spikeinterface 0.100.6__tar.gz → 0.100.7__tar.gz

{spikeinterface-0.100.6/src/spikeinterface.egg-info → spikeinterface-0.100.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.6
+Version: 0.100.7
 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
@@ -20,7 +20,7 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: threadpoolctl>=3.0.0
 Requires-Dist: tqdm
-Requires-Dist: zarr>=0.2.16
+Requires-Dist: zarr<2.18,>=2.16
 Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
@@ -53,11 +53,11 @@ Requires-Dist: scipy; extra == "full"
 Requires-Dist: scikit-learn; extra == "full"
 Requires-Dist: networkx; extra == "full"
 Requires-Dist: distinctipy; extra == "full"
-Requires-Dist: matplotlib; extra == "full"
+Requires-Dist: matplotlib>=3.6; extra == "full"
 Requires-Dist: cuda-python; platform_system != "Darwin" and extra == "full"
 Requires-Dist: numba; extra == "full"
 Provides-Extra: widgets
-Requires-Dist: matplotlib; extra == "widgets"
+Requires-Dist: matplotlib>=3.6; extra == "widgets"
 Requires-Dist: ipympl; extra == "widgets"
 Requires-Dist: ipywidgets; extra == "widgets"
 Requires-Dist: sortingview>=0.12.0; extra == "widgets"

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.6"
+version = "0.100.7"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
@@ -23,7 +23,7 @@ dependencies = [
     "numpy",
     "threadpoolctl>=3.0.0",
     "tqdm",
-    "zarr>=0.2.16",
+    "zarr>=2.16,<2.18",
     "neo>=0.13.0",
     "probeinterface>=0.2.21",
 ]
@@ -94,13 +94,13 @@ full = [
     "scikit-learn",
     "networkx",
     "distinctipy",
-    "matplotlib",
+    "matplotlib>=3.6",
     "cuda-python; platform_system != 'Darwin'",
     "numba",
 ]
 
 widgets = [
-    "matplotlib",
+    "matplotlib>=3.6",
     "ipympl",
     "ipywidgets",
     "sortingview>=0.12.0",

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/core/waveform_extractor.py

@@ -911,9 +911,11 @@ class WaveformExtractor:
             )
             if self.recording.get_probegroup() is not None:
                 probegroup = self.recording.get_probegroup()
+            with_recording = True
         else:
             rec_attributes = deepcopy(self._rec_attributes)
-            probegroup = rec_attributes["probegroup"]
+            probegroup = rec_attributes.pop("probegroup")
+            with_recording = False
 
         if self.is_sparse():
             assert sparsity is None, "WaveformExtractor is already sparse!"
@@ -1026,7 +1028,7 @@ class WaveformExtractor:
                         name=f"sampled_index_{unit_id}", data=sampled_indices, compressor=compressor
                     )
 
-        new_we = WaveformExtractor.load(folder)
+        new_we = WaveformExtractor.load(folder, with_recording=with_recording)
 
         # save waveform extensions
         for ext_name in self.get_available_extension_names():
@@ -1926,10 +1928,16 @@ class BaseWaveformExtractorExtension:
             params = cls.load_params_from_folder(folder)
 
         if "sparsity" in params and params["sparsity"] is not None:
-            params["sparsity"] = ChannelSparsity.from_dict(params["sparsity"])
-
-        # if waveform_extractor is None:
-        #     waveform_extractor = WaveformExtractor.load(folder)
+            sparsity_params = params["sparsity"]
+            # handle old sparsity version
+            if "unit_ids" not in params["sparsity"]:
+                sparsity_params = {}
+                sparsity_params["unit_ids"] = waveform_extractor.unit_ids
+                sparsity_params["channel_ids"] = waveform_extractor.channel_ids
+                sparsity_params["unit_id_to_channel_ids"] = params["sparsity"]
+            else:
+                sparsity_params = params["sparsity"]
+            params["sparsity"] = ChannelSparsity.from_dict(sparsity_params)
 
         # make instance with params
         ext = cls(waveform_extractor)

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/core/zarrextractors.py

@@ -72,7 +72,7 @@ class ZarrRecordingExtractor(BaseRecording):
             time_kwargs = {}
             time_vector = self._root.get(f"times_seg{segment_index}", None)
             if time_vector is not None:
-                time_kwargs["time_vector"] = time_vector
+                time_kwargs["time_vector"] = time_vector[:]
             else:
                 if t_starts is None:
                     t_start = None

