spikeinterface 0.100.4__tar.gz → 0.100.6__tar.gz

{spikeinterface-0.100.4/src/spikeinterface.egg-info → spikeinterface-0.100.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.4
+Version: 0.100.6
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface
@@ -25,7 +25,7 @@ Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
 Requires-Dist: MEArec>=1.8; extra == "extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "extractors"
 Requires-Dist: pyedflib>=0.1.30; extra == "extractors"
 Requires-Dist: sonpy; python_version < "3.10" and extra == "extractors"
@@ -41,7 +41,7 @@ Requires-Dist: ibllib>=2.21.0; extra == "streaming-extractors"
 Requires-Dist: fsspec; extra == "streaming-extractors"
 Requires-Dist: aiohttp; extra == "streaming-extractors"
 Requires-Dist: requests; extra == "streaming-extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "streaming-extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "streaming-extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "streaming-extractors"
 Requires-Dist: remfile; extra == "streaming-extractors"
 Requires-Dist: s3fs; extra == "streaming-extractors"

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.4"
+version = "0.100.6"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
@@ -59,7 +59,7 @@ changelog = "https://spikeinterface.readthedocs.io/en/latest/whatisnew.html"
 
 extractors = [
     "MEArec>=1.8",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "pyedflib>=0.1.30",
     "sonpy;python_version<'3.10'",
@@ -80,7 +80,7 @@ streaming_extractors = [
     "fsspec",
     "aiohttp",
     "requests",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "remfile",
     "s3fs"

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/core/core_tools.py

@@ -7,6 +7,7 @@ import datetime
 import json
 from copy import deepcopy
 
+from math import prod
 
 import numpy as np
 from tqdm import tqdm
@@ -163,7 +164,8 @@ def make_shared_array(shape, dtype):
     from multiprocessing.shared_memory import SharedMemory
 
     dtype = np.dtype(dtype)
-    nbytes = int(np.prod(shape) * dtype.itemsize)
+    shape = tuple(int(x) for x in shape)  # We need to be sure that shape comes in int instead of numpy scalars
+    nbytes = prod(shape) * dtype.itemsize
     shm = SharedMemory(name=None, create=True, size=nbytes)
     arr = np.ndarray(shape=shape, dtype=dtype, buffer=shm.buf)
     arr[:] = 0

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/core/waveform_tools.py

@@ -483,7 +483,7 @@ def extract_waveforms_to_single_buffer(
     if sparsity_mask is None:
         num_chans = recording.get_num_channels()
     else:
-        num_chans = max(np.sum(sparsity_mask, axis=1))
+        num_chans = int(max(np.sum(sparsity_mask, axis=1)))  # This is a numpy scalar, so we cast to int
     shape = (num_spikes, nsamples, num_chans)
 
     if mode == "memmap":
@@ -696,6 +696,8 @@ def has_exceeding_spikes(recording, sorting):
         if len(spike_vector_seg) > 0:
             if spike_vector_seg["sample_index"][-1] > recording.get_num_samples(segment_index=segment_index) - 1:
                 return True
+            if spike_vector_seg["sample_index"][0] < 0:
+                return True
     return False
 
 

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/curation/remove_excess_spikes.py

@@ -61,7 +61,8 @@ class RemoveExcessSpikesSorting(BaseSorting):
         for segment_index in range(num_segments):
             spike_vector = parent_spike_vector[segments_bounds[segment_index] : segments_bounds[segment_index + 1]]
             end = np.searchsorted(spike_vector["sample_index"], self._num_samples[segment_index])
-            list_spike_vectors.append(spike_vector[:end])
+            start = np.searchsorted(spike_vector["sample_index"], 0)
+            list_spike_vectors.append(spike_vector[start:end])
 
         spike_vector = np.concatenate(list_spike_vectors)
         self._cached_spike_vector = spike_vector
@@ -78,8 +79,9 @@ class RemoveExcessSpikesSortingSegment(BaseSortingSegment):
     ) -> np.ndarray:
         spike_train = self._parent_segment.get_unit_spike_train(unit_id, start_frame=start_frame, end_frame=end_frame)
         max_spike = np.searchsorted(spike_train, self._num_samples, side="left")
+        min_spike = np.searchsorted(spike_train, 0, side="left")
 
