def accept(self):
""" Start item creation for current subject
"""
subject = self.experiment.active_subject
selected_spectrum = self.selected_spectrum
params = {}
try:
params['name'] = validate_name(self.ui.lineEditName.text())
except Exception as exc:
exc_messagebox(self, exc)
return
params['peak_width_low'] = self.ui.doubleSpinBoxPeakWidthLow.value()
params['peak_width_high'] = self.ui.doubleSpinBoxPeakWidthHigh.value()
params['peak_threshold'] = self.ui.doubleSpinBoxPeakThreshold.value()
params['max_n_peaks'] = self.ui.spinBoxMaxNPeaks.value()
params['aperiodic_mode'] = self.ui.comboBoxAperiodicMode.currentText()
params['minfreq'] = self.ui.doubleSpinBoxFreqMin.value()
params['maxfreq'] = self.ui.doubleSpinBoxFreqMax.value()
try:
self.handler(subject, params)
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
# Update experiment file and the window
self.parent.initialize_ui()
self.close()
def accept(self):
""" Add new subjects. """
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, basename,
raw_path)
_create_subject(do_meanwhile=self.parent.update_ui)
except Exception as exc:
exc_messagebox(self.parent, exc)
logging.getLogger('ui_logger').exception(str(exc))
self.parent.experiment.save_experiment_settings()
self.parent.initialize_ui()
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 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):
"""
"""
experiment = self.experiment
raw = experiment.active_subject.get_raw()
selection = self.ui.comboBoxChannel.currentText()
@threaded
def rereference_fun():
if selection == 'Use average':
raw.set_eeg_reference(ref_channels='average', projection=False)
elif selection == '':
raise Exception('Empty selection')
else:
raw.set_eeg_reference(ref_channels=[selection])
try:
rereference_fun(do_meanwhile=self.parent.update_ui)
except Exception as exc:
exc_messagebox(self.parent, exc)
self.close()
return
experiment.active_subject.save()
experiment.active_subject.rereferenced = True
experiment.save_experiment_settings()
self.parent.initialize_ui()
logging.getLogger('ui_logger').info('Finished.')
self.close()
def run(self):
subject = self.experiment.active_subject
try:
self.handler(subject, {})
except Exception as exc:
exc_messagebox(self.window, exc)
def accept(self):
if not self.ica:
return
raw = self.experiment.active_subject.get_raw()
indices = [self.component_info[name] for name in self.removed]
try:
@threaded
def apply_ica_wrapper():
self.ica.apply(raw, exclude=indices)
apply_ica_wrapper(do_meanwhile=self.parent.update_ui)
self.experiment.active_subject.save()
self.experiment.active_subject.ica_applied = True
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
self.parent.initialize_ui()
# for logging purposes, call the handler
if self.on_apply:
self.params['exclude'] = indices
self.on_apply(self.experiment.active_subject, self.params)
self._reset()
self.close()
def acceptBatch(self):
experiment = self.experiment
selection = self.ui.comboBoxChannel.currentText()
selected_subject_names = self.batching_widget.selected_subjects
for name, subject in experiment.subjects.items():
if name in selected_subject_names:
try:
params = {'selection': selection}
self.handler(subject, params)
subject.release_memory()
except Exception as exc:
self.batching_widget.failed_subjects.append(
(subject, str(exc)))
logging.getLogger('ui_logger').exception('')
self.batching_widget.cleanup()
try:
experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self.parent, exc)
self.parent.initialize_ui()
self.close()
def __init__(self, application):
QtWidgets.QMainWindow.__init__(self)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# set default ratio of splitter
self.ui.splitterTopBottom.setStretchFactor(0, 2)
self.ui.splitterTopBottom.setStretchFactor(1, 1)
self.experiment = None
self._setup_loggers()
# Direct output to console
if not sys.argv[-1] == 'debug':
self._direct_output()