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/preprocessing/common_reference.py

@@ -189,12 +189,12 @@ class CommonReferenceRecordingSegment(BasePreprocessorSegment):
                 shift = traces[:, self.ref_channel_indices]
                 re_referenced_traces = traces[:, channel_indices] - shift
             else:  # then it must be local
-                re_referenced_traces = np.zeros_like(traces[:, channel_indices])
                 channel_indices_array = np.arange(traces.shape[1])[channel_indices]
-                for channel_index in channel_indices_array:
+                re_referenced_traces = np.zeros((traces.shape[0], len(channel_indices_array)), dtype="float32")
+                for i, channel_index in enumerate(channel_indices_array):
                     channel_neighborhood = self.neighbors[channel_index]
                     channel_shift = self.operator_func(traces[:, channel_neighborhood], axis=1)
-                    re_referenced_traces[:, channel_index] = traces[:, channel_index] - channel_shift
+                    re_referenced_traces[:, i] = traces[:, channel_index] - channel_shift
 
             return re_referenced_traces.astype(self.dtype, copy=False)
 

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/sorters/external/kilosort4.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 from pathlib import Path
 from typing import Union
-from packaging.version import parse
 
 from ..basesorter import BaseSorter
 from .kilosortbase import KilosortBase
@@ -37,6 +36,7 @@ class Kilosort4Sorter(BaseSorter):
         "template_sizes": 5,
         "nearest_chans": 10,
         "nearest_templates": 100,
+        "max_channel_distance": None,
         "templates_from_data": True,
         "n_templates": 6,
         "n_pcs": 6,
@@ -45,7 +45,8 @@ class Kilosort4Sorter(BaseSorter):
         "ccg_threshold": 0.25,
         "cluster_downsampling": 20,
         "cluster_pcs": 64,
-        "duplicate_spike_bins": 15,
+        "x_centers": None,
+        "duplicate_spike_bins": 7,
         "do_correction": True,
         "keep_good_only": False,
         "save_extra_kwargs": False,
@@ -74,6 +75,7 @@ class Kilosort4Sorter(BaseSorter):
         "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.",
         "nearest_templates": "Number of nearest spike template locations to consider when finding local maxima during spike detection. Default value: 100.",
+        "max_channel_distance": "Templates farther away than this from their nearest channel will not be used. Also limits distance between compared channels during clustering. Default value: None.",
         "templates_from_data": "Indicates whether spike shapes used in universal templates should be estimated from the data or loaded from the predefined templates. Default value: True.",
         "n_templates": "Number of single-channel templates to use for the universal templates (only used if templates_from_data is True). Default value: 6.",
         "n_pcs": "Number of single-channel PCs to use for extracting spike features (only used if templates_from_data is True). Default value: 6.",
@@ -82,7 +84,8 @@ class Kilosort4Sorter(BaseSorter):
         "ccg_threshold": "Fraction of refractory period violations that are allowed in the CCG compared to baseline; used to perform splits and merges. Default value: 0.25.",
         "cluster_downsampling": "Inverse fraction of nodes used as landmarks during clustering (can be 1, but that slows down the optimization). Default value: 20.",
         "cluster_pcs": "Maximum number of spatiotemporal PC features used for clustering. Default value: 64.",
-        "duplicate_spike_bins": "Number of bins for which subsequent spikes from the same cluster are assumed to be artifacts. A value of 0 disables this step. Default value: 15.",
+        "x_centers": "Number of x-positions to use when determining center points for template groupings. If None, this will be determined automatically by finding peaks in channel density. For 2D array type probes, we recommend specifying this so that centers are placed every few hundred microns.",
+        "duplicate_spike_bins": "Number of bins for which subsequent spikes from the same cluster are assumed to be artifacts. A value of 0 disables this step. Default value: 7.",
         "keep_good_only": "If True only 'good' units are returned",
         "do_correction": "If True, drift correction is performed",
         "save_extra_kwargs": "If True, additional kwargs are saved to the output",

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/sortingcomponents/clustering/clustering_tools.py

@@ -61,7 +61,7 @@ def _split_waveforms(
         local_feature_plot = local_feature
 
         unique_lab = np.unique(local_labels_with_noise)
-        cmap = plt.get_cmap("jet", unique_lab.size)
+        cmap = plt.colormaps["jet"].resampled(unique_lab.size)
         cmap = {k: cmap(l) for l, k in enumerate(unique_lab)}
         cmap[-1] = "k"
         active_ind = np.arange(local_feature.shape[0])
@@ -144,7 +144,7 @@ def _split_waveforms_nested(
             local_feature_plot = reducer.fit_transform(local_feature)
 
             unique_lab = np.unique(active_labels_with_noise)
-            cmap = plt.get_cmap("jet", unique_lab.size)
+            cmap = plt.colormaps["jet"].resampled(unique_lab.size)
             cmap = {k: cmap(l) for l, k in enumerate(unique_lab)}
             cmap[-1] = "k"
             cmap[-2] = "b"
@@ -275,7 +275,7 @@ def auto_split_clustering(
 
             fig, ax = plt.subplots()
             plot_labels_set = np.unique(local_labels_with_noise)
-            cmap = plt.get_cmap("jet", plot_labels_set.size)
+            cmap = plt.colormaps["jet"].resampled(unique_lab.size)
             cmap = {k: cmap(l) for l, k in enumerate(plot_labels_set)}
             cmap[-1] = "k"
             cmap[-2] = "b"

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/sortingcomponents/clustering/sliding_hdbscan.py

@@ -347,7 +347,7 @@ class SlidingHdbscanClustering:
                 wfs_no_noise = wfs[: -noise.shape[0]]
 
                 fig, axs = plt.subplots(ncols=3)
-                cmap = plt.get_cmap("jet", np.unique(local_labels).size)
+                cmap = plt.colormaps["jet"].resampled(np.unique(local_labels).size)
                 cmap = {label: cmap(l) for l, label in enumerate(local_labels_set)}
                 cmap[-1] = "k"
                 for label in local_labels_set:

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/sortingcomponents/clustering/split.py

@@ -249,7 +249,7 @@ class LocalFeatureClustering:
             import matplotlib.pyplot as plt
 
             labels_set = np.setdiff1d(possible_labels, [-1])
-            colors = plt.get_cmap("tab10", len(labels_set))
+            colors = plt.colormaps["tab10"].resampled(len(labels_set))
             colors = {k: colors(i) for i, k in enumerate(labels_set)}
             colors[-1] = "k"
             fix, axs = plt.subplots(nrows=2)

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/widgets/collision.py

@@ -136,7 +136,7 @@ class ComparisonCollisionBySimilarityWidget(BaseWidget):
 
             ax1.set_xlabel("lag (ms)")
         elif dp.mode == "lines":
-            my_cmap = plt.get_cmap(dp.cmap)
+            my_cmap = plt.colormaps[dp.cmap]
             cNorm = matplotlib.colors.Normalize(vmin=dp.similarity_bins.min(), vmax=dp.similarity_bins.max())
             scalarMap = plt.cm.ScalarMappable(norm=cNorm, cmap=my_cmap)
 
@@ -245,7 +245,7 @@ class StudyComparisonCollisionBySimilarityWidget(BaseWidget):
 
         study = dp.study
 
-        my_cmap = plt.get_cmap(dp.cmap)
+        my_cmap = plt.colormaps[dp.cmap]
         cNorm = matplotlib.colors.Normalize(vmin=dp.similarity_bins.min(), vmax=dp.similarity_bins.max())
         scalarMap = plt.cm.ScalarMappable(norm=cNorm, cmap=my_cmap)
         study.precompute_scores_by_similarities(

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/widgets/motion.py

@@ -128,7 +128,7 @@ class MotionWidget(BaseWidget):
             if dp.scatter_decimate is not None:
                 amps = amps[:: dp.scatter_decimate]
                 amps_abs = amps_abs[:: dp.scatter_decimate]
-            cmap = plt.get_cmap(dp.amplitude_cmap)
+            cmap = plt.colormaps[dp.amplitude_cmap]
             if dp.amplitude_clim is None:
                 amps = amps_abs
                 amps /= q_95

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/widgets/multicomparison.py

@@ -87,7 +87,7 @@ class MultiCompGraphWidget(BaseWidget):
             nodelist=sorted(g.nodes),
             edge_color=edge_col,
             alpha=dp.alpha_edges,
-            edge_cmap=plt.cm.get_cmap(dp.edge_cmap),
+            edge_cmap=plt.colormaps[dp.edge_cmap],
             edge_vmin=mcmp.match_score,
             edge_vmax=1,
             ax=self.ax,
@@ -106,7 +106,7 @@ class MultiCompGraphWidget(BaseWidget):
             import matplotlib.pyplot as plt
 
             norm = mpl_colors.Normalize(vmin=mcmp.match_score, vmax=1)
-            cmap = plt.cm.get_cmap(dp.edge_cmap)
+            cmap = plt.colormaps[dp.edge_cmap]
             m = plt.cm.ScalarMappable(norm=norm, cmap=cmap)
             self.figure.colorbar(m)
 
