Merge pull request #99 from int-brain-lab/filter_spurious_units

Filter "spurious" units from alignment gui
int-brain-lab · Sep 26, 2023 · f372bc5 · f372bc5
2 parents cafba88 + 3b53981
commit f372bc5
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Showing 2 changed files with 18 additions and 3 deletions.
diff --git a/atlaselectrophysiology/load_data.py b/atlaselectrophysiology/load_data.py
@@ -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
@@ -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')

diff --git a/atlaselectrophysiology/plot_data.py b/atlaselectrophysiology/plot_data.py
@@ -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
@@ -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])