conflicts

src/spikeinterface/sorters/internal/spyking_circus2.py

@@ -314,7 +314,9 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
 
                 motion_info = load_motion_info(motion_folder)
                 motion = motion_info["motion"]
-                max_motion = max(np.max(np.abs(motion.displacement[seg_index])) for seg_index in range(len(motion.displacement)))
+                max_motion = max(
+                    np.max(np.abs(motion.displacement[seg_index])) for seg_index in range(len(motion.displacement))
+                )
                 merging_params["maximum_distance_um"] = max(50, 2 * max_motion)
 
             # peak_sign = params['detection'].get('peak_sign', 'neg')

src/spikeinterface/sortingcomponents/benchmark/benchmark_motion_estimation.py

@@ -55,13 +55,9 @@ def get_gt_motion_from_unit_displacement(
             gt_displacement[t, :] = f(spatial_bins_um)
 
     gt_motion = Motion(
-        gt_displacement,
-        temporal_bins_s,
-        spatial_bins_um,
-        direction="xyz"[direction_dim],
-        interpolation_method="linear"
+        gt_displacement, temporal_bins_s, spatial_bins_um, direction="xyz"[direction_dim], interpolation_method="linear"
     )
-    
+
     return gt_motion
 
 
@@ -102,9 +98,7 @@ def run(self, **job_kwargs):
         t2 = time.perf_counter()
         peak_locations = localize_peaks(self.recording, selected_peaks, **p["localize_kwargs"], **job_kwargs)
         t3 = time.perf_counter()
-        motion = estimate_motion(
-            self.recording, selected_peaks, peak_locations, **p["estimate_motion_kwargs"]
-        )
+        motion = estimate_motion(self.recording, selected_peaks, peak_locations, **p["estimate_motion_kwargs"])
         t4 = time.perf_counter()
 
         step_run_times = dict(
@@ -263,8 +257,12 @@ def plot_errors(self, case_keys=None, figsize=None, lim=None):
                 aspect="auto",
                 interpolation="nearest",
                 origin="lower",
-                extent=(motion.temporal_bins_s[0][0], motion.temporal_bins_s[0][-1],
-                        motion.spatial_bins_um[0], motion.spatial_bins_um[-1]),
+                extent=(
+                    motion.temporal_bins_s[0][0],
+                    motion.temporal_bins_s[0][-1],
+                    motion.spatial_bins_um[0],
+                    motion.spatial_bins_um[-1],
+                ),
             )
             plt.colorbar(im, ax=ax, label="error")
             ax.set_ylabel("depth (um)")

src/spikeinterface/sortingcomponents/benchmark/benchmark_motion_interpolation.py

@@ -44,9 +44,7 @@ def run(self, **job_kwargs):
             recording = self.drifting_recording
         elif self.params["recording_source"] == "corrected":
             correct_motion_kwargs = self.params["correct_motion_kwargs"]
-            recording = InterpolateMotionRecording(
-                self.drifting_recording, self.motion, **correct_motion_kwargs
-            )
+            recording = InterpolateMotionRecording(self.drifting_recording, self.motion, **correct_motion_kwargs)
         else:
             raise ValueError("recording_source")
 

src/spikeinterface/sortingcomponents/benchmark/tests/test_benchmark_motion_estimation.py

@@ -70,6 +70,7 @@ def test_benchmark_motion_estimaton(create_cache_folder):
     study.plot_summary_errors()
 
     import matplotlib.pyplot as plt
+
     plt.show()
 
 

src/spikeinterface/sortingcomponents/benchmark/tests/test_benchmark_motion_interpolation.py

@@ -134,6 +134,7 @@ def test_benchmark_motion_interpolation(create_cache_folder):
     study.plot_sorting_accuracy(mode="depth", mode_best_merge=True)
 
     import matplotlib.pyplot as plt
+
     plt.show()
 
 

src/spikeinterface/sortingcomponents/motion_utils.py

@@ -220,11 +220,11 @@ def __eq__(self, other):
             return False
 
         return True
-    
+
     def copy(self):
         return Motion(
             self.displacement.copy(),
             self.temporal_bins_s.copy(),
             self.spatial_bins_um.copy(),
-            interpolation_method=self.interpolation_method
+            interpolation_method=self.interpolation_method,
         )

src/spikeinterface/sortingcomponents/tests/test_motion_utils.py

@@ -14,29 +14,28 @@
 
 
 def make_fake_motion():
-    displacement_sampling_frequency = 5.
-    spatial_bins_um = np.array([100.0, 200.0, 300., 400.])    
+    displacement_sampling_frequency = 5.0
+    spatial_bins_um = np.array([100.0, 200.0, 300.0, 400.0])
 
     displacement_vector = make_one_displacement_vector(
         drift_mode="zigzag",
         duration=50.0,
         amplitude_factor=1.0,
         displacement_sampling_frequency=displacement_sampling_frequency,
-        period_s=25.,
+        period_s=25.0,
     )
     temporal_bins_s = np.arange(displacement_vector.size) / displacement_sampling_frequency
     displacement = np.zeros((temporal_bins_s.size, spatial_bins_um.size))
-    
+
     n = spatial_bins_um.size
     for i in range(n):
-        displacement[:, i] = displacement_vector * ((i +1 ) / n)
+        displacement[:, i] = displacement_vector * ((i + 1) / n)
 
     motion = Motion(displacement, temporal_bins_s, spatial_bins_um, direction="y")
 
     return motion
 
 
-
 def test_Motion():
 
     temporal_bins_s = np.arange(0.0, 10.0, 1.0)

src/spikeinterface/widgets/motion.py

@@ -4,6 +4,7 @@
 
 from .base import BaseWidget, to_attr
 
+
 class MotionWidget(BaseWidget):
     """
     Plot the Motion object
@@ -18,6 +19,7 @@ class MotionWidget(BaseWidget):
         How to plot map or lines.
         "auto" make it automatic if the number of depth is too high.
     """
+
     def __init__(
         self,
         motion,
@@ -26,10 +28,11 @@ def __init__(
         motion_lim=None,
         backend=None,
         **backend_kwargs,
-
-    ):  
+    ):
         if isinstance(motion, dict):
-            raise ValueError("The API has changed, plot_motion() used Motion object now, maybe you want plot_motion_info(motion_info)")
+            raise ValueError(
+                "The API has changed, plot_motion() used Motion object now, maybe you want plot_motion_info(motion_info)"
+            )
 
         if segment_index is None:
             if len(motion.displacement) == 1:
@@ -43,7 +46,7 @@ def __init__(
             mode=mode,
         )
 
-        BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)        
+        BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         import matplotlib.pyplot as plt
@@ -59,7 +62,6 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
 
         self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
 
-
         displacement = motion.displacement[dp.segment_index]
         temporal_bins_s = motion.temporal_bins_s[dp.segment_index]
         depth = motion.spatial_bins_um
@@ -69,7 +71,6 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         else:
             motion_lim = dp.motion_lim
 
-
         ax = self.ax
         fig = self.figure
         if dp.mode == "line":
@@ -84,10 +85,10 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
                 aspect="auto",
                 origin="lower",
                 extent=(temporal_bins_s[0], temporal_bins_s[-1], depth[0], depth[-1]),
-                cmap="PiYG"
+                cmap="PiYG",
             )
             im.set_clim(-motion_lim, motion_lim)
-            
+
             cbar = fig.colorbar(im)
             cbar.ax.set_ylabel("motion [um]")
             ax.set_xlabel("Times [s]")
@@ -106,8 +107,13 @@ class MotionInfoWidget(BaseWidget):
     ----------
     motion_info : dict
         The motion info return by correct_motion() or load back with load_motion_info()
+<<<<<<< HEAD
     segment_index : int, default: None
         The segment index to display.
+=======
+    segment_index:
+
+>>>>>>> 257950d5859521730ed1da746b6fd32b7b6335bb
     recording : RecordingExtractor, default: None
         The recording extractor object (only used to get "real" times)
     segment_index : int, default: 0
@@ -145,7 +151,7 @@ def __init__(
         backend=None,
         **backend_kwargs,
     ):
-        
+
         motion = motion_info["motion"]
         if segment_index is None:
             if len(motion.displacement) == 1:
@@ -192,7 +198,6 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
 
         motion = dp.motion
 
-
         displacement = motion.displacement[dp.segment_index]
         temporal_bins_s = motion.temporal_bins_s[dp.segment_index]
         spatial_bins_um = motion.spatial_bins_um
@@ -202,7 +207,6 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         else:
             motion_lim = dp.motion_lim
 
-
         is_rigid = displacement.shape[1] == 1
 
         gs = fig.add_gridspec(2, 2, wspace=0.3, hspace=0.5)

src/spikeinterface/widgets/tests/test_widgets.py

@@ -579,47 +579,40 @@ def test_plot_multicomparison(self):
 
                 _, axes = plt.subplots(len(mcmp.object_list), 1)
                 sw.plot_multicomparison_agreement_by_sorter(mcmp, axes=axes)
-    
+
     def test_plot_motion(self):
         from spikeinterface.sortingcomponents.tests.test_motion_utils import make_fake_motion
+
         motion = make_fake_motion()
 
         possible_backends = list(sw.MotionWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_motion(motion, backend=backend, mode='line')
-                sw.plot_motion(motion, backend=backend, mode='map')
+                sw.plot_motion(motion, backend=backend, mode="line")
+                sw.plot_motion(motion, backend=backend, mode="map")
 
     def test_plot_motion_info(self):
         from spikeinterface.sortingcomponents.tests.test_motion_utils import make_fake_motion
 
-
         motion = make_fake_motion()
         rng = np.random.default_rng(seed=2205)
         peak_locations = np.zeros(self.peaks.size, dtype=[("x", "float64"), ("y", "float64")])
-        peak_locations['y'] = rng.uniform(motion.spatial_bins_um[0],
-                                          motion.spatial_bins_um[-1],
-                                          size=self.peaks.size)
-
+        peak_locations["y"] = rng.uniform(motion.spatial_bins_um[0], motion.spatial_bins_um[-1], size=self.peaks.size)
+
         motion_info = dict(
             motion=motion,
-            parameters=dict(sampling_frequency=30000.),
+            parameters=dict(sampling_frequency=30000.0),
             run_times=dict(),
             peaks=self.peaks,
             peak_locations=peak_locations,
         )
 
-
         possible_backends = list(sw.MotionWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
                 sw.plot_motion_info(motion_info, recording=self.recording, backend=backend)
 
 
-
-
-
-
 if __name__ == "__main__":
     # unittest.main()
     import matplotlib.pyplot as plt