-        return spike_train[:max_spike]
+        return spike_train[min_spike:max_spike]
 
 
 def remove_excess_spikes(sorting, recording):

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/extractors/neoextractors/openephys.py

@@ -180,6 +180,9 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
             exp_id = exp_ids[0]
         else:
             exp_id = exp_ids[block_index]
+        rec_ids = sorted(
+            list(self.neo_reader.folder_structure[record_node]["experiments"][exp_id]["recordings"].keys())
+        )
 
         # do not load probe for NIDQ stream or if load_sync_channel is True
         if "NI-DAQmx" not in stream_name and not load_sync_channel:
@@ -229,10 +232,8 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
         # load synchronized timestamps and set_times to recording
         recording_folder = Path(folder_path) / record_node
         stream_folders = []
-        for segment_index in range(self.get_num_segments()):
-            stream_folder = (
-                recording_folder / f"experiment{exp_id}" / f"recording{segment_index+1}" / "continuous" / oe_stream
-            )
+        for segment_index, rec_id in enumerate(rec_ids):
+            stream_folder = recording_folder / f"experiment{exp_id}" / f"recording{rec_id}" / "continuous" / oe_stream
             stream_folders.append(stream_folder)
             if load_sync_timestamps:
                 if (stream_folder / "sample_numbers.npy").is_file():
@@ -245,7 +246,7 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
                     sync_times = None
                 try:
                     self.set_times(times=sync_times, segment_index=segment_index, with_warning=False)
-                except AssertionError:
+                except:
                     warnings.warn(f"Could not load synchronized timestamps for {stream_name}")
 
         self._stream_folders = stream_folders

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/extractors/nwbextractors.py

@@ -842,7 +842,8 @@ class NwbRecordingExtractor(BaseRecording):
         data_attributes = self.electrical_series["data"].attrs
         electrical_series_conversion = data_attributes["conversion"]
         gains = electrical_series_conversion * 1e6
-        if "channel_conversion" in data_attributes:
+        channel_conversion = self.electrical_series.get("channel_conversion", None)
+        if channel_conversion:
             gains *= self.electrical_series["channel_conversion"][:]
 
         # Channel offsets

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/sorters/external/kilosort4.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
 from pathlib import Path
-import os
 from typing import Union
+from packaging.version import parse
 
 from ..basesorter import BaseSorter
 from .kilosortbase import KilosortBase
@@ -32,7 +32,7 @@ class Kilosort4Sorter(BaseSorter):
         "sig_interp": 20,
         "nt0min": None,
         "dmin": None,
-        "dminx": None,
+        "dminx": 32,
         "min_template_size": 10,
         "template_sizes": 5,
         "nearest_chans": 10,
@@ -51,10 +51,11 @@ class Kilosort4Sorter(BaseSorter):
         "save_extra_kwargs": False,
         "skip_kilosort_preprocessing": False,
         "scaleproc": None,
+        "torch_device": "auto",
     }
 
     _params_description = {
-        "batch_size": "Number of samples per batch. Default value: 60000.",
+        "batch_size": "Number of samples included in each batch of data.",
         "nblocks": "Number of non-overlapping blocks for drift correction (additional nblocks-1 blocks are created in the overlaps). Default value: 1.",
         "Th_universal": "Spike detection threshold for universal templates. Th(1) in previous versions of Kilosort. Default value: 9.",
         "Th_learned": "Spike detection threshold for learned templates. Th(2) in previous versions of Kilosort. Default value: 8.",
@@ -68,7 +69,7 @@ class Kilosort4Sorter(BaseSorter):
         "sig_interp": "For drift correction, sigma for interpolation (spatial standard deviation). Approximate smoothness scale in units of microns. Default value: 20.",
         "nt0min": "Sample index for aligning waveforms, so that their minimum or maximum value happens here. Default of 20. Default value: None.",
         "dmin": "Vertical spacing of template centers used for spike detection, in microns. Determined automatically by default. Default value: None.",
-        "dminx": "Horizontal spacing of template centers used for spike detection, in microns. Determined automatically by default. Default value: None.",
+        "dminx": "Horizontal spacing of template centers used for spike detection, in microns. Default value: 32.",
         "min_template_size": "Standard deviation of the smallest, spatial envelope Gaussian used for universal templates. Default value: 10.",
         "template_sizes": "Number of sizes for universal spike templates (multiples of the min_template_size). Default value: 5.",
         "nearest_chans": "Number of nearest channels to consider when finding local maxima during spike detection. Default value: 10.",
@@ -87,6 +88,7 @@ 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.",
+        "torch_device": "Select the torch device auto/cuda/cpu",
     }
 
     sorter_description = """Kilosort4 is a Python package for spike sorting on GPUs with template matching.
@@ -152,7 +154,10 @@ class Kilosort4Sorter(BaseSorter):
 
         probe_filename = sorter_output_folder / "probe.prb"
 
-        device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+        torch_device = params["torch_device"]
+        if torch_device == "auto":
+            torch_device = "cuda" if torch.cuda.is_available() else "cpu"
+        device = torch.device(torch_device)
 
         # load probe
         recording = cls.load_recording_from_folder(sorter_output_folder.parent, with_warnings=False)
@@ -222,39 +227,14 @@ class Kilosort4Sorter(BaseSorter):
         torch.cuda.manual_seed_all(1)
         torch.random.manual_seed(1)
         # if not params["skip_kilosort_preprocessing"]:
-        if params["do_correction"]:
-            # this function applies both preprocessing and drift correction
-            ops, bfile, st0 = compute_drift_correction(
-                ops, device, tic0=tic0, progress_bar=progress_bar, file_object=file_object
-            )
-        else:
+        if not params["do_correction"]:
             print("Skipping drift correction.")
-            hp_filter = ops["preprocessing"]["hp_filter"]
-            whiten_mat = ops["preprocessing"]["whiten_mat"]
-
-            bfile = BinaryFiltered(
-                ops["filename"],
-                n_chan_bin,
-                fs,
-                NT,
-                nt,
-                twav_min,
-                chan_map,
-                hp_filter=hp_filter,
-                whiten_mat=whiten_mat,
-                device=device,
-                do_CAR=do_CAR,
-                invert_sign=invert,
-                dtype=dtype,
-                tmin=tmin,
-                tmax=tmax,
-                artifact_threshold=artifact,
-                file_object=file_object,
-            )
+            ops["nblocks"] = 0
 
-        # TODO: don't think we need to do this actually
-        # Save intermediate `ops` for use by GUI plots
-        # io.save_ops(ops, results_dir)
+        # this function applies both preprocessing and drift correction
+        ops, bfile, st0 = compute_drift_correction(
+            ops, device, tic0=tic0, progress_bar=progress_bar, file_object=file_object
+        )
 
         # Sort spikes and save results
         st, tF, _, _ = detect_spikes(ops, device, bfile, tic0=tic0, progress_bar=progress_bar)
@@ -263,39 +243,8 @@ class Kilosort4Sorter(BaseSorter):
             ops["preprocessing"] = dict(
                 hp_filter=torch.as_tensor(np.zeros(1)), whiten_mat=torch.as_tensor(np.eye(recording.get_num_channels()))
             )
-        ops, similar_templates, is_ref, est_contam_rate = save_sorting(
-            ops, results_dir, st, clu, tF, Wall, bfile.imin, tic0, save_extra_vars=save_extra_vars
-        )
-
-        # # Clean-up temporary files
-        # if params["delete_recording_dat"] and (recording_file := sorter_output_folder / "recording.dat").exists():
-        #     recording_file.unlink()
-
-        # all_tmp_files = ("matlab_files", "temp_wh.dat")
-
-        # if isinstance(params["delete_tmp_files"], bool):
-        #     if params["delete_tmp_files"]:
-        #         tmp_files_to_remove = all_tmp_files
-        #     else:
-        #         tmp_files_to_remove = ()
-        # else:
-        #     assert isinstance(
-        #         params["delete_tmp_files"], (tuple, list)
-        #     ), "`delete_tmp_files` must be a `Bool`, `Tuple` or `List`."
-
-        #     for name in params["delete_tmp_files"]:
-        #         assert name in all_tmp_files, f"{name} is not a valid option, must be one of: {all_tmp_files}"
-
-        #     tmp_files_to_remove = params["delete_tmp_files"]
-
-        # if "temp_wh.dat" in tmp_files_to_remove:
-        #     if (temp_wh_file := sorter_output_folder / "temp_wh.dat").exists():
-        #         temp_wh_file.unlink()
 
-        # if "matlab_files" in tmp_files_to_remove:
-        #     for ext in ["*.m", "*.mat"]:
-        #         for temp_file in sorter_output_folder.glob(ext):
-        #             temp_file.unlink()
+        _ = 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):

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/sorters/external/mountainsort5.py

@@ -3,14 +3,15 @@ from __future__ import annotations
 from pathlib import Path
 from packaging.version import parse
 
-from tempfile import TemporaryDirectory
 
+import shutil
 import numpy as np
+from warnings import warn
 
 from spikeinterface.preprocessing import bandpass_filter, whiten
 
 from spikeinterface.core.baserecording import BaseRecording
-from ..basesorter import BaseSorter
+from ..basesorter import BaseSorter, get_job_kwargs
 
 from spikeinterface.extractors import NpzSortingExtractor
 
@@ -43,8 +44,7 @@ class Mountainsort5Sorter(BaseSorter):
         "freq_max": 6000,
         "filter": True,
         "whiten": True,  # Important to do whitening
-        "temporary_base_dir": None,
-        "n_jobs_for_preprocessing": -1,
+        "delete_temporary_recording": True,
     }
 
     _params_description = {
@@ -68,8 +68,7 @@ class Mountainsort5Sorter(BaseSorter):
         "freq_max": "Low-pass filter cutoff frequency",
         "filter": "Enable or disable filter",
         "whiten": "Enable or disable whitening",
-        "temporary_base_dir": "Temporary directory base directory for storing cached recording",
-        "n_jobs_for_preprocessing": "Number of parallel jobs for creating the cached recording",
+        "delete_temporary_recording": "If True, the temporary recording file is deleted after sorting (this may fail on Windows requiring the end-user to delete the file themselves later)",
     }
 
     sorter_description = "MountainSort5 uses Isosplit clustering. It is an updated version of MountainSort4. See https://doi.org/10.1016/j.neuron.2017.08.030"
@@ -186,21 +185,26 @@ class Mountainsort5Sorter(BaseSorter):
             block_sorting_parameters=scheme2_sorting_parameters, block_duration_sec=p["scheme3_block_duration_sec"]
         )
 
