Merge branch 'refactor_GTStudy' of github.com:samuelgarcia/spikeinter…

…face into refactor_GTStudy

doc/modules/benchmark.rst

@@ -103,7 +103,7 @@ The all mechanism is based on an intrinsic organization into a "study_folder" wi
         # some plots
         m = comp.get_confusion_matrix()
         w_comp = sw.plot_agreement_matrix(sorting_comparison=comp)
-    
+
     # Collect synthetic dataframes and display
     # As shown previously, the performance is returned as a pandas dataframe.
     # The spikeinterface.comparison.get_performance_by_unit() function,

doc/modules/comparison.rst

@@ -412,7 +412,3 @@ sorting analyzers from day 1 (:code:`analyzer_day1`) to day 5 (:code:`analyzer_d
     # match all
     m_tcmp = sc.compare_multiple_templates(waveform_list=analyzer_list,
                                            name_list=["D1", "D2", "D3", "D4", "D5"])
-
-
-
-

src/spikeinterface/benchmark/__init__.py

@@ -4,4 +4,4 @@
   * some sorting components (clustering, motion, template matching)
 """
 
-from .benchmark_sorter import SorterStudy
+from .benchmark_sorter import SorterStudy

src/spikeinterface/benchmark/benchmark_base.py

@@ -259,6 +259,7 @@ def get_run_times(self, case_keys=None):
 
     def plot_run_times(self, case_keys=None):
         from .benchmark_plot_tools import plot_run_times
+
         return plot_run_times(self, case_keys=case_keys)
 
     def compute_results(self, case_keys=None, verbose=False, **result_params):
@@ -445,4 +446,3 @@ def run(self):
     def compute_result(self):
         # run becnhmark result
         raise NotImplementedError
-

src/spikeinterface/benchmark/benchmark_clustering.py

@@ -163,16 +163,18 @@ def get_count_units(self, case_keys=None, well_detected_score=None, redundant_sc
     # plotting by methods
     def plot_unit_counts(self, **kwargs):
         from .benchmark_plot_tools import plot_unit_counts
+
         return plot_unit_counts(self, **kwargs)
 
     def plot_agreement_matrix(self, **kwargs):
         from .benchmark_plot_tools import plot_agreement_matrix
+
         return plot_agreement_matrix(self, **kwargs)
 
     def plot_performances_vs_snr(self, **kwargs):
         from .benchmark_plot_tools import plot_performances_vs_snr
-        return plot_performances_vs_snr(self, **kwargs)
 
+        return plot_performances_vs_snr(self, **kwargs)
 
     def plot_error_metrics(self, metric="cosine", case_keys=None, figsize=(15, 5)):
 

src/spikeinterface/benchmark/benchmark_matching.py

@@ -63,12 +63,13 @@ def create_benchmark(self, key):
 
     def plot_agreement_matrix(self, **kwargs):
         from .benchmark_plot_tools import plot_agreement_matrix
+
         return plot_agreement_matrix(self, **kwargs)
 
     def plot_performances_vs_snr(self, **kwargs):
         from .benchmark_plot_tools import plot_performances_vs_snr
-        return plot_performances_vs_snr(self, **kwargs)
 
+        return plot_performances_vs_snr(self, **kwargs)
 
     def plot_collisions(self, case_keys=None, figsize=None):
         if case_keys is None:

src/spikeinterface/benchmark/benchmark_peak_selection.py

@@ -10,6 +10,7 @@
 
 from .benchmark_base import Benchmark, BenchmarkStudy
 
+
 class PeakSelectionBenchmark(Benchmark):
 
     def __init__(self, recording, gt_sorting, params, indices, exhaustive_gt=True):

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -1,7 +1,6 @@
 import numpy as np
 
 
-
 def _simpleaxis(ax):
     ax.spines["top"].set_visible(False)
     ax.spines["right"].set_visible(False)
@@ -28,7 +27,6 @@ def plot_run_times(study, case_keys=None):
     run_times = study.get_run_times(case_keys=case_keys)
 
     colors = study.get_colors()
-
 
     fig, ax = plt.subplots()
     labels = []
@@ -58,7 +56,6 @@ def plot_unit_counts(study, case_keys=None):
     if case_keys is None:
         case_keys = list(study.cases.keys())
 
