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Fix: save a copy of group ids in CommonReferenceRecording #2215

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merged 4 commits into from
Nov 22, 2023
Merged

Fix: save a copy of group ids in CommonReferenceRecording #2215

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116af53
Fix: save a copy of group ids in CommonReferenceRecording
oaaij-gnahz Nov 15, 2023
ac3ae7c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 15, 2023
89acc59
Update src/spikeinterface/preprocessing/common_reference.py
oaaij-gnahz Nov 21, 2023
1badc49
Fix variable naming inconsistency
oaaij-gnahz Nov 21, 2023
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22 changes: 16 additions & 6 deletions src/spikeinterface/preprocessing/common_reference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,15 +98,17 @@ def __init__(

# tranforms groups (ids) to groups (indices)
if groups is not None:
groups = [self.ids_to_indices(g) for g in groups]
group_indices = [self.ids_to_indices(g) for g in groups]
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@oaaij-gnahz same name change should apply to all other groups_inds!

else:
group_indices = None
if ref_channel_ids is not None:
ref_channel_inds = self.ids_to_indices(ref_channel_ids)
else:
ref_channel_inds = None

for parent_segment in recording._recording_segments:
rec_segment = CommonReferenceRecordingSegment(
parent_segment, reference, operator, groups, ref_channel_inds, local_radius, neighbors, dtype_
parent_segment, reference, operator, group_indices, ref_channel_inds, local_radius, neighbors, dtype_
)
self.add_recording_segment(rec_segment)

Expand All @@ -123,13 +125,21 @@ def __init__(

class CommonReferenceRecordingSegment(BasePreprocessorSegment):
def __init__(
self, parent_recording_segment, reference, operator, groups, ref_channel_inds, local_radius, neighbors, dtype
self,
parent_recording_segment,
reference,
operator,
group_indices,
ref_channel_inds,
local_radius,
neighbors,
dtype,
):
BasePreprocessorSegment.__init__(self, parent_recording_segment)

self.reference = reference
self.operator = operator
self.groups = groups
self.group_indices = group_indices
self.ref_channel_inds = ref_channel_inds
self.local_radius = local_radius
self.neighbors = neighbors
Expand Down Expand Up @@ -175,8 +185,8 @@ def get_traces(self, start_frame, end_frame, channel_indices):
def _groups(self, channel_indices):
selected_groups = []
selected_channels = []
if self.groups:
for chan_inds in self.groups:
if self.group_indices:
for chan_inds in self.group_indices:
sel_inds = [ind for ind in channel_indices if ind in chan_inds]
# if no channels are in a group, do not return the group
if len(sel_inds) > 0:
Expand Down