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Compute quality metrics after pipeline nodes #2773

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merged 2 commits into from
May 13, 2024
Merged

Compute quality metrics after pipeline nodes #2773

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a1439e7
Compute quality metrics after pipeline nodes
alejoe91 Apr 29, 2024
6f6f4f7
Update src/spikeinterface/core/sortinganalyzer.py
alejoe91 Apr 29, 2024
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19 changes: 18 additions & 1 deletion src/spikeinterface/core/sortinganalyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -968,7 +968,13 @@ def compute_several_extensions(self, extensions, save=True, **job_kwargs):

extensions_with_pipeline = {}
extensions_without_pipeline = {}
extensions_post_pipeline = {}
for extension_name, extension_params in extensions.items():
if extension_name == "quality_metrics":
# PATCH: the quality metric is computed after the pipeline, since some of the metrics optionally require
# the output of the pipeline extensions (e.g., spike_amplitudes, spike_locations).
extensions_post_pipeline[extension_name] = extension_params
continue
extension_class = get_extension_class(extension_name)
if extension_class.use_nodepipeline:
extensions_with_pipeline[extension_name] = extension_params
Expand Down Expand Up @@ -1020,6 +1026,17 @@ def compute_several_extensions(self, extensions, save=True, **job_kwargs):
if save:
extension_instance.save()

# PATCH: the quality metric is computed after the pipeline, since some of the metrics optionally require
# the output of the pipeline extensions (e.g., spike_amplitudes, spike_locations).
# An alternative could be to extend the "depend_on" attribute to use optional and to check if an extension
# depends on the output of the pipeline nodes (e.g. depend_on=["spike_amplitudes[optional]"])
Comment on lines +1029 to +1032
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perfect

for extension_name, extension_params in extensions_post_pipeline.items():
extension_class = get_extension_class(extension_name)
if extension_class.need_job_kwargs:
self.compute_one_extension(extension_name, save=save, **extension_params, **job_kwargs)
else:
self.compute_one_extension(extension_name, save=save, **extension_params)

def get_saved_extension_names(self):
"""
Get extension names saved in folder or zarr that can be loaded.
Expand Down Expand Up @@ -1173,7 +1190,7 @@ def _get_children_dependencies(extension_name):
This function is making the reverse way : get all children that depend of a
particular extension.

This is recurssive so this includes : children and so grand children and grand grand children
This is recursive so this includes : children and so grand children and great grand children

This function is usefull for deleting on recompute.
For instance recompute the "waveforms" need to delete "template"
Expand Down