Merge branch 'main' into cap_python_proyect_toml

Author: h-mayorquin

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
     -   id: black
         files: ^src/

src/spikeinterface/benchmark/benchmark_matching.py

@@ -33,7 +33,7 @@ def run(self, **job_kwargs):
         sorting["unit_index"] = spikes["cluster_index"]
         sorting["segment_index"] = spikes["segment_index"]
         sorting = NumpySorting(sorting, self.recording.sampling_frequency, unit_ids)
-        self.result = {"sorting": sorting}
+        self.result = {"sorting": sorting, "spikes": spikes}
         self.result["templates"] = self.templates
 
     def compute_result(self, with_collision=False, **result_params):
@@ -45,6 +45,7 @@ def compute_result(self, with_collision=False, **result_params):
 
     _run_key_saved = [
         ("sorting", "sorting"),
+        ("spikes", "npy"),
         ("templates", "zarr_templates"),
     ]
     _result_key_saved = [("gt_collision", "pickle"), ("gt_comparison", "pickle")]
@@ -71,9 +72,15 @@ def plot_performances_vs_snr(self, **kwargs):
 
         return plot_performances_vs_snr(self, **kwargs)
 
+    def plot_performances_comparison(self, **kwargs):
+        from .benchmark_plot_tools import plot_performances_comparison
+
+        return plot_performances_comparison(self, **kwargs)
+
     def plot_collisions(self, case_keys=None, figsize=None):
         if case_keys is None:
             case_keys = list(self.cases.keys())
+        import matplotlib.pyplot as plt
 
         fig, axs = plt.subplots(ncols=len(case_keys), nrows=1, figsize=figsize, squeeze=False)
 
@@ -90,70 +97,6 @@ def plot_collisions(self, case_keys=None, figsize=None):
 
         return fig
 
-    def plot_comparison_matching(
-        self,
-        case_keys=None,
-        performance_names=["accuracy", "recall", "precision"],
-        colors=["g", "b", "r"],
-        ylim=(-0.1, 1.1),
-        figsize=None,
-    ):
-
-        if case_keys is None:
-            case_keys = list(self.cases.keys())
-
-        num_methods = len(case_keys)
-        import pylab as plt
-
-        fig, axs = plt.subplots(ncols=num_methods, nrows=num_methods, figsize=(10, 10))
-        for i, key1 in enumerate(case_keys):
-            for j, key2 in enumerate(case_keys):
-                if len(axs.shape) > 1:
-                    ax = axs[i, j]
-                else:
-                    ax = axs[j]
-                comp1 = self.get_result(key1)["gt_comparison"]
-                comp2 = self.get_result(key2)["gt_comparison"]
-                if i <= j:
-                    for performance, color in zip(performance_names, colors):
-                        perf1 = comp1.get_performance()[performance]
-                        perf2 = comp2.get_performance()[performance]
-                        ax.plot(perf2, perf1, ".", label=performance, color=color)
-
-                    ax.plot([0, 1], [0, 1], "k--", alpha=0.5)
-                    ax.set_ylim(ylim)
-                    ax.set_xlim(ylim)
-                    ax.spines[["right", "top"]].set_visible(False)
-                    ax.set_aspect("equal")
-
-                    label1 = self.cases[key1]["label"]
-                    label2 = self.cases[key2]["label"]
-                    if j == i:
-                        ax.set_ylabel(f"{label1}")
-                    else:
-                        ax.set_yticks([])
-                    if i == j:
-                        ax.set_xlabel(f"{label2}")
-                    else:
-                        ax.set_xticks([])
-                    if i == num_methods - 1 and j == num_methods - 1:
-                        patches = []
-                        import matplotlib.patches as mpatches
-
-                        for color, name in zip(colors, performance_names):
-                            patches.append(mpatches.Patch(color=color, label=name))
-                        ax.legend(handles=patches, bbox_to_anchor=(1.05, 1), loc="upper left", borderaxespad=0.0)
-                else:
-                    ax.spines["bottom"].set_visible(False)
-                    ax.spines["left"].set_visible(False)
-                    ax.spines["top"].set_visible(False)
-                    ax.spines["right"].set_visible(False)
-                    ax.set_xticks([])
-                    ax.set_yticks([])
-        plt.tight_layout(h_pad=0, w_pad=0)
-
-        return fig
-
     def get_count_units(self, case_keys=None, well_detected_score=None, redundant_score=None, overmerged_score=None):
         import pandas as pd
 
@@ -196,6 +139,7 @@ def plot_unit_counts(self, case_keys=None, figsize=None):
         plot_study_unit_counts(self, case_keys, figsize=figsize)
 
     def plot_unit_losses(self, before, after, metric=["precision"], figsize=None):
+        import matplotlib.pyplot as plt
 
         fig, axs = plt.subplots(ncols=1, nrows=len(metric), figsize=figsize, squeeze=False)
 

