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 run(self, payload, next_elem):
spif_params_dict = {}
probe_file = None
for param in self.param_list:
if param["name"] == "probe_path":
probe_file = param["value"]
elif param["name"] == "channel_map":
channel_map = param["value"]
elif param["name"] == "channel_groups":
channel_groups = param["value"]
else:
spif_params_dict[param["name"]] = param["value"]
recording = self._spif_class(**spif_params_dict)
if probe_file:
recording = recording.load_probe_file(probe_file, channel_map,
channel_groups)
else:
if channel_map:
assert np.all([
chan in channel_map
for chan in recording.get_channel_ids()
]), ("all channel_ids in "
"'channel_map' must be in recording channel ids")
recording = se.SubRecordingExtractor(recording,
channel_ids=channel_map)
if channel_groups:
recording.set_channel_groups(recording.get_channel_ids(),
channel_groups)
return recording
def run(self):
code = ''.join(
random.choice(string.ascii_uppercase) for x in range(10))
tmpdir = os.environ.get('TEMPDIR', '/tmp') + '/yass-tmp-' + code
# num_workers = os.environ.get('NUM_WORKERS', 1)
# print('num_workers: {}'.format(num_workers))
try:
recording = SFMdaRecordingExtractor(self.recording_dir)
if len(self.channels) > 0:
recording = se.SubRecordingExtractor(
parent_recording=recording, channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting, _ = yass_helper(recording=recording,
output_folder=tmpdir,
probe_file=None,
file_name=None,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
template_width_ms=self.template_width_ms,
filter=self.filter)
SFMdaSortingExtractor.write_sorting(sorting=sorting,
save_path=self.firings_out)
# shutil.copyfile(yaml_file, self.paramfile_out)
except:
if os.path.exists(tmpdir):
# shutil.rmtree(tmpdir)
print('not deleted tmpdir1')
raise
if not getattr(self, '_keep_temp_files', False):
# shutil.rmtree(tmpdir)
print('not deleted tmpdir2')
def old_fetch_average_waveform_plot_data(recording_object, sorting_object,
unit_id):
import labbox_ephys as le
R = le.LabboxEphysRecordingExtractor(recording_object)
S = le.LabboxEphysSortingExtractor(sorting_object)
start_frame = 0
end_frame = R.get_sampling_frequency() * 30
R0 = se.SubRecordingExtractor(parent_recording=R,
start_frame=start_frame,
end_frame=end_frame)
S0 = se.SubSortingExtractor(parent_sorting=S,
start_frame=start_frame,
end_frame=end_frame)
times0 = S0.get_unit_spike_train(unit_id=unit_id)
if len(times0) == 0:
# no waveforms found
return dict(channel_id=None, average_waveform=None)
try:
average_waveform = st.postprocessing.get_unit_templates(
recording=R0, sorting=S0, unit_ids=[unit_id])[0]
except:
raise Exception(f'Error getting unit templates for unit {unit_id}')
channel_maximums = np.max(np.abs(average_waveform), axis=1)
maxchan_index = np.argmax(channel_maximums)
maxchan_id = R0.get_channel_ids()[maxchan_index]
return dict(channel_id=maxchan_id,
average_waveform=average_waveform[maxchan_index, :].tolist())
def run(self):
code=''.join(random.choice(string.ascii_uppercase) for x in range(10))
tmpdir=os.environ.get('TEMPDIR','/tmp')+'/ironclust-tmp-'+code
num_workers=os.environ.get('NUM_WORKERS',2)
try:
recording=si.MdaRecordingExtractor(self.recording_dir)
if len(self.channels)>0:
recording=si.SubRecordingExtractor(parent_recording=recording,channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting=sf.sorters.spyking_circus(
recording=recording,
output_folder=tmpdir,
probe_file=None,
file_name=None,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
spike_thresh=self.spike_thresh,
template_width_ms=self.template_width_ms,
filter=self.filter,
merge_spikes=True,
n_cores=num_workers,
electrode_dimensions=None,
whitening_max_elts=self.whitening_max_elts,
clustering_max_elts=self.clustering_max_elts
)
