Final cleaning of mixtures for lupin/tdc/sc

src/spikeinterface/benchmark/benchmark_clustering.py

@@ -29,9 +29,14 @@ def __init__(self, recording, gt_sorting, params, indices, peaks, exhaustive_gt=
         self.method_kwargs = params["method_kwargs"]
         self.result = {}
 
-    def run(self, **job_kwargs):
+    def run(self, verbose=True, **job_kwargs):
         labels, peak_labels = find_clusters_from_peaks(
-            self.recording, self.peaks, method=self.method, method_kwargs=self.method_kwargs, job_kwargs=job_kwargs
+            self.recording,
+            self.peaks,
+            method=self.method,
+            method_kwargs=self.method_kwargs,
+            verbose=verbose,
+            job_kwargs=job_kwargs,
         )
         self.result["peak_labels"] = peak_labels
 

src/spikeinterface/benchmark/benchmark_matching.py

@@ -26,9 +26,14 @@ def __init__(self, recording, gt_sorting, params):
         self.method_kwargs = params["method_kwargs"]
         self.result = {}
 
-    def run(self, **job_kwargs):
+    def run(self, verbose=True, **job_kwargs):
         spikes = find_spikes_from_templates(
-            self.recording, self.templates, method=self.method, method_kwargs=self.method_kwargs, job_kwargs=job_kwargs
+            self.recording,
+            self.templates,
+            method=self.method,
+            method_kwargs=self.method_kwargs,
+            verbose=verbose,
+            job_kwargs=job_kwargs,
         )
         unit_ids = self.templates.unit_ids
         sorting = np.zeros(spikes.size, dtype=minimum_spike_dtype)

src/spikeinterface/sorters/internal/lupin.py

@@ -54,8 +54,10 @@ class LupinSorter(ComponentsBasedSorter):
         "clustering_recursive_depth": 3,
         "ms_before": 1.0,
         "ms_after": 2.5,
-        "sparsity_threshold": 1.5,
-        "template_min_snr": 2.5,
+        "template_sparsify_threshold": 1.5,
+        "template_min_snr_ptp": 4.0,
+        "template_max_jitter_ms": 0.2,
+        "min_firing_rate": 0.1,
         "gather_mode": "memory",
         "job_kwargs": {},
         "seed": None,
@@ -80,8 +82,10 @@ class LupinSorter(ComponentsBasedSorter):
         "clustering_recursive_depth": "Clustering recussivity",
         "ms_before": "Milliseconds before the spike peak for template matching",
         "ms_after": "Milliseconds after the spike peak for template matching",
-        "sparsity_threshold": "Threshold to sparsify templates before template matching",
-        "template_min_snr": "Threshold to remove templates before template matching",
+        "template_sparsify_threshold": "Threshold to sparsify templates before template matching",
+        "template_min_snr_ptp": "Threshold to remove templates before template matching",
+        "template_max_jitter_ms": "Threshold on jitters to remove templates before template matching",
+        "min_firing_rate": "To remove small cluster in size before template matching",
         "gather_mode": "How to accumalte spike in matching : memory/npy",
         "job_kwargs": "The famous and fabulous job_kwargs",
         "seed": "Seed for random number",
@@ -232,6 +236,12 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         clustering_kwargs["peaks_svd"]["n_components"] = params["n_svd_components_per_channel"]
         clustering_kwargs["split"]["recursive_depth"] = params["clustering_recursive_depth"]
         clustering_kwargs["split"]["method_kwargs"]["n_pca_features"] = params["n_pca_features"]
+        clustering_kwargs["clean_templates"]["sparsify_threshold"] = params["template_sparsify_threshold"]
+        clustering_kwargs["clean_templates"]["min_snr"] = params["template_min_snr_ptp"]
+        clustering_kwargs["clean_templates"]["max_jitter_ms"] = params["template_max_jitter_ms"]
+        clustering_kwargs["noise_levels"] = noise_levels
+        clustering_kwargs["clean_low_firing"]["min_firing_rate"] = params["min_firing_rate"]
+        clustering_kwargs["clean_low_firing"]["subsampling_factor"] = all_peaks.size / peaks.size
 
