Merge branch 'main' into add-BaseRasterWidget

Author: chrishalcrow

.github/scripts/test_kilosort4_ci.py

@@ -20,7 +20,7 @@
 
 import pytest
 import copy
-from typing import Any
+from packaging.version import parse
 from inspect import signature
 
 import numpy as np
@@ -84,8 +84,6 @@
     "duplicate_spike_ms": 0.3,
 }
 
-PARAMS_TO_TEST = list(PARAMS_TO_TEST_DICT.keys())
-
 PARAMETERS_NOT_AFFECTING_RESULTS = [
     "artifact_threshold",
     "ccg_threshold",
@@ -95,13 +93,24 @@
     "duplicate_spike_ms",  # this is because ground-truth spikes don't have violations
 ]
 
-# THIS IS A PLACEHOLDER FOR FUTURE PARAMS TO TEST
-# if parse(version("kilosort")) >= parse("4.0.X"):
-#     PARAMS_TO_TEST_DICT.update(
-#         [
-#             {"new_param": new_value},
-#         ]
-#     )
+
+# Add/Remove version specific parameters
+if parse(kilosort.__version__) >= parse("4.0.22"):
+    PARAMS_TO_TEST_DICT.update(
+        {"position_limit": 50}
+    )
+    # Position limit only affects computing spike locations after sorting
+    PARAMETERS_NOT_AFFECTING_RESULTS.append("position_limit")
+
+if parse(kilosort.__version__) >= parse("4.0.24"):
+    PARAMS_TO_TEST_DICT.update(
+        {"max_peels": 200},
+    )
+    # max_peels is not affecting the results in this short dataset
+    PARAMETERS_NOT_AFFECTING_RESULTS.append("max_peels")
+
+
+PARAMS_TO_TEST = list(PARAMS_TO_TEST_DICT.keys())
 
 
 class TestKilosort4Long:

pyproject.toml

@@ -159,12 +159,16 @@ test = [
     "s3fs",
 
     # tridesclous
-    "numba",
+    "numba<0.61.0;python_version<'3.13'",
+    "numba>=0.61.0;python_version>='3.13'",
     "hdbscan>=0.8.33",  # Previous version had a broken wheel
 
     # for sortingview backend
     "sortingview",
 
+    # for motion and sortingcomponents
+    "torch",
+
     # curation
     "skops",
     "huggingface_hub",

src/spikeinterface/core/base.py

@@ -79,6 +79,31 @@ def __init__(self, main_ids: Sequence) -> None:
         # preferred context for multiprocessing
         self._preferred_mp_context = None
 
+    def _repr_html_(self, display_name=True):
+        pass
+
+    def _get_common_repr_html(self, common_style):
+        html_annotations = f"<details style='{common_style}'>  <summary><strong>Annotations</strong></summary><ul>"
+        for key, value in self._annotations.items():
+            html_annotations += f"<li> <strong> {key} </strong>: {value}</li>"
+        html_annotations += f"</details>"
+
+        html_properties = f"<details style='{common_style}'><summary><strong>Properties</strong></summary><ul>"
+        for key, value in self._properties.items():
+            # Add a further indent for each property
+            value_formatted = np.asarray(value)
+            html_properties += f"<details><summary><strong>{key}</strong></summary>{value_formatted}</details>"
+        html_properties += "</ul></details>"
+
+        if self.get_parent():
+            html_parent = f"<details style='{common_style}'>  <summary><strong>Parent</strong></summary><ul>"
+            display_name = self.name != self.get_parent().name
+            html_parent += self.get_parent()._repr_html_(display_name=display_name)
+            html_parent += "</ul></details>"
+        else:
+            html_parent = ""
+        return html_annotations + html_properties + html_parent
+
     @property
     def name(self):
         name = self._annotations.get("name", None)

src/spikeinterface/core/baserecording.py

@@ -89,7 +89,7 @@ def list_to_string(lst, max_size=6):
 
         return txt
 
-    def _repr_header(self):
+    def _repr_header(self, display_name=True):
         num_segments = self.get_num_segments()
         num_channels = self.get_num_channels()
         dtype = self.get_dtype()
@@ -105,8 +105,13 @@ def _repr_header(self):
             # Khz for high sampling rate and Hz for LFP
             sampling_frequency_repr = f"{(sf_hz/1000.0):0.1f}kHz" if sf_hz > 10_000.0 else f"{sf_hz:0.1f}Hz"
 
