Dredge lfp and dredge ap

doc/modules/sortingcomponents.rst

@@ -193,7 +193,7 @@ Here is an example with non-rigid motion estimation:
     from spikeinterface.sortingcomponents.motion_estimation import estimate_motion
     motion, temporal_bins, spatial_bins,
                 extra_check = estimate_motion(recording=recording, peaks=peaks, peak_locations=peak_locations,
-                                              direction='y', bin_duration_s=10., bin_um=10., margin_um=0.,
+                                              direction='y', bin_s=10., bin_um=10., margin_um=0.,
                                               method='decentralized_registration',
                                               rigid=False, win_shape='gaussian', win_step_um=50., win_sigma_um=150.,
                                               progress_bar=True, verbose=True)

src/spikeinterface/generation/hybrid_tools.py

@@ -15,7 +15,7 @@
 )
 from spikeinterface.core.template_tools import get_template_extremum_channel
 
-from spikeinterface.sortingcomponents.motion_utils import Motion
+from spikeinterface.sortingcomponents.motion import Motion
 
 from spikeinterface.generation.drift_tools import (
     InjectDriftingTemplatesRecording,

src/spikeinterface/preprocessing/motion.py

@@ -19,8 +19,8 @@
             method="locally_exclusive",
             peak_sign="neg",
             detect_threshold=8.0,
-            exclude_sweep_ms=0.1,
-            radius_um=50,
+            exclude_sweep_ms=0.8,
+            radius_um=80.,
         ),
         "select_kwargs": dict(),
         "localize_peaks_kwargs": dict(
@@ -35,16 +35,13 @@
         "estimate_motion_kwargs": dict(
             method="decentralized",
             direction="y",
-            bin_duration_s=2.0,
+            bin_s=1.0,
             rigid=False,
             bin_um=5.0,
-            margin_um=0.0,
-            # win_shape="gaussian",
-            # win_step_um=50.0,
-            # win_sigma_um=150.0,
+            hist_margin_um=20.0,
             win_shape="gaussian",
-            win_step_um=100.0,
-            win_sigma_um=200.0,
+            win_step_um=200.0,
+            win_scale_um=300.0,
             histogram_depth_smooth_um=5.0,
             histogram_time_smooth_s=None,
             pairwise_displacement_method="conv",
@@ -78,13 +75,14 @@
             method="locally_exclusive",
             peak_sign="neg",
             detect_threshold=8.0,
-            exclude_sweep_ms=0.5,
-            radius_um=50,
+            exclude_sweep_ms=0.8,
+            radius_um=80.,
         ),
         "select_kwargs": dict(),
         "localize_peaks_kwargs": dict(
             method="grid_convolution",
-            radius_um=40.0,
+            # radius_um=40.0,
+            radius_um=80.0,
             upsampling_um=5.0,
             sigma_ms=0.25,
             margin_um=30.0,
@@ -94,16 +92,13 @@
         "estimate_motion_kwargs": dict(
             method="decentralized",
             direction="y",
-            bin_duration_s=2.0,
+            bin_s=2.0,
             rigid=False,
             bin_um=5.0,
-            margin_um=0.0,
-            # win_shape="gaussian",
-            # win_step_um=50.0,
-            # win_sigma_um=150.0,
+            hist_margin_um=0.0,
             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",
@@ -149,7 +144,7 @@
         ),
         "estimate_motion_kwargs": dict(
             method="decentralized",
-            bin_duration_s=10.0,
+            bin_s=10.0,
             rigid=True,
         ),
         "interpolate_motion_kwargs": dict(
@@ -179,11 +174,11 @@
         ),
         "estimate_motion_kwargs": dict(
             method="iterative_template",
-            bin_duration_s=2.0,
+            bin_s=2.0,
             rigid=False,
             win_step_um=50.0,
-            win_sigma_um=150.0,
-            margin_um=0,
+            win_scale_um=150.0,
+            hist_margin_um=0,
             win_shape="rect",
         ),
         "interpolate_motion_kwargs": dict(
@@ -201,6 +196,7 @@
 }
 
 
+
 def correct_motion(
     recording,
     preset="nonrigid_accurate",
@@ -241,8 +237,8 @@ def correct_motion(
       * :py:func:`~spikeinterface.sortingcomponents.peak_detection.detect_peaks`
       * :py:func:`~spikeinterface.sortingcomponents.peak_selection.select_peaks`
       * :py:func:`~spikeinterface.sortingcomponents.peak_localization.localize_peaks`
-      * :py:func:`~spikeinterface.sortingcomponents.motion_estimation.estimate_motion`
-      * :py:func:`~spikeinterface.sortingcomponents.motion_interpolation.interpolate_motion`
+      * :py:func:`~spikeinterface.sortingcomponents.motion.motion_estimation.estimate_motion`
+      * :py:func:`~spikeinterface.sortingcomponents.motion.motion_interpolation.interpolate_motion`
 
 
     Possible presets : {}
@@ -286,8 +282,7 @@ def correct_motion(
     from spikeinterface.sortingcomponents.peak_detection import detect_peaks, detect_peak_methods
     from spikeinterface.sortingcomponents.peak_selection import select_peaks
     from spikeinterface.sortingcomponents.peak_localization import localize_peaks, localize_peak_methods
-    from spikeinterface.sortingcomponents.motion_estimation import estimate_motion
-    from spikeinterface.sortingcomponents.motion_interpolation import InterpolateMotionRecording
+    from spikeinterface.sortingcomponents.motion import estimate_motion, InterpolateMotionRecording
     from spikeinterface.core.node_pipeline import ExtractDenseWaveforms, run_node_pipeline
 
     # get preset params and update if necessary
@@ -431,7 +426,7 @@ def save_motion_info(motion_info, folder, overwrite=False):
 
 
 def load_motion_info(folder):
-    from spikeinterface.sortingcomponents.motion_utils import Motion
+    from spikeinterface.sortingcomponents.motion import Motion
 
     folder = Path(folder)
 

src/spikeinterface/sortingcomponents/benchmark/benchmark_motion_estimation.py

@@ -9,13 +9,13 @@
 
 from spikeinterface.core import get_noise_levels
 from spikeinterface.sortingcomponents.benchmark.benchmark_tools import Benchmark, BenchmarkStudy, _simpleaxis
-from spikeinterface.sortingcomponents.motion_estimation import estimate_motion
+from spikeinterface.sortingcomponents.motion import estimate_motion
 from spikeinterface.sortingcomponents.peak_detection import detect_peaks
 from spikeinterface.sortingcomponents.peak_selection import select_peaks
 from spikeinterface.sortingcomponents.peak_localization import localize_peaks
 from spikeinterface.widgets import plot_probe_map
 
-from spikeinterface.sortingcomponents.motion_utils import Motion
+from spikeinterface.sortingcomponents.motion import Motion
 
 # import MEArec as mr
 

src/spikeinterface/sortingcomponents/benchmark/benchmark_motion_interpolation.py

@@ -6,7 +6,7 @@
 from spikeinterface.sorters import run_sorter
 
 from spikeinterface.comparison import GroundTruthComparison
-from spikeinterface.sortingcomponents.motion_interpolation import InterpolateMotionRecording
+from spikeinterface.sortingcomponents.motion.motion_interpolation import InterpolateMotionRecording
 from spikeinterface.curation import MergeUnitsSorting
 
 

src/spikeinterface/sortingcomponents/benchmark/benchmark_tools.py

@@ -443,7 +443,7 @@ def load_folder(cls, folder):
 
                 result[k] = load_extractor(folder / k)
             elif format == "Motion":
-                from spikeinterface.sortingcomponents.motion_utils import Motion
+                from spikeinterface.sortingcomponents.motion import Motion
 
                 result[k] = Motion.load(folder / k)
             elif format == "zarr_templates":

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

@@ -41,11 +41,11 @@ def test_benchmark_motion_estimaton(create_cache_folder):
                 localize_kwargs=dict(method=loc_method),
                 estimate_motion_kwargs=dict(
                     method=est_method,
-                    bin_duration_s=1.0,
+                    bin_s=1.0,
                     bin_um=5.0,
                     rigid=False,
                     win_step_um=50.0,
-                    win_sigma_um=200.0,
+                    win_scale_um=200.0,
                 ),
             ),
         )

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

@@ -56,7 +56,7 @@ def test_benchmark_motion_interpolation(create_cache_folder):
     # plt.show()
 
     cases = {}
-    bin_duration_s = 1.0
+    bin_s = 1.0
 
     cases["static_SC2"] = dict(
         label="No drift - no correction - SC2",

src/spikeinterface/sortingcomponents/motion/__init__.py

@@ -0,0 +1,5 @@
+from .motion_utils import Motion
+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