Calibration with first benchmarks

SpikeInterface · Nov 29, 2024 · d310021 · d310021
1 parent cdac4b9
commit d310021
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/src/spikeinterface/sorters/internal/spyking_circus2.py b/src/spikeinterface/sorters/internal/spyking_circus2.py
@@ -346,10 +346,10 @@ def final_cleaning_circus(
     sorting,
     templates,
     similarity_kwargs={"method": "l2", "support": "union", "max_lag_ms": 0.1},
-    apply_merge_kwargs={"sparsity_overlap": 0.5, "censor_ms": 3.0},
+    apply_merge_kwargs={"sparsity_overlap": 0.1, "censor_ms": 3.0},
     correlograms_kwargs={},
     max_distance_um=50,
-    template_diff_thresh=np.arange(0.05, 0.25, 0.05),
+    template_diff_thresh=np.arange(0.05, 0.5, 0.05),
     **job_kwargs,
 ):
 

diff --git a/src/spikeinterface/sortingcomponents/peak_detection.py b/src/spikeinterface/sortingcomponents/peak_detection.py
@@ -118,7 +118,7 @@ def detect_peaks(
         squeeze_output = True
     else:
         squeeze_output = False
-        job_name += f"  + {len(pipeline_nodes)} nodes"
+        job_name += f" + {len(pipeline_nodes)} nodes"
 
         # because node are modified inplace (insert parent) they need to copy incase
         # the same pipeline is run several times

diff --git a/src/spikeinterface/sortingcomponents/tools.py b/src/spikeinterface/sortingcomponents/tools.py
@@ -169,7 +169,9 @@ def create_sorting_analyzer_with_existing_templates(sorting, recording, template
         non_empty_sorting = sorting
 
     sa = create_sorting_analyzer(non_empty_sorting, recording, format="memory", sparsity=sparsity)
+    sa.compute("random_spikes")
     sa.extensions["templates"] = ComputeTemplates(sa)
     sa.extensions["templates"].params = {"ms_before": templates.ms_before, "ms_after": templates.ms_after}
     sa.extensions["templates"].data["average"] = templates_array
+    sa.extensions["templates"].data["std"] = np.zeros(templates_array.shape, dtype=np.float32)
     return sa