spikeinterface 0.103.2__tar.gz → 0.104.0__tar.gz

{spikeinterface-0.103.2/src/spikeinterface.egg-info → spikeinterface-0.104.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spikeinterface
-Version: 0.103.2
+Version: 0.104.0
 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
@@ -14,7 +14,7 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.20; python_version < "3.13"
@@ -22,8 +22,8 @@ Requires-Dist: numpy>=2.0.0; python_version >= "3.13"
 Requires-Dist: threadpoolctl>=3.0.0
 Requires-Dist: tqdm
 Requires-Dist: zarr<3,>=2.18
-Requires-Dist: neo>=0.14.3
-Requires-Dist: probeinterface>=0.3.1
+Requires-Dist: neo>=0.14.4
+Requires-Dist: probeinterface>=0.3.2
 Requires-Dist: packaging
 Requires-Dist: pydantic
 Requires-Dist: numcodecs<0.16.0
@@ -51,9 +51,9 @@ Provides-Extra: preprocessing
 Requires-Dist: scipy; extra == "preprocessing"
 Provides-Extra: full
 Requires-Dist: h5py; extra == "full"
-Requires-Dist: pandas; extra == "full"
+Requires-Dist: pandas<3; extra == "full"
 Requires-Dist: scipy; extra == "full"
-Requires-Dist: scikit-learn; extra == "full"
+Requires-Dist: scikit-learn<1.8; extra == "full"
 Requires-Dist: networkx; extra == "full"
 Requires-Dist: distinctipy; extra == "full"
 Requires-Dist: matplotlib>=3.6; extra == "full"
@@ -65,15 +65,15 @@ Provides-Extra: widgets
 Requires-Dist: matplotlib; extra == "widgets"
 Requires-Dist: ipympl; extra == "widgets"
 Requires-Dist: ipywidgets; extra == "widgets"
-Requires-Dist: sortingview>=0.12.0; extra == "widgets"
-Provides-Extra: qualitymetrics
-Requires-Dist: scikit-learn; extra == "qualitymetrics"
-Requires-Dist: scipy; extra == "qualitymetrics"
-Requires-Dist: pandas; extra == "qualitymetrics"
-Requires-Dist: numba; extra == "qualitymetrics"
+Requires-Dist: figpack; extra == "widgets"
+Requires-Dist: figpack-spike-sorting; extra == "widgets"
+Provides-Extra: metrics
+Requires-Dist: scikit-learn<1.8; extra == "metrics"
+Requires-Dist: scipy; extra == "metrics"
+Requires-Dist: pandas<3; extra == "metrics"
+Requires-Dist: numba; extra == "metrics"
 Provides-Extra: test-core
 Requires-Dist: pytest<8.4.0; extra == "test-core"
-Requires-Dist: pytest-dependency; extra == "test-core"
 Requires-Dist: psutil; extra == "test-core"
 Requires-Dist: pytest-mock; extra == "test-core"
 Provides-Extra: test-extractors
@@ -82,9 +82,10 @@ Requires-Dist: datalad>=1.0.2; extra == "test-extractors"
 Provides-Extra: test-preprocessing
 Requires-Dist: ibllib>=3.4.1; python_version >= "3.10" and extra == "test-preprocessing"
 Requires-Dist: torch; extra == "test-preprocessing"
+Requires-Dist: pooch; extra == "test-preprocessing"
+Requires-Dist: datalad; extra == "test-preprocessing"
 Provides-Extra: test
 Requires-Dist: pytest<8.4.0; extra == "test"
-Requires-Dist: pytest-dependency; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: psutil; extra == "test"
 Requires-Dist: ibllib>=3.4.1; python_version >= "3.10" and extra == "test"
@@ -97,6 +98,7 @@ Requires-Dist: sortingview>=0.12.0; extra == "test"
 Requires-Dist: torch; extra == "test"
 Requires-Dist: skops; extra == "test"
 Requires-Dist: huggingface_hub; extra == "test"
+Requires-Dist: sortingview; extra == "test"
 Requires-Dist: pytest-mock; extra == "test"
 Provides-Extra: docs
 Requires-Dist: Sphinx; extra == "docs"
@@ -108,12 +110,13 @@ Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: sphinxcontrib-jquery; extra == "docs"
 Requires-Dist: autodoc_pydantic; extra == "docs"
 Requires-Dist: MEArec; extra == "docs"
-Requires-Dist: pandas; extra == "docs"
+Requires-Dist: pandas<3; extra == "docs"
 Requires-Dist: hdbscan>=0.8.33; extra == "docs"
 Requires-Dist: numba; extra == "docs"
 Requires-Dist: networkx; extra == "docs"
+Requires-Dist: seaborn; extra == "docs"
 Requires-Dist: skops; extra == "docs"
-Requires-Dist: scikit-learn; extra == "docs"
+Requires-Dist: scikit-learn<1.8; extra == "docs"
 Requires-Dist: huggingface_hub; extra == "docs"
 Provides-Extra: dev
 Requires-Dist: spikeinterface[test]; extra == "dev"
@@ -168,35 +171,39 @@ Dynamic: license-file
 </tr>
 </table>
 
