def acceptBatch(self):
"""
"""
experiment = self.experiment
if self.ui.listWidgetEvents.count() == 0:
message = 'Cannot create epochs from empty list.'
messagebox(self.parent, message)
return
try:
params = self.collect_parameter_values()
except Exception as exc:
exc_messagebox(self, exc)
return
selected_subject_names = self.batching_widget.selected_subjects
for name, subject in self.experiment.subjects.items():
if name in selected_subject_names:
try:
self.calculate_epochs(subject, params)
subject.release_memory()
except Exception as exc:
self.batching_widget.failed_subjects.append(
(subject, str(exc)))
logging.getLogger('ui_logger').exception(str(exc))
self.batching_widget.cleanup()
self.experiment.save_experiment_settings()
self.parent.initialize_ui()
logging.getLogger('ui_logger').info('Finished.')
self.close()
def on_pushButtonRemoveSubject_clicked(self, checked=None):
""" Completely removes selected subjects from the experiment """
if checked is None:
return
selIndexes = self.ui.listWidgetSubjects.selectedIndexes()
if selIndexes == []:
return
message = 'Permanently remove the selected subjects and the related files?'
reply = QtWidgets.QMessageBox.question(
self, 'Delete selected subjects', message,
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
failures = []
if reply == QtWidgets.QMessageBox.Yes:
for index in selIndexes:
subject_name = index.data()
try:
self.experiment.remove_subject(subject_name)
except Exception:
failures.append(subject_name)
if failures:
msg = ''.join([
'Could not remove the contents of the subject ',
'folder for following subjects: ', '\n'.join(failures)
])
messagebox(self, msg)
self.experiment.save_experiment_settings()
self.initialize_ui()
def _open_mne_coreg(window, on_close, raw_path, subjects_dir):
""" Opens mne coreg with some small changes.
"""
# Open the mne coregistration UI
open_message = (
"An external coregistration GUI is now opened. You should "
"fit the digization points to the scalp and then click save "
"on the right panel. The trans file should be saved as "
"`experiment_folder`/`subject_name`/coregistrations/"
"`coreg_name`/`subject_name`-trans.fif")
messagebox(window, open_message)
logging.getLogger('ui_logger').info('Opening coregistration utility.')
gui = mne.gui.coregistration(inst=raw_path,
subject='fsaverage',
subjects_dir=subjects_dir)
def close_wrapper(*args, **kwargs):
if not gui._accept_close_event:
return
logging.getLogger('ui_logger').info('Coregistration utility closed.')
on_close()
gui._renderer._window_close_connect(close_wrapper)
def on_pushButtonPreview_clicked(self, checked=None):
"""
Draws the preview.
"""
if checked is None:
return
params = self.collect_parameter_values()
if not params:
message = 'No filter(s) selected.'
messagebox(self.parent, message)
return
subject = self.experiment.active_subject
# mne-python's filter_data takes filter_length in human-readable format
params = deepcopy(params)
params['length'] = params['length'] + 's'
params['bandstop_length'] = params['bandstop_length'] + 's'
try:
raw_to = filter_data(params,
subject,
preview=True,
do_meanwhile=self.parent.update_ui)
raw_from = subject.get_raw()
compare_raws(raw_from, raw_to)
except Exception as exc:
exc_messagebox(self.parent, exc)
def accept(self):
if self.ui.lineEditExperimentName.text() == '':
message = 'Give experiment a name.'
messagebox(self.parent, message)
return
selected_pipeline = ""
for button_idx, radio_button in enumerate(self.pipeline_buttons):
if radio_button.isChecked():
selected_pipeline = self.pipelines[button_idx][0]
break
try:
experiment = initialize_new_experiment(
self.ui.lineEditExperimentName.text(),
self.ui.lineEditAuthor.text(), self.parent.prefs)
experiment.selected_pipeline = selected_pipeline
experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
self.parent.experiment = experiment
self.parent.reconstruct_tabs()
self.parent.initialize_ui()
self.close()
def on_pushButtonActivateSubject_clicked(self, checked=None):
if checked is None:
return
items = self.ui.listWidgetSubjects.selectedItems()
if not items:
return
subject_name = items[0].text()
if self.experiment.active_subject:
if subject_name == self.experiment.active_subject.name:
return
previous_subject = self.experiment.active_subject
try:
@threaded
def activate(subject_name):
self.experiment.activate_subject(subject_name)
activate(subject_name, do_meanwhile=self.update_ui)
self.reconstruct_tabs()
except Exception as exc:
self.experiment.active_subject = None
messagebox(self, "Could not activate the subject.")
