Merge branch 'main' into import-cleanup-again

Author: h-mayorquin

doc/how_to/handle_drift.rst

@@ -1455,38 +1455,32 @@ Plot the results
 We load back the results and use the widgets module to explore the
 estimated drift motion.
 
-For all methods we have 4 plots: \* top left: time vs estimated peak
-depth \* top right: time vs peak depth after motion correction \* bottom
-left: the average motion vector across depths and all motion across
-spatial depths (for non-rigid estimation) \* bottom right: if motion
-correction is non rigid, the motion vector across depths is plotted as a
-map, with the color code representing the motion in micrometers.
-
-A few comments on the figures: \* the preset **‘rigid_fast’** has only
-one motion vector for the entire probe because it is a “rigid” case. The
-motion amplitude is globally underestimated because it averages across
-depths. However, the corrected peaks are flatter than the non-corrected
-ones, so the job is partially done. The big jump at=600s when the probe
-start moving is recovered quite well. \* The preset **kilosort_like**
-gives better results because it is a non-rigid case. The motion vector
-is computed for different depths. The corrected peak locations are
-flatter than the rigid case. The motion vector map is still be a bit
-noisy at some depths (e.g around 1000um). \* The preset **dredge** is
-offcial DREDge re-implementation in spikeinterface. It give the best
-result : very fast and smooth motion estimation. Very few noise. This
-method also capture very well the non rigid motion gradient along the
-probe. The best method on the market at the moement. An enormous thanks
-to the dream team : Charlie Windolf, Julien Boussard, Erdem Varol, Liam
-Paninski. Note that in the first part of the recording before the
-imposed motion (0-600s) we clearly have a non-rigid motion: the upper
-part of the probe (2000-3000um) experience some drifts, but the lower
-part (0-1000um) is relatively stable. The method defined by this preset
-is able to capture this. \* The preset **nonrigid_accurate** this is the
-ancestor of “dredge” before it was published. It seems to give the good
-results on this recording but with bit more noise. \* The preset
-**dredge_fast** similar than dredge but faster (using grid_convolution).
-\* The preset **nonrigid_fast_and_accurate** a variant of
-nonrigid_accurate but faster (using grid_convolution).
+For all methods we have 4 plots:
+    * top left: time vs estimated peak
+    * top right: time vs peak depth after motion correction
+    * bottom left: the average motion vector across depths and all motion across spatial depths (for non-rigid estimation)
+    * bottom right: if motion correction is non rigid, the motion vector across depths is plotted as a map,
+      with the color code representing the motion in micrometers.
+
+A few comments on the figures:
+    * the preset **‘rigid_fast’** has only one motion vector for the entire probe because it is a “rigid” case. The
+      motion amplitude is globally underestimated because it averages across depths. However, the corrected peaks
+      are flatter than the non-corrected ones, so the job is partially done. The big jump at=600s when the probe start
+      moving is recovered quite well.
+    * The preset **kilosort_like** gives better results because it is a non-rigid case. The motion vector is computed
+      for different depths. The corrected peak locations are flatter than the rigid case. The motion vector map is still
+      be a bit noisy at some depths (e.g around 1000um).
+    * The preset **dredge** is official DREDge re-implementation in spikeinterface. It give the best result : very fast
+      and smooth motion estimation. Very few noise. This method also capture very well the non rigid motion gradient along
+      the probe. The best method on the market at the moement. An enormous thanks to the dream team : Charlie Windolf,
+      Julien Boussard, Erdem Varol, Liam Paninski. Note that in the first part of the recording before the imposed motion
+      (0-600s) we clearly have a non-rigid motion: the upper part of the probe (2000-3000um) experience some drifts, but the
+      lower part (0-1000um) is relatively stable. The method defined by this preset is able to capture this.
+    * The preset **nonrigid_accurate** this is the ancestor of “dredge” before it was published. It seems to give good results
+      on this recording but with bit more noise.
+    * The preset **dredge_fast** similar than dredge but faster (using grid_convolution).
+    * The preset **nonrigid_fast_and_accurate** a variant of
+      nonrigid_accurate but faster (using grid_convolution).
 