-[![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge&logo=Twitter&logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge&logo=mastodon&logoColor=white)](https://fosstodon.org/@spikeinterface)
-
 
-> :rocket::rocket::rocket:
-> **New features!**: after months of development and testing, we are happy to announce that
-> the latest release (0.101.0) includes a major API improvement: the `SortingAnalyzer`!
-> To read more about why we did this, checkout the
-> [SpikeInterface Enhancement Proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).
-> Please follow this guide to transition from the old API to the new one:
-> [Updating from legacy](https://spikeinterface.readthedocs.io/en/0.101.0/tutorials/waveform_extractor_to_sorting_analyzer.html).
+[![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge&logo=Twitter&logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge&logo=mastodon&logoColor=white)](https://fosstodon.org/@spikeinterface)
 
+Please [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!
 
-SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
+SpikeInterface is a Python package designed to unify preexisting spike sorting technologies into a single code base. If you use SpikeInterface, you are also using code and ideas from many other projects. Our codebase would be tiny without the amazing algorithms and formats that we interface with. See them all, and how to cite them, on our [references page](https://spikeinterface.readthedocs.io/en/latest/references.html). In the past year, we have added support for the following tools:
 
-Please [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!
+- Bombcell [Bombcell: automated curation and cell classification of spike-sorted electrophysiology data](https://doi.org/10.5281/zenodo.8172822>) ([docs](https://spikeinterface.readthedocs.io/en/latest/how_to/auto_label_units.html#bombcell))
+- SLAy. [SLAy-ing oversplitting errors in high-density electrophysiology spike sorting](https://www.biorxiv.org/content/10.1101/2025.06.20.660590v2) ([docs](https://spikeinterface.readthedocs.io/en/latest/modules/curation.html#auto-merging-units))
+- Lupin, Spykingcicus2 and Tridesclous2. [Opening the black box: a modular approach to spike sorting](https://www.biorxiv.org/content/10.64898/2026.01.23.701239v1) ([docs](https://spikeinterface.readthedocs.io/en/stable/modules/sorters.html#supported-spike-sorters))
+- rtsort. [RT-Sort: An action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312438) ([docs](https://spikeinterface.readthedocs.io/en/stable/modules/sorters.html#supported-spike-sorters))
+- MEDiCINe. [MEDiCINe: Motion Correction for Neural Electrophysiology Recordings](https://www.eneuro.org/content/12/3/ENEURO.0529-24.2025) ([docs](https://spikeinterface.readthedocs.io/en/latest/how_to/handle_drift.html))
+- UnitRefine. [UnitRefine: A Community Toolbox for Automated Spike Sorting Curation](https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2) ([docs](https://spikeinterface.readthedocs.io/en/latest/tutorials_custom_index.html#automated-curation-tutorials))
 
+If you would like us to add another tool, or you would like to integrate your project with our package, please [open an issue](https://github.com/SpikeInterface/spikeinterface/issues).
 
