''Get the param as an array of 8-bit unsigned integers.'''
+    return self._data._as_array(self.dtypes.uint8)
      
+
      
 
      
 
      var uint8_value
      
 
      
 
      Get the param as an 8-bit unsigned integer.
      
+
      
+
+Expand source code
+
+
      @property
+def uint8_value(self):
+    '''Get the param as an 8-bit unsigned integer.'''
+    return self._data._as(self.dtypes.uint8)
      
+
      
 
      
 
      var uint_array
      
 
      
 
      Get the param as an array of integer values.
      
+
      
+
+Expand source code
+
+
      @property
+def uint_array(self):
+    '''Get the param as an array of integer values.'''
+    # Convert float data if not IEEE processor
+    if self.bytes_per_element == 1:
+        return self.uint8_array
+    elif self.bytes_per_element == 2:
+        return self.uint16_array
+    elif self.bytes_per_element == 4:
+        return self.uint32_array
+    elif self.bytes_per_element == 8:
+        return self.uint64_array
+    else:
+        raise TypeError("Parsing parameter bytes to an array with %i bit integer values is not unsupported." %
+                        self.bytes_per_element)
      
+
      
 
      
 
      var uint_value
      
 
      
 
      Get the param as a unsigned integer of appropriate type.
      
+
      
+
+Expand source code
+
+
      @property
+def uint_value(self):
+    ''' Get the param as a unsigned integer of appropriate type. '''
+    if self.total_bytes >= 4:
+        return self.uint32_value
+    elif self.total_bytes >= 2:
+        return self.uint16_value
+    else:
+        return self.uint8_value
      
+
      
 
      
 
 
    
diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html
index a9eac9d..0b868b0 100644
--- a/docs/c3d/reader.html
+++ b/docs/c3d/reader.html
@@ -5,7 +5,7 @@
 
 
 c3d.reader API documentation
-
+
 
 
 
@@ -22,7 +22,349 @@
 
    Module c3d.reader
    
 
 
    
-
    A Python module for reading and writing C3D files.
    
+
    Contains the Reader class for reading C3D files.
    
+
    
+
+Expand source code
+
+
    '''Contains the Reader class for reading C3D files.'''
+
+import io
+import numpy as np
+import struct
+import warnings
+from .manager import Manager
+from .header import Header
+from .dtypes import DataTypes
+from .utils import DEC_to_IEEE_BYTES
+
+
+class Reader(Manager):
+    '''This class provides methods for reading the data in a C3D file.
+
+    A C3D file contains metadata and frame-based data describing 3D motion.
+
+    You can iterate over the frames in the file by calling `read_frames()` after
+    construction:
+
+    >>> r = c3d.Reader(open('capture.c3d', 'rb'))
+    >>> for frame_no, points, analog in r.read_frames():
+    ...     print('{0.shape} points in this frame'.format(points))
+    '''
+
+    def __init__(self, handle):
+        '''Initialize this C3D file by reading header and parameter data.
+
+        Parameters
+        ----------
+        handle : file handle
+            Read metadata and C3D motion frames from the given file handle. This
+            handle is assumed to be `seek`-able and `read`-able. The handle must
+            remain open for the life of the `Reader` instance. The `Reader` does
+            not `close` the handle.
+
+        Raises
+        ------
+        AssertionError
+            If the metadata in the C3D file is inconsistent.
+        '''
+        super(Reader, self).__init__(Header(handle))
+
+        self._handle = handle
+
+        def seek_param_section_header():
+            ''' Seek to and read the first 4 byte of the parameter header section '''
+            self._handle.seek((self._header.parameter_block - 1) * 512)
+            # metadata header
+            return self._handle.read(4)
+
+        # Begin by reading the processor type:
+        buf = seek_param_section_header()
+        _, _, parameter_blocks, processor = struct.unpack('BBBB', buf)
+        self._dtypes = DataTypes(processor)
+        # Convert header parameters in accordance with the processor type (MIPS format re-reads the header)
+        self._header._processor_convert(self._dtypes, handle)
+
+        # Restart reading the parameter header after parsing processor type
+        buf = seek_param_section_header()
+
+        start_byte = self._handle.tell()
+        endbyte = start_byte + 512 * parameter_blocks - 4
+        while self._handle.tell() < endbyte:
+            chars_in_name, group_id = struct.unpack('bb', self._handle.read(2))
+            if group_id == 0 or chars_in_name == 0:
+                # we've reached the end of the parameter section.
+                break
+            name = self._dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper()
+
+            # Read the byte segment associated with the parameter and create a
+            # separate binary stream object from the data.
+            offset_to_next, = struct.unpack(['<h', '>h'][self._dtypes.is_mips], self._handle.read(2))
+            if offset_to_next == 0:
+                # Last parameter, as number of bytes are unknown,
+                # read the remaining bytes in the parameter section.
+                bytes = self._handle.read(endbyte - self._handle.tell())
+            else:
+                bytes = self._handle.read(offset_to_next - 2)
+            buf = io.BytesIO(bytes)
+
+            if group_id > 0:
+                # We've just started reading a parameter. If its group doesn't
+                # exist, create a blank one. add the parameter to the group.
+                group = super(Reader, self).get(group_id)
+                if group is None:
+                    group = self._add_group(group_id)
+                group.add_param(name, handle=buf)
+            else:
+                # We've just started reading a group. If a group with the
+                # appropriate numerical id exists already (because we've
+                # already created it for a parameter), just set the name of
+                # the group. Otherwise, add a new group.
+                group_id = abs(group_id)
+                size, = struct.unpack('B', buf.read(1))
+                desc = size and buf.read(size) or ''
+                group = super(Reader, self).get(group_id)
+                if group is not None:
+                    self._rename_group(group, name)  # Inserts name key
+                    group.desc = desc
+                else:
+                    self._add_group(group_id, name, desc)
+
+        self._check_metadata()
+
+    def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False):
+        '''Iterate over the data frames from our C3D file handle.
+
+        Parameters
+        ----------
+        copy : bool
+            If False, the reader returns a reference to the same data buffers
+            for every frame. The default is True, which causes the reader to
+            return a unique data buffer for each frame. Set this to False if you
+            consume frames as you iterate over them, or True if you store them
+            for later.
+        analog_transform : bool, default=True
+            If True, ANALOG:SCALE, ANALOG:GEN_SCALE, and ANALOG:OFFSET transforms
+            available in the file are applied to the analog channels.
+        check_nan : bool, default=True
+            If True, point x,y,z coordinates with nan values will be marked invalidated
+            and residuals will be set to -1.
+        camera_sum : bool, default=False
+            Camera flag bits will be summed, converting the fifth column to a camera visibility counter.
+
+        Returns
+        -------
+        frames : sequence of (frame number, points, analog)
+            This method generates a sequence of (frame number, points, analog)
+            tuples, one tuple per frame. The first element of each tuple is the
+            frame number. The second is a numpy array of parsed, 5D point data
+            and the third element of each tuple is a numpy array of analog
+            values that were recorded during the frame. (Often the analog data
+            are sampled at a higher frequency than the 3D point data, resulting
+            in multiple analog frames per frame of point data.)
+
+            The first three columns in the returned point data are the (x, y, z)
+            coordinates of the observed motion capture point. The fourth column
+            is an estimate of the error for this particular point, and the fifth
+            column is the number of cameras that observed the point in question.
+            Both the fourth and fifth values are -1 if the point is considered
+            to be invalid.
+        '''
+        # Point magnitude scalar, if scale parameter is < 0 data is floating point
+        # (in which case the magnitude is the absolute value)
+        scale_mag = abs(self.point_scale)
+        is_float = self.point_scale < 0
+
+        if is_float:
+            point_word_bytes = 4
+        else:
+            point_word_bytes = 2
+        points = np.zeros((self.point_used, 5), np.float32)
+
+        # TODO: handle ANALOG:BITS parameter here!
+        p = self.get('ANALOG:FORMAT')
+        analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED'
+        if is_float:
+            analog_dtype = self._dtypes.float32
+            analog_word_bytes = 4
+        elif analog_unsigned:
+            # Note*: Floating point is 'always' defined for both analog and point data, according to the standard.
+            analog_dtype = self._dtypes.uint16
+            analog_word_bytes = 2
+            # Verify BITS parameter for analog
+            p = self.get('ANALOG:BITS')
+            if p and p._as_integer_value / 8 != analog_word_bytes:
+                raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value))
+        else:
+            analog_dtype = self._dtypes.int16
+            analog_word_bytes = 2
+
+        analog = np.array([], float)
+        analog_scales, analog_offsets = self.get_analog_transform()
+
+        # Seek to the start point of the data blocks
+        self._handle.seek((self._header.data_block - 1) * 512)
+        # Number of values (words) read in regard to POINT/ANALOG data
+        N_point = 4 * self.point_used
+        N_analog = self.analog_used * self.analog_per_frame
+
+        # Total bytes per frame
+        point_bytes = N_point * point_word_bytes
+        analog_bytes = N_analog * analog_word_bytes
+        # Parse the data blocks
+        for frame_no in range(self.first_frame, self.last_frame + 1):
+            # Read the byte data (used) for the block
+            raw_bytes = self._handle.read(N_point * point_word_bytes)
+            raw_analog = self._handle.read(N_analog * analog_word_bytes)
+            # Verify read pointers (any of the two can be assumed to be 0)
+            if len(raw_bytes) < point_bytes:
+                warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                                 and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+                return
+            if len(raw_analog) < analog_bytes:
+                warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                                 and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+                return
+
+            if is_float:
+                # Convert every 4 byte words to a float-32 reprensentation
+                # (the fourth column is still not a float32 representation)
+                if self._dtypes.is_dec:
+                    # Convert each of the first 6 16-bit words from DEC to IEEE float
+                    points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4))
+                else:  # If IEEE or MIPS:
+                    # Convert each of the first 6 16-bit words to native float
+                    points[:, :4] = np.frombuffer(raw_bytes,
+                                                  dtype=self._dtypes.float32,
+                                                  count=N_point).reshape((self.point_used, 4))
+
+                # Cast last word to signed integer in system endian format
+                last_word = points[:, 3].astype(np.int32)
+
+            else:
+                # View the bytes as signed 16-bit integers
+                raw = np.frombuffer(raw_bytes,
+                                    dtype=self._dtypes.int16,
+                                    count=N_point).reshape((self.point_used, 4))
+                # Read the first six 16-bit words as x, y, z coordinates
+                points[:, :3] = raw[:, :3] * scale_mag
+                # Cast last word to signed integer in system endian format
+                last_word = raw[:, 3].astype(np.int16)
+
+            # Parse camera-observed bits and residuals.
+            # Notes:
+            # - Invalid sample if residual is equal to -1 (check if word < 0).
+            # - A residual of 0.0 represent modeled data (filtered or interpolated).
+            # - Camera and residual words are always 8-bit (1 byte), never 16-bit.
+            # - If floating point, the byte words are encoded in an integer cast to a float,
+            #    and are written directly in byte form (see the MLS guide).
+            ##
+            # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded).
+            residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8
+
+            # Fourth value is floating-point (scaled) error estimate (residual)
+            points[:, 3] = residual_byte * scale_mag
+
+            # Determine invalid samples
+            invalid = last_word < 0
+            if check_nan:
+                is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1)
+                points[is_nan, :3] = 0.0
+                invalid &= is_nan
+            # Update discarded - sign
+            points[invalid, 3] = -1
+
+
+            # Fifth value is the camera-observation byte
+            if camera_sum:
+                # Convert to observation sum
+                points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7))
+            else:
+                points[:, 4] = camera_byte #.astype(np.float32)
+
+            # Check if analog data exist, and parse if so
+            if N_analog > 0:
+                if is_float and self._dtypes.is_dec:
+                    # Convert each of the 16-bit words from DEC to IEEE float
+                    analog = DEC_to_IEEE_BYTES(raw_analog)
+                else:
+                    # Integer or INTEL/MIPS floating point data can be parsed directly
+                    analog = np.frombuffer(raw_analog, dtype=analog_dtype, count=N_analog)
+
+                # Reformat and convert
+                analog = analog.reshape((-1, self.analog_used)).T
+                analog = analog.astype(float)
+                # Convert analog
+                analog = (analog - analog_offsets) * analog_scales
+
+            # Output buffers
+            if copy:
+                yield frame_no, points.copy(), analog  # .copy(), a new array is generated per frame for analog data.
+            else:
+                yield frame_no, points, analog
+
+        # Function evaluating EOF, note that data section is written in blocks of 512
+        final_byte_index = self._handle.tell()
+        self._handle.seek(0, 2)  # os.SEEK_END)
+        # Check if more then 1 block remain
+        if self._handle.tell() - final_byte_index >= 512:
+            warnings.warn('incomplete reading of data blocks. {} bytes remained after all datablocks were read!'.format(
+                self._handle.tell() - final_byte_index))
+
+    @property
+    def proc_type(self) -> int:
+        '''Get the processory type associated with the data format in the file.
+        '''
+        return self._dtypes.proc_type
+
+    def to_writer(self, conversion=None):
+        ''' Converts the reader to a `c3d.writer.Writer` instance using the conversion mode.
+
+        See `c3d.writer.Writer.from_reader()` for supported conversion modes.
+        '''
+        from .writer import Writer
+        return Writer.from_reader(self, conversion=conversion)
+
+    def get(self, key, default=None):
+        '''Get a readonly group or parameter.
+
+        Parameters
+        ----------
+        key : str
+            If this string contains a period (.), then the part before the
+            period will be used to retrieve a group, and the part after the
+            period will be used to retrieve a parameter from that group. If this
+            string does not contain a period, then just a group will be
+            returned.
+        default : any
+            Return this value if the named group and parameter are not found.
+
+        Returns
+        -------
+        value : `c3d.group.GroupReadonly` or `c3d.parameter.ParamReadonly`
+            Either a group or parameter with the specified name(s). If neither
+            is found, returns the default value.
+        '''
+        val = super(Reader, self).get(key)
+        if val:
+            return val.readonly()
+        return default
+
+    def items(self):
+        ''' Get iterable over pairs of (str, `c3d.group.GroupReadonly`) entries.
+        '''
+        return ((k, v.readonly()) for k, v in super(Reader, self).items())
+
+    def values(self):
+        ''' Get iterable over `c3d.group.GroupReadonly` entries.
+        '''
+        return (v.readonly() for k, v in super(Reader, self).items())
+
+    def listed(self):
+        ''' Get iterable over pairs of (int, `c3d.group.GroupReadonly`) entries.
+        '''
+        return ((k, v.readonly()) for k, v in super(Reader, self).listed())
    
+
    
 
    
 
    
 
    
@@ -60,6 +402,336 @@ 
    Raises
    
 
    AssertionError
    
 
    If the metadata in the C3D file is inconsistent.
    
 
+
    
+
+Expand source code
+
+
    class Reader(Manager):
+    '''This class provides methods for reading the data in a C3D file.
+
+    A C3D file contains metadata and frame-based data describing 3D motion.
+
+    You can iterate over the frames in the file by calling `read_frames()` after
+    construction:
+
+    >>> r = c3d.Reader(open('capture.c3d', 'rb'))
+    >>> for frame_no, points, analog in r.read_frames():
+    ...     print('{0.shape} points in this frame'.format(points))
+    '''
+
+    def __init__(self, handle):
+        '''Initialize this C3D file by reading header and parameter data.
+
+        Parameters
+        ----------
+        handle : file handle
+            Read metadata and C3D motion frames from the given file handle. This
+            handle is assumed to be `seek`-able and `read`-able. The handle must
+            remain open for the life of the `Reader` instance. The `Reader` does
+            not `close` the handle.
+
+        Raises
+        ------
+        AssertionError
+            If the metadata in the C3D file is inconsistent.
+        '''
+        super(Reader, self).__init__(Header(handle))
+
+        self._handle = handle
+
+        def seek_param_section_header():
+            ''' Seek to and read the first 4 byte of the parameter header section '''
+            self._handle.seek((self._header.parameter_block - 1) * 512)
+            # metadata header
+            return self._handle.read(4)
+
+        # Begin by reading the processor type:
+        buf = seek_param_section_header()
+        _, _, parameter_blocks, processor = struct.unpack('BBBB', buf)
+        self._dtypes = DataTypes(processor)
+        # Convert header parameters in accordance with the processor type (MIPS format re-reads the header)
+        self._header._processor_convert(self._dtypes, handle)
+
+        # Restart reading the parameter header after parsing processor type
+        buf = seek_param_section_header()
+
+        start_byte = self._handle.tell()
+        endbyte = start_byte + 512 * parameter_blocks - 4
+        while self._handle.tell() < endbyte:
+            chars_in_name, group_id = struct.unpack('bb', self._handle.read(2))
+            if group_id == 0 or chars_in_name == 0:
+                # we've reached the end of the parameter section.
+                break
+            name = self._dtypes.decode_string(self._handle.read(abs(chars_in_name))).upper()
+
+            # Read the byte segment associated with the parameter and create a
+            # separate binary stream object from the data.
+            offset_to_next, = struct.unpack(['<h', '>h'][self._dtypes.is_mips], self._handle.read(2))
+            if offset_to_next == 0:
+                # Last parameter, as number of bytes are unknown,
+                # read the remaining bytes in the parameter section.
+                bytes = self._handle.read(endbyte - self._handle.tell())
+            else:
+                bytes = self._handle.read(offset_to_next - 2)
+            buf = io.BytesIO(bytes)
+
+            if group_id > 0:
+                # We've just started reading a parameter. If its group doesn't
+                # exist, create a blank one. add the parameter to the group.
+                group = super(Reader, self).get(group_id)
+                if group is None:
+                    group = self._add_group(group_id)
+                group.add_param(name, handle=buf)
+            else:
+                # We've just started reading a group. If a group with the
+                # appropriate numerical id exists already (because we've
+                # already created it for a parameter), just set the name of
+                # the group. Otherwise, add a new group.
+                group_id = abs(group_id)
+                size, = struct.unpack('B', buf.read(1))
+                desc = size and buf.read(size) or ''
+                group = super(Reader, self).get(group_id)
+                if group is not None:
+                    self._rename_group(group, name)  # Inserts name key
+                    group.desc = desc
+                else:
+                    self._add_group(group_id, name, desc)
+
+        self._check_metadata()
+
+    def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False):
+        '''Iterate over the data frames from our C3D file handle.
+
+        Parameters
+        ----------
+        copy : bool
+            If False, the reader returns a reference to the same data buffers
+            for every frame. The default is True, which causes the reader to
+            return a unique data buffer for each frame. Set this to False if you
+            consume frames as you iterate over them, or True if you store them
+            for later.
+        analog_transform : bool, default=True
+            If True, ANALOG:SCALE, ANALOG:GEN_SCALE, and ANALOG:OFFSET transforms
+            available in the file are applied to the analog channels.
+        check_nan : bool, default=True
+            If True, point x,y,z coordinates with nan values will be marked invalidated
+            and residuals will be set to -1.
+        camera_sum : bool, default=False
+            Camera flag bits will be summed, converting the fifth column to a camera visibility counter.
+
+        Returns
+        -------
+        frames : sequence of (frame number, points, analog)
+            This method generates a sequence of (frame number, points, analog)
+            tuples, one tuple per frame. The first element of each tuple is the
+            frame number. The second is a numpy array of parsed, 5D point data
+            and the third element of each tuple is a numpy array of analog
+            values that were recorded during the frame. (Often the analog data
+            are sampled at a higher frequency than the 3D point data, resulting
+            in multiple analog frames per frame of point data.)
+
+            The first three columns in the returned point data are the (x, y, z)
+            coordinates of the observed motion capture point. The fourth column
+            is an estimate of the error for this particular point, and the fifth
+            column is the number of cameras that observed the point in question.
+            Both the fourth and fifth values are -1 if the point is considered
+            to be invalid.
+        '''
+        # Point magnitude scalar, if scale parameter is < 0 data is floating point
+        # (in which case the magnitude is the absolute value)
+        scale_mag = abs(self.point_scale)
+        is_float = self.point_scale < 0
+
+        if is_float:
+            point_word_bytes = 4
+        else:
+            point_word_bytes = 2
+        points = np.zeros((self.point_used, 5), np.float32)
+
+        # TODO: handle ANALOG:BITS parameter here!
+        p = self.get('ANALOG:FORMAT')
+        analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED'
+        if is_float:
+            analog_dtype = self._dtypes.float32
+            analog_word_bytes = 4
+        elif analog_unsigned:
+            # Note*: Floating point is 'always' defined for both analog and point data, according to the standard.
+            analog_dtype = self._dtypes.uint16
+            analog_word_bytes = 2
+            # Verify BITS parameter for analog
+            p = self.get('ANALOG:BITS')
+            if p and p._as_integer_value / 8 != analog_word_bytes:
+                raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value))
+        else:
+            analog_dtype = self._dtypes.int16
+            analog_word_bytes = 2
+
+        analog = np.array([], float)
+        analog_scales, analog_offsets = self.get_analog_transform()
+
+        # Seek to the start point of the data blocks
+        self._handle.seek((self._header.data_block - 1) * 512)
+        # Number of values (words) read in regard to POINT/ANALOG data
+        N_point = 4 * self.point_used
+        N_analog = self.analog_used * self.analog_per_frame
+
+        # Total bytes per frame
+        point_bytes = N_point * point_word_bytes
+        analog_bytes = N_analog * analog_word_bytes
+        # Parse the data blocks
+        for frame_no in range(self.first_frame, self.last_frame + 1):
+            # Read the byte data (used) for the block
+            raw_bytes = self._handle.read(N_point * point_word_bytes)
+            raw_analog = self._handle.read(N_analog * analog_word_bytes)
+            # Verify read pointers (any of the two can be assumed to be 0)
+            if len(raw_bytes) < point_bytes:
+                warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                                 and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+                return
+            if len(raw_analog) < analog_bytes:
+                warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                                 and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+                return
+
+            if is_float:
+                # Convert every 4 byte words to a float-32 reprensentation
+                # (the fourth column is still not a float32 representation)
+                if self._dtypes.is_dec:
+                    # Convert each of the first 6 16-bit words from DEC to IEEE float
+                    points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4))
+                else:  # If IEEE or MIPS:
+                    # Convert each of the first 6 16-bit words to native float
+                    points[:, :4] = np.frombuffer(raw_bytes,
+                                                  dtype=self._dtypes.float32,
+                                                  count=N_point).reshape((self.point_used, 4))
+
+                # Cast last word to signed integer in system endian format
+                last_word = points[:, 3].astype(np.int32)
+
+            else:
+                # View the bytes as signed 16-bit integers
+                raw = np.frombuffer(raw_bytes,
+                                    dtype=self._dtypes.int16,
+                                    count=N_point).reshape((self.point_used, 4))
+                # Read the first six 16-bit words as x, y, z coordinates
+                points[:, :3] = raw[:, :3] * scale_mag
+                # Cast last word to signed integer in system endian format
+                last_word = raw[:, 3].astype(np.int16)
+
+            # Parse camera-observed bits and residuals.
+            # Notes:
+            # - Invalid sample if residual is equal to -1 (check if word < 0).
+            # - A residual of 0.0 represent modeled data (filtered or interpolated).
+            # - Camera and residual words are always 8-bit (1 byte), never 16-bit.
+            # - If floating point, the byte words are encoded in an integer cast to a float,
+            #    and are written directly in byte form (see the MLS guide).
+            ##
+            # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded).
+            residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8
+
+            # Fourth value is floating-point (scaled) error estimate (residual)
+            points[:, 3] = residual_byte * scale_mag
+
+            # Determine invalid samples
+            invalid = last_word < 0
+            if check_nan:
+                is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1)
+                points[is_nan, :3] = 0.0
+                invalid &= is_nan
+            # Update discarded - sign
+            points[invalid, 3] = -1
+
+
+            # Fifth value is the camera-observation byte
+            if camera_sum:
+                # Convert to observation sum
+                points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7))
+            else:
+                points[:, 4] = camera_byte #.astype(np.float32)
+
+            # Check if analog data exist, and parse if so
+            if N_analog > 0:
+                if is_float and self._dtypes.is_dec:
+                    # Convert each of the 16-bit words from DEC to IEEE float
+                    analog = DEC_to_IEEE_BYTES(raw_analog)
+                else:
+                    # Integer or INTEL/MIPS floating point data can be parsed directly
+                    analog = np.frombuffer(raw_analog, dtype=analog_dtype, count=N_analog)
+
+                # Reformat and convert
+                analog = analog.reshape((-1, self.analog_used)).T
+                analog = analog.astype(float)
+                # Convert analog
+                analog = (analog - analog_offsets) * analog_scales
+
+            # Output buffers
+            if copy:
+                yield frame_no, points.copy(), analog  # .copy(), a new array is generated per frame for analog data.
+            else:
+                yield frame_no, points, analog
+
+        # Function evaluating EOF, note that data section is written in blocks of 512
+        final_byte_index = self._handle.tell()
+        self._handle.seek(0, 2)  # os.SEEK_END)
+        # Check if more then 1 block remain
+        if self._handle.tell() - final_byte_index >= 512:
+            warnings.warn('incomplete reading of data blocks. {} bytes remained after all datablocks were read!'.format(
+                self._handle.tell() - final_byte_index))
+
+    @property
+    def proc_type(self) -> int:
+        '''Get the processory type associated with the data format in the file.
+        '''
+        return self._dtypes.proc_type
+
+    def to_writer(self, conversion=None):
+        ''' Converts the reader to a `c3d.writer.Writer` instance using the conversion mode.
+
+        See `c3d.writer.Writer.from_reader()` for supported conversion modes.
+        '''
+        from .writer import Writer
+        return Writer.from_reader(self, conversion=conversion)
+
+    def get(self, key, default=None):
+        '''Get a readonly group or parameter.
+
+        Parameters
+        ----------
+        key : str
+            If this string contains a period (.), then the part before the
+            period will be used to retrieve a group, and the part after the
+            period will be used to retrieve a parameter from that group. If this
+            string does not contain a period, then just a group will be
+            returned.
+        default : any
+            Return this value if the named group and parameter are not found.
+
+        Returns
+        -------
+        value : `c3d.group.GroupReadonly` or `c3d.parameter.ParamReadonly`
+            Either a group or parameter with the specified name(s). If neither
+            is found, returns the default value.
+        '''
+        val = super(Reader, self).get(key)
+        if val:
+            return val.readonly()
+        return default
+
+    def items(self):
+        ''' Get iterable over pairs of (str, `c3d.group.GroupReadonly`) entries.
+        '''
+        return ((k, v.readonly()) for k, v in super(Reader, self).items())
+
+    def values(self):
+        ''' Get iterable over `c3d.group.GroupReadonly` entries.
+        '''
+        return (v.readonly() for k, v in super(Reader, self).items())
+
+    def listed(self):
+        ''' Get iterable over pairs of (int, `c3d.group.GroupReadonly`) entries.
+        '''
+        return ((k, v.readonly()) for k, v in super(Reader, self).listed())
    
+
    
 
    Ancestors
    
 
      
 
    • Manager
      • 
@@ -69,6 +741,16 @@ 
      Instance variables
      
 
      var proc_type : int
      
 
      
 
      Get the processory type associated with the data format in the file.
      
+
      
+
+Expand source code
+
+
      @property
+def proc_type(self) -> int:
+    '''Get the processory type associated with the data format in the file.
+    '''
+    return self._dtypes.proc_type
      
+
      
 
      
 
 
      Methods
      
@@ -95,18 +777,65 @@ 
      Returns
      
 
      Either a group or parameter with the specified name(s). If neither
 is found, returns the default value.
      
 
+
      
+
+Expand source code
+
+
      def get(self, key, default=None):
+    '''Get a readonly group or parameter.
+
+    Parameters
+    ----------
+    key : str
+        If this string contains a period (.), then the part before the
+        period will be used to retrieve a group, and the part after the
+        period will be used to retrieve a parameter from that group. If this
+        string does not contain a period, then just a group will be
+        returned.
+    default : any
+        Return this value if the named group and parameter are not found.
+
+    Returns
+    -------
+    value : `c3d.group.GroupReadonly` or `c3d.parameter.ParamReadonly`
+        Either a group or parameter with the specified name(s). If neither
+        is found, returns the default value.
+    '''
+    val = super(Reader, self).get(key)
+    if val:
+        return val.readonly()
+    return default
      
+
      
 
 
      
 def items(self)
 
      
 
      
 
      Get iterable over pairs of (str, GroupReadonly) entries.
      
+
      
+
+Expand source code
+
+
      def items(self):
+    ''' Get iterable over pairs of (str, `c3d.group.GroupReadonly`) entries.
+    '''
+    return ((k, v.readonly()) for k, v in super(Reader, self).items())
      
+
      
 
      
 
      
 def listed(self)
 
      
 
      
 
      Get iterable over pairs of (int, GroupReadonly) entries.
      
+
      
+
+Expand source code
+
+
      def listed(self):
+    ''' Get iterable over pairs of (int, `c3d.group.GroupReadonly`) entries.
+    '''
+    return ((k, v.readonly()) for k, v in super(Reader, self).listed())
      
+
      
 
      
 
      
 def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False)
@@ -149,6 +878,189 @@ 
      Returns
      
 to be invalid.
      
 
 
+
      
+
+Expand source code
+
+
      def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_sum=False):
+    '''Iterate over the data frames from our C3D file handle.
+
+    Parameters
+    ----------
+    copy : bool
+        If False, the reader returns a reference to the same data buffers
+        for every frame. The default is True, which causes the reader to
+        return a unique data buffer for each frame. Set this to False if you
+        consume frames as you iterate over them, or True if you store them
+        for later.
+    analog_transform : bool, default=True
+        If True, ANALOG:SCALE, ANALOG:GEN_SCALE, and ANALOG:OFFSET transforms
+        available in the file are applied to the analog channels.
+    check_nan : bool, default=True
+        If True, point x,y,z coordinates with nan values will be marked invalidated
+        and residuals will be set to -1.
+    camera_sum : bool, default=False
+        Camera flag bits will be summed, converting the fifth column to a camera visibility counter.
+
+    Returns
+    -------
+    frames : sequence of (frame number, points, analog)
+        This method generates a sequence of (frame number, points, analog)
+        tuples, one tuple per frame. The first element of each tuple is the
+        frame number. The second is a numpy array of parsed, 5D point data
+        and the third element of each tuple is a numpy array of analog
+        values that were recorded during the frame. (Often the analog data
+        are sampled at a higher frequency than the 3D point data, resulting
+        in multiple analog frames per frame of point data.)
+
+        The first three columns in the returned point data are the (x, y, z)
+        coordinates of the observed motion capture point. The fourth column
+        is an estimate of the error for this particular point, and the fifth
+        column is the number of cameras that observed the point in question.
+        Both the fourth and fifth values are -1 if the point is considered
+        to be invalid.
+    '''
+    # Point magnitude scalar, if scale parameter is < 0 data is floating point
+    # (in which case the magnitude is the absolute value)
+    scale_mag = abs(self.point_scale)
+    is_float = self.point_scale < 0
+
+    if is_float:
+        point_word_bytes = 4
+    else:
+        point_word_bytes = 2
+    points = np.zeros((self.point_used, 5), np.float32)
+
+    # TODO: handle ANALOG:BITS parameter here!
+    p = self.get('ANALOG:FORMAT')
+    analog_unsigned = p and p.string_value.strip().upper() == 'UNSIGNED'
+    if is_float:
+        analog_dtype = self._dtypes.float32
+        analog_word_bytes = 4
+    elif analog_unsigned:
+        # Note*: Floating point is 'always' defined for both analog and point data, according to the standard.
+        analog_dtype = self._dtypes.uint16
+        analog_word_bytes = 2
+        # Verify BITS parameter for analog
+        p = self.get('ANALOG:BITS')
+        if p and p._as_integer_value / 8 != analog_word_bytes:
+            raise NotImplementedError('Analog data using {} bits is not supported.'.format(p._as_integer_value))
+    else:
+        analog_dtype = self._dtypes.int16
+        analog_word_bytes = 2
+
+    analog = np.array([], float)
+    analog_scales, analog_offsets = self.get_analog_transform()
+
+    # Seek to the start point of the data blocks
+    self._handle.seek((self._header.data_block - 1) * 512)
+    # Number of values (words) read in regard to POINT/ANALOG data
+    N_point = 4 * self.point_used
+    N_analog = self.analog_used * self.analog_per_frame
+
+    # Total bytes per frame
+    point_bytes = N_point * point_word_bytes
+    analog_bytes = N_analog * analog_word_bytes
+    # Parse the data blocks
+    for frame_no in range(self.first_frame, self.last_frame + 1):
+        # Read the byte data (used) for the block
+        raw_bytes = self._handle.read(N_point * point_word_bytes)
+        raw_analog = self._handle.read(N_analog * analog_word_bytes)
+        # Verify read pointers (any of the two can be assumed to be 0)
+        if len(raw_bytes) < point_bytes:
+            warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                             and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+            return
+        if len(raw_analog) < analog_bytes:
+            warnings.warn('''reached end of file (EOF) while reading POINT data at frame index {}
+                             and file pointer {}!'''.format(frame_no - self.first_frame, self._handle.tell()))
+            return
+
+        if is_float:
+            # Convert every 4 byte words to a float-32 reprensentation
+            # (the fourth column is still not a float32 representation)
+            if self._dtypes.is_dec:
+                # Convert each of the first 6 16-bit words from DEC to IEEE float
+                points[:, :4] = DEC_to_IEEE_BYTES(raw_bytes).reshape((self.point_used, 4))
+            else:  # If IEEE or MIPS:
+                # Convert each of the first 6 16-bit words to native float
+                points[:, :4] = np.frombuffer(raw_bytes,
+                                              dtype=self._dtypes.float32,
+                                              count=N_point).reshape((self.point_used, 4))
+
+            # Cast last word to signed integer in system endian format
+            last_word = points[:, 3].astype(np.int32)
+
+        else:
+            # View the bytes as signed 16-bit integers
+            raw = np.frombuffer(raw_bytes,
+                                dtype=self._dtypes.int16,
+                                count=N_point).reshape((self.point_used, 4))
+            # Read the first six 16-bit words as x, y, z coordinates
+            points[:, :3] = raw[:, :3] * scale_mag
+            # Cast last word to signed integer in system endian format
+            last_word = raw[:, 3].astype(np.int16)
+
+        # Parse camera-observed bits and residuals.
+        # Notes:
+        # - Invalid sample if residual is equal to -1 (check if word < 0).
+        # - A residual of 0.0 represent modeled data (filtered or interpolated).
+        # - Camera and residual words are always 8-bit (1 byte), never 16-bit.
+        # - If floating point, the byte words are encoded in an integer cast to a float,
+        #    and are written directly in byte form (see the MLS guide).
+        ##
+        # Read the residual and camera byte words (Note* if 32 bit word negative sign is discarded).
+        residual_byte, camera_byte = (last_word & 0x00ff), (last_word & 0x7f00) >> 8
+
+        # Fourth value is floating-point (scaled) error estimate (residual)
+        points[:, 3] = residual_byte * scale_mag
+
+        # Determine invalid samples
+        invalid = last_word < 0
+        if check_nan:
+            is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1)
+            points[is_nan, :3] = 0.0
+            invalid &= is_nan
+        # Update discarded - sign
+        points[invalid, 3] = -1
+
+
+        # Fifth value is the camera-observation byte
+        if camera_sum:
+            # Convert to observation sum
+            points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7))
+        else:
+            points[:, 4] = camera_byte #.astype(np.float32)
+
+        # Check if analog data exist, and parse if so
+        if N_analog > 0:
+            if is_float and self._dtypes.is_dec:
+                # Convert each of the 16-bit words from DEC to IEEE float
+                analog = DEC_to_IEEE_BYTES(raw_analog)
+            else:
+                # Integer or INTEL/MIPS floating point data can be parsed directly
+                analog = np.frombuffer(raw_analog, dtype=analog_dtype, count=N_analog)
+
+            # Reformat and convert
+            analog = analog.reshape((-1, self.analog_used)).T
+            analog = analog.astype(float)
+            # Convert analog
+            analog = (analog - analog_offsets) * analog_scales
+
+        # Output buffers
+        if copy:
+            yield frame_no, points.copy(), analog  # .copy(), a new array is generated per frame for analog data.
+        else:
+            yield frame_no, points, analog
+
+    # Function evaluating EOF, note that data section is written in blocks of 512
+    final_byte_index = self._handle.tell()
+    self._handle.seek(0, 2)  # os.SEEK_END)
+    # Check if more then 1 block remain
+    if self._handle.tell() - final_byte_index >= 512:
+        warnings.warn('incomplete reading of data blocks. {} bytes remained after all datablocks were read!'.format(
+            self._handle.tell() - final_byte_index))
      
+
      
 
 
      
 def to_writer(self, conversion=None)
@@ -156,12 +1068,33 @@ 
      Returns
      
 
      
 
      Converts the reader to a Writer instance using the conversion mode.
      
