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Extend and refactor waveform metrics #1993

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merged 12 commits into from
Oct 16, 2023
Merged

Extend and refactor waveform metrics #1993

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f96e2b7
Extend and refactor waveform metrics
alejoe91 Sep 13, 2023
87b2b10
update main
alejoe91 Sep 14, 2023
e2d3a8b
1D -> single channel; 2D -> multi-channel
alejoe91 Sep 22, 2023
226ad85
Update tests
alejoe91 Sep 22, 2023
3e7c16c
Merge branch 'main' into extended-template-metrics
alejoe91 Sep 25, 2023
00f91eb
Do not save/overwrite params in read-only mode
alejoe91 Sep 25, 2023
7ba84ad
updates
alejoe91 Sep 28, 2023
c1cd889
Add 'column_range' and simplify dimension handling
alejoe91 Sep 29, 2023
9662e1f
Merge branch 'main' into extended-template-metrics
alejoe91 Sep 29, 2023
ac84b25
Fix docstrings
alejoe91 Oct 1, 2023
4e3140f
Remove comment
alejoe91 Oct 2, 2023
3a1f540
Merge branch 'main' into extended-template-metrics
alejoe91 Oct 6, 2023
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27 changes: 23 additions & 4 deletions src/spikeinterface/core/waveform_extractor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -833,14 +833,30 @@ def select_units(self, unit_ids, new_folder=None, use_relative_path: bool = Fals
sparsity = ChannelSparsity(mask, unit_ids, self.channel_ids)
else:
sparsity = None
we = WaveformExtractor.create(self.recording, sorting, folder=None, mode="memory", sparsity=sparsity)
we.set_params(**self._params)
if self.has_recording():
we = WaveformExtractor.create(self.recording, sorting, folder=None, mode="memory", sparsity=sparsity)
else:
we = WaveformExtractor(
recording=None,
sorting=sorting,
folder=None,
sparsity=sparsity,
rec_attributes=self._rec_attributes,
allow_unfiltered=True,
)
we._params = self._params
# copy memory objects
if self.has_waveforms():
we._memory_objects = {"wfs_arrays": {}, "sampled_indices": {}}
for unit_id in unit_ids:
we._memory_objects["wfs_arrays"][unit_id] = self._memory_objects["wfs_arrays"][unit_id]
we._memory_objects["sampled_indices"][unit_id] = self._memory_objects["sampled_indices"][unit_id]
if self.format == "memory":
we._memory_objects["wfs_arrays"][unit_id] = self._memory_objects["wfs_arrays"][unit_id]
we._memory_objects["sampled_indices"][unit_id] = self._memory_objects["sampled_indices"][
unit_id
]
else:
we._memory_objects["wfs_arrays"][unit_id] = self.get_waveforms(unit_id)
we._memory_objects["sampled_indices"][unit_id] = self.get_sampled_indices(unit_id)

# finally select extensions data
for ext_name in self.get_available_extension_names():
Expand Down Expand Up @@ -2016,6 +2032,9 @@ def set_params(self, **params):
params = self._set_params(**params)
self._params = params

if self.waveform_extractor.is_read_only():
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Maybe we should run error instead no ?
set_params on read only should be allowed.

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It is allowed, but only in mem in this case

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henestly set_params to a read only should be not aalowed.
What is the use here ?

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It skips saving to disk!

return

params_to_save = params.copy()
if "sparsity" in params and params["sparsity"] is not None:
assert isinstance(
Expand Down
1 change: 0 additions & 1 deletion src/spikeinterface/postprocessing/__init__.py
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Expand Up @@ -10,7 +10,6 @@
from .template_metrics import (
TemplateMetricsCalculator,
compute_template_metrics,
calculate_template_metrics,
get_template_metric_names,
)

Expand Down
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