-        with TemporaryDirectory(dir=p["temporary_base_dir"]) as tmpdir:
-            # cache the recording to a temporary directory for efficient reading (so we don't have to re-filter)
-            recording_cached = create_cached_recording(
-                recording=recording, folder=tmpdir, n_jobs=p["n_jobs_for_preprocessing"]
-            )
-
-            scheme = p["scheme"]
-            if scheme == "1":
-                sorting = ms5.sorting_scheme1(recording=recording_cached, sorting_parameters=scheme1_sorting_parameters)
-            elif p["scheme"] == "2":
-                sorting = ms5.sorting_scheme2(recording=recording_cached, sorting_parameters=scheme2_sorting_parameters)
-            elif p["scheme"] == "3":
-                sorting = ms5.sorting_scheme3(recording=recording_cached, sorting_parameters=scheme3_sorting_parameters)
-            else:
-                raise ValueError(f"Invalid scheme: {scheme} given. scheme must be one of '1', '2' or '3'")
+        if not recording.is_binary_compatible():
+            recording_cached = recording.save(folder=sorter_output_folder / "recording", **get_job_kwargs(p, verbose))
+        else:
+            recording_cached = recording
+
+        if p["scheme"] == "1":
+            sorting = ms5.sorting_scheme1(recording=recording_cached, sorting_parameters=scheme1_sorting_parameters)
+        elif p["scheme"] == "2":
+            sorting = ms5.sorting_scheme2(recording=recording_cached, sorting_parameters=scheme2_sorting_parameters)
+        elif p["scheme"] == "3":
+            sorting = ms5.sorting_scheme3(recording=recording_cached, sorting_parameters=scheme3_sorting_parameters)
+        else:
+            raise ValueError(f"Invalid scheme: {p['scheme']} given. scheme must be one of '1', '2' or '3'")
+
+        if p["delete_temporary_recording"]:
+            if not recording.is_binary_compatible():
+                del recording_cached
+                shutil.rmtree(sorter_output_folder / "recording", ignore_errors=True)
+                if Path(sorter_output_folder / "recording").is_dir():
+                    warn("cleanup failed, please remove file yourself if desired")
 
         NpzSortingExtractor.write_sorting(sorting, str(sorter_output_folder / "firings.npz"))
 

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface/widgets/spikes_on_traces.py

@@ -183,8 +183,7 @@ class SpikesOnTracesWidget(BaseWidget):
                 spike_times_to_plot = sorting.get_unit_spike_train(
                     unit, segment_index=segment_index, return_times=True
                 )[spike_start:spike_end]
-                unit_y_loc = min_y + max_y - dp.unit_locations[unit][1]
-                # markers = np.ones_like(spike_frames_to_plot) * (min_y + max_y - dp.unit_locations[unit][1])
+                unit_y_loc = dp.unit_locations[unit][1]
                 width = 2 * 1e-3
                 ellipse_kwargs = dict(width=width, height=10, fc="none", ec=dp.unit_colors[unit], lw=2)
                 patches = [Ellipse((s, unit_y_loc), **ellipse_kwargs) for s in spike_times_to_plot]

{spikeinterface-0.100.4 → spikeinterface-0.100.6/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.4
+Version: 0.100.6
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface
@@ -25,7 +25,7 @@ Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
 Requires-Dist: MEArec>=1.8; extra == "extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "extractors"
 Requires-Dist: pyedflib>=0.1.30; extra == "extractors"
 Requires-Dist: sonpy; python_version < "3.10" and extra == "extractors"
@@ -41,7 +41,7 @@ Requires-Dist: ibllib>=2.21.0; extra == "streaming-extractors"
 Requires-Dist: fsspec; extra == "streaming-extractors"
 Requires-Dist: aiohttp; extra == "streaming-extractors"
 Requires-Dist: requests; extra == "streaming-extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "streaming-extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "streaming-extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "streaming-extractors"
 Requires-Dist: remfile; extra == "streaming-extractors"
 Requires-Dist: s3fs; extra == "streaming-extractors"

{spikeinterface-0.100.4 → spikeinterface-0.100.6}/src/spikeinterface.egg-info/requires.txt

@@ -26,7 +26,7 @@ numba
 
 [extractors]
 MEArec>=1.8
-pynwb>=2.3.0
+pynwb>=2.6.0
 hdmf-zarr>=0.5.0
 pyedflib>=0.1.30
 lxml
@@ -67,7 +67,7 @@ ibllib>=2.21.0
 fsspec
 aiohttp
 requests
-pynwb>=2.3.0
+pynwb>=2.6.0
 hdmf-zarr>=0.5.0
 remfile
 s3fs