def __init__(self, group):
vd.Component.__init__(self)
self._group = group
SF = sf.SFData()
a = kb.loadObject(
key=dict(name='spikeforest_batch_group', group_name=group))
for recordings_name in a['recordings_names']:
try:
SF.loadRecordings(key=dict(name=recordings_name))
except:
raise
print('Warning: unable to load recordings: ' + recordings_name)
for batch_name in a['batch_names']:
try:
SF.loadProcessingBatch(batch_name=batch_name)
except:
print('Warning: unable to load processing batch: ' +
batch_name)
self._SF_data = SF
self._accuracy_threshold_input = vd.components.LineEdit(
value=0.8, dtype=float, style=dict(width='70px'))
self._update_button = vd.components.Button(onclick=self._on_update,
class_='button',
label='Update')
self._study_sorter_fig = StudySorterFigure(SF)
self._study_sorter_table = vd.div() # dummy
vd.devel.loadBootstrap()
self._update_accuracy_table()
def _on_group_changed(self, value=None):
group_name = self._SEL_group.value()
if not group_name:
return
if self._CB_use_summarized_recordings.checked():
a = kb.loadObject(
key=dict(name='summarized_recordings', group_name=group_name)
)
else:
a = kb.loadObject(
key=dict(name='spikeforest_recording_group',
group_name=group_name)
)
if not a:
print('ERROR: unable to open recording group: '+group_name)
return
if ('recordings' not in a) or ('studies' not in a):
print('ERROR: problem with recording group: '+group_name)
return
studies = a['studies']
recordings = a['recordings']
SF = sf.SFData()
SF.loadStudies(studies)
SF.loadRecordings2(recordings)
self._SF = SF
self._SEL_study.setOptions(SF.studyNames())
self._on_study_changed(value=self._SEL_study.value())
def _on_group_changed(self, value):
group_name = self._SEL_group.value()
if not group_name:
return
a = ca.loadObject(key=dict(name='spikeforest_recording_group',
group_name=group_name))
# key=dict(name='spikeforest_results', output_id='spikeforest_test2'))
SF = sf.SFData()
SF.loadStudies(a['studies'])
SF.loadRecordings2(a['recordings'])
self._SF = SF
self._SEL_study.setOptions(SF.studyNames())
self._on_study_changed(value=self._SEL_study.value())
def __init__(self, group):
vd.Component.__init__(self)
self._sorter_names = kb.loadObject(key=dict(
name='spikeforest_sorter_names'))
group_name = group
self._group = group_name
a = kb.loadObject(
key=dict(name='summarized_recordings', group_name=group_name))
if not a:
print('ERROR: unable to open recording group: ' + group_name)
return
if ('recordings' not in a) or ('studies' not in a):
print('ERROR: problem with recording group: ' + group_name)
return
studies = a['studies']
recordings = a['recordings']
SF = sf.SFData()
SF.loadStudies(studies)
SF.loadRecordings2(recordings)
sorter_names = self._sorter_names[group_name]
for sorter_name in sorter_names:
print('Loading sorting results for sorter: ' + sorter_name)
b = kb.loadObject(key=dict(name='sorting_results',
group_name=group_name,
sorter_name=sorter_name))
if not b:
print('WARNING: unable to open sorting results for sorter: ' +
sorter_name)
break
SF.loadSortingResults(b['sorting_results'])
self._SF_data = SF
self._accuracy_threshold_input = vd.components.LineEdit(
value=0.8, dtype=float, style=dict(width='70px'))
self._update_button = vd.components.Button(onclick=self._on_update,
class_='button',
label='Update')
self._study_sorter_fig = StudySorterFigure(SF)
self._study_sorter_table = vd.div() # dummy
vd.devel.loadBootstrap()
self._update_accuracy_table()
def _on_output_id_changed(self, value):
output_id = self._SEL_output_id.value()
if not output_id:
return
key = dict(name='spikeforest_results', output_id=output_id)
a = ca.loadObject(key=key)
if a is None:
raise Exception(
'Unable to load spikeforest result: {}'.format(output_id))
SF = sf.SFData()
SF.loadStudies(a['studies'])
SF.loadRecordings2(a['recordings'])
SF.loadSortingResults(a['sorting_results'])
self._SF = SF
self._SEL_study.setOptions(SF.studyNames())
self._on_study_changed(value=self._SEL_study.value())
def __init__(self, output_id):
vd.Component.__init__(self)
self._output_id = output_id
a = ca.loadObject(key=dict(name='spikeforest_results'),
subkey=output_id)
if not a:
print('ERROR: unable to open results: ' + output_id)
return
if ('recordings' not in a) or ('studies'
not in a) or ('sorting_results'
not in a):
print('ERROR: problem with output: ' + output_id)
return
studies = a['studies']
recordings = a['recordings']
sorting_results = a['sorting_results']
SF = sf.SFData()
SF.loadStudies(studies)
SF.loadRecordings2(recordings)
SF.loadSortingResults(sorting_results)
# sorter_names=[]
# for SR in sorting_results:
# sorter_names.append(SR['sorter']['name'])
# sorter_names=list(set(sorter_names))
# sorter_names.sort()
self._SF_data = SF
self._accuracy_threshold_input = vd.components.LineEdit(
value=0.8, dtype=float, style=dict(width='70px'))
self._update_button = vd.components.Button(onclick=self._on_update,
class_='button',
label='Update')
self._study_sorter_fig = StudySorterFigure(SF)
self._study_sorter_table = vd.div() # dummy
vd.devel.loadBootstrap()
self._update_accuracy_table()
def _on_group_changed(self, value):
group_name = self._SEL_group.value()
a = kb.loadObject(