 
      See Writer.from_reader() for supported conversion modes.
      
+
      
+
+Expand source code
+
+
      def to_writer(self, conversion=None):
+    ''' Converts the reader to a `c3d.writer.Writer` instance using the conversion mode.
+
+    See `c3d.writer.Writer.from_reader()` for supported conversion modes.
+    '''
+    from .writer import Writer
+    return Writer.from_reader(self, conversion=conversion)
      
+
      
 
      
 
      
 def values(self)
 
      
 
      
 
      Get iterable over GroupReadonly entries.
      
+
      
+
+Expand source code
+
+
      def values(self):
+    ''' Get iterable over `c3d.group.GroupReadonly` entries.
+    '''
+    return (v.readonly() for k, v in super(Reader, self).items())
      
+
      
 
      
 
 
      Inherited members
      
diff --git a/docs/c3d/utils.html b/docs/c3d/utils.html
index 9560227..466598c 100644
--- a/docs/c3d/utils.html
+++ b/docs/c3d/utils.html
@@ -23,6 +23,159 @@ 
      Module c3d.utils
      
 
 
      
 
      Trailing utility functions.
      
+
      
+
+Expand source code
+
+
      ''' Trailing utility functions.
+'''
+import numpy as np
+import struct
+
+def is_integer(value):
+    '''Check if value input is integer.'''
+    return isinstance(value, (int, np.int32, np.int64))
+
+
+def is_iterable(value):
+    '''Check if value is iterable.'''
+    return hasattr(value, '__iter__')
+
+
+def type_npy2struct(dtype):
+    ''' Convert numpy dtype format to a struct package format string.
+    '''
+    return dtype.byteorder + dtype.char
+
+
+def pack_labels(labels):
+    ''' Static method used to pack and pad the set of `labels` strings before
+        passing the output into a `c3d.group.Group.add_str`.
+
+    Parameters
+    ----------
+    labels : iterable
+        List of strings to pack and pad into a single string suitable for encoding in a Parameter entry.
+
+    Example
+    -------
+    >>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3']
+    >>> param_str, label_max_size = Writer.pack_labels(labels)
+    >>> writer.point_group.add_str('LABELS',
+                                   'Point labels.',
+                                   label_str,
+                                   label_max_size,
+                                   len(labels))
+
+    Returns
+    -------
+    param_str : str
+        String containing `labels` packed into a single variable where
+        each string is padded to match the longest `labels` string.
+    label_max_size : int
+        Number of bytes associated with the longest `label` string, all strings are padded to this length.
+    '''
+    labels = np.ravel(labels)
+    # Get longest label name
+    label_max_size = 0
+    label_max_size = max(label_max_size, np.max([len(label) for label in labels]))
+    label_str = ''.join(label.ljust(label_max_size) for label in labels)
+    return label_str, label_max_size
+
+class Decorator(object):
+    '''Base class for extending (decorating) a python object.
+    '''
+    def __init__(self, decoratee):
+        self._decoratee = decoratee
+    def __getattr__(self, name):
+        return getattr(self._decoratee, name)
+
+def UNPACK_FLOAT_IEEE(uint_32):
+    '''Unpacks a single 32 bit unsigned int to a IEEE float representation
+    '''
+    return struct.unpack('f', struct.pack("<I", uint_32))[0]
+
+def UNPACK_FLOAT_MIPS(uint_32):
+    '''Unpacks a single 32 bit unsigned int to a IEEE float representation
+    '''
+    return struct.unpack('f', struct.pack(">I", uint_32))[0]
+
+def DEC_to_IEEE(uint_32):
+    '''Convert the 32 bit representation of a DEC float to IEEE format.
+
+    Params:
+    ----
+    uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits.
+    Returns : IEEE formated floating point of the same shape as the input.
+    '''
+    # Follows the bit pattern found:
+    #   http://home.fnal.gov/~yang/Notes/ieee_vs_dec_float.txt
+    # Further formating descriptions can be found:
+    #   http://www.irig106.org/docs/106-07/appendixO.pdf
+    # In accodance with the first ref. first & second 16 bit words are placed
+    # in a big endian 16 bit word representation, and needs to be inverted.
+    # Second reference describe the DEC->IEEE conversion.
+
+    # Warning! Unsure if NaN numbers are managed appropriately.
+
+    # Shuffle the first two bit words from DEC bit representation to an ordered representation.
+    # Note that the most significant fraction bits are placed in the first 7 bits.
+    #
+    # Below are the DEC layout in accordance with the references:
+    # ___________________________________________________________________________________
+    # |         Mantissa (16:0)         |       SIGN    |       Exponent (8:0)  |       Mantissa (23:17)        |
+    # ___________________________________________________________________________________
+    # |32-                                        -16|   15        |14-                           -7|6-                                   -0|
+    #
+    # Legend:
+    # _______________________________________________________
+    # | Part (left bit of segment : right bit) | Part | ..
+    # _______________________________________________________
+    # |Bit adress -     ..       - Bit adress | Bit adress - ..
+    ####
+
+    # Swap the first and last 16  bits for a consistent alignment of the fraction
+    reshuffled = ((uint_32 & 0xFFFF0000) >> 16) | ((uint_32 & 0x0000FFFF) << 16)
+    # After the shuffle each part are in little-endian and ordered as: SIGN-Exponent-Fraction
+    exp_bits = ((reshuffled & 0xFF000000) - 1) & 0xFF000000
+    reshuffled = (reshuffled & 0x00FFFFFF) | exp_bits
+    return UNPACK_FLOAT_IEEE(reshuffled)
+
+
+def DEC_to_IEEE_BYTES(bytes):
+    '''Convert byte array containing 32 bit DEC floats to IEEE format.
+
+    Params:
+    ----
+    bytes : Byte array where every 4 bytes represent a single precision DEC float.
+    Returns : IEEE formated floating point of the same shape as the input.
+    '''
+
+    # See comments in DEC_to_IEEE() for DEC format definition
+
+    # Reshuffle
+    bytes = memoryview(bytes)
+    reshuffled = np.empty(len(bytes), dtype=np.dtype('B'))
+    reshuffled[::4] = bytes[2::4]
+    reshuffled[1::4] = bytes[3::4]
+    reshuffled[2::4] = bytes[::4]
+    # Decrement exponent by 2, if exp. > 1
+    reshuffled[3::4] = bytes[1::4] + (np.bitwise_and(bytes[1::4], 0x7f) == 0) - 1
+
+    # There are different ways to adjust for differences in DEC/IEEE representation
+    # after reshuffle. Two simple methods are:
+    # 1) Decrement exponent bits by 2, then convert to IEEE.
+    # 2) Convert to IEEE directly and divide by four.
+    # 3) Handle edge cases, expensive in python...
+    # However these are simple methods, and do not accurately convert when:
+    # 1) Exponent < 2 (without bias), impossible to decrement exponent without adjusting fraction/mantissa.
+    # 2) Exponent == 0, DEC numbers are then 0 or undefined while IEEE is not. NaN are produced when exponent == 255.
+    # Here method 1) is used, which mean that only small numbers will be represented incorrectly.
+
+    return np.frombuffer(reshuffled.tobytes(),
+                         dtype=np.float32,
+                         count=int(len(bytes) / 4))
      
+
      
 
      
 
      
 
      
@@ -39,6 +192,51 @@ 
      Functions
      
 
      Params:
      
 
      uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits.
 Returns : IEEE formated floating point of the same shape as the input.
      
+
      
+
+Expand source code
+
+
      def DEC_to_IEEE(uint_32):
+    '''Convert the 32 bit representation of a DEC float to IEEE format.
+
+    Params:
+    ----
+    uint_32 : 32 bit unsigned integer containing the DEC single precision float point bits.
+    Returns : IEEE formated floating point of the same shape as the input.
+    '''
+    # Follows the bit pattern found:
+    #   http://home.fnal.gov/~yang/Notes/ieee_vs_dec_float.txt
+    # Further formating descriptions can be found:
+    #   http://www.irig106.org/docs/106-07/appendixO.pdf
+    # In accodance with the first ref. first & second 16 bit words are placed
+    # in a big endian 16 bit word representation, and needs to be inverted.
+    # Second reference describe the DEC->IEEE conversion.
+
+    # Warning! Unsure if NaN numbers are managed appropriately.
+
+    # Shuffle the first two bit words from DEC bit representation to an ordered representation.
+    # Note that the most significant fraction bits are placed in the first 7 bits.
+    #
+    # Below are the DEC layout in accordance with the references:
+    # ___________________________________________________________________________________
+    # |         Mantissa (16:0)         |       SIGN    |       Exponent (8:0)  |       Mantissa (23:17)        |
+    # ___________________________________________________________________________________
+    # |32-                                        -16|   15        |14-                           -7|6-                                   -0|
+    #
+    # Legend:
+    # _______________________________________________________
+    # | Part (left bit of segment : right bit) | Part | ..
+    # _______________________________________________________
+    # |Bit adress -     ..       - Bit adress | Bit adress - ..
+    ####
+
+    # Swap the first and last 16  bits for a consistent alignment of the fraction
+    reshuffled = ((uint_32 & 0xFFFF0000) >> 16) | ((uint_32 & 0x0000FFFF) << 16)
+    # After the shuffle each part are in little-endian and ordered as: SIGN-Exponent-Fraction
+    exp_bits = ((reshuffled & 0xFF000000) - 1) & 0xFF000000
+    reshuffled = (reshuffled & 0x00FFFFFF) | exp_bits
+    return UNPACK_FLOAT_IEEE(reshuffled)
      
+
      
 
 
      
 def DEC_to_IEEE_BYTES(bytes)
@@ -48,30 +246,102 @@ 
      Params:
      
 
      Params:
      
 
      bytes : Byte array where every 4 bytes represent a single precision DEC float.
 Returns : IEEE formated floating point of the same shape as the input.
      
+
      
+
+Expand source code
+
+
      def DEC_to_IEEE_BYTES(bytes):
+    '''Convert byte array containing 32 bit DEC floats to IEEE format.
+
+    Params:
+    ----
+    bytes : Byte array where every 4 bytes represent a single precision DEC float.
+    Returns : IEEE formated floating point of the same shape as the input.
+    '''
+
+    # See comments in DEC_to_IEEE() for DEC format definition
+
+    # Reshuffle
+    bytes = memoryview(bytes)
+    reshuffled = np.empty(len(bytes), dtype=np.dtype('B'))
+    reshuffled[::4] = bytes[2::4]
+    reshuffled[1::4] = bytes[3::4]
+    reshuffled[2::4] = bytes[::4]
+    # Decrement exponent by 2, if exp. > 1
+    reshuffled[3::4] = bytes[1::4] + (np.bitwise_and(bytes[1::4], 0x7f) == 0) - 1
+
+    # There are different ways to adjust for differences in DEC/IEEE representation
+    # after reshuffle. Two simple methods are:
+    # 1) Decrement exponent bits by 2, then convert to IEEE.
+    # 2) Convert to IEEE directly and divide by four.
+    # 3) Handle edge cases, expensive in python...
+    # However these are simple methods, and do not accurately convert when:
+    # 1) Exponent < 2 (without bias), impossible to decrement exponent without adjusting fraction/mantissa.
+    # 2) Exponent == 0, DEC numbers are then 0 or undefined while IEEE is not. NaN are produced when exponent == 255.
+    # Here method 1) is used, which mean that only small numbers will be represented incorrectly.
+
+    return np.frombuffer(reshuffled.tobytes(),
+                         dtype=np.float32,
+                         count=int(len(bytes) / 4))
      
+
      
 
 
      
 def UNPACK_FLOAT_IEEE(uint_32)
 
      
 
      
 
      Unpacks a single 32 bit unsigned int to a IEEE float representation
      
+
      
+
+Expand source code
+
+
      def UNPACK_FLOAT_IEEE(uint_32):
+    '''Unpacks a single 32 bit unsigned int to a IEEE float representation
+    '''
+    return struct.unpack('f', struct.pack("<I", uint_32))[0]
      
+
      
 
      
 
      
 def UNPACK_FLOAT_MIPS(uint_32)
 
      
 
      
 
      Unpacks a single 32 bit unsigned int to a IEEE float representation
      
+
      
+
+Expand source code
+
+
      def UNPACK_FLOAT_MIPS(uint_32):
+    '''Unpacks a single 32 bit unsigned int to a IEEE float representation
+    '''
+    return struct.unpack('f', struct.pack(">I", uint_32))[0]
      
+
      
 
      
 
      
 def is_integer(value)
 
      
 
      
 
      Check if value input is integer.
      
+
      
+
+Expand source code
+
+
      def is_integer(value):
+    '''Check if value input is integer.'''
+    return isinstance(value, (int, np.int32, np.int64))
      
+
      
 
      
 
      
 def is_iterable(value)
 
      
 
      
 
      Check if value is iterable.
      
+
      
+
+Expand source code
+
+
      def is_iterable(value):
+    '''Check if value is iterable.'''
+    return hasattr(value, '__iter__')
      
+
      
 
      
 
      
 def pack_labels(labels)
@@ -101,12 +371,59 @@ 
      Returns
      
 
      label_max_size : int
      
 
      Number of bytes associated with the longest label string, all strings are padded to this length.
      
 
+
      
+
+Expand source code
+
+
      def pack_labels(labels):
+    ''' Static method used to pack and pad the set of `labels` strings before
+        passing the output into a `c3d.group.Group.add_str`.
+
+    Parameters
+    ----------
+    labels : iterable
+        List of strings to pack and pad into a single string suitable for encoding in a Parameter entry.
+
+    Example
+    -------
+    >>> labels = ['RFT1', 'RFT2', 'RFT3', 'LFT1', 'LFT2', 'LFT3']
+    >>> param_str, label_max_size = Writer.pack_labels(labels)
+    >>> writer.point_group.add_str('LABELS',
+                                   'Point labels.',
+                                   label_str,
+                                   label_max_size,
+                                   len(labels))
+
+    Returns
+    -------
+    param_str : str
+        String containing `labels` packed into a single variable where
+        each string is padded to match the longest `labels` string.
+    label_max_size : int
+        Number of bytes associated with the longest `label` string, all strings are padded to this length.
+    '''
+    labels = np.ravel(labels)
+    # Get longest label name
+    label_max_size = 0
+    label_max_size = max(label_max_size, np.max([len(label) for label in labels]))
+    label_str = ''.join(label.ljust(label_max_size) for label in labels)
+    return label_str, label_max_size
      
+
      
 
 
      
 def type_npy2struct(dtype)
 
      
 
      
 
      Convert numpy dtype format to a struct package format string.
      
+
      
+
+Expand source code
+
+
      def type_npy2struct(dtype):
+    ''' Convert numpy dtype format to a struct package format string.
+    '''
+    return dtype.byteorder + dtype.char
      
+
      
 
      
 
 
@@ -119,6 +436,18 @@ 
      Classes
      
       
 
      
 
      Base class for extending (decorating) a python object.
      
+
      
+
+Expand source code
+
+
      class Decorator(object):
+    '''Base class for extending (decorating) a python object.
+    '''
+    def __init__(self, decoratee):
+        self._decoratee = decoratee
+    def __getattr__(self, name):
+        return getattr(self._decoratee, name)
      
+
      
 
      
 
 
diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html
index 2ba71a3..3ffe26f 100644
--- a/docs/c3d/writer.html
+++ b/docs/c3d/writer.html
@@ -5,7 +5,7 @@
 
 
 c3d.writer API documentation
-
+
 
 
 
@@ -22,7 +22,519 @@
 
      Module c3d.writer
      
 
 
      
-
      A Python module for reading and writing C3D files.
      
+
      Contains the Writer class for writing C3D files.
      
+
      
+
+Expand source code
+
+
      '''Contains the Writer class for writing C3D files.'''
+
+import copy
+import numpy as np
+import struct
+#import warnings
+from . import utils
+from .manager import Manager
+from .dtypes import DataTypes
+
+class Writer(Manager):
+    '''This class writes metadata and frames to a C3D file.
+
+    For example, to read an existing C3D file, apply some sort of data
+    processing to the frames, and write out another C3D file::
+
+    >>> r = c3d.Reader(open('data.c3d', 'rb'))
+    >>> w = c3d.Writer()
+    >>> w.add_frames(process_frames_somehow(r.read_frames()))
+    >>> with open('smoothed.c3d', 'wb') as handle:
+    >>>     w.write(handle)
+
+    Parameters
+    ----------
+    point_rate : float, optional
+        The frame rate of the data. Defaults to 480.
+    analog_rate : float, optional
+        The number of analog samples per frame. Defaults to 0.
+    point_scale : float, optional
+        The scale factor for point data. Defaults to -1 (i.e., "check the
+        POINT:SCALE parameter").
+    point_units : str, optional
+        The units that the point numbers represent. Defaults to ``'mm  '``.
+    gen_scale : float, optional
+        General scaling factor for analog data. Defaults to 1.
+    '''
+
+    def __init__(self,
+                 point_rate=480.,
+                 analog_rate=0.,
+                 point_scale=-1.):
+        '''Set minimal metadata for this writer.
+
+        '''
+        self._dtypes = DataTypes() # Only support INTEL format from writing
+        super(Writer, self).__init__()
+
+        # Header properties
+        self._header.frame_rate = np.float32(point_rate)
+        self._header.scale_factor = np.float32(point_scale)
+        self.analog_rate = analog_rate
+        self._frames = []
+
+    @staticmethod
+    def from_reader(reader, conversion=None):
+        '''
+
+        Parameters
+        ----------
+        source : `c3d.manager.Manager`
+            Source to copy.
+        conversion : str
+            Conversion mode, None is equivalent to the default mode. Supported modes are:
+
+                'consume'       - (Default) Reader object will be
+                                  consumed and explicitly deleted.
+
+                'copy'          - Reader objects will be deep copied.
+
+                'copy_metadata' - Similar to 'copy' but only copies metadata and
+                                  not point and analog frame data.
+
+                'copy_shallow'  - Similar to 'copy' but group parameters are
+                                  not copied.
+
+                'copy_header'   - Similar to 'copy_shallow' but only the
+                                  header is copied (frame data is not copied).
+
+        Returns
+        -------
+        param : :class:`Writer`
+            A writeable and persistent representation of the 'Reader' object.
+
+        Raises
+        ------
+        ValueError
+            If mode string is not equivalent to one of the supported modes.
+            If attempting to convert non-Intel files using mode other than 'shallow_copy'.
+        '''
+        writer = Writer()
+        # Modes
+        is_header_only = conversion == 'copy_header'
+        is_meta_copy = conversion == 'copy_metadata'
+        is_meta_only = is_header_only or is_meta_copy
+        is_consume = conversion == 'consume' or conversion is None
+        is_shallow_copy = conversion == 'shallow_copy' or is_header_only
+        is_deep_copy = conversion == 'copy' or is_meta_copy
+        # Verify mode
+        if not (is_consume or is_shallow_copy or is_deep_copy):
+            raise ValueError(
+                "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(
+                conversion))
+        if not reader._dtypes.is_ieee and not is_shallow_copy:
+            # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data.
+            raise ValueError(
+                "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format(
+                reader._dtypes.proc_type))
+
+        if is_consume:
+            writer._header = reader._header
+            writer._groups = reader._groups
+        elif is_deep_copy:
+            writer._header = copy.deepcopy(reader._header)
+            writer._groups = copy.deepcopy(reader._groups)
+        elif is_shallow_copy:
+            # Only copy header (no groups)
+            writer._header = copy.deepcopy(reader._header)
+            # Reformat header events
+            writer._header.encode_events(writer._header.events)
+
+            # Transfer a minimal set parameters
+            writer.set_start_frame(reader.first_frame)
+            writer.set_point_labels(reader.point_labels)
+            writer.set_analog_labels(reader.analog_labels)
+
+            gen_scale, analog_scales, analog_offsets = reader.get_analog_transform_parameters()
+            writer.set_analog_general_scale(gen_scale)
+            writer.set_analog_scales(analog_scales)
+            writer.set_analog_offsets(analog_offsets)
+
+        if not is_meta_only:
+            # Copy frames
+            for (i, point, analog) in reader.read_frames(copy=True, camera_sum=False):
+                writer.add_frames((point, analog))
+        if is_consume:
+            # Cleanup
+            reader._header = None
+            reader._groups = None
+            del reader
+        return writer
+
+    @property
+    def analog_rate(self):
+        return super(Writer, self).analog_rate
+
+    @analog_rate.setter
+    def analog_rate(self, value):
+        per_frame_rate = value / self.point_rate
+        assert float(per_frame_rate).is_integer(), "Analog rate must be a multiple of the point rate."
+        self._header.analog_per_frame = np.uint16(per_frame_rate)
+
+    @property
+    def numeric_key_max(self):
+        ''' Get the largest numeric key.
+        '''
+        num = 0
+        if len(self._groups) > 0:
+            for i in self._groups.keys():
+                if isinstance(i, int):
+                    num = max(i, num)
+        return num
+
+    @property
+    def numeric_key_next(self):
+        ''' Get a new unique numeric group key.
+        '''
+        return self.numeric_key_max + 1
+
+    def get_create(self, label):
+        ''' Get or create a parameter `c3d.group.Group`.'''
+        label = label.upper()
+        group = self.get(label)
+        if group is None:
+            group = self.add_group(self.numeric_key_next, label, label + ' group')
+        return group
+
+    @property
+    def point_group(self):
+        ''' Get or create the POINT parameter group.'''
+        return self.get_create('POINT')
+
+    @property
+    def analog_group(self):
+        ''' Get or create the ANALOG parameter group.'''
+        return self.get_create('ANALOG')
+
+    @property
+    def trial_group(self):
+        ''' Get or create the TRIAL parameter group.'''
+        return self.get_create('TRIAL')
+
+    def add_group(self, group_id, name, desc):
+        '''Add a new parameter group. See Manager.add_group() for more information.
+
+        Returns
+        -------
+        group : `c3d.group.Group`
+            An editable group instance.
+        '''
+        return super(Writer, self)._add_group(group_id, name, desc)
+
+    def rename_group(self, *args):
+        ''' Rename a specified parameter group (see Manager._rename_group for args). '''
+        super(Writer, self)._rename_group(*args)
+
+    def remove_group(self, *args):
+        '''Remove the parameter group. (see Manager._rename_group for args). '''
+        super(Writer, self)._remove_group(*args)
+
+    def add_frames(self, frames, index=None):
+        '''Add frames to this writer instance.
+
+        Parameters
+        ----------
+        frames : Single or sequence of (point, analog) pairs
+            A sequence or frame of frame data to add to the writer.
+        index : int or None
+            Insert the frame or sequence at the index (the first sequence frame will be inserted at the given `index`).
+            Note that the index should be relative to 0 rather then the frame number provided by read_frames()!
+        '''
+        sh = np.shape(frames)
+        # Single frame
+        if len(sh) < 2:
+            frames = [frames]
+            sh = np.shape(frames)
+
+        # Check data shapes match
+        if len(self._frames) > 0:
+            point0, analog0 = self._frames[0]
+            psh, ash = np.shape(point0), np.shape(analog0)
+            for f in frames:
+                if np.shape(f[0]) != psh:
+                    raise ValueError(
+                        'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                        str(psh), str(np.shape(f[0]))
+                        ))
+                if np.shape(f[1]) != ash:
+                    raise ValueError(
+                        'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                        str(ash), str(np.shape(f[1]))
+                        ))
+
+        # Sequence of invalid shape
+        if sh[1] != 2:
+            raise ValueError(
+                'Expected frame input to be sequence of point and analog pairs on form (None, 2). ' +
+                'Input was of shape {}.'.format(str(sh)))
+
+        if index is not None:
+            self._frames[index:index] = frames
+        else:
+            self._frames.extend(frames)
+
+    def set_point_labels(self, labels):
+        ''' Set point data labels.
+
+        Parameters
+        ----------
+        labels : iterable
+            Set POINT:LABELS parameter entry from a set of string labels.
+        '''
+        grp = self.point_group
+        if labels is None:
+            grp.add_empty_array('LABELS', 'Point labels.', -1)
+        else:
+            label_str, label_max_size = utils.pack_labels(labels)
+            grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels))
+
+    def set_analog_labels(self, labels):
+        ''' Set analog data labels.
+
+        Parameters
+        ----------
+        labels : iterable
+            Set ANALOG:LABELS parameter entry from a set of string labels.
+        '''
+        grp = self.analog_group
+        if labels is None:
+            grp.add_empty_array('LABELS', 'Analog labels.', -1)
+        else:
+            label_str, label_max_size = utils.pack_labels(labels)
+            grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels))
+
+    def set_analog_general_scale(self, value):
+        ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor).
+        '''
+        self.analog_group.set('GEN_SCALE', 'Analog general scale factor', 4, '<f', value)
+
+    def set_analog_scales(self, values):
+        ''' Set ANALOG:SCALE factors (per channel scale factor).
+
+        Parameters
+        ----------
+        values : iterable or None
+            Iterable containing individual scale factors (float32) for scaling analog channel data.
+        '''
+        if utils.is_iterable(values):
+            data = np.array([v for v in values], dtype=np.float32)
+            self.analog_group.set_array('SCALE', 'Analog channel scale factors', data)
+        elif values is None:
+            self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4)
+        else:
+            raise ValueError('Expected iterable containing analog scale factors.')
+
+    def set_analog_offsets(self, values):
+        ''' Set ANALOG:OFFSET offsets (per channel offset).
+
+        Parameters
+        ----------
+        values : iterable or None
+            Iterable containing individual offsets (int16) for encoding analog channel data.
+        '''
+        if utils.is_iterable(values):
+            data = np.array([v for v in values], dtype=np.int16)
+            self.analog_group.set_array('OFFSET', 'Analog channel offsets', data)
+        elif values is None:
+            self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2)
+        else:
+            raise ValueError('Expected iterable containing analog data offsets.')
+
+    def set_start_frame(self, frame=1):
+        ''' Set the 'TRIAL:ACTUAL_START_FIELD' parameter and header.first_frame entry.
+
+        Parameters
+        ----------
+        frame : int
+            Number for the first frame recorded in the file.
+            Frame counter for a trial recording always start at 1 for the first frame.
+        '''
+        self.trial_group.set('ACTUAL_START_FIELD', 'Actual start frame', 2, '<I', frame, 2)
+        if frame < 65535:
+            self._header.first_frame = np.uint16(frame)
+        else:
+            self._header.first_frame = np.uint16(65535)
+
+    def _set_last_frame(self, frame):
+        ''' Sets the 'TRIAL:ACTUAL_END_FIELD' parameter and header.last_frame entry.
+        '''
+        self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, '<I', frame, 2)
+        self._header.last_frame = np.uint16(min(frame, 65535))
+
+
+    def set_screen_axis(self, X='+X', Y='+Y'):
+        ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+        Parameters
+        ----------
+        X : str
+            Two byte string with first character indicating positive or negative axis (+/-),
+            and the second axis (X/Y/Z). Example strings '+X' or '-Y'
+        Y : str
+            Second axis string with same format as Y. Determines the second Y screen axis.
+        '''
+        if len(X) != 2:
+            raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter.')
+        if len(Y) != 2:
+            raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter.')
+        group = self.point_group
+        group.set_str('X_SCREEN', 'X_SCREEN parameter', X)
+        group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y)
+
+    def write(self, handle):
+        '''Write metadata, point and analog frames to a file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        if not self._frames:
+            raise RuntimeError('Attempted to write empty file.')
+
+        points, analog = self._frames[0]
+        ppf = len(points)
+        apf = len(analog)
+
+
+        first_frame = self.first_frame
+        if first_frame <= 0: # Bad value
+            first_frame = 1
+        nframes = len(self._frames)
+        last_frame = first_frame + nframes - 1
+
+        UINT16_MAX = 65535
+
+        # POINT group
+        group = self.point_group
+        group.set('USED', 'Number of point samples', 2, '<H', ppf)
+        group.set('FRAMES', 'Total frame count', 2, '<H', min(UINT16_MAX, nframes))
+        if nframes >= UINT16_MAX:
+            # Should be floating point
+            group.set('LONG_FRAMES', 'Total frame count', 4, '<f', nframes)
+        elif 'LONG_FRAMES' in group:
+            # Docs states it should not exist if frame_count < 65535
+            group.remove_param('LONG_FRAMES')
+        group.set('DATA_START', 'First data block containing frame samples.', 2, '<H', 0)
+        group.set('SCALE', 'Point data scaling factor', 4, '<f', self.point_scale)
+        group.set('RATE', 'Point data sample rate', 4, '<f', self.point_rate)
+        # Optional
+        if 'UNITS' not in group:
+            group.add_str('UNITS', 'Units used for point data measurements.', 'mm')
+        if 'DESCRIPTIONS' not in group:
+            group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * ppf, 2, ppf)
+
+        # ANALOG group
+        group = self.analog_group
+        group.set('USED', 'Analog channel count', 2, '<H', apf)
+        group.set('RATE', 'Analog samples per second', 4, '<f', self.analog_rate)
+        if 'GEN_SCALE' not in group:
+            self.set_analog_general_scale(1.0)
+        # Optional
+        if 'SCALE' not in group:
+            self.set_analog_scales(None)
+        if 'OFFSET' not in group:
+            self.set_analog_offsets(None)
+        if 'DESCRIPTIONS' not in group:
+            group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * apf, 2, apf)
+
+        # TRIAL group
+        self.set_start_frame(first_frame)
+        self._set_last_frame(last_frame)
+
+        # sync parameter information to header.
+        start_block = self.parameter_blocks() + 2
+        self.get('POINT:DATA_START').bytes = struct.pack('<H', start_block)
+        self._header.data_block = np.uint16(start_block)
+        self._header.point_count = np.uint16(ppf)
+        self._header.analog_count = np.uint16(np.prod(np.shape(analog)))
+
+        self._write_metadata(handle)
+        self._write_frames(handle)
+
+    def _pad_block(self, handle):
+        '''Pad the file with 0s to the end of the next block boundary.'''
+        extra = handle.tell() % 512
+        if extra:
+            handle.write(b'\x00' * (512 - extra))
+
+    def _write_metadata(self, handle):
+        '''Write metadata to a file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        self._check_metadata()
+
+        # Header
+        self._header.write(handle)
+        self._pad_block(handle)
+        assert handle.tell() == 512
+
+        # Groups
+        handle.write(struct.pack(
+            'BBBB', 0, 0, self.parameter_blocks(), self._dtypes.processor))
+        for group_id, group in self.listed():
+            group._data.write(group_id, handle)
+
+        # Padding
+        self._pad_block(handle)
+        while handle.tell() != 512 * (self.header.data_block - 1):
+            handle.write(b'\x00' * 512)
+
+    def _write_frames(self, handle):
+        '''Write our frame data to the given file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        assert handle.tell() == 512 * (self._header.data_block - 1)
+        scale_mag = abs(self.point_scale)
+        is_float = self.point_scale < 0
+        if is_float:
+            point_dtype = self._dtypes.float32
+            point_scale = 1.0
+        else:
+            point_dtype = self._dtypes.int16
+            point_scale = scale_mag
+        raw = np.zeros((self.point_used, 4), point_dtype)
+
+        analog_scales, analog_offsets = self.get_analog_transform()
+        analog_scales_inv = 1.0 / analog_scales
+
+        for points, analog in self._frames:
+            # Transform point data
+            valid = points[:, 3] >= 0.0
+            raw[~valid, 3] = -1
+            raw[valid, :3] = points[valid, :3] / point_scale
+            raw[valid, 3] = np.bitwise_or(np.rint(points[valid, 3] / scale_mag).astype(np.uint8),
+                                          (points[valid, 4].astype(np.uint16) << 8),
+                                          dtype=np.uint16)
+
+            # Transform analog data
+            analog = analog * analog_scales_inv + analog_offsets
+            analog = analog.T
+
+            # Write
+            analog = analog.astype(point_dtype)
+            handle.write(raw.tobytes())
+            handle.write(analog.tobytes())
+        self._pad_block(handle)
      
+
      
 
      
 
      
 
      
@@ -63,6 +575,508 @@ 
      Parameters
      
 
      General scaling factor for analog data. Defaults to 1.
      
 
 
      Set minimal metadata for this writer.
      
