def acceptBatch(self):
tfr_name = self.ui.lineEditTFRName.text()
try:
validate_name(tfr_name)
except Exception as exc:
exc_messagebox(self, exc)
return
minfreq = self.ui.doubleSpinBoxMinFreq.value()
maxfreq = self.ui.doubleSpinBoxMaxFreq.value()
decim = self.ui.spinBoxDecim.value()
interval = self.ui.doubleSpinBoxFreqInterval.value()
freqs = np.arange(minfreq, maxfreq, interval)
subtract_evoked = self.ui.checkBoxSubtractEvoked.isChecked()
if self.ui.radioButtonFixed.isChecked():
n_cycles = self.ui.doubleSpinBoxNcycles.value()
elif self.ui.radioButtonAdapted.isChecked():
n_cycles = freqs / self.ui.doubleSpinBoxCycleFactor.value()
params = {}
params['freqs'] = freqs
params['decim'] = decim
params['subtract_evoked'] = subtract_evoked
params['n_cycles'] = n_cycles
params['name'] = tfr_name
params['conditions'] = self.epoch_names
experiment = self.experiment
selected_subject_names = self.batching_widget.selected_subjects
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:
experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self.parent, exc)
self.parent.initialize_ui()
self.close()
def acceptBatch(self):
"""
"""
tfr_name = self.ui.lineEditTFRName.text()
try:
validate_name(tfr_name)
except Exception as exc:
exc_messagebox(self, exc)
return
minfreq = self.ui.doubleSpinBoxMinFreq.value()
maxfreq = self.ui.doubleSpinBoxMaxFreq.value()
decim = self.ui.spinBoxDecim.value()
interval = self.ui.doubleSpinBoxFreqInterval.value()
freqs = np.arange(minfreq, maxfreq, interval)
subtract_evoked = self.ui.checkBoxSubtractEvoked.isChecked()
if self.ui.radioButtonFixed.isChecked():
n_cycles = self.ui.doubleSpinBoxNcycles.value()
elif self.ui.radioButtonAdapted.isChecked():
n_cycles = freqs / self.ui.doubleSpinBoxCycleFactor.value()
experiment = self.experiment
selected_subject_names = self.batching_widget.selected_subjects
for name, subject in self.experiment.subjects.items():
if name in selected_subject_names:
try:
create_tfr(subject, tfr_name,
self.epoch_names, freqs=freqs,
decim=decim, n_cycles=n_cycles,
subtract_evoked=subtract_evoked,
do_meanwhile=self.parent.update_ui)
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()
experiment.save_experiment_settings()
self.parent.initialize_ui()
logging.getLogger('ui_logger').info('Finished')
self.close()
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, *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 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 _collect_parameter_values(self):
tmin = float(self.ui.doubleSpinBoxTmin.value())
tmax = float(self.ui.doubleSpinBoxTmax.value())
bstart = float(self.ui.doubleSpinBoxBaselineStart.value())
bend = float(self.ui.doubleSpinBoxBaselineEnd.value())
delay = float(self.ui.doubleSpinBoxDelay.value())
mag = self.ui.checkBoxMag.isChecked()
grad = self.ui.checkBoxGrad.isChecked()
eeg = self.ui.checkBoxEeg.isChecked()
collection_name = validate_name(
str(self.ui.lineEditCollectionName.text()))
reject = dict()
if mag:
reject['mag'] = self.ui.doubleSpinBoxMagReject.value()
if grad:
reject['grad'] = self.ui.doubleSpinBoxGradReject.value()
if eeg:
reject['eeg'] = self.ui.doubleSpinBoxEEGReject.value()
params = {'mag': mag, 'grad': grad, 'eeg': eeg,
'reject': reject,
'tmin': tmin, 'tmax': tmax,
'bstart': bstart, 'bend': bend,
'delay': delay,
'collection_name': collection_name,
'events': self.events}
return params
def accept(self):
"""
"""
tfr_name = self.ui.lineEditTFRName.text()
try:
validate_name(tfr_name)
except Exception as exc:
exc_messagebox(self, exc)
return
minfreq = self.ui.doubleSpinBoxMinFreq.value()
maxfreq = self.ui.doubleSpinBoxMaxFreq.value()
decim = self.ui.spinBoxDecim.value()
interval = self.ui.doubleSpinBoxFreqInterval.value()
freqs = np.arange(minfreq, maxfreq, interval)
subtract_evoked = self.ui.checkBoxSubtractEvoked.isChecked()
if self.ui.radioButtonFixed.isChecked():
n_cycles = self.ui.doubleSpinBoxNcycles.value()
elif self.ui.radioButtonAdapted.isChecked():
n_cycles = freqs / self.ui.doubleSpinBoxCycleFactor.value()
experiment = self.experiment
subject = experiment.active_subject
try:
create_tfr(subject, tfr_name, self.epoch_names,
freqs=freqs, decim=decim, n_cycles=n_cycles,
subtract_evoked=subtract_evoked,
do_meanwhile=self.parent.update_ui)
except Exception as exc:
exc_messagebox(self.parent, exc)
return
experiment.save_experiment_settings()
self.parent.initialize_ui()
logging.getLogger('ui_logger').info('Finished.')
