motion_estimation() : refactoring party.

Move method into separated files. Change, refactor (and rename some) kwargs from common to specific methos. Add dredge_lfp class.
SpikeInterface · Jun 26, 2024 · 1ac451c · 1ac451c
1 parent 13c81ac
commit 1ac451c
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Showing 11 changed files with 1,543 additions and 1,406 deletions.
diff --git a/src/spikeinterface/preprocessing/motion.py b/src/spikeinterface/preprocessing/motion.py
@@ -40,10 +40,10 @@
             margin_um=0.0,
             # win_shape="gaussian",
             # win_step_um=50.0,
-            # win_sigma_um=150.0,
+            # win_scale_um=150.0,
             win_shape="gaussian",
             win_step_um=100.0,
-            win_sigma_um=200.0,
+            win_scale_um=200.0,
             histogram_depth_smooth_um=5.0,
             histogram_time_smooth_s=None,
             pairwise_displacement_method="conv",
@@ -99,10 +99,10 @@
             margin_um=0.0,
             # win_shape="gaussian",
             # win_step_um=50.0,
-            # win_sigma_um=150.0,
+            # win_scale_um=150.0,
             win_shape="gaussian",
             win_step_um=100.0,
-            win_sigma_um=200.0,
+            win_scale_um=200.0,
             histogram_depth_smooth_um=5.0,
             histogram_time_smooth_s=None,
             pairwise_displacement_method="conv",
@@ -181,7 +181,7 @@
             bin_duration_s=2.0,
             rigid=False,
             win_step_um=50.0,
-            win_sigma_um=150.0,
+            win_scale_um=150.0,
             margin_um=0,
             win_shape="rect",
         ),

diff --git a/src/spikeinterface/sortingcomponents/benchmark/tests/test_benchmark_motion_estimation.py b/src/spikeinterface/sortingcomponents/benchmark/tests/test_benchmark_motion_estimation.py
@@ -45,7 +45,7 @@ def test_benchmark_motion_estimaton(create_cache_folder):
                     bin_um=5.0,
                     rigid=False,
                     win_step_um=50.0,
-                    win_sigma_um=200.0,
+                    win_scale_um=200.0,
                 ),
             ),
         )

diff --git a/src/spikeinterface/sortingcomponents/motion/__init__.py b/src/spikeinterface/sortingcomponents/motion/__init__.py
@@ -2,3 +2,4 @@
 from .motion_estimation import estimate_motion
 from .motion_interpolation import (correct_motion_on_peaks, interpolate_motion_on_traces,
                                    InterpolateMotionRecording, interpolate_motion)
+from .motion_cleaner import clean_motion_vector