# For storing and handling program wide preferences.
self.prefs = PreferencesHandler()
auto_load = self.prefs.auto_load_last_open_experiment
previous_name = self.prefs.previous_experiment_name
if auto_load and previous_name:
try:
exp = open_existing_experiment(self.prefs)
self.experiment = exp
self.prefs.previous_experiment_name = exp.path
self.prefs.write_preferences_to_disk()
logging.getLogger('ui_logger').info('Opening experiment ' + exp.path)
except Exception as exc:
self.prefs.previous_experiment_name = ''
exc_messagebox(self, exc)
self.reconstruct_tabs()
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 acceptBatch(self):
experiment = self.experiment
try:
evoked_name = validate_name(self.ui.lineEditName.text())
except Exception as exc:
exc_messagebox(self, exc)
return
selected_subject_names = self.batching_widget.selected_subjects
params = {'name': evoked_name}
for name, subject in self.experiment.subjects.items():
if name in selected_subject_names:
try:
self.handler(subject, params)
subject.release_memory()
except Exception as exc:
self.batching_widget.failed_subjects.append(
(subject, str(exc)))
logging.getLogger('ui_logger').exception('')
self.batching_widget.cleanup()
try:
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self, exc)
return
self.parent.initialize_ui()
self.close()
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_actionOpenExperiment_triggered(self, checked=None):
"""
"""
if checked is None:
return
if self.experiment is not None:
directory = self.experiment.workspace
else:
directory = ''
path = QtCore.QDir.toNativeSeparators(
str(
QtWidgets.QFileDialog.getExistingDirectory(
self, "Select experiment directory", directory)))
if path == '':
return
logging.getLogger('ui_logger').info('Opening experiment ' + path)
try:
exp = self.experimentHandler.open_existing_experiment(
self.preferencesHandler, path=path)
self.experiment = exp
self.initialize_ui()
except Exception as exc:
exc_messagebox(self, exc)
self.preferencesHandler.write_preferences_to_disk()
def accept(self, *args, **kwargs):
try:
spectrum_name = validate_name(self.ui.lineEditName.text())
except Exception as exc:
exc_messagebox(self, exc)
return
intervals = self.intervals
if not intervals:
return
fmin = self.ui.spinBoxFmin.value()
fmax = self.ui.spinBoxFmax.value()
subject = self.experiment.active_subject
params = dict()
params['fmin'] = fmin
params['fmax'] = fmax
params['nfft'] = self.ui.spinBoxNfft.value()
params['overlap'] = self.ui.spinBoxOverlap.value()
params['intervals'] = intervals
params['name'] = spectrum_name
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 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 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 on_pushButtonCompute_clicked(self, checked=None):
"""
"""
if checked is None:
return
# start by clearing out the previous things
self.reset()
n_components = self.ui.doubleSpinBoxNComponents.value()
method = 'fastica'
max_iter = self.ui.spinBoxMaxIter.value()
raw = self.experiment.active_subject.get_raw()
@threaded
def _compute_ica():
return compute_ica(raw, n_components, method, max_iter)
try:
self.ica = _compute_ica(do_meanwhile=self.parent.update_ui)
except Exception as exc:
exc_messagebox(self, exc)
return
for idx in range(self.ica.n_components_):
label = 'Component ' + str(idx)
self.ui.listWidgetNotRemoved.addItem(label)
self.component_info[label] = idx
self.not_removed.append(label)
logging.getLogger('ui_logger').info('ICA finished.')
