Solve conflicts

Author: alejoe91

src/spikeinterface/benchmark/benchmark_base.py

@@ -457,27 +457,6 @@ def compute_results(self, case_keys=None, verbose=False, **result_params):
             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"]

src/spikeinterface/benchmark/benchmark_clustering.py

@@ -222,11 +222,21 @@ def plot_performances_ordered(self, *args, **kwargs):
 
         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)
 
@@ -263,7 +273,7 @@ def plot_metrics_vs_snr(self, metric="agreement", 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
 
         if axes is None:
             fig, axes = plt.subplots(ncols=len(case_keys), nrows=1, figsize=figsize, squeeze=False)
@@ -322,7 +332,7 @@ def plot_metrics_vs_depth_and_snr(self, metric="agreement", case_keys=None, figs
 
         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)
 
@@ -391,81 +401,3 @@ def plot_metrics_vs_depth_and_snr(self, metric="agreement", case_keys=None, figs
         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

src/spikeinterface/benchmark/benchmark_peak_localization.py

@@ -86,7 +86,7 @@ def plot_comparison_positions(self, case_keys=None):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         fig, axs = plt.subplots(ncols=3, nrows=1, figsize=(15, 5))
 
@@ -222,7 +222,7 @@ def plot_template_errors(self, case_keys=None, show_probe=True):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         fig, axs = plt.subplots(ncols=3, nrows=1, figsize=(15, 5))
 
@@ -248,7 +248,7 @@ def plot_comparison_positions(self, case_keys=None):
 
         if case_keys is None:
             case_keys = list(self.cases.keys())
-        import pylab as plt
+        import matplotlib.pyplot as plt
 
         fig, axs = plt.subplots(ncols=3, nrows=1, figsize=(15, 5))
 
@@ -416,7 +416,7 @@ def plot_comparison_positions(self, case_keys=None):
 
 
 # def plot_comparison_precision(benchmarks):
-#     import pylab as plt
+#     import matplotlib.pyplot as plt
 
 #     fig, axes = plt.subplots(ncols=2, nrows=1, figsize=(15, 10), squeeze=False)
 
@@ -487,7 +487,7 @@ def plot_comparison_positions(self, case_keys=None):
 #         norms = np.linalg.norm(benchmark.gt_positions[:, :2], axis=1)
 #         cell_ind = np.argsort(norms)[0]
 
-#     import pylab as plt
+#     import matplotlib.pyplot as plt
 
 #     fig, axs = plt.subplots(ncols=2, nrows=2, figsize=(15, 10))
 #     plot_probe_map(benchmark.recording, ax=axs[0, 0])

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -842,6 +842,7 @@ def plot_performances_comparison(
     performance_colors={"accuracy": "g", "recall": "b", "precision": "r"},
     levels_to_group_by=None,
     ylim=(-0.1, 1.1),
+    axs=None,
 ):
     """
     Plot performances comparison for a study.
@@ -881,7 +882,8 @@ def plot_performances_comparison(
         [key in performance_colors for key in performance_names]
     ), f"performance_colors must have a color for each performance name: {performance_names}"
 
-    fig, axs = plt.subplots(ncols=num_methods - 1, nrows=num_methods - 1, figsize=figsize, squeeze=False)
+    if axs is None:
+        fig, axs = plt.subplots(ncols=num_methods - 1, nrows=num_methods - 1, figsize=figsize, squeeze=False)
     for i, key1 in enumerate(case_keys):
         for j, key2 in enumerate(case_keys):
             if i < j:
@@ -897,7 +899,8 @@ def plot_performances_comparison(
                         comp1 = study.get_result(sub_key1)["gt_comparison"]
                         comp2 = study.get_result(sub_key2)["gt_comparison"]
 
-                        for performance_name, color in performance_colors.items():
+                        for performance_name in performance_names:
+                            color = performance_colors[performance_name]
                             perf1 = comp1.get_performance()[performance_name]
                             perf2 = comp2.get_performance()[performance_name]
                             ax.scatter(perf2, perf1, marker=".", label=performance_name, color=color)
@@ -923,9 +926,11 @@ def plot_performances_comparison(
     patches = []
     from matplotlib.patches import Patch
 
-    for name, color in performance_colors.items():
-        patches.append(Patch(color=color, label=name))
+    for performance_name in performance_names:
+        color = performance_colors[performance_name]
+        patches.append(Patch(color=color, label=performance_name))
     ax.legend(handles=patches)
+    fig = ax.figure
     fig.subplots_adjust(hspace=0.1, wspace=0.1)
     return fig
 
@@ -964,7 +969,7 @@ def plot_performances_vs_depth_and_snr(
     fig : matplotlib.figure.Figure
         The resulting figure containing the plots.
     """
-    import pylab as plt
+    import matplotlib.pyplot as plt
 
     if case_keys is None:
         case_keys = list(study.cases.keys())
@@ -1082,3 +1087,102 @@ def plot_performance_losses(
     despine(axs)
 
     return fig
+
+
+def plot_some_over_merged(study, case_keys=None, overmerged_score=0.05, max_units=5, figsize=None):
+    """
+    Plot some waveforms of overmerged units.
+    """
+
+    if case_keys is None:
+        case_keys = list(study.cases.keys())
+    import matplotlib.pyplot as plt
+
+    figs = []
+    for count, key in enumerate(case_keys):
+        label = study.cases[key]["label"]
+        comp = study.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, squeeze=False)
+            axs = axs[:, 0]
+            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 = study.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(study, case_keys=None, oversplit_score=0.05, max_units=5, figsize=None):
+    """
+    Plot some waveforms of over-splitted units.
+    """
+    if case_keys is None:
+        case_keys = list(study.cases.keys())
+    import matplotlib.pyplot as plt
+
+    print(case_keys)
+    figs = []
+    for count, key in enumerate(case_keys):
+        print(key)
+        label = study.cases[key]["label"]
+        comp = study.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, squeeze=False)
+            axs = axs[:, 0]
+            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}")
+
+                results = study.get_result(key)
+                if "clustering_templates" in results:
+                    # ClusteringBenchmark has this
+                    templates = results["clustering_templates"]
+                elif "sorter_analyzer" in results:
+                    # SorterBenchmark has this
+                    templates = results["sorter_analyzer"].get_extension("templates").get_data(outputs="Templates")
+                else:
+                    raise ValueError("This benchmark do not have templates computed")
+
+                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