 With SpikeInterface, users can:
 
 - read/write many extracellular file formats.
 - pre-process extracellular recordings.
-- run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).
-- post-process sorted datasets.
+- run many popular, semi-automatic spike sorters (kilosort1-4, mountainsort4-5, spykingcircus,
+  tridesclous, ironclust, herdingspikes, yass, waveclus)
+- run sorters developed in house (lupin, spkykingcicus2, tridesclous2, simple) that compete with kilosort4
+- run theses polar sorters without installation using containers (Docker/Singularity).
+- post-process sorted datasets using th SortingAnalyzer
 - compare and benchmark spike sorting outputs.
 - compute quality metrics to validate and curate spike sorting outputs.
 - visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
 - export a report and/or export to phy
-- offer a powerful Qt-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)
+- curate your sorting with several strategies (ml-based, metrics based, manual, ...)
+- offer a powerful Qt-based or we-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui) for manual curation that replace phy.
 - have powerful sorting components to build your own sorter.
+- have a full motion/drift correction framework
 
 
 ## Documentation

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/README.md

@@ -43,35 +43,39 @@
 </tr>
 </table>
 
-[![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge&logo=Twitter&logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge&logo=mastodon&logoColor=white)](https://fosstodon.org/@spikeinterface)
-
 
-> :rocket::rocket::rocket:
-> **New features!**: after months of development and testing, we are happy to announce that
-> the latest release (0.101.0) includes a major API improvement: the `SortingAnalyzer`!
-> To read more about why we did this, checkout the
-> [SpikeInterface Enhancement Proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).
-> Please follow this guide to transition from the old API to the new one:
-> [Updating from legacy](https://spikeinterface.readthedocs.io/en/0.101.0/tutorials/waveform_extractor_to_sorting_analyzer.html).
+[![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge&logo=Twitter&logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge&logo=mastodon&logoColor=white)](https://fosstodon.org/@spikeinterface)
 
+Please [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!
 
-SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
+SpikeInterface is a Python package designed to unify preexisting spike sorting technologies into a single code base. If you use SpikeInterface, you are also using code and ideas from many other projects. Our codebase would be tiny without the amazing algorithms and formats that we interface with. See them all, and how to cite them, on our [references page](https://spikeinterface.readthedocs.io/en/latest/references.html). In the past year, we have added support for the following tools:
 
-Please [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!
+- Bombcell [Bombcell: automated curation and cell classification of spike-sorted electrophysiology data](https://doi.org/10.5281/zenodo.8172822>) ([docs](https://spikeinterface.readthedocs.io/en/latest/how_to/auto_label_units.html#bombcell))
+- SLAy. [SLAy-ing oversplitting errors in high-density electrophysiology spike sorting](https://www.biorxiv.org/content/10.1101/2025.06.20.660590v2) ([docs](https://spikeinterface.readthedocs.io/en/latest/modules/curation.html#auto-merging-units))
+- Lupin, Spykingcicus2 and Tridesclous2. [Opening the black box: a modular approach to spike sorting](https://www.biorxiv.org/content/10.64898/2026.01.23.701239v1) ([docs](https://spikeinterface.readthedocs.io/en/stable/modules/sorters.html#supported-spike-sorters))
+- rtsort. [RT-Sort: An action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312438) ([docs](https://spikeinterface.readthedocs.io/en/stable/modules/sorters.html#supported-spike-sorters))
+- MEDiCINe. [MEDiCINe: Motion Correction for Neural Electrophysiology Recordings](https://www.eneuro.org/content/12/3/ENEURO.0529-24.2025) ([docs](https://spikeinterface.readthedocs.io/en/latest/how_to/handle_drift.html))
+- UnitRefine. [UnitRefine: A Community Toolbox for Automated Spike Sorting Curation](https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2) ([docs](https://spikeinterface.readthedocs.io/en/latest/tutorials_custom_index.html#automated-curation-tutorials))
 
+If you would like us to add another tool, or you would like to integrate your project with our package, please [open an issue](https://github.com/SpikeInterface/spikeinterface/issues).
 