si.MdaSortingExtractor.writeSorting(sorting=sorting,save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
raise
shutil.rmtree(tmpdir)
def run(self):
_keep_temp_files = True
code = ''.join(
random.choice(string.ascii_uppercase) for x in range(10))
tmpdir = os.environ.get('TEMPDIR', '/tmp') + '/kilosort2-tmp-' + code
try:
recording = SFMdaRecordingExtractor(self.recording_dir)
if len(self.channels) > 0:
recording = se.SubRecordingExtractor(
parent_recording=recording, channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting = kilosort2_helper(recording=recording,
tmpdir=tmpdir,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
detect_threshold=self.detect_threshold,
merge_thresh=self.merge_thresh,
freq_min=self.freq_min,
freq_max=self.freq_max,
pc_per_chan=self.pc_per_chan,
minFR=self.minFR)
SFMdaSortingExtractor.write_sorting(sorting=sorting,
save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
if not _keep_temp_files:
print('removing tmpdir1')
shutil.rmtree(tmpdir)
raise
if not _keep_temp_files:
print('removing tmpdir2')
shutil.rmtree(tmpdir)
def run(self):
ironclust_src=os.environ.get('IRONCLUST_SRC',None)
if not ironclust_src:
raise Exception('Environment variable not set: IRONCLUST_SRC')
code=''.join(random.choice(string.ascii_uppercase) for x in range(10))
tmpdir=os.environ.get('TEMPDIR','/tmp')+'/ironclust-tmp-'+code
try:
recording=si.MdaRecordingExtractor(self.recording_dir)
if len(self.channels)>0:
recording=si.SubRecordingExtractor(parent_recording=recording,channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting=sf.sorters.ironclust(
recording=recording,
tmpdir=tmpdir, ## TODO
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
detect_threshold=self.detect_threshold,
merge_thresh=self.merge_thresh,
freq_min=self.freq_min,
freq_max=self.freq_max,
pc_per_chan=self.pc_per_chan,
prm_template_name=self.prm_template_name,
ironclust_src=ironclust_src
)
si.MdaSortingExtractor.writeSorting(sorting=sorting,save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
raise
shutil.rmtree(tmpdir)
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):
code = ''.join(
random.choice(string.ascii_uppercase) for x in range(10))
tmpdir = os.environ.get('TEMPDIR', '/tmp') + '/kilosort-tmp-' + code
try:
recording = si.MdaRecordingExtractor(self.recording_dir)
if len(self.channels) > 0:
recording = si.SubRecordingExtractor(
parent_recording=recording, channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting = sorters.kilosort(recording=recording,
tmpdir=tmpdir,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
detect_threshold=self.detect_threshold,
merge_thresh=self.merge_thresh,
freq_min=self.freq_min,
freq_max=self.freq_max,
pc_per_chan=self.pc_per_chan)
si.MdaSortingExtractor.writeSorting(sorting=sorting,
save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
raise
shutil.rmtree(tmpdir)
def run(self):
tmpdir = _get_tmpdir('jrclust')
try:
recording = SFMdaRecordingExtractor(self.recording_dir)
params = read_dataset_params(self.recording_dir)
if len(self.channels) > 0:
recording = se.SubRecordingExtractor(
parent_recording=recording, channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
all_params = dict()
for param0 in self.PARAMETERS:
all_params[param0.name] = getattr(self, param0.name)
sorting = jrclust_helper(
recording=recording,
tmpdir=tmpdir,
params=params,
**all_params,
)
SFMdaSortingExtractor.write_sorting(sorting=sorting,
save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
if not getattr(self, '_keep_temp_files', False):
shutil.rmtree(tmpdir)
raise
if not getattr(self, '_keep_temp_files', False):
shutil.rmtree(tmpdir)
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 _on_view_timeseries(self):
rx = self._recording.recordingExtractor()
sf = rx.getSamplingFrequency()