@@ -159,7 +159,7 @@ class MultiCompGlobalAgreementWidget(BaseWidget):
         self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
 
         mcmp = dp.multi_comparison
-        cmap = plt.get_cmap(dp.cmap)
+        cmap = plt.colormaps[dp.cmap]
         colors = np.array([cmap(i) for i in np.linspace(0.1, 0.8, len(mcmp.name_list))])
         sg_names, sg_units = mcmp.compute_subgraphs()
         # fraction of units with agreement > threshold
@@ -242,7 +242,7 @@ class MultiCompAgreementBySorterWidget(BaseWidget):
         backend_kwargs["ncols"] = len(name_list)
         self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
 
-        cmap = plt.get_cmap(dp.cmap)
+        cmap = plt.colormaps[dp.cmap]
         colors = np.array([cmap(i) for i in np.linspace(0.1, 0.8, len(mcmp.name_list))])
         sg_names, sg_units = mcmp.compute_subgraphs()
         # fraction of units with agreement > threshold

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface/widgets/utils.py

@@ -76,7 +76,7 @@ def get_some_colors(keys, color_engine="auto", map_name="gist_ncar", format="RGB
     elif color_engine == "matplotlib":
         # some map have black or white at border so +10
         margin = max(4, int(N * 0.08))
-        cmap = plt.get_cmap(map_name, N + 2 * margin)
+        cmap = plt.colormaps[map_name].resampled(N + 2 * margin)
         colors = [cmap(i + margin) for i, key in enumerate(keys)]
 
     elif color_engine == "colorsys":
@@ -153,7 +153,7 @@ def array_to_image(
     num_channels = data.shape[1]
     spacing = int(num_channels * spatial_zoom[1] * row_spacing)
 
-    cmap = plt.get_cmap(colormap)
+    cmap = plt.colormaps[colormap]
     zoomed_data = zoom(data, spatial_zoom)
     num_timepoints_after_scaling, num_channels_after_scaling = zoomed_data.shape
     num_timepoints_per_row_after_scaling = int(np.min([num_timepoints_per_row, num_timepoints]) * spatial_zoom[0])

{spikeinterface-0.100.6 → spikeinterface-0.100.7/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.6
+Version: 0.100.7
 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
@@ -20,7 +20,7 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: threadpoolctl>=3.0.0
 Requires-Dist: tqdm
-Requires-Dist: zarr>=0.2.16
+Requires-Dist: zarr<2.18,>=2.16
 Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
@@ -53,11 +53,11 @@ Requires-Dist: scipy; extra == "full"
 Requires-Dist: scikit-learn; extra == "full"
 Requires-Dist: networkx; extra == "full"
 Requires-Dist: distinctipy; extra == "full"
-Requires-Dist: matplotlib; extra == "full"
+Requires-Dist: matplotlib>=3.6; extra == "full"
 Requires-Dist: cuda-python; platform_system != "Darwin" and extra == "full"
 Requires-Dist: numba; extra == "full"
 Provides-Extra: widgets
-Requires-Dist: matplotlib; extra == "widgets"
+Requires-Dist: matplotlib>=3.6; extra == "widgets"
 Requires-Dist: ipympl; extra == "widgets"
 Requires-Dist: ipywidgets; extra == "widgets"
 Requires-Dist: sortingview>=0.12.0; extra == "widgets"

{spikeinterface-0.100.6 → spikeinterface-0.100.7}/src/spikeinterface.egg-info/requires.txt

@@ -1,7 +1,7 @@
 numpy
 threadpoolctl>=3.0.0
 tqdm
-zarr>=0.2.16
+zarr<2.18,>=2.16
 neo>=0.13.0
 probeinterface>=0.2.21
 
@@ -49,7 +49,7 @@ scipy
 scikit-learn
 networkx
 distinctipy
-matplotlib
+matplotlib>=3.6
 numba
 
 [full:platform_system != "Darwin"]
@@ -92,7 +92,7 @@ pytest
 psutil
 
 [widgets]
-matplotlib
+matplotlib>=3.6
 ipympl
 ipywidgets
 sortingview>=0.12.0