diff --git a/invokers/invoker_estimate_noise_cov_matrix.py b/invokers/invoker_estimate_noise_cov_matrix.py index be170dfe..c0f8570c 100644 --- a/invokers/invoker_estimate_noise_cov_matrix.py +++ b/invokers/invoker_estimate_noise_cov_matrix.py @@ -1,8 +1,6 @@ from pathlib import Path -from colorama import Fore from kymata.io.yaml import load_config -from kymata.io.cli import print_with_color from kymata.preproc.data_cleansing import estimate_noise_cov diff --git a/invokers/invoker_run_hexel_current_estimation.py b/invokers/invoker_run_hexel_current_estimation.py index 68c7baad..119c7a1f 100644 --- a/invokers/invoker_run_hexel_current_estimation.py +++ b/invokers/invoker_run_hexel_current_estimation.py @@ -3,7 +3,7 @@ from kymata.io.yaml import load_config from kymata.io.cli import print_with_color -from kymata.preproc.hexel_current_estimation import create_current_estimation_prerequisites, create_forward_model_and_inverse_solution, create_hexel_morph_maps +from kymata.preproc.hexel_current_estimation import create_forward_model_and_inverse_solution, create_hexel_morph_maps # noinspection DuplicatedCode diff --git a/invokers/run_gridsearch.py b/invokers/run_gridsearch.py index 3f088369..f1a2b777 100644 --- a/invokers/run_gridsearch.py +++ b/invokers/run_gridsearch.py @@ -7,7 +7,6 @@ from kymata.io.functions import load_function from kymata.preproc.source import load_emeg_pack from kymata.io.nkg import save_expression_set -from kymata.io.yaml import load_config from kymata.plot.plot import expression_plot _default_output_dir = Path(data_root_path(), "output") @@ -64,7 +63,7 @@ def main(): args = parser.parse_args() # TODO: use config for ppt lists etc - config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml"))) + #config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml"))) participants = [ 'pilot_01', @@ -98,8 +97,8 @@ def main(): if (len(emeg_filenames) > 1) and (not args.morph) and (args.ave_mode == "ave") and (args.inverse_operator_dir is not None): raise ValueError( - f"Averaging source-space results without morphing to a common space. " - f"If you are averaging over multiple participants you must morph to a common space.") + "Averaging source-space results without morphing to a common space. " + + "If you are averaging over multiple participants you must morph to a common space.") # Load data emeg_path = Path(args.base_dir, args.emeg_dir) diff --git a/kymata/datasets/sample.py b/kymata/datasets/sample.py index 0e276a72..c002fc3a 100644 --- a/kymata/datasets/sample.py +++ b/kymata/datasets/sample.py @@ -141,7 +141,7 @@ def delete_dataset(local_dataset: SampleDataset): # Make sure it's not silent print(f"Deleting dataset {local_dataset.name}") # Only allow deletion if the specified url is within the data dir - assert data_root_path() in local_dataset.path.parents, f"Cannot delete dataset outside of data root directory" + assert data_root_path() in local_dataset.path.parents, "Cannot delete dataset outside of data root directory" if not local_dataset.path.exists(): # Nothing to delete print(f"{str(local_dataset.path)} doesn't exist") diff --git a/kymata/gridsearch/plain.py b/kymata/gridsearch/plain.py index a5908136..eef2c44c 100644 --- a/kymata/gridsearch/plain.py +++ b/kymata/gridsearch/plain.py @@ -43,7 +43,9 @@ def do_gridsearch( n_samples_per_split = int(seconds_per_split * emeg_sample_rate * 2 // downsample_rate) if ave_mode == 'add': - n_reps = len(EMEG_paths) + # TODO: hard-code hack, fix as part of https://github.com/kymata-atlas/kymata-toolbox/issues/128 + #n_reps = len(EMEG_paths) + n_reps = 1 else: n_reps = 1 diff --git a/kymata/io/functions.py b/kymata/io/functions.py index 92f99e1c..688a9f84 100644 --- a/kymata/io/functions.py +++ b/kymata/io/functions.py @@ -1,6 +1,5 @@ from pathlib import Path -from numpy import array, float16, convolve, mean import numpy as np from numpy.typing import NDArray from scipy.io import loadmat @@ -26,7 +25,6 @@ def load_function(function_path_without_suffix: path_type, func_name: str, n_der n_chans = func.shape[0] new_mr_arr = np.zeros((n_chans, 400_000)) new_ft_arr = np.zeros((n_chans, 400_000)) - T_end = tt[0, -1] if func_name == 'neurogram_mr': for i in range(n_chans): new_mr_arr[i] = np.interp(np.linspace(0, 400, 400_000 + 1)[:-1], tt[0], func[i]) diff --git a/kymata/io/nkg.py b/kymata/io/nkg.py index 36ee3189..5205596c 100644 --- a/kymata/io/nkg.py +++ b/kymata/io/nkg.py @@ -263,7 +263,7 @@ def _load_data_current(from_path_or_file: path_type | file_type) -> dict[str, An with TextIOWrapper(zf.open("_metadata/expression-set-type.txt"), encoding="utf-8") as f: return_dict[_Keys.expressionset_type] = str(f.read()).strip() with TextIOWrapper(zf.open("/blocks.txt"), encoding="utf-8") as f: - blocks = [str(l.strip()) for l in f.readlines()] + blocks = [str(line.strip()) for line in f.readlines()] with TextIOWrapper(zf.open("/latencies.txt"), encoding="utf-8") as