if self._recording.recordingFileIsLocal():
rx = se.SubRecordingExtractor(parent_recording=rx,
start_frame=int(sf * 0),
end_frame=int(sf * 10))
else:
rx = se.SubRecordingExtractor(parent_recording=rx,
start_frame=int(sf * 0),
end_frame=int(sf * 1))
rx = st.preprocessing.bandpass_filter(recording=rx,
freq_min=300,
freq_max=6000)
self._view = SFW.TimeseriesWidget(recording=rx)
self.refresh()
def test_ttl_frames_in_sub_multi(self):
# sub recording
start_frame = self.example_info['num_frames'] // 3
end_frame = 2 * self.example_info['num_frames'] // 3
RX_sub = se.SubRecordingExtractor(self.RX,
start_frame=start_frame,
end_frame=end_frame)
original_ttls = self.RX.get_ttl_events()[0]
ttls_in_sub = original_ttls[np.where((original_ttls >= start_frame)
& (original_ttls < end_frame))[0]]
self.assertTrue(
np.array_equal(RX_sub.get_ttl_events()[0],
ttls_in_sub - start_frame))
# multirecording
RX_multi = se.MultiRecordingTimeExtractor(
recordings=[self.RX, self.RX, self.RX])
ttls_originals = self.RX.get_ttl_events()[0]
num_ttls = len(ttls_originals)
self.assertEqual(len(RX_multi.get_ttl_events()[0]), 3 * num_ttls)
self.assertTrue(
np.array_equal(RX_multi.get_ttl_events()[0][:num_ttls],
ttls_originals))
self.assertTrue(
np.array_equal(RX_multi.get_ttl_events()[0][num_ttls:2 * num_ttls],
ttls_originals + self.RX.get_num_frames()))
self.assertTrue(
np.array_equal(RX_multi.get_ttl_events()[0][2 * num_ttls:],
ttls_originals + 2 * self.RX.get_num_frames()))
def recordingExtractor(self, download=False):
X = si.MdaRecordingExtractor(dataset_directory=self.directory(),
download=download)
if 'channels' in self._obj:
if self._obj['channels']:
X = si.SubRecordingExtractor(parent_recording=X,
channel_ids=self._obj['channels'])
return X
def __init__(self, context):
vd.Component.__init__(self)
self._context = context
rx = self._context.recording.recordingExtractor()
sf = rx.getSamplingFrequency()
print(self._context.recording.recordingFileIsLocal())
if self._context.recording.recordingFileIsLocal():
rx = se.SubRecordingExtractor(parent_recording=rx,
start_frame=int(sf * 0),
end_frame=int(sf * 10))
else:
rx = se.SubRecordingExtractor(parent_recording=rx,
start_frame=int(sf * 0),
end_frame=int(sf * 1))
rx = st.preprocessing.bandpass_filter(recording=rx,
freq_min=300,
freq_max=6000)
self._timeseries_widget = TimeseriesWidget(recording=rx)
def run(self):
ret={}
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)
ret['samplerate']=recording.getSamplingFrequency()
ret['num_channels']=len(recording.getChannelIds())
ret['duration_sec']=recording.getNumFrames()/ret['samplerate']
write_json_file(self.json_out,ret)
def createSession(self):
recording = SFMdaRecordingExtractor(
dataset_directory=self._recording_directory, download=False)
recording = se.SubRecordingExtractor(
parent_recording=recording, start_frame=0, end_frame=10000)
recording = se.NumpyRecordingExtractor(
timeseries=recording.get_traces(), samplerate=recording.get_sampling_frequency())
W = SFW.TimeseriesWidget(recording=recording)
_make_full_browser(W)
return W
def compute_units_info(*, recording, sorting, channel_ids=[], unit_ids=[]):
if (channel_ids) and (len(channel_ids) > 0):
recording = si.SubRecordingExtractor(parent_recording=recording,
channel_ids=channel_ids)
# load into memory
print('Loading recording into RAM...')
recording = si.NumpyRecordingExtractor(
timeseries=recording.get_traces(),
samplerate=recording.get_sampling_frequency())
# do filtering
print('Filtering...')
recording = bandpass_filter(recording=recording,
freq_min=300,
freq_max=6000)
recording = si.NumpyRecordingExtractor(
timeseries=recording.get_traces(),
samplerate=recording.get_sampling_frequency())
if (not unit_ids) or (len(unit_ids) == 0):
unit_ids = sorting.get_unit_ids()
print('Computing channel noise levels...')
