Add highpass_cutoff and fix KS tests

.github/scripts/test_kilosort4_ci.py

@@ -21,19 +21,21 @@
 
 import copy
 from typing import Any
-import spikeinterface.full as si
 import numpy as np
 import torch
 import kilosort
 from kilosort.io import load_probe
 import pandas as pd
-from spikeinterface.sorters.external.kilosort4 import Kilosort4Sorter
 import pytest
-from probeinterface.io import write_prb
-from kilosort.parameters import DEFAULT_SETTINGS
 from packaging.version import parse
 from importlib.metadata import version
 from inspect import signature
+
+import spikeinterface.full as si
+from spikeinterface.sorters.external.kilosort4 import Kilosort4Sorter
+from probeinterface.io import write_prb
+
+from kilosort.parameters import DEFAULT_SETTINGS
 from kilosort.run_kilosort import (
     set_files,
     initialize_ops,
@@ -66,6 +68,7 @@
     ("nt", 93),
     ("nskip", 1),
     ("whitening_range", 16),
+    ("highpass_cutoff", 200),
     ("sig_interp", 5),
     ("nt0min", 25),
     ("dmin", 15),
@@ -87,10 +90,11 @@
     ("ccg_threshold", 1e12),
     ("acg_threshold", 1e12),
     ("cluster_downsampling", 2),
-    ("duplicate_spike_bins", 5),
+    ("duplicate_spike_ms", 0.3),
     ("drift_smoothing", [250, 250, 250]),
-    ("bad_channels", None),
     ("save_preprocessed_copy", False),
+    ("shift", 0),
+    ("scale", 1),
 ]
 
 
@@ -194,7 +198,10 @@ def test_params_to_test(self):
                 continue
 
             if param_key not in RUN_KILOSORT_ARGS:
-                assert DEFAULT_SETTINGS[param_key] != param_value, f"{param_key} values should be different in test."
+                assert DEFAULT_SETTINGS[param_key] != param_value, (
+                    f"{param_key} values should be different in test: "
+                    f"{param_value} vs. {DEFAULT_SETTINGS[param_key]}"
+                )
 
     def test_default_settings_all_represented(self):
         """
@@ -227,7 +234,7 @@ def test_spikeinterface_defaults_against_kilsort(self):
 
     # Testing Arguments ###
     def test_set_files_arguments(self):
-        self._check_arguments(set_files, ["settings", "filename", "probe", "probe_name", "data_dir", "results_dir"])
+        self._check_arguments(set_files, ["settings", "filename", "probe", "probe_name", "data_dir", "results_dir", "bad_channels"])
 
     def test_initialize_ops_arguments(self):
         expected_arguments = [
@@ -249,13 +256,13 @@ def test_compute_preprocessing_arguments(self):
         self._check_arguments(compute_preprocessing, ["ops", "device", "tic0", "file_object"])
 
     def test_compute_drift_location_arguments(self):
-        self._check_arguments(compute_drift_correction, ["ops", "device", "tic0", "progress_bar", "file_object"])
+        self._check_arguments(compute_drift_correction, ["ops", "device", "tic0", "progress_bar", "file_object", "clear_cache"])
 
     def test_detect_spikes_arguments(self):
-        self._check_arguments(detect_spikes, ["ops", "device", "bfile", "tic0", "progress_bar"])
+        self._check_arguments(detect_spikes, ["ops", "device", "bfile", "tic0", "progress_bar", "clear_cache"])
 
     def test_cluster_spikes_arguments(self):
-        self._check_arguments(cluster_spikes, ["st", "tF", "ops", "device", "bfile", "tic0", "progress_bar"])
+        self._check_arguments(cluster_spikes, ["st", "tF", "ops", "device", "bfile", "tic0", "progress_bar", "clear_cache"])
 
     def test_save_sorting_arguments(self):
         expected_arguments = ["ops", "results_dir", "st", "clu", "tF", "Wall", "imin", "tic0", "save_extra_vars"]

src/spikeinterface/sorters/external/kilosort4.py

@@ -35,6 +35,7 @@ class Kilosort4Sorter(BaseSorter):
         "artifact_threshold": None,
         "nskip": 25,
         "whitening_range": 32,
+        "highpass_cutoff": 300,
         "binning_depth": 5,
         "sig_interp": 20,
         "drift_smoothing": [0.5, 0.5, 0.5],
@@ -55,7 +56,7 @@ class Kilosort4Sorter(BaseSorter):
         "cluster_downsampling": 20,
         "cluster_pcs": 64,
         "x_centers": None,
-        "duplicate_spike_bins": 7,
+        "duplicate_spike_ms": 0.25,
         "do_correction": True,
         "keep_good_only": False,
         "save_extra_kwargs": False,
@@ -80,6 +81,7 @@ class Kilosort4Sorter(BaseSorter):
         "artifact_threshold": "If a batch contains absolute values above this number, it will be zeroed out under the assumption that a recording artifact is present. By default, the threshold is infinite (so that no zeroing occurs). Default value: None.",
         "nskip": "Batch stride for computing whitening matrix. Default value: 25.",
         "whitening_range": "Number of nearby channels used to estimate the whitening matrix. Default value: 32.",
+        "highpass_cutoff": "High-pass filter cutoff frequency in Hz. Default value: 300.",
         "binning_depth": "For drift correction, vertical bin size in microns used for 2D histogram. Default value: 5.",
         "sig_interp": "For drift correction, sigma for interpolation (spatial standard deviation). Approximate smoothness scale in units of microns. Default value: 20.",
         "drift_smoothing": "Amount of gaussian smoothing to apply to the spatiotemporal drift estimation, for x,y,time axes in units of registration blocks (for x,y axes) and batch size (for time axis). The x,y smoothing has no effect for `nblocks = 1`.",