 .. code:: ipython3
 

examples/how_to/handle_drift.py

@@ -133,32 +133,33 @@ def preprocess_chain(rec):
 # We load back the results and use the widgets module to explore the estimated drift motion.
 #
 # For all methods we have 4 plots:
+#
 #   * top left: time vs estimated peak depth
 #   * top right: time vs peak depth after motion correction
 #   * bottom left: the average motion vector across depths and all motion across spatial depths (for non-rigid estimation)
 #   * bottom right: if motion correction is non rigid, the motion vector across depths is plotted as a map, with the color code representing the motion in micrometers.
 #
 # A few comments on the figures:
-# * the preset **'rigid_fast'** has only one motion vector for the entire probe because it is a "rigid" case.
-#   The motion amplitude is globally underestimated because it averages across depths.
-#   However, the corrected peaks are flatter than the non-corrected ones, so the job is partially done.
-#   The big jump at=600s when the probe start moving is recovered quite well.
-# * The preset **kilosort_like** gives better results because it is a non-rigid case.
-#   The motion vector is computed for different depths.
-#   The corrected peak locations are flatter than the rigid case.
-#   The motion vector map is still be a bit noisy at some depths (e.g around 1000um).
-# * The preset **dredge** is offcial DREDge re-implementation in spikeinterface.
-#   It give the best result : very fast and smooth motion estimation. Very few noise.
-#   This method also capture very well the non rigid motion gradient along the probe.
-#   The best method on the market at the moement.
-#   An enormous thanks to the dream team :  Charlie Windolf, Julien Boussard, Erdem Varol, Liam Paninski.
-#   Note that in the first part of the recording before the imposed motion (0-600s) we clearly have a non-rigid motion:
-#   the upper part of the probe (2000-3000um) experience some drifts, but the lower part (0-1000um) is relatively stable.
-#   The method defined by this preset is able to capture this.
-# * The preset **nonrigid_accurate** this is the ancestor of "dredge" before it was published.
-#   It seems to give the good results on this recording but with bit more noise.
-# * The preset **dredge_fast** similar than dredge but faster (using grid_convolution).
-# * The preset **nonrigid_fast_and_accurate** a variant of nonrigid_accurate but faster (using grid_convolution).
+#   * the preset **'rigid_fast'** has only one motion vector for the entire probe because it is a "rigid" case.
+#     The motion amplitude is globally underestimated because it averages across depths.
+#     However, the corrected peaks are flatter than the non-corrected ones, so the job is partially done.
+#     The big jump at=600s when the probe start moving is recovered quite well.
+#   * The preset **kilosort_like** gives better results because it is a non-rigid case.
+#     The motion vector is computed for different depths.
+#     The corrected peak locations are flatter than the rigid case.
+#     The motion vector map is still be a bit noisy at some depths (e.g around 1000um).
+#   * The preset **dredge** is offcial DREDge re-implementation in spikeinterface.
+#     It give the best result : very fast and smooth motion estimation. Very few noise.
+#     This method also capture very well the non rigid motion gradient along the probe.
+#     The best method on the market at the moement.
+#     An enormous thanks to the dream team :  Charlie Windolf, Julien Boussard, Erdem Varol, Liam Paninski.
+#     Note that in the first part of the recording before the imposed motion (0-600s) we clearly have a non-rigid motion:
+#     the upper part of the probe (2000-3000um) experience some drifts, but the lower part (0-1000um) is relatively stable.
+#     The method defined by this preset is able to capture this.
+#   * The preset **nonrigid_accurate** this is the ancestor of "dredge" before it was published.
+#     It seems to give the good results on this recording but with bit more noise.
+#   * The preset **dredge_fast** similar than dredge but faster (using grid_convolution).
+#   * The preset **nonrigid_fast_and_accurate** a variant of nonrigid_accurate but faster (using grid_convolution).
 #
 #
 
@@ -205,6 +206,7 @@ def preprocess_chain(rec):
 # We can see here that some clusters seem to be more compact on the 'y' axis, especially for the preset "nonrigid_accurate".
 #
 # Be aware that there are two ways to correct for the motion:
+#
 #   1. Interpolate traces and detect/localize peaks again  (`interpolate_recording()`)
 #   2. Compensate for drifts directly on peak locations (`correct_motion_on_peaks()`)
 #

src/spikeinterface/extractors/neoextractors/spikeglx.py

@@ -75,13 +75,18 @@ def __init__(
 
         self._kwargs.update(dict(folder_path=str(Path(folder_path).absolute()), load_sync_channel=load_sync_channel))
 
+        stream_is_nidq_or_sync = "nidq" in self.stream_id or "SYNC" in self.stream_id
+        if stream_is_nidq_or_sync:
+            # Do not add probe information for the sync or nidq stream. Early return
+            return None
+
         # Checks if the probe information is available and adds location, shanks and sample shift if available.
         signals_info_dict = {e["stream_name"]: e for e in self.neo_reader.signals_info_list}
         meta_filename = signals_info_dict[self.stream_id]["meta_file"]
+
         ap_meta_filename = meta_filename.replace(".lf", ".ap") if "lf" in self.stream_id else meta_filename
         ap_meta_file_exists = Path(ap_meta_filename).exists()
-        stream_is_not_nidq = "nidq" not in self.stream_id
-        add_probe_properties = ap_meta_file_exists and stream_is_not_nidq and not load_sync_channel
+        add_probe_properties = ap_meta_file_exists and not load_sync_channel
 
         if add_probe_properties:
             probe = probeinterface.read_spikeglx(ap_meta_filename)

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -101,9 +101,9 @@ class SpikeGLXRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     downloads = ["spikeglx"]
     entities = [
         ("spikeglx/Noise4Sam_g0", {"stream_id": "imec0.ap"}),
-        ("spikeglx/Noise4Sam_g0", {"stream_id": "imec0.ap", "load_sync_channel": True}),
         ("spikeglx/Noise4Sam_g0", {"stream_id": "imec0.lf"}),
         ("spikeglx/Noise4Sam_g0", {"stream_id": "nidq"}),
+        ("spikeglx/Noise4Sam_g0", {"stream_id": "imec0.ap-SYNC"}),
     ]