self.close()
def accept(self):
tfr_name = self.ui.lineEditTFRName.text()
try:
validate_name(tfr_name)
except Exception as exc:
exc_messagebox(self, exc)
return
minfreq = self.ui.doubleSpinBoxMinFreq.value()
maxfreq = self.ui.doubleSpinBoxMaxFreq.value()
interval = self.ui.doubleSpinBoxFreqInterval.value()
freqs = np.arange(minfreq, maxfreq, interval)
decim = self.ui.spinBoxDecim.value()
subtract_evoked = self.ui.checkBoxSubtractEvoked.isChecked()
if self.ui.radioButtonFixed.isChecked():
n_cycles = self.ui.doubleSpinBoxNcycles.value()
elif self.ui.radioButtonAdapted.isChecked():
n_cycles = freqs / self.ui.doubleSpinBoxCycleFactor.value()
params = {}
params['freqs'] = freqs
params['decim'] = decim
params['subtract_evoked'] = subtract_evoked
params['n_cycles'] = n_cycles
params['name'] = tfr_name
params['conditions'] = self.epoch_names
experiment = self.experiment
subject = experiment.active_subject
try:
self.handler(subject, params)
experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self.parent, exc)
return
self.parent.initialize_ui()
self.close()
def acceptBatch(self, *args):
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()
update_ui = self.parent.update_ui
selected_subject_names = self.batching_widget.selected_subjects
for name, subject in self.experiment.subjects.items():
if name in selected_subject_names:
try:
create_power_spectrum(subject,
spectrum_name,
params,
intervals,
do_meanwhile=update_ui)
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 acceptBatch(self):
""" Start item creation of all subjects selected in the batching widget
"""
selected_spectrum = self.selected_spectrum
experiment = self.experiment
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()
selected_subject_names = self.batching_widget.selected_subjects
# Loop through every subject creating items and collecting info from
# failed cases
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(str(exc))
# if any fails, tell user about them
self.batching_widget.cleanup()
# and update experiment file and the UI
try:
self.experiment.save_experiment_settings()
except Exception as exc:
exc_messagebox(self.parent, exc)
self.parent.initialize_ui()
self.close()
def accept(self, *args, **kwargs):
""" Starts the computation.
"""
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
update_ui = self.parent.update_ui
params = dict()
params['fmin'] = fmin
params['fmax'] = fmax
params['nfft'] = self.ui.spinBoxNfft.value()
params['overlap'] = self.ui.spinBoxOverlap.value()
try:
create_power_spectrum(subject,
spectrum_name,
params,
intervals,
do_meanwhile=update_ui)
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):
subject = self.experiment.active_subject
try:
evoked_name = validate_name(self.ui.lineEditName.text())
except Exception as exc:
exc_messagebox(self, exc)
return
try:
params = {'name': evoked_name}
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 accept(self):
groups = {}
for idx, subject in enumerate(self.subjects):
selected = getattr(self.ui,
'checkBoxGroup_' + str(idx)).checkState()
if selected != QtCore.Qt.Checked:
continue
group_id = getattr(self.ui, 'spinBoxGroup_' + str(idx)).value()
if group_id in groups:
groups[group_id].append(subject)
else:
groups[group_id] = [subject]
try:
name = validate_name(self.ui.lineEditName.text())
except Exception as exc:
exc_messagebox(self, exc)
return
self.handler(name, groups)
self.close()
def create_evoked(self, subject, selected_epochs):
time_arrays = []
for name in selected_epochs:
epochs = subject.epochs.get(name)
if epochs:
time_arrays.append(epochs.content.times)
assert_arrays_same(time_arrays)
evokeds = {}
for name in selected_epochs:
try:
epochs = subject.epochs[name]
except KeyError:
raise KeyError('No epoch collection called ' + str(name))
mne_epochs = epochs.content
@threaded
def average():
return mne_epochs.average()
mne_evoked = average(do_meanwhile=self.parent.update_ui)
mne_evoked.comment = name
evokeds[name] = mne_evoked
evoked_name = validate_name(self.ui.lineEditName.text())
params = {'conditions': selected_epochs}
evoked_directory = subject.evoked_directory
evoked = Evoked(evoked_name, evoked_directory, params, content=evokeds)
evoked.save_content()
subject.add(evoked, 'evoked')
def collect_parameter_values(self):
"""Collect the parameter values for epoch creation from the ui.