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -235,9 +235,71 @@ def plot_performances_vs_snr(study, case_keys=None, figsize=None, metrics=["accu
             ax.scatter(x, y, marker=".", label=label)
             ax.set_title(k)
 
-        ax.set_ylim(0, 1.05)
+        ax.set_ylim(-0.05, 1.05)
 
         if count == 2:
             ax.legend()
 
     return fig
+
+
+def plot_performances_comparison(
+    study,
+    case_keys=None,
+    figsize=None,
+    metrics=["accuracy", "recall", "precision"],
+    colors=["g", "b", "r"],
+    ylim=(-0.1, 1.1),
+):
+    import matplotlib.pyplot as plt
+
+    if case_keys is None:
+        case_keys = list(study.cases.keys())
+
+    num_methods = len(case_keys)
+    assert num_methods >= 2, "plot_performances_comparison need at least 2 cases!"
+
+    fig, axs = plt.subplots(ncols=num_methods - 1, nrows=num_methods - 1, figsize=(10, 10), squeeze=False)
+    for i, key1 in enumerate(case_keys):
+        for j, key2 in enumerate(case_keys):
+
+            if i < j:
+                ax = axs[i, j - 1]
+
+                comp1 = study.get_result(key1)["gt_comparison"]
+                comp2 = study.get_result(key2)["gt_comparison"]
+
+                for performance, color in zip(metrics, colors):
+                    perf1 = comp1.get_performance()[performance]
+                    perf2 = comp2.get_performance()[performance]
+                    ax.scatter(perf2, perf1, marker=".", label=performance, color=color)
+
+                ax.plot([0, 1], [0, 1], "k--", alpha=0.5)
+                ax.set_ylim(ylim)
+                ax.set_xlim(ylim)
+                ax.spines[["right", "top"]].set_visible(False)
+                ax.set_aspect("equal")
+
+                label1 = study.cases[key1]["label"]
+                label2 = study.cases[key2]["label"]
+
+                if i == j - 1:
+                    ax.set_xlabel(label2)
+                    ax.set_ylabel(label1)
+
+            else:
+                if j >= 1 and i < num_methods - 1:
+                    ax = axs[i, j - 1]
+                    ax.spines[["right", "top", "left", "bottom"]].set_visible(False)
+                    ax.set_xticks([])
+                    ax.set_yticks([])
+
+    ax = axs[num_methods - 2, 0]
+    patches = []
+    from matplotlib.patches import Patch
+
+    for color, name in zip(colors, metrics):
+        patches.append(Patch(color=color, label=name))
+    ax.legend(handles=patches)
+    fig.tight_layout()
+    return fig

src/spikeinterface/benchmark/tests/test_benchmark_sorter.py

@@ -64,10 +64,10 @@ def test_SorterStudy(setup_module):
     print(study)
 
     # # this run the sorters
-    # study.run()
+    study.run()
 
     # # this run comparisons
-    # study.compute_results()
+    study.compute_results()
     print(study)
 
     # this is from the base class
@@ -84,5 +84,7 @@ def test_SorterStudy(setup_module):
 
 if __name__ == "__main__":
     study_folder = Path(__file__).resolve().parents[4] / "cache_folder" / "benchmarks" / "test_SorterStudy"
+    if study_folder.exists():
+        shutil.rmtree(study_folder)
     create_a_study(study_folder)
     test_SorterStudy(study_folder)

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -9,6 +9,7 @@
 from .mearec import MEArecRecordingExtractor, MEArecSortingExtractor, read_mearec
 from .mcsraw import MCSRawRecordingExtractor, read_mcsraw
 from .neuralynx import NeuralynxRecordingExtractor, NeuralynxSortingExtractor, read_neuralynx, read_neuralynx_sorting
+from .neuronexus import NeuroNexusRecordingExtractor, read_neuronexus
 from .neuroscope import (
     NeuroScopeRecordingExtractor,
     NeuroScopeSortingExtractor,
@@ -54,6 +55,7 @@
     MCSRawRecordingExtractor,
     NeuralynxRecordingExtractor,
     NeuroScopeRecordingExtractor,
+    NeuroNexusRecordingExtractor,
     NixRecordingExtractor,
     OpenEphysBinaryRecordingExtractor,
     OpenEphysLegacyRecordingExtractor,