-
     count_units = study.get_count_units(case_keys=case_keys)
 
     fig, ax = plt.subplots()
@@ -95,6 +92,7 @@ def plot_unit_counts(study, case_keys=None):
 
     return fig
 
+
 def plot_performances(study, mode="ordered", performance_names=("accuracy", "precision", "recall"), case_keys=None):
     """
     Plot performances over case for a study.
@@ -121,10 +119,9 @@ def plot_performances(study, mode="ordered", performance_names=("accuracy", "pre
     if case_keys is None:
         case_keys = list(study.cases.keys())
 
-    perfs=study.get_performance_by_unit(case_keys=case_keys)
+    perfs = study.get_performance_by_unit(case_keys=case_keys)
     colors = study.get_colors()
 
-
     if mode in ("ordered", "snr"):
         num_axes = len(performance_names)
         fig, axs = plt.subplots(ncols=num_axes)
@@ -195,7 +192,6 @@ def plot_agreement_matrix(study, ordered=True, case_keys=None):
     if case_keys is None:
         case_keys = list(study.cases.keys())
 
-
     num_axes = len(case_keys)
     fig, axs = plt.subplots(ncols=num_axes)
 
@@ -238,9 +234,9 @@ def plot_performances_vs_snr(study, case_keys=None, figsize=None, metrics=["accu
             y = study.get_result(key)["gt_comparison"].get_performance()[k].values
             ax.scatter(x, y, marker=".", label=label)
             ax.set_title(k)
-        
+
         ax.set_ylim(0, 1.05)
-        
+
         if count == 2:
             ax.legend()
 

src/spikeinterface/benchmark/benchmark_sorter.py

@@ -2,7 +2,6 @@
 This replace the previous `GroundTruthStudy`
 """
 
-
 import numpy as np
 from ..core import NumpySorting
 from .benchmark_base import Benchmark, BenchmarkStudy
@@ -40,6 +39,7 @@ def compute_result(self):
         ("gt_comparison", "pickle"),
     ]
 
+
 class SorterStudy(BenchmarkStudy):
     """
     This class is used to tests several sorter in several situtation.
@@ -121,15 +121,15 @@ def get_count_units(self, case_keys=None, well_detected_score=None, redundant_sc
     # plotting as methods
     def plot_unit_counts(self, **kwargs):
         from .benchmark_plot_tools import plot_unit_counts
+
         return plot_unit_counts(self, **kwargs)
 
     def plot_performances(self, **kwargs):
         from .benchmark_plot_tools import plot_performances
+
         return plot_performances(self, **kwargs)
 
     def plot_agreement_matrix(self, **kwargs):
         from .benchmark_plot_tools import plot_agreement_matrix
-        return plot_agreement_matrix(self, **kwargs)
-
-
 
+        return plot_agreement_matrix(self, **kwargs)

src/spikeinterface/benchmark/tests/test_benchmark_peak_selection.py

@@ -2,6 +2,7 @@
 
 from pathlib import Path
 
+
 @pytest.mark.skip()
 def test_benchmark_peak_selection(create_cache_folder):
     cache_folder = create_cache_folder

src/spikeinterface/benchmark/tests/test_benchmark_sorter.py

@@ -15,6 +15,7 @@ def setup_module(tmp_path_factory):
     create_a_study(study_folder)
     return study_folder
 
+
 def simple_preprocess(rec):
     return bandpass_filter(rec)
 
@@ -75,14 +76,11 @@ def test_SorterStudy(setup_module):
     # import matplotlib.pyplot as plt
     # plt.show()
 
-
     perf_by_unit = study.get_performance_by_unit()
     # print(perf_by_unit)
     count_units = study.get_count_units()
     # print(count_units)
 
-
-
 
 if __name__ == "__main__":
     study_folder = Path(__file__).resolve().parents[4] / "cache_folder" / "benchmarks" / "test_SorterStudy"

src/spikeinterface/comparison/collision.py

@@ -171,6 +171,7 @@ def compute_collision_by_similarity(self, similarity_matrix, unit_ids=None, good
 
         return similarities, recall_scores, pair_names
 
+
 # This is removed at the moment.
 # We need to move this maybe one day in benchmark.
 # please do not delete this

src/spikeinterface/comparison/groundtruthstudy.py

@@ -1,5 +1,3 @@
-
-
 _txt_error_message = """
 GroundTruthStudy has been replaced by SorterStudy with similar API but not back compatible folder loading.
 You can do:
@@ -13,6 +11,7 @@
 ...
 """
 
