Merge branch 'SpikeInterface:main' into sortingview-curation-fix

src/spikeinterface/sorters/external/kilosort4.py

@@ -56,6 +56,7 @@ class Kilosort4Sorter(BaseSorter):
         "save_extra_kwargs": False,
         "skip_kilosort_preprocessing": False,
         "scaleproc": None,
+        "save_preprocessed_copy": False,
         "torch_device": "auto",
     }
 
@@ -98,6 +99,7 @@ class Kilosort4Sorter(BaseSorter):
         "save_extra_kwargs": "If True, additional kwargs are saved to the output",
         "skip_kilosort_preprocessing": "Can optionally skip the internal kilosort preprocessing",
         "scaleproc": "int16 scaling of whitened data, if None set to 200.",
+        "save_preprocessed_copy": "save a pre-processed copy of the data (including drift correction) to temp_wh.dat in the results directory and format Phy output to use that copy of the data",
         "torch_device": "Select the torch device auto/cuda/cpu",
     }
 
@@ -153,7 +155,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             save_sorting,
             get_run_parameters,
         )
-        from kilosort.io import load_probe, RecordingExtractorAsArray, BinaryFiltered
+        from kilosort.io import load_probe, RecordingExtractorAsArray, BinaryFiltered, save_preprocessing
         from kilosort.parameters import DEFAULT_SETTINGS
 
         import time
@@ -186,6 +188,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         do_CAR = params["do_CAR"]
         invert_sign = params["invert_sign"]
         save_extra_vars = params["save_extra_kwargs"]
+        save_preprocessed_copy = params["save_preprocessed_copy"]
         progress_bar = None
         settings_ks = {k: v for k, v in params.items() if k in DEFAULT_SETTINGS}
         settings_ks["n_chan_bin"] = recording.get_num_channels()
@@ -207,7 +210,15 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         results_dir = sorter_output_folder
         filename, data_dir, results_dir, probe = set_files(settings, filename, probe, probe_name, data_dir, results_dir)
         if version.parse(cls.get_sorter_version()) >= version.parse("4.0.12"):
-            ops = initialize_ops(settings, probe, recording.get_dtype(), do_CAR, invert_sign, device, False)
+            ops = initialize_ops(
+                settings,
+                probe,
+                recording.get_dtype(),
+                do_CAR,
+                invert_sign,
+                device,
+                save_preprocesed_copy=save_preprocessed_copy,  # this kwarg is correct (typo)
+            )
             n_chan_bin, fs, NT, nt, twav_min, chan_map, dtype, do_CAR, invert, _, _, tmin, tmax, artifact, _, _ = (
                 get_run_parameters(ops)
             )
@@ -257,6 +268,9 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             ops, device, tic0=tic0, progress_bar=progress_bar, file_object=file_object
         )
 
+        if save_preprocessed_copy:
+            save_preprocessing(results_dir / "temp_wh.dat", ops, bfile)
+
         # Sort spikes and save results
         st, tF, _, _ = detect_spikes(ops, device, bfile, tic0=tic0, progress_bar=progress_bar)
         clu, Wall = cluster_spikes(st, tF, ops, device, bfile, tic0=tic0, progress_bar=progress_bar)
@@ -265,7 +279,21 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                 hp_filter=torch.as_tensor(np.zeros(1)), whiten_mat=torch.as_tensor(np.eye(recording.get_num_channels()))
             )
 
-        _ = save_sorting(ops, results_dir, st, clu, tF, Wall, bfile.imin, tic0, save_extra_vars=save_extra_vars)
+        if version.parse(cls.get_sorter_version()) >= version.parse("4.0.12"):
+            _ = save_sorting(
+                ops,
+                results_dir,
+                st,
+                clu,
+                tF,
+                Wall,
+                bfile.imin,
+                tic0,
+                save_extra_vars=save_extra_vars,
+                save_preprocessed_copy=save_preprocessed_copy,
+            )
+        else:
+            _ = save_sorting(ops, results_dir, st, clu, tF, Wall, bfile.imin, tic0, save_extra_vars=save_extra_vars)
 
     @classmethod
     def _get_result_from_folder(cls, sorter_output_folder):