f: return_dict[_Keys.latencies] = [LatencyDType(lat.strip()) for lat in f.readlines()] with TextIOWrapper(zf.open("/functions.txt"), encoding="utf-8") as f: diff --git a/kymata/io/nkg_compatibility.py b/kymata/io/nkg_compatibility.py index f887aa61..f69cbaa4 100644 --- a/kymata/io/nkg_compatibility.py +++ b/kymata/io/nkg_compatibility.py @@ -37,7 +37,7 @@ def _load_data_0_3(from_path_or_file: path_type | file_type) -> dict[str, Any]: with TextIOWrapper(zf.open("_metadata/expression-set-type.txt"), encoding="utf-8") as f: return_dict["expressionset-type"] = str(f.read()).strip() with TextIOWrapper(zf.open("/layers.txt"), encoding="utf-8") as f: - layers = [str(l.strip()) for l in f.readlines()] + layers = [str(line.strip()) for line in f.readlines()] with TextIOWrapper(zf.open("/channels.txt"), encoding="utf-8") as f: return_dict["channels"] = [c.strip() for c in f.readlines()] with TextIOWrapper(zf.open("/latencies.txt"), encoding="utf-8") as f: @@ -76,7 +76,7 @@ def _load_data_0_2(from_path_or_file: path_type | file_type) -> dict[str, Any]: with TextIOWrapper(zf.open("_metadata/expression-set-type.txt"), encoding="utf-8") as f: return_dict["expressionset-type"] = str(f.read()).strip() with TextIOWrapper(zf.open("/layers.txt"), encoding="utf-8") as f: - layers = [str(l.strip()) for l in f.readlines()] + layers = [str(line.strip()) for line in f.readlines()] with TextIOWrapper(zf.open("/channels.txt"), encoding="utf-8") as f: return_dict["channels"] = [c.strip() for c in f.readlines()] with TextIOWrapper(zf.open("/latencies.txt"), encoding="utf-8") as f: diff --git a/kymata/ippm/__init__.py b/kymata/ippm/__init__.py index e69de29b..8b137891 100644 --- a/kymata/ippm/__init__.py +++ b/kymata/ippm/__init__.py @@ -0,0 +1 @@ + diff --git a/kymata/ippm/data_tools.py b/kymata/ippm/data_tools.py index 845e8014..76f30467 100644 --- a/kymata/ippm/data_tools.py +++ b/kymata/ippm/data_tools.py @@ -10,7 +10,6 @@ import pandas as pd from sklearn.preprocessing import normalize from sklearn.metrics.pairwise import euclidean_distances -from copy import deepcopy import requests import seaborn as sns from matplotlib.lines import Line2D @@ -102,7 +101,7 @@ def build_hexel_dict_from_expression_set(expression_set: HexelExpressionSet) -> func = row[DIM_FUNCTION] latency = row[DIM_LATENCY] * 1000 # convert to ms pval = row["value"] - if not func in hexels: + if func not in hexels: hexels[func] = IPPMHexel(func) hexels[func].add_pairing(hemi, (latency, pval)) return hexels @@ -127,7 +126,7 @@ def build_hexel_dict_from_api_response(dict_: Dict) -> Dict[str, IPPMHexel]: for (_, latency, pval, func) in dict_[hemi]: # we have id, latency (ms), pvalue (log_10), function name. # discard id as it conveys no useful information - if not func in hexels: + if func not in hexels: # first time seeing function, so create key and hexel object. hexels[func] = IPPMHexel(func) @@ -209,7 +208,7 @@ def stem_plot( right_hem_expression_plot.invert_yaxis() left_hem_expression_plot.text(-180, y_limit * 10000000, 'left hemisphere', style='italic', verticalalignment='center') right_hem_expression_plot.text(-180, y_limit * 10000000, 'right hemisphere', style='italic', verticalalignment='center') - y_axis_label = f'p-value (with α at 5-sigma, Bonferroni corrected)' + y_axis_label = 'p-value (with α at 5-sigma, Bonferroni corrected)' left_hem_expression_plot.text(-275, 1, y_axis_label, verticalalignment='center',rotation='vertical') right_hem_expression_plot.text(0, 1, ' onset of environment ', color='white', fontsize='x-small', bbox={'facecolor': 'grey', 'edgecolor': 'none'}, verticalalignment='center', horizontalalignment='center', rotation='vertical') left_hem_expression_plot.legend(handles=custom_handles, labels=custom_labels, fontsize='x-small', bbox_to_anchor=(1.2, 1)) @@ -265,7 +264,7 @@ def function_recall(hexels: Dict[str, IPPMHexel], funcs: List[str], ippm_dict: D for func in funcs: pairings = hexels[func].right_best_pairings if hemi == 'rightHemisphere' else hexels[func].left_best_pairings for latency, spike in pairings: - if spike <= alpha: + if spike <= bonferroni_corrected_alpha: funcs_present_in_data += 1 # Step 2: Found a function, look in ippm_dict.keys() for the function. @@ -291,7 +290,7 @@ def convert_to_power10(hexels: Dict[str, IPPMHexel]) -> Dict[str, IPPMHexel]: def remove_excess_funcs(to_retain: List[str], hexels: Dict[str, IPPMHexel]) -> Dict[str, IPPMHexel]: funcs = list(hexels.keys()) for func in funcs: - if not func in to_retain: + if func not in to_retain: # delete hexels.pop(func) return hexels diff --git a/kymata/ippm/denoiser.py b/kymata/ippm/denoiser.py index 745683af..ad3e703b 100644 --- a/kymata/ippm/denoiser.py +++ b/kymata/ippm/denoiser.py @@ -6,7 +6,7 @@ import pandas as pd from sklearn.cluster import DBSCAN as DBSCAN_, MeanShift as MeanShift_ from sklearn.mixture import GaussianMixture -from sklearn.preprocessing import StandardScaler, normalize +from sklearn.preprocessing import normalize from .data_tools import IPPMHexel @@ -155,7 +155,7 @@ def _check_hemi(self, hemi): ------ ValueError if invalid hemi input. """ - if not hemi in ['rightHemisphere', 'leftHemisphere']: + if hemi not in ['rightHemisphere', 'leftHemisphere']: print('Hemisphere needs to be rightHemisphere or leftHemisphere') raise ValueError @@ -206,7 +206,7 @@ def _get_cluster_mins(self, df: pd.DataFrame) -> List[Tuple[float, float]]: # label = -1 indicates anomaly, so exclude. continue - if not label in class_mins.keys(): + if label not in class_mins.keys(): # first time seeing this class. class_mins[label] = [float(row['Mag']), float(row['Latency'])] elif class_mins[label][0] > row['Mag']: @@ -236,13 +236,15 @@ def __init__(self, **kwargs): bin_sz : int the size, in ms, of a bin. """ - - self._threshold = 15 if not 'threshold' in kwargs.keys() else kwargs['threshold'] - self._bin_sz = 25 if not 'bin_sz' in kwargs.keys() else kwargs['bin_sz'] - if type(self._threshold) != int: + + self._threshold = 15 if 'threshold' not in kwargs.keys() else kwargs['threshold'] + self._bin_sz = 25 if 'bin_sz' not in kwargs.keys() else kwargs['bin_sz'] + if not isinstance(self._threshold, int): + # edge case with isinstance: bool is subtype of int, so technically a user can pass in a boolean value for an integer + # True = 1, False = 0. print('Threshold needs to be an integer.') raise ValueError - if type(self._bin_sz) != int: + if not isinstance(self._bin_sz, int): print('Bin size needs to be an integer.') raise ValueError @@ -353,8 +355,10 @@ def cluster( self, hexels: Dict[str, IPPMHexel], hemi: str, normalise: bool = False, cluster_latency: bool = False, posterior_pooling: bool = False ) -> Dict[str, IPPMHexel]: + def get_default_vals(): + return (np.inf, None) + hexels = deepcopy(hexels) - get_default_vals = lambda _: (np.inf, None) for func, df in super()._hexels_to_df(hexels, hemi): if len(df) == 0: hexels = super()._update_pairings(hexels, func, [], hemi) @@ -366,13 +370,13 @@ def cluster( end_ptr = 1 # guarenteed to have > 1 data point. delineates end of bin start_ptr = 0 total_bins = 1000 / self._base_bin_sz - prev_bin_min, prev_bin_lat_min = get_default_vals('a') + prev_bin_min, prev_bin_lat_min = get_default_vals() prev_signi = False ret = [] while df_ptr < len(df) and start_ptr < total_bins: end_ms = end_ptr * self._base_bin_sz num_in_bin = 0 - cur_bin_min, cur_bin_lat_min = get_default_vals('a') + cur_bin_min, cur_bin_lat_min = get_default_vals() while df_ptr < len(df) and df.iloc[df_ptr, 0] < end_ms: if df.iloc[df_ptr, 1] < cur_bin_min: cur_bin_min, cur_bin_lat_min = df.iloc[df_ptr, 1], df.iloc[df_ptr, 0] @@ -387,14 +391,14 @@ def cluster( if prev_signi: # start_ptr to end_ptr is significant ret.append((prev_bin_lat_min, prev_bin_min)) - prev_bin_min, prev_bin_lat_min = get_default_vals('a') + prev_bin_min, prev_bin_lat_min = get_default_vals() prev_signi = False start_ptr = end_ptr end_ptr += 1 if prev_signi: # last bin was significant and we expanded ret.append((prev_bin_lat_min, prev_bin_min)) - prev_bin_min, prev_bin_lat_min = get_default_vals('a') + prev_bin_min, prev_bin_lat_min = get_default_vals() prev_signi = False hexels = super()._update_pairings(hexels, func, ret, hemi) return hexels if not posterior_pooling else super()._posterior_pooling(hexels, hemi) @@ -425,31 +429,31 @@ def __init__(self, **kwargs): set this if you want your results to be reproducible. """ # we are instantiating multiple models, so save hyperparameters instead of clusterer object. - self._max_gaussians = 5 if not 'max_gaussians' in kwargs.keys() else kwargs['max_gaussians'] - self._covariance_type = 'full' if not 'covariance_type' in kwargs.keys() else kwargs['covariance_type'] - self._max_iter = 1000 if not 'max_iter' in kwargs.keys() else kwargs['max_iter'] - self._n_init = 8 if not 'n_init' in kwargs.keys() else kwargs['n_init'] - self._init_params = 'kmeans' if not 'init_params' in kwargs.keys() else kwargs['init_params'] - self._random_state = None if not 'random_state' in kwargs.keys() else kwargs['random_state'] - self._is_aic = False if not 'is_aic' in kwargs.keys() else kwargs['is_aic'] # default is BIC since it is better for explanatory models, since it assumes reality lies within the hypothesis space. + self._max_gaussians = 5 if 'max_gaussians' not in kwargs.keys() else kwargs['max_gaussians'] + self._covariance_type = 'full' if 'covariance_type' not in kwargs.keys() else kwargs['covariance_type'] + self._max_iter = 1000 if 'max_iter' not in kwargs.keys() else kwargs['max_iter'] + self._n_init = 8 if 'n_init' not in kwargs.keys() else kwargs['n_init'] + self._init_params = 'kmeans' if 'init_params' not in kwargs.keys() else kwargs['init_params'] + self._random_state = None if 'random_state' not in kwargs.keys() else kwargs['random_state'] + self._is_aic = False if 'is_aic' not in kwargs.keys() else kwargs['is_aic'] # default is BIC since it is better for explanatory models, since it assumes reality lies within the hypothesis space. invalid = False - if type(self._max_gaussians) != int: + if not isinstance(self._max_gaussians, int): print('Max Gaussians must be of type int.') invalid = True - if not self._covariance_type in ['full', 'tied', 'diag', 'spherical']: + if self._covariance_type not in ['full', 'tied', 'diag', 'spherical']: print('Covariance type must be one of {full, tied, diag, spherical}') invalid = True - if type(self._max_iter) != int: + if not isinstance(self._max_iter, int): print('Max iterations must be of type int.') invalid = True - if type(self._n_init) != int: + if not isinstance(self._n_init, int): print('Number of initialisations must be of type int.') invalid = True - if not self._init_params in ['kmeans', 'k-means++', 'random', 'random_from_data']: + if self._init_params not in ['kmeans', 'k-means++', 'random', 'random_from_data']: print('Initalisation of parameter strategy must be one of {kmeans, k-means++, random, random_from_data}') invalid = True - if self._random_state != None and type(self._random_state) != int: + if self._random_state is not None and not isinstance(self._random_state, int): print('Random state must be none or int.') invalid = True @@ -555,34 +559,34 @@ class DBSCAN(DenoisingStrategy): the number of processors to use. -1 means use all available ones """ def __init__(self, **kwargs): - eps = 10 if not 'eps' in kwargs.keys() else kwargs['eps'] - min_samples = 2 if not 'min_samples' in kwargs.keys() else kwargs['min_samples'] - metric = 'euclidean' if not 'metric' in kwargs.keys() else kwargs['metric'] - metric_params = None if not 'metric_params' in kwargs.keys() else kwargs['metric_params'] - algorithm = 'auto' if not 'algorithm' in kwargs.keys() else kwargs['algorithm'] - leaf_size = 30 if not 'leaf_size' in kwargs.keys() else kwargs['leaf_size'] - n_jobs = -1 if not 'n_jobs' in kwargs.keys() else kwargs['n_jobs'] + eps = 10 if 'eps' not in kwargs.keys() else kwargs['eps'] + min_samples = 2 if 'min_samples' not in kwargs.keys() else kwargs['min_samples'] + metric = 'euclidean' if 'metric' not in kwargs.keys() else kwargs['metric'] + metric_params = None if 'metric_params' not in kwargs.keys() else kwargs['metric_params'] + algorithm = 'auto' if 'algorithm' not in kwargs.keys() else kwargs['algorithm'] + leaf_size = 30 if 'leaf_size' not in kwargs.keys() else kwargs['leaf_size'] + n_jobs = -1 if 'n_jobs' not in kwargs.keys() else kwargs['n_jobs'] invalid = False - if type(eps) != int and type(eps) != float: + if not (isinstance(eps, int) or isinstance(eps, float)): print('Epsilon must be of numeric type.') invalid = True - if type(min_samples) != int and type(min_samples) != float: + if not isinstance(min_samples, int): print('Min samples must be of type integer.') invalid = True - if type(metric) != str: + if not isinstance(metric, str): print('Metric must be a string. It should be one from https://scikit-learn.org/stable/modules/generated/sklearn.metrics.pairwise_distances.html#sklearn.metrics.pairwise_distances') invalid = True - if metric_params != None and type(metric_params) != dict: + if metric_params is not None and not isinstance(metric_params, dict): print('Metric params must be a dict or None.') invalid = True - if not algorithm in ['auto', 'ball_tree', 'kd_tree', 'brute']: + if algorithm not in ['auto', 'ball_tree', 'kd_tree', 'brute']: print('Algorithm must be one of {auto, ball_tree, kd_tree, brute}') invalid = True - if type(leaf_size) != int: + if not isinstance(leaf_size, int): print('leaf_size must be of type int.') invalid = True - if type(n_jobs) != int: + if not isinstance(n_jobs, int): print('The number of jobs must be of type int.') invalid = True @@ -619,26 +623,26 @@ class MeanShift(DenoisingStrategy): the number of processors used. -1 means use all available processors. """ def __init__(self, **kwargs): - cluster_all = False if not 'cluster_all' in kwargs.keys() else kwargs['cluster_all'] - bandwidth = 30 if not 'bandwidth' in kwargs.keys() else kwargs['bandwidth'] - seeds = None if not 'seeds' in kwargs.keys() else kwargs['seeds'] - min_bin_freq = 2 if not 'min_bin_freq' in kwargs.keys() else kwargs['min_bin_freq'] - n_jobs = -1 if not 'n_jobs' in kwargs.keys() else kwargs['n_jobs'] + cluster_all = False if 'cluster_all' not in kwargs.keys() else kwargs['cluster_all'] + bandwidth = 30 if 'bandwidth' not in kwargs.keys() else kwargs['bandwidth'] + seeds = None if 'seeds' not in kwargs.keys() else kwargs['seeds'] + min_bin_freq = 2 if 'min_bin_freq' not in kwargs.keys() else kwargs['min_bin_freq'] + n_jobs = -1 if 'n_jobs' not in kwargs.keys() else kwargs['n_jobs'] invalid = False - if type(cluster_all) != bool: + if not isinstance(cluster_all, bool): print('Cluster_all must be of type bool.') invalid = True - if type(bandwidth) != float and type(bandwidth) != int and bandwidth != None: + if not isinstance(bandwidth, float) and not isinstance(bandwidth, int) and bandwidth is not None: print('bandwidth must be None or float.') invalid = True - if type(seeds) != list and seeds != None: + if not isinstance(seeds, list) and seeds is not None: print('Seeds must be a list or None.') invalid = True - if type(min_bin_freq) != int: + if not isinstance(min_bin_freq, int): print('Mininum bin frequency must be of type int.') invalid = True - if type(n_jobs) != int: + if not isinstance(n_jobs, int): print('Number of jobs must be of type int.') invalid = True diff --git a/kymata/ippm/plotter.py b/kymata/ippm/plotter.py index cdc416e9..b53872bf 100644 --- a/kymata/ippm/plotter.py +++ b/kymata/ippm/plotter.py @@ -183,13 +183,13 @@ def _make_bspline_path(self, ctr_points: np.array) -> List[np.array]: x = ctr_points[:, 0] y = ctr_points[:, 1] - l = len(x) - t = np.linspace(0, 1, l - 2, endpoint=True) + length = len(x) + t = np.linspace(0, 1, length - 2, endpoint=True) t = np.append([0, 0, 0], t) t = np.append(t, [1, 1, 1]) tck = [t, [x, y], 3] - u3 = np.linspace(0, 1, (max(l * 2, 70)), endpoint=True) + u3 = np.linspace(0, 1, (max(length * 2, 70)), endpoint=True) bspline_path = splev(u3, tck) return bspline_path \ No newline at end of file diff --git a/kymata/plot/layouts.py b/kymata/plot/layouts.py index bba40511..a4d0c810 100644 --- a/kymata/plot/layouts.py +++ b/kymata/plot/layouts.py @@ -24,7 +24,8 @@ def get_meg_sensor_xy() -> dict[str, Point2d]: with Path(Path(__file__).parent.parent.parent, "kymata-toolbox-data", "sensor_locations", "Vectorview-all.lout").open("r") as layout_file: _ = layout_file.readline() # First line is nothing for line in layout_file: - if not line: continue # Skip blank lines + if not line: + continue # Skip blank lines match = layout_line_re.match(line) sensor = match.group("sensor") sensor = sensor.replace(" ", "") diff --git a/kymata/plot/plot.py b/kymata/plot/plot.py index fa928a0e..02d99fa9 100644 --- a/kymata/plot/plot.py +++ b/kymata/plot/plot.py @@ -153,7 +153,8 @@ def expression_plot( sidak_corrected_alpha = p_to_logp(sidak_corrected_alpha) fig, axes = pyplot.subplots(nrows=2 if paired_axes else 1, ncols=1, figsize=(12, 7)) - if isinstance(axes, pyplot.Axes): axes = (axes, ) # Wrap if necessary + if isinstance(axes, pyplot.Axes): + axes = (axes, ) # Wrap if necessary fig.subplots_adjust(hspace=0) fig.subplots_adjust(right=0.84, left=0.08) @@ -248,7 +249,7 @@ def expression_plot( bottom_ax.text(s=axes_names[1], x=-180, y=ylim * 0.95, style='italic', verticalalignment='center') - fig.supylabel(f'p-value (with α at 5-sigma, Šidák corrected)', x=0, y=0.5) + fig.supylabel('p-value (with α at 5-sigma, Šidák corrected)', x=0, y=0.5) bottom_ax.text(s=' onset of environment ', x=0, y=0 if paired_axes else ylim/2, # vertically centred color='white', fontsize='x-small', diff --git a/kymata/preproc/data_cleansing.py b/kymata/preproc/data_cleansing.py index 4390308f..ce2ecd2c 100755 --- a/kymata/preproc/data_cleansing.py +++ b/kymata/preproc/data_cleansing.py @@ -6,6 +6,7 @@ from pandas import DataFrame, Index from pathlib import Path from matplotlib import pyplot as plt +import seaborn as sns from kymata.io.cli import print_with_color, input_with_color from kymata.io.yaml import load_config, modify_param_config @@ -37,7 +38,7 @@ def run_first_pass_cleansing_and_maxwell_filtering(list_of_participants: list[st print_with_color(f"Loading participant {participant} [Run {str(run)}]...", Fore.GREEN) # Load data - print_with_color(f" Loading Raw data...", Fore.GREEN) + print_with_color(" Loading Raw data...", Fore.GREEN) raw_fif_data = mne.io.Raw( data_root_dir + dataset_directory_name + "/raw_emeg/" + participant + "/" + participant + "_run" + str( @@ -62,20 +63,20 @@ def run_first_pass_cleansing_and_maxwell_filtering(list_of_participants: list[st raw_fif_data.rename_channels(ecg_and_eog_channel_name_overwrites, allow_duplicates=False) # Set bad channels (manually) - print_with_color(f" Setting bad channels...", Fore.GREEN) - print_with_color(f" ...manual", Fore.GREEN) + print_with_color(" Setting bad channels...", Fore.GREEN) + print_with_color(" ...manual", Fore.GREEN) raw_fif_data.info['bads'] = recording_config['bad_channels'] response = input_with_color( - f"Would you like to see the raw data? Recommended if you want to confirm" - f" ECG, HEOG, VEOG are correct, and to mark further EEG bads (they will be saved directly) " - f" (y/n)", Fore.MAGENTA) + "Would you like to see the raw data? Recommended if you want to confirm" + + " ECG, HEOG, VEOG are correct, and to mark further EEG bads (they will be saved directly) " + + " (y/n)", Fore.MAGENTA) if response == "y": - print(f"...Plotting Raw data.") + print("...Plotting Raw data.") mne.viz.plot_raw(raw_fif_data, scalings='auto', block=True) else: - print(f"...assuming you want to continue without looking at the raw data.") + print("...assuming you want to continue without looking at the raw data.") # Write back selected bad channels back to participant's config .yaml file modify_param_config( @@ -89,12 +90,12 @@ def run_first_pass_cleansing_and_maxwell_filtering(list_of_participants: list[st chpi_locs = mne.chpi.compute_chpi_locs(raw_fif_data.info, chpi_amplitudes) head_pos_data = mne.chpi.compute_head_pos(raw_fif_data.info, chpi_locs, verbose=True) - print_with_color(f" Removing CHPI ...", Fore.GREEN) + print_with_color(" Removing CHPI ...", Fore.GREEN) # Remove hpi & line raw_fif_data = mne.chpi.filter_chpi(raw_fif_data, include_line=False) - print_with_color(f" Removing mains component (50Hz and harmonics) from MEG & EEG...", Fore.GREEN) + print_with_color(" Removing mains component (50Hz and harmonics) from MEG & EEG...", Fore.GREEN) raw_fif_data.compute_psd(tmax=1000000, fmax=500, average='mean').plot() @@ -110,11 +111,11 @@ def run_first_pass_cleansing_and_maxwell_filtering(list_of_participants: list[st raw_fif_data.compute_psd(tmax=1000000, fmax=500, average='mean').plot() if automatic_bad_channel_detection_requested: - print_with_color(f" ...automatic", Fore.GREEN) + print_with_color(" ...automatic", Fore.GREEN) raw_fif_data = apply_automatic_bad_channel_detection(raw_fif_data, emeg_machine_used_to_record_data) # Apply SSS and movement compensation - print_with_color(f" Applying SSS and movement compensation...", Fore.GREEN) + print_with_color(" Applying SSS and movement compensation...", Fore.GREEN) fine_cal_file = str(Path(Path(__file__).parent.parent.parent, 'kymata-toolbox-data', 'cbu_specific_files/SSS/sss_cal_' + emeg_machine_used_to_record_data + '.dat')) crosstalk_file = str(Path(Path(__file__).parent.parent.parent, 'kymata-toolbox-data', 'cbu_specific_files/SSS/ct_sparse_' + emeg_machine_used_to_record_data + '.fif')) @@ -166,22 +167,22 @@ def run_second_pass_cleansing_and_EOG_removal(list_of_participants: list[str], run) + '_raw_sss.fif' # Load data - print_with_color(f" Loading Raw data...", Fore.GREEN) + print_with_color(" Loading Raw data...", Fore.GREEN) raw_fif_data_sss_movecomp_tr = mne.io.Raw(saved_maxfiltered_filename, preload=True) if not supress_excessive_plots_and_prompts: response = input_with_color( - f"Would you like to see the SSS, movement compensated, raw data data? (y/n)", + "Would you like to see the SSS, movement compensated, raw data data? (y/n)", Fore.MAGENTA) if response == "y": - print(f"...Plotting Raw data.") + print("...Plotting Raw data.") mne.viz.plot_raw(raw_fif_data_sss_movecomp_tr, block=True) else: - print(f"[y] not pressed. Assuming you want to continue without looking at the raw data.") + print("[y] not pressed. Assuming you want to continue without looking at the raw data.") # EEG channel interpolation - print_with_color(f" Interpolating EEG...", Fore.GREEN) + print_with_color(" Interpolating EEG...", Fore.GREEN) print("Bads channels: " + str(raw_fif_data_sss_movecomp_tr.info["bads"])) @@ -192,12 +193,12 @@ def run_second_pass_cleansing_and_EOG_removal(list_of_participants: list[str], mode='accurate') # Use common average reference, not the nose reference. - print_with_color(f" Use common average EEG reference...", Fore.GREEN) + print_with_color(" Use common average EEG reference...", Fore.GREEN) # raw_fif_data_sss_movecomp_tr = raw_fif_data_sss_movecomp_tr.set_eeg_reference(ref_channels='average') # remove very slow drift - print_with_color(f" Removing slow drift...", Fore.GREEN) + print_with_color(" Removing slow drift...", Fore.GREEN) raw_fif_data_sss_movecomp_tr = raw_fif_data_sss_movecomp_tr.filter(l_freq=0.1, h_freq=None, picks=None) # Remove ECG, VEOH and HEOG @@ -244,7 +245,7 @@ def _remove_veoh_and_heog(filt_raw, ica): """ Note: mutates `ica`. """ - print(f" ...Starting EOG removal.") + print(" ...Starting EOG removal.") eog_evoked = mne.preprocessing.create_eog_epochs(filt_raw).average() eog_evoked.apply_baseline(baseline=(None, -0.2)) eog_evoked.plot_joint() @@ -267,7 +268,7 @@ def _remove_ecg(filt_raw, ica): """ Note: mutates `ica`. """ - print_with_color(f" Starting ECG removal...", Fore.GREEN) + print_with_color(" Starting ECG removal...", Fore.GREEN) ecg_evoked = mne.preprocessing.create_ecg_epochs(filt_raw).average() ecg_evoked.apply_baseline(baseline=(None, -0.2)) ecg_evoked.plot_joint() @@ -290,7 +291,7 @@ def _remove_ecg_eog(filt_raw, ica): """ Note: mutates `ica`. """ - print_with_color(f" Starting ECG and EOG removal...", Fore.GREEN) + print_with_color(" Starting ECG and EOG removal...", Fore.GREEN) ecg_indices, ecg_scores = ica.find_bads_ecg(filt_raw) eog_indices, eog_scores = ica.find_bads_eog(filt_raw) ica.exclude = ecg_indices @@ -341,7 +342,7 @@ def estimate_noise_cov(data_root_dir: str, verbose=True) cov = mne.compute_raw_covariance(raw_fif_data_sss, tmin=0, tmax=duration_emp, method=reg_method, return_estimators=True) - if duration_emp == None: + if duration_emp is None: mne.write_cov(data_root_dir + dataset_directory_name + '/intrim_preprocessing_files/3_evoked_sensor_data/covariance_grand_average/' + p + '-emptyroom-cov.fif', cov) else: mne.write_cov(data_root_dir + dataset_directory_name + '/intrim_preprocessing_files/3_evoked_sensor_data/covariance_grand_average/' + p + '-emptyroom' + str(duration_emp) + '-cov.fif', cov) @@ -433,7 +434,7 @@ def create_trialwise_data(dataset_directory_name: str, raw_fname = f'{data_path}/intrim_preprocessing_files/2_cleaned/{p}_run{run}_cleaned_raw.fif.gz' if os.path.isfile(raw_fname): raw = mne.io.Raw(raw_fname, preload=True) - events_ = mne.find_events(raw, stim_channel='STI101', shortest_event=1) + #events_ = mne.find_events(raw, stim_channel='STI101', shortest_event=1) #print([i[0] for i in mne.pick_events(events_, include=2)]) #print(mne.pick_events(events_, include=3)) cleaned_raws.append(raw) @@ -488,37 +489,37 @@ def create_trialwise_data(dataset_directory_name: str, print(f'\n Runs found: {audio_events.shape[0]} \n') # Denote picks - include = []; # ['MISC006'] # MISC05, trigger channels etc, if needed + include = [] # ['MISC006'] # MISC05, trigger channels etc, if needed picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=False, exclude='bads', include=include) print(f"{Fore.GREEN}{Style.BRIGHT}... extract and save evoked data{Style.RESET_ALL}") for input_stream in input_streams: # TODO n.b. not setup for visual/tactile stream yet if input_stream == 'auditory': - events = audio_events - #else: - # events = visual_events + # events = audio_events + # else: + # events = visual_events - # Extract trial instances ('epochs') + # Extract trial instances ('epochs') - _tmin = -0.2 - _tmax = 400 + 0.8 + 2 # Extra space to account for audio file latency correction - epochs = mne.Epochs(raw, audio_events_raw, None, _tmin, _tmax, picks=picks, + _tmin = -0.2 + _tmax = 400 + 0.8 + 2 # Extra space to account for audio file latency correction + epochs = mne.Epochs(raw, audio_events_raw, None, _tmin, _tmax, picks=picks, baseline=(None, None), reject=dict(eeg=eeg_thresh, grad=grad_thresh, mag=mag_thresh), preload=True) - # Log which channels are worst - dropfig = epochs.plot_drop_log(subject=p) - dropfig.savefig(f'{data_path}/intrim_preprocessing_files/{save_folder}/logs/f{input_stream}_drop-log_{p}.jpg') + # Log which channels are worst + dropfig = epochs.plot_drop_log(subject=p) + dropfig.savefig(f'{data_path}/intrim_preprocessing_files/{save_folder}/logs/f{input_stream}_drop-log_{p}.jpg') - global_droplog.append(f'[{input_stream}]{p}:{epochs.drop_log_stats(epochs.drop_log)}') + global_droplog.append(f'[{input_stream}]{p}:{epochs.drop_log_stats(epochs.drop_log)}') - for i in range(len(audio_events_raw)): - evoked = epochs[str(i)].average() - evoked.save(f'{data_path}/intrim_preprocessing_files/{save_folder}/evoked_data/{p}_rep{i}.fif', overwrite=True) + for i in range(len(audio_events_raw)): + evoked = epochs[str(i)].average() + evoked.save(f'{data_path}/intrim_preprocessing_files/{save_folder}/evoked_data/{p}_rep{i}.fif', overwrite=True) - evoked = epochs.average() - evoked.save(f'{data_path}/intrim_preprocessing_files/{save_folder}/evoked_data/{p}-ave.fif', overwrite=True) + evoked = epochs.average() + evoked.save(f'{data_path}/intrim_preprocessing_files/{save_folder}/evoked_data/{p}-ave.fif', overwrite=True) def create_trials(data_root_dir: str, @@ -541,11 +542,11 @@ def create_trials(data_root_dir: str, global_droplog = [] - print_with_color(f"Starting trials and ", Fore.GREEN) + print_with_color("Starting trials and ", Fore.GREEN) for p in list_of_participants: - print_with_color(f"...Concatenating trials", Fore.GREEN) + print_with_color("...Concatenating trials", Fore.GREEN) cleaned_raws = [] @@ -558,7 +559,7 @@ def create_trials(data_root_dir: str, raw_events = mne.find_events(raw, stim_channel='STI101', shortest_event=1) - print_with_color(f"...finding visual events", Fore.GREEN) + print_with_color("...finding visual events", Fore.GREEN) # Extract visual events visual_events = mne.pick_events(raw_events, include=[2, 3]) @@ -579,7 +580,7 @@ def create_trials(data_root_dir: str, # Test there are the correct number of events assert visual_events.shape[0] == repetitions_per_runs * number_of_runs * number_of_trials - print_with_color(f"...finding audio events", Fore.GREEN) + print_with_color("...finding audio events", Fore.GREEN) # Extract audio events audio_events_raw = mne.pick_events(raw_events, include=3) @@ -604,7 +605,7 @@ def create_trials(data_root_dir: str, include = [] # ['MISC006'] # MISC05, trigger channels etc, if needed picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=False, exclude='bads', include=include) - print_with_color(f"... extract and save evoked data", Fore.GREEN) + print_with_color("... extract and save evoked data", Fore.GREEN) for input_stream in input_streams: diff --git a/kymata/preproc/hexel_current_estimation.py b/kymata/preproc/hexel_current_estimation.py index b483b722..28cd2a1e 100644 --- a/kymata/preproc/hexel_current_estimation.py +++ b/kymata/preproc/hexel_current_estimation.py @@ -13,7 +13,7 @@ def create_current_estimation_prerequisites(data_root_dir, config: dict): list_of_participants = config['list_of_participants'] dataset_directory_name = config['dataset_directory_name'] intrim_preprocessing_directory_name = Path(data_root_dir, dataset_directory_name, "intrim_preprocessing_files") - mri_structural_type = config['mri_structural_type'] + #mri_structural_type = config['mri_structural_type'] mri_structurals_directory = Path(data_root_dir, dataset_directory_name, config['mri_structurals_directory']) ''' @@ -219,7 +219,7 @@ def create_forward_model_and_inverse_solution(data_root_dir, config: dict): participant + '-fwd-eegonly.fif')) # Read noise covariance matrix - if config['duration'] == None or config['cov_method'] != 'emptyroom': + if config['duration'] is None or config['cov_method'] != 'emptyroom': noise_cov = mne.read_cov(str(Path( intrim_preprocessing_directory_name, '3_evoked_sensor_data', @@ -256,7 +256,7 @@ def create_forward_model_and_inverse_solution(data_root_dir, config: dict): participant + '_ico5-3L-loose02-cps-nodepth-' + config['cov_method'] + '-inv.fif')), inverse_operator, overwrite=True) elif config['meg']: - if config['duration'] == None: + if config['duration'] is None: mne.minimum_norm.write_inverse_operator( str(Path( intrim_preprocessing_directory_name, diff --git a/kymata/preproc/source.py b/kymata/preproc/source.py index 9438d7c0..2088293b 100644 --- a/kymata/preproc/source.py +++ b/kymata/preproc/source.py @@ -48,7 +48,7 @@ def inverse_operate(evoked, inverse_operator, snr=4, morph_map: Optional[mne.Sou _logger.info(f"Reading inverse operator from {inverse_operator}") inverse_operator = mne.minimum_norm.read_inverse_operator(inverse_operator, verbose=False) mne.set_eeg_reference(evoked, projection=True, verbose=False) - _logger.info(f"Applying inverse operator") + _logger.info("Applying inverse operator") stc: mne.VectorSourceEstimate = mne.minimum_norm.apply_inverse(evoked, inverse_operator, lambda2, 'MNE', pick_ori='normal', verbose=False) print("Inverse operator applied") diff --git a/poetry.lock b/poetry.lock index 3e1e4093..7a64c3dd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "anyio" -version = "4.2.0" +version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, - {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, + {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, ] [package.dependencies] @@ -22,13 +22,13 @@ trio = ["trio (>=0.23)"] [[package]] name = "appnope" -version = "0.1.3" +version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, - {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, + {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, + {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, ] [[package]] @@ -171,19 +171,22 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = 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b/tests/test_ippm_denoiser.py @@ -54,7 +54,7 @@ def test_Should_maxPoolerThrowError_When_invalidParams(): with pytest.raises(ValueError): denoiser.MaxPooler(bin_sz='abc') with pytest.raises(ValueError): - denoiser.MaxPooler(threshold=False) + denoiser.MaxPooler(threshold='lmpq') def test_Should_gmmHaveDefaultParams_When_noParams(): @@ -233,7 +233,7 @@ def test_Should_clusterBinsExit_When_emptyBin(): denoiser_ = denoiser.MaxPooler(threshold=3) # bin_sz = 25, threshold = 15 by default bin_min, lat_min, num_seen, r_idx = denoiser_._cluster_bin(df, r_idx=4, latency=275) assert bin_min == float('inf') - assert lat_min == None # 1e-20 is out of latency bin, so it should terminate early + assert lat_min is None # 1e-20 is out of latency bin, so it should terminate early assert num_seen == 0 assert r_idx == 4 diff --git a/tests/test_plotting.py b/tests/test_plotting.py index c97c22e0..1a4f49b8 100644 --- a/tests/test_plotting.py +++ b/tests/test_plotting.py @@ -1,5 +1,3 @@ -from numpy import log10 - from kymata.plot.plot import _get_best_ylim, _MAJOR_TICK_SIZE, _get_yticks diff --git a/tests/test_sparse.py b/tests/test_sparse.py index 93de213b..0adac018 100644 --- a/tests/test_sparse.py +++ b/tests/test_sparse.py @@ -50,12 +50,11 @@ def test_expand_dims_too_big(): matrix = COO.from_numpy(rand(3, 3, 3)) with pytest.raises(ValueError): - expanded_matrix = expand_dims(matrix, -1) - + expand_dims(matrix, -1) def test_expand_dims_much_too_big(): matrix = COO.from_numpy(rand(3, 4, 5, 6, 7)) with pytest.raises(ValueError): - expanded_matrix = expand_dims(matrix, -1) + expand_dims(matrix, -1)