+
      
+
+Expand source code
+
+
      class Writer(Manager):
+    '''This class writes metadata and frames to a C3D file.
+
+    For example, to read an existing C3D file, apply some sort of data
+    processing to the frames, and write out another C3D file::
+
+    >>> r = c3d.Reader(open('data.c3d', 'rb'))
+    >>> w = c3d.Writer()
+    >>> w.add_frames(process_frames_somehow(r.read_frames()))
+    >>> with open('smoothed.c3d', 'wb') as handle:
+    >>>     w.write(handle)
+
+    Parameters
+    ----------
+    point_rate : float, optional
+        The frame rate of the data. Defaults to 480.
+    analog_rate : float, optional
+        The number of analog samples per frame. Defaults to 0.
+    point_scale : float, optional
+        The scale factor for point data. Defaults to -1 (i.e., "check the
+        POINT:SCALE parameter").
+    point_units : str, optional
+        The units that the point numbers represent. Defaults to ``'mm  '``.
+    gen_scale : float, optional
+        General scaling factor for analog data. Defaults to 1.
+    '''
+
+    def __init__(self,
+                 point_rate=480.,
+                 analog_rate=0.,
+                 point_scale=-1.):
+        '''Set minimal metadata for this writer.
+
+        '''
+        self._dtypes = DataTypes() # Only support INTEL format from writing
+        super(Writer, self).__init__()
+
+        # Header properties
+        self._header.frame_rate = np.float32(point_rate)
+        self._header.scale_factor = np.float32(point_scale)
+        self.analog_rate = analog_rate
+        self._frames = []
+
+    @staticmethod
+    def from_reader(reader, conversion=None):
+        '''
+
+        Parameters
+        ----------
+        source : `c3d.manager.Manager`
+            Source to copy.
+        conversion : str
+            Conversion mode, None is equivalent to the default mode. Supported modes are:
+
+                'consume'       - (Default) Reader object will be
+                                  consumed and explicitly deleted.
+
+                'copy'          - Reader objects will be deep copied.
+
+                'copy_metadata' - Similar to 'copy' but only copies metadata and
+                                  not point and analog frame data.
+
+                'copy_shallow'  - Similar to 'copy' but group parameters are
+                                  not copied.
+
+                'copy_header'   - Similar to 'copy_shallow' but only the
+                                  header is copied (frame data is not copied).
+
+        Returns
+        -------
+        param : :class:`Writer`
+            A writeable and persistent representation of the 'Reader' object.
+
+        Raises
+        ------
+        ValueError
+            If mode string is not equivalent to one of the supported modes.
+            If attempting to convert non-Intel files using mode other than 'shallow_copy'.
+        '''
+        writer = Writer()
+        # Modes
+        is_header_only = conversion == 'copy_header'
+        is_meta_copy = conversion == 'copy_metadata'
+        is_meta_only = is_header_only or is_meta_copy
+        is_consume = conversion == 'consume' or conversion is None
+        is_shallow_copy = conversion == 'shallow_copy' or is_header_only
+        is_deep_copy = conversion == 'copy' or is_meta_copy
+        # Verify mode
+        if not (is_consume or is_shallow_copy or is_deep_copy):
+            raise ValueError(
+                "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(
+                conversion))
+        if not reader._dtypes.is_ieee and not is_shallow_copy:
+            # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data.
+            raise ValueError(
+                "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format(
+                reader._dtypes.proc_type))
+
+        if is_consume:
+            writer._header = reader._header
+            writer._groups = reader._groups
+        elif is_deep_copy:
+            writer._header = copy.deepcopy(reader._header)
+            writer._groups = copy.deepcopy(reader._groups)
+        elif is_shallow_copy:
+            # Only copy header (no groups)
+            writer._header = copy.deepcopy(reader._header)
+            # Reformat header events
+            writer._header.encode_events(writer._header.events)
+
+            # Transfer a minimal set parameters
+            writer.set_start_frame(reader.first_frame)
+            writer.set_point_labels(reader.point_labels)
+            writer.set_analog_labels(reader.analog_labels)
+
+            gen_scale, analog_scales, analog_offsets = reader.get_analog_transform_parameters()
+            writer.set_analog_general_scale(gen_scale)
+            writer.set_analog_scales(analog_scales)
+            writer.set_analog_offsets(analog_offsets)
+
+        if not is_meta_only:
+            # Copy frames
+            for (i, point, analog) in reader.read_frames(copy=True, camera_sum=False):
+                writer.add_frames((point, analog))
+        if is_consume:
+            # Cleanup
+            reader._header = None
+            reader._groups = None
+            del reader
+        return writer
+
+    @property
+    def analog_rate(self):
+        return super(Writer, self).analog_rate
+
+    @analog_rate.setter
+    def analog_rate(self, value):
+        per_frame_rate = value / self.point_rate
+        assert float(per_frame_rate).is_integer(), "Analog rate must be a multiple of the point rate."
+        self._header.analog_per_frame = np.uint16(per_frame_rate)
+
+    @property
+    def numeric_key_max(self):
+        ''' Get the largest numeric key.
+        '''
+        num = 0
+        if len(self._groups) > 0:
+            for i in self._groups.keys():
+                if isinstance(i, int):
+                    num = max(i, num)
+        return num
+
+    @property
+    def numeric_key_next(self):
+        ''' Get a new unique numeric group key.
+        '''
+        return self.numeric_key_max + 1
+
+    def get_create(self, label):
+        ''' Get or create a parameter `c3d.group.Group`.'''
+        label = label.upper()
+        group = self.get(label)
+        if group is None:
+            group = self.add_group(self.numeric_key_next, label, label + ' group')
+        return group
+
+    @property
+    def point_group(self):
+        ''' Get or create the POINT parameter group.'''
+        return self.get_create('POINT')
+
+    @property
+    def analog_group(self):
+        ''' Get or create the ANALOG parameter group.'''
+        return self.get_create('ANALOG')
+
+    @property
+    def trial_group(self):
+        ''' Get or create the TRIAL parameter group.'''
+        return self.get_create('TRIAL')
+
+    def add_group(self, group_id, name, desc):
+        '''Add a new parameter group. See Manager.add_group() for more information.
+
+        Returns
+        -------
+        group : `c3d.group.Group`
+            An editable group instance.
+        '''
+        return super(Writer, self)._add_group(group_id, name, desc)
+
+    def rename_group(self, *args):
+        ''' Rename a specified parameter group (see Manager._rename_group for args). '''
+        super(Writer, self)._rename_group(*args)
+
+    def remove_group(self, *args):
+        '''Remove the parameter group. (see Manager._rename_group for args). '''
+        super(Writer, self)._remove_group(*args)
+
+    def add_frames(self, frames, index=None):
+        '''Add frames to this writer instance.
+
+        Parameters
+        ----------
+        frames : Single or sequence of (point, analog) pairs
+            A sequence or frame of frame data to add to the writer.
+        index : int or None
+            Insert the frame or sequence at the index (the first sequence frame will be inserted at the given `index`).
+            Note that the index should be relative to 0 rather then the frame number provided by read_frames()!
+        '''
+        sh = np.shape(frames)
+        # Single frame
+        if len(sh) < 2:
+            frames = [frames]
+            sh = np.shape(frames)
+
+        # Check data shapes match
+        if len(self._frames) > 0:
+            point0, analog0 = self._frames[0]
+            psh, ash = np.shape(point0), np.shape(analog0)
+            for f in frames:
+                if np.shape(f[0]) != psh:
+                    raise ValueError(
+                        'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                        str(psh), str(np.shape(f[0]))
+                        ))
+                if np.shape(f[1]) != ash:
+                    raise ValueError(
+                        'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                        str(ash), str(np.shape(f[1]))
+                        ))
+
+        # Sequence of invalid shape
+        if sh[1] != 2:
+            raise ValueError(
+                'Expected frame input to be sequence of point and analog pairs on form (None, 2). ' +
+                'Input was of shape {}.'.format(str(sh)))
+
+        if index is not None:
+            self._frames[index:index] = frames
+        else:
+            self._frames.extend(frames)
+
+    def set_point_labels(self, labels):
+        ''' Set point data labels.
+
+        Parameters
+        ----------
+        labels : iterable
+            Set POINT:LABELS parameter entry from a set of string labels.
+        '''
+        grp = self.point_group
+        if labels is None:
+            grp.add_empty_array('LABELS', 'Point labels.', -1)
+        else:
+            label_str, label_max_size = utils.pack_labels(labels)
+            grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels))
+
+    def set_analog_labels(self, labels):
+        ''' Set analog data labels.
+
+        Parameters
+        ----------
+        labels : iterable
+            Set ANALOG:LABELS parameter entry from a set of string labels.
+        '''
+        grp = self.analog_group
+        if labels is None:
+            grp.add_empty_array('LABELS', 'Analog labels.', -1)
+        else:
+            label_str, label_max_size = utils.pack_labels(labels)
+            grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels))
+
+    def set_analog_general_scale(self, value):
+        ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor).
+        '''
+        self.analog_group.set('GEN_SCALE', 'Analog general scale factor', 4, '<f', value)
+
+    def set_analog_scales(self, values):
+        ''' Set ANALOG:SCALE factors (per channel scale factor).
+
+        Parameters
+        ----------
+        values : iterable or None
+            Iterable containing individual scale factors (float32) for scaling analog channel data.
+        '''
+        if utils.is_iterable(values):
+            data = np.array([v for v in values], dtype=np.float32)
+            self.analog_group.set_array('SCALE', 'Analog channel scale factors', data)
+        elif values is None:
+            self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4)
+        else:
+            raise ValueError('Expected iterable containing analog scale factors.')
+
+    def set_analog_offsets(self, values):
+        ''' Set ANALOG:OFFSET offsets (per channel offset).
+
+        Parameters
+        ----------
+        values : iterable or None
+            Iterable containing individual offsets (int16) for encoding analog channel data.
+        '''
+        if utils.is_iterable(values):
+            data = np.array([v for v in values], dtype=np.int16)
+            self.analog_group.set_array('OFFSET', 'Analog channel offsets', data)
+        elif values is None:
+            self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2)
+        else:
+            raise ValueError('Expected iterable containing analog data offsets.')
+
+    def set_start_frame(self, frame=1):
+        ''' Set the 'TRIAL:ACTUAL_START_FIELD' parameter and header.first_frame entry.
+
+        Parameters
+        ----------
+        frame : int
+            Number for the first frame recorded in the file.
+            Frame counter for a trial recording always start at 1 for the first frame.
+        '''
+        self.trial_group.set('ACTUAL_START_FIELD', 'Actual start frame', 2, '<I', frame, 2)
+        if frame < 65535:
+            self._header.first_frame = np.uint16(frame)
+        else:
+            self._header.first_frame = np.uint16(65535)
+
+    def _set_last_frame(self, frame):
+        ''' Sets the 'TRIAL:ACTUAL_END_FIELD' parameter and header.last_frame entry.
+        '''
+        self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, '<I', frame, 2)
+        self._header.last_frame = np.uint16(min(frame, 65535))
+
+
+    def set_screen_axis(self, X='+X', Y='+Y'):
+        ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+        Parameters
+        ----------
+        X : str
+            Two byte string with first character indicating positive or negative axis (+/-),
+            and the second axis (X/Y/Z). Example strings '+X' or '-Y'
+        Y : str
+            Second axis string with same format as Y. Determines the second Y screen axis.
+        '''
+        if len(X) != 2:
+            raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter.')
+        if len(Y) != 2:
+            raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter.')
+        group = self.point_group
+        group.set_str('X_SCREEN', 'X_SCREEN parameter', X)
+        group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y)
+
+    def write(self, handle):
+        '''Write metadata, point and analog frames to a file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        if not self._frames:
+            raise RuntimeError('Attempted to write empty file.')
+
+        points, analog = self._frames[0]
+        ppf = len(points)
+        apf = len(analog)
+
+
+        first_frame = self.first_frame
+        if first_frame <= 0: # Bad value
+            first_frame = 1
+        nframes = len(self._frames)
+        last_frame = first_frame + nframes - 1
+
+        UINT16_MAX = 65535
+
+        # POINT group
+        group = self.point_group
+        group.set('USED', 'Number of point samples', 2, '<H', ppf)
+        group.set('FRAMES', 'Total frame count', 2, '<H', min(UINT16_MAX, nframes))
+        if nframes >= UINT16_MAX:
+            # Should be floating point
+            group.set('LONG_FRAMES', 'Total frame count', 4, '<f', nframes)
+        elif 'LONG_FRAMES' in group:
+            # Docs states it should not exist if frame_count < 65535
+            group.remove_param('LONG_FRAMES')
+        group.set('DATA_START', 'First data block containing frame samples.', 2, '<H', 0)
+        group.set('SCALE', 'Point data scaling factor', 4, '<f', self.point_scale)
+        group.set('RATE', 'Point data sample rate', 4, '<f', self.point_rate)
+        # Optional
+        if 'UNITS' not in group:
+            group.add_str('UNITS', 'Units used for point data measurements.', 'mm')
+        if 'DESCRIPTIONS' not in group:
+            group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * ppf, 2, ppf)
+
+        # ANALOG group
+        group = self.analog_group
+        group.set('USED', 'Analog channel count', 2, '<H', apf)
+        group.set('RATE', 'Analog samples per second', 4, '<f', self.analog_rate)
+        if 'GEN_SCALE' not in group:
+            self.set_analog_general_scale(1.0)
+        # Optional
+        if 'SCALE' not in group:
+            self.set_analog_scales(None)
+        if 'OFFSET' not in group:
+            self.set_analog_offsets(None)
+        if 'DESCRIPTIONS' not in group:
+            group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * apf, 2, apf)
+
+        # TRIAL group
+        self.set_start_frame(first_frame)
+        self._set_last_frame(last_frame)
+
+        # sync parameter information to header.
+        start_block = self.parameter_blocks() + 2
+        self.get('POINT:DATA_START').bytes = struct.pack('<H', start_block)
+        self._header.data_block = np.uint16(start_block)
+        self._header.point_count = np.uint16(ppf)
+        self._header.analog_count = np.uint16(np.prod(np.shape(analog)))
+
+        self._write_metadata(handle)
+        self._write_frames(handle)
+
+    def _pad_block(self, handle):
+        '''Pad the file with 0s to the end of the next block boundary.'''
+        extra = handle.tell() % 512
+        if extra:
+            handle.write(b'\x00' * (512 - extra))
+
+    def _write_metadata(self, handle):
+        '''Write metadata to a file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        self._check_metadata()
+
+        # Header
+        self._header.write(handle)
+        self._pad_block(handle)
+        assert handle.tell() == 512
+
+        # Groups
+        handle.write(struct.pack(
+            'BBBB', 0, 0, self.parameter_blocks(), self._dtypes.processor))
+        for group_id, group in self.listed():
+            group._data.write(group_id, handle)
+
+        # Padding
+        self._pad_block(handle)
+        while handle.tell() != 512 * (self.header.data_block - 1):
+            handle.write(b'\x00' * 512)
+
+    def _write_frames(self, handle):
+        '''Write our frame data to the given file handle.
+
+        Parameters
+        ----------
+        handle : file
+            Write metadata and C3D motion frames to the given file handle. The
+            writer does not close the handle.
+        '''
+        assert handle.tell() == 512 * (self._header.data_block - 1)
+        scale_mag = abs(self.point_scale)
+        is_float = self.point_scale < 0
+        if is_float:
+            point_dtype = self._dtypes.float32
+            point_scale = 1.0
+        else:
+            point_dtype = self._dtypes.int16
+            point_scale = scale_mag
+        raw = np.zeros((self.point_used, 4), point_dtype)
+
+        analog_scales, analog_offsets = self.get_analog_transform()
+        analog_scales_inv = 1.0 / analog_scales
+
+        for points, analog in self._frames:
+            # Transform point data
+            valid = points[:, 3] >= 0.0
+            raw[~valid, 3] = -1
+            raw[valid, :3] = points[valid, :3] / point_scale
+            raw[valid, 3] = np.bitwise_or(np.rint(points[valid, 3] / scale_mag).astype(np.uint8),
+                                          (points[valid, 4].astype(np.uint16) << 8),
+                                          dtype=np.uint16)
+
+            # Transform analog data
+            analog = analog * analog_scales_inv + analog_offsets
+            analog = analog.T
+
+            # Write
+            analog = analog.astype(point_dtype)
+            handle.write(raw.tobytes())
+            handle.write(analog.tobytes())
+        self._pad_block(handle)
      
+
      
 
      Ancestors
      
 
        
 
      • Manager
        • 
@@ -105,6 +1119,98 @@ 
        Raises
        
 
        If mode string is not equivalent to one of the supported modes.
 If attempting to convert non-Intel files using mode other than 'shallow_copy'.
        
 
+
        
+
+Expand source code
+
+
        @staticmethod
+def from_reader(reader, conversion=None):
+    '''
+
+    Parameters
+    ----------
+    source : `c3d.manager.Manager`
+        Source to copy.
+    conversion : str
+        Conversion mode, None is equivalent to the default mode. Supported modes are:
+
+            'consume'       - (Default) Reader object will be
+                              consumed and explicitly deleted.
+
+            'copy'          - Reader objects will be deep copied.
+
+            'copy_metadata' - Similar to 'copy' but only copies metadata and
+                              not point and analog frame data.
+
+            'copy_shallow'  - Similar to 'copy' but group parameters are
+                              not copied.
+
+            'copy_header'   - Similar to 'copy_shallow' but only the
+                              header is copied (frame data is not copied).
+
+    Returns
+    -------
+    param : :class:`Writer`
+        A writeable and persistent representation of the 'Reader' object.
+
+    Raises
+    ------
+    ValueError
+        If mode string is not equivalent to one of the supported modes.
+        If attempting to convert non-Intel files using mode other than 'shallow_copy'.
+    '''
+    writer = Writer()
+    # Modes
+    is_header_only = conversion == 'copy_header'
+    is_meta_copy = conversion == 'copy_metadata'
+    is_meta_only = is_header_only or is_meta_copy
+    is_consume = conversion == 'consume' or conversion is None
+    is_shallow_copy = conversion == 'shallow_copy' or is_header_only
+    is_deep_copy = conversion == 'copy' or is_meta_copy
+    # Verify mode
+    if not (is_consume or is_shallow_copy or is_deep_copy):
+        raise ValueError(
+            "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(
+            conversion))
+    if not reader._dtypes.is_ieee and not is_shallow_copy:
+        # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data.
+        raise ValueError(
+            "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format(
+            reader._dtypes.proc_type))
+
+    if is_consume:
+        writer._header = reader._header
+        writer._groups = reader._groups
+    elif is_deep_copy:
+        writer._header = copy.deepcopy(reader._header)
+        writer._groups = copy.deepcopy(reader._groups)
+    elif is_shallow_copy:
+        # Only copy header (no groups)
+        writer._header = copy.deepcopy(reader._header)
+        # Reformat header events
+        writer._header.encode_events(writer._header.events)
+
+        # Transfer a minimal set parameters
+        writer.set_start_frame(reader.first_frame)
+        writer.set_point_labels(reader.point_labels)
+        writer.set_analog_labels(reader.analog_labels)
+
+        gen_scale, analog_scales, analog_offsets = reader.get_analog_transform_parameters()
+        writer.set_analog_general_scale(gen_scale)
+        writer.set_analog_scales(analog_scales)
+        writer.set_analog_offsets(analog_offsets)
+
+    if not is_meta_only:
+        # Copy frames
+        for (i, point, analog) in reader.read_frames(copy=True, camera_sum=False):
+            writer.add_frames((point, analog))
+    if is_consume:
+        # Cleanup
+        reader._header = None
+        reader._groups = None
+        del reader
+    return writer
        
+
        
 
 
 
        Instance variables
        
@@ -112,22 +1218,74 @@ 
        Instance variables
        
 
        var analog_group
        
 
        
 
        Get or create the ANALOG parameter group.
        
+
        
+
+Expand source code
+
+
        @property
+def analog_group(self):
+    ''' Get or create the ANALOG parameter group.'''
+    return self.get_create('ANALOG')
        
+
        
 
        
 
        var numeric_key_max
        
 
        
 
        Get the largest numeric key.
        
+
        
+
+Expand source code
+
+
        @property
+def numeric_key_max(self):
+    ''' Get the largest numeric key.
+    '''
+    num = 0
+    if len(self._groups) > 0:
+        for i in self._groups.keys():
+            if isinstance(i, int):
+                num = max(i, num)
+    return num
        
+
        
 
        
 
        var numeric_key_next
        
 
        
 
        Get a new unique numeric group key.
        
+
        
+
+Expand source code
+
+
        @property
+def numeric_key_next(self):
+    ''' Get a new unique numeric group key.
+    '''
+    return self.numeric_key_max + 1
        
+
        
 
        
 
        var point_group
        
 
        
 
        Get or create the POINT parameter group.
        
+
        
+
+Expand source code
+
+
        @property
+def point_group(self):
+    ''' Get or create the POINT parameter group.'''
+    return self.get_create('POINT')
        
+
        
 
        
 
        var trial_group
        
 
        
 
        Get or create the TRIAL parameter group.
        
+
        
+
+Expand source code
+
+
        @property
+def trial_group(self):
+    ''' Get or create the TRIAL parameter group.'''
+    return self.get_create('TRIAL')
        
+
        
 
        
 
 
        Methods
        
@@ -145,6 +1303,54 @@ 
        Parameters
        
 
        Insert the frame or sequence at the index (the first sequence frame will be inserted at the given index).
 Note that the index should be relative to 0 rather then the frame number provided by read_frames()!
        
 
+
        
+
+Expand source code
+
+
        def add_frames(self, frames, index=None):
+    '''Add frames to this writer instance.
+
+    Parameters
+    ----------
+    frames : Single or sequence of (point, analog) pairs
+        A sequence or frame of frame data to add to the writer.
+    index : int or None
+        Insert the frame or sequence at the index (the first sequence frame will be inserted at the given `index`).
+        Note that the index should be relative to 0 rather then the frame number provided by read_frames()!
+    '''
+    sh = np.shape(frames)
+    # Single frame
+    if len(sh) < 2:
+        frames = [frames]
+        sh = np.shape(frames)
+
+    # Check data shapes match
+    if len(self._frames) > 0:
+        point0, analog0 = self._frames[0]
+        psh, ash = np.shape(point0), np.shape(analog0)
+        for f in frames:
+            if np.shape(f[0]) != psh:
+                raise ValueError(
+                    'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                    str(psh), str(np.shape(f[0]))
+                    ))
+            if np.shape(f[1]) != ash:
+                raise ValueError(
+                    'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
+                    str(ash), str(np.shape(f[1]))
+                    ))
+
+    # Sequence of invalid shape
+    if sh[1] != 2:
+        raise ValueError(
+            'Expected frame input to be sequence of point and analog pairs on form (None, 2). ' +
+            'Input was of shape {}.'.format(str(sh)))
+
+    if index is not None:
+        self._frames[index:index] = frames
+    else:
+        self._frames.extend(frames)
        
+
        
 
 
        
 def add_group(self, group_id, name, desc)
@@ -153,33 +1359,84 @@ 
        Parameters
        
 
        Add a new parameter group. See Manager.add_group() for more information.
        
 
        Returns
        
 
        
-
        group : :class:Group``
        
+
        group : Group
        
 
        An editable group instance.
        
 
        
+
        
+
+Expand source code
+
+
        def add_group(self, group_id, name, desc):
+    '''Add a new parameter group. See Manager.add_group() for more information.
+
+    Returns
+    -------
+    group : `c3d.group.Group`
+        An editable group instance.
+    '''
+    return super(Writer, self)._add_group(group_id, name, desc)
        
+
        
 
 
        
 def get_create(self, label)
 
        
 
        
-
        Get or create the specified parameter group.
        
+
        Get or create a parameter Group.
        
+
        
+
+Expand source code
+
+
        def get_create(self, label):
+    ''' Get or create a parameter `c3d.group.Group`.'''
+    label = label.upper()
+    group = self.get(label)
+    if group is None:
+        group = self.add_group(self.numeric_key_next, label, label + ' group')
+    return group
        
+
        
 
        
 
        
 def remove_group(self, *args)
 
        
 
        
 
        Remove the parameter group. (see Manager._rename_group for args).
        
+
        
+
+Expand source code
+
+
        def remove_group(self, *args):
+    '''Remove the parameter group. (see Manager._rename_group for args). '''
+    super(Writer, self)._remove_group(*args)
        
+
        
 
        
 
        
 def rename_group(self, *args)
 
        
 
        
 
        Rename a specified parameter group (see Manager._rename_group for args).
        
+
        
+
+Expand source code
+
+
        def rename_group(self, *args):
+    ''' Rename a specified parameter group (see Manager._rename_group for args). '''
+    super(Writer, self)._rename_group(*args)
        
+
        
 
        
 
        
 def set_analog_general_scale(self, value)
 
        
 
        
 
        Set ANALOG:GEN_SCALE factor (uniform analog scale factor).
        
+
        
+
+Expand source code
+
+
        def set_analog_general_scale(self, value):
+    ''' Set ANALOG:GEN_SCALE factor (uniform analog scale factor).
+    '''
+    self.analog_group.set('GEN_SCALE', 'Analog general scale factor', 4, '<f', value)
        
+
        
 
        
 
        
 def set_analog_labels(self, labels)
@@ -191,6 +1448,25 @@ 
        Parameters
        
 
        labels : iterable
        
 
        Set ANALOG:LABELS parameter entry from a set of string labels.
        
 
+
        
+
+Expand source code
+
+
        def set_analog_labels(self, labels):
+    ''' Set analog data labels.
+
+    Parameters
+    ----------
+    labels : iterable
+        Set ANALOG:LABELS parameter entry from a set of string labels.
+    '''
+    grp = self.analog_group
+    if labels is None:
+        grp.add_empty_array('LABELS', 'Analog labels.', -1)
+    else:
+        label_str, label_max_size = utils.pack_labels(labels)
+        grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels))
        
+
        
 
 
        
 def set_analog_offsets(self, values)
@@ -200,8 +1476,28 @@ 
        Parameters
        
 
        Parameters
        
 
        
 
        values : iterable or None
        
-
        Iterable containing individual offsets for encoding analog channel data.
        
+
        Iterable containing individual offsets (int16) for encoding analog channel data.
        
 
        
+
        
+
+Expand source code
+
+
        def set_analog_offsets(self, values):
+    ''' Set ANALOG:OFFSET offsets (per channel offset).
+
+    Parameters
+    ----------
+    values : iterable or None
+        Iterable containing individual offsets (int16) for encoding analog channel data.
+    '''
+    if utils.is_iterable(values):
+        data = np.array([v for v in values], dtype=np.int16)
+        self.analog_group.set_array('OFFSET', 'Analog channel offsets', data)
+    elif values is None:
+        self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2)
+    else:
+        raise ValueError('Expected iterable containing analog data offsets.')
        
+
        
 
 
        
 def set_analog_scales(self, values)
@@ -211,8 +1507,28 @@ 
        Parameters
        
 
        Parameters
        
 
        
 
        values : iterable or None
        
-
        Iterable containing individual scale factors for encoding analog channel data.
        
+
        Iterable containing individual scale factors (float32) for scaling analog channel data.
        
 
        
+
        
+
+Expand source code
+
+
        def set_analog_scales(self, values):
+    ''' Set ANALOG:SCALE factors (per channel scale factor).
+
+    Parameters
+    ----------
+    values : iterable or None
+        Iterable containing individual scale factors (float32) for scaling analog channel data.
+    '''
+    if utils.is_iterable(values):
+        data = np.array([v for v in values], dtype=np.float32)
+        self.analog_group.set_array('SCALE', 'Analog channel scale factors', data)
+    elif values is None:
+        self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4)
+    else:
+        raise ValueError('Expected iterable containing analog scale factors.')
        
+
        
 
 
        
 def set_point_labels(self, labels)
@@ -224,6 +1540,25 @@ 
        Parameters
        
 
        labels : iterable
        
 
        Set POINT:LABELS parameter entry from a set of string labels.
        
 
+
        
+
+Expand source code
+
+
        def set_point_labels(self, labels):
+    ''' Set point data labels.
+
+    Parameters
+    ----------
+    labels : iterable
+        Set POINT:LABELS parameter entry from a set of string labels.
+    '''
+    grp = self.point_group
+    if labels is None:
+        grp.add_empty_array('LABELS', 'Point labels.', -1)
+    else:
+        label_str, label_max_size = utils.pack_labels(labels)
+        grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels))
        
+
        
 
 
        
 def set_screen_axis(self, X='+X', Y='+Y')
@@ -238,6 +1573,29 @@ 
        Parameters
        
 
        Y : str
        
 
        Second axis string with same format as Y. Determines the second Y screen axis.
        
 
+
        
+
+Expand source code
+
+
        def set_screen_axis(self, X='+X', Y='+Y'):
+    ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group.
+
+    Parameters
+    ----------
+    X : str
+        Two byte string with first character indicating positive or negative axis (+/-),
+        and the second axis (X/Y/Z). Example strings '+X' or '-Y'
+    Y : str
+        Second axis string with same format as Y. Determines the second Y screen axis.
+    '''
+    if len(X) != 2:
+        raise ValueError('Expected string literal to be a 2 character string for the X_SCREEN parameter.')
+    if len(Y) != 2:
+        raise ValueError('Expected string literal to be a 2 character string for the Y_SCREEN parameter.')
+    group = self.point_group
+    group.set_str('X_SCREEN', 'X_SCREEN parameter', X)
+    group.set_str('Y_SCREEN', 'Y_SCREEN parameter', Y)
        
+
        
 
 
        
 def set_start_frame(self, frame=1)
@@ -250,6 +1608,25 @@ 
        Parameters
        
 
        Number for the first frame recorded in the file.
 Frame counter for a trial recording always start at 1 for the first frame.
        
 
+
        
+
+Expand source code
+
+
        def set_start_frame(self, frame=1):
+    ''' Set the 'TRIAL:ACTUAL_START_FIELD' parameter and header.first_frame entry.
+
+    Parameters
+    ----------
+    frame : int
+        Number for the first frame recorded in the file.
+        Frame counter for a trial recording always start at 1 for the first frame.
+    '''
+    self.trial_group.set('ACTUAL_START_FIELD', 'Actual start frame', 2, '<I', frame, 2)
+    if frame < 65535:
+        self._header.first_frame = np.uint16(frame)
+    else:
+        self._header.first_frame = np.uint16(65535)
        
+
        
 
 
        
 def write(self, handle)
@@ -262,6 +1639,82 @@ 
        Parameters
        
 
        Write metadata and C3D motion frames to the given file handle. The
 writer does not close the handle.
        
 
+
        
+
+Expand source code
+
+
        def write(self, handle):
+    '''Write metadata, point and analog frames to a file handle.
+
+    Parameters
+    ----------
+    handle : file
+        Write metadata and C3D motion frames to the given file handle. The
+        writer does not close the handle.
+    '''
+    if not self._frames:
+        raise RuntimeError('Attempted to write empty file.')
+
+    points, analog = self._frames[0]
+    ppf = len(points)
+    apf = len(analog)
+
+
+    first_frame = self.first_frame
+    if first_frame <= 0: # Bad value
+        first_frame = 1
+    nframes = len(self._frames)
+    last_frame = first_frame + nframes - 1
+
+    UINT16_MAX = 65535
+
+    # POINT group
+    group = self.point_group
+    group.set('USED', 'Number of point samples', 2, '<H', ppf)
+    group.set('FRAMES', 'Total frame count', 2, '<H', min(UINT16_MAX, nframes))
+    if nframes >= UINT16_MAX:
+        # Should be floating point
+        group.set('LONG_FRAMES', 'Total frame count', 4, '<f', nframes)
+    elif 'LONG_FRAMES' in group:
+        # Docs states it should not exist if frame_count < 65535
+        group.remove_param('LONG_FRAMES')
+    group.set('DATA_START', 'First data block containing frame samples.', 2, '<H', 0)
+    group.set('SCALE', 'Point data scaling factor', 4, '<f', self.point_scale)
+    group.set('RATE', 'Point data sample rate', 4, '<f', self.point_rate)
+    # Optional
+    if 'UNITS' not in group:
+        group.add_str('UNITS', 'Units used for point data measurements.', 'mm')
+    if 'DESCRIPTIONS' not in group:
+        group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * ppf, 2, ppf)
+
+    # ANALOG group
+    group = self.analog_group
+    group.set('USED', 'Analog channel count', 2, '<H', apf)
+    group.set('RATE', 'Analog samples per second', 4, '<f', self.analog_rate)
+    if 'GEN_SCALE' not in group:
+        self.set_analog_general_scale(1.0)
+    # Optional
+    if 'SCALE' not in group:
+        self.set_analog_scales(None)
+    if 'OFFSET' not in group:
+        self.set_analog_offsets(None)
+    if 'DESCRIPTIONS' not in group:
+        group.add_str('DESCRIPTIONS', 'Channel descriptions.', '  ' * apf, 2, apf)
+
+    # TRIAL group
+    self.set_start_frame(first_frame)
+    self._set_last_frame(last_frame)
+
+    # sync parameter information to header.
+    start_block = self.parameter_blocks() + 2
+    self.get('POINT:DATA_START').bytes = struct.pack('<H', start_block)
+    self._header.data_block = np.uint16(start_block)
+    self._header.point_count = np.uint16(ppf)
+    self._header.analog_count = np.uint16(np.prod(np.shape(analog)))
+
+    self._write_metadata(handle)
+    self._write_frames(handle)
        
+
        
 
 
 
        Inherited members
        
diff --git a/docs/examples.md b/docs/examples.md
index d9d63e4..274f517 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -2,7 +2,7 @@ Examples
 ========
 
 Access to data blocks in a .c3d file is provided through the `c3d.reader.Reader` and `c3d.writer.Writer` classes.
-Runnable implementation of the examples are provided in the [examples/] directory in the github repository.
+Implementation of the examples below are provided in the [examples/] directory in the github repository.
 
 [examples/]: https://github.com/EmbodiedCognition/py-c3d/tree/master/examples
 
@@ -61,10 +61,11 @@ Editing
 -------
 
 Editing c3d files is possible by combining the use of `c3d.reader.Reader` and `c3d.writer.Writer`
-instances through the use of `c3d.reader.Reader.to_writer`. Opening a .c3d file stream through
-a reader instance, `c3d.reader.Reader.to_writer` can be used to create an independent Writer instance
-containing a heap copy of the file contents. Rereading the data frames from the file
-and inserting into the writer in reverse, a looped version of the .c3d file can be created!
+instances through the `c3d.reader.Reader.to_writer` method. To edit a file, open a file stream and pass
+it to a `c3d.reader.Reader` instance. Convert it using the `c3d.reader.Reader.to_writer` method to create
+an independent `c3d.writer.Writer` instance containing a heap copy of the file contents.
+Rereading the data frames from the reader and inserting them in reverse into
+the writer will then create a looped version of the .c3d file!
 
     import c3d
 
@@ -76,3 +77,48 @@ and inserting into the writer in reverse, a looped version of the .c3d file can
 
     with open('my-looped-motion.c3d', 'wb') as h:
         writer.write(h)
+
+
+Accessing metadata
+----------------
+
+Metadata in a .c3d file exists in two forms, a `c3d.header.Header` and `c3d.parameter.ParamData`.
+Reading metadata fields can be done though the `c3d.reader.Reader` but editing requires a
+`c3d.writer.Writer` instance.
+
+`c3d.header.Header` fields can be accessed from the common `c3d.manager.Manager.header` attribute.
+Parameters are available through a parameter `c3d.group.Group`, and can be accessed
+through the `c3d.manager.Manager.get` method:
+
+    group = reader.get('POINT')
+    param = group.get('LABELS')
+
+or use the simpler method
+
+    param = reader.get('POINT:LABELS')
+
+Note that for accessing parameters in the `c3d.reader.Reader`, `c3d.reader.Reader.get`
+returns a `c3d.group.GroupReadonly` instance. Convenience functions are provided
+for some of the common metadata fields
+such as `c3d.manager.Manager.frame_count`. In the case you require specific
+metadata fields, consider visiting the documentation for the [C3D format] and/or inspect
+the file using the c3d-metadata script.
+
+[C3D format]: https://c3d.org/docs/C3D_User_Guide.pdf
+
+Writing metadata
+----------------
+
+Once a `c3d.writer.Writer` instance is created, to edit
+parameter data `c3d.writer.Writer.get_create` a group:
+
+    group = writer.get_create('ANALOG')
+
+and to write a float32 entry, use the `c3d.group.Group.add` or `c3d.group.Group.set` functions
+
+    group.set('GEN_SCALE', 'Analog general scale factor', 4, '
Date: Sun, 4 Jul 2021 22:07:13 +0200
Subject: [PATCH 087/120] pycodestyle ./c3d --max-line-length 120

---
 c3d/dtypes.py    |  1 +
 c3d/group.py     |  4 ++++
 c3d/header.py    |  7 ++++---
 c3d/manager.py   |  7 +++----
 c3d/parameter.py |  3 +++
 c3d/reader.py    |  3 +--
 c3d/utils.py     |  6 ++++++
 c3d/writer.py    | 19 ++++++++++---------
 8 files changed, 32 insertions(+), 18 deletions(-)

diff --git a/c3d/dtypes.py b/c3d/dtypes.py
index 9071d0d..193615e 100644
--- a/c3d/dtypes.py
+++ b/c3d/dtypes.py
@@ -10,6 +10,7 @@
 PROCESSOR_DEC = 85
 PROCESSOR_MIPS = 86
 
+
 class DataTypes(object):
     ''' Container defining the data types used when parsing byte data.
         Data types depend on the processor format the file is stored in.
diff --git a/c3d/group.py b/c3d/group.py
index 46b539f..853e9ec 100644
--- a/c3d/group.py
+++ b/c3d/group.py
@@ -5,6 +5,7 @@
 from .parameter import ParamData, Param
 from .utils import Decorator
 
+
 class GroupData(object):
     '''A group of parameters stored in a C3D file.
 
@@ -147,6 +148,7 @@ def write(self, group_id, handle):
         for param in self._params.values():
             param._data.write(group_id, handle)
 
+
 class GroupReadonly(object):
     ''' Wrapper exposing readonly attributes of a `c3d.group.GroupData` entry.
     '''
@@ -237,6 +239,7 @@ def get_string(self, key):
         '''Get the value of the given parameter as a string.'''
         return self._data[key.upper()].string_value
 
+
 class Group(GroupReadonly):
     ''' Wrapper exposing readable and writeable attributes of a `c3d.group.GroupData` entry.
     '''
@@ -289,6 +292,7 @@ def get(self, key, default=None):
             A parameter from the current group.
         '''
         return self._data._params.get(key, default)
+
     #
     #  Forward param editing
     #
diff --git a/c3d/header.py b/c3d/header.py
index 25a3718..29ac894 100644
--- a/c3d/header.py
+++ b/c3d/header.py
@@ -6,6 +6,7 @@
 import numpy as np
 from .utils import UNPACK_FLOAT_IEEE, DEC_to_IEEE
 
+
 class Header(object):
     '''Header information from a C3D file.
 
@@ -260,7 +261,7 @@ def encode_events(self, events):
                                   str(18) + 's',      # Flags
                                   'H',                # __
                                   str(18 * 4) + 's'   # Labels
-                                 )
+                                  )
         # Pack bytes
         event_timings = np.zeros(18, dtype=np.float32)
         event_disp_flags = np.zeros(18, dtype=np.uint8)
@@ -280,7 +281,7 @@ def encode_events(self, events):
         event_disp_flags[:write_count] = 1
 
         # Update event headers in self
-        self.long_event_labels = 0x3039 # Magic number
+        self.long_event_labels = 0x3039  # Magic number
         self.event_count = write_count
         # Update event block
         self.event_timings = event_timings[:write_count]
@@ -291,4 +292,4 @@ def encode_events(self, events):
                                        event_disp_flags.tobytes(),
                                        0,
                                        label_bytes
-                                      )
+                                       )
diff --git a/c3d/manager.py b/c3d/manager.py
index eb858a3..47ab6ef 100644
--- a/c3d/manager.py
+++ b/c3d/manager.py
@@ -118,7 +118,6 @@ def check_parameters(params):
             elif lab.num_elements > 0:
                 warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries')
 
-
     def _add_group(self, group_id, name=None, desc=None):
         '''Add a new parameter group.
 
@@ -150,7 +149,7 @@ def _add_group(self, group_id, name=None, desc=None):
                 raise TypeError('Expected Group name key to be string, was %s.' % type(name))
         else:
             name = name.upper()
-        group_id = int(group_id) # Asserts python int
+        group_id = int(group_id)  # Asserts python int
         if group_id in self._groups:
             raise KeyError('Group with numerical key {} already exists'.format(group_id))
         if name in self._groups:
@@ -206,7 +205,7 @@ def _rename_group(self, group_id, new_group_id):
                 del self._groups[grp.name]
             grp.name = new_group_id
         elif is_integer(new_group_id):
-            new_group_id = int(new_group_id) # Ensure python int
+            new_group_id = int(new_group_id)  # Ensure python int
             del self._groups[group_id]
         else:
             raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id)))
@@ -356,7 +355,7 @@ def last_frame(self) -> int:
             # Encoded as 2 16 bit words (rather then 1 32 bit word)
             words = param.uint16_array
             end_frame[1] = words[0] + words[1] * 65536
-            #end_frame[1] = param.uint32_value
+            # end_frame[1] = param.uint32_value
         param = self.get('POINT:LONG_FRAMES')
         if param is not None:
             # Encoded as float
diff --git a/c3d/parameter.py b/c3d/parameter.py
index 542d6c6..9e2e0f1 100644
--- a/c3d/parameter.py
+++ b/c3d/parameter.py
@@ -4,6 +4,7 @@
 import numpy as np
 from .utils import DEC_to_IEEE, DEC_to_IEEE_BYTES
 
+
 class ParamData(object):
     '''A class representing a single named parameter from a C3D file.
 
