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@@ -915,26 +915,27 @@ class ReachGraspIO(BlackrockIO):
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filter_type=filter_type
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))
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- # Get rejection bands
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- sec = self.odmldoc['PreProcessing']
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- bands = sec.properties['LFPBands'].values
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+ self.__annotate_electrode_rejections(asig)
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- if hasattr(bands, '__iter__'):
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- for band in bands:
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- sec = self.odmldoc['PreProcessing'][band]
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+ def __annotate_electrode_rejections(self, obj):
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+ # Get rejection bands
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+ sec = self.odmldoc['PreProcessing']
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+ bands = sec.properties['LFPBands'].values
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- # default: No rejection information present
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- rej = np.full((asig.shape[-1]), None)
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-
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- if sec.properties['RejElectrodes'].values:
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- rej_els = np.asarray(sec.properties['RejElectrodes'].values, dtype=int)
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- rej = np.isin(asig.array_annotations['channel_ids'], rej_els)
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- else:
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- raise ValueError(
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- "Invalid entry %s in odML for rejected electrodes "
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- "in LFP band %s." % (sec.properties['RejElectrodes'].values, band))
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+ if hasattr(bands, '__iter__'):
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+ for band in bands:
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+ sec = self.odmldoc['PreProcessing'][band]
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+ rej_els = np.asarray(sec.properties['RejElectrodes'].values, dtype=int)
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- asig.array_annotations.update({str('electrode_reject_' + band): rej})
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+ if 'channel_id' in obj.annotations:
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+ rejection_value = bool(obj.annotations['channel_id'] in rej_els)
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+ obj.annotations['electrode_reject_' + band] = rejection_value
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+ elif hasattr(obj, 'array_annotations') and 'channel_ids' in obj.array_annotations:
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+ rej = np.isin(obj.array_annotations['channel_ids'], rej_els)
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+ obj.array_annotations.update({str('electrode_reject_' + band): rej})
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+ else:
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+ warnings.warn(
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+ 'Could not annotate {} with electrode rejection information.'.format(obj))
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def __convert_chids_and_coordinates(self, channel_ids):
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nchan = len(channel_ids)
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@@ -1667,6 +1668,9 @@ class ReachGraspIO(BlackrockIO):
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if correct_filter_shifts:
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self.__correct_filter_shifts(asig)
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+ for st in seg.spiketrains:
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+ self.__annotate_electrode_rejections(st)
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+
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for ev in seg.events:
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# Modify digital trial events to include semantic event information
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if ev.name == 'digital_input_port':
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