def handler(ch_name, title, legend, ylim, window, window_len):
try:
ch_idx = info['ch_names'].index(ch_name)
# create new evoked based on old
new_evokeds = {}
for key, evoked in content.items():
new_evoked = evoked.copy()
# smoothen
if window:
try:
new_evoked.data[ch_idx] = smooth_signal(
new_evoked.data[ch_idx],
window_len=window_len,
window=window)
except ValueError as exc:
exc_messagebox(window, exc)
new_evoked.comment = legend[key]
new_evokeds[legend[key]] = new_evoked
ylim = {ch_types[ch_name]: ylim}
mne.viz.plot_compare_evokeds(new_evokeds,
title=title,
picks=[ch_idx],
colors=colors,
ylim=ylim,
show_sensors=False)
except Exception as exc:
exc_messagebox(window, exc)
def evs_from_annots():
try:
events_from_annotations(subject, self.items)
except Exception as exc:
exc_messagebox(self, exc)
return
subject.save()
def handler(selected_option):
try:
if selected_option == 'channel_averages':
_plot_evoked_averages(experiment, evoked)
else:
_plot_evoked_topo(experiment, evoked)
except Exception as exc:
exc_messagebox(window, exc)
def option_handler(params):
params['channel_groups'] = self.experiment.channel_groups
params['name'] = selected_name
try:
self.handler(self.experiment.active_subject, params)
except Exception as exc:
exc_messagebox(self.window, exc)
def option_handler(selected_option):
params = {'name': selected_name,
'output_option': selected_option,
'channel_groups': self.experiment.channel_groups}
try:
self.handler(self.experiment.active_subject, params)
except Exception as exc:
exc_messagebox(self.window, exc)
def handler(selected_option):
try:
if selected_option == 'channel_averages':
save_channel_averages(experiment, selected_name)
else:
save_all_channels(experiment, selected_name)
except Exception as exc:
exc_messagebox(window, exc)
def handler(selected_option):
try:
if selected_option == 'channel_averages':
plot_spectrum_averages(experiment, selected_name)
else:
plot_spectrum_topo(experiment, selected_name)
except Exception as exc:
exc_messagebox(window, exc)
def group_handler(groups):
params = {'based_on': selected_name,
'name': name,
'groups': groups}
try:
self.handler(self.experiment.active_subject, params)
self.experiment.save_experiment_settings()
self.window.initialize_ui()
except Exception as exc:
exc_messagebox(self.window, exc)
def update_contents(self):
try:
logfile_path = os.path.join(self.parent.experiment.workspace,
self.parent.experiment.name, 'meggie.log')
log_file = open(logfile_path, 'r')
# logging.getLogger('ui_logger').info(
# 'Showing last 10000 lines of ' + logfile_path)
last_lines = filemanager.tail(log_file, lines=self.lines)
# track lines that start log entries as there can be multiline
# entries.
meggie_idxs = []
mne_idxs = []
mne_call_idxs = []
all_idxs = []
for line_idx, line in enumerate(last_lines):
if line.startswith('Meggie:'):
meggie_idxs.append(line_idx)
all_idxs.append(line_idx)
elif line.startswith('MNE call:'):
mne_call_idxs.append(line_idx)
all_idxs.append(line_idx)
elif line.startswith('MNE:'):
mne_idxs.append(line_idx)
all_idxs.append(line_idx)
self.ui.textEditBrowser.clear()
selected_lines = []
for idx_idx, line_idx in enumerate(all_idxs):
if idx_idx != len(all_idxs) - 1:
next_idx = all_idxs[idx_idx + 1]
else:
next_idx = -1
if line_idx in meggie_idxs:
if self.show_meggie:
selected_lines.extend(
last_lines[line_idx:next_idx])
elif line_idx in mne_idxs:
if self.show_mne:
selected_lines.extend(
last_lines[line_idx:next_idx])
elif line_idx in mne_call_idxs:
if self.show_mne_call:
selected_lines.extend(
last_lines[line_idx:next_idx])
for line in selected_lines:
self.ui.textEditBrowser.append(line.strip('\n'))
except Exception as exc:
exc_messagebox(self, exc)
def on_pushButtonPlotTopographies_clicked(self, checked=None):
if checked is None:
return
raw = self.experiment.active_subject.get_raw()
try:
plot_topographies(self.ica, len(self.component_info))
except Exception as exc:
exc_messagebox(self, exc)
return
def on_pushButtonPlotSources_clicked(self, checked=None):
if checked is None:
return
raw = self.experiment.active_subject.get_raw()
try:
plot_sources(raw, self.ica)
except Exception as exc:
exc_messagebox(self, exc)
return
def run(self):
try:
selected_name = self.data['outputs']['epochs'][0]
except IndexError as exc:
return
subject = self.experiment.active_subject
try:
self.handler(subject, {'name': selected_name})
except Exception as exc:
exc_messagebox(self.window, exc)
def handler(output, condition, blmode, blstart, blend, tmin, tmax, fmin,
fmax):
try:
if output == 'all_channels':
save_tse_all_channels(experiment, selected_name, blmode,
blstart, blend, tmin, tmax, fmin, fmax)
else:
save_tse_channel_averages(experiment, selected_name, blmode,
blstart, blend, tmin, tmax, fmin,
fmax)
except Exception as exc:
exc_messagebox(window, exc)