 With SpikeInterface, users can:
 
 - read/write many extracellular file formats.
 - pre-process extracellular recordings.
-- run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).
-- post-process sorted datasets.
+- run many popular, semi-automatic spike sorters (kilosort1-4, mountainsort4-5, spykingcircus,
+  tridesclous, ironclust, herdingspikes, yass, waveclus)
+- run sorters developed in house (lupin, spkykingcicus2, tridesclous2, simple) that compete with kilosort4
+- run theses polar sorters without installation using containers (Docker/Singularity).
+- post-process sorted datasets using th SortingAnalyzer
 - compare and benchmark spike sorting outputs.
 - compute quality metrics to validate and curate spike sorting outputs.
 - visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
 - export a report and/or export to phy
-- offer a powerful Qt-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)
+- curate your sorting with several strategies (ml-based, metrics based, manual, ...)
+- offer a powerful Qt-based or we-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui) for manual curation that replace phy.
 - have powerful sorting components to build your own sorter.
+- have a full motion/drift correction framework
 
 
 ## Documentation

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "spikeinterface"
-version = "0.103.2"
+version = "0.104.0"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",
@@ -25,8 +25,8 @@ dependencies = [
     "threadpoolctl>=3.0.0",
     "tqdm",
     "zarr>=2.18,<3",
-    "neo>=0.14.3",
-    "probeinterface>=0.3.1",
+    "neo>=0.14.4",
+    "probeinterface>=0.3.2",
     "packaging",
     "pydantic",
     "numcodecs<0.16.0", # For supporting zarr < 3
@@ -94,9 +94,9 @@ preprocessing = [
 
 full = [
     "h5py",
-    "pandas",
+    "pandas<3",
     "scipy",
-    "scikit-learn",
+    "scikit-learn<1.8",
     "networkx",
     "distinctipy",
     "matplotlib>=3.6", # matplotlib.colormaps
@@ -110,19 +110,19 @@ widgets = [
     "matplotlib",
     "ipympl",
     "ipywidgets",
-    "sortingview>=0.12.0",
+    "figpack",
+    "figpack-spike-sorting"
 ]
 
-qualitymetrics = [
-    "scikit-learn",
+metrics = [
+    "scikit-learn<1.8",
     "scipy",
-    "pandas",
+    "pandas<3",
     "numba",
 ]
 
 test_core = [
     "pytest<8.4.0",
-    "pytest-dependency",
     "psutil",
 
     # for github test : probeinterface and neo from master
@@ -146,12 +146,14 @@ test_extractors = [
 test_preprocessing = [
     "ibllib>=3.4.1;python_version>='3.10'", # streaming IBL
     "torch",
+    # for IBL data fetching
+    "pooch",
+    "datalad"
 ]
 
 
 test = [
     "pytest<8.4.0",
-    "pytest-dependency",
     "pytest-cov",
     "psutil",
 
@@ -183,6 +185,9 @@ test = [
     "skops",
     "huggingface_hub",
 
+    # widgets
+    "sortingview",
+
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
     # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
@@ -204,12 +209,13 @@ docs = [
 
     # for notebooks in the gallery
     "MEArec", # Use as an example
-    "pandas", # in the modules gallery comparison tutorial
+    "pandas<3", # in the modules gallery comparison tutorial
     "hdbscan>=0.8.33",   # For sorters spykingcircus2 + tridesclous
     "numba", # For many postprocessing functions
     "networkx",
+    "seaborn",
     "skops", # For automated curation
-    "scikit-learn", # For automated curation
+    "scikit-learn<1.8", # For automated curation
     "huggingface_hub", # For automated curation
 
     # for release we need pypi, so this needs to be commented
@@ -232,7 +238,7 @@ markers = [
     "extractors",
     "preprocessing",
     "postprocessing",
-    "qualitymetrics",
+    "mertrics",
     "sorters",
     "sorters_external",
     "sorters_internal",

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_base.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from pathlib import Path
 import shutil
 import json
@@ -50,6 +48,29 @@ class BenchmarkStudy:
         self.labels_by_levels = {}
         self.scan_folder()
 
