Merge branch 'main' into support_python_3.13

Author: alejoe91

src/spikeinterface/widgets/sorting_summary.py

@@ -2,6 +2,8 @@
 
 import numpy as np
 
+import warnings
+
 from .base import BaseWidget, to_attr
 
 from .amplitudes import AmplitudesWidget
@@ -14,6 +16,9 @@
 from ..core import SortingAnalyzer
 
 
+_default_displayed_unit_properties = ["firing_rate", "num_spikes", "x", "y", "amplitude_median", "snr", "rp_violation"]
+
+
 class SortingSummaryWidget(BaseWidget):
     """
     Plots spike sorting summary.
@@ -42,14 +47,24 @@ class SortingSummaryWidget(BaseWidget):
     label_choices : list or None, default: None
         List of labels to be added to the curation table
         (sortingview backend)
-    unit_table_properties : list or None, default: None
+    displayed_unit_properties : list or None, default: None
         List of properties to be added to the unit table.
         These may be drawn from the sorting extractor, and, if available,
-        the quality_metrics and template_metrics extensions of the SortingAnalyzer.
+        the quality_metrics/template_metrics/unit_locations extensions of the SortingAnalyzer.
         See all properties available with sorting.get_property_keys(), and, if available,
         analyzer.get_extension("quality_metrics").get_data().columns and
         analyzer.get_extension("template_metrics").get_data().columns.
-        (sortingview backend)
+    extra_unit_properties : dict or None, default: None
+        A dict with extra units properties to display.
+    curation_dict : dict or None, default: None
+        When curation is True, optionaly the viewer can get a previous 'curation_dict'
+        to continue/check  previous curations on this analyzer.
+        In this case label_definitions must be None beacuse it is already included in the curation_dict.
+        (spikeinterface_gui backend)
+    label_definitions : dict or None, default: None
+        When curation is True, optionaly the user can provide a label_definitions dict.
+        This replaces the label_choices in the curation_format.
+        (spikeinterface_gui backend)
     """
 
     def __init__(
@@ -60,11 +75,24 @@ def __init__(
         max_amplitudes_per_unit=None,
         min_similarity_for_correlograms=0.2,
         curation=False,
-        unit_table_properties=None,
+        displayed_unit_properties=None,
+        extra_unit_properties=None,
         label_choices=None,
+        curation_dict=None,
+        label_definitions=None,
         backend=None,
+        unit_table_properties=None,
         **backend_kwargs,
     ):
+
+        if unit_table_properties is not None:
+            warnings.warn(
+                "plot_sorting_summary() : unit_table_properties is deprecated, use displayed_unit_properties instead",
+                category=DeprecationWarning,
+                stacklevel=2,
+            )
+            displayed_unit_properties = unit_table_properties
+
         sorting_analyzer = self.ensure_sorting_analyzer(sorting_analyzer)
         self.check_extensions(
             sorting_analyzer, ["correlograms", "spike_amplitudes", "unit_locations", "template_similarity"]
@@ -74,18 +102,29 @@ def __init__(
         if unit_ids is None:
             unit_ids = sorting.get_unit_ids()
 
-        plot_data = dict(
+        if curation_dict is not None and label_definitions is not None:
+            raise ValueError("curation_dict and label_definitions are mutualy exclusive, they cannot be not None both")
+
+        if displayed_unit_properties is None:
+            displayed_unit_properties = list(_default_displayed_unit_properties)
+            if extra_unit_properties is not None:
+                displayed_unit_properties += list(extra_unit_properties.keys())
+
+        data_plot = dict(
             sorting_analyzer=sorting_analyzer,
             unit_ids=unit_ids,
             sparsity=sparsity,
             min_similarity_for_correlograms=min_similarity_for_correlograms,
-            unit_table_properties=unit_table_properties,
+            displayed_unit_properties=displayed_unit_properties,
+            extra_unit_properties=extra_unit_properties,
             curation=curation,
             label_choices=label_choices,
             max_amplitudes_per_unit=max_amplitudes_per_unit,
+            curation_dict=curation_dict,
+            label_definitions=label_definitions,
         )
 
-        BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
+        BaseWidget.__init__(self, data_plot, backend=backend, **backend_kwargs)
 
     def plot_sortingview(self, data_plot, **backend_kwargs):
         import sortingview.views as vv
@@ -156,7 +195,7 @@ def plot_sortingview(self, data_plot, **backend_kwargs):
 
         # unit ids
         v_units_table = generate_unit_table_view(
-            dp.sorting_analyzer, dp.unit_table_properties, similarity_scores=similarity_scores
+            dp.sorting_analyzer, dp.displayed_unit_properties, similarity_scores=similarity_scores
         )
 
         if dp.curation:
@@ -190,9 +229,14 @@ def plot_sortingview(self, data_plot, **backend_kwargs):
     def plot_spikeinterface_gui(self, data_plot, **backend_kwargs):
         sorting_analyzer = data_plot["sorting_analyzer"]
 
-        import spikeinterface_gui
+        from spikeinterface_gui import run_mainwindow
 
-        app = spikeinterface_gui.mkQApp()
-        win = spikeinterface_gui.MainWindow(sorting_analyzer, curation=data_plot["curation"])
-        win.show()
-        app.exec_()
+        run_mainwindow(
+            sorting_analyzer,
+            with_traces=True,
+            curation=data_plot["curation"],
+            curation_dict=data_plot["curation_dict"],
+            label_definitions=data_plot["label_definitions"],
+            extra_unit_properties=data_plot["extra_unit_properties"],
+            displayed_unit_properties=data_plot["displayed_unit_properties"],
+        )

src/spikeinterface/widgets/tests/test_widgets.py

@@ -73,7 +73,9 @@ def setUpClass(cls):
             spike_amplitudes=dict(),
             unit_locations=dict(),
             spike_locations=dict(),
-            quality_metrics=dict(metric_names=["snr", "isi_violation", "num_spikes", "amplitude_cutoff"]),
+            quality_metrics=dict(
+                metric_names=["snr", "isi_violation", "num_spikes", "firing_rate", "amplitude_cutoff"]
+            ),
             template_metrics=dict(),
             correlograms=dict(),
             template_similarity=dict(),
@@ -531,26 +533,37 @@ def test_plot_sorting_summary(self):
         possible_backends = list(sw.SortingSummaryWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_sorting_summary(self.sorting_analyzer_dense, backend=backend, **self.backend_kwargs[backend])
-                sw.plot_sorting_summary(self.sorting_analyzer_sparse, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_sorting_summary(
+                    self.sorting_analyzer_dense,
+                    displayed_unit_properties=[],
+                    backend=backend,
+                    **self.backend_kwargs[backend],
+                )
+                sw.plot_sorting_summary(
+                    self.sorting_analyzer_sparse,
+                    displayed_unit_properties=[],
+                    backend=backend,
+                    **self.backend_kwargs[backend],
+                )
                 sw.plot_sorting_summary(
                     self.sorting_analyzer_sparse,
                     sparsity=self.sparsity_strict,
+                    displayed_unit_properties=[],
                     backend=backend,
                     **self.backend_kwargs[backend],
                 )
-                # add unit_properties
+                # select unit_properties
                 sw.plot_sorting_summary(
                     self.sorting_analyzer_sparse,
-                    unit_table_properties=["firing_rate", "snr"],
+                    displayed_unit_properties=["firing_rate", "snr"],
                     backend=backend,
                     **self.backend_kwargs[backend],
                 )
                 # adding a missing property should raise a warning
                 with self.assertWarns(UserWarning):
                     sw.plot_sorting_summary(
                         self.sorting_analyzer_sparse,
-                        unit_table_properties=["missing_property"],
+                        displayed_unit_properties=["missing_property"],
                         backend=backend,
                         **self.backend_kwargs[backend],
                     )
@@ -688,9 +701,9 @@ def test_plot_motion_info(self):
     # mytest.test_plot_unit_presence()
     # mytest.test_plot_peak_activity()
     # mytest.test_plot_multicomparison()
-    # mytest.test_plot_sorting_summary()
+    mytest.test_plot_sorting_summary()
     # mytest.test_plot_motion()
-    mytest.test_plot_motion_info()
-    plt.show()
+    # mytest.test_plot_motion_info()
+    # plt.show()
 
     # TestWidgets.tearDownClass()

src/spikeinterface/widgets/utils.py

@@ -243,3 +243,93 @@ def array_to_image(
             output_image = np.frombuffer(image.tobytes(), dtype=np.uint8).reshape(output_image.shape)
 
     return output_image
+
+
+def make_units_table_from_sorting(sorting, units_table=None):
+    """
+    Make a DataFrame from sorting properties.
+    Only for properties with ndim=1
+
+    Parameters
+    ----------
+    sorting : Sorting
+        The Sorting object
+    units_table : None | pd.DataFrame
+        Optionally a existing dataframe.
+
+    Returns
+    -------
+    units_table : pd.DataFrame
+        Table containing all columns.
+    """
+
+    if units_table is None:
+        import pandas as pd
+
+        units_table = pd.DataFrame(index=sorting.unit_ids)
+
+    for col in sorting.get_property_keys():
+        values = sorting.get_property(col)
+        if values.dtype.kind in "iuUSfb" and values.ndim == 1:
+            units_table.loc[:, col] = values
+
+    return units_table
+
+
+def make_units_table_from_analyzer(
+    analyzer,
+    extra_properties=None,
+):
+    """
+    Make a DataFrame by aggregating :
+      * quality metrics
+      * template metrics
+      * unit_position
+      * sorting properties
+      * extra columns
+
+    This used in sortingview and spikeinterface-gui to display the units table in a flexible way.
+
+    Parameters
+    ----------
+    sorting_analyzer : SortingAnalyzer
+        The SortingAnalyzer object
+    extra_properties : None | dict
+        Extra columns given as dict.
+
+    Returns
+    -------
+    units_table : pd.DataFrame
+        Table containing all columns.
+    """
+    import pandas as pd
+
+    all_df = []
+
+    if analyzer.get_extension("unit_locations") is not None:
+        locs = analyzer.get_extension("unit_locations").get_data()
+        df = pd.DataFrame(locs[:, :2], columns=["x", "y"], index=analyzer.unit_ids)
+        all_df.append(df)
+
+    if analyzer.get_extension("quality_metrics") is not None:
+        df = analyzer.get_extension("quality_metrics").get_data()
+        all_df.append(df)
+
+    if analyzer.get_extension("template_metrics") is not None:
+        df = analyzer.get_extension("template_metrics").get_data()
+        all_df.append(df)
+
+    if len(all_df) > 0:
+        units_table = pd.concat(all_df, axis=1)
+    else:
+        units_table = pd.DataFrame(index=analyzer.unit_ids)
+
+    make_units_table_from_sorting(analyzer.sorting, units_table=units_table)
+
+    if extra_properties is not None:
+        for col, values in extra_properties.items():
+            # the ndim = 1 is important because we need  column only for the display in gui.
+            if values.dtype.kind in "iuUSfb" and values.ndim == 1:
+                units_table.loc[:, col] = values
+
+    return units_table