if previous_subject:
message = "Couldn't activate the subject, resuming to previous one."
logging.getLogger('ui_logger').info(message)
self.experiment.activate_subject(previous_subject.name)
self.initialize_ui()
def handler(accepted):
if not accepted:
return
n_successful = 0
for index in selIndexes:
subject_name = index.data()
try:
self.experiment.remove_subject(subject_name)
n_successful += 1
except Exception:
logging.getLogger('ui_logger').exception('')
try:
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
n_total = len(selIndexes)
if n_successful != n_total:
message = ("Could not remove all subjects completely. "
"Please check console below for details.")
messagebox(self, message)
self.initialize_ui()
def accept(self):
"""
"""
if self.ui.listWidgetEvents.count() == 0:
message = 'Cannot create epochs from empty list.'
messagebox(self.parent, message)
return
try:
params = self.collect_parameter_values()
except Exception as exc:
exc_messagebox(self, exc)
return
subject = self.experiment.active_subject
if params['collection_name'] in subject.epochs:
message = 'Epoch collection with the name exists.'
messagebox(self.parent, message)
return
try:
self.calculate_epochs(subject, params)
except Exception as exc:
exc_messagebox(self, exc)
return
self.experiment.save_experiment_settings()
self.parent.initialize_ui()
logging.getLogger('ui_logger').info('Finished.')
self.close()
def accept(self):
workspace = self.ui.LineEditFilePath.text()
if not os.path.isdir(workspace):
message = 'Workspace must be set to proper path.'
messagebox(self.parent, message)
return
self.prefs.workspace = workspace
if self.ui.checkBoxAutomaticOpenPreviousExperiment.isChecked():
autoLoadLastOpenExp = True
else:
autoLoadLastOpenExp = False
self.prefs.auto_load_last_open_experiment = autoLoadLastOpenExp # noqa
self.prefs.active_plugins = self.active_plugins
try:
self.prefs.write_preferences_to_disk()
except Exception as exc:
exc_messagebox(self.parent, exc)
return
# Plugins can add new actions to existing pipelines.
self.parent.reconstruct_tabs()
self.parent.initialize_ui()
self.close()
def handler(self, subject, params):
raw = subject.get_raw()
if not raw.info['projs']:
messagebox(self.window, "Data does not contain any projection vectors")
return
fig = raw.plot_projs_topomap()
elems = ['projections', subject.name]
fig.canvas.set_window_title('_'.join(elems))
fig.suptitle(' '.join(elems))
def on_actionShowLog_triggered(self, checked=None):
if checked is None:
return
if not self.experiment:
message = 'Please open an experiment first.'
messagebox(self, message)
return
dialog = LogDialog(self)
dialog.show()
def on_pushButtonAdd_clicked(self, checked=None):
if checked is None:
return
group = str(self.ui.comboBoxAvgGroup.currentText())
tmin = self.ui.doubleSpinBoxTmin.value()
tmax = self.ui.doubleSpinBoxTmax.value()
if tmin >= tmax:
messagebox(self.parent,
"End time must be higher than the starting time")
return
self.add_intervals([('fixed', (group, tmin, tmax))])
def on_pushButtonAddSubjects_clicked(self, checked=None):
if checked is None:
return
# Check that we have an experiment that we can add a subject to
if not self.experiment:
msg = ('No active experiment to add a subject to. Load an '
'experiment or make a new one, then try again.')
messagebox(self, msg)
return
dialog = AddSubjectDialog(self)
dialog.show()
def on_actionCreateExperiment_triggered(self, checked=None):
if checked is None:
return
if not self.prefs.workspace:
messagebox(self,
"Please set up a workspace "
"(a place where experiments are stored) in preferences "
"before creating experiments")
dialog = PreferencesDialog(self)
dialog.show()
else:
dialog = CreateExperimentDialog(self)
dialog.show()
def projections(experiment, data, window):
"""
"""
subject = experiment.active_subject
raw = subject.get_raw()
if not raw.info['projs']:
messagebox(window, "Raw contains no projection vectors")
return
fig = raw.plot_projs_topomap()
title = 'projections_{0}'.format(subject.name)
fig.canvas.set_window_title(title)
fig.suptitle(title)
def cleanup(self, parent=None):
if len(self.failed_subjects) > 0:
rows = []
rows.append('Failed calculation for subjects:')
for subject, message in self.failed_subjects:
rows.append(subject.name + ' (' + message + ')')
if not parent:
parent = self.parent.parent
messagebox(parent, '\n'.join(rows))
self.failed_subjects = []
self.ui.checkBoxBatch.setChecked(False)
self.ui.functionalityWidget.hide()
def on_actionCreateExperiment_triggered(self, checked=None):
"""
"""
if checked is None:
return
if not self.preferencesHandler.working_directory:
messagebox(
self,
"Please set up a working directory before creating experiments"
)
self.check_workspace()
else:
dialog = CreateExperimentDialog(self)
dialog.experimentCreated.connect(self.set_experiment)
dialog.show()
def accept(self):
subject = self.experiment.active_subject
params = self._collect_parameter_values()
if not params:
message = 'No filter(s) selected'
messagebox(self.parent, message)
return
try:
self.handler(subject, params)
except Exception as exc:
exc_messagebox(self.parent, exc)
return
self.parent.initialize_ui()
self.close()
def cleanup(self):
""" Cleans the batching widget after use.
"""
if len(self.failed_subjects) > 0:
rows = []
rows.append('Failed calculation for subjects:')
for subject, message in self.failed_subjects:
rows.append(subject.name + ' (' + message + ')')
parent = self.parent.parent
messagebox(parent, '\n'.join(rows))
self.failed_subjects = []
self.ui.checkBoxBatch.setChecked(False)
self.ui.functionalityWidget.hide()
def accept(self):
n_successful = 0
for i in range(self.ui.listWidgetFileNames.count()):
item = self.ui.listWidgetFileNames.item(i)
raw_path = item.text()
basename = os.path.basename(raw_path)
subject_name = basename.split('.')[0]
experiment = self.parent.experiment
old_names = experiment.subjects.keys()
try:
subject_name = next_available_name(old_names, subject_name)
@threaded
def _create_subject():
experiment.create_subject(subject_name, raw_path)
_create_subject(do_meanwhile=self.parent.update_ui)
n_successful += 1
except Exception as exc:
logging.getLogger('ui_logger').exception('')
try:
self.parent.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
n_total = self.ui.listWidgetFileNames.count()
if n_total != n_successful:
message = ("Only {0} / {1} subjects added successfully. "
"Please check console below for details.")
messagebox(self.parent, message.format(n_successful, n_total))
message = ('{0} / {1} subjects added successfully.').format(
n_successful, n_total)
logging.getLogger('ui_logger').info(message)
self.parent.initialize_ui()
self.close()
def on_treeWidgetActions_itemDoubleClicked(self, item):
if item.childCount() == 0:
# try creating a pretty formatted details dialog
try:
match = re.compile("([a-zA-Z0-9_]*): (.*)").match(item.text(0))
if not match:
return
key = match.group(1)
val = match.group(2)
try:
obj = json.loads(val)
except Exception as exc:
obj = val
message = pformat(obj)
messagebox(self, message)
except Exception as exc:
logging.getLogger('ui_logger').exception("")
return
def accept(self):
"""
Get the parameters dictionary and relay it to filter_data to
actually do the filtering.
"""
subject = self.experiment.active_subject
params = self.collect_parameter_values()
if not params:
message = 'No filter(s) selected'
messagebox(self.parent, message)
return
try:
self.filter(subject, params)
except Exception as exc:
exc_messagebox(self.parent, exc)
logging.getLogger('ui_logger').exception(str(exc))
self.parent.initialize_ui()
self.close()
def on_pushButtonPreview_clicked(self, checked=None):
if checked is None:
return
params = self._collect_parameter_values()
if not params:
message = 'No filter(s) selected.'
messagebox(self.parent, message)
return
subject = self.experiment.active_subject
try:
raw_to = filter_data(subject,
params,
preview=True)
raw_from = subject.get_raw()
compare_raws(raw_from, raw_to)
except Exception as exc:
exc_messagebox(self.parent, exc)
def acceptBatch(self):
subject_names = self.batching_widget.selected_subjects
params = self._collect_parameter_values()
if not params:
message = 'No filter(s) selected'
messagebox(self.parent, message)
return
for name, subject in self.experiment.subjects.items():
if name in subject_names:
try:
self.handler(subject, params)
subject.release_memory()
except Exception as exc:
logging.getLogger('ui_logger').exception('')
self.batching_widget.failed_subjects.append(
(subject, str(exc)))
self.batching_widget.cleanup()
self.parent.initialize_ui()
self.close()
def on_pushButtonHelp_clicked(self, checked=None):
if checked is None:
return
help_message = (
"Events are found in a following way. If only event "
"id is set, events with exactly the same binary representation as "
"event id are included in the final event list. If also mask is "
"set, event list will also include events where binary digits in "
"the places specified by the mask are not the same as in the "
"event id, or in other words, only events where the digits we "
"are interested in are the same as in the list of all events, "
"are included. Binary representations are assumed to be 16 digits "
"long. \n\nFor example event id of 0000010000010000 = 1040 and "
"mask of 0000000000000011 = 3 would mean that first (rightmost) "
"two digits can be 1 or 0, but anything else must be exactly as "
"in the event id. Thus events with following id's would be allowed:"
"\n\n0000010000010000 = 1040\n0000010000010001 = 1041\n"
"0000010000010010 = 1042\n0000010000010011 = 1043")
messagebox(self.parent, help_message, 'Mask help')
def accept(self):
"""Send parameters to experimentHandler for the creation of a
new experiment."""
if self.ui.lineEditExperimentName.text() == '':
message = 'Give experiment a name.'
messagebox(self.parent, message)
return
expDict = {
'name': self.ui.lineEditExperimentName.text(),
'author': self.ui.lineEditAuthor.text(),
}
try:
experiment = self.parent.experimentHandler.initialize_new_experiment(
expDict, )
except Exception as exc:
exc_messagebox(self, exc)
return
self.experimentCreated.emit(experiment)
self.close()
def on_pushButtonReset_clicked(self, checked=None):
if checked is None:
return
subject = self.parent.experiment.active_subject
if not subject:
messagebox(self.parent, 'To reset, active subject is needed')
return
info = subject.get_raw().info
if self.ui.radioButtonEEG.isChecked():
self.eeg_channel_groups = get_default_channel_groups(info, 'eeg')
self.ui.listWidgetChannelGroups.clear()
for ch_name in sorted(self.eeg_channel_groups.keys()):
self.ui.listWidgetChannelGroups.addItem(ch_name)
else:
meg_defaults = get_default_channel_groups(info, 'meg')
self.meg_channel_groups = meg_defaults
self.ui.listWidgetChannelGroups.clear()
for ch_name in sorted(self.meg_channel_groups.keys()):
self.ui.listWidgetChannelGroups.addItem(ch_name)
def accept(self):
if self.ui.listWidgetEvents.count() == 0:
message = 'Cannot create epochs from empty list.'
messagebox(self.parent, message)
return
try:
params = self._collect_parameter_values()
except Exception as exc:
exc_messagebox(self, exc)
return
subject = self.experiment.active_subject
try:
self.handler(subject, params)
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
self.parent.initialize_ui()
self.close()
def run(self):
""" Called when action is initiated
"""
messagebox("Running action " + self.action_spec['id'])
def on_pushButtonSetChannels_clicked(self, checked=None):
if checked is None:
return
subject = self.parent.experiment.active_subject
if not subject:
messagebox(self.parent, 'To set channels, active subject is needed')
return
try:
selected_item = self.ui.listWidgetChannelGroups.selectedItems()[0]
except IndexError:
messagebox(self.parent, 'Select a channel group first')
return
info = subject.get_raw().info
if self.ui.radioButtonEEG.isChecked():
if mne.pick_types(info, meg=False, eeg=True).size == 0:
messagebox(self.parent, 'No EEG channels found')
return
ch_names = self.eeg_channel_groups[selected_item.text()]
try:
ch_idxs = [info['ch_names'].index(ch_name) for ch_name in ch_names]
except ValueError:
messagebox(self.parent, "Channel names in the group "
"and the current subject don't match")
return
ch_groups = [[], ch_idxs]
try:
fig, selection = mne.viz.plot_sensors(info, kind='select', ch_type='eeg',
ch_groups=ch_groups, show=False)
except RuntimeError:
messagebox(self.parent, 'Could not plot sensors. Is the montage set?')
return
else:
if mne.pick_types(info, meg=True, eeg=False).size == 0:
messagebox(self.parent, 'No MEG channels found')
return
ch_names = self.meg_channel_groups[selected_item.text()]
try:
ch_idxs = [info['ch_names'].index(ch_name) for ch_name in ch_names]
except ValueError:
messagebox(self.parent, "Channel names in the group "
"and the current subject don't match")
return
ch_groups = [[], ch_idxs]
fig, selection = mne.viz.plot_sensors(info, kind='select', ch_type='mag',
ch_groups=ch_groups, show=False)
# make markers bigger
for child in fig.axes[0].get_children():
if isinstance(child, mpl.collections.PathCollection):
child.set_sizes([100])
child.set_lw([1])
break
plt.show(block=True)
if self.ui.radioButtonMEG.isChecked():
if selection:
all_megs = []
for ch_name in selection:
all_megs.extend(get_triplet_from_mag(info, ch_name))
self.meg_channel_groups[selected_item.text()] = all_megs
else:
if selection:
self.eeg_channel_groups[selected_item.text()] = selection