src/spikeinterface/extractors/neoextractors/neuronexus.py

@@ -0,0 +1,66 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from spikeinterface.core.core_tools import define_function_from_class
+
+from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor
+
+
+class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading data from NeuroNexus Allego.
+
+    Based on :py:class:`neo.rawio.NeuronexusRawIO`
+
+    Parameters
+    ----------
+    file_path : str | Path
+        The file path to the metadata .xdat.json file of an Allego session
+    stream_id : str | None, default: None
+        If there are several streams, specify the stream id you want to load.
+    stream_name : str | None, default: None
+        If there are several streams, specify the stream name you want to load.
+    all_annotations : bool, default: False
+        Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
+
+        In Neuronexus the ids provided by NeoRawIO are the hardware channel ids stored as `ntv_chan_name` within
+        the metada and the names are the `chan_names`
+
+
+    """
+
+    NeoRawIOClass = "NeuroNexusRawIO"
+
+    def __init__(
+        self,
+        file_path: str | Path,
+        stream_id: str | None = None,
+        stream_name: str | None = None,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
+    ):
+        neo_kwargs = self.map_to_neo_kwargs(file_path)
+        NeoBaseRecordingExtractor.__init__(
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
+        )
+
+        self._kwargs.update(dict(file_path=str(Path(file_path).resolve())))
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+
+        neo_kwargs = {"filename": str(file_path)}
+
+        return neo_kwargs
+
+
+read_neuronexus = define_function_from_class(source_class=NeuroNexusRecordingExtractor, name="read_neuronexus")

src/spikeinterface/extractors/neoextractors/plexon2.py

@@ -28,6 +28,10 @@ class Plexon2RecordingExtractor(NeoBaseRecordingExtractor):
             ids: ["source3.1" , "source3.2", "source3.3", "source3.4"]
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    reading_attempts : int, default: 25
+        Number of attempts to read the file before raising an error
+        This opening process is somewhat unreliable and might fail occasionally. Adjust this higher
+        if you encounter problems in opening the file.
 
     Examples
     --------
@@ -37,8 +41,16 @@ class Plexon2RecordingExtractor(NeoBaseRecordingExtractor):
 
     NeoRawIOClass = "Plexon2RawIO"
 
-    def __init__(self, file_path, stream_id=None, stream_name=None, use_names_as_ids=True, all_annotations=False):
-        neo_kwargs = self.map_to_neo_kwargs(file_path)
+    def __init__(
+        self,
+        file_path,
+        stream_id=None,
+        stream_name=None,
+        use_names_as_ids=True,
+        all_annotations=False,
+        reading_attempts: int = 25,
+    ):
+        neo_kwargs = self.map_to_neo_kwargs(file_path, reading_attempts=reading_attempts)
         NeoBaseRecordingExtractor.__init__(
             self,
             stream_id=stream_id,
@@ -50,8 +62,18 @@ def __init__(self, file_path, stream_id=None, stream_name=None, use_names_as_ids
         self._kwargs.update({"file_path": str(file_path)})
 
     @classmethod
-    def map_to_neo_kwargs(cls, file_path):
+    def map_to_neo_kwargs(cls, file_path, reading_attempts: int = 25):
+
         neo_kwargs = {"filename": str(file_path)}
+
+        from packaging.version import Version
+        import neo
+
+        neo_version = Version(neo.__version__)
+
+        if neo_version > Version("0.13.3"):
+            neo_kwargs["reading_attempts"] = reading_attempts
+
         return neo_kwargs
 
 

src/spikeinterface/extractors/tests/common_tests.py

@@ -52,8 +52,11 @@ def test_open(self):
                 num_samples = rec.get_num_samples(segment_index=segment_index)
 
                 full_traces = rec.get_traces(segment_index=segment_index)
-                assert full_traces.shape == (num_samples, num_chans)
-                assert full_traces.dtype == dtype
+                assert full_traces.shape == (
+                    num_samples,
+                    num_chans,
+                ), f"{full_traces.shape} != {(num_samples, num_chans)}"
+                assert full_traces.dtype == dtype, f"{full_traces.dtype} != {dtype=}"
 
                 traces_sample_first = rec.get_traces(segment_index=segment_index, start_frame=0, end_frame=1)
                 assert traces_sample_first.shape == (1, num_chans)

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -181,6 +181,14 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class NeuroNexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = NeuroNexusRecordingExtractor
+    downloads = ["neuronexus"]
+    entities = [
+        ("neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json", {"stream_id": "0"}),
+    ]
+
+
 class PlexonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = PlexonRecordingExtractor
     downloads = ["plexon"]
@@ -360,7 +368,7 @@ class Plexon2RecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = Plexon2RecordingExtractor
     downloads = ["plexon"]
     entities = [
-        ("plexon/4chDemoPL2.pl2", {"stream_id": "3"}),
+        ("plexon/4chDemoPL2.pl2", {"stream_name": "WB-Wideband"}),
     ]