+    @classmethod
+    def _check_cases(cls, cases, levels=None, reference=None):
+        if reference is None:
+            reference = list(cases.keys())[0]
+        for key in cases.keys():
+            if isinstance(reference, str):
+                assert isinstance(key, str), f"Case key {key} for cases is not homogeneous"
+                if levels is None:
+                    levels = "level0"
+                else:
+                    assert isinstance(levels, str)
+            elif isinstance(reference, tuple):
+                assert isinstance(key, tuple), f"Case key {key} for cases is not homogeneous"
+                num_levels = len(reference)
+                assert len(key) == num_levels, f"Case key {key} for cases is not homogeneous, tuple negth differ"
+                if levels is None:
+                    levels = [f"level{i}" for i in range(num_levels)]
+                else:
+                    levels = list(levels)
+            else:
+                raise ValueError("Keys for cases must str or tuple")
+        return levels
+
     @classmethod
     def create(cls, study_folder, datasets={}, cases={}, levels=None):
         """
@@ -76,27 +97,7 @@ class BenchmarkStudy:
         study : BenchmarkStudy
             The created study.
         """
-        # check that cases keys are homogeneous
-        key0 = list(cases.keys())[0]
-        if isinstance(key0, str):
-            assert all(isinstance(key, str) for key in cases.keys()), "Keys for cases are not homogeneous"
-            if levels is None:
-                levels = "level0"
-            else:
-                assert isinstance(levels, str)
-        elif isinstance(key0, tuple):
-            assert all(isinstance(key, tuple) for key in cases.keys()), "Keys for cases are not homogeneous"
-            num_levels = len(key0)
-            assert all(
-                len(key) == num_levels for key in cases.keys()
-            ), "Keys for cases are not homogeneous, tuple negth differ"
-            if levels is None:
-                levels = [f"level{i}" for i in range(num_levels)]
-            else:
-                levels = list(levels)
-                assert len(levels) == num_levels
-        else:
-            raise ValueError("Keys for cases must str or tuple")
+        levels = cls._check_cases(cases, levels)
 
         study_folder = Path(study_folder)
         study_folder.mkdir(exist_ok=False, parents=True)
@@ -272,6 +273,25 @@ class BenchmarkStudy:
                 f.unlink()
         self.benchmarks[key] = None
 
+    def add_cases(self, cases):
+
+        _ = self._check_cases(cases, reference=list(self.cases.keys())[0])
+        for case in cases.values():
+            dataset = case["dataset"]
+            assert dataset in list(self.datasets.keys()), f"Unknown dataset {dataset} for the Study"
+        self.cases.update(cases)
+        for key in cases.keys():
+            benchmark = self.create_benchmark(key=key)
+            self.benchmarks[key] = benchmark
+        (self.folder / "cases.pickle").write_bytes(pickle.dumps(self.cases))
+
+    def remove_cases(self, case_keys):
+        for key in case_keys:
+            assert key in list(self.cases.keys()), f"Case {key} is not in the cases of the Study"
+            self.cases.pop(key)
+            self.remove_benchmark(key)
+        (self.folder / "cases.pickle").write_bytes(pickle.dumps(self.cases))
+
     def run(self, case_keys=None, keep=True, verbose=False, **job_kwargs):
         if case_keys is None:
             case_keys = list(self.cases.keys())
@@ -435,27 +455,6 @@ class BenchmarkStudy:
             benchmark.compute_result(**result_params)
             benchmark.save_result(self.folder / "results" / self.key_to_str(key))
 
-    def create_sorting_analyzer_gt(self, case_keys=None, return_in_uV=True, random_params={}, **job_kwargs):
-        print("###### Study.create_sorting_analyzer_gt() is not used anymore!!!!!!")
-        # if case_keys is None:
-        #     case_keys = self.cases.keys()
-
-        # base_folder = self.folder / "sorting_analyzer"
-        # base_folder.mkdir(exist_ok=True)
-
-        # dataset_keys = [self.cases[key]["dataset"] for key in case_keys]
-        # dataset_keys = set(dataset_keys)
-        # for dataset_key in dataset_keys:
-        #     # the waveforms depend on the dataset key
-        #     folder = base_folder / self.key_to_str(dataset_key)
-        #     recording, gt_sorting = self.datasets[dataset_key]
-        #     sorting_analyzer = create_sorting_analyzer(
-        #         gt_sorting, recording, format="binary_folder", folder=folder, return_in_uV=return_in_uV
-        #     )
-        #     sorting_analyzer.compute("random_spikes", **random_params)
-        #     sorting_analyzer.compute("templates", **job_kwargs)
-        #     sorting_analyzer.compute("noise_levels")
-
     def get_sorting_analyzer(self, case_key=None, dataset_key=None):
         if case_key is not None:
             dataset_key = self.cases[case_key]["dataset"]
@@ -655,8 +654,6 @@ class Benchmark:
                     with open(file, mode="rb") as f:
                         result[k] = pickle.load(f)
             elif format == "sorting":
-                from spikeinterface.core import load_extractor
-
                 sorting_folder = folder / k
                 if sorting_folder.exists():
                     result[k] = load(sorting_folder)