key=dict(name='spikeforest_batch_group', group_name=group_name))
SF = sf.SFData()
for recordings_name in a['recordings_names']:
try:
SF.loadRecordings(key=dict(name=recordings_name))
except:
print('Warning: unable to load recordings: '+recordings_name)
for batch_name in a['batch_names']:
try:
SF.loadProcessingBatch(batch_name=batch_name)
except:
print('Warning: unable to load processing batch: '+batch_name)
self._SF = SF
self._SEL_study.setOptions(SF.studyNames())
self._on_study_changed(value=self._SEL_study.value())
def _on_group_changed(self, value):
group_name = self._SEL_group.value()
if not group_name:
return
a = kb.loadObject(
key=dict(name='summarized_recordings', group_name=group_name))
if not a:
print('ERROR: unable to open recording group: ' + group_name)
return
if ('recordings' not in a) or ('studies' not in a):
print('ERROR: problem with recording group: ' + group_name)
return
studies = a['studies']
recordings = a['recordings']
SF = sf.SFData()
SF.loadStudies(studies)
SF.loadRecordings2(recordings)
sorter_names = self._sorter_names[group_name]
for sorter_name in sorter_names:
print('Loading sorting results for sorter: ' + sorter_name)
b = kb.loadObject(key=dict(name='sorting_results',
group_name=group_name,
sorter_name=sorter_name))
if not b:
print('WARNING: unable to open sorting results for sorter: ' +
sorter_name)
break
SF.loadSortingResults(b['sorting_results'])
self._SF = SF
self._SEL_study.setOptions(SF.studyNames())
self._on_study_changed(value=self._SEL_study.value())
def aggregate_sorting_results(studies, recordings, sorting_results):
SF = sf.SFData()
SF.loadStudies(studies=studies)
SF.loadRecordings2(recordings=recordings)
SF.loadSortingResults(sorting_results=sorting_results)
aggregated_sorting_results = dict(
recording_sorting_results=[],
study_sorting_results=[]
)
for study_name in SF.studyNames():
print('study: '+study_name)
S = SF.study(study_name)
first_recording = S.recording(S.recordingNames()[0])
sorter_names = first_recording.sortingResultNames()
for srname in sorter_names:
print('sorter: '+srname)
study_results0=dict(
recording_indices = [],
true_unit_ids = [],
true_unit_snrs = [],
true_unit_firing_rates = [],
num_matches = [],
num_false_positives = [],
num_false_negatives = []
)
for recording_index,rname in enumerate(S.recordingNames()):
print('recording: '+rname)
rec = S.recording(rname)
true_units_info = rec.trueUnitsInfo(format='json')
true_units_info_by_id = dict()
for true_unit in true_units_info:
true_units_info_by_id[true_unit['unit_id']] = true_unit
SR = rec.sortingResult(srname)
comparison = SR.comparisonWithTruth(format='json')
recording_results0=dict(
true_unit_ids = [],
true_unit_snrs = [],
true_unit_firing_rates = [],
num_matches = [],
num_false_positives = [],
num_false_negatives = []
)
ok = True
for i in comparison:
unit = comparison[i]
best_unit = unit['best_unit']
unit_id = unit['unit_id']
true_unit = true_units_info_by_id[unit_id]
recording_results0['true_unit_ids'].append(unit_id)
recording_results0['true_unit_snrs'].append(round(true_unit['snr'], 3))
recording_results0['true_unit_firing_rates'].append(
round(true_unit['firing_rate'], 3))
if 'num_false_positives' in unit:
recording_results0['num_matches'].append(unit['num_matches'])
recording_results0['num_false_positives'].append(unit['num_false_positives'])
recording_results0['num_false_negatives'].append(unit['num_false_negatives'])
else:
ok = False
error = 'missing field: num_false_positives'
break
if ok:
recording_sorting_result = dict(
study=study_name,
recording=rname,
sorter=srname,
true_unit_ids=recording_results0['true_unit_ids'],
true_unit_snrs=recording_results0['true_unit_snrs'],
true_unit_firing_rates=recording_results0['true_unit_firing_rates'],
num_matches=recording_results0['num_matches'],
num_false_positives=recording_results0['num_false_positives'],
num_false_negatives=recording_results0['num_false_negatives']
)
aggregated_sorting_results['recording_sorting_results'].append(recording_sorting_result)
else:
print('Warning: '+error)
study_results0['recording_indices'].extend([recording_index]*len(recording_results0['true_unit_ids']))
study_results0['true_unit_ids'].extend(recording_results0['true_unit_ids'])
study_results0['true_unit_snrs'].extend(recording_results0['true_unit_snrs'])
study_results0['true_unit_firing_rates'].extend(recording_results0['true_unit_firing_rates'])
study_results0['num_matches'].extend(recording_results0['num_matches'])
study_results0['num_false_positives'].extend(recording_results0['num_false_positives'])
study_results0['num_false_negatives'].extend(recording_results0['num_false_negatives'])
study_sorting_result = dict(
study=study_name,
sorter=srname,
true_unit_recording_indices=study_results0['recording_indices'],
true_unit_ids=study_results0['true_unit_ids'],
true_unit_snrs=study_results0['true_unit_snrs'],
true_unit_firing_rates=study_results0['true_unit_firing_rates'],
num_matches=study_results0['num_matches'],
num_false_positives=study_results0['num_false_positives'],
num_false_negatives=study_results0['num_false_negatives']
)
aggregated_sorting_results['study_sorting_results'].append(study_sorting_result)
return aggregated_sorting_results