+        if display_name and self.name != self.__class__.__name__:
+            name = f"{self.name} ({self.__class__.__name__})"
+        else:
+            name = self.__class__.__name__
+
         txt = (
-            f"{self.name}: "
+            f"{name}: "
             f"{num_channels} channels - "
             f"{sampling_frequency_repr} - "
             f"{num_segments} segments - "
@@ -118,11 +123,11 @@ def _repr_header(self):
 
         return txt
 
-    def _repr_html_(self):
+    def _repr_html_(self, display_name=True):
         common_style = "margin-left: 10px;"
         border_style = "border:1px solid #ddd; padding:10px;"
 
-        html_header = f"<div style='{border_style}'><strong>{self._repr_header()}</strong></div>"
+        html_header = f"<div style='{border_style}'><strong>{self._repr_header(display_name)}</strong></div>"
 
         html_segments = ""
         if self.get_num_segments() > 1:
@@ -143,19 +148,8 @@ def _repr_html_(self):
         html_channel_ids = f"<details style='{common_style}'>  <summary><strong>Channel IDs</strong></summary><ul>"
         html_channel_ids += f"{self.channel_ids} </details>"
 
-        html_annotations = f"<details style='{common_style}'>  <summary><strong>Annotations</strong></summary><ul>"
-        for key, value in self._annotations.items():
-            html_annotations += f"<li> <strong> {key} </strong>: {value}</li>"
-        html_annotations += "</ul> </details>"
-
-        html_properties = f"<details style='{common_style}'><summary><strong>Channel Properties</strong></summary><ul>"
-        for key, value in self._properties.items():
-            # Add a further indent for each property
-            value_formatted = np.asarray(value)
-            html_properties += f"<details><summary> <strong> {key} </strong> </summary>{value_formatted}</details>"
-        html_properties += "</ul></details>"
-
-        html_repr = html_header + html_segments + html_channel_ids + html_annotations + html_properties
+        html_extra = self._get_common_repr_html(common_style)
+        html_repr = html_header + html_segments + html_channel_ids + html_extra
         return html_repr
 
     def get_num_segments(self) -> int:

src/spikeinterface/core/basesorting.py

@@ -30,38 +30,33 @@ def __init__(self, sampling_frequency: float, unit_ids: List):
         self._cached_spike_trains = {}
 
     def __repr__(self):
+        return self._repr_header()
+
+    def _repr_header(self, display_name=True):
         nseg = self.get_num_segments()
         nunits = self.get_num_units()
         sf_khz = self.get_sampling_frequency() / 1000.0
-        txt = f"{self.name}: {nunits} units - {nseg} segments - {sf_khz:0.1f}kHz"
+        if display_name and self.name != self.__class__.__name__:
+            name = f"{self.name} ({self.__class__.__name__})"
+        else:
+            name = self.__class__.__name__
+        txt = f"{name}: {nunits} units - {nseg} segments - {sf_khz:0.1f}kHz"
         if "file_path" in self._kwargs:
             txt += "\n  file_path: {}".format(self._kwargs["file_path"])
         return txt
 
-    def _repr_html_(self):
+    def _repr_html_(self, display_name=True):
         common_style = "margin-left: 10px;"
         border_style = "border:1px solid #ddd; padding:10px;"
 
-        html_header = f"<div style='{border_style}'><strong>{self.__repr__()}</strong></div>"
+        html_header = f"<div style='{border_style}'><strong>{self._repr_header(display_name)}</strong></div>"
 
         html_unit_ids = f"<details style='{common_style}'>  <summary><strong>Unit IDs</strong></summary><ul>"
         html_unit_ids += f"{self.unit_ids} </details>"
 
-        html_annotations = f"<details style='{common_style}'>  <summary><strong>Annotations</strong></summary><ul>"
-        for key, value in self._annotations.items():
-            html_annotations += f"<li> <strong> {key} </strong>: {value}</li>"
-        html_annotations += f"</details>"
-
-        html_unit_properties = (
-            f"<details style='{common_style}'><summary><strong>Unit Properties</strong></summary><ul>"
-        )
-        for key, value in self._properties.items():
-            # Add a further indent for each property
-            value_formatted = np.asarray(value)
-            html_unit_properties += f"<details><summary><strong>{key}</strong></summary>{value_formatted}</details>"
-        html_unit_properties += "</ul></details>"
+        html_extra = self._get_common_repr_html(common_style)
 