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_clustering.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.sortingcomponents.clustering import find_clusters_from_peaks
 from spikeinterface.core import NumpySorting
 from spikeinterface.comparison import GroundTruthComparison
@@ -29,9 +27,14 @@ class ClusteringBenchmark(Benchmark):
         self.method_kwargs = params["method_kwargs"]
         self.result = {}
 
-    def run(self, **job_kwargs):
+    def run(self, verbose=True, **job_kwargs):
         labels, peak_labels = find_clusters_from_peaks(
-            self.recording, self.peaks, method=self.method, method_kwargs=self.method_kwargs, job_kwargs=job_kwargs
+            self.recording,
+            self.peaks,
+            method=self.method,
+            method_kwargs=self.method_kwargs,
+            verbose=verbose,
+            job_kwargs=job_kwargs,
         )
         self.result["peak_labels"] = peak_labels
 
@@ -217,11 +220,21 @@ class ClusteringStudy(BenchmarkStudy, MixinStudyUnitCount):
 
         return plot_performances_ordered(self, *args, **kwargs)
 
+    def plot_some_over_merged(self, *args, **kwargs):
+        from .benchmark_plot_tools import plot_some_over_merged
+
+        return plot_some_over_merged(self, *args, **kwargs)
+
+    def plot_some_over_splited(self, *args, **kwargs):
+        from .benchmark_plot_tools import plot_some_over_splited
+
+        return plot_some_over_splited(self, *args, **kwargs)
+
     def plot_error_metrics(self, metric="cosine", case_keys=None, figsize=(15, 5)):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         fig, axes = plt.subplots(ncols=len(case_keys), nrows=1, figsize=figsize, squeeze=False)
 
@@ -258,7 +271,7 @@ class ClusteringStudy(BenchmarkStudy, MixinStudyUnitCount):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         if axes is None:
             fig, axes = plt.subplots(ncols=len(case_keys), nrows=1, figsize=figsize, squeeze=False)
@@ -317,7 +330,7 @@ class ClusteringStudy(BenchmarkStudy, MixinStudyUnitCount):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         fig, axes = plt.subplots(ncols=len(case_keys), nrows=1, figsize=figsize, squeeze=False)
 
@@ -386,81 +399,3 @@ class ClusteringStudy(BenchmarkStudy, MixinStudyUnitCount):
         fig.colorbar(im, cax=cbar_ax, label=metric)
 