channel_noise_levels = compute_channel_noise_levels(recording=recording)
# No longer use subset to compute the templates
print('Computing unit templates...')
templates = compute_unit_templates(recording=recording,
sorting=sorting,
unit_ids=unit_ids,
max_num=100)
print(recording.get_channel_ids())
ret = []
for i, unit_id in enumerate(unit_ids):
print('Unit {} of {} (id={})'.format(i + 1, len(unit_ids), unit_id))
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.get_channel_ids()[peak_channel_index]
peak_signal = np.max(np.abs(template[peak_channel_index, :]))
info0 = dict()
info0['unit_id'] = int(unit_id)
info0['snr'] = peak_signal / channel_noise_levels[peak_channel_index]
info0['peak_channel'] = int(recording.get_channel_ids()[peak_channel])
train = sorting.get_unit_spike_train(unit_id=unit_id)
info0['num_events'] = int(len(train))
info0['firing_rate'] = float(
len(train) /
(recording.get_num_frames() / recording.get_sampling_frequency()))
ret.append(info0)
return ret
def run(self):
R0=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=False)
if len(self.channels)>0:
R0=si.SubRecordingExtractor(parent_recording=R0,channel_ids=self.channels)
R=sw.lazyfilters.bandpass_filter(recording=R0,freq_min=300,freq_max=6000)
N=R.getNumFrames()
N2=int(N/2)
channels=R.getChannelIds()
if len(channels)>20: channels=channels[0:20]
sw.TimeseriesWidget(recording=R,trange=[N2-4000,N2+0],channels=channels,width=12,height=5).plot()
save_plot(self.jpg_out)
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 __init__(self, arg: Union[str, dict], download: bool=False):
super().__init__()
obj = _create_object_for_arg(arg)
assert obj is not None
self._object: dict = obj
recording_format = self._object['recording_format']
data: dict = self._object['data']
if recording_format == 'mda':
self._recording: se.RecordingExtractor = MdaRecordingExtractor(timeseries_path=data['raw'], samplerate=data['params']['samplerate'], geom=np.array(data['geom']), download=download)
elif recording_format == 'nrs':
self._recording: se.RecordingExtractor = NrsRecordingExtractor(**data)
# elif recording_format == 'nwb':
# path0 = kp.load_file(data['path'])
# self._recording: se.RecordingExtractor = NwbRecordingExtractor(path0, electrical_series_name='e-series')
elif recording_format == 'bin1':
self._recording: se.RecordingExtractor = Bin1RecordingExtractor(**data, p2p=True)
elif recording_format == 'snippets1':
self._recording: se.RecordingExtractor = Snippets1RecordingExtractor(snippets_h5_uri=data['snippets_h5_uri'], p2p=True)
elif recording_format == 'subrecording':
R = LabboxEphysRecordingExtractor(data['recording'], download=download)
if 'channel_ids' in data:
channel_ids = np.array(data['channel_ids'])
elif 'group' in data:
channel_ids = np.array(R.get_channel_ids())
groups = R.get_channel_groups(channel_ids=R.get_channel_ids())
group = int(data['group'])
inds = np.where(np.array(groups) == group)[0]
channel_ids = channel_ids[inds]
elif 'groups' in data:
raise Exception('This case not yet handled.')
else:
channel_ids = None
if 'start_frame' in data:
start_frame = data['start_frame']
end_frame = data['end_frame']
else:
start_frame = None
end_frame = None
self._recording: se.RecordingExtractor = se.SubRecordingExtractor(
parent_recording=R,
channel_ids=channel_ids,
start_frame=start_frame,
end_frame=end_frame
)
elif recording_format == 'filtered':
R = LabboxEphysRecordingExtractor(data['recording'], download=download)
self._recording: se.RecordingExtractor = _apply_filters(recording=R, filters=data['filters'])
else:
raise Exception(f'Unexpected recording format: {recording_format}')
self.copy_channel_properties(recording=self._recording)
def get_unit_waveforms(recording, sorting, unit_ids, channel_ids_by_unit,
snippet_len):
if not isinstance(snippet_len, list) and not isinstance(
snippet_len, tuple):
b = int(snippet_len / 2)
a = int(snippet_len) - b
snippet_len = [a, b]
num_channels = recording.get_num_channels()
num_frames = recording.get_num_frames()
num_bytes_per_chunk = 1000 * 1000 * 1000 # ? how to choose this
num_bytes_per_frame = num_channels * 2
chunk_size = num_bytes_per_chunk / num_bytes_per_frame
padding_size = 100 + snippet_len[0] + snippet_len[
1] # a bit excess padding
chunks = _divide_recording_into_time_chunks(num_frames=num_frames,
chunk_size=chunk_size,
padding_size=padding_size)
all_unit_waveforms = [[] for ii in range(len(unit_ids))]
for ii, chunk in enumerate(chunks):
# chunk: {istart, iend, istart_with_padding, iend_with_padding} # include padding
print(
f'Processing chunk {ii + 1} of {len(chunks)}; chunk-range: {chunk["istart_with_padding"]} {chunk["iend_with_padding"]}; num-frames: {num_frames}'
)
recording_chunk = se.SubRecordingExtractor(
parent_recording=recording,
start_frame=chunk['istart_with_padding'],
end_frame=chunk['iend_with_padding'])
# note that the efficiency of this operation may need improvement (really depends on sorting extractor implementation)
sorting_chunk = se.SubSortingExtractor(parent_sorting=sorting,
start_frame=chunk['istart'],
end_frame=chunk['iend'])
print(f'Getting unit waveforms for chunk {ii + 1} of {len(chunks)}')
# num_events_in_chunk x num_channels_in_nbhd[unit_id] x len_of_one_snippet
unit_waveforms = _get_unit_waveforms_for_chunk(
recording=recording_chunk,
sorting=sorting_chunk,
frame_offset=chunk['istart'] - chunk[
'istart_with_padding'], # just the padding size (except 0 for first chunk)
unit_ids=unit_ids,
snippet_len=snippet_len,
channel_ids_by_unit=channel_ids_by_unit)
for i_unit, x in enumerate(unit_waveforms):
all_unit_waveforms[i_unit].append(x)
# concatenate the results over the chunks
unit_waveforms = [
# tot_num_events_for_unit x num_channels_in_nbhd[unit_id] x len_of_one_snippet
np.concatenate(all_unit_waveforms[i_unit], axis=0)
for i_unit in range(len(unit_ids))
]
return unit_waveforms
def run(self):
R0=si.MdaRecordingExtractor(dataset_directory=self.recording_dir,download=True)
if len(self.channels)>0:
R0=si.SubRecordingExtractor(parent_recording=R0,channel_ids=self.channels)
R=sw.lazyfilters.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]
if len(self.units)>0:
units=self.units
else:
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 test_multi_sub_recording_extractor(self):
RX_multi = se.MultiRecordingTimeExtractor(
recordings=[self.RX, self.RX, self.RX],
epoch_names=['A', 'B', 'C'])
RX_sub = RX_multi.get_epoch('C')
self._check_recordings_equal(self.RX, RX_sub)
self.assertEqual(4, len(RX_sub.get_channel_ids()))
RX_multi = se.MultiRecordingChannelExtractor(
recordings=[self.RX, self.RX2, self.RX3], groups=[1, 2, 3])
print(RX_multi.get_channel_groups())
RX_sub = se.SubRecordingExtractor(RX_multi,
channel_ids=[4, 5, 6, 7],
renamed_channel_ids=[0, 1, 2, 3])
self._check_recordings_equal(self.RX2, RX_sub)
self.assertEqual([2, 2, 2, 2], RX_sub.get_channel_groups())
self.assertEqual(12, len(RX_multi.get_channel_ids()))
def get_max_channels_per_waveforms(recording, grouping_property, channel_ids, max_channels_per_waveforms):
if grouping_property is None:
if max_channels_per_waveforms is None:
n_channels = len(channel_ids)