@@ -147,6 +148,7 @@ def _as_any(self, dtype):
                 return data.flatten()
             return data
 
+
 class ParamReadonly(object):
     ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry.
     '''
@@ -431,6 +433,7 @@ def _as_integer_or_float_value(self):
         else:
             return self.uint8_value
 
+
 class Param(ParamReadonly):
     ''' Wrapper exposing both readable and writable attributes of a `c3d.parameter.ParamData` entry.
     '''
diff --git a/c3d/reader.py b/c3d/reader.py
index 5a94992..0668673 100644
--- a/c3d/reader.py
+++ b/c3d/reader.py
@@ -245,13 +245,12 @@ def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_s
             # Update discarded - sign
             points[invalid, 3] = -1
 
-
             # Fifth value is the camera-observation byte
             if camera_sum:
                 # Convert to observation sum
                 points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7))
             else:
-                points[:, 4] = camera_byte #.astype(np.float32)
+                points[:, 4] = camera_byte  # .astype(np.float32)
 
             # Check if analog data exist, and parse if so
             if N_analog > 0:
diff --git a/c3d/utils.py b/c3d/utils.py
index 8f81e9a..63f684e 100644
--- a/c3d/utils.py
+++ b/c3d/utils.py
@@ -3,6 +3,7 @@
 import numpy as np
 import struct
 
+
 def is_integer(value):
     '''Check if value input is integer.'''
     return isinstance(value, (int, np.int32, np.int64))
@@ -53,24 +54,29 @@ def pack_labels(labels):
     label_str = ''.join(label.ljust(label_max_size) for label in labels)
     return label_str, label_max_size
 
+
 class Decorator(object):
     '''Base class for extending (decorating) a python object.
     '''
     def __init__(self, decoratee):
         self._decoratee = decoratee
+
     def __getattr__(self, name):
         return getattr(self._decoratee, name)
 
+
 def UNPACK_FLOAT_IEEE(uint_32):
     '''Unpacks a single 32 bit unsigned int to a IEEE float representation
     '''
     return struct.unpack('f', struct.pack("I", uint_32))[0]
 
+
 def DEC_to_IEEE(uint_32):
     '''Convert the 32 bit representation of a DEC float to IEEE format.
 
diff --git a/c3d/writer.py b/c3d/writer.py
index 3a76a22..5f6898f 100644
--- a/c3d/writer.py
+++ b/c3d/writer.py
@@ -3,11 +3,12 @@
 import copy
 import numpy as np
 import struct
-#import warnings
+# import warnings
 from . import utils
 from .manager import Manager
 from .dtypes import DataTypes
 
+
 class Writer(Manager):
     '''This class writes metadata and frames to a C3D file.
 
@@ -42,7 +43,7 @@ def __init__(self,
         '''Set minimal metadata for this writer.
 
         '''
-        self._dtypes = DataTypes() # Only support INTEL format from writing
+        self._dtypes = DataTypes()  # Only support INTEL format from writing
         super(Writer, self).__init__()
 
         # Header properties
@@ -99,12 +100,14 @@ def from_reader(reader, conversion=None):
         if not (is_consume or is_shallow_copy or is_deep_copy):
             raise ValueError(
                 "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format(
-                conversion))
+                    conversion
+                ))
         if not reader._dtypes.is_ieee and not is_shallow_copy:
             # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data.
             raise ValueError(
                 "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format(
-                reader._dtypes.proc_type))
+                    reader._dtypes.proc_type
+                ))
 
         if is_consume:
             writer._header = reader._header
@@ -232,12 +235,12 @@ def add_frames(self, frames, index=None):
                 if np.shape(f[0]) != psh:
                     raise ValueError(
                         'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
-                        str(psh), str(np.shape(f[0]))
+                            str(psh), str(np.shape(f[0]))
                         ))
                 if np.shape(f[1]) != ash:
                     raise ValueError(
                         'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format(
-                        str(ash), str(np.shape(f[1]))
+                            str(ash), str(np.shape(f[1]))
                         ))
 
         # Sequence of invalid shape
@@ -339,7 +342,6 @@ def _set_last_frame(self, frame):
         self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, '
Date: Sun, 4 Jul 2021 22:11:21 +0200
Subject: [PATCH 088/120] Code style

---
 c3d/README.rst | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 c3d/README.rst

diff --git a/c3d/README.rst b/c3d/README.rst
new file mode 100644
index 0000000..d912137
--- /dev/null
+++ b/c3d/README.rst
@@ -0,0 +1,10 @@
+Code style
+----------
+
+Use pycodestyle with the settings
+
+    pycodestyle . --max-line-length 120
+
+Pycodestyle can be installed from pip:
+
+    pip install pycodestyle

From 9afe8d5f42efbefd9c54e9846ebe774d1f8ae627 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 22:12:18 +0200
Subject: [PATCH 089/120] pip command

---
 c3d/README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/c3d/README.rst b/c3d/README.rst
index d912137..6e39c5e 100644
--- a/c3d/README.rst
+++ b/c3d/README.rst
@@ -5,6 +5,6 @@ Use pycodestyle with the settings
 
     pycodestyle . --max-line-length 120
 
-Pycodestyle can be installed from pip:
+Pycodestyle can be installed with the pip command
 
     pip install pycodestyle

From d0ed984d671e39ef65b2e47820ee2dd2984b42ad Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 4 Jul 2021 22:13:40 +0200
Subject: [PATCH 090/120] Update README.rst

--config show_source_code=True
---
 docs/README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/README.rst b/docs/README.rst
index 2003a97..f484e1e 100644
--- a/docs/README.rst
+++ b/docs/README.rst
@@ -1,7 +1,7 @@
 Reading the docs
 -----------------
 
-Documentation is available at: https://mattiasfredriksson.github.io/py-c3d/c3d/
+Online documentation can be accessed at: https://mattiasfredriksson.github.io/py-c3d/c3d/
 
 Building the docs
 -----------------
@@ -13,7 +13,7 @@ Building the docs requires the pdoc3 package::
 
 Once installed, documentation can be updated from the root directory with the command::
 
-    pdoc --html c3d --force --config show_source_code=False  --output-dir docs
+    pdoc --html c3d --force --config show_source_code=True  --output-dir docs
 
 Once updated you can access the documentation in the `docs/c3d/`_ folder.
 

From 7a6d36a8b07cca4d8ee5edfb0b56f152f8b85dba Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 22:14:24 +0200
Subject: [PATCH 091/120] Pycodestyles doc update

---
 docs/c3d/dtypes.html    |  1 +
 docs/c3d/group.html     |  5 +++++
 docs/c3d/header.html    | 19 ++++++++--------
 docs/c3d/manager.html   | 16 ++++++--------
 docs/c3d/parameter.html |  3 +++
 docs/c3d/reader.html    |  9 +++-----
 docs/c3d/utils.html     |  7 ++++++
 docs/c3d/writer.html    | 48 +++++++++++++++++++++--------------------
 8 files changed, 61 insertions(+), 47 deletions(-)

diff --git a/docs/c3d/dtypes.html b/docs/c3d/dtypes.html
index 81ca407..c9473d4 100644
--- a/docs/c3d/dtypes.html
+++ b/docs/c3d/dtypes.html
@@ -39,6 +39,7 @@ 
        Module c3d.dtypes
        
 PROCESSOR_DEC = 85
 PROCESSOR_MIPS = 86
 
+
 class DataTypes(object):
     ''' Container defining the data types used when parsing byte data.
         Data types depend on the processor format the file is stored in.
diff --git a/docs/c3d/group.html b/docs/c3d/group.html
index 833dd60..bce40b9 100644
--- a/docs/c3d/group.html
+++ b/docs/c3d/group.html
@@ -34,6 +34,7 @@ 
        Module c3d.group
        
 from .parameter import ParamData, Param
 from .utils import Decorator
 
+
 class GroupData(object):
     '''A group of parameters stored in a C3D file.
 
@@ -176,6 +177,7 @@ 
        Module c3d.group
        
         for param in self._params.values():
             param._data.write(group_id, handle)
 
+
 class GroupReadonly(object):
     ''' Wrapper exposing readonly attributes of a `c3d.group.GroupData` entry.
     '''
@@ -266,6 +268,7 @@ 
        Module c3d.group
        
         '''Get the value of the given parameter as a string.'''
         return self._data[key.upper()].string_value
 
+
 class Group(GroupReadonly):
     ''' Wrapper exposing readable and writeable attributes of a `c3d.group.GroupData` entry.
     '''
@@ -318,6 +321,7 @@ 
        Module c3d.group
        
             A parameter from the current group.
         '''
         return self._data._params.get(key, default)
+
     #
     #  Forward param editing
     #
@@ -562,6 +566,7 @@ 
        Classes
        
             A parameter from the current group.
         '''
         return self._data._params.get(key, default)
+
     #
     #  Forward param editing
     #
diff --git a/docs/c3d/header.html b/docs/c3d/header.html
index dd42c47..95ee820 100644
--- a/docs/c3d/header.html
+++ b/docs/c3d/header.html
@@ -35,6 +35,7 @@ 
        Module c3d.header
        
 import numpy as np
 from .utils import UNPACK_FLOAT_IEEE, DEC_to_IEEE
 
+
 class Header(object):
     '''Header information from a C3D file.
 
@@ -289,7 +290,7 @@ 
        Module c3d.header
        
                                   str(18) + 's',      # Flags
                                   'H',                # __
                                   str(18 * 4) + 's'   # Labels
-                                 )
+                                  )
         # Pack bytes
         event_timings = np.zeros(18, dtype=np.float32)
         event_disp_flags = np.zeros(18, dtype=np.uint8)
@@ -309,7 +310,7 @@ 
        Module c3d.header
        
         event_disp_flags[:write_count] = 1
 
         # Update event headers in self
-        self.long_event_labels = 0x3039 # Magic number
+        self.long_event_labels = 0x3039  # Magic number
         self.event_count = write_count
         # Update event block
         self.event_timings = event_timings[:write_count]
@@ -320,7 +321,7 @@ 
        Module c3d.header
        
                                        event_disp_flags.tobytes(),
                                        0,
                                        label_bytes
-                                      )
    + )
    @@ -645,7 +646,7 @@

    Parameters

    str(18) + 's', # Flags 'H', # __ str(18 * 4) + 's' # Labels - ) + ) # Pack bytes event_timings = np.zeros(18, dtype=np.float32) event_disp_flags = np.zeros(18, dtype=np.uint8) @@ -665,7 +666,7 @@

    Parameters

    event_disp_flags[:write_count] = 1 # Update event headers in self - self.long_event_labels = 0x3039 # Magic number + self.long_event_labels = 0x3039 # Magic number self.event_count = write_count # Update event block self.event_timings = event_timings[:write_count] @@ -676,7 +677,7 @@

    Parameters

    event_disp_flags.tobytes(), 0, label_bytes - )     + )

    Class variables

    @@ -755,7 +756,7 @@

    Parameters

    str(18) + 's', # Flags 'H', # __ str(18 * 4) + 's' # Labels - ) + ) # Pack bytes event_timings = np.zeros(18, dtype=np.float32) event_disp_flags = np.zeros(18, dtype=np.uint8) @@ -775,7 +776,7 @@

    Parameters

    event_disp_flags[:write_count] = 1 # Update event headers in self - self.long_event_labels = 0x3039 # Magic number + self.long_event_labels = 0x3039 # Magic number self.event_count = write_count # Update event block self.event_timings = event_timings[:write_count] @@ -786,7 +787,7 @@

    Parameters

    event_disp_flags.tobytes(), 0, label_bytes - ) + )
    diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html index 41cfcbe..bd64c3b 100644 --- a/docs/c3d/manager.html +++ b/docs/c3d/manager.html @@ -147,7 +147,6 @@

    Module c3d.manager

    elif lab.num_elements > 0: warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries') - def _add_group(self, group_id, name=None, desc=None): '''Add a new parameter group. @@ -179,7 +178,7 @@

    Module c3d.manager

    raise TypeError('Expected Group name key to be string, was %s.' % type(name)) else: name = name.upper() - group_id = int(group_id) # Asserts python int + group_id = int(group_id) # Asserts python int if group_id in self._groups: raise KeyError('Group with numerical key {} already exists'.format(group_id)) if name in self._groups: @@ -235,7 +234,7 @@

    Module c3d.manager

    del self._groups[grp.name] grp.name = new_group_id elif is_integer(new_group_id): - new_group_id = int(new_group_id) # Ensure python int + new_group_id = int(new_group_id) # Ensure python int del self._groups[group_id] else: raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id))) @@ -385,7 +384,7 @@

    Module c3d.manager

    # Encoded as 2 16 bit words (rather then 1 32 bit word) words = param.uint16_array end_frame[1] = words[0] + words[1] * 65536 - #end_frame[1] = param.uint32_value + # end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: # Encoded as float @@ -619,7 +618,6 @@

    Attributes

    elif lab.num_elements > 0: warnings.warn('No analog data found in file, but file contains ANALOG:LABELS entries') - def _add_group(self, group_id, name=None, desc=None): '''Add a new parameter group. @@ -651,7 +649,7 @@

    Attributes

    raise TypeError('Expected Group name key to be string, was %s.' % type(name)) else: name = name.upper() - group_id = int(group_id) # Asserts python int + group_id = int(group_id) # Asserts python int if group_id in self._groups: raise KeyError('Group with numerical key {} already exists'.format(group_id)) if name in self._groups: @@ -707,7 +705,7 @@

    Attributes

    del self._groups[grp.name] grp.name = new_group_id elif is_integer(new_group_id): - new_group_id = int(new_group_id) # Ensure python int + new_group_id = int(new_group_id) # Ensure python int del self._groups[group_id] else: raise KeyError('Invalid group identifier of type: %s' % str(type(new_group_id))) @@ -857,7 +855,7 @@

    Attributes

    # Encoded as 2 16 bit words (rather then 1 32 bit word) words = param.uint16_array end_frame[1] = words[0] + words[1] * 65536 - #end_frame[1] = param.uint32_value + # end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: # Encoded as float @@ -1100,7 +1098,7 @@

    Instance variables

    # Encoded as 2 16 bit words (rather then 1 32 bit word) words = param.uint16_array end_frame[1] = words[0] + words[1] * 65536 - #end_frame[1] = param.uint32_value + # end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: # Encoded as float diff --git a/docs/c3d/parameter.html b/docs/c3d/parameter.html index f32c8ab..8a28333 100644 --- a/docs/c3d/parameter.html +++ b/docs/c3d/parameter.html @@ -33,6 +33,7 @@

    Module c3d.parameter

    import numpy as np from .utils import DEC_to_IEEE, DEC_to_IEEE_BYTES + class ParamData(object): '''A class representing a single named parameter from a C3D file. @@ -176,6 +177,7 @@

    Module c3d.parameter

    return data.flatten() return data + class ParamReadonly(object): ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry. ''' @@ -460,6 +462,7 @@

    Module c3d.parameter

    else: return self.uint8_value + class Param(ParamReadonly): ''' Wrapper exposing both readable and writable attributes of a `c3d.parameter.ParamData` entry. ''' diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html index 0b868b0..de72e63 100644 --- a/docs/c3d/reader.html +++ b/docs/c3d/reader.html @@ -274,13 +274,12 @@

    Module c3d.reader

    # Update discarded - sign points[invalid, 3] = -1 - # Fifth value is the camera-observation byte if camera_sum: # Convert to observation sum points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7)) else: - points[:, 4] = camera_byte #.astype(np.float32) + points[:, 4] = camera_byte # .astype(np.float32) # Check if analog data exist, and parse if so if N_analog > 0: @@ -641,13 +640,12 @@

    Raises

    # Update discarded - sign points[invalid, 3] = -1 - # Fifth value is the camera-observation byte if camera_sum: # Convert to observation sum points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7)) else: - points[:, 4] = camera_byte #.astype(np.float32) + points[:, 4] = camera_byte # .astype(np.float32) # Check if analog data exist, and parse if so if N_analog > 0: @@ -1024,13 +1022,12 @@

    Returns

    # Update discarded - sign points[invalid, 3] = -1 - # Fifth value is the camera-observation byte if camera_sum: # Convert to observation sum points[:, 4] = sum((camera_byte & (1 << k)) >> k for k in range(7)) else: - points[:, 4] = camera_byte #.astype(np.float32) + points[:, 4] = camera_byte # .astype(np.float32) # Check if analog data exist, and parse if so if N_analog > 0: diff --git a/docs/c3d/utils.html b/docs/c3d/utils.html index 466598c..dff3183 100644 --- a/docs/c3d/utils.html +++ b/docs/c3d/utils.html @@ -32,6 +32,7 @@

    Module c3d.utils

    import numpy as np import struct + def is_integer(value): '''Check if value input is integer.''' return isinstance(value, (int, np.int32, np.int64)) @@ -82,24 +83,29 @@

    Module c3d.utils

    label_str = ''.join(label.ljust(label_max_size) for label in labels) return label_str, label_max_size + class Decorator(object): '''Base class for extending (decorating) a python object. ''' def __init__(self, decoratee): self._decoratee = decoratee + def __getattr__(self, name): return getattr(self._decoratee, name) + def UNPACK_FLOAT_IEEE(uint_32): '''Unpacks a single 32 bit unsigned int to a IEEE float representation ''' return struct.unpack('f', struct.pack("<I", uint_32))[0] + def UNPACK_FLOAT_MIPS(uint_32): '''Unpacks a single 32 bit unsigned int to a IEEE float representation ''' return struct.unpack('f', struct.pack(">I", uint_32))[0] + def DEC_to_IEEE(uint_32): '''Convert the 32 bit representation of a DEC float to IEEE format. @@ -445,6 +451,7 @@

    Classes

    ''' def __init__(self, decoratee): self._decoratee = decoratee + def __getattr__(self, name): return getattr(self._decoratee, name)     diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html index 3ffe26f..35d06ae 100644 --- a/docs/c3d/writer.html +++ b/docs/c3d/writer.html @@ -32,11 +32,12 @@

    Module c3d.writer

    import copy import numpy as np import struct -#import warnings +# import warnings from . import utils from .manager import Manager from .dtypes import DataTypes + class Writer(Manager): '''This class writes metadata and frames to a C3D file. @@ -71,7 +72,7 @@

    Module c3d.writer

    '''Set minimal metadata for this writer. ''' - self._dtypes = DataTypes() # Only support INTEL format from writing + self._dtypes = DataTypes() # Only support INTEL format from writing super(Writer, self).__init__() # Header properties @@ -128,12 +129,14 @@

    Module c3d.writer

    if not (is_consume or is_shallow_copy or is_deep_copy): raise ValueError( "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format( - conversion)) + conversion + )) if not reader._dtypes.is_ieee and not is_shallow_copy: # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. raise ValueError( "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( - reader._dtypes.proc_type)) + reader._dtypes.proc_type + )) if is_consume: writer._header = reader._header @@ -261,12 +264,12 @@

    Module c3d.writer

    if np.shape(f[0]) != psh: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(psh), str(np.shape(f[0])) + str(psh), str(np.shape(f[0])) )) if np.shape(f[1]) != ash: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(ash), str(np.shape(f[1])) + str(ash), str(np.shape(f[1])) )) # Sequence of invalid shape @@ -368,7 +371,6 @@

    Module c3d.writer

    self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, '<I', frame, 2) self._header.last_frame = np.uint16(min(frame, 65535)) - def set_screen_axis(self, X='+X', Y='+Y'): ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. @@ -404,9 +406,8 @@

    Module c3d.writer

    ppf = len(points) apf = len(analog) - first_frame = self.first_frame - if first_frame <= 0: # Bad value + if first_frame <= 0: # Bad value first_frame = 1 nframes = len(self._frames) last_frame = first_frame + nframes - 1 @@ -613,7 +614,7 @@

    Parameters

    '''Set minimal metadata for this writer. ''' - self._dtypes = DataTypes() # Only support INTEL format from writing + self._dtypes = DataTypes() # Only support INTEL format from writing super(Writer, self).__init__() # Header properties @@ -670,12 +671,14 @@

    Parameters

    if not (is_consume or is_shallow_copy or is_deep_copy): raise ValueError( "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format( - conversion)) + conversion + )) if not reader._dtypes.is_ieee and not is_shallow_copy: # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. raise ValueError( "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( - reader._dtypes.proc_type)) + reader._dtypes.proc_type + )) if is_consume: writer._header = reader._header @@ -803,12 +806,12 @@

    Parameters

    if np.shape(f[0]) != psh: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(psh), str(np.shape(f[0])) + str(psh), str(np.shape(f[0])) )) if np.shape(f[1]) != ash: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(ash), str(np.shape(f[1])) + str(ash), str(np.shape(f[1])) )) # Sequence of invalid shape @@ -910,7 +913,6 @@

    Parameters

    self.trial_group.set('ACTUAL_END_FIELD', 'Actual end frame', 2, '<I', frame, 2) self._header.last_frame = np.uint16(min(frame, 65535)) - def set_screen_axis(self, X='+X', Y='+Y'): ''' Set the X_SCREEN and Y_SCREEN parameters in the POINT group. @@ -946,9 +948,8 @@

    Parameters

    ppf = len(points) apf = len(analog) - first_frame = self.first_frame - if first_frame <= 0: # Bad value + if first_frame <= 0: # Bad value first_frame = 1 nframes = len(self._frames) last_frame = first_frame + nframes - 1 @@ -1171,12 +1172,14 @@

    Raises

    if not (is_consume or is_shallow_copy or is_deep_copy): raise ValueError( "Unknown mode argument %s. Supported modes are: 'consume', 'copy', or 'shallow_copy'".format( - conversion)) + conversion + )) if not reader._dtypes.is_ieee and not is_shallow_copy: # Can't copy/consume non-Intel files due to the uncertainty of converting parameter data. raise ValueError( "File was read in %s format and only 'shallow_copy' mode is supported for non Intel files!".format( - reader._dtypes.proc_type)) + reader._dtypes.proc_type + )) if is_consume: writer._header = reader._header @@ -1332,12 +1335,12 @@

    Parameters

    if np.shape(f[0]) != psh: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(psh), str(np.shape(f[0])) + str(psh), str(np.shape(f[0])) )) if np.shape(f[1]) != ash: raise ValueError( 'Shape of analog data does not previous frames. Expexted shape {}, was {}.'.format( - str(ash), str(np.shape(f[1])) + str(ash), str(np.shape(f[1])) )) # Sequence of invalid shape @@ -1659,9 +1662,8 @@

    Parameters

    ppf = len(points) apf = len(analog) - first_frame = self.first_frame - if first_frame <= 0: # Bad value + if first_frame <= 0: # Bad value first_frame = 1 nframes = len(self._frames) last_frame = first_frame + nframes - 1 From 67598431dace48dd98932d35de93d959d5b86cd0 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 22:16:08 +0200 Subject: [PATCH 092/120] Update README.rst --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 0af68d9..cc3117c 100644 --- a/README.rst +++ b/README.rst @@ -59,8 +59,8 @@ Caveats The package is tested against the `software examples`_ but may still not support every possible format. For example, parameters serialized in multiple parameters -are not handled automatically (such as POINT:LABELS and POINT:LABELS2). Reading and -writing files from a big-endian system is also not supported. +are not handled automatically (such as a LABELS field stored in both POINT:LABELS and +POINT:LABELS2). Reading and writing files from a big-endian system is also not supported. Tests are currently only run on Windows, which means that Linux and Mac users may experience some issues. If you experience issues with a file or feature, feel free From dd5a627c0e4246d0e5da4a3dceda71a2cb92c777 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 23:22:16 +0200 Subject: [PATCH 093/120] Update README.rst --- c3d/README.rst | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/c3d/README.rst b/c3d/README.rst index 6e39c5e..a0c6c4a 100644 --- a/c3d/README.rst +++ b/c3d/README.rst @@ -8,3 +8,47 @@ Use pycodestyle with the settings Pycodestyle can be installed with the pip command pip install pycodestyle + +Docstrings +----------- + +Use `numpy style`_ doc strings + +.. _numpy style: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard + +Docstring example +----------- + + def my_function(aparam, bparam): + ''' Short summary. + + Description, classes can be referred to through package/module `c3d.reader.Reader`. + Methods can be referred to in the same way e.g. `c3d.reader.Reader.read_frames`. + + Parameters + ---------- + aparam : `c3d.reader.Reader` + This is the first input parameter. + bparam : str + The second parameter should be a string. + + Returns + ------- + aarg : `c3d.writer.Writer` + First return argument is a Writer instance. + barg : int + Second return argument is of type int. + + Raises + ------ + ValueError + It occurs for some reason. + ''' + + ... + some_code + ... + + return aarg, barg + + From c697676d3473409d2926268281ff433fc0f96f4f Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 23:23:56 +0200 Subject: [PATCH 094/120] Docstrings --- c3d/writer.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/c3d/writer.py b/c3d/writer.py index 5f6898f..6b6edf5 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -54,12 +54,12 @@ def __init__(self, @staticmethod def from_reader(reader, conversion=None): - ''' + ''' Convert a `c3d.reader.Reader` to a persistent `c3d.writer.Writer` instance. Parameters ---------- - source : `c3d.manager.Manager` - Source to copy. + source : `c3d.reader.Reader` + Source to copy data from. conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: @@ -79,8 +79,8 @@ def from_reader(reader, conversion=None): Returns ------- - param : :class:`Writer` - A writeable and persistent representation of the 'Reader' object. + param : `c3d.writer.Writer` + A writeable and persistent representation of the `c3d.reader.Reader` object. Raises ------ From ebb119a824e074e968859c43cb25a8a011f77080 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 23:25:08 +0200 Subject: [PATCH 095/120] Test readme.md --- c3d/{README.rst => README.md} | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) rename c3d/{README.rst => README.md} (86%) diff --git a/c3d/README.rst b/c3d/README.md similarity index 86% rename from c3d/README.rst rename to c3d/README.md index a0c6c4a..4554f88 100644 --- a/c3d/README.rst +++ b/c3d/README.md @@ -8,20 +8,20 @@ Use pycodestyle with the settings Pycodestyle can be installed with the pip command pip install pycodestyle - + Docstrings ----------- -Use `numpy style`_ doc strings +Use [numpy style] doc strings -.. _numpy style: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard +[numpy style] https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard Docstring example ----------- def my_function(aparam, bparam): ''' Short summary. - + Description, classes can be referred to through package/module `c3d.reader.Reader`. Methods can be referred to in the same way e.g. `c3d.reader.Reader.read_frames`. @@ -44,11 +44,9 @@ Docstring example ValueError It occurs for some reason. ''' - + ... some_code ... - + return aarg, barg - - From 24f5005b2f22aac8b2d3acda99faccba57ee8831 Mon Sep 17 00:00:00 2001 From: MattiasFredriksson Date: Sun, 4 Jul 2021 23:27:21 +0200 Subject: [PATCH 096/120] .md worked --- c3d/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/c3d/README.md b/c3d/README.md index 4554f88..05c168c 100644 --- a/c3d/README.md +++ b/c3d/README.md @@ -12,9 +12,9 @@ Pycodestyle can be installed with the pip command Docstrings ----------- -Use [numpy style] doc strings +Use [numpy style] doc strings. -[numpy style] https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard +[numpy style]: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard Docstring example ----------- From 5f7120aca08eab876d6c6f8aeddb855752824893 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 23:30:01 +0200 Subject: [PATCH 097/120] Updated docs --- docs/c3d/writer.html | 41 +++++++++++++++++++++-------------------- 1 file changed, 21 insertions(+), 20 deletions(-) diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html index 35d06ae..9a5dc36 100644 --- a/docs/c3d/writer.html +++ b/docs/c3d/writer.html @@ -83,12 +83,12 @@

    Module c3d.writer

    @staticmethod def from_reader(reader, conversion=None): - ''' + ''' Convert a `c3d.reader.Reader` to a persistent `c3d.writer.Writer` instance. Parameters ---------- - source : `c3d.manager.Manager` - Source to copy. + source : `c3d.reader.Reader` + Source to copy data from. conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: @@ -108,8 +108,8 @@

    Module c3d.writer

    Returns ------- - param : :class:`Writer` - A writeable and persistent representation of the 'Reader' object. + param : `c3d.writer.Writer` + A writeable and persistent representation of the `c3d.reader.Reader` object. Raises ------ @@ -625,12 +625,12 @@

    Parameters

    @staticmethod def from_reader(reader, conversion=None): - ''' + ''' Convert a `c3d.reader.Reader` to a persistent `c3d.writer.Writer` instance. Parameters ---------- - source : `c3d.manager.Manager` - Source to copy. + source : `c3d.reader.Reader` + Source to copy data from. conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: @@ -650,8 +650,8 @@

    Parameters

    Returns ------- - param : :class:`Writer` - A writeable and persistent representation of the 'Reader' object. + param : `c3d.writer.Writer` + A writeable and persistent representation of the `c3d.reader.Reader` object. Raises ------ @@ -1088,10 +1088,11 @@

    Static methods

    def from_reader(reader, conversion=None)
    -

    Parameters

    +

    Convert a Reader to a persistent Writer instance.

    +

    Parameters

    -
    source : Manager
    -
    Source to copy.
    +
    source : Reader
    +
    Source to copy data from.
    conversion : str
    Conversion mode, None is equivalent to the default mode. Supported modes are:
    'consume'       - (Default) Reader object will be
                   consumed and explicitly deleted.
@@ -1111,8 +1112,8 @@ 
    Static methods

    Returns

    -
    param : :class:Writer``
    -
    A writeable and persistent representation of the 'Reader' object.
    +
    param : Writer
    +
    A writeable and persistent representation of the Reader object.

    Raises

    @@ -1126,12 +1127,12 @@

    Raises

    @staticmethod
 def from_reader(reader, conversion=None):
-    '''
+    ''' Convert a `c3d.reader.Reader` to a persistent `c3d.writer.Writer` instance.
 
     Parameters
     ----------
-    source : `c3d.manager.Manager`
-        Source to copy.
+    source : `c3d.reader.Reader`
+        Source to copy data from.
     conversion : str
         Conversion mode, None is equivalent to the default mode. Supported modes are:
 
@@ -1151,8 +1152,8 @@ 
    Raises
    
 
     Returns
     -------
-    param : :class:`Writer`
-        A writeable and persistent representation of the 'Reader' object.
+    param : `c3d.writer.Writer`
+        A writeable and persistent representation of the `c3d.reader.Reader` object.
 
     Raises
     ------

From 4faef087e20777248cfc146b96601100bffd0fe0 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 23:34:20 +0200
Subject: [PATCH 098/120] documentation -> manual

---
 docs/c3d/index.html | 2 +-
 docs/examples.md    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index 1b42573..caac219 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -110,7 +110,7 @@ 
    Accessing Metadata
    
 returns a GroupReadonly instance. Convenience functions are provided
 for some of the common metadata fields
 such as Manager.frame_count. In the case you require specific
-metadata fields, consider visiting the documentation for the C3D format and/or inspect
+metadata fields, consider exploring the C3D format manual and/or inspect
 the file using the c3d-metadata script.
    
 
    Writing Metadata
    
 
    Once a Writer instance is created, to edit
diff --git a/docs/examples.md b/docs/examples.md
index 274f517..d5a429f 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -101,10 +101,10 @@ Note that for accessing parameters in the `c3d.reader.Reader`, `c3d.reader.Reade
 returns a `c3d.group.GroupReadonly` instance. Convenience functions are provided
 for some of the common metadata fields
 such as `c3d.manager.Manager.frame_count`. In the case you require specific
-metadata fields, consider visiting the documentation for the [C3D format] and/or inspect
+metadata fields, consider exploring the [C3D format manual] and/or inspect
 the file using the c3d-metadata script.
 
-[C3D format]: https://c3d.org/docs/C3D_User_Guide.pdf
+[C3D format manual]: https://c3d.org/docs/C3D_User_Guide.pdf
 
 Writing metadata
 ----------------

From 08b8269396ef4b6967bb660dd6fe51914187e631 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 23:53:41 +0200
Subject: [PATCH 099/120] Update example documentation

---
 docs/c3d/index.html | 21 ++++++++++-----------
 docs/examples.md    | 21 ++++++++++-----------
 2 files changed, 20 insertions(+), 22 deletions(-)

diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index caac219..380d143 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -78,10 +78,10 @@ 
    Writing
    
 
    Editing
    
 
    Editing c3d files is possible by combining the use of Reader and Writer
 instances through the Reader.to_writer() method. To edit a file, open a file stream and pass
-it to a Reader instance. Convert it using the Reader.to_writer() method to create
-an independent Writer instance containing a heap copy of the file contents.
-Rereading the data frames from the reader and inserting them in reverse into
-the writer will then create a looped version of the .c3d file!
    
+it to the Reader constructor. Use the Reader.to_writer() method to create
+an independent Writer instance containing a heap copy of its file contents.
+Rereading data frames from the reader and inserting them in reverse will then create a
+looped version of the original motion sequence!
    
 
    import c3d
 
 with open('my-motion.c3d', 'rb') as file:
@@ -99,19 +99,18 @@ 
    Accessing Metadata
    
 Writer instance.
    
 
    Header fields can be accessed from the common Manager.header attribute.
 Parameters are available through a parameter Group, and can be accessed
-through the Manager.get() method:
    
+through the Manager.get() and Group.get() methods:
    
 
    group = reader.get('POINT')
 param = group.get('LABELS')
 
    
-
    or use the simpler method
    
+
    or simply use
    
 
    param = reader.get('POINT:LABELS')
 
    
 
    Note that for accessing parameters in the Reader, Reader.get()
 returns a GroupReadonly instance. Convenience functions are provided
-for some of the common metadata fields
-such as Manager.frame_count. In the case you require specific
-metadata fields, consider exploring the C3D format manual and/or inspect
-the file using the c3d-metadata script.
    
+for some of the common metadata fields such as Manager.frame_count.
+In the case you require specific metadata fields, consider exploring
+the C3D format manual and/or inspect the file using the c3d-metadata script.
    
 
    Writing Metadata
    
 
    Once a Writer instance is created, to edit
 parameter data Writer.get_create() a group:
    
@@ -121,7 +120,7 @@ 
    Writing Metadata
    
 
    group.set('GEN_SCALE', 'Analog general scale factor', 4, '<f', value)
 
    
 
    In this case, one can use the Writer.set_analog_general_scale() method instead.
-For serializing other types, see the source code for some of the convenience functions such as
+For serializing other types, see the source code for some of the convenience functions. For example:
 Writer.set_point_labels() (2D string array) or
 Writer.set_analog_scales() (1D float array).
    
 
    
diff --git a/docs/examples.md b/docs/examples.md
index d5a429f..ca8eb42 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -62,10 +62,10 @@ Editing
 
 Editing c3d files is possible by combining the use of `c3d.reader.Reader` and `c3d.writer.Writer`
 instances through the `c3d.reader.Reader.to_writer` method. To edit a file, open a file stream and pass
-it to a `c3d.reader.Reader` instance. Convert it using the `c3d.reader.Reader.to_writer` method to create
-an independent `c3d.writer.Writer` instance containing a heap copy of the file contents.
-Rereading the data frames from the reader and inserting them in reverse into
-the writer will then create a looped version of the .c3d file!
+it to the `c3d.reader.Reader` constructor. Use the `c3d.reader.Reader.to_writer` method to create
+an independent `c3d.writer.Writer` instance containing a heap copy of its file contents.
+Rereading data frames from the reader and inserting them in reverse will then create a
+looped version of the original motion sequence!
 
     import c3d
 
@@ -88,21 +88,20 @@ Reading metadata fields can be done though the `c3d.reader.Reader` but editing r
 
 `c3d.header.Header` fields can be accessed from the common `c3d.manager.Manager.header` attribute.
 Parameters are available through a parameter `c3d.group.Group`, and can be accessed
-through the `c3d.manager.Manager.get` method:
+through the `c3d.manager.Manager.get` and `c3d.group.Group.get` methods:
 
     group = reader.get('POINT')
     param = group.get('LABELS')
 
-or use the simpler method
+or simply use
 
     param = reader.get('POINT:LABELS')
 
 Note that for accessing parameters in the `c3d.reader.Reader`, `c3d.reader.Reader.get`
 returns a `c3d.group.GroupReadonly` instance. Convenience functions are provided
-for some of the common metadata fields
-such as `c3d.manager.Manager.frame_count`. In the case you require specific
-metadata fields, consider exploring the [C3D format manual] and/or inspect
-the file using the c3d-metadata script.
+for some of the common metadata fields such as `c3d.manager.Manager.frame_count`.
+In the case you require specific metadata fields, consider exploring
+the [C3D format manual] and/or inspect the file using the c3d-metadata script.
 
