Add read_kilosort4_motion function

src/spikeinterface/sorters/external/kilosort4.py

@@ -1,7 +1,9 @@
 import warnings
+from pathlib import Path
 from packaging import version
 
-from spikeinterface.core import write_binary_recording
+
+from spikeinterface.core import write_binary_recording, Motion, BaseRecording
 from spikeinterface.sorters.basesorter import BaseSorter, get_job_kwargs
 from .kilosortbase import KilosortBase
 from spikeinterface.sorters.basesorter import get_job_kwargs
@@ -453,6 +455,11 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             if (sorter_output_folder / "recording.dat").is_file():
                 (sorter_output_folder / "recording.dat").unlink()
 
+        # close logger
+        for handler in logger.handlers.copy():
+            logger.removeHandler(handler)
+            handler.close()
+
     @classmethod
     def _get_result_from_folder(cls, sorter_output_folder):
         return KilosortBase._get_result_from_folder(sorter_output_folder)
@@ -484,3 +491,47 @@ def _setup_json_probe_map(cls, recording, sorter_output_folder):
             "n_chan": n_chan,
         }
         save_probe(probe, str(sorter_output_folder / "chanMap.json"))
+
+
+def read_kilosort4_motion(sorter_output_folder: str | Path, recording: BaseRecording | None = None) -> Motion:
+    """Reads the motion information from a Kilosort4 output folder and returns a Motion object.
+
+    Parameters
+    ----------
+    sorter_output_folder: str or Path
+        The path to the Kilosort4 output folder.
+    recording: BaseRecording, optional
+        The recording object. If provided, the temporal bins will be estimated based on the recording's
+        start and end times. If not provided, the temporal bins will be estimated based on the number
+        of batches in the ops file.
+
+    Returns
+    -------
+    Motion
+        A Motion object containing the displacement, temporal bins, and spatial bins.
+
+    """
+    sorter_output_folder = Path(sorter_output_folder)
+    ops_file = sorter_output_folder / "ops.npy"
+    if not ops_file.is_file():
+        raise FileNotFoundError("'ops.npy' file not found!")
+    ops = np.load(ops_file, allow_pickle=True).item()
+    yblk = ops.get("yblk")
+    dshift = ops.get("dshift")
+    if yblk is None or dshift is None:
+        raise Exception("'yblk' and 'dshift' fields not found in ops file!")
+    displacement = dshift + yblk
+    spatial_bins_um = yblk
+    # estimate temporal bins
+    batch_size = ops["batch_size"]
+    fs = ops["fs"]
+    t_bin = batch_size / fs
+    if recording is not None:
+        t_start = recording.get_start_time()
+        t_end = recording.get_end_time()
+        temporal_bins_s = np.linspace(t_start + t_bin / 2, t_end - t_bin / 2)
+    else:
+        temporal_bins_s = np.arange(displacement.shape[0]) * t_bin + t_bin / 2
+
+    motion = Motion(displacement=displacement, temporal_bins_s=temporal_bins_s, spatial_bins_um=spatial_bins_um)
+    return motion

src/spikeinterface/sorters/sorterlist.py

@@ -6,7 +6,7 @@
 from .external.kilosort2 import Kilosort2Sorter
 from .external.kilosort2_5 import Kilosort2_5Sorter
 from .external.kilosort3 import Kilosort3Sorter
-from .external.kilosort4 import Kilosort4Sorter
+from .external.kilosort4 import Kilosort4Sorter, read_kilosort4_motion
 from .external.pykilosort import PyKilosortSorter
 from .external.klusta import KlustaSorter
 from .external.mountainsort4 import Mountainsort4Sorter