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SpikeInterface · Oct 29, 2024 · e301e1a · e301e1a
2 parents 0a5f32f + 94d869a
commit e301e1a
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Showing 3 changed files with 16 additions and 23 deletions.
diff --git a/src/spikeinterface/benchmark/benchmark_merging.py b/src/spikeinterface/benchmark/benchmark_merging.py
@@ -29,8 +29,8 @@ def run(self, **job_kwargs):
         sorting_analyzer.compute(["random_spikes", "templates"], **job_kwargs)
         sorting_analyzer.compute("unit_locations", method="monopolar_triangulation")
         sorting_analyzer.compute("template_similarity", **{"method": "l2", "support": "union", "max_lag_ms": 0.1})
-        #sorting_analyzer.compute("correlograms", **correlograms_kwargs)
-        
+        # sorting_analyzer.compute("correlograms", **correlograms_kwargs)
+
         merged_analyzer, self.result["merges"], self.result["outs"] = auto_merge_units(
             sorting_analyzer,
             extra_outputs=True,
@@ -160,4 +160,3 @@ def plot_potential_merges(self, case_key, min_snr=None, backend="ipywidgets"):
         from spikeinterface.widgets import plot_potential_merges
 
         plot_potential_merges(analyzer, mylist, backend=backend)
-
diff --git a/src/spikeinterface/curation/auto_merge.py b/src/spikeinterface/curation/auto_merge.py
@@ -347,7 +347,6 @@ def compute_merge_unit_groups(
             outs["pairs_decreased_score"] = pairs_decreased_score
 
         ind1, ind2 = np.nonzero(pair_mask)
-        print(step, len(ind1))
 
     # FINAL STEP : create the final list from pair_mask boolean matrix
     ind1, ind2 = np.nonzero(pair_mask)
@@ -390,7 +389,7 @@ def auto_merge_units_internal(
     -------
     sorting_analyzer:
         The new sorting analyzer where all the merges from all the presets have been applied
-    
+
     merges, outs:
         Returned only when extra_outputs=True
         A list with the merges performed, and dictionaries that contains data for debugging and plotting.
@@ -626,7 +625,7 @@ def auto_merge_units(
     steps_params: dict = None,
     steps: list[str] | None = None,
     apply_merge_kwargs: dict = {},
-    recursive : bool = False,
+    recursive : bool = True,
     extra_outputs: bool = False,
     **job_kwargs,
 ) -> SortingAnalyzer:
@@ -660,7 +659,7 @@ def auto_merge_units(
         presets = [presets]
 
     if (steps is not None) and (presets is not None):
-        raise Exception('presets and steps are mutually exclusive')
+        raise Exception("presets and steps are mutually exclusive")
 
     if presets is not None:
         to_be_launched = presets
@@ -672,26 +671,23 @@ def auto_merge_units(
     if steps_params is not None:
         assert len(steps_params) == len(to_be_launched), f"steps params should have the same size as {launch_mode}"
     else:
-        steps_params = [None]*len(to_be_launched)
+        steps_params = [None] * len(to_be_launched)
 
     if extra_outputs:
         all_merging_groups = []
         all_outs = []
 
     for to_launch, params in zip(to_be_launched, steps_params):
-        
+
         if launch_mode == "presets":
-            compute_merge_kwargs = {"preset" : to_launch}
+            compute_merge_kwargs = {"preset": to_launch}
         elif launch_mode == "steps":
-            compute_merge_kwargs = {"steps" : to_launch}
+            compute_merge_kwargs = {"steps": to_launch}
 
         compute_merge_kwargs.update({"steps_params": params})
-        sorting_analyzer = auto_merge_units_internal(sorting_analyzer, 
-                                                     compute_merge_kwargs, 
-                                                     apply_merge_kwargs, 
-                                                     recursive,
-                                                     extra_outputs, 
-                                                     **job_kwargs)
+        sorting_analyzer = auto_merge_units_internal(
+            sorting_analyzer, compute_merge_kwargs, apply_merge_kwargs, recursive, extra_outputs, **job_kwargs
+        )
 
         if extra_outputs:
             sorting_analyzer, merge_unit_groups, outs = sorting_analyzer

diff --git a/src/spikeinterface/sorters/internal/spyking_circus2.py b/src/spikeinterface/sorters/internal/spyking_circus2.py
@@ -362,10 +362,8 @@ def final_cleaning_circus(
 
     template_diff_thresh = np.arange(0.05, 0.25, 0.05)
     presets = ["x_contaminations"] * len(template_diff_thresh)
-    steps_params = [{"template_similarity": {"template_diff_thresh": i}} for i in template_diff_thresh
-    ]
-    final_sa = auto_merge_units(analyzer, 
-                                presets=presets, 
-                                steps_params=steps_params, 
-                                apply_merge_kwargs=apply_merge_kwargs)
+    steps_params = [{"template_similarity": {"template_diff_thresh": i}} for i in template_diff_thresh]
+    final_sa = auto_merge_units(
+        analyzer, presets=presets, steps_params=steps_params, apply_merge_kwargs=apply_merge_kwargs
+    )
     return final_sa.sorting