         if params["debug"]:
             clustering_kwargs["debug_folder"] = sorter_output_folder
@@ -290,10 +300,10 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         # this spasify more
         templates = clean_templates(
             templates,
-            sparsify_threshold=params["sparsity_threshold"],
+            sparsify_threshold=params["template_sparsify_threshold"],
             noise_levels=noise_levels,
-            min_snr=params["template_min_snr"],
-            max_jitter_ms=None,
+            min_snr=params["template_min_snr_ptp"],
+            max_jitter_ms=params["template_max_jitter_ms"],
             remove_empty=True,
         )
 

src/spikeinterface/sorters/internal/spyking_circus2.py

@@ -39,7 +39,8 @@ class Spykingcircus2Sorter(ComponentsBasedSorter):
         "motion_correction": {"preset": "dredge_fast"},
         "merging": {"max_distance_um": 50},
         "clustering": {"method": "iterative-hdbscan", "method_kwargs": dict()},
-        "cleaning": {"min_snr": 5, "max_jitter_ms": 0.1, "sparsify_threshold": None},
+        "cleaning": {"min_snr": 5, "max_jitter_ms": 0.2, "sparsify_threshold": 1, "mean_sd_ratio_threshold": 3},
+        "min_firing_rate": 0.1,
         "matching": {"method": "circus-omp", "method_kwargs": dict(), "pipeline_kwargs": dict()},
         "apply_preprocessing": True,
         "apply_whitening": True,
@@ -103,6 +104,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         from spikeinterface.sortingcomponents.peak_detection import detect_peaks
         from spikeinterface.sortingcomponents.peak_selection import select_peaks
         from spikeinterface.sortingcomponents.clustering import find_clusters_from_peaks
+        from spikeinterface.sortingcomponents.clustering.tools import remove_small_cluster
         from spikeinterface.sortingcomponents.matching import find_spikes_from_templates
         from spikeinterface.sortingcomponents.tools import check_probe_for_drift_correction
         from spikeinterface.sortingcomponents.tools import clean_templates
@@ -118,8 +120,6 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         ms_before = params["general"].get("ms_before", 0.5)
         ms_after = params["general"].get("ms_after", 1.5)
         radius_um = params["general"].get("radius_um", 100.0)
-        detect_threshold = params["detection"]["method_kwargs"].get("detect_threshold", 5)
-        peak_sign = params["detection"].get("peak_sign", "neg")
         deterministic = params["deterministic_peaks_detection"]
         debug = params["debug"]
         seed = params["seed"]
@@ -310,6 +310,9 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             if verbose:
                 print("Kept %d peaks for clustering" % len(selected_peaks))
 
+            cleaning_kwargs = params.get("cleaning", {}).copy()
+            cleaning_kwargs["remove_empty"] = True
+
             if clustering_method in [
                 "iterative-hdbscan",
                 "iterative-isosplit",
@@ -319,6 +322,10 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                 clustering_params.update(verbose=verbose)
                 clustering_params.update(seed=seed)
                 clustering_params.update(peaks_svd=params["general"])
+                if clustering_method in ["iterative-hdbscan", "iterative-isosplit"]:
+                    clustering_params.update(clean_templates=cleaning_kwargs)
+                    clustering_params["noise_levels"] = noise_levels
+
                 if debug:
                     clustering_params["debug_folder"] = sorter_output_folder / "clustering"
 
@@ -328,6 +335,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                 method=clustering_method,
                 method_kwargs=clustering_params,
                 extra_outputs=True,
+                verbose=verbose,
                 job_kwargs=job_kwargs,
             )
 
@@ -365,7 +373,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             else:
                 from spikeinterface.sortingcomponents.clustering.tools import get_templates_from_peaks_and_svd
 
