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PR to restore the "no matching" functionality in circus2 #4095

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PR to restore the "no matching" functionality in circus2 #4095

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c752529
WIP
yger Jul 30, 2025
d5478d5
Merge branch 'main' of https://github.com/SpikeInterface/spikeinterfa…
yger Jul 31, 2025
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24 changes: 13 additions & 11 deletions src/spikeinterface/sorters/internal/spyking_circus2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -322,7 +322,11 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
),
}

outputs = find_cluster_from_peaks(
matching_method = params["matching"].pop("method")
if matching_method is None:
templates_from_svd = True

clustering_outputs = find_cluster_from_peaks(
recording_w,
selected_peaks,
method=clustering_method,
Expand All @@ -331,8 +335,8 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
**job_kwargs,
)

if len(outputs) == 2:
_, peak_labels = outputs
if len(clustering_outputs) == 2:
_, peak_labels = clustering_outputs
from spikeinterface.sortingcomponents.clustering.tools import get_templates_from_peaks_and_recording

templates = get_templates_from_peaks_and_recording(
Expand All @@ -346,8 +350,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
else:
from spikeinterface.sortingcomponents.clustering.tools import get_templates_from_peaks_and_svd

# _, peak_labels, svd_model, svd_features, sparsity_mask = outputs
_, peak_labels, more_outs = outputs
_, peak_labels, more_outs = clustering_outputs

templates, _ = get_templates_from_peaks_and_svd(
recording_w,
Expand All @@ -360,9 +363,6 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
more_outs["peak_svd_sparse_mask"],
operator="median",
)
# this release the peak_svd memmap file
del more_outs
del outputs

templates = clean_templates(
templates,
Expand All @@ -379,7 +379,6 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
templates.to_zarr(folder_path=clustering_folder / "templates")

## We launch a OMP matching pursuit by full convolution of the templates and the raw traces
matching_method = params["matching"].pop("method")
gather_mode = params["matching"].pop("gather_mode", "memory")
gather_kwargs = params["matching"].pop("gather_kwargs", {})
matching_params = params["matching"].get("method_kwargs", {}).copy()
Expand Down Expand Up @@ -421,8 +420,8 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
recording_w,
peaks,
templates=templates,
svd_model=svd_model,
sparse_mask=sparsity_mask,
svd_model=more_outs["svd_model"],
sparse_mask=more_outs["peak_svd_sparse_mask"],
**job_kwargs,
)

Expand All @@ -435,6 +434,9 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
sorting["segment_index"] = peaks["segment_index"]
sorting = NumpySorting(sorting, sampling_frequency, templates.unit_ids)

# this release the peak_svd memmap file
del clustering_outputs

merging_params = params["merging"].copy()
merging_params["debug_folder"] = sorter_output_folder / "merging"

Expand Down
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