"""
tmin = float(self.ui.doubleSpinBoxTmin.value())
tmax = float(self.ui.doubleSpinBoxTmax.value())
bstart = float(self.ui.doubleSpinBoxBaselineStart.value())
bend = float(self.ui.doubleSpinBoxBaselineEnd.value())
mag = self.ui.checkBoxMag.isChecked()
grad = self.ui.checkBoxGrad.isChecked()
eeg = self.ui.checkBoxEeg.isChecked()
collection_name = validate_name(
str(self.ui.lineEditCollectionName.text()))
reject = dict()
if mag:
reject['mag'] = self.ui.doubleSpinBoxMagReject.value()
if grad:
reject['grad'] = self.ui.doubleSpinBoxGradReject.value()
if eeg:
reject['eeg'] = self.ui.doubleSpinBoxEEGReject.value()
params = {
'mag': mag,
'grad': grad,
'eeg': eeg,
'reject': reject,
'tmin': float(tmin),
'tmax': float(tmax),
'bstart': float(bstart),
'bend': float(bend),
'collection_name': collection_name,
'events': self.events
}
return params
def author(self, author):
"""
"""
self._author = validate_name(author, minlength=0, fieldname='author')
def name(self, name):
"""
"""
self._name = validate_name(name, fieldname='name')
def create_report(self, subject, selected_spectrum):
""" Collect parameters from the dialog and creates an FOOOFReport item
"""
report_name = validate_name(self.ui.lineEditName.text())
spectrum = subject.spectrum.get(selected_spectrum)
peak_width_low = self.ui.doubleSpinBoxPeakWidthLow.value()
peak_width_high = self.ui.doubleSpinBoxPeakWidthHigh.value()
peak_threshold = self.ui.doubleSpinBoxPeakThreshold.value()
max_n_peaks = self.ui.spinBoxMaxNPeaks.value()
aperiodic_mode = self.ui.comboBoxAperiodicMode.currentText()
minfreq = self.ui.doubleSpinBoxFreqMin.value()
maxfreq = self.ui.doubleSpinBoxFreqMax.value()
peak_width_limits = [peak_width_low, peak_width_high]
peak_threshold = peak_threshold
max_n_peaks = max_n_peaks
aperiodic_mode = aperiodic_mode
freq_range = [minfreq, maxfreq]
# As meggie spectrum items can contain data for multiple conditions,
# reports are also created for all those conditions, and dict is used.
report_content = {}
for key, data in spectrum.content.items():
fg = FOOOFGroup(peak_width_limits=peak_width_limits,
peak_threshold=peak_threshold,
max_n_peaks=max_n_peaks,
aperiodic_mode=aperiodic_mode,
verbose=False)
@threaded
def fit(**kwargs):
""" Run fitting in a separate thread so that UI stays responsive
"""
fg.fit(spectrum.freqs, data, freq_range)
fit(do_meanwhile=self.parent.update_ui)
logging.getLogger('ui_logger').info('FOOOF results for ' +
subject.name + ', ' +
'condition: ' + key)
# Log the textual report
logging.getLogger('ui_logger').info(
gen_results_fg_str(fg, concise=True))
report_content[key] = fg
params = {
'conditions': list(spectrum.content.keys()),
'based_on': selected_spectrum,
'ch_names': spectrum.ch_names,
}
fooof_directory = subject.fooof_report_directory
# Create a container item that meggie understands,
# and which holds the report data
report = FOOOFReport(report_name, fooof_directory, params,
report_content)
# save report data to fs
report.save_content()
# and add the report item to subject
subject.add(report, 'fooof_report')