-                dense_templates, new_sparse_mask = get_templates_from_peaks_and_svd(
+                dense_templates, new_sparse_mask, max_std_per_channel = get_templates_from_peaks_and_svd(
                     recording_w,
                     selected_peaks,
                     peak_labels,
@@ -375,16 +383,30 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                     more_outs["peaks_svd"],
                     more_outs["peak_svd_sparse_mask"],
                     operator="median",
+                    return_max_std_per_channel=True,
                 )
                 # this release the peak_svd memmap file
                 templates = dense_templates.to_sparse(new_sparse_mask)
 
             del more_outs
 
-            cleaning_kwargs = params.get("cleaning", {}).copy()
-            cleaning_kwargs["noise_levels"] = noise_levels
-            cleaning_kwargs["remove_empty"] = True
-            templates = clean_templates(templates, **cleaning_kwargs)
+            before_clean_ids = templates.unit_ids.copy()
+            cleaning_kwargs["max_std_per_channel"] = max_std_per_channel
+            cleaning_kwargs["verbose"] = verbose
+            templates = clean_templates(templates, noise_levels=noise_levels, **cleaning_kwargs)
+            remove_peak_mask = ~np.isin(peak_labels, templates.unit_ids)
+            peak_labels[remove_peak_mask] = -1
+
+            if params["min_firing_rate"] is not None:
+                peak_labels, to_keep = remove_small_cluster(
+                    recording_w,
+                    selected_peaks,
+                    peak_labels,
+                    min_firing_rate=params["min_firing_rate"],
+                    subsampling_factor=peaks.size / selected_peaks.size,
+                    verbose=verbose,
+                )
+                templates = templates.select_units(to_keep)
 
             if verbose:
                 print("Kept %d clean clusters" % len(templates.unit_ids))
@@ -508,5 +530,4 @@ def final_cleaning_circus(
         sparsity_overlap=sparsity_overlap,
         **job_kwargs,
     )
-
     return final_sa

src/spikeinterface/sorters/internal/tridesclous2.py

@@ -51,13 +51,15 @@ class Tridesclous2Sorter(ComponentsBasedSorter):
         "clustering": {
             "recursive_depth": 3,
         },
+        "min_firing_rate": 0.1,
         "templates": {
             "ms_before": 2.0,
             "ms_after": 3.0,
             "max_spikes_per_unit": 400,
             "sparsity_threshold": 1.5,
-            "min_snr": 2.5,
+            "min_snr": 3.5,
             "radius_um": 100.0,
+            "max_jitter_ms": 0.2,
         },
         "matching": {"method": "tdc-peeler", "method_kwargs": {}, "gather_mode": "memory"},
         "job_kwargs": {},
@@ -93,7 +95,6 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         from spikeinterface.sortingcomponents.peak_detection import detect_peaks
         from spikeinterface.sortingcomponents.peak_selection import select_peaks
         from spikeinterface.sortingcomponents.clustering.main import find_clusters_from_peaks, clustering_methods
-        from spikeinterface.sortingcomponents.tools import remove_empty_templates
         from spikeinterface.preprocessing import correct_motion
         from spikeinterface.sortingcomponents.motion import InterpolateMotionRecording
         from spikeinterface.sortingcomponents.tools import clean_templates, compute_sparsity_from_peaks_and_label
@@ -194,6 +195,9 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         clustering_kwargs["split"].update(params["clustering"])
         if params["debug"]:
             clustering_kwargs["debug_folder"] = sorter_output_folder
+        clustering_kwargs["noise_levels"] = noise_levels
+        clustering_kwargs["clean_low_firing"]["min_firing_rate"] = params["min_firing_rate"]
+        clustering_kwargs["clean_low_firing"]["subsampling_factor"] = all_peaks.size / peaks.size
 
         # if clustering_kwargs["clustering"]["clusterer"] == "isosplit6":
         #    have_sisosplit6 = importlib.util.find_spec("isosplit6") is not None
@@ -262,13 +266,13 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             is_in_uV=False,
         )
 
