def run(self):
sorting=si.MdaSortingExtractor(firings_file=self.firings)
sorting_true=si.MdaSortingExtractor(firings_file=self.firings_true)
if len(self.units_true)>0:
sorting_true=si.SubSortingExtractor(parent_sorting=sorting_true,unit_ids=self.units_true)
SC=st.comparison.SortingComparison(sorting_true,sorting)
df=sw.SortingComparisonTable(comparison=SC).getDataframe()
json=df.transpose().to_dict()
html=df.to_html(index=False)
_write_json_file(json,self.json_out)
_write_json_file(html,self.html_out)
def spikeforest_sort(
recording_dirname, # The recording extractor
sorter,
sorting_params,
_force_run=False,
_force_save=False
):
recording_signature=kb.computeDirHash(recording_dirname)
signature_obj=dict(
sorter_name=sorter.name,
sorter_version=sorter.version,
recording=recording_signature,
sorting_params=sorting_params
)
if not _force_run:
print('Looking up in cache...')
firings=kb.realizeFile(key=signature_obj)
if firings:
print('Found')
if _force_save:
print('Saving')
kb.saveFile(fname=firings,key=signature_obj)
return si.MdaSortingExtractor(firings_file=firings)
recording=si.MdaRecordingExtractor(recording_dirname)
sorting=sorter(recording=recording,**sorting_params)
si.MdaSortingExtractor.writeSorting(sorting=sorting,save_path='tmp_firings.mda')
kb.saveFile(fname='tmp_firings.mda',key=signature_obj)
return sorting
def run(self):
recording=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=False)
if len(self.channels)>0:
recording=si.SubRecordingExtractor(parent_recording=recording,channel_ids=self.channels)
sorting=si.MdaSortingExtractor(firings_file=self.firings)
sw.CrossCorrelogramsWidget(samplerate=recording.getSamplingFrequency(),sorting=sorting).plot()
fname=save_plot(self.plot_out)
def run(self):
recording=si.MdaRecordingExtractor(dataset_directory=self.recording_dir)
if len(self.channels)>0:
recording=si.SubRecordingExtractor(parent_recording=recording,channel_ids=self.channels)
sorting=si.MdaSortingExtractor(firings_file=self.firings)
sw.UnitWaveformsWidget(recording=recording,sorting=sorting).plot()
fname=save_plot(self.plot_out)
def run(self):
R0=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=True)
if (self.channel_ids) and (len(self.channel_ids)>0):
R0=si.SubRecordingExtractor(parent_recording=R0,channel_ids=self.channel_ids)
recording=sw.lazyfilters.bandpass_filter(recording=R0,freq_min=300,freq_max=6000)
sorting=si.MdaSortingExtractor(firings_file=self.firings)
ef=int(1e6)
recording_sub=si.SubRecordingExtractor(parent_recording=recording,start_frame=0,end_frame=ef)
recording_sub=MemoryRecordingExtractor(parent_recording=recording_sub)
sorting_sub=si.SubSortingExtractor(parent_sorting=sorting,start_frame=0,end_frame=ef)
unit_ids=self.unit_ids
if (not unit_ids) or (len(unit_ids)==0):
unit_ids=sorting.getUnitIds()
channel_noise_levels=compute_channel_noise_levels(recording=recording)
print('computing templates...')
templates=compute_unit_templates(recording=recording_sub,sorting=sorting_sub,unit_ids=unit_ids)
print('.')
ret=[]
for i,unit_id in enumerate(unit_ids):
template=templates[i]
info0=dict()
info0['unit_id']=int(unit_id)
info0['snr']=compute_template_snr(template,channel_noise_levels)
peak_channel_index=np.argmax(np.max(np.abs(template),axis=1))
info0['peak_channel']=int(recording.getChannelIds()[peak_channel_index])
train=sorting.getUnitSpikeTrain(unit_id=unit_id)
info0['num_events']=int(len(train))
info0['firing_rate']=float(len(train)/(recording.getNumFrames()/recording.getSamplingFrequency()))
ret.append(info0)
write_json_file(self.json_out,ret)
def getSortingTrue(self):
D2=mlp.readDir(self._kbucket_path)
if 'firings_true.mda' in D2['files']:
ret=si.MdaSortingExtractor(firings_file=self._kbucket_path+'/firings_true.mda')
else:
ret=None
return ret
def test_mda_extractor(self):
path1 = self.test_dir + '/mda'
path2 = path1 + '/firings_true.mda'
se.MdaRecordingExtractor.write_recording(self.RX, path1)
se.MdaSortingExtractor.write_sorting(self.SX, path2)
RX_mda = se.MdaRecordingExtractor(path1)
SX_mda = se.MdaSortingExtractor(path2)
self._check_recording_return_types(RX_mda)
self._check_recordings_equal(self.RX, RX_mda)
self._check_sorting_return_types(SX_mda)
self._check_sortings_equal(self.SX, SX_mda)
