Merge branch 'refactor_GTStudy' of github.com:samuelgarcia/spikeinterface into refactor_GTStudy

Author: samuelgarcia

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