 [C3D format manual]: https://c3d.org/docs/C3D_User_Guide.pdf
 
@@ -119,6 +118,6 @@ and to write a float32 entry, use the `c3d.group.Group.add` or `c3d.group.Group.
     group.set('GEN_SCALE', 'Analog general scale factor', 4, '
Date: Sun, 4 Jul 2021 23:55:14 +0200
Subject: [PATCH 100/120] Update README.md

---
 c3d/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/c3d/README.md b/c3d/README.md
index 05c168c..1e74339 100644
--- a/c3d/README.md
+++ b/c3d/README.md
@@ -29,8 +29,8 @@ Docstring example
         ----------
         aparam : `c3d.reader.Reader`
             This is the first input parameter.
-        bparam : str
-            The second parameter should be a string.
+        bparam : str, optional
+            The second parameter is an optional string argument.
 
         Returns
         -------

From 15411e2f80c3923de13b737e4e8fe6e901b77f95 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Sun, 4 Jul 2021 23:57:46 +0200
Subject: [PATCH 101/120] Test .. code-block:: python

---
 c3d/{README.md => README.rst} | 2 ++
 1 file changed, 2 insertions(+)
 rename c3d/{README.md => README.rst} (98%)

diff --git a/c3d/README.md b/c3d/README.rst
similarity index 98%
rename from c3d/README.md
rename to c3d/README.rst
index 1e74339..349ac6d 100644
--- a/c3d/README.md
+++ b/c3d/README.rst
@@ -19,6 +19,8 @@ Use [numpy style] doc strings.
 Docstring example
 -----------
 
+.. code-block:: python
+
     def my_function(aparam, bparam):
         ''' Short summary.
 

From 08f15f32db4cb3224e7bee6faf2a6047e5fbb8c6 Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 4 Jul 2021 23:59:33 +0200
Subject: [PATCH 102/120] Update README.rst

.rst working with .. code-block:: python
---
 c3d/README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/c3d/README.rst b/c3d/README.rst
index 349ac6d..75880ce 100644
--- a/c3d/README.rst
+++ b/c3d/README.rst
@@ -12,9 +12,9 @@ Pycodestyle can be installed with the pip command
 Docstrings
 -----------
 
-Use [numpy style] doc strings.
+Use `numpy style`_ doc strings.
 
-[numpy style]: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard
+.. _`numpy style`: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard
 
 Docstring example
 -----------

From 56c99da702782d10b0793eb394dfb0b8e32db94a Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Mon, 5 Jul 2021 14:47:41 +0200
Subject: [PATCH 103/120] Manager.get_screen_xy_strings
 Manager.get_screen_xy_axis

---
 c3d/manager.py          |  73 ++++++--
 c3d/parameter.py        | 105 ++++++-----
 docs/c3d/dtypes.html    |   1 +
 docs/c3d/group.html     |   1 +
 docs/c3d/header.html    |   1 +
 docs/c3d/index.html     |   1 +
 docs/c3d/manager.html   | 175 +++++++++++++++++--
 docs/c3d/parameter.html | 375 +++++++++++++++++++++++++---------------
 docs/c3d/reader.html    |   2 +
 docs/c3d/utils.html     |   1 +
 docs/c3d/writer.html    |   2 +
 test/test_c3d.py        |   2 +-
 12 files changed, 528 insertions(+), 211 deletions(-)

diff --git a/c3d/manager.py b/c3d/manager.py
index 47ab6ef..9b196f9 100644
--- a/c3d/manager.py
+++ b/c3d/manager.py
@@ -1,4 +1,4 @@
-''' Manager base class defining common attributes for both the Reader and Writer instances.
+''' Manager base class defining common attributes for both Reader and Writer instances.
 '''
 import numpy as np
 import warnings
@@ -337,8 +337,7 @@ def first_frame(self) -> int:
         param = self.get('TRIAL:ACTUAL_START_FIELD')
         if param is not None:
             # ACTUAL_START_FIELD is encoded in two 16 byte words...
-            words = param.uint16_array
-            return words[0] + words[1] * 65535
+            return param.uint32_value
         return self.header.first_frame
 
     @property
@@ -353,30 +352,35 @@ def last_frame(self) -> int:
         param = self.get('TRIAL:ACTUAL_END_FIELD')
         if param is not None:
             # Encoded as 2 16 bit words (rather then 1 32 bit word)
-            words = param.uint16_array
-            end_frame[1] = words[0] + words[1] * 65536
-            # end_frame[1] = param.uint32_value
+            #words = param.uint16_array
+            #end_frame[1] = words[0] + words[1] * 65536
+            end_frame[1] = param.uint32_value
         param = self.get('POINT:LONG_FRAMES')
         if param is not None:
-            # Encoded as float
-            end_frame[2] = int(param.float_value)
+            # 'Should be' encoded as float
+            if param.bytes_per_element >= 4:
+                end_frame[2] = int(param.float_value)
+            else:
+                end_frame[2] = param.uint16_value
         param = self.get('POINT:FRAMES')
         if param is not None:
             # Can be encoded either as 32 bit float or 16 bit uint
-            if param.bytes_per_element == 2:
-                end_frame[3] = param.uint16_value
-            else:
+            if param.bytes_per_element == 4:
                 end_frame[3] = int(param.float_value)
+            else:
+                end_frame[3] = param.uint16_value
         # Return the largest of the all (queue bad reading...)
         return int(np.max(end_frame))
 
-    def get_screen_axis(self):
-        ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+    def get_screen_xy_strings(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
+
+        See `Manager.get_screen_xy_axis` to get numpy vectors instead.
 
         Returns
         -------
         value : (str, str) or None
-            Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+            Touple containing X_SCREEN and Y_SCREEN strings, or None (if no parameters could be found).
         '''
         X = self.get('POINT:X_SCREEN')
         Y = self.get('POINT:Y_SCREEN')
@@ -384,6 +388,47 @@ def get_screen_axis(self):
             return (X.string_value, Y.string_value)
         return None
 
+    def get_screen_xy_axis(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
+
+        Z axis can be computed using the cross product:
+
+        \[ z = x \\times y \]
+
+        To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
+
+        \[ p = | x^T y^T z^T |^T p_s  \]
+
+
+        See `Manager.get_screen_xy_strings` to get the parameter as string values instead.
+
+        Returns
+        -------
+        value : ([3,], [3,]) or None
+            Touple $(x, y)$ containing X_SCREEN and Y_SCREEN as row vectors, or None.
+        '''
+        # Axis conversion dictionary.
+        AXIS_DICT = {
+            'X': np.array([1.0, 0, 0]),
+            '+X': np.array([1.0, 0, 0]),
+            '-X': np.array([-1.0, 0, 0]),
+            'Y': np.array([0, 1.0, 0]),
+            '+Y': np.array([0, 1.0, 0]),
+            '-Y': np.array([0, -1.0, 0]),
+            'Z': np.array([0, 0, 1.0]),
+            '+Z': np.array([0, 0, 1.0]),
+            '-Z': np.array([0, 0, -1.0]),
+        }
+
+        val = self.get_screen_xy()
+        if val is None:
+            return None
+        axis_x, axis_y  = val
+
+        # Interpret using both X/Y_SCREEN
+        return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
+
+
     def get_analog_transform_parameters(self):
         ''' Parse analog data transform parameters. '''
         # Offsets
diff --git a/c3d/parameter.py b/c3d/parameter.py
index 9e2e0f1..f0031a5 100644
--- a/c3d/parameter.py
+++ b/c3d/parameter.py
@@ -176,7 +176,7 @@ def dtypes(self):
 
     @property
     def dimensions(self) -> (int, ...):
-        ''' Shape of the parameter data (Fortran shape). '''
+        ''' Shape of the parameter data (Fortran format). '''
         return self._data.dimensions
 
     @property
@@ -201,63 +201,86 @@ def binary_size(self) -> int:
 
     @property
     def int8_value(self):
-        '''Get the param as an 8-bit signed integer.'''
+        '''Get the parameter data as an 8-bit signed integer.'''
         return self._data._as(self.dtypes.int8)
 
     @property
     def uint8_value(self):
-        '''Get the param as an 8-bit unsigned integer.'''
+        '''Get the parameter data as an 8-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint8)
 
     @property
     def int16_value(self):
-        '''Get the param as a 16-bit signed integer.'''
+        '''Get the parameter data as a 16-bit signed integer.'''
         return self._data._as(self.dtypes.int16)
 
     @property
     def uint16_value(self):
-        '''Get the param as a 16-bit unsigned integer.'''
+        '''Get the parameter data as a 16-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint16)
 
     @property
     def int32_value(self):
-        '''Get the param as a 32-bit signed integer.'''
+        '''Get the parameter data as a 32-bit signed integer.'''
         return self._data._as(self.dtypes.int32)
 
     @property
     def uint32_value(self):
-        '''Get the param as a 32-bit unsigned integer.'''
+        '''Get the parameter data as a 32-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint32)
 
+    @property
+    def any_value(self):
+        ''' Get the parameter data as a value of 'traditional type'.
+
+        Traditional types are defined in the Parameter section in the [user manual].
+
+        Returns
+        -------
+        value : int, float, or str
+            Depending on the `bytes_per_element` field, a traditional type can
+            be a either a signed byte, signed short, 32-bit float, or a string.
+
+        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+        '''
+        if self.bytes_per_element >= 4:
+            return self.float_value
+        elif self.bytes_per_element >= 2:
+            return self.int16_value
+        elif self.bytes_per_element == -1:
+            return self.string_value
+        else:
+            return self.int8_value
+
     @property
     def uint_value(self):
-        ''' Get the param as a unsigned integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a unsigned integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
 
     @property
     def int_value(self):
-        ''' Get the param as a signed integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a signed integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.int32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.int16_value
         else:
             return self.int8_value
 
     @property
     def float_value(self):
-        '''Get the param as a floating point value of appropriate type.'''
-        if self.total_bytes > 4:
+        '''Get the parameter data as a floating point value of appropriate type.'''
+        if self.bytes_per_element > 4:
             if self.dtypes.is_dec:
                 raise AttributeError("64 bit DEC floating point is not supported.")
             # 64-bit floating point is not a standard
             return self._data._as(self.dtypes.float64)
-        elif self.total_bytes == 4:
+        elif self.bytes_per_element == 4:
             if self.dtypes.is_dec:
                 return DEC_to_IEEE(self._data._as(np.uint32))
             else:  # is_mips or is_ieee
@@ -266,58 +289,58 @@ def float_value(self):
             raise AttributeError("Only 32 and 64 bit floating point is supported.")
 
     @property
-    def bytes_value(self):
-        '''Get the param as a raw byte string.'''
+    def bytes_value(self) -> bytes:
+        '''Get the raw byte string.'''
         return self._data.bytes
 
     @property
     def string_value(self):
-        '''Get the param as a unicode string.'''
+        '''Get the parameter data as a unicode string.'''
         return self.dtypes.decode_string(self._data.bytes)
 
     @property
     def int8_array(self):
-        '''Get the param as an array of 8-bit signed integers.'''
+        '''Get the parameter data as an array of 8-bit signed integers.'''
         return self._data._as_array(self.dtypes.int8)
 
     @property
     def uint8_array(self):
-        '''Get the param as an array of 8-bit unsigned integers.'''
+        '''Get the parameter data as an array of 8-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint8)
 
     @property
     def int16_array(self):
-        '''Get the param as an array of 16-bit signed integers.'''
+        '''Get the parameter data as an array of 16-bit signed integers.'''
         return self._data._as_array(self.dtypes.int16)
 
     @property
     def uint16_array(self):
-        '''Get the param as an array of 16-bit unsigned integers.'''
+        '''Get the parameter data as an array of 16-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint16)
 
     @property
     def int32_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int32)
 
     @property
     def uint32_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint32)
 
     @property
     def int64_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int64)
 
     @property
     def uint64_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint64)
 
     @property
     def float32_array(self):
-        '''Get the param as an array of 32-bit floats.'''
+        '''Get the parameter data as an array of 32-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             # _as_array but for DEC
@@ -329,7 +352,7 @@ def float32_array(self):
 
     @property
     def float64_array(self):
-        '''Get the param as an array of 64-bit floats.'''
+        '''Get the parameter data as an array of 64-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
@@ -338,7 +361,7 @@ def float64_array(self):
 
     @property
     def float_array(self):
-        '''Get the param as an array of 32 or 64 bit floats.'''
+        '''Get the parameter data as an array of 32 or 64 bit floats.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 4:
             return self.float32_array
@@ -350,7 +373,7 @@ def float_array(self):
 
     @property
     def int_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.int8_array
@@ -366,7 +389,7 @@ def int_array(self):
 
     @property
     def uint_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.uint8_array
@@ -382,7 +405,7 @@ def uint_array(self):
 
     @property
     def bytes_array(self):
-        '''Get the param as an array of raw byte strings.'''
+        '''Get the parameter data as an array of raw byte strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -403,7 +426,7 @@ def bytes_array(self):
 
     @property
     def string_array(self):
-        '''Get the param as a python array of unicode strings.'''
+        '''Get the parameter data as a python array of unicode strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -418,17 +441,17 @@ def string_array(self):
             return byte_arr
 
     @property
-    def _as_integer_or_float_value(self):
-        ''' Get the param as either 32 bit float or unsigned integer.
-            Evaluates if an integer is stored as a floating point representation.
+    def _as_any_uint(self):
+        ''' Attempt to parse the parameter data as any unsigned integer format.
+            Checks if the integer is stored as a floating point value.
         '''
-        if self.total_bytes >= 4:
+        if self.bytes_per_element >= 4:
             # Check if float value representation is an integer
             value = self.float_value
-            if int(value) == value:
-                return value
+            if float(value).is_integer():
+                return int(value)
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
diff --git a/docs/c3d/dtypes.html b/docs/c3d/dtypes.html
index c9473d4..a7953c6 100644
--- a/docs/c3d/dtypes.html
+++ b/docs/c3d/dtypes.html
@@ -12,6 +12,7 @@
 
 
 
+
 
 
 
diff --git a/docs/c3d/group.html b/docs/c3d/group.html
index bce40b9..08e892e 100644
--- a/docs/c3d/group.html
+++ b/docs/c3d/group.html
@@ -12,6 +12,7 @@
 
 
 
+
 
 
 
diff --git a/docs/c3d/header.html b/docs/c3d/header.html
index 95ee820..df07378 100644
--- a/docs/c3d/header.html
+++ b/docs/c3d/header.html
@@ -12,6 +12,7 @@
 
 
 
+
 
 
 
diff --git a/docs/c3d/index.html b/docs/c3d/index.html
index 380d143..c737ba7 100644
--- a/docs/c3d/index.html
+++ b/docs/c3d/index.html
@@ -13,6 +13,7 @@
 
 
 
+
 
 
 
diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html
index bd64c3b..ed487ff 100644
--- a/docs/c3d/manager.html
+++ b/docs/c3d/manager.html
@@ -12,6 +12,7 @@
 
 
 
+
 
 
 
@@ -399,13 +400,15 @@ 
    Module c3d.manager
    
         # Return the largest of the all (queue bad reading...)
         return int(np.max(end_frame))
 
-    def get_screen_axis(self):
-        ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+    def get_screen_xy(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
+
+        See `Manager.get_screen_axis` to get numpy vectors instead.
 
         Returns
         -------
         value : (str, str) or None
-            Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+            Touple containing X_SCREEN and Y_SCREEN strings, or None (if no parameters could be found).
         '''
         X = self.get('POINT:X_SCREEN')
         Y = self.get('POINT:Y_SCREEN')
@@ -413,6 +416,47 @@ 
    Module c3d.manager
    
             return (X.string_value, Y.string_value)
         return None
 
+    def get_screen_axis(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
+
+        Z axis can be computed using the cross product:
+
+        \[ z = x \\times y \]
+
+        To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
+
+        \[ p = | x^T y^T z^T |^T p_s  \]
+
+
+        See `Manager.get_screen_xy` to get the parameter as string values instead.
+
+        Returns
+        -------
+        value : ([3,], [3,]) or None
+            Touple $(x, y)$ containing X_SCREEN and Y_SCREEN as row vectors, or None.
+        '''
+        # Axis conversion dictionary.
+        AXIS_DICT = {
+            'X': np.array([1.0, 0, 0]),
+            '+X': np.array([1.0, 0, 0]),
+            '-X': np.array([-1.0, 0, 0]),
+            'Y': np.array([0, 1.0, 0]),
+            '+Y': np.array([0, 1.0, 0]),
+            '-Y': np.array([0, -1.0, 0]),
+            'Z': np.array([0, 0, 1.0]),
+            '+Z': np.array([0, 0, 1.0]),
+            '-Z': np.array([0, 0, -1.0]),
+        }
+
+        val = self.get_screen_xy()
+        if val is None:
+            return None
+        axis_x, axis_y  = val
+
+        # Interpret using both X/Y_SCREEN
+        return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
+
+
     def get_analog_transform_parameters(self):
         ''' Parse analog data transform parameters. '''
         # Offsets
@@ -870,13 +914,15 @@ 
    Attributes
    
         # Return the largest of the all (queue bad reading...)
         return int(np.max(end_frame))
 
-    def get_screen_axis(self):
-        ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+    def get_screen_xy(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
+
+        See `Manager.get_screen_axis` to get numpy vectors instead.
 
         Returns
         -------
         value : (str, str) or None
-            Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+            Touple containing X_SCREEN and Y_SCREEN strings, or None (if no parameters could be found).
         '''
         X = self.get('POINT:X_SCREEN')
         Y = self.get('POINT:Y_SCREEN')
@@ -884,6 +930,47 @@ 
    Attributes
    
             return (X.string_value, Y.string_value)
         return None
 
+    def get_screen_axis(self):
+        ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
+
+        Z axis can be computed using the cross product:
+
+        \[ z = x \\times y \]
+
+        To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
+
+        \[ p = | x^T y^T z^T |^T p_s  \]
+
+
+        See `Manager.get_screen_xy` to get the parameter as string values instead.
+
+        Returns
+        -------
+        value : ([3,], [3,]) or None
+            Touple $(x, y)$ containing X_SCREEN and Y_SCREEN as row vectors, or None.
+        '''
+        # Axis conversion dictionary.
+        AXIS_DICT = {
+            'X': np.array([1.0, 0, 0]),
+            '+X': np.array([1.0, 0, 0]),
+            '-X': np.array([-1.0, 0, 0]),
+            'Y': np.array([0, 1.0, 0]),
+            '+Y': np.array([0, 1.0, 0]),
+            '-Y': np.array([0, -1.0, 0]),
+            'Z': np.array([0, 0, 1.0]),
+            '+Z': np.array([0, 0, 1.0]),
+            '-Z': np.array([0, 0, -1.0]),
+        }
+
+        val = self.get_screen_xy()
+        if val is None:
+            return None
+        axis_x, axis_y  = val
+
+        # Interpret using both X/Y_SCREEN
+        return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
+
+
     def get_analog_transform_parameters(self):
         ''' Parse analog data transform parameters. '''
         # Offsets
@@ -1366,23 +1453,88 @@ 
    Returns
    
 def get_screen_axis(self)
     
 
    
-
    Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
    
+
    Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
    
+
    Z axis can be computed using the cross product:
    
+
     z = x \times y 
    
+
    To move a point coordinate $p_s$ as read from Reader.read_frames() out of the system basis do:
    
+
     p = | x^T y^T z^T |^T p_s
+
    
+
    See Manager.get_screen_xy() to get the parameter as string values instead.
    
 
    Returns
    
 
    
-
    value : (str, str) or None
    
-
    Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
    
+
    value : ([3,], [3,]) or None
    
+
    Touple $(x, y)$ containing X_SCREEN and Y_SCREEN as row vectors, or None.
    
 
    
 
    
 
 Expand source code
 
 
    def get_screen_axis(self):
-    ''' Get the X_SCREEN and Y_SCREEN parameters in the POINT group.
+    ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
+
+    Z axis can be computed using the cross product:
+
+    \[ z = x \\times y \]
+
+    To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
+
+    \[ p = | x^T y^T z^T |^T p_s  \]
+
+
+    See `Manager.get_screen_xy` to get the parameter as string values instead.
+
+    Returns
+    -------
+    value : ([3,], [3,]) or None
+        Touple $(x, y)$ containing X_SCREEN and Y_SCREEN as row vectors, or None.
+    '''
+    # Axis conversion dictionary.
+    AXIS_DICT = {
+        'X': np.array([1.0, 0, 0]),
+        '+X': np.array([1.0, 0, 0]),
+        '-X': np.array([-1.0, 0, 0]),
+        'Y': np.array([0, 1.0, 0]),
+        '+Y': np.array([0, 1.0, 0]),
+        '-Y': np.array([0, -1.0, 0]),
+        'Z': np.array([0, 0, 1.0]),
+        '+Z': np.array([0, 0, 1.0]),
+        '-Z': np.array([0, 0, -1.0]),
+    }
+
+    val = self.get_screen_xy()
+    if val is None:
+        return None
+    axis_x, axis_y  = val
+
+    # Interpret using both X/Y_SCREEN
+    return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
    
+
    
+
    
+
    
+def get_screen_xy(self)
+
    
+
    
+
    Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
    
+
    See Manager.get_screen_axis() to get numpy vectors instead.
    
+
    Returns
    
+
    
+
    value : (str, str) or None
    
+
    Touple containing X_SCREEN and Y_SCREEN strings, or None (if no parameters could be found).
    
+
    
+
    
+
+Expand source code
+
+
    def get_screen_xy(self):
+    ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
+
+    See `Manager.get_screen_axis` to get numpy vectors instead.
 
     Returns
     -------
     value : (str, str) or None
-        Touple containing X_SCREEN and Y_SCREEN strings, or None if no parameters could be found.
+        Touple containing X_SCREEN and Y_SCREEN strings, or None (if no parameters could be found).
     '''
     X = self.get('POINT:X_SCREEN')
     Y = self.get('POINT:Y_SCREEN')
@@ -1559,6 +1711,7 @@ 
    Manager
 
  • get_int32
    • 
 
  • get_int8
    • 
 
  • get_screen_axis
    • 
+
  • get_screen_xy
    • 
 
  • get_string
    • 
 
  • get_uint16
    • 
 
  • get_uint32
    • 
diff --git a/docs/c3d/parameter.html b/docs/c3d/parameter.html
index 8a28333..c86b866 100644
--- a/docs/c3d/parameter.html
+++ b/docs/c3d/parameter.html
@@ -12,6 +12,7 @@
 
 
 
+
 
 
 
@@ -205,7 +206,7 @@ 
    Module c3d.parameter
    
 
     @property
     def dimensions(self) -> (int, ...):
-        ''' Shape of the parameter data (Fortran shape). '''
+        ''' Shape of the parameter data (Fortran format). '''
         return self._data.dimensions
 
     @property
@@ -230,63 +231,86 @@ 
    Module c3d.parameter
    
 
     @property
     def int8_value(self):
-        '''Get the param as an 8-bit signed integer.'''
+        '''Get the parameter data as an 8-bit signed integer.'''
         return self._data._as(self.dtypes.int8)
 
     @property
     def uint8_value(self):
-        '''Get the param as an 8-bit unsigned integer.'''
+        '''Get the parameter data as an 8-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint8)
 
     @property
     def int16_value(self):
-        '''Get the param as a 16-bit signed integer.'''
+        '''Get the parameter data as a 16-bit signed integer.'''
         return self._data._as(self.dtypes.int16)
 
     @property
     def uint16_value(self):
-        '''Get the param as a 16-bit unsigned integer.'''
+        '''Get the parameter data as a 16-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint16)
 
     @property
     def int32_value(self):
-        '''Get the param as a 32-bit signed integer.'''
+        '''Get the parameter data as a 32-bit signed integer.'''
         return self._data._as(self.dtypes.int32)
 
     @property
     def uint32_value(self):
-        '''Get the param as a 32-bit unsigned integer.'''
+        '''Get the parameter data as a 32-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint32)
 
+    @property
+    def any_value(self):
+        ''' Get the parameter data as a value of 'traditional type'.
+
+        Traditional types are defined in the Parameter section in the [user manual].
+
+        Returns
+        -------
+        value : int, float, or str
+            Depending on the `bytes_per_element` field, a traditional type can
+            be a either a signed byte, signed short, 32-bit float, or a string.
+
+        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+        '''
+        if self.bytes_per_element >= 4:
+            return self.float_value
+        elif self.bytes_per_element >= 2:
+            return self.int16_value
+        elif self.bytes_per_element == -1:
+            return self.string_value
+        else:
+            return self.int8_value
+
     @property
     def uint_value(self):
-        ''' Get the param as a unsigned integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a unsigned integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
 
     @property
     def int_value(self):
-        ''' Get the param as a signed integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a signed integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.int32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.int16_value
         else:
             return self.int8_value
 
     @property
     def float_value(self):
-        '''Get the param as a floating point value of appropriate type.'''
-        if self.total_bytes > 4:
+        '''Get the parameter data as a floating point value of appropriate type.'''
+        if self.bytes_per_element > 4:
             if self.dtypes.is_dec:
                 raise AttributeError("64 bit DEC floating point is not supported.")
             # 64-bit floating point is not a standard
             return self._data._as(self.dtypes.float64)
-        elif self.total_bytes == 4:
+        elif self.bytes_per_element == 4:
             if self.dtypes.is_dec:
                 return DEC_to_IEEE(self._data._as(np.uint32))
             else:  # is_mips or is_ieee
@@ -295,58 +319,58 @@ 
    Module c3d.parameter
    
             raise AttributeError("Only 32 and 64 bit floating point is supported.")
 
     @property
-    def bytes_value(self):
-        '''Get the param as a raw byte string.'''
+    def bytes_value(self) -> bytes:
+        '''Get the raw byte string.'''
         return self._data.bytes
 
     @property
     def string_value(self):
-        '''Get the param as a unicode string.'''
+        '''Get the parameter data as a unicode string.'''
         return self.dtypes.decode_string(self._data.bytes)
 
     @property
     def int8_array(self):
-        '''Get the param as an array of 8-bit signed integers.'''
+        '''Get the parameter data as an array of 8-bit signed integers.'''
         return self._data._as_array(self.dtypes.int8)
 
     @property
     def uint8_array(self):
-        '''Get the param as an array of 8-bit unsigned integers.'''
+        '''Get the parameter data as an array of 8-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint8)
 
     @property
     def int16_array(self):
-        '''Get the param as an array of 16-bit signed integers.'''
+        '''Get the parameter data as an array of 16-bit signed integers.'''
         return self._data._as_array(self.dtypes.int16)
 
     @property
     def uint16_array(self):
-        '''Get the param as an array of 16-bit unsigned integers.'''
+        '''Get the parameter data as an array of 16-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint16)
 
     @property
     def int32_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int32)
 
     @property
     def uint32_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint32)
 
     @property
     def int64_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int64)
 
     @property
     def uint64_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint64)
 
     @property
     def float32_array(self):
-        '''Get the param as an array of 32-bit floats.'''
+        '''Get the parameter data as an array of 32-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             # _as_array but for DEC
@@ -358,7 +382,7 @@ 
    Module c3d.parameter
    
 
     @property
     def float64_array(self):
-        '''Get the param as an array of 64-bit floats.'''
+        '''Get the parameter data as an array of 64-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
@@ -367,7 +391,7 @@ 
    Module c3d.parameter
    
 
     @property
     def float_array(self):
-        '''Get the param as an array of 32 or 64 bit floats.'''
+        '''Get the parameter data as an array of 32 or 64 bit floats.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 4:
             return self.float32_array
@@ -379,7 +403,7 @@ 
    Module c3d.parameter
    
 
     @property
     def int_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.int8_array
@@ -395,7 +419,7 @@ 
    Module c3d.parameter
    
 
     @property
     def uint_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.uint8_array
@@ -411,7 +435,7 @@ 
    Module c3d.parameter
    
 
     @property
     def bytes_array(self):
-        '''Get the param as an array of raw byte strings.'''
+        '''Get the parameter data as an array of raw byte strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -432,7 +456,7 @@ 
    Module c3d.parameter
    
 
     @property
     def string_array(self):
-        '''Get the param as a python array of unicode strings.'''
+        '''Get the parameter data as a python array of unicode strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -447,17 +471,17 @@ 
    Module c3d.parameter
    
             return byte_arr
 
     @property
-    def _as_integer_or_float_value(self):
-        ''' Get the param as either 32 bit float or unsigned integer.
-            Evaluates if an integer is stored as a floating point representation.
+    def _as_any_uint(self):
+        ''' Attempt to parse the parameter data as any unsigned integer format.
+            Checks if the integer is stored as a floating point value.
         '''
-        if self.total_bytes >= 4:
+        if self.bytes_per_element >= 4:
             # Check if float value representation is an integer
             value = self.float_value
-            if int(value) == value:
-                return value
+            if float(value).is_integer():
+                return int(value)
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
@@ -562,6 +586,7 @@ 
    Inherited members
    
 
      
 
    • ParamReadonly:
 
        
+
      • any_value
        • 
 
      • binary_size
        • 
 
      • bytes_array
        • 
 
      • bytes_per_element
        • 
@@ -936,7 +961,7 @@ 
        Parameters
        
 
     @property
     def dimensions(self) -> (int, ...):
-        ''' Shape of the parameter data (Fortran shape). '''
+        ''' Shape of the parameter data (Fortran format). '''
         return self._data.dimensions
 
     @property
@@ -961,63 +986,86 @@ 
        Parameters
        
 
     @property
     def int8_value(self):
-        '''Get the param as an 8-bit signed integer.'''
+        '''Get the parameter data as an 8-bit signed integer.'''
         return self._data._as(self.dtypes.int8)
 
     @property
     def uint8_value(self):
-        '''Get the param as an 8-bit unsigned integer.'''
+        '''Get the parameter data as an 8-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint8)
 
     @property
     def int16_value(self):
-        '''Get the param as a 16-bit signed integer.'''
+        '''Get the parameter data as a 16-bit signed integer.'''
         return self._data._as(self.dtypes.int16)
 
     @property
     def uint16_value(self):
-        '''Get the param as a 16-bit unsigned integer.'''
+        '''Get the parameter data as a 16-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint16)
 
     @property
     def int32_value(self):
-        '''Get the param as a 32-bit signed integer.'''
+        '''Get the parameter data as a 32-bit signed integer.'''
         return self._data._as(self.dtypes.int32)
 
     @property
     def uint32_value(self):
-        '''Get the param as a 32-bit unsigned integer.'''
+        '''Get the parameter data as a 32-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint32)
 
+    @property
+    def any_value(self):
+        ''' Get the parameter data as a value of 'traditional type'.
+
+        Traditional types are defined in the Parameter section in the [user manual].
+
+        Returns
+        -------
+        value : int, float, or str
+            Depending on the `bytes_per_element` field, a traditional type can
+            be a either a signed byte, signed short, 32-bit float, or a string.
+
+        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+        '''
+        if self.bytes_per_element >= 4:
+            return self.float_value
+        elif self.bytes_per_element >= 2:
+            return self.int16_value
+        elif self.bytes_per_element == -1:
+            return self.string_value
+        else:
+            return self.int8_value
+
     @property
     def uint_value(self):
-        ''' Get the param as a unsigned integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a unsigned integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
 
     @property
     def int_value(self):
-        ''' Get the param as a signed integer of appropriate type. '''
-        if self.total_bytes >= 4:
+        ''' Get the parameter data as a signed integer of appropriate type. '''
+        if self.bytes_per_element >= 4:
             return self.int32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.int16_value
         else:
             return self.int8_value
 
     @property
     def float_value(self):
-        '''Get the param as a floating point value of appropriate type.'''
-        if self.total_bytes > 4:
+        '''Get the parameter data as a floating point value of appropriate type.'''
+        if self.bytes_per_element > 4:
             if self.dtypes.is_dec:
                 raise AttributeError("64 bit DEC floating point is not supported.")
             # 64-bit floating point is not a standard
             return self._data._as(self.dtypes.float64)
-        elif self.total_bytes == 4:
+        elif self.bytes_per_element == 4:
             if self.dtypes.is_dec:
                 return DEC_to_IEEE(self._data._as(np.uint32))
             else:  # is_mips or is_ieee
@@ -1026,58 +1074,58 @@ 
        Parameters
        
             raise AttributeError("Only 32 and 64 bit floating point is supported.")
 
     @property
-    def bytes_value(self):
-        '''Get the param as a raw byte string.'''
+    def bytes_value(self) -> bytes:
+        '''Get the raw byte string.'''
         return self._data.bytes
 
     @property
     def string_value(self):
-        '''Get the param as a unicode string.'''
+        '''Get the parameter data as a unicode string.'''
         return self.dtypes.decode_string(self._data.bytes)
 
     @property
     def int8_array(self):
-        '''Get the param as an array of 8-bit signed integers.'''
+        '''Get the parameter data as an array of 8-bit signed integers.'''
         return self._data._as_array(self.dtypes.int8)
 
     @property
     def uint8_array(self):
-        '''Get the param as an array of 8-bit unsigned integers.'''
+        '''Get the parameter data as an array of 8-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint8)
 
     @property
     def int16_array(self):
-        '''Get the param as an array of 16-bit signed integers.'''
+        '''Get the parameter data as an array of 16-bit signed integers.'''
         return self._data._as_array(self.dtypes.int16)
 
     @property
     def uint16_array(self):
-        '''Get the param as an array of 16-bit unsigned integers.'''
+        '''Get the parameter data as an array of 16-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint16)
 
     @property
     def int32_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int32)
 
     @property
     def uint32_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint32)
 
     @property
     def int64_array(self):
-        '''Get the param as an array of 32-bit signed integers.'''
+        '''Get the parameter data as an array of 32-bit signed integers.'''
         return self._data._as_array(self.dtypes.int64)
 
     @property
     def uint64_array(self):
-        '''Get the param as an array of 32-bit unsigned integers.'''
+        '''Get the parameter data as an array of 32-bit unsigned integers.'''
         return self._data._as_array(self.dtypes.uint64)
 
     @property
     def float32_array(self):
-        '''Get the param as an array of 32-bit floats.'''
+        '''Get the parameter data as an array of 32-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             # _as_array but for DEC
@@ -1089,7 +1137,7 @@ 
        Parameters
        
 
     @property
     def float64_array(self):
-        '''Get the param as an array of 64-bit floats.'''
+        '''Get the parameter data as an array of 64-bit floats.'''
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
@@ -1098,7 +1146,7 @@ 
        Parameters
        
 
     @property
     def float_array(self):
-        '''Get the param as an array of 32 or 64 bit floats.'''
+        '''Get the parameter data as an array of 32 or 64 bit floats.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 4:
             return self.float32_array
@@ -1110,7 +1158,7 @@ 
        Parameters
        
 
     @property
     def int_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.int8_array
@@ -1126,7 +1174,7 @@ 
        Parameters
        
 
     @property
     def uint_array(self):
-        '''Get the param as an array of integer values.'''
+        '''Get the parameter data as an array of integer values.'''
         # Convert float data if not IEEE processor
         if self.bytes_per_element == 1:
             return self.uint8_array
@@ -1142,7 +1190,7 @@ 
        Parameters
        
 
     @property
     def bytes_array(self):
-        '''Get the param as an array of raw byte strings.'''
+        '''Get the parameter data as an array of raw byte strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -1163,7 +1211,7 @@ 
        Parameters
        
 
     @property
     def string_array(self):
-        '''Get the param as a python array of unicode strings.'''
+        '''Get the parameter data as a python array of unicode strings.'''
         # Decode different dimensions
         if len(self.dimensions) == 0:
             return np.array([])
@@ -1178,17 +1226,17 @@ 
        Parameters
        
             return byte_arr
 
     @property
-    def _as_integer_or_float_value(self):
-        ''' Get the param as either 32 bit float or unsigned integer.
-            Evaluates if an integer is stored as a floating point representation.
+    def _as_any_uint(self):
+        ''' Attempt to parse the parameter data as any unsigned integer format.
+            Checks if the integer is stored as a floating point value.
         '''
-        if self.total_bytes >= 4:
+        if self.bytes_per_element >= 4:
             # Check if float value representation is an integer
             value = self.float_value
-            if int(value) == value:
-                return value
+            if float(value).is_integer():
+                return int(value)
             return self.uint32_value
-        elif self.total_bytes >= 2:
+        elif self.bytes_per_element >= 2:
             return self.uint16_value
         else:
             return self.uint8_value
    
@@ -1199,6 +1247,44 @@ 
    Subclasses
    
 
 
    Instance variables
    
 
    
+
    var any_value
    
+
    
+
    Get the parameter data as a value of 'traditional type'.
    
+
    Traditional types are defined in the Parameter section in the user manual.
    
+
    Returns
    
+
    
+
    value : int, float, or str
    
+
    Depending on the bytes_per_element field, a traditional type can
+be a either a signed byte, signed short, 32-bit float, or a string.
    
+
    
+
    
+
+Expand source code
+
+
    @property
+def any_value(self):
+    ''' Get the parameter data as a value of 'traditional type'.
+
+    Traditional types are defined in the Parameter section in the [user manual].
+
+    Returns
+    -------
+    value : int, float, or str
+        Depending on the `bytes_per_element` field, a traditional type can
+        be a either a signed byte, signed short, 32-bit float, or a string.
+
+    [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+    '''
+    if self.bytes_per_element >= 4:
+        return self.float_value
+    elif self.bytes_per_element >= 2:
+        return self.int16_value
+    elif self.bytes_per_element == -1:
+        return self.string_value
+    else:
+        return self.int8_value
    
+
    
+
    
 
    var binary_size : int
    
 
    
 
    Return the number of bytes needed to store this parameter.
    
@@ -1214,14 +1300,14 @@ 
    Instance variables
    
 
    
 
    var bytes_array
    
 
    
-
    Get the param as an array of raw byte strings.
    
+
    Get the parameter data as an array of raw byte strings.
    
 
    
 
 Expand source code
 
 
    @property
 def bytes_array(self):
-    '''Get the param as an array of raw byte strings.'''
+    '''Get the parameter data as an array of raw byte strings.'''
     # Decode different dimensions
     if len(self.dimensions) == 0:
         return np.array([])
@@ -1254,16 +1340,16 @@ 
    Instance variables
    
     return self._data.bytes_per_element
    
 
    
 
    
-
    var bytes_value
    
+
    var bytes_value : bytes
    
 
    
-
    Get the param as a raw byte string.
    
+
    Get the raw byte string.
    
 
    
 
 Expand source code
 
 
    @property
-def bytes_value(self):
-    '''Get the param as a raw byte string.'''
+def bytes_value(self) -> bytes:
+    '''Get the raw byte string.'''
     return self._data.bytes
    
 
    
 
    
@@ -1282,14 +1368,14 @@ 
    Instance variables
    
 
    
 
    var dimensions : (, Ellipsis)
    
 
    
-
    Shape of the parameter data (Fortran shape).
    
+
    Shape of the parameter data (Fortran format).
    
 
    
 
 Expand source code
 
 
    @property
 def dimensions(self) -> (int, ...):
-    ''' Shape of the parameter data (Fortran shape). '''
+    ''' Shape of the parameter data (Fortran format). '''
     return self._data.dimensions
    
 
    
 
    
@@ -1308,14 +1394,14 @@ 
    Instance variables
    var float32_array
    -

    Get the param as an array of 32-bit floats.

    +

    Get the parameter data as an array of 32-bit floats.

    Expand source code 
    @property
 def float32_array(self):
-    '''Get the param as an array of 32-bit floats.'''
+    '''Get the parameter data as an array of 32-bit floats.'''
     # Convert float data if not IEEE processor
     if self.dtypes.is_dec:
         # _as_array but for DEC
@@ -1328,14 +1414,14 @@ 
    Instance variables
    var float64_array
    -

    Get the param as an array of 64-bit floats.

    +

    Get the parameter data as an array of 64-bit floats.

    Expand source code 
    @property
 def float64_array(self):
-    '''Get the param as an array of 64-bit floats.'''
+    '''Get the parameter data as an array of 64-bit floats.'''
     # Convert float data if not IEEE processor
     if self.dtypes.is_dec:
         raise ValueError('Unable to convert bytes encoded in a 64 bit floating point DEC format.')
@@ -1345,14 +1431,14 @@ 
    Instance variables
    var float_array
    -

    Get the param as an array of 32 or 64 bit floats.

    +

    Get the parameter data as an array of 32 or 64 bit floats.

    Expand source code 
    @property
 def float_array(self):
-    '''Get the param as an array of 32 or 64 bit floats.'''
+    '''Get the parameter data as an array of 32 or 64 bit floats.'''
     # Convert float data if not IEEE processor
     if self.bytes_per_element == 4:
         return self.float32_array
@@ -1365,20 +1451,20 @@ 
    Instance variables
    var float_value
    -

    Get the param as a floating point value of appropriate type.

    +

    Get the parameter data as a floating point value of appropriate type.

    Expand source code 
    @property
 def float_value(self):
-    '''Get the param as a floating point value of appropriate type.'''
-    if self.total_bytes > 4:
+    '''Get the parameter data as a floating point value of appropriate type.'''
+    if self.bytes_per_element > 4:
         if self.dtypes.is_dec:
             raise AttributeError("64 bit DEC floating point is not supported.")
         # 64-bit floating point is not a standard
         return self._data._as(self.dtypes.float64)
-    elif self.total_bytes == 4:
+    elif self.bytes_per_element == 4:
         if self.dtypes.is_dec:
             return DEC_to_IEEE(self._data._as(np.uint32))
         else:  # is_mips or is_ieee
@@ -1389,105 +1475,105 @@ 
    Instance variables
    var int16_array
    -

    Get the param as an array of 16-bit signed integers.

    +

    Get the parameter data as an array of 16-bit signed integers.

    Expand source code 
    @property
 def int16_array(self):
-    '''Get the param as an array of 16-bit signed integers.'''
+    '''Get the parameter data as an array of 16-bit signed integers.'''
     return self._data._as_array(self.dtypes.int16)
    var int16_value
    -

    Get the param as a 16-bit signed integer.

    +

    Get the parameter data as a 16-bit signed integer.

    Expand source code 
    @property
 def int16_value(self):
-    '''Get the param as a 16-bit signed integer.'''
+    '''Get the parameter data as a 16-bit signed integer.'''
     return self._data._as(self.dtypes.int16)
    var int32_array
    -

    Get the param as an array of 32-bit signed integers.

    +

    Get the parameter data as an array of 32-bit signed integers.

    Expand source code 
    @property
 def int32_array(self):
-    '''Get the param as an array of 32-bit signed integers.'''
+    '''Get the parameter data as an array of 32-bit signed integers.'''
     return self._data._as_array(self.dtypes.int32)
    var int32_value
    -

    Get the param as a 32-bit signed integer.

    +

    Get the parameter data as a 32-bit signed integer.

    Expand source code 
    @property
 def int32_value(self):
-    '''Get the param as a 32-bit signed integer.'''
+    '''Get the parameter data as a 32-bit signed integer.'''
     return self._data._as(self.dtypes.int32)
    var int64_array
    -

    Get the param as an array of 32-bit signed integers.

    +

    Get the parameter data as an array of 32-bit signed integers.

    Expand source code 
    @property
 def int64_array(self):
-    '''Get the param as an array of 32-bit signed integers.'''
+    '''Get the parameter data as an array of 32-bit signed integers.'''
     return self._data._as_array(self.dtypes.int64)
    var int8_array
    -

    Get the param as an array of 8-bit signed integers.

    +

    Get the parameter data as an array of 8-bit signed integers.

    Expand source code 
    @property
 def int8_array(self):
-    '''Get the param as an array of 8-bit signed integers.'''
+    '''Get the parameter data as an array of 8-bit signed integers.'''
     return self._data._as_array(self.dtypes.int8)
    var int8_value
    -

    Get the param as an 8-bit signed integer.

    +

    Get the parameter data as an 8-bit signed integer.

    Expand source code 
    @property
 def int8_value(self):
-    '''Get the param as an 8-bit signed integer.'''
+    '''Get the parameter data as an 8-bit signed integer.'''
     return self._data._as(self.dtypes.int8)
    var int_array
    -

    Get the param as an array of integer values.

    +

    Get the parameter data as an array of integer values.

    Expand source code 
    @property
 def int_array(self):
-    '''Get the param as an array of integer values.'''
+    '''Get the parameter data as an array of integer values.'''
     # Convert float data if not IEEE processor
     if self.bytes_per_element == 1:
         return self.int8_array
@@ -1504,17 +1590,17 @@ 
    Instance variables
    var int_value
    -

    Get the param as a signed integer of appropriate type.

    +

    Get the parameter data as a signed integer of appropriate type.

    Expand source code 
    @property
 def int_value(self):
-    ''' Get the param as a signed integer of appropriate type. '''
-    if self.total_bytes >= 4:
+    ''' Get the parameter data as a signed integer of appropriate type. '''
+    if self.bytes_per_element >= 4:
         return self.int32_value
-    elif self.total_bytes >= 2:
+    elif self.bytes_per_element >= 2:
         return self.int16_value
     else:
         return self.int8_value
    @@ -1548,14 +1634,14 @@

    Instance variables

    var string_array
    -

    Get the param as a python array of unicode strings.

    +

    Get the parameter data as a python array of unicode strings.

    Expand source code 
    @property
 def string_array(self):
-    '''Get the param as a python array of unicode strings.'''
+    '''Get the parameter data as a python array of unicode strings.'''
     # Decode different dimensions
     if len(self.dimensions) == 0:
         return np.array([])
@@ -1572,14 +1658,14 @@ 
    Instance variables
    var string_value
    -

    Get the param as a unicode string.

    +

    Get the parameter data as a unicode string.

    Expand source code 
    @property
 def string_value(self):
-    '''Get the param as a unicode string.'''
+    '''Get the parameter data as a unicode string.'''
     return self.dtypes.decode_string(self._data.bytes)
    @@ -1598,105 +1684,105 @@

    Instance variables

    var uint16_array
    -

    Get the param as an array of 16-bit unsigned integers.

    +

    Get the parameter data as an array of 16-bit unsigned integers.

    Expand source code 
    @property
 def uint16_array(self):
-    '''Get the param as an array of 16-bit unsigned integers.'''
+    '''Get the parameter data as an array of 16-bit unsigned integers.'''
     return self._data._as_array(self.dtypes.uint16)
    var uint16_value
    -

    Get the param as a 16-bit unsigned integer.

    +

    Get the parameter data as a 16-bit unsigned integer.

    Expand source code 
    @property
 def uint16_value(self):
-    '''Get the param as a 16-bit unsigned integer.'''
+    '''Get the parameter data as a 16-bit unsigned integer.'''
     return self._data._as(self.dtypes.uint16)
    var uint32_array
    -

    Get the param as an array of 32-bit unsigned integers.

    +

    Get the parameter data as an array of 32-bit unsigned integers.

    Expand source code 
    @property
 def uint32_array(self):
-    '''Get the param as an array of 32-bit unsigned integers.'''
+    '''Get the parameter data as an array of 32-bit unsigned integers.'''
     return self._data._as_array(self.dtypes.uint32)
    var uint32_value
    -

    Get the param as a 32-bit unsigned integer.

    +

    Get the parameter data as a 32-bit unsigned integer.

    Expand source code 
    @property
 def uint32_value(self):
-    '''Get the param as a 32-bit unsigned integer.'''
+    '''Get the parameter data as a 32-bit unsigned integer.'''
     return self._data._as(self.dtypes.uint32)
    var uint64_array
    -

    Get the param as an array of 32-bit unsigned integers.

    +

    Get the parameter data as an array of 32-bit unsigned integers.

    Expand source code 
    @property
 def uint64_array(self):
-    '''Get the param as an array of 32-bit unsigned integers.'''
+    '''Get the parameter data as an array of 32-bit unsigned integers.'''
     return self._data._as_array(self.dtypes.uint64)
    var uint8_array
    -

    Get the param as an array of 8-bit unsigned integers.

    +

    Get the parameter data as an array of 8-bit unsigned integers.

    Expand source code 
    @property
 def uint8_array(self):
-    '''Get the param as an array of 8-bit unsigned integers.'''
+    '''Get the parameter data as an array of 8-bit unsigned integers.'''
     return self._data._as_array(self.dtypes.uint8)
    var uint8_value
    -

    Get the param as an 8-bit unsigned integer.

    +

    Get the parameter data as an 8-bit unsigned integer.

    Expand source code 
    @property
 def uint8_value(self):
-    '''Get the param as an 8-bit unsigned integer.'''
+    '''Get the parameter data as an 8-bit unsigned integer.'''
     return self._data._as(self.dtypes.uint8)
    var uint_array
    -

    Get the param as an array of integer values.

    +

    Get the parameter data as an array of integer values.

    Expand source code 
    @property
 def uint_array(self):
-    '''Get the param as an array of integer values.'''
+    '''Get the parameter data as an array of integer values.'''
     # Convert float data if not IEEE processor
     if self.bytes_per_element == 1:
         return self.uint8_array
@@ -1713,17 +1799,17 @@ 
    Instance variables
    var uint_value
    -

    Get the param as a unsigned integer of appropriate type.

    +

    Get the parameter data as a unsigned integer of appropriate type.

    Expand source code 
    @property
 def uint_value(self):
-    ''' Get the param as a unsigned integer of appropriate type. '''
-    if self.total_bytes >= 4:
+    ''' Get the parameter data as a unsigned integer of appropriate type. '''
+    if self.bytes_per_element >= 4:
         return self.uint32_value
-    elif self.total_bytes >= 2:
+    elif self.bytes_per_element >= 2:
         return self.uint16_value
     else:
         return self.uint8_value
    @@ -1767,6 +1853,7 @@

    Par

  • ParamReadonly

      +
    • any_value
    • binary_size
    • bytes_array
    • bytes_per_element
      • diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html index de72e63..d676f0c 100644 --- a/docs/c3d/reader.html +++ b/docs/c3d/reader.html @@ -12,6 +12,7 @@ + @@ -1113,6 +1114,7 @@

      Inherited members

    • get_int32
    • get_int8
    • get_screen_axis
      • +
    • get_screen_xy
    • get_string
    • get_uint16
    • get_uint32
      • diff --git a/docs/c3d/utils.html b/docs/c3d/utils.html index dff3183..a79fbe9 100644 --- a/docs/c3d/utils.html +++ b/docs/c3d/utils.html @@ -12,6 +12,7 @@ + diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html index 9a5dc36..96a5aff 100644 --- a/docs/c3d/writer.html +++ b/docs/c3d/writer.html @@ -12,6 +12,7 @@ + @@ -1740,6 +1741,7 @@

      Inherited members

    • get_int32
    • get_int8
    • get_screen_axis
      • +
    • get_screen_xy
    • get_string
    • get_uint16
    • get_uint32
      • diff --git a/test/test_c3d.py b/test/test_c3d.py index da5a6a4..90c2e8d 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -124,7 +124,7 @@ def test_set_params(self): X, Y = '-Y', '+Z' w.set_screen_axis() w.set_screen_axis(X, Y) - X_v, Y_v = w.get_screen_axis() + X_v, Y_v = w.get_screen_xy_strings() assert X_v == X and Y == Y_v, 'Mismatch between set & get screen axis.' assert np.all(np.equal(r.point_labels, w.point_labels)), 'Expected labels to be equal.' From 4ddaa30a6162cf03f016baf38f7aa41cff93ac9e Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 5 Jul 2021 18:19:20 +0200 Subject: [PATCH 104/120] Returns array of single element if dimensions is empty. ParamReadonly.any_value() ParamReadonly.any_array() --- c3d/group.py | 4 +- c3d/manager.py | 2 +- c3d/parameter.py | 98 ++++++++++++++++++++++++++---------------------- c3d/writer.py | 8 ++-- 4 files changed, 60 insertions(+), 52 deletions(-) diff --git a/c3d/group.py b/c3d/group.py index 853e9ec..0390493 100644 --- a/c3d/group.py +++ b/c3d/group.py @@ -407,7 +407,7 @@ def add_str(self, name, desc, data, *dimensions): bytes=data.encode('utf-8'), dimensions=shape or [len(data)]) - def add_empty_array(self, name, desc='', bpe=1): + def add_empty_array(self, name, desc=''): ''' Add an empty parameter block. Parameters @@ -416,7 +416,7 @@ def add_empty_array(self, name, desc='', bpe=1): Parameter name. ''' self.add_param(name, desc=desc, - bytes_per_element=bpe, dimensions=[0]) + bytes_per_element=0, dimensions=[0]) # # Convenience functions for adding or overwriting parameters. diff --git a/c3d/manager.py b/c3d/manager.py index 9b196f9..b6c4759 100644 --- a/c3d/manager.py +++ b/c3d/manager.py @@ -420,7 +420,7 @@ def get_screen_xy_axis(self): '-Z': np.array([0, 0, -1.0]), } - val = self.get_screen_xy() + val = self.get_screen_xy_strings() if val is None: return None axis_x, axis_y = val diff --git a/c3d/parameter.py b/c3d/parameter.py index f0031a5..4aef7db 100644 --- a/c3d/parameter.py +++ b/c3d/parameter.py @@ -121,8 +121,8 @@ def _as(self, dtype): def _as_array(self, dtype, copy=True): '''Unpack the raw bytes of this param using the given data format.''' - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, dtype) + if not self.dimensions: + return [self._as(dtype)] elems = np.frombuffer(self.bytes, dtype=dtype) # Reverse shape as the shape is defined in fortran format view = elems.reshape(self.dimensions[::-1]) @@ -130,24 +130,6 @@ def _as_array(self, dtype, copy=True): return view.copy() return view - def _as_any(self, dtype): - '''Unpack the raw bytes of this param as either array or single value.''' - if 0 in self.dimensions[:]: # Check if any dimension is 0 (empty buffer) - return [] # Buffer is empty - - if len(self.dimensions) == 0: # Parse data as a single value - if dtype == np.float32: # Floats need to be parsed separately! - return self.float_value - return self._data._as(dtype) - else: # Parse data as array - if dtype == np.float32: - data = self.float_array - else: - data = self._data._as_array(dtype) - if len(self.dimensions) < 2: # Check if data is contained in a single dimension - return data.flatten() - return data - class ParamReadonly(object): ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry. @@ -229,29 +211,6 @@ def uint32_value(self): '''Get the parameter data as a 32-bit unsigned integer.''' return self._data._as(self.dtypes.uint32) - @property - def any_value(self): - ''' Get the parameter data as a value of 'traditional type'. - - Traditional types are defined in the Parameter section in the [user manual]. - - Returns - ------- - value : int, float, or str - Depending on the `bytes_per_element` field, a traditional type can - be a either a signed byte, signed short, 32-bit float, or a string. - - [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf - ''' - if self.bytes_per_element >= 4: - return self.float_value - elif self.bytes_per_element >= 2: - return self.int16_value - elif self.bytes_per_element == -1: - return self.string_value - else: - return self.int8_value - @property def uint_value(self): ''' Get the parameter data as a unsigned integer of appropriate type. ''' @@ -344,8 +303,8 @@ def float32_array(self): # Convert float data if not IEEE processor if self.dtypes.is_dec: # _as_array but for DEC - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32) + if not self.dimensions: + return [self.float_value] return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format else: # is_ieee or is_mips return self._data._as_array(self.dtypes.float32) @@ -440,10 +399,59 @@ def string_array(self): byte_arr[i] = self.dtypes.decode_string(byte_arr[i]) return byte_arr + @property + def any_value(self): + ''' Get the parameter data as a value of 'traditional type'. + + Traditional types are defined in the Parameter section in the [user manual]. + + Returns + ------- + value : int, float, or str + Depending on the `bytes_per_element` field, a traditional type can + be a either a signed byte, signed short, 32-bit float, or a string. + + [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf + ''' + if self.bytes_per_element >= 4: + return self.float_value + elif self.bytes_per_element >= 2: + return self.int16_value + elif self.bytes_per_element == -1: + return self.string_value + else: + return self.int8_value + + @property + def any_array(self): + ''' Get the parameter data as an array of 'traditional type'. + + Traditional types are defined in the Parameter section in the [user manual]. + + Returns + ------- + value : array + Depending on the `bytes_per_element` field, a traditional type can + be a either a signed byte, signed short, 32-bit float, or a string. + + [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf + ''' + if self.bytes_per_element >= 4: + return self.float_array + elif self.bytes_per_element >= 2: + return self.int16_array + elif self.bytes_per_element == -1: + return self.string_array + else: + return self.int8_array + @property def _as_any_uint(self): ''' Attempt to parse the parameter data as any unsigned integer format. Checks if the integer is stored as a floating point value. + + Can be used to read 'POINT:FRAMES' or 'POINT:LONG_FRAMES' + when not accessed through `c3d.manager.Manager.last_frame`. ''' if self.bytes_per_element >= 4: # Check if float value representation is an integer diff --git a/c3d/writer.py b/c3d/writer.py index 6b6edf5..896a95e 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -264,7 +264,7 @@ def set_point_labels(self, labels): ''' grp = self.point_group if labels is None: - grp.add_empty_array('LABELS', 'Point labels.', -1) + grp.add_empty_array('LABELS', 'Point labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) @@ -279,7 +279,7 @@ def set_analog_labels(self, labels): ''' grp = self.analog_group if labels is None: - grp.add_empty_array('LABELS', 'Analog labels.', -1) + grp.add_empty_array('LABELS', 'Analog labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) @@ -301,7 +301,7 @@ def set_analog_scales(self, values): data = np.array([v for v in values], dtype=np.float32) self.analog_group.set_array('SCALE', 'Analog channel scale factors', data) elif values is None: - self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4) + self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors') else: raise ValueError('Expected iterable containing analog scale factors.') @@ -317,7 +317,7 @@ def set_analog_offsets(self, values): data = np.array([v for v in values], dtype=np.int16) self.analog_group.set_array('OFFSET', 'Analog channel offsets', data) elif values is None: - self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2) + self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets') else: raise ValueError('Expected iterable containing analog data offsets.') From fb5ed86957e56950f782d12365f4f1cea3f337f1 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 5 Jul 2021 18:19:47 +0200 Subject: [PATCH 105/120] &= -> |= !!!!!!!!!!!!!! --- c3d/reader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/c3d/reader.py b/c3d/reader.py index 0668673..da5fff4 100644 --- a/c3d/reader.py +++ b/c3d/reader.py @@ -241,7 +241,7 @@ def read_frames(self, copy=True, analog_transform=True, check_nan=True, camera_s if check_nan: is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) points[is_nan, :3] = 0.0 - invalid &= is_nan + invalid |= is_nan # Update discarded - sign points[invalid, 3] = -1 From 51a5f79bff5b39e1f8cadb8232cc2f6e110a157e Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 5 Jul 2021 20:22:17 +0200 Subject: [PATCH 106/120] License doc --- c3d/LICENSE | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 c3d/LICENSE diff --git a/c3d/LICENSE b/c3d/LICENSE new file mode 100644 index 0000000..b263f7c --- /dev/null +++ b/c3d/LICENSE @@ -0,0 +1,22 @@ +The MIT License (MIT) + +Copyright (c) 2013-2015 UT Vision, Cognition, and Action Lab + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + From fd74ca7c597ceccf00df949771e063822d0735d3 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 5 Jul 2021 20:47:27 +0200 Subject: [PATCH 107/120] pycodestyles, updated docs --- c3d/manager.py | 11 +- docs/README.rst | 2 +- docs/c3d/group.html | 14 +-- docs/c3d/index.html | 2 +- docs/c3d/manager.html | 138 ++++++++++++----------- docs/c3d/parameter.html | 242 +++++++++++++++++++++++++--------------- docs/c3d/reader.html | 10 +- docs/c3d/writer.html | 28 ++--- test/README.rst | 2 + 9 files changed, 255 insertions(+), 194 deletions(-) diff --git a/c3d/manager.py b/c3d/manager.py index b6c4759..97df4cf 100644 --- a/c3d/manager.py +++ b/c3d/manager.py @@ -352,8 +352,8 @@ def last_frame(self) -> int: param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) - #words = param.uint16_array - #end_frame[1] = words[0] + words[1] * 65536 + # words = param.uint16_array + # end_frame[1] = words[0] + words[1] * 65536 end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: @@ -393,11 +393,11 @@ def get_screen_xy_axis(self): Z axis can be computed using the cross product: - \[ z = x \\times y \] + $$ z = x \\times y $$ To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do: - \[ p = | x^T y^T z^T |^T p_s \] + $$ p = | x^T y^T z^T |^T p_s $$ See `Manager.get_screen_xy_strings` to get the parameter as string values instead. @@ -423,12 +423,11 @@ def get_screen_xy_axis(self): val = self.get_screen_xy_strings() if val is None: return None - axis_x, axis_y = val + axis_x, axis_y = val # Interpret using both X/Y_SCREEN return AXIS_DICT[axis_x], AXIS_DICT[axis_y] - def get_analog_transform_parameters(self): ''' Parse analog data transform parameters. ''' # Offsets diff --git a/docs/README.rst b/docs/README.rst index f484e1e..d6acdf7 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -13,7 +13,7 @@ Building the docs requires the pdoc3 package:: Once installed, documentation can be updated from the root directory with the command:: - pdoc --html c3d --force --config show_source_code=True --output-dir docs + pdoc --html c3d --force --config show_source_code=True --output-dir docs -c latex_math=True Once updated you can access the documentation in the `docs/c3d/`_ folder. diff --git a/docs/c3d/group.html b/docs/c3d/group.html index 08e892e..95d99b0 100644 --- a/docs/c3d/group.html +++ b/docs/c3d/group.html @@ -437,7 +437,7 @@

      Module c3d.group

      bytes=data.encode('utf-8'), dimensions=shape or [len(data)]) - def add_empty_array(self, name, desc='', bpe=1): + def add_empty_array(self, name, desc=''): ''' Add an empty parameter block. Parameters @@ -446,7 +446,7 @@

      Module c3d.group

      Parameter name. ''' self.add_param(name, desc=desc, - bytes_per_element=bpe, dimensions=[0]) + bytes_per_element=0, dimensions=[0]) # # Convenience functions for adding or overwriting parameters. @@ -682,7 +682,7 @@

      Classes

      bytes=data.encode('utf-8'), dimensions=shape or [len(data)]) - def add_empty_array(self, name, desc='', bpe=1): + def add_empty_array(self, name, desc=''): ''' Add an empty parameter block. Parameters @@ -691,7 +691,7 @@

      Classes

      Parameter name. ''' self.add_param(name, desc=desc, - bytes_per_element=bpe, dimensions=[0]) + bytes_per_element=0, dimensions=[0]) # # Convenience functions for adding or overwriting parameters. @@ -886,7 +886,7 @@

      Parameters

    • -def add_empty_array(self, name, desc='', bpe=1) +def add_empty_array(self, name, desc='')

    Add an empty parameter block.

    @@ -899,7 +899,7 @@

    Parameters

    Expand source code -
    def add_empty_array(self, name, desc='', bpe=1):
+
    def add_empty_array(self, name, desc=''):
     ''' Add an empty parameter block.
 
     Parameters
@@ -908,7 +908,7 @@ 
    Parameters
    
         Parameter name.
     '''
     self.add_param(name, desc=desc,
-                   bytes_per_element=bpe, dimensions=[0])
    
+                   bytes_per_element=0, dimensions=[0])
    diff --git a/docs/c3d/index.html b/docs/c3d/index.html index c737ba7..69cd6bf 100644 --- a/docs/c3d/index.html +++ b/docs/c3d/index.html @@ -176,7 +176,7 @@

    Sub-modules

    c3d.manager
    -

    Manager base class defining common attributes for both the Reader and Writer instances.

    +

    Manager base class defining common attributes for both Reader and Writer instances.

    c3d.parameter
    diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html index ed487ff..f4e33c9 100644 --- a/docs/c3d/manager.html +++ b/docs/c3d/manager.html @@ -5,7 +5,7 @@ c3d.manager API documentation - + @@ -23,12 +23,12 @@

    Module c3d.manager

    -

    Manager base class defining common attributes for both the Reader and Writer instances.

    +

    Manager base class defining common attributes for both Reader and Writer instances.

    Expand source code -
    ''' Manager base class defining common attributes for both the Reader and Writer instances.
+
    ''' Manager base class defining common attributes for both Reader and Writer instances.
 '''
 import numpy as np
 import warnings
@@ -367,8 +367,7 @@ 
    Module c3d.manager
    
         param = self.get('TRIAL:ACTUAL_START_FIELD')
         if param is not None:
             # ACTUAL_START_FIELD is encoded in two 16 byte words...
-            words = param.uint16_array
-            return words[0] + words[1] * 65535
+            return param.uint32_value
         return self.header.first_frame
 
     @property
@@ -383,27 +382,30 @@ 
    Module c3d.manager
    
         param = self.get('TRIAL:ACTUAL_END_FIELD')
         if param is not None:
             # Encoded as 2 16 bit words (rather then 1 32 bit word)
-            words = param.uint16_array
-            end_frame[1] = words[0] + words[1] * 65536
-            # end_frame[1] = param.uint32_value
+            # words = param.uint16_array
+            # end_frame[1] = words[0] + words[1] * 65536
+            end_frame[1] = param.uint32_value
         param = self.get('POINT:LONG_FRAMES')
         if param is not None:
-            # Encoded as float
-            end_frame[2] = int(param.float_value)
+            # 'Should be' encoded as float
+            if param.bytes_per_element >= 4:
+                end_frame[2] = int(param.float_value)
+            else:
+                end_frame[2] = param.uint16_value
         param = self.get('POINT:FRAMES')
         if param is not None:
             # Can be encoded either as 32 bit float or 16 bit uint
-            if param.bytes_per_element == 2:
-                end_frame[3] = param.uint16_value
-            else:
+            if param.bytes_per_element == 4:
                 end_frame[3] = int(param.float_value)
+            else:
+                end_frame[3] = param.uint16_value
         # Return the largest of the all (queue bad reading...)
         return int(np.max(end_frame))
 
-    def get_screen_xy(self):
+    def get_screen_xy_strings(self):
         ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
 
-        See `Manager.get_screen_axis` to get numpy vectors instead.
+        See `Manager.get_screen_xy_axis` to get numpy vectors instead.
 
         Returns
         -------
@@ -416,19 +418,19 @@ 
    Module c3d.manager
    
             return (X.string_value, Y.string_value)
         return None
 
-    def get_screen_axis(self):
+    def get_screen_xy_axis(self):
         ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
 
         Z axis can be computed using the cross product:
 
-        \[ z = x \\times y \]
+        $$ z = x \\times y $$
 
         To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
 
-        \[ p = | x^T y^T z^T |^T p_s  \]
+        $$ p = | x^T y^T z^T |^T p_s  $$
 
 
-        See `Manager.get_screen_xy` to get the parameter as string values instead.
+        See `Manager.get_screen_xy_strings` to get the parameter as string values instead.
 
         Returns
         -------
@@ -448,15 +450,14 @@ 
    Module c3d.manager
    
             '-Z': np.array([0, 0, -1.0]),
         }
 
-        val = self.get_screen_xy()
+        val = self.get_screen_xy_strings()
         if val is None:
             return None
-        axis_x, axis_y  = val
+        axis_x, axis_y = val
 
         # Interpret using both X/Y_SCREEN
         return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
 
-
     def get_analog_transform_parameters(self):
         ''' Parse analog data transform parameters. '''
         # Offsets
@@ -881,8 +882,7 @@ 
    Attributes
    
         param = self.get('TRIAL:ACTUAL_START_FIELD')
         if param is not None:
             # ACTUAL_START_FIELD is encoded in two 16 byte words...
-            words = param.uint16_array
-            return words[0] + words[1] * 65535
+            return param.uint32_value
         return self.header.first_frame
 
     @property
@@ -897,27 +897,30 @@ 
    Attributes
    
         param = self.get('TRIAL:ACTUAL_END_FIELD')
         if param is not None:
             # Encoded as 2 16 bit words (rather then 1 32 bit word)
-            words = param.uint16_array
-            end_frame[1] = words[0] + words[1] * 65536
-            # end_frame[1] = param.uint32_value
+            # words = param.uint16_array
+            # end_frame[1] = words[0] + words[1] * 65536
+            end_frame[1] = param.uint32_value
         param = self.get('POINT:LONG_FRAMES')
         if param is not None:
-            # Encoded as float
-            end_frame[2] = int(param.float_value)
+            # 'Should be' encoded as float
+            if param.bytes_per_element >= 4:
+                end_frame[2] = int(param.float_value)
+            else:
+                end_frame[2] = param.uint16_value
         param = self.get('POINT:FRAMES')
         if param is not None:
             # Can be encoded either as 32 bit float or 16 bit uint
-            if param.bytes_per_element == 2:
-                end_frame[3] = param.uint16_value
-            else:
+            if param.bytes_per_element == 4:
                 end_frame[3] = int(param.float_value)
+            else:
+                end_frame[3] = param.uint16_value
         # Return the largest of the all (queue bad reading...)
         return int(np.max(end_frame))
 
-    def get_screen_xy(self):
+    def get_screen_xy_strings(self):
         ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
 
-        See `Manager.get_screen_axis` to get numpy vectors instead.
+        See `Manager.get_screen_xy_axis` to get numpy vectors instead.
 
         Returns
         -------
@@ -930,19 +933,19 @@ 
    Attributes
    
             return (X.string_value, Y.string_value)
         return None
 
-    def get_screen_axis(self):
+    def get_screen_xy_axis(self):
         ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
 
         Z axis can be computed using the cross product:
 
-        \[ z = x \\times y \]
+        $$ z = x \\times y $$
 
         To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
 
-        \[ p = | x^T y^T z^T |^T p_s  \]
+        $$ p = | x^T y^T z^T |^T p_s  $$
 
 
-        See `Manager.get_screen_xy` to get the parameter as string values instead.
+        See `Manager.get_screen_xy_strings` to get the parameter as string values instead.
 
         Returns
         -------
@@ -962,15 +965,14 @@ 
    Attributes
    
             '-Z': np.array([0, 0, -1.0]),
         }
 
-        val = self.get_screen_xy()
+        val = self.get_screen_xy_strings()
         if val is None:
             return None
-        axis_x, axis_y  = val
+        axis_x, axis_y = val
 
         # Interpret using both X/Y_SCREEN
         return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
 
-
     def get_analog_transform_parameters(self):
         ''' Parse analog data transform parameters. '''
         # Offsets
@@ -1133,8 +1135,7 @@ 
    Instance variables
    
     param = self.get('TRIAL:ACTUAL_START_FIELD')
     if param is not None:
         # ACTUAL_START_FIELD is encoded in two 16 byte words...
-        words = param.uint16_array
-        return words[0] + words[1] * 65535
+        return param.uint32_value
     return self.header.first_frame
    @@ -1183,20 +1184,23 @@

    Instance variables

    param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) - words = param.uint16_array - end_frame[1] = words[0] + words[1] * 65536 - # end_frame[1] = param.uint32_value + # words = param.uint16_array + # end_frame[1] = words[0] + words[1] * 65536 + end_frame[1] = param.uint32_value param = self.get('POINT:LONG_FRAMES') if param is not None: - # Encoded as float - end_frame[2] = int(param.float_value) + # 'Should be' encoded as float + if param.bytes_per_element >= 4: + end_frame[2] = int(param.float_value) + else: + end_frame[2] = param.uint16_value param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint - if param.bytes_per_element == 2: - end_frame[3] = param.uint16_value - else: + if param.bytes_per_element == 4: end_frame[3] = int(param.float_value) + else: + end_frame[3] = param.uint16_value # Return the largest of the all (queue bad reading...) return int(np.max(end_frame))     @@ -1449,8 +1453,8 @@

    Returns

    return self.get(key).int8_value     -
    -def get_screen_axis(self) +
    +def get_screen_xy_axis(self)

    Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.

    @@ -1460,7 +1464,7 @@

    Returns

    p = | x^T y^T z^T |^T p_s

    -

    See Manager.get_screen_xy() to get the parameter as string values instead.

    +

    See Manager.get_screen_xy_strings() to get the parameter as string values instead.

    Returns

    value : ([3,], [3,]) or None
    @@ -1470,19 +1474,19 @@

    Returns

    Expand source code -
    def get_screen_axis(self):
+
    def get_screen_xy_axis(self):
     ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as unit row vectors.
 
     Z axis can be computed using the cross product:
 
-    \[ z = x \\times y \]
+    $$ z = x \\times y $$
 
     To move a point coordinate $p_s$ as read from `c3d.reader.Reader.read_frames` out of the system basis do:
 
-    \[ p = | x^T y^T z^T |^T p_s  \]
+    $$ p = | x^T y^T z^T |^T p_s  $$
 
 
-    See `Manager.get_screen_xy` to get the parameter as string values instead.
+    See `Manager.get_screen_xy_strings` to get the parameter as string values instead.
 
     Returns
     -------
@@ -1502,21 +1506,21 @@ 
    Returns
    
         '-Z': np.array([0, 0, -1.0]),
     }
 
-    val = self.get_screen_xy()
+    val = self.get_screen_xy_strings()
     if val is None:
         return None
-    axis_x, axis_y  = val
+    axis_x, axis_y = val
 
     # Interpret using both X/Y_SCREEN
     return AXIS_DICT[axis_x], AXIS_DICT[axis_y]
    -
    -def get_screen_xy(self) +
    +def get_screen_xy_strings(self)

    Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.

    -

    See Manager.get_screen_axis() to get numpy vectors instead.

    +

    See Manager.get_screen_xy_axis() to get numpy vectors instead.

    Returns

    value : (str, str) or None
    @@ -1526,10 +1530,10 @@

    Returns

    Expand source code -
    def get_screen_xy(self):
+
    def get_screen_xy_strings(self):
     ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings.
 
-    See `Manager.get_screen_axis` to get numpy vectors instead.
+    See `Manager.get_screen_xy_axis` to get numpy vectors instead.
 
     Returns
     -------
@@ -1710,8 +1714,8 @@ 
    Manager
 
  • get_int16
    • 
 
  • get_int32
    • 
 
  • get_int8
    • 
-
  • get_screen_axis
    • 
-
  • get_screen_xy
    • 
+
  • get_screen_xy_axis
    • 
+
  • get_screen_xy_strings
    • 
 
  • get_string
    • 
 
  • get_uint16
    • 
 
  • get_uint32
    • 
diff --git a/docs/c3d/parameter.html b/docs/c3d/parameter.html
index c86b866..4a3c1be 100644
--- a/docs/c3d/parameter.html
+++ b/docs/c3d/parameter.html
@@ -151,8 +151,8 @@ 
    Module c3d.parameter
    
 
     def _as_array(self, dtype, copy=True):
         '''Unpack the raw bytes of this param using the given data format.'''
-        assert self.dimensions, \
-            '{}: cannot get value as {} array!'.format(self.name, dtype)
+        if not self.dimensions:
+            return [self._as(dtype)]
         elems = np.frombuffer(self.bytes, dtype=dtype)
         # Reverse shape as the shape is defined in fortran format
         view = elems.reshape(self.dimensions[::-1])
@@ -160,24 +160,6 @@ 
    Module c3d.parameter
    
             return view.copy()
         return view
 
-    def _as_any(self, dtype):
-        '''Unpack the raw bytes of this param as either array or single value.'''
-        if 0 in self.dimensions[:]:             # Check if any dimension is 0 (empty buffer)
-            return []                                           # Buffer is empty
-
-        if len(self.dimensions) == 0:           # Parse data as a single value
-            if dtype == np.float32:                     # Floats need to be parsed separately!
-                return self.float_value
-            return self._data._as(dtype)
-        else:                                                           # Parse data as array
-            if dtype == np.float32:
-                data = self.float_array
-            else:
-                data = self._data._as_array(dtype)
-            if len(self.dimensions) < 2:    # Check if data is contained in a single dimension
-                return data.flatten()
-            return data
-
 
 class ParamReadonly(object):
     ''' Wrapper exposing readonly attributes of a `c3d.parameter.ParamData` entry.
@@ -259,29 +241,6 @@ 
    Module c3d.parameter
    
         '''Get the parameter data as a 32-bit unsigned integer.'''
         return self._data._as(self.dtypes.uint32)
 
-    @property
-    def any_value(self):
-        ''' Get the parameter data as a value of 'traditional type'.
-
-        Traditional types are defined in the Parameter section in the [user manual].
-
-        Returns
-        -------
-        value : int, float, or str
-            Depending on the `bytes_per_element` field, a traditional type can
-            be a either a signed byte, signed short, 32-bit float, or a string.
-
-        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
-        '''
-        if self.bytes_per_element >= 4:
-            return self.float_value
-        elif self.bytes_per_element >= 2:
-            return self.int16_value
-        elif self.bytes_per_element == -1:
-            return self.string_value
-        else:
-            return self.int8_value
-
     @property
     def uint_value(self):
         ''' Get the parameter data as a unsigned integer of appropriate type. '''
@@ -374,8 +333,8 @@ 
    Module c3d.parameter
    
         # Convert float data if not IEEE processor
         if self.dtypes.is_dec:
             # _as_array but for DEC
-            assert self.dimensions, \
-                '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32)
+            if not self.dimensions:
+                return [self.float_value]
             return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1])  # Reverse fortran format
         else:  # is_ieee or is_mips
             return self._data._as_array(self.dtypes.float32)
@@ -470,10 +429,59 @@ 
    Module c3d.parameter
    
                 byte_arr[i] = self.dtypes.decode_string(byte_arr[i])
             return byte_arr
 
+    @property
+    def any_value(self):
+        ''' Get the parameter data as a value of 'traditional type'.
+
+        Traditional types are defined in the Parameter section in the [user manual].
+
+        Returns
+        -------
+        value : int, float, or str
+            Depending on the `bytes_per_element` field, a traditional type can
+            be a either a signed byte, signed short, 32-bit float, or a string.
+
+        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+        '''
+        if self.bytes_per_element >= 4:
+            return self.float_value
+        elif self.bytes_per_element >= 2:
+            return self.int16_value
+        elif self.bytes_per_element == -1:
+            return self.string_value
+        else:
+            return self.int8_value
+
+    @property
+    def any_array(self):
+        ''' Get the parameter data as an array of 'traditional type'.
+
+        Traditional types are defined in the Parameter section in the [user manual].
+
+        Returns
+        -------
+        value : array
+            Depending on the `bytes_per_element` field, a traditional type can
+            be a either a signed byte, signed short, 32-bit float, or a string.
+
+        [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+        '''
+        if self.bytes_per_element >= 4:
+            return self.float_array
+        elif self.bytes_per_element >= 2:
+            return self.int16_array
+        elif self.bytes_per_element == -1:
+            return self.string_array
+        else:
+            return self.int8_array
+
     @property
     def _as_any_uint(self):
         ''' Attempt to parse the parameter data as any unsigned integer format.
             Checks if the integer is stored as a floating point value.
+
+            Can be used to read 'POINT:FRAMES' or 'POINT:LONG_FRAMES'
+            when not accessed through `c3d.manager.Manager.last_frame`.
         '''
         if self.bytes_per_element >= 4:
             # Check if float value representation is an integer
@@ -586,6 +594,7 @@ 
    Inherited members
    
 
      
 
    • ParamReadonly:
 
        
+
      • any_array
        • 
 
      • any_value
        • 
 
      • binary_size
        • 
 
      • bytes_array
        • 
@@ -771,32 +780,14 @@ 
        Attributes
        
 
     def _as_array(self, dtype, copy=True):
         '''Unpack the raw bytes of this param using the given data format.'''
-        assert self.dimensions, \
-            '{}: cannot get value as {} array!'.format(self.name, dtype)
+        if not self.dimensions:
+            return [self._as(dtype)]
         elems = np.frombuffer(self.bytes, dtype=dtype)
         # Reverse shape as the shape is defined in fortran format
         view = elems.reshape(self.dimensions[::-1])
         if copy:
             return view.copy()
-        return view
-
-    def _as_any(self, dtype):
-        '''Unpack the raw bytes of this param as either array or single value.'''
-        if 0 in self.dimensions[:]:             # Check if any dimension is 0 (empty buffer)
-            return []                                           # Buffer is empty
-
-        if len(self.dimensions) == 0:           # Parse data as a single value
-            if dtype == np.float32:                     # Floats need to be parsed separately!
-                return self.float_value
-            return self._data._as(dtype)
-        else:                                                           # Parse data as array
-            if dtype == np.float32:
-                data = self.float_array
-            else:
-                data = self._data._as_array(dtype)
-            if len(self.dimensions) < 2:    # Check if data is contained in a single dimension
-                return data.flatten()
-            return data
    
+        return view

    Instance variables

    @@ -1014,29 +1005,6 @@

    Parameters

    '''Get the parameter data as a 32-bit unsigned integer.''' return self._data._as(self.dtypes.uint32) - @property - def any_value(self): - ''' Get the parameter data as a value of 'traditional type'. - - Traditional types are defined in the Parameter section in the [user manual]. - - Returns - ------- - value : int, float, or str - Depending on the `bytes_per_element` field, a traditional type can - be a either a signed byte, signed short, 32-bit float, or a string. - - [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf - ''' - if self.bytes_per_element >= 4: - return self.float_value - elif self.bytes_per_element >= 2: - return self.int16_value - elif self.bytes_per_element == -1: - return self.string_value - else: - return self.int8_value - @property def uint_value(self): ''' Get the parameter data as a unsigned integer of appropriate type. ''' @@ -1129,8 +1097,8 @@

    Parameters

    # Convert float data if not IEEE processor if self.dtypes.is_dec: # _as_array but for DEC - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32) + if not self.dimensions: + return [self.float_value] return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format else: # is_ieee or is_mips return self._data._as_array(self.dtypes.float32) @@ -1225,10 +1193,59 @@

    Parameters

    byte_arr[i] = self.dtypes.decode_string(byte_arr[i]) return byte_arr + @property + def any_value(self): + ''' Get the parameter data as a value of 'traditional type'. + + Traditional types are defined in the Parameter section in the [user manual]. + + Returns + ------- + value : int, float, or str + Depending on the `bytes_per_element` field, a traditional type can + be a either a signed byte, signed short, 32-bit float, or a string. + + [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf + ''' + if self.bytes_per_element >= 4: + return self.float_value + elif self.bytes_per_element >= 2: + return self.int16_value + elif self.bytes_per_element == -1: + return self.string_value + else: + return self.int8_value + + @property + def any_array(self): + ''' Get the parameter data as an array of 'traditional type'. + + Traditional types are defined in the Parameter section in the [user manual]. + + Returns + ------- + value : array + Depending on the `bytes_per_element` field, a traditional type can + be a either a signed byte, signed short, 32-bit float, or a string. + + [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf + ''' + if self.bytes_per_element >= 4: + return self.float_array + elif self.bytes_per_element >= 2: + return self.int16_array + elif self.bytes_per_element == -1: + return self.string_array + else: + return self.int8_array + @property def _as_any_uint(self): ''' Attempt to parse the parameter data as any unsigned integer format. Checks if the integer is stored as a floating point value. + + Can be used to read 'POINT:FRAMES' or 'POINT:LONG_FRAMES' + when not accessed through `c3d.manager.Manager.last_frame`. ''' if self.bytes_per_element >= 4: # Check if float value representation is an integer @@ -1247,6 +1264,44 @@

    Subclasses

    Instance variables

    +
    var any_array
    +
    +

    Get the parameter data as an array of 'traditional type'.

    +

    Traditional types are defined in the Parameter section in the user manual.

    +

    Returns

    +
    +
    value : array
    +
    Depending on the bytes_per_element field, a traditional type can +be a either a signed byte, signed short, 32-bit float, or a string.
    +
    +
    + +Expand source code + +
    @property
+def any_array(self):
+    ''' Get the parameter data as an array of 'traditional type'.
+
+    Traditional types are defined in the Parameter section in the [user manual].
+
+    Returns
+    -------
+    value : array
+        Depending on the `bytes_per_element` field, a traditional type can
+        be a either a signed byte, signed short, 32-bit float, or a string.
+
+    [user manual]: https://www.c3d.org/docs/C3D_User_Guide.pdf
+    '''
+    if self.bytes_per_element >= 4:
+        return self.float_array
+    elif self.bytes_per_element >= 2:
+        return self.int16_array
+    elif self.bytes_per_element == -1:
+        return self.string_array
+    else:
+        return self.int8_array
    +
    +
    var any_value

    Get the parameter data as a value of 'traditional type'.

    @@ -1405,8 +1460,8 @@

    Returns

    # Convert float data if not IEEE processor if self.dtypes.is_dec: # _as_array but for DEC - assert self.dimensions, \ - '{}: cannot get value as {} array!'.format(self.name, self.dtypes.float32) + if not self.dimensions: + return [self.float_value] return DEC_to_IEEE_BYTES(self._data.bytes).reshape(self.dimensions[::-1]) # Reverse fortran format else: # is_ieee or is_mips return self._data._as_array(self.dtypes.float32)     @@ -1853,6 +1908,7 @@

    Par

  • ParamReadonly

      +
    • any_array
    • any_value
    • binary_size
    • bytes_array
      • diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html index d676f0c..2e8d643 100644 --- a/docs/c3d/reader.html +++ b/docs/c3d/reader.html @@ -271,7 +271,7 @@

      Module c3d.reader

      if check_nan: is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) points[is_nan, :3] = 0.0 - invalid &= is_nan + invalid |= is_nan # Update discarded - sign points[invalid, 3] = -1 @@ -637,7 +637,7 @@

      Raises

      if check_nan: is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) points[is_nan, :3] = 0.0 - invalid &= is_nan + invalid |= is_nan # Update discarded - sign points[invalid, 3] = -1 @@ -1019,7 +1019,7 @@

      Returns

      if check_nan: is_nan = ~np.all(np.isfinite(points[:, :4]), axis=1) points[is_nan, :3] = 0.0 - invalid &= is_nan + invalid |= is_nan # Update discarded - sign points[invalid, 3] = -1 @@ -1113,8 +1113,8 @@

      Inherited members

    • get_int16
    • get_int32
    • get_int8
      • -
    • get_screen_axis
      • -
    • get_screen_xy
      • +
    • get_screen_xy_axis
      • +
    • get_screen_xy_strings
    • get_string
    • get_uint16
    • get_uint32
      • diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html index 96a5aff..7c9aae2 100644 --- a/docs/c3d/writer.html +++ b/docs/c3d/writer.html @@ -294,7 +294,7 @@

      Module c3d.writer

      ''' grp = self.point_group if labels is None: - grp.add_empty_array('LABELS', 'Point labels.', -1) + grp.add_empty_array('LABELS', 'Point labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) @@ -309,7 +309,7 @@

      Module c3d.writer

      ''' grp = self.analog_group if labels is None: - grp.add_empty_array('LABELS', 'Analog labels.', -1) + grp.add_empty_array('LABELS', 'Analog labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) @@ -331,7 +331,7 @@

      Module c3d.writer

      data = np.array([v for v in values], dtype=np.float32) self.analog_group.set_array('SCALE', 'Analog channel scale factors', data) elif values is None: - self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4) + self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors') else: raise ValueError('Expected iterable containing analog scale factors.') @@ -347,7 +347,7 @@

      Module c3d.writer

      data = np.array([v for v in values], dtype=np.int16) self.analog_group.set_array('OFFSET', 'Analog channel offsets', data) elif values is None: - self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2) + self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets') else: raise ValueError('Expected iterable containing analog data offsets.') @@ -836,7 +836,7 @@

      Parameters

      ''' grp = self.point_group if labels is None: - grp.add_empty_array('LABELS', 'Point labels.', -1) + grp.add_empty_array('LABELS', 'Point labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) @@ -851,7 +851,7 @@

      Parameters

      ''' grp = self.analog_group if labels is None: - grp.add_empty_array('LABELS', 'Analog labels.', -1) + grp.add_empty_array('LABELS', 'Analog labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels)) @@ -873,7 +873,7 @@

      Parameters

      data = np.array([v for v in values], dtype=np.float32) self.analog_group.set_array('SCALE', 'Analog channel scale factors', data) elif values is None: - self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4) + self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors') else: raise ValueError('Expected iterable containing analog scale factors.') @@ -889,7 +889,7 @@

      Parameters

      data = np.array([v for v in values], dtype=np.int16) self.analog_group.set_array('OFFSET', 'Analog channel offsets', data) elif values is None: - self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2) + self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets') else: raise ValueError('Expected iterable containing analog data offsets.') @@ -1467,7 +1467,7 @@

      Parameters

      ''' grp = self.analog_group if labels is None: - grp.add_empty_array('LABELS', 'Analog labels.', -1) + grp.add_empty_array('LABELS', 'Analog labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Analog labels.', label_str, label_max_size, len(labels))       @@ -1499,7 +1499,7 @@

      Parameters

      data = np.array([v for v in values], dtype=np.int16) self.analog_group.set_array('OFFSET', 'Analog channel offsets', data) elif values is None: - self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets', 2) + self.analog_group.set_empty_array('OFFSET', 'Analog channel offsets') else: raise ValueError('Expected iterable containing analog data offsets.') @@ -1530,7 +1530,7 @@

      Parameters

      data = np.array([v for v in values], dtype=np.float32) self.analog_group.set_array('SCALE', 'Analog channel scale factors', data) elif values is None: - self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors', 4) + self.analog_group.set_empty_array('SCALE', 'Analog channel scale factors') else: raise ValueError('Expected iterable containing analog scale factors.')       @@ -1559,7 +1559,7 @@

      Parameters

      ''' grp = self.point_group if labels is None: - grp.add_empty_array('LABELS', 'Point labels.', -1) + grp.add_empty_array('LABELS', 'Point labels.') else: label_str, label_max_size = utils.pack_labels(labels) grp.add_str('LABELS', 'Point labels.', label_str, label_max_size, len(labels)) @@ -1740,8 +1740,8 @@

      Inherited members

    • get_int16
    • get_int32
    • get_int8
      • -
    • get_screen_axis
      • -
    • get_screen_xy
      • +
    • get_screen_xy_axis
      • +
    • get_screen_xy_strings
    • get_string
    • get_uint16
    • get_uint32
      • diff --git a/test/README.rst b/test/README.rst index bf286c0..ed74c76 100644 --- a/test/README.rst +++ b/test/README.rst @@ -8,3 +8,5 @@ To run tests, use the following command from the root of the package directory:: Test scripts will automatically download test files from `c3d.org`_. .. _c3d.org: https://www.c3d.org/sampledata.html + +Currently no code style is enforced. From cb800a895b0df44697e1881abf1136d4f50ce963 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Mon, 5 Jul 2021 20:54:23 +0200 Subject: [PATCH 108/120] README --- README.rst | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/README.rst b/README.rst index cc3117c..859c9ee 100644 --- a/README.rst +++ b/README.rst @@ -49,7 +49,7 @@ To use the C3D library, just import the package and create a ``Reader`` and/or print('frame {}: point {}, analog {}'.format( i, points.shape, analog.shape)) -You can also get and set metadata fields using the library; see the `package +You can also edit metadata fields using the library; see the `package documentation`_ for more details. .. _package documentation: https://mattiasfredriksson.github.io/py-c3d/c3d/ @@ -58,17 +58,16 @@ Caveats ------- The package is tested against the `software examples`_ but may still not support -every possible format. For example, parameters serialized in multiple parameters -are not handled automatically (such as a LABELS field stored in both POINT:LABELS and -POINT:LABELS2). Reading and writing files from a big-endian system is also not supported. +every possible format. For example, parameters serialized in multiple parameters +are not handled automatically (LABELS field stored in both POINT:LABELS and +POINT:LABELS2). Reading and writing files from a big-endian system is also not supported. -Tests are currently only run on Windows, which means that Linux and Mac users may -experience some issues. If you experience issues with a file or feature, feel free -to post an issue (preferably by including example file/code/python exception) +Tests are currently only run on Windows, which means that Linux and Mac users may +experience some issues. If you experience issues with a file or feature, feel free +to post an issue (preferably by including example file/code/python exception) or make a pull request! -The package is also Python only, for other languages there are other packages such as `ezc3d`_. +The package is also Python only, for other languages there are other packages for example `ezc3d`_. .. _software examples: https://www.c3d.org/sampledata.html .. _ezc3d: https://github.com/pyomeca/ezc3d - From 509944d757e3a96c986fcf0b42e6027c1f2ca708 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Tue, 6 Jul 2021 14:56:46 +0200 Subject: [PATCH 109/120] Updated Manager.last_frame to comply better with documentation, removed convenience functions giving direct access to value attributes from `c3d.manager.Manager` --- c3d/manager.py | 68 ++++++++++++++---------------------------------- test/test_c3d.py | 8 +++--- 2 files changed, 23 insertions(+), 53 deletions(-) diff --git a/c3d/manager.py b/c3d/manager.py index 97df4cf..031063c 100644 --- a/c3d/manager.py +++ b/c3d/manager.py @@ -88,7 +88,7 @@ def _check_metadata(self): )) try: - start = self.get_uint16('POINT:DATA_START') + start = self.get('POINT:DATA_START').uint16_value if self._header.data_block != start: warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( self._header.data_block, start)) @@ -177,7 +177,7 @@ def _rename_group(self, group_id, new_group_id): Parameters ---------- - group_id : int, str, or 'Group' + group_id : int, str, or `c3d.group.Group` Group instance, name, or numerical identifier for the group. new_group_id : str, or int If string, it is the new name for the group. If integer, it will replace its numerical group id. @@ -344,33 +344,39 @@ def first_frame(self) -> int: def last_frame(self) -> int: ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values - if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: - return self.header.last_frame + #if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: + # return self.header.last_frame - # Check different parameter options where the frame can be encoded - end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] + # Try different parameters where the frame can be encoded + hlf = self.header.last_frame param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) # words = param.uint16_array # end_frame[1] = words[0] + words[1] * 65536 - end_frame[1] = param.uint32_value + end_frame = param.uint32_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:LONG_FRAMES') if param is not None: # 'Should be' encoded as float if param.bytes_per_element >= 4: - end_frame[2] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[2] = param.uint16_value + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint if param.bytes_per_element == 4: - end_frame[3] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[3] = param.uint16_value - # Return the largest of the all (queue bad reading...) - return int(np.max(end_frame)) + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame + # Return header value by default + return hlf def get_screen_xy_strings(self): ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings. @@ -456,39 +462,3 @@ def get_analog_transform(self): analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) return analog_scales, analog_offsets - - def get_int8(self, key): - '''Get a parameter value as an 8-bit signed integer.''' - return self.get(key).int8_value - - def get_uint8(self, key): - '''Get a parameter value as an 8-bit unsigned integer.''' - return self.get(key).uint8_value - - def get_int16(self, key): - '''Get a parameter value as a 16-bit signed integer.''' - return self.get(key).int16_value - - def get_uint16(self, key): - '''Get a parameter value as a 16-bit unsigned integer.''' - return self.get(key).uint16_value - - def get_int32(self, key): - '''Get a parameter value as a 32-bit signed integer.''' - return self.get(key).int32_value - - def get_uint32(self, key): - '''Get a parameter value as a 32-bit unsigned integer.''' - return self.get(key).uint32_value - - def get_float(self, key): - '''Get a parameter value as a 32-bit float.''' - return self.get(key).float_value - - def get_bytes(self, key): - '''Get a parameter value as a byte string.''' - return self.get(key).bytes_value - - def get_string(self, key): - '''Get a parameter value as a string.''' - return self.get(key).string_value diff --git a/test/test_c3d.py b/test/test_c3d.py index 90c2e8d..1152dd1 100644 --- a/test/test_c3d.py +++ b/test/test_c3d.py @@ -56,8 +56,8 @@ def test_paramsb(self): assert r.point_used == 26 assert r.point_rate == 50 assert r.analog_used == 16 - assert r.get_float('POINT:RATE') == 50 - assert r.get_float('ANALOG:RATE') == 200 + assert r.get('POINT:RATE').float_value == 50 + assert r.get('ANALOG:RATE').float_value == 200 def test_paramsc(self): r = c3d.Reader(Zipload._get('sample08.zip', 'TESTCPI.c3d')) @@ -102,7 +102,7 @@ def test_add_frames(self): h = io.BytesIO() w.set_point_labels(r.point_labels) w.set_analog_labels(r.analog_labels) - w.set_analog_general_scale(r.get_float('ANALOG:GEN_SCALE')) + w.set_analog_general_scale(r.get('ANALOG:GEN_SCALE').float_value) w.write(h) def test_set_params(self): @@ -118,7 +118,7 @@ def test_set_params(self): w.set_start_frame(255) w.set_point_labels(r.point_labels) w.set_analog_labels(r.analog_labels) - w.set_analog_general_scale(r.get_float('ANALOG:GEN_SCALE')) + w.set_analog_general_scale(r.get('ANALOG:GEN_SCALE').float_value) # Screen axis X, Y = '-Y', '+Z' From 9587aac5657b4a60f08bdcc7148cd3945a63e74e Mon Sep 17 00:00:00 2001 From: MattiasF Date: Tue, 6 Jul 2021 16:19:39 +0200 Subject: [PATCH 110/120] Updated docs --- docs/c3d/manager.html | 303 ++++++++---------------------------------- docs/c3d/reader.html | 9 -- docs/c3d/writer.html | 9 -- 3 files changed, 57 insertions(+), 264 deletions(-) diff --git a/docs/c3d/manager.html b/docs/c3d/manager.html index f4e33c9..eb17ef0 100644 --- a/docs/c3d/manager.html +++ b/docs/c3d/manager.html @@ -118,7 +118,7 @@

      Module c3d.manager

      )) try: - start = self.get_uint16('POINT:DATA_START') + start = self.get('POINT:DATA_START').uint16_value if self._header.data_block != start: warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( self._header.data_block, start)) @@ -207,7 +207,7 @@

      Module c3d.manager

      Parameters ---------- - group_id : int, str, or 'Group' + group_id : int, str, or `c3d.group.Group` Group instance, name, or numerical identifier for the group. new_group_id : str, or int If string, it is the new name for the group. If integer, it will replace its numerical group id. @@ -374,33 +374,39 @@

      Module c3d.manager

      def last_frame(self) -> int: ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values - if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: - return self.header.last_frame + #if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: + # return self.header.last_frame - # Check different parameter options where the frame can be encoded - end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] + # Try different parameters where the frame can be encoded + hlf = self.header.last_frame param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) # words = param.uint16_array # end_frame[1] = words[0] + words[1] * 65536 - end_frame[1] = param.uint32_value + end_frame = param.uint32_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:LONG_FRAMES') if param is not None: # 'Should be' encoded as float if param.bytes_per_element >= 4: - end_frame[2] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[2] = param.uint16_value + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint if param.bytes_per_element == 4: - end_frame[3] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[3] = param.uint16_value - # Return the largest of the all (queue bad reading...) - return int(np.max(end_frame)) + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame + # Return header value by default + return hlf def get_screen_xy_strings(self): ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings. @@ -485,43 +491,7 @@

      Module c3d.manager

      analog_scales *= gen_scale analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) - return analog_scales, analog_offsets - - def get_int8(self, key): - '''Get a parameter value as an 8-bit signed integer.''' - return self.get(key).int8_value - - def get_uint8(self, key): - '''Get a parameter value as an 8-bit unsigned integer.''' - return self.get(key).uint8_value - - def get_int16(self, key): - '''Get a parameter value as a 16-bit signed integer.''' - return self.get(key).int16_value - - def get_uint16(self, key): - '''Get a parameter value as a 16-bit unsigned integer.''' - return self.get(key).uint16_value - - def get_int32(self, key): - '''Get a parameter value as a 32-bit signed integer.''' - return self.get(key).int32_value - - def get_uint32(self, key): - '''Get a parameter value as a 32-bit unsigned integer.''' - return self.get(key).uint32_value - - def get_float(self, key): - '''Get a parameter value as a 32-bit float.''' - return self.get(key).float_value - - def get_bytes(self, key): - '''Get a parameter value as a byte string.''' - return self.get(key).bytes_value - - def get_string(self, key): - '''Get a parameter value as a string.''' - return self.get(key).string_value       + return analog_scales, analog_offsets

    • @@ -633,7 +603,7 @@

    Attributes

    )) try: - start = self.get_uint16('POINT:DATA_START') + start = self.get('POINT:DATA_START').uint16_value if self._header.data_block != start: warnings.warn('inconsistent data block! {} header != {} POINT:DATA_START'.format( self._header.data_block, start)) @@ -722,7 +692,7 @@

    Attributes

    Parameters ---------- - group_id : int, str, or 'Group' + group_id : int, str, or `c3d.group.Group` Group instance, name, or numerical identifier for the group. new_group_id : str, or int If string, it is the new name for the group. If integer, it will replace its numerical group id. @@ -889,33 +859,39 @@

    Attributes

    def last_frame(self) -> int: ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values - if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: - return self.header.last_frame + #if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: + # return self.header.last_frame - # Check different parameter options where the frame can be encoded - end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] + # Try different parameters where the frame can be encoded + hlf = self.header.last_frame param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) # words = param.uint16_array # end_frame[1] = words[0] + words[1] * 65536 - end_frame[1] = param.uint32_value + end_frame = param.uint32_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:LONG_FRAMES') if param is not None: # 'Should be' encoded as float if param.bytes_per_element >= 4: - end_frame[2] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[2] = param.uint16_value + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint if param.bytes_per_element == 4: - end_frame[3] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[3] = param.uint16_value - # Return the largest of the all (queue bad reading...) - return int(np.max(end_frame)) + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame + # Return header value by default + return hlf def get_screen_xy_strings(self): ''' Get the POINT:X_SCREEN and POINT:Y_SCREEN parameters as strings. @@ -1000,43 +976,7 @@

    Attributes

    analog_scales *= gen_scale analog_scales = np.broadcast_to(analog_scales[:, np.newaxis], (self.analog_used, self.analog_per_frame)) analog_offsets = np.broadcast_to(analog_offsets[:, np.newaxis], (self.analog_used, self.analog_per_frame)) - return analog_scales, analog_offsets - - def get_int8(self, key): - '''Get a parameter value as an 8-bit signed integer.''' - return self.get(key).int8_value - - def get_uint8(self, key): - '''Get a parameter value as an 8-bit unsigned integer.''' - return self.get(key).uint8_value - - def get_int16(self, key): - '''Get a parameter value as a 16-bit signed integer.''' - return self.get(key).int16_value - - def get_uint16(self, key): - '''Get a parameter value as a 16-bit unsigned integer.''' - return self.get(key).uint16_value - - def get_int32(self, key): - '''Get a parameter value as a 32-bit signed integer.''' - return self.get(key).int32_value - - def get_uint32(self, key): - '''Get a parameter value as a 32-bit unsigned integer.''' - return self.get(key).uint32_value - - def get_float(self, key): - '''Get a parameter value as a 32-bit float.''' - return self.get(key).float_value - - def get_bytes(self, key): - '''Get a parameter value as a byte string.''' - return self.get(key).bytes_value - - def get_string(self, key): - '''Get a parameter value as a string.''' - return self.get(key).string_value     + return analog_scales, analog_offsets

    Subclasses

      @@ -1176,33 +1116,39 @@

      Instance variables

      def last_frame(self) -> int: ''' Trial frame corresponding to the last frame recorded in the data (inclusive). ''' # Number of frames can be represented in many formats, first check if valid header values - if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: - return self.header.last_frame + #if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535: + # return self.header.last_frame - # Check different parameter options where the frame can be encoded - end_frame = [self.header.last_frame, 0.0, 0.0, 0.0] + # Try different parameters where the frame can be encoded + hlf = self.header.last_frame param = self.get('TRIAL:ACTUAL_END_FIELD') if param is not None: # Encoded as 2 16 bit words (rather then 1 32 bit word) # words = param.uint16_array # end_frame[1] = words[0] + words[1] * 65536 - end_frame[1] = param.uint32_value + end_frame = param.uint32_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:LONG_FRAMES') if param is not None: # 'Should be' encoded as float if param.bytes_per_element >= 4: - end_frame[2] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[2] = param.uint16_value + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame param = self.get('POINT:FRAMES') if param is not None: # Can be encoded either as 32 bit float or 16 bit uint if param.bytes_per_element == 4: - end_frame[3] = int(param.float_value) + end_frame = int(param.float_value) else: - end_frame[3] = param.uint16_value - # Return the largest of the all (queue bad reading...) - return int(np.max(end_frame)) + end_frame = param.uint16_value + if hlf <= end_frame: + return end_frame + # Return header value by default + return hlf
      var point_labels : list
      @@ -1383,76 +1329,6 @@

      Returns

      return gen_scale, analog_scales, analog_offsets -
      -def get_bytes(self, key) -
      -
      -

      Get a parameter value as a byte string.

      -
      - -Expand source code - -
      def get_bytes(self, key):
-    '''Get a parameter value as a byte string.'''
-    return self.get(key).bytes_value
      -
      -
      -
      -def get_float(self, key) -
      -
      -

      Get a parameter value as a 32-bit float.

      -
      - -Expand source code - -
      def get_float(self, key):
-    '''Get a parameter value as a 32-bit float.'''
-    return self.get(key).float_value
      -
      -
      -
      -def get_int16(self, key) -
      -
      -

      Get a parameter value as a 16-bit signed integer.

      -
      - -Expand source code - -
      def get_int16(self, key):
-    '''Get a parameter value as a 16-bit signed integer.'''
-    return self.get(key).int16_value
      -
      -
      -
      -def get_int32(self, key) -
      -
      -

      Get a parameter value as a 32-bit signed integer.

      -
      - -Expand source code - -
      def get_int32(self, key):
-    '''Get a parameter value as a 32-bit signed integer.'''
-    return self.get(key).int32_value
      -
      -
      -
      -def get_int8(self, key) -
      -
      -

      Get a parameter value as an 8-bit signed integer.

      -
      - -Expand source code - -
      def get_int8(self, key):
-    '''Get a parameter value as an 8-bit signed integer.'''
-    return self.get(key).int8_value
      -
      -
      def get_screen_xy_axis(self)
      @@ -1547,62 +1423,6 @@

      Returns

      return None -
      -def get_string(self, key) -
      -
      -

      Get a parameter value as a string.

      -
      - -Expand source code - -
      def get_string(self, key):
-    '''Get a parameter value as a string.'''
-    return self.get(key).string_value
      -
      -
      -
      -def get_uint16(self, key) -
      -
      -

      Get a parameter value as a 16-bit unsigned integer.

      -
      - -Expand source code - -
      def get_uint16(self, key):
-    '''Get a parameter value as a 16-bit unsigned integer.'''
-    return self.get(key).uint16_value
      -
      -
      -
      -def get_uint32(self, key) -
      -
      -

      Get a parameter value as a 32-bit unsigned integer.

      -
      - -Expand source code - -
      def get_uint32(self, key):
-    '''Get a parameter value as a 32-bit unsigned integer.'''
-    return self.get(key).uint32_value
      -
      -
      -
      -def get_uint8(self, key) -
      -
      -

      Get a parameter value as an 8-bit unsigned integer.

      -
      - -Expand source code - -
      def get_uint8(self, key):
-    '''Get a parameter value as an 8-bit unsigned integer.'''
-    return self.get(key).uint8_value
      -
      -
      def items(self)
      @@ -1709,17 +1529,8 @@

      Manager
    • get
    • get_analog_transform
    • get_analog_transform_parameters
      • -
    • get_bytes
      • -
    • get_float
      • -
    • get_int16
      • -
    • get_int32
      • -
    • get_int8
    • get_screen_xy_axis
    • get_screen_xy_strings
      • -
    • get_string
      • -
    • get_uint16
      • -
    • get_uint32
      • -
    • get_uint8
    • header
    • items
    • keys
      • diff --git a/docs/c3d/reader.html b/docs/c3d/reader.html index 2e8d643..359809b 100644 --- a/docs/c3d/reader.html +++ b/docs/c3d/reader.html @@ -1108,17 +1108,8 @@

      Inherited members

    • frame_count
    • get_analog_transform
    • get_analog_transform_parameters
      • -
    • get_bytes
      • -
    • get_float
      • -
    • get_int16
      • -
    • get_int32
      • -
    • get_int8
    • get_screen_xy_axis
    • get_screen_xy_strings
      • -
    • get_string
      • -
    • get_uint16
      • -
    • get_uint32
      • -
    • get_uint8
    • header
    • keys
    • last_frame
      • diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html index 7c9aae2..2b0e1b7 100644 --- a/docs/c3d/writer.html +++ b/docs/c3d/writer.html @@ -1735,17 +1735,8 @@

      Inherited members

    • get
    • get_analog_transform
    • get_analog_transform_parameters
      • -
    • get_bytes
      • -
    • get_float
      • -
    • get_int16
      • -
    • get_int32
      • -
    • get_int8
    • get_screen_xy_axis
    • get_screen_xy_strings
      • -
    • get_string
      • -
    • get_uint16
      • -
    • get_uint32
      • -
    • get_uint8
    • header
    • items
    • keys
      • From 673b2e2eb0cddfa66784aa3a7d4c0c1a9f1ed607 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 11 Jul 2021 12:30:18 +0200 Subject: [PATCH 111/120] consume -> convert in Writer.from_reader() --- c3d/writer.py | 6 +++--- docs/c3d/index.html | 4 ++-- docs/c3d/writer.html | 22 +++++++++++----------- docs/examples.md | 4 ++-- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/c3d/writer.py b/c3d/writer.py index 896a95e..742474a 100644 --- a/c3d/writer.py +++ b/c3d/writer.py @@ -63,8 +63,8 @@ def from_reader(reader, conversion=None): conversion : str Conversion mode, None is equivalent to the default mode. Supported modes are: - 'consume' - (Default) Reader object will be - consumed and explicitly deleted. + 'convert' - (Default) Convert the Reader to a Writer + instance and explicitly delete the Reader. 'copy' - Reader objects will be deep copied. @@ -93,7 +93,7 @@ def from_reader(reader, conversion=None): is_header_only = conversion == 'copy_header' is_meta_copy = conversion == 'copy_metadata' is_meta_only = is_header_only or is_meta_copy - is_consume = conversion == 'consume' or conversion is None + is_consume = conversion == 'convert' or conversion is None is_shallow_copy = conversion == 'shallow_copy' or is_header_only is_deep_copy = conversion == 'copy' or is_meta_copy # Verify mode diff --git a/docs/c3d/index.html b/docs/c3d/index.html index 69cd6bf..7a90562 100644 --- a/docs/c3d/index.html +++ b/docs/c3d/index.html @@ -81,8 +81,8 @@

      Editing

      instances through the Reader.to_writer() method. To edit a file, open a file stream and pass it to the Reader constructor. Use the Reader.to_writer() method to create an independent Writer instance containing a heap copy of its file contents. -Rereading data frames from the reader and inserting them in reverse will then create a -looped version of the original motion sequence!

      +To edit the sequence, one can now reread the data frames from the reader and through inserting the +frames in reverse to create a looped version of the original motion sequence!

      import c3d
 
 with open('my-motion.c3d', 'rb') as file:
diff --git a/docs/c3d/writer.html b/docs/c3d/writer.html
index 2b0e1b7..0d7b9e6 100644
--- a/docs/c3d/writer.html
+++ b/docs/c3d/writer.html
@@ -93,8 +93,8 @@ 
      Module c3d.writer
      
         conversion : str
             Conversion mode, None is equivalent to the default mode. Supported modes are:
 
-                'consume'       - (Default) Reader object will be
-                                  consumed and explicitly deleted.
+                'convert'       - (Default) Convert the Reader to a Writer
+                                  instance and explicitly delete the Reader.
 
                 'copy'          - Reader objects will be deep copied.
 
@@ -123,7 +123,7 @@ 
      Module c3d.writer
      
         is_header_only = conversion == 'copy_header'
         is_meta_copy = conversion == 'copy_metadata'
         is_meta_only = is_header_only or is_meta_copy
-        is_consume = conversion == 'consume' or conversion is None
+        is_consume = conversion == 'convert' or conversion is None
         is_shallow_copy = conversion == 'shallow_copy' or is_header_only
         is_deep_copy = conversion == 'copy' or is_meta_copy
         # Verify mode
@@ -635,8 +635,8 @@ 
      Parameters
      
         conversion : str
             Conversion mode, None is equivalent to the default mode. Supported modes are:
 
-                'consume'       - (Default) Reader object will be
-                                  consumed and explicitly deleted.
+                'convert'       - (Default) Convert the Reader to a Writer
+                                  instance and explicitly delete the Reader.
 
                 'copy'          - Reader objects will be deep copied.
 
@@ -665,7 +665,7 @@ 
      Parameters
      
         is_header_only = conversion == 'copy_header'
         is_meta_copy = conversion == 'copy_metadata'
         is_meta_only = is_header_only or is_meta_copy
-        is_consume = conversion == 'consume' or conversion is None
+        is_consume = conversion == 'convert' or conversion is None
         is_shallow_copy = conversion == 'shallow_copy' or is_header_only
         is_deep_copy = conversion == 'copy' or is_meta_copy
         # Verify mode
@@ -1095,8 +1095,8 @@ 
      Parameters
      
 
      source : Reader
      
 
      Source to copy data from.
      
 
      conversion : str
      
-
      Conversion mode, None is equivalent to the default mode. Supported modes are:
      'consume'       - (Default) Reader object will be
-                  consumed and explicitly deleted.
+
      Conversion mode, None is equivalent to the default mode. Supported modes are:
      'convert'       - (Default) Convert the Reader to a Writer
+                  instance and explicitly delete the Reader.
 
 'copy'          - Reader objects will be deep copied.
 
@@ -1137,8 +1137,8 @@ 
      Raises
      
     conversion : str
         Conversion mode, None is equivalent to the default mode. Supported modes are:
 
-            'consume'       - (Default) Reader object will be
-                              consumed and explicitly deleted.
+            'convert'       - (Default) Convert the Reader to a Writer
+                              instance and explicitly delete the Reader.
 
             'copy'          - Reader objects will be deep copied.
 
@@ -1167,7 +1167,7 @@ 
      Raises
      
     is_header_only = conversion == 'copy_header'
     is_meta_copy = conversion == 'copy_metadata'
     is_meta_only = is_header_only or is_meta_copy
-    is_consume = conversion == 'consume' or conversion is None
+    is_consume = conversion == 'convert' or conversion is None
     is_shallow_copy = conversion == 'shallow_copy' or is_header_only
     is_deep_copy = conversion == 'copy' or is_meta_copy
     # Verify mode
diff --git a/docs/examples.md b/docs/examples.md
index ca8eb42..8b1ceba 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -64,8 +64,8 @@ Editing c3d files is possible by combining the use of `c3d.reader.Reader` and `c
 instances through the `c3d.reader.Reader.to_writer` method. To edit a file, open a file stream and pass
 it to the `c3d.reader.Reader` constructor. Use the `c3d.reader.Reader.to_writer` method to create
 an independent `c3d.writer.Writer` instance containing a heap copy of its file contents.
-Rereading data frames from the reader and inserting them in reverse will then create a
-looped version of the original motion sequence!
+To edit the sequence, one can now reread the data frames from the reader and through inserting the
+frames in reverse to create a looped version of the original motion sequence!
 
     import c3d
 

From c27874491df5dc151f82f2a745608457d5726c04 Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 11 Jul 2021 12:37:29 +0200
Subject: [PATCH 112/120] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 859c9ee..b4b9035 100644
--- a/README.rst
+++ b/README.rst
@@ -67,7 +67,7 @@ experience some issues. If you experience issues with a file or feature, feel fr
 to post an issue (preferably by including example file/code/python exception)
 or make a pull request!
 
-The package is also Python only, for other languages there are other packages for example `ezc3d`_.
+The package is Python only, support for other languages is available in other packages, for example see `ezc3d`_.
 
 .. _software examples: https://www.c3d.org/sampledata.html
 .. _ezc3d: https://github.com/pyomeca/ezc3d

From fbc00053630a06364d0264f024fe8d1fce377398 Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 11 Jul 2021 12:38:11 +0200
Subject: [PATCH 113/120] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index b4b9035..4378b6a 100644
--- a/README.rst
+++ b/README.rst
@@ -59,7 +59,7 @@ Caveats
 
 The package is tested against the `software examples`_ but may still not support
 every possible format. For example, parameters serialized in multiple parameters
-are not handled automatically (LABELS field stored in both POINT:LABELS and
+are not handled automatically (such as a LABELS field stored in both POINT:LABELS and
 POINT:LABELS2). Reading and writing files from a big-endian system is also not supported.
 
 Tests are currently only run on Windows, which means that Linux and Mac users may

From f4479c0c49990a2a2c1d8ee23b1bfcdc155d73ac Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 11 Jul 2021 12:40:09 +0200
Subject: [PATCH 114/120] Update README.rst

---
 README.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.rst b/README.rst
index 4378b6a..da0c0d2 100644
--- a/README.rst
+++ b/README.rst
@@ -49,15 +49,15 @@ To use the C3D library, just import the package and create a ``Reader`` and/or
             print('frame {}: point {}, analog {}'.format(
                   i, points.shape, analog.shape))
 
-You can also edit metadata fields using the library; see the `package
-documentation`_ for more details.
+The librart also provide functionality for editing both frame and metadata fields; 
+see the `package documentation`_ for more details.
 
 .. _package documentation: https://mattiasfredriksson.github.io/py-c3d/c3d/
 
 Caveats
 -------
 
-The package is tested against the `software examples`_ but may still not support
+The package is tested against the available `software examples`_ but may still not support
 every possible format. For example, parameters serialized in multiple parameters
 are not handled automatically (such as a LABELS field stored in both POINT:LABELS and
 POINT:LABELS2). Reading and writing files from a big-endian system is also not supported.

From f0f5c50076d1d1c6060680bd5cafa67b9446c6fe Mon Sep 17 00:00:00 2001
From: MattiasFredriksson 
Date: Sun, 11 Jul 2021 12:40:54 +0200
Subject: [PATCH 115/120] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index da0c0d2..1c81c8a 100644
--- a/README.rst
+++ b/README.rst
@@ -49,7 +49,7 @@ To use the C3D library, just import the package and create a ``Reader`` and/or
             print('frame {}: point {}, analog {}'.format(
                   i, points.shape, analog.shape))
 
-The librart also provide functionality for editing both frame and metadata fields; 
+The library also provide functionality for editing both frame and metadata fields; 
 see the `package documentation`_ for more details.
 
 .. _package documentation: https://mattiasfredriksson.github.io/py-c3d/c3d/

From 10038432ce8a581441ec02662d493a008fb8099d Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Thu, 15 Jul 2021 11:29:00 +0200
Subject: [PATCH 116/120] pycodestyle comments

---
 c3d/manager.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/c3d/manager.py b/c3d/manager.py
index 031063c..816d6d6 100644
--- a/c3d/manager.py
+++ b/c3d/manager.py
@@ -342,16 +342,15 @@ def first_frame(self) -> int:
 
     @property
     def last_frame(self) -> int:
-        ''' Trial frame corresponding to the last frame recorded in the data (inclusive). '''
-        # Number of frames can be represented in many formats, first check if valid header values
-        #if self.header.first_frame < self.header.last_frame and self.header.last_frame != 65535:
-        #    return self.header.last_frame
-
-        # Try different parameters where the frame can be encoded
+        ''' Trial frame corresponding to the last frame recorded in the data (inclusive).
+        '''
+        # Number of frames can be represented in many formats.
+        # Start of by  different parameters where the frame can be encoded
         hlf = self.header.last_frame
         param = self.get('TRIAL:ACTUAL_END_FIELD')
         if param is not None:
             # Encoded as 2 16 bit words (rather then 1 32 bit word)
+            # Manual refer to parsing the parameter as 2 16-bit words, but its equivalent to an uint32
             # words = param.uint16_array
             # end_frame[1] = words[0] + words[1] * 65536
             end_frame = param.uint32_value

From 37a21e46f3b203fb4aafe975fa7fc1c2dac590b8 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Thu, 15 Jul 2021 13:08:31 +0200
Subject: [PATCH 117/120] pycodestyles

---
 examples/write.py                         |  2 +-
 scripts/c3d-metadata.py                   |  2 +-
 scripts/c3d-viewer.py                     |  6 +--
 scripts/c3d2npz.py                        |  6 ++-
 test/test_c3d.py                          |  2 +-
 test/test_examples.py                     |  1 +
 test/test_group_accessors.py              | 12 +++---
 test/test_parameter_accessors.py          |  8 ++--
 test/test_parameter_bytes_conversion.py   | 47 ++++++++++++-----------
 test/test_software_examples_write_read.py |  1 -
 test/verify.py                            | 10 ++---
 11 files changed, 49 insertions(+), 48 deletions(-)

diff --git a/examples/write.py b/examples/write.py
index 6a05b73..644d770 100644
--- a/examples/write.py
+++ b/examples/write.py
@@ -17,7 +17,7 @@
 writer.set_point_labels(['RFT1', 'RFT2', 'RFT3', 'RFT4', 'LFT1', 'LFT2', 'LFT3', 'LFT4',
                          'RSK1', 'RSK2', 'RSK3', 'RSK4', 'LSK1', 'LSK2', 'LSK3', 'LSK4',
                          'RTH1', 'RTH2', 'RTH3', 'RTH4', 'LTH1', 'LTH2', 'LTH3', 'LTH4'
-                        ])
+                         ])
 writer.set_analog_labels(None)
 
 with open('random-points.c3d', 'wb') as h:
diff --git a/scripts/c3d-metadata.py b/scripts/c3d-metadata.py
index cb054f6..388fd6e 100644
--- a/scripts/c3d-metadata.py
+++ b/scripts/c3d-metadata.py
@@ -15,7 +15,7 @@
 
 parser = argparse.ArgumentParser(description='Display C3D group and parameter information.')
 parser.add_argument('input', default='-', metavar='FILE', nargs='+',
-                help='process C3D data from this input FILE')
+                    help='process C3D data from this input FILE')
 
 
 def print_metadata(reader):
diff --git a/scripts/c3d-viewer.py b/scripts/c3d-viewer.py
index b215e36..c7b252c 100644
--- a/scripts/c3d-viewer.py
+++ b/scripts/c3d-viewer.py
@@ -112,7 +112,7 @@ def __init__(self, c3d_reader, trace=None, paused=False):
         self.ry = 30
         self.rz = 30
 
-        #self.fps = pyglet.clock.ClockDisplay()
+        # self.fps = pyglet.clock.ClockDisplay()
 
         self.on_resize(self.width, self.height)
 
@@ -158,7 +158,8 @@ def __init__(self, c3d_reader, trace=None, paused=False):
             len(vtx) // 3, idx, ('v3f/static', vtx), ('n3f/static', nrm))
 
     def on_mouse_scroll(self, x, y, dx, dy):
-        if dy == 0: return
+        if dy == 0:
+            return
         self.zoom *= 1.1 ** (-1 if dy < 0 else 1)
 
     def on_mouse_drag(self, x, y, dx, dy, buttons, modifiers):
@@ -170,7 +171,6 @@ def on_mouse_drag(self, x, y, dx, dy, buttons, modifiers):
             # roll
             self.ry += 0.2 * -dy
             self.rz += 0.2 * dx
-        #print('z', self.zoom, 't', self.ty, self.tz, 'r', self.ry, self.rz)
 
     def on_resize(self, width, height):
         glViewport(0, 0, width, height)
diff --git a/scripts/c3d2npz.py b/scripts/c3d2npz.py
index 4629b3c..843f83b 100644
--- a/scripts/c3d2npz.py
+++ b/scripts/c3d2npz.py
@@ -21,6 +21,7 @@
 parser.add_argument('input', default='-', metavar='FILE', nargs='+', help='process data from this input FILE')
 parser.add_argument("-v", "--verbose", help="increase output verbosity", action="store_true")
 
+
 def convert(filename, args):
     input = sys.stdin
     outname = '-'
@@ -38,12 +39,13 @@ def convert(filename, args):
 
     np.savez(outname, points=points, analog=analog)
     print(outname + ': saved', len(points), "x", str(points[0].shape), "points,",
-        len(analog), analog[0].shape, 'analog' if len(analog) else ()
-    )
+          len(analog), analog[0].shape, 'analog' if len(analog) else ()
+          )
 
     if filename != '-':
         input.close()
 
+
 def main(args):
     if args.verbose:
         logging.basicConfig(level=logging.DEBUG)
diff --git a/test/test_c3d.py b/test/test_c3d.py
index 1152dd1..c8bda28 100644
--- a/test/test_c3d.py
+++ b/test/test_c3d.py
@@ -135,8 +135,8 @@ def test_set_params(self):
         assert w.point_group.get(test_name).total_bytes == len(test_string), \
                "Mismatch in number of bytes encoded by 'Group.add_str'"
 
-
         w.write(h)
 
+
 if __name__ == '__main__':
     unittest.main()
diff --git a/test/test_examples.py b/test/test_examples.py
index 7700b39..4724f40 100644
--- a/test/test_examples.py
+++ b/test/test_examples.py
@@ -46,5 +46,6 @@ def test_edit(self):
         # Raises 'FileNotFound' if the file was not generated
         os.remove(path)
 
+
 if __name__ == '__main__':
     unittest.main()
diff --git a/test/test_group_accessors.py b/test/test_group_accessors.py
index 8d92531..a4e0a62 100644
--- a/test/test_group_accessors.py
+++ b/test/test_group_accessors.py
@@ -7,6 +7,7 @@
 from test.zipload import Zipload
 from test.base import Base
 
+
 class GroupSample():
     ''' Helper object to verify group entries persist or terminate properly. '''
     def __init__(self, manager):
@@ -38,13 +39,13 @@ def sample(self):
         '''Call before applying changes. '''
         self.s_grp_items, self.s_grp_list = self.fetch_groups
 
-
     def assert_entry_count(self, delta=0):
         '''Assert all values in group still exist.
 
         Arguments
         ---------
-        delta:  Number of entries added (+) or removed (-) since last sample.
+        delta : int
+            Number of entries added (+) or removed (-) since last sample.
         '''
         grp_items, grp_list = self.fetch_groups
 
@@ -193,7 +194,7 @@ def test_Manager_rename_group(self):
             writer.rename_group(new_names[0], new_names[1])
             raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.')
         except ValueError as e:
-            pass # Correct
+            pass  # Correct
 
     def test_Manager_renumber_group(self):
         '''Test if renaming (renumbering) groups acts as intended.'''
@@ -221,10 +222,7 @@ def test_Manager_renumber_group(self):
             writer.rename_group(max_key + 1, max_key + 2)
             raise RuntimeError('Overwriting existing numerical ID should raise a KeyError.')
         except ValueError as e:
-            pass # Correct
-
-
-
+            pass  # Correct
 
 
 if __name__ == '__main__':
diff --git a/test/test_parameter_accessors.py b/test/test_parameter_accessors.py
index 1be26ae..cbfa451 100644
--- a/test/test_parameter_accessors.py
+++ b/test/test_parameter_accessors.py
@@ -10,10 +10,12 @@
 
 rnd = np.random.default_rng()
 
+
 def add_dummy_param(group, name='TEST_NAME', shape=(10, 2), flt_range=(-1e6, 1e6)):
     arr = rnd.uniform(*flt_range, size=shape).astype(np.float32)
     group.add_param(name, bytes_per_element=4, dimensions=arr.shape, bytes=arr.T.tobytes())
 
+
 class ParamSample():
     ''' Helper object to verify parameter entries persist or terminate properly. '''
     def __init__(self, group):
@@ -129,7 +131,7 @@ def test_Group_remove_param(self):
             ref.verify_add_parameter(100)
 
     def test_Group_rename_param(self):
-        '''Test if renaming groups acts as intended.'''
+        ''' Test if renaming groups acts as intended.'''
         reader = c3d.Reader(Zipload._get(self.ZIP, self.INTEL_REAL))
 
         writer = reader.to_writer()
@@ -149,9 +151,7 @@ def test_Group_rename_param(self):
                 g.rename_param(new_names[0], new_names[1])
                 raise RuntimeError('Overwriting existing numerical ID should raise a ValueError.')
             except ValueError as e:
-                pass # Correct
-
-
+                pass  # Correct
 
 
 if __name__ == '__main__':
diff --git a/test/test_parameter_bytes_conversion.py b/test/test_parameter_bytes_conversion.py
index 3525ccf..026dfc4 100644
--- a/test/test_parameter_bytes_conversion.py
+++ b/test/test_parameter_bytes_conversion.py
@@ -6,7 +6,7 @@
 
 
 def genByteWordArr(word, shape):
-    '''    Generate a multi-dimensional byte array from a specific word.
+    ''' Generate a multi-dimensional byte array from a specific word.
     '''
     arr = np.array(word)
     for d in shape[::-1]:
@@ -15,7 +15,7 @@ def genByteWordArr(word, shape):
 
 
 def genRndByteArr(wordlen, shape, pad):
-    '''    Generate a multi-dimensional byte array with random data.
+    ''' Generate a multi-dimensional byte array with random data.
     '''
     tot_len = wordlen + pad*wordlen
     arr = np.empty(shape, dtype=np.dtype('S'+str(tot_len)))
@@ -28,16 +28,17 @@ def genRndByteArr(wordlen, shape, pad):
 
 
 def genRndFloatArr(shape, rnd, range=(-1e6, 1e6)):
-    '''    Generate a multi-dimensional array of 32 bit floating point data.
+    ''' Generate a multi-dimensional array of 32 bit floating point data.
     '''
     return rnd.uniform(range[0], range[1], shape)
 
+
 def make_param(*args, **kwargs):
     return ParamReadonly(ParamData(*args, **kwargs))
 
 
 class ParameterValueTest(unittest.TestCase):
-    '''    Test read Parameter arrays
+    ''' Test read Parameter arrays
     '''
 
     RANGE_8_BIT = (-127, 127)
@@ -53,7 +54,7 @@ def setUp(self):
         self.dtypes = DataTypes(PROCESSOR_INTEL)
 
     def test_a_param_float32(self):
-        '''    Verify a single 32 bit floating point value is parsed correctly
+        ''' Verify a single 32 bit floating point value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.float32(self.rnd.uniform(*ParameterValueTest.RANGE_32_BIT))
@@ -64,7 +65,7 @@ def test_a_param_float32(self):
                 (value_out, value)
 
     def test_b_param_int32(self):
-        '''    Verify a single 32 bit integer value is parsed correctly
+        ''' Verify a single 32 bit integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.int32(self.rnd.uniform(*ParameterValueTest.RANGE_32_BIT))
@@ -75,7 +76,7 @@ def test_b_param_int32(self):
                 (value_out, value)
 
     def test_b_param_uint32(self):
-        '''    Verify a single 32 bit unsigned integer value is parsed correctly
+        ''' Verify a single 32 bit unsigned integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.uint32(self.rnd.uniform(*ParameterValueTest.RANGE_32_UNSIGNED_BIT))
@@ -86,7 +87,7 @@ def test_b_param_uint32(self):
                 (value_out, value)
 
     def test_b_param_int16(self):
-        '''    Verify a single 16 bit integer value is parsed correctly
+        ''' Verify a single 16 bit integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.int16(self.rnd.uniform(*ParameterValueTest.RANGE_16_BIT))
@@ -97,7 +98,7 @@ def test_b_param_int16(self):
                 (value_out, value)
 
     def test_b_param_uint16(self):
-        '''    Verify a single 16 bit unsigned integer value is parsed correctly
+        ''' Verify a single 16 bit unsigned integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.uint16(self.rnd.uniform(*ParameterValueTest.RANGE_16_UNSIGNED_BIT))
@@ -108,7 +109,7 @@ def test_b_param_uint16(self):
                 (value_out, value)
 
     def test_b_param_int8(self):
-        '''    Verify a single 8 bit integer value is parsed correctly
+        ''' Verify a single 8 bit integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.int8(self.rnd.uniform(*ParameterValueTest.RANGE_8_BIT))
@@ -119,7 +120,7 @@ def test_b_param_int8(self):
                 (value_out, value)
 
     def test_b_param_uint8(self):
-        '''    Verify a single 8 bit unsigned integer value is parsed correctly
+        ''' Verify a single 8 bit unsigned integer value is parsed correctly
         '''
         for i in range(ParameterValueTest.TEST_ITERATIONS):
             value = np.uint8(self.rnd.uniform(*ParameterValueTest.RANGE_8_UNSIGNED_BIT))
@@ -131,7 +132,7 @@ def test_b_param_uint8(self):
 
 
 class ParameterArrayTest(unittest.TestCase):
-    '''    Test read Parameter arrays
+    ''' Test read Parameter arrays
     '''
 
     SHAPES = [[7, 6, 5], [7, 5, 3], [7, 3], [19]]
@@ -141,7 +142,7 @@ def setUp(self):
         self.dtypes = DataTypes(PROCESSOR_INTEL)
 
     def test_a_parse_float32_array(self):
-        '''    Verify array of 32 bit floating point values are parsed correctly
+        ''' Verify array of 32 bit floating point values are parsed correctly
         '''
         flt_range = (-1e6, 1e6)
 
@@ -153,7 +154,7 @@ def test_a_parse_float32_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading float array'
 
     def test_b_parse_float64_array(self):
-        '''    Verify array of 64 bit floating point values are parsed correctly
+        ''' Verify array of 64 bit floating point values are parsed correctly
         '''
         flt_range = (-1e6, 1e6)
 
@@ -165,7 +166,7 @@ def test_b_parse_float64_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading float array'
 
     def test_c_parse_int32_array(self):
-        '''    Verify array of 32 bit integer values are parsed correctly
+        ''' Verify array of 32 bit integer values are parsed correctly
         '''
         flt_range = (-1e6, 1e6)
 
@@ -177,7 +178,7 @@ def test_c_parse_int32_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array'
 
     def test_d_parse_uint32_array(self):
-        '''    Verify array of 32 bit unsigned integer values are parsed correctly
+        ''' Verify array of 32 bit unsigned integer values are parsed correctly
         '''
         flt_range = (0, 1e6)
 
@@ -189,7 +190,7 @@ def test_d_parse_uint32_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array'
 
     def test_e_parse_int16_array(self):
-        '''    Verify array of 16 bit integer values are parsed correctly
+        ''' Verify array of 16 bit integer values are parsed correctly
         '''
         flt_range = (-1e4, 1e4)
 
@@ -201,7 +202,7 @@ def test_e_parse_int16_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array'
 
     def test_f_parse_uint16_array(self):
-        '''    Verify array of 16 bit unsigned integer values are parsed correctly
+        ''' Verify array of 16 bit unsigned integer values are parsed correctly
         '''
         flt_range = (0, 1e4)
 
@@ -213,7 +214,7 @@ def test_f_parse_uint16_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array'
 
     def test_g_parse_int8_array(self):
-        '''    Verify array of 8 bit integer values are parsed correctly
+        ''' Verify array of 8 bit integer values are parsed correctly
         '''
         flt_range = (-127, 127)
 
@@ -225,7 +226,7 @@ def test_g_parse_int8_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading int32 array'
 
     def test_h_parse_uint8_array(self):
-        '''    Verify array of 8 bit unsigned integer values are parsed correctly
+        ''' Verify array of 8 bit unsigned integer values are parsed correctly
         '''
         flt_range = (0, 255)
 
@@ -237,7 +238,7 @@ def test_h_parse_uint8_array(self):
             assert np.all(arr.T == arr_out), 'Value mismatch when reading uint32 array'
 
     def test_i_parse_byte_array(self):
-        '''    Verify byte arrays are parsed correctly
+        ''' Verify byte arrays are parsed correctly
         '''
         word = b'WRIST'
 
@@ -269,7 +270,7 @@ def test_i_parse_byte_array(self):
             assert np.all(arr[i[::-1]] == arr_out[i]), "Mismatch in 'bytes_array' converted value at index %s" % str(i)
 
     def test_j_parse_string_array(self):
-        '''    Verify repeated word arrays are parsed correctly
+        ''' Verify repeated word arrays are parsed correctly
         '''
         word = b'ANCLE'
 
@@ -307,7 +308,7 @@ def test_j_parse_string_array(self):
                 "Mismatch in 'string_array' converted value at index %s" % str(i)
 
     def test_k_parse_random_string_array(self):
-        '''    Verify random word arrays are parsed correctly
+        ''' Verify random word arrays are parsed correctly
         '''
         ##
         # RND
diff --git a/test/test_software_examples_write_read.py b/test/test_software_examples_write_read.py
index 3f02ae9..df6125a 100644
--- a/test/test_software_examples_write_read.py
+++ b/test/test_software_examples_write_read.py
@@ -89,6 +89,5 @@ def test_read_write_examples(self):
         print('Done.')
 
 
-
 if __name__ == '__main__':
     unittest.main()
diff --git a/test/verify.py b/test/verify.py
index 807ee80..37de442 100644
--- a/test/verify.py
+++ b/test/verify.py
@@ -110,13 +110,13 @@ def check_zipfile(file_path):
                     analog_min = np.min(analog)
                     analog_max = np.max(analog)
 
-            assert np.all(npoint == reader.frame_count), '\n' + \
+            assert np.all(npoint == reader.frame_count), '\n' +\
                 'Failed verifying POINT data in range ({}, {}).\n'.format(min_range, max_range) +\
                 'Found a total of {} values outside plausible range.\n'.format(
                  np.sum(np.abs(npoint - reader.frame_count), axis=0)) +\
                 'Range for data was ({}, {})'.format(point_min, point_max)
 
-            assert np.all(nanalog == reader.analog_sample_count),'\n' + \
+            assert np.all(nanalog == reader.analog_sample_count), '\n' +\
                 'Failed verifying ANALOG data in range ({}, {}).\n'.format(min_range, max_range) +\
                 'Found a total of {} values outside plausible range.\n'.format(
                  np.abs(nanalog - reader.analog_sample_count)) +\
@@ -311,7 +311,7 @@ def data_is_equal(areader, breader, alabel, blabel):
         assert axis_notclose == 0, '\n' +\
             'Mismatched coordinates on {} axis between {} and {}.\n'.format(c[i], alabel, blabel) +\
             'Samples with absolute difference larger then {:0.4f}: {} of {}.\n'.format(
-            atol, axis_notclose, tot_points) +\
+                atol, axis_notclose, tot_points) +\
             'Maximum difference: {}'.format(np.max(np.abs(apoint[:, i] - bpoint[:, i])))
 
     # Word 4 (residual + camera bits)
@@ -321,8 +321,8 @@ def data_is_equal(areader, breader, alabel, blabel):
 
     # Camera bit errors (warn if non identical, allow 1 cam bit diff, might be bad DEC implementation, or bad data)
     if cam_diff_non_equal > 0:
-        #print(apoint[~cam_close, 4])
-        #print(bpoint[~cam_close, 4])
+        # print(apoint[~cam_close, 4])
+        # print(bpoint[~cam_close, 4])
         cam_close = np.isclose(apoint[:, 4], bpoint[:, 4], atol=1.001)
         cam_diff = tot_points - np.sum(cam_close)
         assert cam_diff == 0, '\n' + \

From e103f4fb8cd64471250b48d3674ab153cea0601e Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Thu, 15 Jul 2021 13:12:35 +0200
Subject: [PATCH 118/120] pycodestyles

---
 test/README.rst | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/README.rst b/test/README.rst
index ed74c76..bf286c0 100644
--- a/test/README.rst
+++ b/test/README.rst
@@ -8,5 +8,3 @@ To run tests, use the following command from the root of the package directory::
 Test scripts will automatically download test files from `c3d.org`_.
 
 .. _c3d.org: https://www.c3d.org/sampledata.html
-
-Currently no code style is enforced.

From 4b4715dfd9ad6d0df373a32abbe62c0a4678ba08 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Thu, 15 Jul 2021 15:40:06 +0200
Subject: [PATCH 119/120] missing sys in c3d2npz and added info print to
 c3d-viewer.py

---
 scripts/c3d-viewer.py | 8 +++++---
 scripts/c3d2npz.py    | 1 +
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/scripts/c3d-viewer.py b/scripts/c3d-viewer.py
index b215e36..f3cc943 100644
--- a/scripts/c3d-viewer.py
+++ b/scripts/c3d-viewer.py
@@ -12,9 +12,11 @@
 import collections
 import contextlib
 import numpy as np
-import pyglet
-
-from pyglet.gl import *
+try:
+    import pyglet
+    from pyglet.gl import *
+except ModuleNotFoundError as e:
+    sys.stdout.write("View requires pyglet to be installed. Install pyglet through the command 'pip insall pyglet'")
 
 parser = argparse.ArgumentParser(description='A simple OpenGL viewer for C3D files.')
 parser.add_argument('inputs', nargs='+', metavar='FILE', help='show these c3d files')
diff --git a/scripts/c3d2npz.py b/scripts/c3d2npz.py
index 4629b3c..730c35d 100644
--- a/scripts/c3d2npz.py
+++ b/scripts/c3d2npz.py
@@ -9,6 +9,7 @@
 import logging
 import gzip
 import numpy as np
+import sys
 from tempfile import TemporaryFile
 try:
     import c3d

From 36c377763edcfa348fb6e272a8455a69d63ef225 Mon Sep 17 00:00:00 2001
From: MattiasF 
Date: Thu, 15 Jul 2021 15:52:22 +0200
Subject: [PATCH 120/120] removed the added info msg

---
 scripts/c3d-viewer.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/scripts/c3d-viewer.py b/scripts/c3d-viewer.py
index 18cf8d2..6096019 100644
--- a/scripts/c3d-viewer.py
+++ b/scripts/c3d-viewer.py
@@ -12,11 +12,8 @@
 import collections
 import contextlib
 import numpy as np
-try:
-    import pyglet
-    from pyglet.gl import *
-except ModuleNotFoundError as e:
-    sys.stdout.write("View requires pyglet to be installed. Install pyglet through the command 'pip insall pyglet'")
+import pyglet
+from pyglet.gl import *
 
 parser = argparse.ArgumentParser(description='A simple OpenGL viewer for C3D files.')
 parser.add_argument('inputs', nargs='+', metavar='FILE', help='show these c3d files')

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z37)FHll$0de?;$NA@e%=@Adz~e^+(n8J3w~ZGXcjyO-QBqSsG1{NMaru`K&vUp}bc XO(lbF8(cEzo&hEQ_2K`c|Ka}t!@My? literal 0 HcmV?d00001 diff --git a/examples/read.py b/examples/read.py new file mode 100644 index 0000000..e85e885 --- /dev/null +++ b/examples/read.py @@ -0,0 +1,18 @@ +import numpy as np +import os +try: + import c3d +except ModuleNotFoundError: + # Force load package with no instalation + import sys + sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..\\')) + import c3d + +# My motion == Sample01.Eb015pi.c3d +file_path = os.path.join(os.path.dirname(__file__), 'my-motion.c3d') + +with open(file_path, 'rb') as file: + reader = c3d.Reader(file) + for i, points, analog in reader.read_frames(): + print('frame {}: point {}, analog {}'.format( + i, points.shape, analog.shape)) diff --git a/test/test_examples.py b/test/test_examples.py index aad4f8c..848857e 100644 --- a/test/test_examples.py +++ b/test/test_examples.py @@ -30,6 +30,16 @@ def test_write(self): # Raises 'FileNotFound' if the file was not generated os.remove(path) + def test_edit(self): + import edit + path = 'my-looped-motion.c3d' + + with open(path, 'rb') as f: + reader = c3d.Reader(f) + assert reader.frame_count == 900, \ + 'Expected 900 point frames in edit.py test, was {}'.format(reader.frame_count) + # Raises 'FileNotFound' if the file was not generated + os.remove(path) if __name__ == '__main__': unittest.main() From 914fb568986c05aeb4c337b39a8644a0259abfe2 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 15:37:16 +0200 Subject: [PATCH 068/120] Exclude looped motion --- .gitignore | 3 ++- examples/my-looped-motion.c3d | Bin 311808 -> 0 bytes 2 files changed, 2 insertions(+), 1 deletion(-) delete mode 100644 examples/my-looped-motion.c3d diff --git a/.gitignore b/.gitignore index d6eceab..8746a79 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ # C extensions *.so +*.c3d # Packages *.egg @@ -41,4 +42,4 @@ docs/_build .vscode/ # mypy -.mypy_cache/ \ No newline 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z7wet9-LSv(lG;Uny@;QEO-sBC^=Ex^mh&R?eTKEb^FvYojHrjDIYsq+rSqnLa5{$l zx-4o=Ha|Kc?at{5)idn;(cWBsB)^UNn_rL*D1UN4*aqGd?|fc-T6+I{y+!$e?bGmh zr|eP~579V5zO(zznPqltgKbU}`P%)g|0h;_bxB>yPs|Ce<4 td4AIS9+ZE7JO4S;qpzih&gTnuKE#rK&Glc*Pi~5@-y*U4?f>6@{x9Q%fY|^5 From 3bbc73f19ee130b73fb8793ea6730b2aea0029f5 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 15:41:02 +0200 Subject: [PATCH 069/120] Added reference to example/ dir --- docs/examples.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/examples.md b/docs/examples.md index 6917c66..4c77c3a 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -4,6 +4,7 @@ Examples ======== Access to data blocks in a .c3d file is provided through the `c3d.reader.Reader` and `c3d.writer.Writer` classes. +Implementation of the examples are provided in the `example/` in the github repository. Reading ------- From a9e1771ac28d0536e22b96daa7940b9baed45155 Mon Sep 17 00:00:00 2001 From: MattiasF Date: Sun, 4 Jul 2021 15:45:09 +0200 Subject: [PATCH 070/120] Docs --- docs/c3d/dtypes.html | 127 ++++++++++ docs/c3d/group.html | 536 ++++++++++++++++++++++++++++++++++++++++ docs/c3d/header.html | 206 +++++++++++++++ docs/c3d/index.html | 176 +++++++++++++ docs/c3d/manager.html | 306 +++++++++++++++++++++++ docs/c3d/parameter.html | 401 ++++++++++++++++++++++++++++++ docs/c3d/reader.html | 239 ++++++++++++++++++ docs/c3d/utils.html | 163 ++++++++++++ docs/c3d/writer.html | 355 ++++++++++++++++++++++++++ docs/examples.md | 9 +- 10 files changed, 2517 insertions(+), 1 deletion(-) create mode 100644 docs/c3d/dtypes.html create mode 100644 docs/c3d/group.html create mode 100644 docs/c3d/header.html create mode 100644 docs/c3d/index.html create mode 100644 docs/c3d/manager.html create mode 100644 docs/c3d/parameter.html create mode 100644 docs/c3d/reader.html create mode 100644 docs/c3d/utils.html create mode 100644 docs/c3d/writer.html diff --git a/docs/c3d/dtypes.html b/docs/c3d/dtypes.html new file mode 100644 index 0000000..729ad33 --- /dev/null +++ b/docs/c3d/dtypes.html @@ -0,0 +1,127 @@ + + + + + + +c3d.dtypes API documentation + + + + + + + + + + + +