+
 class GroundTruthStudy:
     def __init__(self, study_folder):
         raise RuntimeError(_txt_error_message)

src/spikeinterface/widgets/gtstudy.py

@@ -11,6 +11,7 @@
 
 import warnings
 
+
 class StudyRunTimesWidget(BaseWidget):
     """
     Plot sorter run times for a SorterStudy.
@@ -25,12 +26,15 @@ class StudyRunTimesWidget(BaseWidget):
     """
 
     def __init__(self, study, case_keys=None, backend=None, **backend_kwargs):
-        warnings.warn("plot_study_run_times is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead.")
+        warnings.warn(
+            "plot_study_run_times is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead."
+        )
         plot_data = dict(study=study, case_keys=case_keys)
         BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         from spikeinterface.benchmark.benchmark_plot_tools import plot_run_times
+
         plot_run_times(data_plot["study"], case_keys=data_plot["case_keys"])
 
 
@@ -48,12 +52,15 @@ class StudyUnitCountsWidget(BaseWidget):
     """
 
     def __init__(self, study, case_keys=None, backend=None, **backend_kwargs):
-        warnings.warn("plot_study_unit_counts is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead.")
+        warnings.warn(
+            "plot_study_unit_counts is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead."
+        )
         plot_data = dict(study=study, case_keys=case_keys)
         BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         from spikeinterface.benchmark.benchmark_plot_tools import plot_unit_counts
+
         plot_unit_counts(data_plot["study"], case_keys=data_plot["case_keys"])
 
 
@@ -87,7 +94,9 @@ def __init__(
         backend=None,
         **backend_kwargs,
     ):
-        warnings.warn("plot_study_performances is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead.")
+        warnings.warn(
+            "plot_study_performances is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead."
+        )
         plot_data = dict(
             study=study,
             mode=mode,
@@ -98,13 +107,15 @@ def __init__(
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         from spikeinterface.benchmark.benchmark_plot_tools import plot_performances
+
         plot_performances(
             data_plot["study"],
             mode=data_plot["mode"],
             performance_names=data_plot["performance_names"],
-            case_keys=data_plot["case_keys"]
+            case_keys=data_plot["case_keys"],
         )
 
+
 class StudyAgreementMatrix(BaseWidget):
     """
     Plot agreement matrix.
@@ -128,7 +139,9 @@ def __init__(
         backend=None,
         **backend_kwargs,
     ):
-        warnings.warn("plot_study_agreement_matrix is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead.")
+        warnings.warn(
+            "plot_study_agreement_matrix is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead."
+        )
         plot_data = dict(
             study=study,
             case_keys=case_keys,
@@ -139,11 +152,8 @@ def __init__(
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         from spikeinterface.benchmark.benchmark_plot_tools import plot_agreement_matrix
-        plot_agreement_matrix(
-            data_plot["study"],
-            ordered=data_plot["ordered"],
-            case_keys=data_plot["case_keys"]
-        )
+
+        plot_agreement_matrix(data_plot["study"], ordered=data_plot["ordered"], case_keys=data_plot["case_keys"])
 
 
 class StudySummary(BaseWidget):
@@ -171,16 +181,23 @@ def __init__(
         backend=None,
         **backend_kwargs,
     ):
-
-        warnings.warn("plot_study_summary is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead.")
+
+        warnings.warn(
+            "plot_study_summary is to be deprecated. Use spikeinterface.benchmark.benchmark_plot_tools instead."
+        )
         plot_data = dict(study=study, case_keys=case_keys)
         BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         study = data_plot["study"]
         case_keys = data_plot["case_keys"]
 
-        from spikeinterface.benchmark.benchmark_plot_tools import plot_agreement_matrix, plot_performances, plot_unit_counts, plot_run_times
+        from spikeinterface.benchmark.benchmark_plot_tools import (
+            plot_agreement_matrix,
+            plot_performances,
+            plot_unit_counts,
+            plot_run_times,
+        )
 
         plot_performances(study=study, case_keys=case_keys, mode="ordered")
         plot_performances(study=study, case_keys=case_keys, mode="snr")