Merge branch 'main' of https://github.com/cwindolf/spike-psvae

src/dartsort/__init__.py

@@ -1,9 +1,12 @@
+from . import vis
 from .config import *
 from .localize.localize_util import (localize_amplitude_vectors, localize_hdf5,
                                      localize_waveforms)
-from .main import (DARTsortSorting, ObjectiveUpdateTemplateMatchingPeeler,
-                   SubtractionPeeler, check_recording, cluster, dartsort,
-                   match, run_peeler, split_merge, subtract)
+from .main import (ObjectiveUpdateTemplateMatchingPeeler, SubtractionPeeler,
+                   check_recording, cluster, dartsort, match, run_peeler,
+                   split_merge, subtract)
 from .peel.grab import GrabAndFeaturize
+from .templates import TemplateData
 from .transform import WaveformPipeline
+from .util.data_util import DARTsortSorting
 from .util.waveform_util import make_channel_index

src/dartsort/config.py

@@ -123,6 +123,28 @@ class SubtractionConfig:
     )
 
 
+@dataclass(frozen=True)
+class MotionEstimationConfig:
+    """Configure motion estimation.
+
+    You can also make your own and pass it to dartsort() to bypass this
+    """
+    do_motion_estimation: bool = True
+
+    # sometimes spikes can be localized far away from the probe, causing
+    # issues with motion estimation, we will ignore such spikes
+    probe_boundary_padding_um: float = 100.0
+
+    # DREDge parameters
+    spatial_bin_length_um: float = 1.0
+    temporal_bin_length_s: float = 1.0
+    window_step_um: float = 400.0
+    window_scale_um: float = 450.0
+    window_margin_um: Optional[float] = None
+    max_dt_s: float = 0.1
+    max_disp_um: Optional[float] = None
+
+
 @dataclass(frozen=True)
 class TemplateConfig:
     trough_offset_samples: int = 42
@@ -189,7 +211,7 @@ class ClusteringConfig:
     log_c: float = 5.0
     recursive: bool = False
     remove_duplicates: bool = True
-    #remove large clusters in hdbscan?
+    # remove large clusters in hdbscan?
     remove_big_units: bool = True
     zstd_big_units: float = 50.0
 

src/dartsort/main.py

@@ -12,7 +12,7 @@
 from dartsort.peel import (ObjectiveUpdateTemplateMatchingPeeler,
                            SubtractionPeeler)
 from dartsort.templates import TemplateData
-from dartsort.util.data_util import DARTsortSorting, check_recording
+from dartsort.util.data_util import check_recording
 from dartsort.util.peel_util import run_peeler
 
 

src/dartsort/util/registration_util.py

@@ -0,0 +1,14 @@
+try:
+    from dredge import dredge_ap
+    have_dredge = True
+except ImportError:
+    have_dredge = False
+    pass
+
+
+def estimate_motion(recording, sorting, motion_estimation_config=None, localizations_dataset_name="point_source_localizations"):
+    if not motion_estimation_config.do_motion_estimation:
+        return None
+
+    if not have_dredge:
+        raise ValueError("Please install DREDge to use motion estimation.")

tests/test_grab_and_featurize.py

@@ -229,7 +229,7 @@ def test_grab_and_featurize():
         localize_hdf5(
             Path(tempdir) / "grab.h5",
             radius=50.0,
-            amplitude_vectors_dataset_name="amplitude_vectors",
+            amplitude_vectors_dataset_name="peak_amplitude_vectors",
         )
 
         with h5py.File(Path(tempdir) / "grab.h5") as h5:

tests/test_subtract.py

@@ -250,11 +250,12 @@ def test_fakedata_nonn():
             subconf.subtraction_denoising_config, do_tpca_denoise=False
         ),
     )
+    nolocfeatconf = dataclasses.replace(featconf, do_localization=False)
     with tempfile.TemporaryDirectory() as tempdir:
         st0, out_h5 = subtract(
             rec,
             tempdir,
-            featurization_config=dataclasses.replace(featconf, do_localization=False),
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         ns0 = len(st0)
@@ -263,13 +264,13 @@ def test_fakedata_nonn():
         sta, out_h5 = subtract(
             rec.frame_slice(start_frame=0, end_frame=int(20 * fs)),
             tempdir,
-            featurization_config=dataclasses.replace(featconf, do_localization=False),
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         stb, out_h5 = subtract(
             rec,
             tempdir,
-            featurization_config=featconf,
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         assert len(sta) < ns0
@@ -279,13 +280,13 @@ def test_fakedata_nonn():
         sta, out_h5 = subtract(
             rec.frame_slice(start_frame=0, end_frame=int(25 * fs)),
             tempdir,
-            featurization_config=dataclasses.replace(featconf, do_localization=False),
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         stb, out_h5 = subtract(
             rec,
             tempdir,
-            featurization_config=featconf,
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         assert len(sta) < ns0
@@ -295,13 +296,13 @@ def test_fakedata_nonn():
         sta, out_h5 = subtract(
             rec.frame_slice(start_frame=0, end_frame=int(30 * fs)),
             tempdir,
-            featurization_config=dataclasses.replace(featconf, do_localization=False),
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         stb, out_h5 = subtract(
             rec,
             tempdir,
-            featurization_config=featconf,
+            featurization_config=nolocfeatconf,
             subtraction_config=subconf,
         )
         assert len(sta) < ns0