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Filter "spurious" units from alignment gui #99

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merged 2 commits into from
Sep 26, 2023
Merged

Filter "spurious" units from alignment gui #99

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40675f0
filter units
Sep 25, 2023
3b53981
remove clusters from spikes object
mayofaulkner Sep 26, 2023
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17 changes: 16 additions & 1 deletion atlaselectrophysiology/load_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
from neuropixel import trace_header
import ibllib.atlas as atlas
from ibllib.qc.alignment_qc import AlignmentQC
from iblutil.numerical import ismember
from iblutil.util import Bunch
from one.api import ONE
from one.remote import aws
from pathlib import Path
Expand Down Expand Up @@ -259,16 +261,29 @@ def get_data(self):
try:
data['spikes'] = self.one.load_object(self.eid, 'spikes', collection=self.probe_collection,
attribute=['depths', 'amps', 'times', 'clusters'])
data['spikes']['exists'] = True

data['clusters'] = self.one.load_object(self.eid, 'clusters', collection=self.probe_collection,
attribute=['metrics', 'peakToTrough', 'waveforms', 'channels'])

# Remove low firing rate clusters
min_firing_rate = 50. / 3600.
clu_idx = data['clusters'].metrics.firing_rate > min_firing_rate
data['clusters'] = Bunch({k: v[clu_idx] for k, v in data['clusters'].items()})
spike_idx, ib = ismember(data['spikes'].clusters, data['clusters'].metrics.index)
data['clusters'].metrics.reset_index(drop=True, inplace=True)
data['spikes'] = Bunch({k: v[spike_idx] for k, v in data['spikes'].items()})
data['spikes'].clusters = data['clusters'].metrics.index[ib].astype(np.int32)

data['spikes']['exists'] = True
data['clusters']['exists'] = True

data['channels'] = self.one.load_object(self.eid, 'channels', collection=self.probe_collection,
attribute=['rawInd', 'localCoordinates'])
data['channels']['exists'] = True

# Set low firing rate clusters to bad


except alf.exceptions.ALFObjectNotFound:
logger.error(f'Could not load spike sorting for probe insertion {self.probe_id}, GUI'
f' will not work')
Expand Down
4 changes: 2 additions & 2 deletions atlaselectrophysiology/plot_data.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from matplotlib import cm
import numpy as np
from brainbox.processing import bincount2D
from iblutil.numerical import bincount2D
from brainbox.io.spikeglx import Streamer
from brainbox.population.decode import xcorr
from brainbox.task import passive
Expand Down Expand Up @@ -596,7 +596,7 @@ def get_autocorr(self, clust_idx):
autocorr = xcorr(self.data['spikes']['times'][idx], self.data['spikes']['clusters'][idx],
AUTOCORR_BIN_SIZE, AUTOCORR_WIN_SIZE)

return autocorr[0, 0, :], self.clust_id[clust_idx]
return autocorr[0, 0, :], self.data['clusters'].metrics.cluster_id[self.clust_id[clust_idx]]

def get_template_wf(self, clust_idx):
template_wf = (self.data['clusters']['waveforms'][self.clust_id[clust_idx], :, 0])
Expand Down
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