-        # this spasify more
+        # this clean and spasify more
         templates = clean_templates(
             templates,
             sparsify_threshold=params["templates"]["sparsity_threshold"],
             noise_levels=noise_levels,
             min_snr=params["templates"]["min_snr"],
-            max_jitter_ms=None,
+            max_jitter_ms=params["templates"]["max_jitter_ms"],
             remove_empty=True,
         )
 

src/spikeinterface/sortingcomponents/clustering/iterative_hdbscan.py

@@ -9,7 +9,9 @@
 from spikeinterface.sortingcomponents.waveforms.peak_svd import extract_peaks_svd
 from spikeinterface.sortingcomponents.clustering.merging_tools import merge_peak_labels_from_templates
 from spikeinterface.sortingcomponents.clustering.itersplit_tools import split_clusters
-from spikeinterface.sortingcomponents.clustering.tools import get_templates_from_peaks_and_svd
+from spikeinterface.sortingcomponents.clustering.tools import get_templates_from_peaks_and_svd, remove_small_cluster
+from spikeinterface.sortingcomponents.tools import clean_templates
+from spikeinterface.core.recording_tools import get_noise_levels
 
 
 class IterativeHDBSCANClustering:
@@ -30,6 +32,7 @@ class IterativeHDBSCANClustering:
     _default_params = {
         "peaks_svd": {"n_components": 5, "ms_before": 0.5, "ms_after": 1.5, "radius_um": 100.0},
         "seed": None,
+        "noise_levels": None,
         "split": {
             "split_radius_um": 75.0,
             "recursive": True,
@@ -43,8 +46,18 @@ class IterativeHDBSCANClustering:
                 "n_pca_features": 3,
             },
         },
+        "clean_templates": {
+            "sparsify_threshold": 1.0,
+            "min_snr": 2.5,
+            "remove_empty": True,
+            "max_jitter_ms": 0.2,
+        },
         "merge_from_templates": dict(similarity_thresh=0.8, num_shifts=3, use_lags=True),
         "merge_from_features": None,
+        "clean_low_firing": {
+            "min_firing_rate": 0.1,
+            "subsampling_factor": None,
+        },
         "debug_folder": None,
         "verbose": True,
     }
@@ -116,7 +129,7 @@ def main_function(cls, recording, peaks, params, job_kwargs=dict()):
             **split,
         )
 
-        templates, new_sparse_mask = get_templates_from_peaks_and_svd(
+        templates, new_sparse_mask, max_std_per_channel = get_templates_from_peaks_and_svd(
             recording,
             peaks,
             peak_labels,
@@ -126,8 +139,27 @@ def main_function(cls, recording, peaks, params, job_kwargs=dict()):
             peaks_svd,
             sparse_mask,
             operator="median",
+            return_max_std_per_channel=True,
         )
 
+        ## Pre clean using templates (jitter, sparsify_threshold)
+        templates = templates.to_sparse(new_sparse_mask)
+        cleaning_kwargs = params["clean_templates"].copy()
+        cleaning_kwargs["verbose"] = verbose
+        cleaning_kwargs["max_std_per_channel"] = max_std_per_channel
+        if params["noise_levels"] is not None:
+            noise_levels = params["noise_levels"]
+        else:
+            noise_levels = get_noise_levels(recording, return_in_uV=False, **job_kwargs)
+        cleaning_kwargs["noise_levels"] = noise_levels
+        cleaned_templates = clean_templates(templates, **cleaning_kwargs)
+        mask_keep_ids = np.isin(templates.unit_ids, cleaned_templates.unit_ids)
+        to_remove_ids = templates.unit_ids[~mask_keep_ids]
+        to_remove_label_mask = np.isin(peak_labels, to_remove_ids)
+        peak_labels[to_remove_label_mask] = -1
+        templates = cleaned_templates
+        new_sparse_mask = templates.sparsity.mask.copy()
+        templates = templates.to_dense()
         labels = templates.unit_ids
 
         if verbose:
@@ -154,6 +186,21 @@ def main_function(cls, recording, peaks, params, job_kwargs=dict()):
                 is_in_uV=False,
             )
 
+        # clean very small cluster before peeler
+        if (
+            params["clean_low_firing"]["subsampling_factor"] is not None
+            and params["clean_low_firing"]["min_firing_rate"] is not None
+        ):
+            peak_labels, to_keep = remove_small_cluster(
+                recording,
+                peaks,
+                peak_labels,
+                min_firing_rate=params["clean_low_firing"]["min_firing_rate"],
+                subsampling_factor=params["clean_low_firing"]["subsampling_factor"],
+                verbose=verbose,
+            )
+            templates = templates.select_units(to_keep)
+
         labels = templates.unit_ids
 
         if debug_folder is not None: