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fixed small bugs in eels widgets
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@gduscher
gduscher committed Aug 20, 2023
1 parent c6c4ebd commit 19af0b8
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Showing 6 changed files with 394 additions and 93 deletions.
158 changes: 117 additions & 41 deletions notebooks/EELS/Analysis_Core_Loss.ipynb
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188 changes: 151 additions & 37 deletions pyTEMlib/eels_dialog.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,8 @@ def update_element(self, z):
if int(minor_edge[-1]) % 2 == 0 or key[-1] > minor_edge[-1]:
minor_edge = key

all_edges[key] = {'onset': x_section[key]['onset']}
all_edges[key] = {'onset': x_section[key]['onset'], 'original_onset': x_section[key]['onset']}


if major_edge != '':
key = major_edge
Expand Down Expand Up @@ -897,6 +898,87 @@ def get_sidebar():
return side_bar


import ipywidgets

def get_periodic_table_widget(energy_scale=None):

if energy_scale is None:
energy_scale = [100., 150., 200.]

likely_edges = eels_dialog_utilities.get_likely_edges(energy_scale)

pt_info = eels_dialog_utilities.get_periodic_table_info()
table = ipywidgets.GridspecLayout(10, 18,width= '60%', grid_gap="0px")
for symbol, parameter in pt_info.items():
#print(parameter['PT_row'], parameter['PT_col'])
if parameter['PT_row'] > 7:
color = 'warning'
elif '*' in symbol:
color = 'warning'
else:
if symbol in likely_edges:
color = 'primary'
else:
color = 'info'
table[parameter['PT_row'], parameter['PT_col']] = ipywidgets.ToggleButton(description=symbol,
value=False,
button_style=color,
layout=ipywidgets.Layout(width='auto'),
style={"button_width": "30px"})
return table


class PeriodicTableWidget(object):
""" Modal dialog to get a selection of elements.
Elements that are not having a valid cross-sections are disabled.
Parameters
----------
initial_elements: list of str
the elements that are already selected
energy_scale: list or numpy array
energy-scale of spectrum/spectra to determine likely edges
Returns
-------
list of strings: elements.
Example
-------
>> PT_dialog = periodic_table_dialog(None, ['Mn', 'O'])
>> if PT_dialog.exec_() == periodic_table_dialog.Accepted:
>> selected_elements = PT_dialog.get_output()
>> print(selected_elements)
"""

def __init__(self, initial_elements=None, energy_scale=None):

if initial_elements is None:
initial_elements = [' ']
self.elements_selected = initial_elements
if energy_scale is None:
energy_scale = [100., 150., 200.]
self._output = []
self.energy_scale = np.array(energy_scale)
self.pt_info = eels_dialog_utilities.get_periodic_table_info()

self.periodic_table = get_periodic_table_widget(energy_scale)
self.update()

def get_output(self):
self.elements_selected = []
for symbol, parameter in self.pt_info.items():
if self.periodic_table[parameter['PT_row'], parameter['PT_col']].value == True: # [parameter['PT_row'], parameter['PT_col']]
self.elements_selected.append(self.periodic_table[parameter['PT_row'], parameter['PT_col']].description)
return self.elements_selected

def update(self):
for symbol, parameter in self.pt_info.items():
if self.periodic_table[parameter['PT_row'], parameter['PT_col']].description in self.elements_selected:
self.periodic_table[parameter['PT_row'], parameter['PT_col']].value = True


class CompositionWidget(object):
def __init__(self, datasets=None):
self.datasets = datasets
Expand Down Expand Up @@ -930,7 +1012,7 @@ def __init__(self, datasets=None):
self.fig.canvas.toolbar_visible = True
self.key = list(self.datasets.keys())[0]
self.set_dataset()
self.set_action()

self.y_scale = 1.0
self.change_y_scale = 1.0
self.plot(scale=False)
Expand All @@ -944,15 +1026,24 @@ def __init__(self, datasets=None):
self.start_cursor,ipywidgets.Label('eV'),
self.end_cursor, ipywidgets.Label('eV')]),
self.fig.canvas])

self.periodic_table = PeriodicTableWidget(self.energy_scale)
self.elements_cancel_button = ipywidgets.Button(description='Cancel')
self.elements_select_button = ipywidgets.Button(description='Select')
self.elements_auto_button = ipywidgets.Button(description='Auto ID')

self.periodic_table_panel = ipywidgets.VBox([self.periodic_table.periodic_table,
ipywidgets.HBox([self.elements_cancel_button, self.elements_auto_button, self.elements_select_button])])
# Button(description=description, button_style=button_style, layout=Layout(height='auto', width='auto'))

self.app_layout = ipywidgets.AppLayout(
left_sidebar=self.sidebar,
center=self.panel,
center=self.panel, ## can be changed with: self.app_layout.center = self.periodic_table.periodic_table
footer=None,#message_bar,
pane_heights=[0, 10, 0],
pane_widths=[4, 10, 0],
)
IPython.display.display(self.app_layout)
self.set_action()

def line_select_callback(self, x_min, x_max):
self.start_cursor.value = np.round(x_min,3)
Expand Down Expand Up @@ -1131,8 +1222,6 @@ def update_element(self, z=0, index=-1):
self.edges[str(index)]['areal_density'] = 0.0
self.edges[str(index)]['original_onset'] = self.edges[str(index)]['onset']
return True



def sort_elements(self):
onsets = []
Expand All @@ -1159,24 +1248,36 @@ def sort_elements(self):
if edge['end_exclude'] > self.energy_scale[-3]:
edge['end_exclude'] = self.energy_scale[-3]

def set_elements(self, selected_elements):
def set_elements(self, value=0):
selected_elements = self.periodic_table.get_output()
edges = self.edges.copy()
to_delete = []
old_elements = []
if len(selected_elements) > 0:
for key in self.edges:
if key.isdigit():
to_delete.append(key)
old_elements.append(self.edges[key]['element'])

for key in to_delete:
edges[key] = self.edges[key]
del self.edges[key]

for index, elem in enumerate(selected_elements):
self.sidebar[4, 0].value =index
self.update_element(elem)

# self.sort_elements()
if elem in old_elements:
self.edges[str(index)] = edges[str(old_elements.index(elem))]
else:
self.update_element(elem, index=index)
self.sort_elements()
self.update()

self.set_figure_pane()


def set_element(self, elem):
self.update_element(self.sidebar[5, 0].value)
# self.sort_elements()
self.update()

def cursor2energy_scale(self, value):

dispersion = (self.end_cursor.value - self.start_cursor.value) / (self.end_channel - self.start_channel)
self.datasets[self.key].energy_loss *= (self.sidebar[3, 0].value/dispersion)
self.sidebar[3, 0].value = dispersion
Expand All @@ -1199,38 +1300,43 @@ def set_fit_area(self, value):

def set_y_scale(self, value):
self.change_y_scale = 1/self.y_scale
if self.sidebar[12, 0].value:
dispersion = self.energy_scale[1] - self.energy_scale[0]
self.y_scale = 1/self.dataset.metadata['experiment']['flux_ppm'] * dispersion
else:
self.y_scale = 1.0
self.y_scale = 1.0
if self.dataset.metadata['experiment']['flux_ppm'] > 0:
if self.sidebar[12, 0].value:
dispersion = self.energy_scale[1] - self.energy_scale[0]
self.y_scale = 1/self.dataset.metadata['experiment']['flux_ppm'] * dispersion

self.change_y_scale *= self.y_scale
self.update()
self.plot()

def auto_id(self, value=0):
found_edges = eels.auto_id_edges(self.dataset)
if len(found_edges) > 0:
self.periodic_table.elements_selected = found_edges
self.periodic_table.update()

def find_elements(self, value=0):

if '0' not in self.edges:
self.edges['0'] ={}
found_edges = eels.auto_id_edges(self.dataset)

to_delete = []
if len(found_edges) >0:
for key in self.edges:
if key.isdigit():
to_delete.append(key)
for key in to_delete:
del self.edges[key]
if len(to_delete) > 0:
self.edges['0'] = {}
# found_edges = eels.auto_id_edges(self.dataset)
found_edges = {}

selected_elements = []
for key in found_edges:
selected_elements.append(key)
self.set_elements(selected_elements)
elements = self.edges.copy()

self.update()
for key in self.edges:
if key.isdigit():
if 'element' in self.edges[key]:
selected_elements.append(self.edges[key]['element'])
self.periodic_table.elements_selected = selected_elements
self.periodic_table.update()
self.app_layout.center = self.periodic_table_panel # self.periodic_table.periodic_table

def set_figure_pane(self, value=0):

self.app_layout.center = self.panel

def update(self, index=0):

Expand All @@ -1242,10 +1348,10 @@ def update(self, index=0):
self.sidebar[4,0].value = len(self.sidebar[4,0].options)-2
if str(index) not in self.edges:
self.edges[str(index)] = {'z': 0, 'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
'areal_density': 0}
'areal_density': 0, 'chemical_shift':0}
if 'z' not in self.edges[str(index)]:
self.edges[str(index)] = {'z': 0, 'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
'areal_density': 0}
'areal_density': 0, 'chemical_shift':0}
edge = self.edges[str(index)]

self.sidebar[5,0].value = edge['z']
Expand Down Expand Up @@ -1312,6 +1418,8 @@ def modify_onset(self, value=-1):
edge_index = self.sidebar[4, 0].value
edge = self.edges[str(edge_index)]
edge['onset'] = self.sidebar[7,0].value
if 'original_onset' not in edge:
edge['original_onset'] = edge['onset']
edge['chemical_shift'] = edge['onset'] - edge['original_onset']
self.update()

Expand Down Expand Up @@ -1340,7 +1448,9 @@ def modify_areal_density(self, value=-1):
self.model = self.edges['model']['background']
for key in self.edges:
if key.isdigit():
self.model = self.model + self.edges[key]['areal_density'] * self.edges[key]['data']
if 'data' in self.edges[key]:

self.model = self.model + self.edges[key]['areal_density'] * self.edges[key]['data']
self.plot()

def set_action(self):
Expand All @@ -1361,3 +1471,7 @@ def set_action(self):
self.sidebar[0, 0].observe(self.plot)

self.sidebar[12,0].observe(self.set_y_scale)

self.elements_cancel_button.on_click(self.set_figure_pane)
self.elements_auto_button.on_click(self.auto_id)
self.elements_select_button.on_click(self.set_elements)
3 changes: 3 additions & 0 deletions pyTEMlib/eels_dialog_utilities.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -347,6 +347,9 @@ def update(self):
self.axis.figure.canvas.draw()





class RegionSelector(object):
"""Selects fitting region and the regions that are excluded for each edge.
Expand Down
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