elif max_channels_per_waveforms >= len(channel_ids):
n_channels = len(channel_ids)
else:
n_channels = max_channels_per_waveforms
else:
rec = se.SubRecordingExtractor(recording, channel_ids=channel_ids)
rec_groups = np.array(rec.get_channel_groups())
groups, count = np.unique(rec_groups, return_counts=True)
if max_channels_per_waveforms is None:
n_channels = np.max(count)
elif max_channels_per_waveforms >= np.max(count):
n_channels = np.max(count)
else:
n_channels = max_channels_per_waveforms
return n_channels
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):
recording=si.MdaRecordingExtractor(self.recording_dir)
if len(self.channels)>0:
recording=si.SubRecordingExtractor(parent_recording=recording,channel_ids=self.channels)
num_workers=os.environ.get('NUM_WORKERS',None)
if num_workers:
num_workers=int(num_workers)
sorting=sf.sorters.mountainsort4(
recording=recording,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
freq_min=self.freq_min,
freq_max=self.freq_max,
whiten=self.whiten,
clip_size=self.clip_size,
detect_threshold=self.detect_threshold,
detect_interval=self.detect_interval,
noise_overlap_threshold=self.noise_overlap_threshold,
num_workers=num_workers
)
si.MdaSortingExtractor.writeSorting(sorting=sorting,save_path=self.firings_out)
def run(self):
ironclust_path = os.environ.get('IRONCLUST_PATH', None)
if not ironclust_path:
raise Exception('Environment variable not set: IRONCLUST_PATH')
code = ''.join(
random.choice(string.ascii_uppercase) for x in range(10))
tmpdir = os.environ.get('TEMPDIR', '/tmp') + '/ironclust-tmp-' + code
try:
recording = se.MdaRecordingExtractor(self.recording_dir)
params = read_dataset_params(self.recording_dir)
if len(self.channels) > 0:
recording = se.SubRecordingExtractor(
parent_recording=recording, channel_ids=self.channels)
if not os.path.exists(tmpdir):
os.mkdir(tmpdir)
sorting = ironclust_helper(
recording=recording,
tmpdir=tmpdir,
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
detect_threshold=self.detect_threshold,
merge_thresh=self.merge_thresh,
freq_min=self.freq_min,
freq_max=self.freq_max,
pc_per_chan=self.pc_per_chan,
prm_template_name=self.prm_template_name,
ironclust_path=ironclust_path,
params=params,
)
se.MdaSortingExtractor.writeSorting(sorting=sorting,
save_path=self.firings_out)
except:
if os.path.exists(tmpdir):
if not getattr(self, '_keep_temp_files', False):
shutil.rmtree(tmpdir)
raise
if not getattr(self, '_keep_temp_files', False):
shutil.rmtree(tmpdir)
def subset_recording(self, stub_test: bool = False):
"""
Subset a recording extractor according to stub and channel subset options.
Parameters
----------
stub_test : bool, optional (default False)
"""
kwargs = dict()
if stub_test:
num_frames = 100
end_frame = min(
[num_frames,
self.recording_extractor.get_num_frames()])
kwargs.update(end_frame=end_frame)
if self.subset_channels is not None:
kwargs.update(channel_ids=self.subset_channels)
recording_extractor = se.SubRecordingExtractor(
self.recording_extractor, **kwargs)
return recording_extractor
def find_unit_peak_channels(recording, sorting, unit_ids):
# Use the first part of the recording to estimate the peak channels
sorting_shortened = SubsampledSortingExtractor(parent_sorting=sorting, max_events_per_unit=20, method='truncate')
max_time = 0
for unit_id in sorting_shortened.get_unit_ids():
st = sorting_shortened.get_unit_spike_train(unit_id=unit_id)
if len(st) > 0:
max_time = max(max_time, np.max(st))
recording_shortened = se.SubRecordingExtractor(parent_recording=recording, start_frame=0, end_frame=max_time + 1)
unit_waveforms = get_unit_waveforms(
recording=recording_shortened,
sorting=sorting_shortened,
unit_ids=unit_ids,
channel_ids_by_unit=None,
snippet_len=(10, 10)
)
channel_ids = recording.get_channel_ids()
peak_channels = {}
for ii, unit_id in enumerate(unit_ids):
average_waveform = np.median(unit_waveforms[ii], axis=0)
peak_channel_index = int(np.argmax(np.max(average_waveform, axis=1) - np.min(average_waveform, axis=1)))
peak_channels[unit_id] = int(channel_ids[peak_channel_index])
return peak_channels