def get_result_from_folder(output_folder: Union[str, Path]):
output_folder = Path(output_folder)
tmpdir = output_folder / 'tmp'
result_fname = str(tmpdir / 'firings.mda')
samplerate_fname = str(tmpdir / 'samplerate.txt')
with open(samplerate_fname, 'r') as f:
samplerate = float(f.read())
sorting = se.MdaSortingExtractor(file_path=result_fname, sampling_frequency=samplerate)
return sorting
def run(self):
R0=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=True)
R=st.filters.bandpass_filter(recording=R0,freq_min=300,freq_max=6000)
S=si.MdaSortingExtractor(firings_file=self.firings)
channels=R.getChannelIds()
if len(channels)>20:
channels=channels[0:20]
units=S.getUnitIds()
if len(units)>20:
units=units[::int(len(units)/20)]
sw.UnitWaveformsWidget(recording=R,sorting=S,channels=channels,unit_ids=units).plot()
save_plot(self.jpg_out)
def yass_example(download=True, set_id=1):
if set_id in range(1, 7):
dsdir = 'kbucket://15734439d8cf/groundtruth/visapy_mea/set{}'.format(
set_id)
IX = se.MdaRecordingExtractor(dataset_directory=dsdir,
download=download)
path1 = os.path.join(dsdir, 'firings_true.mda')
print(path1)
OX = se.MdaSortingExtractor(path1)
return (IX, OX)
else:
raise Exception(
'Invalid ID for yass_example {} is not betewen 1..6'.format(
set_id))
def test_dump_load_multi_sub_extractor(self):
# generate dumpable formats
path1 = self.test_dir + '/mda'
path2 = path1 + '/firings_true.mda'
se.MdaRecordingExtractor.write_recording(self.RX, path1)
se.MdaSortingExtractor.write_sorting(self.SX, path2)
RX_mda = se.MdaRecordingExtractor(path1)
SX_mda = se.MdaSortingExtractor(path2)
RX_multi_chan = se.MultiRecordingChannelExtractor(recordings=[RX_mda, RX_mda, RX_mda])
check_dumping(RX_multi_chan)
RX_multi_time = se.MultiRecordingTimeExtractor(recordings=[RX_mda, RX_mda, RX_mda], )
check_dumping(RX_multi_time)
RX_multi_chan = se.SubRecordingExtractor(RX_mda, channel_ids=[0, 1])
check_dumping(RX_multi_chan)
SX_sub = se.SubSortingExtractor(SX_mda, unit_ids=[1, 2])
check_dumping(SX_sub)
SX_multi = se.MultiSortingExtractor(sortings=[SX_mda, SX_mda, SX_mda])
check_dumping(SX_multi)
def run(self):
import spikewidgets as sw
R0=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=True)
if (self.channel_ids) and (len(self.channel_ids)>0):
R0=si.SubRecordingExtractor(parent_recording=R0,channel_ids=self.channel_ids)
recording = R0
# recording=sw.lazyfilters.bandpass_filter(recording=R0,freq_min=300,freq_max=6000)
sorting=si.MdaSortingExtractor(firings_file=self.firings)
unit_ids=self.unit_ids
if (not unit_ids) or (len(unit_ids)==0):
unit_ids=sorting.getUnitIds()
channel_noise_levels=compute_channel_noise_levels(recording=recording)
# No longer use subset to compute the templates
templates=compute_unit_templates(recording=recording,sorting=sorting,unit_ids=unit_ids,max_num=100)
ret=[]
for i,unit_id in enumerate(unit_ids):
template=templates[i]
max_p2p_amps_on_channels=np.max(template,axis=1)-np.min(template,axis=1)
peak_channel_index=np.argmax(max_p2p_amps_on_channels)
peak_channel=recording.getChannelIds()[peak_channel_index]
R1=si.SubRecordingExtractor(parent_recording=recording,channel_ids=[peak_channel_index])
R1f=sw.lazyfilters.bandpass_filter(recording=R1,freq_min=300,freq_max=6000)
templates2=compute_unit_templates(recording=R1f,sorting=sorting,unit_ids=[unit_id],max_num=100)
template2=templates2[0]
info0=dict()
info0['unit_id']=int(unit_id)
info0['snr']=np.max(np.abs(template2))/channel_noise_levels[peak_channel_index]
#info0['snr']=compute_template_snr(template,channel_noise_levels)
#peak_channel_index=np.argmax(np.max(np.abs(template),axis=1))
info0['peak_channel']=int(recording.getChannelIds()[peak_channel])
train=sorting.getUnitSpikeTrain(unit_id=unit_id)
info0['num_events']=int(len(train))
info0['firing_rate']=float(len(train)/(recording.getNumFrames()/recording.getSamplingFrequency()))
ret.append(info0)
write_json_file(self.json_out,ret)
def get_result_from_folder(output_folder):
sorting = se.MdaSortingExtractor(str(output_folder / 'firings.mda'))
return sorting
def sorting(self):
return si.MdaSortingExtractor(firings_file=self._obj['firings'])
def sortingTrue(self):
return si.MdaSortingExtractor(firings_file=self.directory() +
'/firings_true.mda')