Merge pull request #2068 from samuelgarcia/widgets

Move more widgets to new widgets API

src/spikeinterface/widgets/_legacy_mpl_widgets/__init__.py

@@ -1,14 +1,6 @@
-# isi/ccg/acg
-from .isidistribution import plot_isi_distribution, ISIDistributionWidget
-
 # peak activity
 from .activity import plot_peak_activity_map, PeakActivityMapWidget
 
-# waveform/PC related
-from .principalcomponent import plot_principal_component
-
-# units on probe
-from .unitprobemap import plot_unit_probe_map, UnitProbeMapWidget
 
 from .multicompgraph import (
     plot_multicomp_graph,

src/spikeinterface/widgets/_legacy_mpl_widgets/tests/test_widgets_legacy.py

@@ -43,9 +43,9 @@ def setUp(self):
     def tearDown(self):
         pass
 
-    def test_plot_unit_probe_map(self):
-        sw.plot_unit_probe_map(self._we, with_channel_ids=True)
-        sw.plot_unit_probe_map(self._we, animated=True)
+    # def test_plot_unit_probe_map(self):
+    #     sw.plot_unit_probe_map(self._we, with_channel_ids=True)
+    #     sw.plot_unit_probe_map(self._we, animated=True)
 
     # def test_plot_units_depth_vs_amplitude(self):
     #     sw.plot_units_depth_vs_amplitude(self._we)
@@ -58,9 +58,6 @@ def test_plot_unit_probe_map(self):
     # def test_amplitudes_distribution(self):
     #     sw.plot_amplitudes_distribution(self._we)
 
-    def test_principal_component(self):
-        sw.plot_principal_component(self._we)
-
     # def test_plot_unit_localization(self):
     #     sw.plot_unit_localization(self._we, with_channel_ids=True)
     #     sw.plot_unit_localization(self._we, method='monopolar_triangulation')
@@ -73,10 +70,10 @@ def test_principal_component(self):
     #     unit_ids = self._sorting.unit_ids[:4]
     #     sw.plot_crosscorrelograms(self._sorting, unit_ids=unit_ids, window_ms=500.0, bin_ms=20.0)
 
-    def test_isi_distribution(self):
-        sw.plot_isi_distribution(self._sorting, bin_ms=5.0, window_ms=500.0)
-        fig, axes = plt.subplots(self.num_units, 1)
-        sw.plot_isi_distribution(self._sorting, axes=axes)
+    # def test_isi_distribution(self):
+    #     sw.plot_isi_distribution(self._sorting, bin_ms=5.0, window_ms=500.0)
+    #     fig, axes = plt.subplots(self.num_units, 1)
+    #     sw.plot_isi_distribution(self._sorting, axes=axes)
 
     def test_plot_peak_activity_map(self):
         sw.plot_peak_activity_map(self._rec, with_channel_ids=True)

src/spikeinterface/widgets/isi_distribution.py

@@ -0,0 +1,71 @@
+import numpy as np
+from warnings import warn
+
+from .base import BaseWidget, to_attr
+from .utils import get_unit_colors
+
+
+class ISIDistributionWidget(BaseWidget):
+    """
+    Plots spike train ISI distribution.
+
+    Parameters
+    ----------
+    sorting: SortingExtractor
+        The sorting extractor object
+    unit_ids: list
+        List of unit ids
+    bins_ms: int
+        Bin size in ms
+    window_ms: float
+        Window size in ms
+
+    """
+
+    def __init__(self, sorting, unit_ids=None, window_ms=100.0, bin_ms=1.0, backend=None, **backend_kwargs):
+        if unit_ids is None:
+            unit_ids = sorting.get_unit_ids()
+
+        plot_data = dict(
+            sorting=sorting,
+            unit_ids=unit_ids,
+            window_ms=window_ms,
+            bin_ms=bin_ms,
+        )
+
+        BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
+
+    def plot_matplotlib(self, data_plot, **backend_kwargs):
+        import matplotlib.pyplot as plt
+        from .utils_matplotlib import make_mpl_figure
+
+        dp = to_attr(data_plot)
+
+        if backend_kwargs.get("axes", None) is None:
+            backend_kwargs["num_axes"] = len(dp.unit_ids)
+
+        self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
+
+        sorting = dp.sorting
+        num_segments = sorting.get_num_segments()
+        fs = sorting.sampling_frequency
+
+        for i, unit_id in enumerate(dp.unit_ids):
+            ax = self.axes.flatten()[i]
+
+            bins = np.arange(0, dp.window_ms, dp.bin_ms)
+            bin_counts = None
+            for segment_index in range(num_segments):
+                times_ms = sorting.get_unit_spike_train(unit_id=unit_id, segment_index=segment_index) / fs * 1000.0
+                isi = np.diff(times_ms)
+
+                bin_counts_, bin_edges = np.histogram(isi, bins=bins, density=True)
+                if segment_index == 0:
+                    bin_counts = bin_counts_
+                else:
+                    bin_counts += bin_counts_
+                    # TODO handle sensity when several segments
+
+            ax.bar(x=bin_edges[:-1], height=bin_counts, width=dp.bin_ms, color="gray", align="edge")
+
+            ax.set_ylabel(f"{unit_id}")

src/spikeinterface/widgets/tests/test_widgets.py

@@ -231,6 +231,20 @@ def test_crosscorrelogram(self):
                     **self.backend_kwargs[backend],
                 )
 
+    def test_isi_distribution(self):
+        possible_backends = list(sw.ISIDistributionWidget.get_possible_backends())
+        for backend in possible_backends:
+            if backend not in self.skip_backends:
+                unit_ids = self.sorting.unit_ids[:4]
+                sw.plot_isi_distribution(
+                    self.sorting,
+                    unit_ids=unit_ids,
+                    window_ms=25.0,
+                    bin_ms=2.0,
+                    backend=backend,
+                    **self.backend_kwargs[backend],
+                )
+
     def test_amplitudes(self):
         possible_backends = list(sw.AmplitudesWidget.get_possible_backends())
         for backend in possible_backends:
@@ -357,6 +371,12 @@ def test_plot_rasters(self):
             if backend not in self.skip_backends:
                 sw.plot_rasters(self.sorting)
 
+    def test_plot_unit_probe_map(self):
+        possible_backends = list(sw.UnitProbeMapWidget.get_possible_backends())
+        for backend in possible_backends:
+            if backend not in self.skip_backends:
+                sw.plot_unit_probe_map(self.we_dense)
+
 
 if __name__ == "__main__":
     # unittest.main()
@@ -374,6 +394,8 @@ def test_plot_rasters(self):
     # mytest.test_plot_unit_depths()
     # mytest.test_plot_unit_templates()
     # mytest.test_plot_unit_summary()
+    # mytest.test_crosscorrelogram()
+    mytest.test_isi_distribution()
     # mytest.test_unit_locations()
     # mytest.test_quality_metrics()
     mytest.test_template_metrics()
@@ -382,6 +404,6 @@ def test_plot_rasters(self):
     # mytest.test_plot_confusion_matrix()
     # mytest.test_plot_probe_map()
     # mytest.test_plot_rasters()
+    # mytest.test_plot_unit_probe_map()
 
-    # plt.ion()
     plt.show()