         return fig
-
-    def plot_some_over_merged(self, case_keys=None, overmerged_score=0.05, max_units=5, figsize=None):
-        if case_keys is None:
-            case_keys = list(self.cases.keys())
-        import pylab as plt
-
-        figs = []
-        for count, key in enumerate(case_keys):
-            label = self.cases[key]["label"]
-            comp = self.get_result(key)["gt_comparison"]
-
-            unit_index = np.flatnonzero(np.sum(comp.agreement_scores.values > overmerged_score, axis=0) > 1)
-            overmerged_ids = comp.sorting2.unit_ids[unit_index]
-
-            n = min(len(overmerged_ids), max_units)
-            if n > 0:
-                fig, axs = plt.subplots(nrows=n, figsize=figsize)
-                for i, unit_id in enumerate(overmerged_ids[:n]):
-                    gt_unit_indices = np.flatnonzero(comp.agreement_scores.loc[:, unit_id].values > overmerged_score)
-                    gt_unit_ids = comp.sorting1.unit_ids[gt_unit_indices]
-                    ax = axs[i]
-                    ax.set_title(f"unit {unit_id} - GTids {gt_unit_ids}")
-
-                    analyzer = self.get_sorting_analyzer(key)
-
-                    wf_template = analyzer.get_extension("templates")
-                    templates = wf_template.get_templates(unit_ids=gt_unit_ids)
-                    if analyzer.sparsity is not None:
-                        chan_mask = np.any(analyzer.sparsity.mask[gt_unit_indices, :], axis=0)
-                        templates = templates[:, :, chan_mask]
-                    ax.plot(templates.swapaxes(1, 2).reshape(templates.shape[0], -1).T)
-                    ax.set_xticks([])
-
-                fig.suptitle(label)
-                figs.append(fig)
-            else:
-                print(key, "no overmerged")
-
-        return figs
-
-    def plot_some_over_splited(self, case_keys=None, oversplit_score=0.05, max_units=5, figsize=None):
-        if case_keys is None:
-            case_keys = list(self.cases.keys())
-        import pylab as plt
-
-        figs = []
-        for count, key in enumerate(case_keys):
-            label = self.cases[key]["label"]
-            comp = self.get_result(key)["gt_comparison"]
-
-            gt_unit_indices = np.flatnonzero(np.sum(comp.agreement_scores.values > oversplit_score, axis=1) > 1)
-            oversplit_ids = comp.sorting1.unit_ids[gt_unit_indices]
-
-            n = min(len(oversplit_ids), max_units)
-            if n > 0:
-                fig, axs = plt.subplots(nrows=n, figsize=figsize)
-                for i, unit_id in enumerate(oversplit_ids[:n]):
-                    unit_indices = np.flatnonzero(comp.agreement_scores.loc[unit_id, :].values > oversplit_score)
-                    unit_ids = comp.sorting2.unit_ids[unit_indices]
-                    ax = axs[i]
-                    ax.set_title(f"Gt unit {unit_id} - unit_ids: {unit_ids}")
-
-                    templates = self.get_result(key)["clustering_templates"]
-
-                    template_arrays = templates.get_dense_templates()[unit_indices, :, :]
-                    if templates.sparsity is not None:
-                        chan_mask = np.any(templates.sparsity.mask[gt_unit_indices, :], axis=0)
-                        template_arrays = template_arrays[:, :, chan_mask]
-
-                    ax.plot(template_arrays.swapaxes(1, 2).reshape(template_arrays.shape[0], -1).T)
-                    ax.set_xticks([])
-
-                fig.suptitle(label)
-                figs.append(fig)
-            else:
-                print(key, "no over splited")
-
-            return figs

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_matching.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import warnings
 
 from spikeinterface.sortingcomponents.matching import find_spikes_from_templates
@@ -12,7 +10,7 @@ from spikeinterface.widgets import (
 
 import numpy as np
 from .benchmark_base import Benchmark, BenchmarkStudy, MixinStudyUnitCount
-from spikeinterface.core.basesorting import minimum_spike_dtype
+from spikeinterface.core.base import minimum_spike_dtype
 
 
 class MatchingBenchmark(Benchmark):
@@ -26,9 +24,14 @@ class MatchingBenchmark(Benchmark):
         self.method_kwargs = params["method_kwargs"]
         self.result = {}
 
-    def run(self, **job_kwargs):
+    def run(self, verbose=True, **job_kwargs):
         spikes = find_spikes_from_templates(
-            self.recording, self.templates, method=self.method, method_kwargs=self.method_kwargs, job_kwargs=job_kwargs
+            self.recording,
+            self.templates,
+            method=self.method,
+            method_kwargs=self.method_kwargs,
+            verbose=verbose,
+            job_kwargs=job_kwargs,
         )
         unit_ids = self.templates.unit_ids
         sorting = np.zeros(spikes.size, dtype=minimum_spike_dtype)

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_merging.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.curation.auto_merge import auto_merge_units
 from spikeinterface.comparison import compare_sorter_to_ground_truth
 from spikeinterface.core.sortinganalyzer import create_sorting_analyzer

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_motion_estimation.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import json
 from pathlib import Path
 import pickle

{spikeinterface-0.103.2 → spikeinterface-0.104.0}/src/spikeinterface/benchmark/benchmark_motion_interpolation.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import numpy as np