-        html_repr = html_header + html_unit_ids + html_annotations + html_unit_properties
+        html_repr = html_header + html_unit_ids + html_extra
         return html_repr
 
     @property

src/spikeinterface/core/channelslice.py

@@ -25,11 +25,10 @@ def __init__(self, parent_recording, channel_ids=None, renamed_channel_ids=None)
                 np.unique(renamed_channel_ids)
             ), "renamed_channel_ids must be unique!"
 
-        self._parent_recording = parent_recording
         self._channel_ids = np.asarray(channel_ids)
         self._renamed_channel_ids = np.asarray(renamed_channel_ids)
 
-        parents_chan_ids = self._parent_recording.get_channel_ids()
+        parents_chan_ids = parent_recording.get_channel_ids()
 
         # some checks
         assert all(
@@ -54,7 +53,7 @@ def __init__(self, parent_recording, channel_ids=None, renamed_channel_ids=None)
         self._parent_channel_indices = parent_recording.ids_to_indices(self._channel_ids)
 
         # link recording segment
-        for parent_segment in self._parent_recording._recording_segments:
+        for parent_segment in parent_recording._recording_segments:
             sub_segment = ChannelSliceRecordingSegment(parent_segment, self._parent_channel_indices)
             self.add_recording_segment(sub_segment)
 

src/spikeinterface/core/recording_tools.py

@@ -586,7 +586,9 @@ def get_random_recording_slices(
         for segment_index in range(num_segments):
             num_frames = recording.get_num_frames(segment_index)
             high = num_frames - chunk_size - margin_frames
-            random_starts = rng.integers(low=low, high=high, size=size)
+            # here we set endpoint to True, because the this represents the start of the
+            # chunk, and should be inclusive
+            random_starts = rng.integers(low=low, high=high, size=size, endpoint=True)
             random_starts = np.sort(random_starts)
             recording_slices += [
                 (segment_index, start_frame, (start_frame + chunk_size)) for start_frame in random_starts

src/spikeinterface/core/segmentutils.py

@@ -243,6 +243,7 @@ def __init__(self, recording: BaseRecording, segment_indices: int | list[int]):
         for segment_index in segment_indices:
             rec_seg = recording._recording_segments[segment_index]
             self.add_recording_segment(rec_seg)
+        self._parent = recording
 
         self._kwargs = {"recording": recording, "segment_indices": segment_indices}
 
@@ -564,6 +565,7 @@ def __init__(self, parent_sorting: BaseSorting, recording_or_recording_list=None
             )
             sliced_segment = sliced_parent_sorting._sorting_segments[0]
             self.add_sorting_segment(sliced_segment)
+        self._parent = parent_sorting
 
         self._kwargs = {"parent_sorting": parent_sorting, "recording_or_recording_list": recording_list}
 

src/spikeinterface/core/zarrextractors.py

@@ -62,8 +62,8 @@ def super_zarr_open(folder_path: str | Path, mode: str = "r", storage_options: d
     else:
         storage_options_to_test = (storage_options,)
 
+    root = None
     if is_path_remote(str(folder_path)):
-        root = None
         for open_func in open_funcs:
             if root is not None:
                 break
@@ -74,6 +74,8 @@ def super_zarr_open(folder_path: str | Path, mode: str = "r", storage_options: d
                 except Exception as e:
                     pass
     else:
+        if not Path(folder_path).is_dir():
+            raise ValueError(f"Folder {folder_path} does not exist")
         for open_func in open_funcs:
             try:
                 root = open_func(str(folder_path), mode=mode, storage_options=storage_options)

src/spikeinterface/preprocessing/basepreprocessor.py

@@ -9,7 +9,6 @@ class BasePreprocessor(BaseRecording):
     def __init__(self, recording, sampling_frequency=None, channel_ids=None, dtype=None):
         assert isinstance(recording, BaseRecording), "'recording' must be a RecordingExtractor"
 
-        self._parent_recording = recording
         if sampling_frequency is None:
             sampling_frequency = recording.get_sampling_frequency()
         if channel_ids is None: