From 507b6b3cf19d0f10069e2415f134dca7fb709b47 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Sun, 3 Nov 2024 19:16:26 -0500
Subject: [PATCH 01/45] Address time bin issue arising in LFP-based reg, which
 AP-based reg doesn't trigger

---
 .../motion/motion_interpolation.py              | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index a5e6ded519..975f43919d 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -3,7 +3,8 @@
 import numpy as np
 from spikeinterface.core.core_tools import define_function_from_class
 from spikeinterface.preprocessing import get_spatial_interpolation_kernel
-from spikeinterface.preprocessing.basepreprocessor import BasePreprocessor, BasePreprocessorSegment
+from spikeinterface.preprocessing.basepreprocessor import (
+    BasePreprocessor, BasePreprocessorSegment)
 from spikeinterface.preprocessing.filter import fix_dtype
 
 
@@ -122,14 +123,18 @@ def interpolate_motion_on_traces(
     time_bins = interpolation_time_bin_centers_s
     if time_bins is None:
         time_bins = motion.temporal_bins_s[segment_index]
+
+    # nearest interpolation bin:
+    # seachsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
+    # hence the -1. doing it with "left" is not as nice.
+    # time_bins are bin centers, so subtract half the bin length. this leads
+    # to snapping to the nearest bin center.
     bin_s = time_bins[1] - time_bins[0]
-    bins_start = time_bins[0] - 0.5 * bin_s
-    # nearest bin center for each frame?
-    bin_inds = (times - bins_start) // bin_s
-    bin_inds = bin_inds.astype(int)
+    bin_inds = np.searchsorted(time_bins - bin_s / 2, times, side="right") - 1
+
     # the time bins may not cover the whole set of times in the recording,
     # so we need to clip these indices to the valid range
-    np.clip(bin_inds, 0, time_bins.size, out=bin_inds)
+    np.clip(bin_inds, 0, time_bins.size - 1, out=bin_inds)
 
     # -- what are the possibilities here anyway?
     bins_here = np.arange(bin_inds[0], bin_inds[-1] + 1)

From 4e38ac18be65051d30d15f3d25bada943af3e31f Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Mon, 4 Nov 2024 11:06:46 -0500
Subject: [PATCH 02/45] Fix LFP-based AP interp bug and allow time_vector in
 interpolation

---
 .../motion/motion_interpolation.py            | 18 +++--
 .../motion/tests/test_motion_interpolation.py | 78 ++++++++++++++++---
 2 files changed, 77 insertions(+), 19 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 975f43919d..4fd42a8b39 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -126,11 +126,16 @@ def interpolate_motion_on_traces(
 
     # nearest interpolation bin:
     # seachsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
-    # hence the -1. doing it with "left" is not as nice.
-    # time_bins are bin centers, so subtract half the bin length. this leads
-    # to snapping to the nearest bin center.
-    bin_s = time_bins[1] - time_bins[0]
-    bin_inds = np.searchsorted(time_bins - bin_s / 2, times, side="right") - 1
+    # hence the -1. doing it with "left" is not as nice -- we want t==b[0]
+    # to lead to i=1 (rounding down).
+    # time_bins are bin centers, but we want to snap to the nearest center.
+    # idea is to get the left bin edges and bin the interp times.
+    # this is like subtracting bin_dt_s/2, but allows non-equally-spaced bins.
+    bin_left = np.zeros_like(time_bins)
+    # it's fine to use the first bin center for the first left edge
+    bin_left[0] = time_bins[0]
+    bin_left[1:] = 0.5 * (time_bins[1:] + time_bins[:-1])
+    bin_inds = np.searchsorted(bin_left, times, side="right") - 1
 
     # the time bins may not cover the whole set of times in the recording,
     # so we need to clip these indices to the valid range
@@ -438,9 +443,6 @@ def __init__(
         self.motion = motion
 
     def get_traces(self, start_frame, end_frame, channel_indices):
-        if self.time_vector is not None:
-            raise NotImplementedError("InterpolateMotionRecording does not yet support recordings with time_vectors.")
-
         if start_frame is None:
             start_frame = 0
         if end_frame is None:
diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
index e022f0cc6c..69f681a1be 100644
--- a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
@@ -1,16 +1,11 @@
-from pathlib import Path
+import warnings
 
 import numpy as np
-import pytest
 import spikeinterface.core as sc
-from spikeinterface import download_dataset
-from spikeinterface.sortingcomponents.motion.motion_interpolation import (
-    InterpolateMotionRecording,
-    correct_motion_on_peaks,
-    interpolate_motion,
-    interpolate_motion_on_traces,
-)
 from spikeinterface.sortingcomponents.motion import Motion
+from spikeinterface.sortingcomponents.motion.motion_interpolation import (
+    InterpolateMotionRecording, correct_motion_on_peaks, interpolate_motion,
+    interpolate_motion_on_traces)
 from spikeinterface.sortingcomponents.tests.common import make_dataset
 
 
@@ -115,6 +110,66 @@ def test_interpolation_simple():
     assert np.all(traces_corrected[:, 2:] == 0)
 
 
+def test_cross_band_interpolation():
+    """Simple version of using LFP to interpolate AP data
+
+    This also tests the time vector implementation in interpolation.
+    The idea is to have two recordings which are all 0s with a 1 that
+    moves from one channel to another after 3s. They're at different
+    sampling frequencies. motion estimation in one sampling frequency
+    applied to the other should still lead to perfect correction.
+    """
+    from spikeinterface.sortingcomponents.motion import estimate_motion
+
+    # sampling freqs and timing for AP and LFP recordings
+    fs_lfp = 50.0
+    fs_ap = 300.0
+    t_start = 10.0
+    total_duration = 5.0
+    nt_lfp = int(fs_lfp * total_duration)
+    nt_ap = int(fs_ap * total_duration)
+    t_switch = 3
+
+    # because interpolation uses bin centers logic, there will be a half
+    # bin offset at the change point in the AP recording.
+    halfbin_ap_lfp = int(0.5 * (fs_ap / fs_lfp))
+
+    # channel geometry
+    nc = 10
+    geom = np.c_[np.zeros(nc), np.arange(nc)]
+
+    # make an LFP recording which drifts a bit
+    traces_lfp = np.zeros((nt_lfp, nc))
+    traces_lfp[: int(t_switch * fs_lfp), 5] = 1.0
+    traces_lfp[int(t_switch * fs_lfp) :, 6] = 1.0
+    rec_lfp = sc.NumpyRecording(traces_lfp, sampling_frequency=fs_lfp)
+    rec_lfp.set_dummy_probe_from_locations(geom)
+
+    # same for AP
+    traces_ap = np.zeros((nt_ap, nc))
+    traces_ap[: int(t_switch * fs_ap) - halfbin_ap_lfp, 5] = 1.0
+    traces_ap[int(t_switch * fs_ap) - halfbin_ap_lfp :, 6] = 1.0
+    rec_ap = sc.NumpyRecording(traces_ap, sampling_frequency=fs_ap)
+    rec_ap.set_dummy_probe_from_locations(geom)
+
+    # set times for both, and silence the warning
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=UserWarning)
+        rec_lfp.set_times(t_start + np.arange(nt_lfp) / fs_lfp)
+        rec_ap.set_times(t_start + np.arange(nt_ap) / fs_ap)
+
+    # estimate motion
+    motion = estimate_motion(rec_lfp, method="dredge_lfp", rigid=True)
+
+    # nearest to keep it simple
+    rec_corrected = interpolate_motion(rec_ap, motion, spatial_interpolation_method="nearest", num_closest=2)
+    traces_corrected = rec_corrected.get_traces()
+    target = np.zeros((nt_ap, nc - 2))
+    target[:, 4] = 1
+    ii, jj = np.nonzero(traces_corrected)
+    assert np.array_equal(traces_corrected, target)
+
+
 def test_InterpolateMotionRecording():
     rec, sorting = make_dataset()
     motion = make_fake_motion(rec)
@@ -148,5 +203,6 @@ def test_InterpolateMotionRecording():
 if __name__ == "__main__":
     # test_correct_motion_on_peaks()
     # test_interpolate_motion_on_traces()
-    test_interpolation_simple()
-    test_InterpolateMotionRecording()
+    # test_interpolation_simple()
+    # test_InterpolateMotionRecording()
+    test_cross_band_interpolation()

From 726170b1526b954b5a26edd70d3162e476ed9f53 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 16:28:44 +0000
Subject: [PATCH 03/45] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../sortingcomponents/motion/motion_interpolation.py       | 3 +--
 .../motion/tests/test_motion_interpolation.py              | 7 +++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 4fd42a8b39..810264d9e4 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -3,8 +3,7 @@
 import numpy as np
 from spikeinterface.core.core_tools import define_function_from_class
 from spikeinterface.preprocessing import get_spatial_interpolation_kernel
-from spikeinterface.preprocessing.basepreprocessor import (
-    BasePreprocessor, BasePreprocessorSegment)
+from spikeinterface.preprocessing.basepreprocessor import BasePreprocessor, BasePreprocessorSegment
 from spikeinterface.preprocessing.filter import fix_dtype
 
 
diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
index 69f681a1be..88af619220 100644
--- a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
@@ -4,8 +4,11 @@
 import spikeinterface.core as sc
 from spikeinterface.sortingcomponents.motion import Motion
 from spikeinterface.sortingcomponents.motion.motion_interpolation import (
-    InterpolateMotionRecording, correct_motion_on_peaks, interpolate_motion,
-    interpolate_motion_on_traces)
+    InterpolateMotionRecording,
+    correct_motion_on_peaks,
+    interpolate_motion,
+    interpolate_motion_on_traces,
+)
 from spikeinterface.sortingcomponents.tests.common import make_dataset
 
 

From e791fe18671c2998fde9d44295c54a5781ca2e46 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Mon, 11 Nov 2024 10:43:48 -0500
Subject: [PATCH 04/45] Cache bin edges in 2 places as discussed with Sam

---
 .../motion/motion_interpolation.py            | 39 +++++++++++++------
 .../sortingcomponents/motion/motion_utils.py  | 24 +++++++++++-
 .../motion/tests/test_motion_interpolation.py | 28 ++++++-------
 3 files changed, 66 insertions(+), 25 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 4fd42a8b39..89696f5041 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -7,6 +7,8 @@
     BasePreprocessor, BasePreprocessorSegment)
 from spikeinterface.preprocessing.filter import fix_dtype
 
+from .motion_utils import ensure_time_bin_edges, ensure_time_bins
+
 
 def correct_motion_on_peaks(peaks, peak_locations, motion, recording) -> np.ndarray:
     """
@@ -55,6 +57,7 @@ def interpolate_motion_on_traces(
     segment_index=None,
     channel_inds=None,
     interpolation_time_bin_centers_s=None,
+    interpolation_time_bin_edges_s=None,
     spatial_interpolation_method="kriging",
     spatial_interpolation_kwargs={},
     dtype=None,
@@ -120,9 +123,11 @@ def interpolate_motion_on_traces(
     total_num_chans = channel_locations.shape[0]
 
     # -- determine the blocks of frames that will land in the same interpolation time bin
-    time_bins = interpolation_time_bin_centers_s
-    if time_bins is None:
-        time_bins = motion.temporal_bins_s[segment_index]
+    if interpolation_time_bin_centers_s is None and interpolation_time_bin_edges_s is None:
+        bin_centers_s = motion.temporal_bin_edges_s[segment_index]
+        bin_edges_s = motion.temporal_bin_edges_s[segment_index]
+    else:
+        bin_centers_s, bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
 
     # nearest interpolation bin:
     # seachsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
@@ -131,15 +136,13 @@ def interpolate_motion_on_traces(
     # time_bins are bin centers, but we want to snap to the nearest center.
     # idea is to get the left bin edges and bin the interp times.
     # this is like subtracting bin_dt_s/2, but allows non-equally-spaced bins.
-    bin_left = np.zeros_like(time_bins)
     # it's fine to use the first bin center for the first left edge
-    bin_left[0] = time_bins[0]
-    bin_left[1:] = 0.5 * (time_bins[1:] + time_bins[:-1])
-    bin_inds = np.searchsorted(bin_left, times, side="right") - 1
+    bin_inds = np.searchsorted(bin_edges_s, times, side="right") - 1
 
     # the time bins may not cover the whole set of times in the recording,
     # so we need to clip these indices to the valid range
-    np.clip(bin_inds, 0, time_bins.size - 1, out=bin_inds)
+    n_bins = bin_edges_s.shape[0] - 1
+    np.clip(bin_inds, 0, n_bins - 1, out=bin_inds)
 
     # -- what are the possibilities here anyway?
     bins_here = np.arange(bin_inds[0], bin_inds[-1] + 1)
@@ -148,7 +151,7 @@ def interpolate_motion_on_traces(
     interp_times = np.empty(total_num_chans)
     current_start_index = 0
     for bin_ind in bins_here:
-        bin_time = time_bins[bin_ind]
+        bin_time = bin_centers_s[bin_ind]
         interp_times.fill(bin_time)
         channel_motions = motion.get_displacement_at_time_and_depth(
             interp_times,
@@ -307,6 +310,7 @@ def __init__(
         p=1,
         num_closest=3,
         interpolation_time_bin_centers_s=None,
+        interpolation_time_bin_edges_s=None,
         interpolation_time_bin_size_s=None,
         dtype=None,
         **spatial_interpolation_kwargs,
@@ -373,9 +377,14 @@ def __init__(
 
         # handle manual interpolation_time_bin_centers_s
         # the case where interpolation_time_bin_size_s is set is handled per-segment below
-        if interpolation_time_bin_centers_s is None:
+        if interpolation_time_bin_centers_s is None and interpolation_time_bin_edges_s is None:
             if interpolation_time_bin_size_s is None:
                 interpolation_time_bin_centers_s = motion.temporal_bins_s
+                interpolation_time_bin_edges_s = motion.temporal_bin_edges_s
+        else:
+            interpolation_time_bin_centers_s, interpolation_time_bin_edges_s = ensure_time_bins(
+                interpolation_time_bin_centers_s, interpolation_time_bin_edges_s
+            )
 
         for segment_index, parent_segment in enumerate(recording._recording_segments):
             # finish the per-segment part of the time bin logic
@@ -385,8 +394,13 @@ def __init__(
                 t_start, t_end = parent_segment.sample_index_to_time(np.array([0, s_end]))
                 halfbin = interpolation_time_bin_size_s / 2.0
                 segment_interpolation_time_bins_s = np.arange(t_start + halfbin, t_end, interpolation_time_bin_size_s)
+                segment_interpolation_time_bin_edges_s = np.arange(
+                    t_start, t_end + halfbin, interpolation_time_bin_size_s
+                )
+                assert segment_interpolation_time_bin_edges_s.shape == (segment_interpolation_time_bins_s.shape[0] + 1,)
             else:
                 segment_interpolation_time_bins_s = interpolation_time_bin_centers_s[segment_index]
+                segment_interpolation_time_bin_edges_s = interpolation_time_bin_edges_s[segment_index]
 
             rec_segment = InterpolateMotionRecordingSegment(
                 parent_segment,
@@ -397,6 +411,7 @@ def __init__(
                 channel_inds,
                 segment_index,
                 segment_interpolation_time_bins_s,
+                segment_interpolation_time_bin_edges_s,
                 dtype=dtype_,
             )
             self.add_recording_segment(rec_segment)
@@ -430,6 +445,7 @@ def __init__(
         channel_inds,
         segment_index,
         interpolation_time_bin_centers_s,
+        interpolation_time_bin_edges_s,
         dtype="float32",
     ):
         BasePreprocessorSegment.__init__(self, parent_recording_segment)
@@ -439,6 +455,7 @@ def __init__(
         self.channel_inds = channel_inds
         self.segment_index = segment_index
         self.interpolation_time_bin_centers_s = interpolation_time_bin_centers_s
+        self.interpolation_time_bin_edges_s = interpolation_time_bin_edges_s
         self.dtype = dtype
         self.motion = motion
 
@@ -460,7 +477,7 @@ def get_traces(self, start_frame, end_frame, channel_indices):
             channel_inds=self.channel_inds,
             spatial_interpolation_method=self.spatial_interpolation_method,
             spatial_interpolation_kwargs=self.spatial_interpolation_kwargs,
-            interpolation_time_bin_centers_s=self.interpolation_time_bin_centers_s,
+            interpolation_time_bin_edges_s=self.interpolation_time_bin_edges_s,
         )
 
         if channel_indices is not None:
diff --git a/src/spikeinterface/sortingcomponents/motion/motion_utils.py b/src/spikeinterface/sortingcomponents/motion/motion_utils.py
index 635624cca8..ec0a55a8f8 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_utils.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_utils.py
@@ -1,5 +1,5 @@
-import warnings
 import json
+import warnings
 from pathlib import Path
 
 import numpy as np
@@ -54,6 +54,7 @@ def __init__(self, displacement, temporal_bins_s, spatial_bins_um, direction="y"
         self.direction = direction
         self.dim = ["x", "y", "z"].index(direction)
         self.check_properties()
+        self.temporal_bin_edges_s = [ensure_time_bin_edges(tbins) for tbins in self.temporal_bins_s]
 
     def check_properties(self):
         assert all(d.ndim == 2 for d in self.displacement)
@@ -576,3 +577,24 @@ def make_3d_motion_histograms(
         motion_histograms = np.log2(1 + motion_histograms)
 
     return motion_histograms, temporal_bin_edges, spatial_bin_edges
+
+
+def ensure_time_bins(time_bin_centers_s=None, time_bin_edges_s=None):
+    if time_bin_centers_s is None and time_bin_edges_s is None:
+        raise ValueError("Need at least one of time_bin_centers_s or time_bin_edges_s.")
+
+    if time_bin_centers_s is None:
+        assert time_bin_edges_s.ndim == 1 and time_bin_edges_s.size >= 2
+        time_bin_centers_s = 0.5 * (time_bin_edges_s[1:] + time_bin_edges_s[:-1])
+
+    if time_bin_edges_s is None:
+        time_bin_edges_s = np.empty(time_bin_centers_s.shape[0] + 1, dtype=time_bin_centers_s.dtype)
+        time_bin_edges_s[[0, -1]] = time_bin_centers_s[[0, -1]]
+        if time_bin_centers_s.size > 2:
+            time_bin_edges_s[1:-1] = 0.5 * (time_bin_centers_s[1:] + time_bin_centers_s[:-1])
+
+    return time_bin_centers_s, time_bin_edges_s
+
+
+def ensure_time_bin_edges(time_bin_centers_s=None, time_bin_edges_s=None):
+    return ensure_time_bins(time_bin_centers_s, time_bin_edges_s)[1]
diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
index 69f681a1be..07cb5b8ab6 100644
--- a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
@@ -62,18 +62,20 @@ def test_interpolate_motion_on_traces():
     times = rec.get_times()[0:30000]
 
     for method in ("kriging", "idw", "nearest"):
-        traces_corrected = interpolate_motion_on_traces(
-            traces,
-            times,
-            channel_locations,
-            motion,
-            channel_inds=None,
-            spatial_interpolation_method=method,
-            # spatial_interpolation_kwargs={},
-            spatial_interpolation_kwargs={"force_extrapolate": True},
-        )
-        assert traces.shape == traces_corrected.shape
-        assert traces.dtype == traces_corrected.dtype
+        for interpolation_time_bin_centers_s in (None, np.linspace(*times[[0, -1]], num=3)):
+            traces_corrected = interpolate_motion_on_traces(
+                traces,
+                times,
+                channel_locations,
+                motion,
+                channel_inds=None,
+                spatial_interpolation_method=method,
+                interpolation_time_bin_centers_s=interpolation_time_bin_centers_s,
+                # spatial_interpolation_kwargs={},
+                spatial_interpolation_kwargs={"force_extrapolate": True},
+            )
+            assert traces.shape == traces_corrected.shape
+            assert traces.dtype == traces_corrected.dtype
 
 
 def test_interpolation_simple():
@@ -202,7 +204,7 @@ def test_InterpolateMotionRecording():
 
 if __name__ == "__main__":
     # test_correct_motion_on_peaks()
-    # test_interpolate_motion_on_traces()
+    test_interpolate_motion_on_traces()
     # test_interpolation_simple()
     # test_InterpolateMotionRecording()
     test_cross_band_interpolation()

From d8f39b5a70dd83f4e1fff71d41036692fba20b38 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Mon, 11 Nov 2024 12:30:32 -0500
Subject: [PATCH 05/45] Sorry if this is shoe-horning in a change...

---
 src/spikeinterface/core/baserecording.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 5e2e9e4014..b95bfb1ad0 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -1,20 +1,17 @@
 from __future__ import annotations
+
 import warnings
 from pathlib import Path
 
 import numpy as np
-from probeinterface import Probe, ProbeGroup, read_probeinterface, select_axes, write_probeinterface
+from probeinterface import (Probe, ProbeGroup, read_probeinterface,
+                            select_axes, write_probeinterface)
 
 from .base import BaseSegment
 from .baserecordingsnippets import BaseRecordingSnippets
-from .core_tools import (
-    convert_bytes_to_str,
-    convert_seconds_to_str,
-)
-from .recording_tools import write_binary_recording
-
-
+from .core_tools import convert_bytes_to_str, convert_seconds_to_str
 from .job_tools import split_job_kwargs
+from .recording_tools import write_binary_recording
 
 
 class BaseRecording(BaseRecordingSnippets):
@@ -921,11 +918,11 @@ def time_to_sample_index(self, time_s):
                 sample_index = time_s * self.sampling_frequency
             else:
                 sample_index = (time_s - self.t_start) * self.sampling_frequency
-            sample_index = round(sample_index)
+            sample_index = np.round(sample_index).astype(int)
         else:
             sample_index = np.searchsorted(self.time_vector, time_s, side="right") - 1
 
-        return int(sample_index)
+        return sample_index
 
     def get_num_samples(self) -> int:
         """Returns the number of samples in this signal segment

From 0a201e17a0b3de283f06c5456010fb20fd8cd209 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 11 Nov 2024 17:31:00 +0000
Subject: [PATCH 06/45] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/core/baserecording.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index b95bfb1ad0..6d4509db12 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -4,8 +4,7 @@
 from pathlib import Path
 
 import numpy as np
-from probeinterface import (Probe, ProbeGroup, read_probeinterface,
-                            select_axes, write_probeinterface)
+from probeinterface import Probe, ProbeGroup, read_probeinterface, select_axes, write_probeinterface
 
 from .base import BaseSegment
 from .baserecordingsnippets import BaseRecordingSnippets

From 530864bceda4b436f5cf16fd5258efd19ccaa76d Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 09:33:03 +0000
Subject: [PATCH 07/45] Replace qm_params with metric_params

---
 .../qualitymetrics/pca_metrics.py             | 36 ++++++++++++-------
 .../quality_metric_calculator.py              | 30 ++++++++++------
 .../tests/test_metrics_functions.py           | 10 +++---
 3 files changed, 47 insertions(+), 29 deletions(-)

diff --git a/src/spikeinterface/qualitymetrics/pca_metrics.py b/src/spikeinterface/qualitymetrics/pca_metrics.py
index 4c68dfea59..b4952bfe6d 100644
--- a/src/spikeinterface/qualitymetrics/pca_metrics.py
+++ b/src/spikeinterface/qualitymetrics/pca_metrics.py
@@ -6,6 +6,7 @@
 from copy import deepcopy
 import platform
 from tqdm.auto import tqdm
+from warnings import warn
 
 import numpy as np
 
@@ -52,6 +53,7 @@ def get_quality_pca_metric_list():
 def compute_pc_metrics(
     sorting_analyzer,
     metric_names=None,
+    metric_params=None,
     qm_params=None,
     unit_ids=None,
     seed=None,
@@ -70,7 +72,7 @@ def compute_pc_metrics(
     metric_names : list of str, default: None
         The list of PC metrics to compute.
         If not provided, defaults to all PC metrics.
-    qm_params : dict or None
+    metric_params : dict or None
         Dictionary with parameters for each PC metric function.
     unit_ids : list of int or None
         List of unit ids to compute metrics for.
@@ -86,6 +88,14 @@ def compute_pc_metrics(
     pc_metrics : dict
         The computed PC metrics.
     """
+
+    if qm_params is not None and metric_params is None:
+        deprecation_msg = (
+            "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+        )
+        metric_params = qm_params
+        warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
+
     pca_ext = sorting_analyzer.get_extension("principal_components")
     assert pca_ext is not None, "calculate_pc_metrics() need extension 'principal_components'"
 
@@ -93,8 +103,8 @@ def compute_pc_metrics(
 
     if metric_names is None:
         metric_names = _possible_pc_metric_names.copy()
-    if qm_params is None:
-        qm_params = _default_params
+    if metric_params is None:
+        metric_params = _default_params
 
     extremum_channels = get_template_extremum_channel(sorting_analyzer)
 
@@ -147,7 +157,7 @@ def compute_pc_metrics(
         pcs = dense_projections[np.isin(all_labels, neighbor_unit_ids)][:, :, neighbor_channel_indices]
         pcs_flat = pcs.reshape(pcs.shape[0], -1)
 
-        func_args = (pcs_flat, labels, non_nn_metrics, unit_id, unit_ids, qm_params, max_threads_per_process)
+        func_args = (pcs_flat, labels, non_nn_metrics, unit_id, unit_ids, metric_params, max_threads_per_process)
         items.append(func_args)
 
     if not run_in_parallel and non_nn_metrics:
@@ -184,7 +194,7 @@ def compute_pc_metrics(
             units_loop = tqdm(units_loop, desc=f"calculate {metric_name} metric", total=len(unit_ids))
 
         func = _nn_metric_name_to_func[metric_name]
-        metric_params = qm_params[metric_name] if metric_name in qm_params else {}
+        metric_params = metric_params[metric_name] if metric_name in metric_params else {}
 
         for _, unit_id in units_loop:
             try:
@@ -213,7 +223,7 @@ def compute_pc_metrics(
 
 
 def calculate_pc_metrics(
-    sorting_analyzer, metric_names=None, qm_params=None, unit_ids=None, seed=None, n_jobs=1, progress_bar=False
+    sorting_analyzer, metric_names=None, metric_params=None, unit_ids=None, seed=None, n_jobs=1, progress_bar=False
 ):
     warnings.warn(
         "The `calculate_pc_metrics` function is deprecated and will be removed in 0.103.0. Please use compute_pc_metrics instead",
@@ -224,7 +234,7 @@ def calculate_pc_metrics(
     pc_metrics = compute_pc_metrics(
         sorting_analyzer,
         metric_names=metric_names,
-        qm_params=qm_params,
+        metric_params=metric_params,
         unit_ids=unit_ids,
         seed=seed,
         n_jobs=n_jobs,
@@ -977,16 +987,16 @@ def _compute_isolation(pcs_target_unit, pcs_other_unit, n_neighbors: int):
 
 
 def pca_metrics_one_unit(args):
-    (pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params, max_threads_per_process) = args
+    (pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params, max_threads_per_process) = args
 
     if max_threads_per_process is None:
-        return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params)
+        return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params)
     else:
         with threadpool_limits(limits=int(max_threads_per_process)):
-            return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params)
+            return _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params)
 
 
-def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_params):
+def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, metric_params):
     pc_metrics = {}
     # metrics
     if "isolation_distance" in metric_names or "l_ratio" in metric_names:
@@ -1015,7 +1025,7 @@ def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_
     if "nearest_neighbor" in metric_names:
         try:
             nn_hit_rate, nn_miss_rate = nearest_neighbors_metrics(
-                pcs_flat, labels, unit_id, **qm_params["nearest_neighbor"]
+                pcs_flat, labels, unit_id, **metric_params["nearest_neighbor"]
             )
         except:
             nn_hit_rate = np.nan
@@ -1024,7 +1034,7 @@ def _pca_metrics_one_unit(pcs_flat, labels, metric_names, unit_id, unit_ids, qm_
         pc_metrics["nn_miss_rate"] = nn_miss_rate
 
     if "silhouette" in metric_names:
-        silhouette_method = qm_params["silhouette"]["method"]
+        silhouette_method = metric_params["silhouette"]["method"]
         if "simplified" in silhouette_method:
             try:
                 unit_silhouette_score = simplified_silhouette_score(pcs_flat, labels, unit_id)
diff --git a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
index b6a50d60f5..eb380304b6 100644
--- a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
+++ b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
@@ -6,6 +6,7 @@
 from copy import deepcopy
 
 import numpy as np
+from warnings import warn
 
 from spikeinterface.core.job_tools import fix_job_kwargs
 from spikeinterface.core.sortinganalyzer import register_result_extension, AnalyzerExtension
@@ -31,7 +32,7 @@ class ComputeQualityMetrics(AnalyzerExtension):
         A SortingAnalyzer object.
     metric_names : list or None
         List of quality metrics to compute.
-    qm_params : dict or None
+    metric_params : dict or None
         Dictionary with parameters for quality metrics calculation.
         Default parameters can be obtained with: `si.qualitymetrics.get_default_qm_params()`
     skip_pc_metrics : bool, default: False
@@ -58,6 +59,7 @@ class ComputeQualityMetrics(AnalyzerExtension):
     def _set_params(
         self,
         metric_names=None,
+        metric_params=None,
         qm_params=None,
         peak_sign=None,
         seed=None,
@@ -65,6 +67,12 @@ def _set_params(
         delete_existing_metrics=False,
         metrics_to_compute=None,
     ):
+        if qm_params is not None and metric_params is None:
+            deprecation_msg = (
+                "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+            )
+            metric_params = qm_params
+            warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
 
         if metric_names is None:
             metric_names = list(_misc_metric_name_to_func.keys())
@@ -80,12 +88,12 @@ def _set_params(
                 if "drift" in metric_names:
                     metric_names.remove("drift")
 
-        qm_params_ = get_default_qm_params()
-        for k in qm_params_:
-            if qm_params is not None and k in qm_params:
-                qm_params_[k].update(qm_params[k])
-            if "peak_sign" in qm_params_[k] and peak_sign is not None:
-                qm_params_[k]["peak_sign"] = peak_sign
+        metric_params_ = get_default_qm_params()
+        for k in metric_params_:
+            if metric_params is not None and k in metric_params:
+                metric_params_[k].update(metric_params[k])
+            if "peak_sign" in metric_params_[k] and peak_sign is not None:
+                metric_params_[k]["peak_sign"] = peak_sign
 
         metrics_to_compute = metric_names
         qm_extension = self.sorting_analyzer.get_extension("quality_metrics")
@@ -101,7 +109,7 @@ def _set_params(
             metric_names=metric_names,
             peak_sign=peak_sign,
             seed=seed,
-            qm_params=qm_params_,
+            metric_params=metric_params_,
             skip_pc_metrics=skip_pc_metrics,
             delete_existing_metrics=delete_existing_metrics,
             metrics_to_compute=metrics_to_compute,
@@ -141,7 +149,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
         """
         import pandas as pd
 
-        qm_params = self.params["qm_params"]
+        metric_params = self.params["metric_params"]
         # sparsity = self.params["sparsity"]
         seed = self.params["seed"]
 
@@ -177,7 +185,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
 
             func = _misc_metric_name_to_func[metric_name]
 
-            params = qm_params[metric_name] if metric_name in qm_params else {}
+            params = metric_params[metric_name] if metric_name in metric_params else {}
             res = func(sorting_analyzer, unit_ids=non_empty_unit_ids, **params)
             # QM with uninstall dependencies might return None
             if res is not None:
@@ -205,7 +213,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
                 # sparsity=sparsity,
                 progress_bar=progress_bar,
                 n_jobs=n_jobs,
-                qm_params=qm_params,
+                metric_params=metric_params,
                 seed=seed,
             )
             for col, values in pc_metrics.items():
diff --git a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
index 4c0890b62b..20869aa44a 100644
--- a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
+++ b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
@@ -69,7 +69,7 @@ def test_compute_new_quality_metrics(small_sorting_analyzer):
     assert calculated_metrics == ["snr"]
 
     small_sorting_analyzer.compute(
-        {"quality_metrics": {"metric_names": list(qm_params.keys()), "qm_params": qm_params}}
+        {"quality_metrics": {"metric_names": list(qm_params.keys()), "metric_params": qm_params}}
     )
     small_sorting_analyzer.compute({"quality_metrics": {"metric_names": ["snr"]}})
 
@@ -96,13 +96,13 @@ def test_compute_new_quality_metrics(small_sorting_analyzer):
     # check that, when parameters are changed, the data and metadata are updated
     old_snr_data = deepcopy(quality_metric_extension.get_data()["snr"].values)
     small_sorting_analyzer.compute(
-        {"quality_metrics": {"metric_names": ["snr"], "qm_params": {"snr": {"peak_mode": "peak_to_peak"}}}}
+        {"quality_metrics": {"metric_names": ["snr"], "metric_params": {"snr": {"peak_mode": "peak_to_peak"}}}}
     )
     new_quality_metric_extension = small_sorting_analyzer.get_extension("quality_metrics")
     new_snr_data = new_quality_metric_extension.get_data()["snr"].values
 
     assert np.all(old_snr_data != new_snr_data)
-    assert new_quality_metric_extension.params["qm_params"]["snr"]["peak_mode"] == "peak_to_peak"
+    assert new_quality_metric_extension.params["metric_params"]["snr"]["peak_mode"] == "peak_to_peak"
 
     # check that all quality metrics are deleted when parents are recomputed, even after
     # recomputation
@@ -280,10 +280,10 @@ def test_unit_id_order_independence(small_sorting_analyzer):
     }
 
     quality_metrics_1 = compute_quality_metrics(
-        small_sorting_analyzer, metric_names=get_quality_metric_list(), qm_params=qm_params
+        small_sorting_analyzer, metric_names=get_quality_metric_list(), metric_params=qm_params
     )
     quality_metrics_2 = compute_quality_metrics(
-        small_sorting_analyzer_2, metric_names=get_quality_metric_list(), qm_params=qm_params
+        small_sorting_analyzer_2, metric_names=get_quality_metric_list(), metric_params=qm_params
     )
 
     for metric, metric_2_data in quality_metrics_2.items():

From 908318a04731f6e8723a9cf3b34914d8e782e900 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 09:38:28 +0000
Subject: [PATCH 08/45] fix tests

---
 .../tests/test_quality_metric_calculator.py          | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py
index a6415c58e8..60f0490f51 100644
--- a/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py
+++ b/src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py
@@ -24,14 +24,14 @@ def test_compute_quality_metrics(sorting_analyzer_simple):
     metrics = compute_quality_metrics(
         sorting_analyzer,
         metric_names=["snr"],
-        qm_params=dict(isi_violation=dict(isi_threshold_ms=2)),
+        metric_params=dict(isi_violation=dict(isi_threshold_ms=2)),
         skip_pc_metrics=True,
         seed=2205,
     )
     # print(metrics)
 
     qm = sorting_analyzer.get_extension("quality_metrics")
-    assert qm.params["qm_params"]["isi_violation"]["isi_threshold_ms"] == 2
+    assert qm.params["metric_params"]["isi_violation"]["isi_threshold_ms"] == 2
     assert "snr" in metrics.columns
     assert "isolation_distance" not in metrics.columns
 
@@ -40,7 +40,7 @@ def test_compute_quality_metrics(sorting_analyzer_simple):
     metrics = compute_quality_metrics(
         sorting_analyzer,
         metric_names=None,
-        qm_params=dict(isi_violation=dict(isi_threshold_ms=2)),
+        metric_params=dict(isi_violation=dict(isi_threshold_ms=2)),
         skip_pc_metrics=False,
         seed=2205,
     )
@@ -54,7 +54,7 @@ def test_compute_quality_metrics_recordingless(sorting_analyzer_simple):
     metrics = compute_quality_metrics(
         sorting_analyzer,
         metric_names=None,
-        qm_params=dict(isi_violation=dict(isi_threshold_ms=2)),
+        metric_params=dict(isi_violation=dict(isi_threshold_ms=2)),
         skip_pc_metrics=False,
         seed=2205,
     )
@@ -68,7 +68,7 @@ def test_compute_quality_metrics_recordingless(sorting_analyzer_simple):
     metrics_norec = compute_quality_metrics(
         sorting_analyzer_norec,
         metric_names=None,
-        qm_params=dict(isi_violation=dict(isi_threshold_ms=2)),
+        metric_params=dict(isi_violation=dict(isi_threshold_ms=2)),
         skip_pc_metrics=False,
         seed=2205,
     )
@@ -101,7 +101,7 @@ def test_empty_units(sorting_analyzer_simple):
     metrics_empty = compute_quality_metrics(
         sorting_analyzer_empty,
         metric_names=None,
-        qm_params=dict(isi_violation=dict(isi_threshold_ms=2)),
+        metric_params=dict(isi_violation=dict(isi_threshold_ms=2)),
         skip_pc_metrics=True,
         seed=2205,
     )

From 2706a0bee9fef9dd3b3a4af99715366aae1c1625 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 09:45:28 +0000
Subject: [PATCH 09/45] Change metrics_kwargs to metric_params and add
 depreciation message

---
 .../postprocessing/template_metrics.py        | 36 +++++++++++--------
 .../tests/test_template_metrics.py            |  2 +-
 2 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 6e7bcf21b8..ef6abfe51f 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -63,8 +63,8 @@ class ComputeTemplateMetrics(AnalyzerExtension):
     include_multi_channel_metrics : bool, default: False
         Whether to compute multi-channel metrics
     delete_existing_metrics : bool, default: False
-        If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metrics_kwargs` are unchanged.
-    metrics_kwargs : dict
+        If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metric_params` are unchanged.
+    metric_params : dict
         Additional arguments to pass to the metric functions. Including:
             * recovery_window_ms: the window in ms after the peak to compute the recovery_slope, default: 0.7
             * peak_relative_threshold: the relative threshold to detect positive and negative peaks, default: 0.2
@@ -109,12 +109,20 @@ def _set_params(
         peak_sign="neg",
         upsampling_factor=10,
         sparsity=None,
+        metric_params=None,
         metrics_kwargs=None,
         include_multi_channel_metrics=False,
         delete_existing_metrics=False,
         **other_kwargs,
     ):
 
+        if metrics_kwargs is not None and metric_params is None:
+            deprecation_msg = (
+                "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+            )
+            metric_params = metrics_kwargs
+            warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
+
         import pandas as pd
 
         # TODO alessio can you check this : this used to be in the function but now we have ComputeTemplateMetrics.function_factory()
@@ -134,27 +142,27 @@ def _set_params(
         if include_multi_channel_metrics:
             metric_names += get_multi_channel_template_metric_names()
 
-        if metrics_kwargs is None:
-            metrics_kwargs_ = _default_function_kwargs.copy()
+        if metric_params is None:
+            metric_params_ = _default_function_kwargs.copy()
             if len(other_kwargs) > 0:
                 for m in other_kwargs:
-                    if m in metrics_kwargs_:
-                        metrics_kwargs_[m] = other_kwargs[m]
+                    if m in metric_params_:
+                        metric_params_[m] = other_kwargs[m]
         else:
-            metrics_kwargs_ = _default_function_kwargs.copy()
-            metrics_kwargs_.update(metrics_kwargs)
+            metric_params_ = _default_function_kwargs.copy()
+            metric_params_.update(metric_params)
 
         metrics_to_compute = metric_names
         tm_extension = self.sorting_analyzer.get_extension("template_metrics")
         if delete_existing_metrics is False and tm_extension is not None:
 
-            existing_params = tm_extension.params["metrics_kwargs"]
+            existing_params = tm_extension.params["metric_params"]
             # checks that existing metrics were calculated using the same params
-            if existing_params != metrics_kwargs_:
+            if existing_params != metric_params_:
                 warnings.warn(
                     f"The parameters used to calculate the previous template metrics are different"
                     f"than those used now.\nPrevious parameters: {existing_params}\nCurrent "
-                    f"parameters:  {metrics_kwargs_}\nDeleting previous template metrics..."
+                    f"parameters:  {metric_params_}\nDeleting previous template metrics..."
                 )
                 tm_extension.params["metric_names"] = []
                 existing_metric_names = []
@@ -171,7 +179,7 @@ def _set_params(
             sparsity=sparsity,
             peak_sign=peak_sign,
             upsampling_factor=int(upsampling_factor),
-            metrics_kwargs=metrics_kwargs_,
+            metric_params=metric_params_,
             delete_existing_metrics=delete_existing_metrics,
             metrics_to_compute=metrics_to_compute,
         )
@@ -273,7 +281,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
                             sampling_frequency=sampling_frequency_up,
                             trough_idx=trough_idx,
                             peak_idx=peak_idx,
-                            **self.params["metrics_kwargs"],
+                            **self.params["metric_params"],
                         )
                     except Exception as e:
                         warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}")
@@ -312,7 +320,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
                         template_upsampled,
                         channel_locations=channel_locations_sparse,
                         sampling_frequency=sampling_frequency_up,
-                        **self.params["metrics_kwargs"],
+                        **self.params["metric_params"],
                     )
                 except Exception as e:
                     warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}")
diff --git a/src/spikeinterface/postprocessing/tests/test_template_metrics.py b/src/spikeinterface/postprocessing/tests/test_template_metrics.py
index 5056d4ff2a..1df723bfe3 100644
--- a/src/spikeinterface/postprocessing/tests/test_template_metrics.py
+++ b/src/spikeinterface/postprocessing/tests/test_template_metrics.py
@@ -47,7 +47,7 @@ def test_compute_new_template_metrics(small_sorting_analyzer):
 
     # check that, when parameters are changed, the old metrics are deleted
     small_sorting_analyzer.compute(
-        {"template_metrics": {"metric_names": ["exp_decay"], "metrics_kwargs": {"recovery_window_ms": 0.6}}}
+        {"template_metrics": {"metric_names": ["exp_decay"], "metric_params": {"recovery_window_ms": 0.6}}}
     )
 
 

From 22460710bca1114e5f11f5ba4cbdad1b82941d70 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 09:46:16 +0000
Subject: [PATCH 10/45] Update warning message (oups)

---
 src/spikeinterface/postprocessing/template_metrics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index ef6abfe51f..9b85f99c0d 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -118,7 +118,7 @@ def _set_params(
 
         if metrics_kwargs is not None and metric_params is None:
             deprecation_msg = (
-                "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+                "`metrics_kwargs` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
             )
             metric_params = metrics_kwargs
             warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)

From 3579934baf43e25759ca1e8ee7f1e3288180be71 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 10:04:02 +0000
Subject: [PATCH 11/45] Make compute work and add `get_default_tm_params`

---
 .../postprocessing/template_metrics.py        | 45 +++++++++----------
 1 file changed, 20 insertions(+), 25 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 9b85f99c0d..25e0d0d490 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -64,22 +64,10 @@ class ComputeTemplateMetrics(AnalyzerExtension):
         Whether to compute multi-channel metrics
     delete_existing_metrics : bool, default: False
         If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metric_params` are unchanged.
-    metric_params : dict
-        Additional arguments to pass to the metric functions. Including:
-            * recovery_window_ms: the window in ms after the peak to compute the recovery_slope, default: 0.7
-            * peak_relative_threshold: the relative threshold to detect positive and negative peaks, default: 0.2
-            * peak_width_ms: the width in samples to detect peaks, default: 0.2
-            * depth_direction: the direction to compute velocity above and below, default: "y" (see notes)
-            * min_channels_for_velocity: the minimum number of channels above or below to compute velocity, default: 5
-            * min_r2_velocity: the minimum r2 to accept the velocity fit, default: 0.7
-            * exp_peak_function: the function to use to compute the peak amplitude for the exp decay, default: "ptp"
-            * min_r2_exp_decay: the minimum r2 to accept the exp decay fit, default: 0.5
-            * spread_threshold: the threshold to compute the spread, default: 0.2
-            * spread_smooth_um: the smoothing in um to compute the spread, default: 20
-            * column_range: the range in um in the horizontal direction to consider channels for velocity, default: None
-                - If None, all channels all channels are considered
-                - If 0 or 1, only the "column" that includes the max channel is considered
-                - If > 1, only channels within range (+/-) um from the max channel horizontal position are used
+    metric_params : dict of dicts
+        metric_params : dict of dicts or None
+        Dictionary with parameters for quality metrics calculation.
+        Default parameters can be obtained with: `si.qualitymetrics.get_default_tm_params()`
 
     Returns
     -------
@@ -116,13 +104,6 @@ def _set_params(
         **other_kwargs,
     ):
 
-        if metrics_kwargs is not None and metric_params is None:
-            deprecation_msg = (
-                "`metrics_kwargs` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
-            )
-            metric_params = metrics_kwargs
-            warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
-
         import pandas as pd
 
         # TODO alessio can you check this : this used to be in the function but now we have ComputeTemplateMetrics.function_factory()
@@ -142,6 +123,13 @@ def _set_params(
         if include_multi_channel_metrics:
             metric_names += get_multi_channel_template_metric_names()
 
+        if metrics_kwargs is not None and metric_params is None:
+            deprecation_msg = (
+                "`metrics_kwargs` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+            )
+            metric_params = dict(zip(metric_names, [metrics_kwargs] * len(metric_names)))
+            warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
+
         if metric_params is None:
             metric_params_ = _default_function_kwargs.copy()
             if len(other_kwargs) > 0:
@@ -281,7 +269,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
                             sampling_frequency=sampling_frequency_up,
                             trough_idx=trough_idx,
                             peak_idx=peak_idx,
-                            **self.params["metric_params"],
+                            **self.params["metric_params"][metric_name],
                         )
                     except Exception as e:
                         warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}")
@@ -320,7 +308,7 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
                         template_upsampled,
                         channel_locations=channel_locations_sparse,
                         sampling_frequency=sampling_frequency_up,
-                        **self.params["metric_params"],
+                        **self.params["metric_params"][metric_name],
                     )
                 except Exception as e:
                     warnings.warn(f"Error computing metric {metric_name} for unit {unit_id}: {e}")
@@ -380,6 +368,13 @@ def _get_data(self):
 )
 
 
+def get_default_tm_params():
+    metric_names = get_single_channel_template_metric_names() + get_multi_channel_template_metric_names()
+    base_tm_params = _default_function_kwargs
+    metric_params = dict(zip(metric_names, [base_tm_params] * len(metric_names)))
+    return metric_params
+
+
 def get_trough_and_peak_idx(template):
     """
     Return the indices into the input template of the detected trough

From 66190c3857bcabf30ca64af994693a3a029c41e1 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 10:18:46 +0000
Subject: [PATCH 12/45] Update compute_name_to_column_names to
 qm_compute_name_to_column_names

---
 .../qualitymetrics/quality_metric_calculator.py             | 6 +++---
 src/spikeinterface/qualitymetrics/quality_metric_list.py    | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
index eb380304b6..365d7bcc09 100644
--- a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
+++ b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
@@ -16,7 +16,7 @@
     compute_pc_metrics,
     _misc_metric_name_to_func,
     _possible_pc_metric_names,
-    compute_name_to_column_names,
+    qm_compute_name_to_column_names,
 )
 from .misc_metrics import _default_params as misc_metrics_params
 from .pca_metrics import _default_params as pca_metrics_params
@@ -32,7 +32,7 @@ class ComputeQualityMetrics(AnalyzerExtension):
         A SortingAnalyzer object.
     metric_names : list or None
         List of quality metrics to compute.
-    metric_params : dict or None
+    metric_params : dict of dicts or None
         Dictionary with parameters for quality metrics calculation.
         Default parameters can be obtained with: `si.qualitymetrics.get_default_qm_params()`
     skip_pc_metrics : bool, default: False
@@ -254,7 +254,7 @@ def _run(self, verbose=False, **job_kwargs):
         # append the metrics which were previously computed
         for metric_name in set(existing_metrics).difference(metrics_to_compute):
             # some metrics names produce data columns with other names. This deals with that.
-            for column_name in compute_name_to_column_names[metric_name]:
+            for column_name in qm_compute_name_to_column_names[metric_name]:
                 computed_metrics[column_name] = qm_extension.data["metrics"][column_name]
 
         self.data["metrics"] = computed_metrics
diff --git a/src/spikeinterface/qualitymetrics/quality_metric_list.py b/src/spikeinterface/qualitymetrics/quality_metric_list.py
index 375dd320ae..fc7e92b50d 100644
--- a/src/spikeinterface/qualitymetrics/quality_metric_list.py
+++ b/src/spikeinterface/qualitymetrics/quality_metric_list.py
@@ -55,7 +55,7 @@
 }
 
 # a dict converting the name of the metric for computation to the output of that computation
-compute_name_to_column_names = {
+qm_compute_name_to_column_names = {
     "num_spikes": ["num_spikes"],
     "firing_rate": ["firing_rate"],
     "presence_ratio": ["presence_ratio"],

From 2de25b47013c8954ece03af1f47250e5db1f7ffb Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 10:19:27 +0000
Subject: [PATCH 13/45] Unify template param checks with quality param checks

---
 .../postprocessing/template_metrics.py        | 63 +++++++++++--------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 25e0d0d490..cfdbd122b3 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -130,33 +130,18 @@ def _set_params(
             metric_params = dict(zip(metric_names, [metrics_kwargs] * len(metric_names)))
             warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
 
-        if metric_params is None:
-            metric_params_ = _default_function_kwargs.copy()
-            if len(other_kwargs) > 0:
-                for m in other_kwargs:
-                    if m in metric_params_:
-                        metric_params_[m] = other_kwargs[m]
-        else:
-            metric_params_ = _default_function_kwargs.copy()
-            metric_params_.update(metric_params)
+        metric_params_ = get_default_tm_params()
+        for k in metric_params_:
+            if metric_params is not None and k in metric_params:
+                metric_params_[k].update(metric_params[k])
+            if "peak_sign" in metric_params_[k] and peak_sign is not None:
+                metric_params_[k]["peak_sign"] = peak_sign
 
         metrics_to_compute = metric_names
         tm_extension = self.sorting_analyzer.get_extension("template_metrics")
         if delete_existing_metrics is False and tm_extension is not None:
 
-            existing_params = tm_extension.params["metric_params"]
-            # checks that existing metrics were calculated using the same params
-            if existing_params != metric_params_:
-                warnings.warn(
-                    f"The parameters used to calculate the previous template metrics are different"
-                    f"than those used now.\nPrevious parameters: {existing_params}\nCurrent "
-                    f"parameters:  {metric_params_}\nDeleting previous template metrics..."
-                )
-                tm_extension.params["metric_names"] = []
-                existing_metric_names = []
-            else:
-                existing_metric_names = tm_extension.params["metric_names"]
-
+            existing_metric_names = tm_extension.params["metric_names"]
             existing_metric_names_propogated = [
                 metric_name for metric_name in existing_metric_names if metric_name not in metrics_to_compute
             ]
@@ -322,8 +307,8 @@ def _compute_metrics(self, sorting_analyzer, unit_ids=None, verbose=False, metri
 
     def _run(self, verbose=False):
 
-        delete_existing_metrics = self.params["delete_existing_metrics"]
         metrics_to_compute = self.params["metrics_to_compute"]
+        delete_existing_metrics = self.params["delete_existing_metrics"]
 
         # compute the metrics which have been specified by the user
         computed_metrics = self._compute_metrics(
@@ -339,9 +324,21 @@ def _run(self, verbose=False):
         ):
             existing_metrics = tm_extension.params["metric_names"]
 
+        existing_metrics = []
+        # here we get in the loaded via the dict only (to avoid full loading from disk after params reset)
+        tm_extension = self.sorting_analyzer.extensions.get("template_metrics", None)
+        if (
+            delete_existing_metrics is False
+            and tm_extension is not None
+            and tm_extension.data.get("metrics") is not None
+        ):
+            existing_metrics = tm_extension.params["metric_names"]
+
         # append the metrics which were previously computed
         for metric_name in set(existing_metrics).difference(metrics_to_compute):
-            computed_metrics[metric_name] = tm_extension.data["metrics"][metric_name]
+            # some metrics names produce data columns with other names. This deals with that.
+            for column_name in tm_compute_name_to_column_names[metric_name]:
+                computed_metrics[column_name] = tm_extension.data["metrics"][column_name]
 
         self.data["metrics"] = computed_metrics
 
@@ -369,12 +366,28 @@ def _get_data(self):
 
 
 def get_default_tm_params():
-    metric_names = get_single_channel_template_metric_names() + get_multi_channel_template_metric_names()
+    metric_names = get_template_metric_names()
     base_tm_params = _default_function_kwargs
     metric_params = dict(zip(metric_names, [base_tm_params] * len(metric_names)))
     return metric_params
 
 
+# a dict converting the name of the metric for computation to the output of that computation
+tm_compute_name_to_column_names = {
+    "peak_to_valley": ["peak_to_valley"],
+    "peak_trough_ratio": ["peak_trough_ratio"],
+    "half_width": ["half_width"],
+    "repolarization_slope": ["repolarization_slope"],
+    "recovery_slope": ["recovery_slope"],
+    "num_positive_peaks": ["num_positive_peaks"],
+    "num_negative_peaks": ["num_negative_peaks"],
+    "velocity_above": ["velocity_above"],
+    "velocity_below": ["velocity_below"],
+    "exp_decay": ["exp_decay"],
+    "spread": ["spread"],
+}
+
+
 def get_trough_and_peak_idx(template):
     """
     Return the indices into the input template of the detected trough

From 8f6602423d53dc625689da2183a24fe43cbb8629 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:07:27 +0000
Subject: [PATCH 14/45] add some tests

---
 .../tests/test_template_metrics.py            | 47 ++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/postprocessing/tests/test_template_metrics.py b/src/spikeinterface/postprocessing/tests/test_template_metrics.py
index 1df723bfe3..1bf49f64c1 100644
--- a/src/spikeinterface/postprocessing/tests/test_template_metrics.py
+++ b/src/spikeinterface/postprocessing/tests/test_template_metrics.py
@@ -1,5 +1,5 @@
 from spikeinterface.postprocessing.tests.common_extension_tests import AnalyzerExtensionCommonTestSuite
-from spikeinterface.postprocessing import ComputeTemplateMetrics
+from spikeinterface.postprocessing import ComputeTemplateMetrics, compute_template_metrics
 import pytest
 import csv
 
@@ -8,6 +8,49 @@
 template_metrics = list(_single_channel_metric_name_to_func.keys())
 
 
+def test_different_params_template_metrics(small_sorting_analyzer):
+    """
+    Computes template metrics using different params, and check that they are
+    actually calculated using the different params.
+    """
+    compute_template_metrics(
+        sorting_analyzer=small_sorting_analyzer,
+        metric_names=["exp_decay", "spread", "half_width"],
+        metric_params={"exp_decay": {"recovery_window_ms": 0.8}, "spread": {"spread_smooth_um": 15}},
+    )
+
+    tm_extension = small_sorting_analyzer.get_extension("template_metrics")
+    tm_params = tm_extension.params["metric_params"]
+
+    assert tm_params["exp_decay"]["recovery_window_ms"] == 0.8
+    assert tm_params["spread"]["recovery_window_ms"] == 0.7
+    assert tm_params["half_width"]["recovery_window_ms"] == 0.7
+
+    assert tm_params["spread"]["spread_smooth_um"] == 15
+    assert tm_params["exp_decay"]["spread_smooth_um"] == 20
+    assert tm_params["half_width"]["spread_smooth_um"] == 20
+
+
+def test_backwards_compat_params_template_metrics(small_sorting_analyzer):
+    """
+    Computes template metrics using the metrics_kwargs keyword
+    """
+    compute_template_metrics(
+        sorting_analyzer=small_sorting_analyzer,
+        metric_names=["exp_decay", "spread"],
+        metrics_kwargs={"recovery_window_ms": 0.8},
+    )
+
+    tm_extension = small_sorting_analyzer.get_extension("template_metrics")
+    tm_params = tm_extension.params["metric_params"]
+
+    assert tm_params["exp_decay"]["recovery_window_ms"] == 0.8
+    assert tm_params["spread"]["recovery_window_ms"] == 0.8
+
+    assert tm_params["spread"]["spread_smooth_um"] == 20
+    assert tm_params["exp_decay"]["spread_smooth_um"] == 20
+
+
 def test_compute_new_template_metrics(small_sorting_analyzer):
     """
     Computes template metrics then computes a subset of template metrics, and checks
@@ -17,6 +60,8 @@ def test_compute_new_template_metrics(small_sorting_analyzer):
     are deleted.
     """
 
+    small_sorting_analyzer.delete_extension("template_metrics")
+
     # calculate just exp_decay
     small_sorting_analyzer.compute({"template_metrics": {"metric_names": ["exp_decay"]}})
     template_metric_extension = small_sorting_analyzer.get_extension("template_metrics")

From fdc01f5adb81f55c5787166fa469100d7bc06239 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 15:00:15 +0000
Subject: [PATCH 15/45] little fixes

---
 .../postprocessing/template_metrics.py        | 31 +++++++++++--------
 .../qualitymetrics/pca_metrics.py             |  4 +--
 2 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index cfdbd122b3..cbcf38d19d 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -66,8 +66,8 @@ class ComputeTemplateMetrics(AnalyzerExtension):
         If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metric_params` are unchanged.
     metric_params : dict of dicts
         metric_params : dict of dicts or None
-        Dictionary with parameters for quality metrics calculation.
-        Default parameters can be obtained with: `si.qualitymetrics.get_default_tm_params()`
+        Dictionary with parameters for template metrics calculation.
+        Default parameters can be obtained with: `si.postprocessing.template_metrics.get_default_tm_params()`
 
     Returns
     -------
@@ -124,18 +124,17 @@ def _set_params(
             metric_names += get_multi_channel_template_metric_names()
 
         if metrics_kwargs is not None and metric_params is None:
-            deprecation_msg = (
-                "`metrics_kwargs` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
-            )
-            metric_params = dict(zip(metric_names, [metrics_kwargs] * len(metric_names)))
-            warnings.warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
+            deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use metric_params instead"
+            warnings.warn(deprecation_msg, category=DeprecationWarning)
+
+            metric_params = {}
+            for metric_name in metric_names:
+                metric_params[metric_name] = deepcopy(metrics_kwargs)
 
-        metric_params_ = get_default_tm_params()
+        metric_params_ = get_default_tm_params(metric_names)
         for k in metric_params_:
             if metric_params is not None and k in metric_params:
                 metric_params_[k].update(metric_params[k])
-            if "peak_sign" in metric_params_[k] and peak_sign is not None:
-                metric_params_[k]["peak_sign"] = peak_sign
 
         metrics_to_compute = metric_names
         tm_extension = self.sorting_analyzer.get_extension("template_metrics")
@@ -365,10 +364,16 @@ def _get_data(self):
 )
 
 
-def get_default_tm_params():
-    metric_names = get_template_metric_names()
+def get_default_tm_params(metric_names):
+    if metric_names is None:
+        metric_names = get_template_metric_names()
+
     base_tm_params = _default_function_kwargs
-    metric_params = dict(zip(metric_names, [base_tm_params] * len(metric_names)))
+
+    metric_params = {}
+    for metric_name in metric_names:
+        metric_params[metric_name] = deepcopy(base_tm_params)
+
     return metric_params
 
 
diff --git a/src/spikeinterface/qualitymetrics/pca_metrics.py b/src/spikeinterface/qualitymetrics/pca_metrics.py
index b4952bfe6d..ca21f1e45f 100644
--- a/src/spikeinterface/qualitymetrics/pca_metrics.py
+++ b/src/spikeinterface/qualitymetrics/pca_metrics.py
@@ -91,10 +91,10 @@ def compute_pc_metrics(
 
     if qm_params is not None and metric_params is None:
         deprecation_msg = (
-            "`qm_params` is deprecated and will be removed in version 0.104.0 Please use metric_params instead"
+            "`qm_params` is deprecated and will be removed in version 0.104.0. Please use metric_params instead"
         )
-        metric_params = qm_params
         warn(deprecation_msg, category=DeprecationWarning, stacklevel=2)
+        metric_params = qm_params
 
     pca_ext = sorting_analyzer.get_extension("principal_components")
     assert pca_ext is not None, "calculate_pc_metrics() need extension 'principal_components'"

From 9db0b83f7c7ad2c773c8673fa3dd09e5c3cdecb6 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 14 Nov 2024 15:11:01 +0000
Subject: [PATCH 16/45] backwards compatible loading

---
 .../postprocessing/template_metrics.py               | 12 ++++++++++++
 .../qualitymetrics/quality_metric_calculator.py      |  7 +++++++
 2 files changed, 19 insertions(+)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index cbcf38d19d..477ad04440 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -344,6 +344,18 @@ def _run(self, verbose=False):
     def _get_data(self):
         return self.data["metrics"]
 
+    def load_params(self):
+        AnalyzerExtension.load_params(self)
+        # For backwards compatibility - this reformats metrics_kwargs as metric_params
+        if (metrics_kwargs := self.params.get("metrics_kwargs")) is not None:
+
+            metric_params = {}
+            for metric_name in self.params["metric_names"]:
+                metric_params[metric_name] = deepcopy(metrics_kwargs)
+            self.params["metric_params"] = metric_params
+
+            del self.params["metrics_kwargs"]
+
 
 register_result_extension(ComputeTemplateMetrics)
 compute_template_metrics = ComputeTemplateMetrics.function_factory()
diff --git a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
index 365d7bcc09..e7e7c244ea 100644
--- a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
+++ b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
@@ -262,6 +262,13 @@ def _run(self, verbose=False, **job_kwargs):
     def _get_data(self):
         return self.data["metrics"]
 
+    def load_params(self):
+        AnalyzerExtension.load_params(self)
+        # For backwards compatibility - this renames qm_params as metric_params
+        if (qm_params := self.params.get("qm_params")) is not None:
+            self.params["metric_params"] = qm_params
+            del self.params["qm_params"]
+
 
 register_result_extension(ComputeQualityMetrics)
 compute_quality_metrics = ComputeQualityMetrics.function_factory()

From 9b2875fd06782bd6da722fed1f524dfda4203f0a Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 21 Nov 2024 11:53:01 +0100
Subject: [PATCH 17/45] Add stream_mode as extra_requirements for NWB wghen
 streaming

---
 src/spikeinterface/extractors/nwbextractors.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/spikeinterface/extractors/nwbextractors.py b/src/spikeinterface/extractors/nwbextractors.py
index d797e64910..171992f6b1 100644
--- a/src/spikeinterface/extractors/nwbextractors.py
+++ b/src/spikeinterface/extractors/nwbextractors.py
@@ -599,6 +599,8 @@ def __init__(
         else:
             gains, offsets, locations, groups = self._fetch_main_properties_backend()
             self.extra_requirements.append("h5py")
+        if stream_mode is not None:
+            self.extra_requirements.append(stream_mode)
         self.set_channel_gains(gains)
         self.set_channel_offsets(offsets)
         if locations is not None:
@@ -1100,6 +1102,8 @@ def __init__(
             for property_name, property_values in properties.items():
                 values = [x.decode("utf-8") if isinstance(x, bytes) else x for x in property_values]
                 self.set_property(property_name, values)
+        if stream_mode is not None:
+            self.extra_requirements.append(stream_mode)
 
         if stream_mode is None and file_path is not None:
             file_path = str(Path(file_path).resolve())

From ad00beb182967ebe68f59ebfd7f1abad3002a10e Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:44:20 +0000
Subject: [PATCH 18/45] Update `interpolate_motion_on_traces` docstring

---
 .../sortingcomponents/motion/motion_interpolation.py           | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index d207dced08..7c6f0ba71a 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -83,6 +83,9 @@ def interpolate_motion_on_traces(
     interpolation_time_bin_centers_s : None or np.array
         Manually specify the time bins which the interpolation happens
         in for this segment. If None, these are the motion estimate's time bins.
+    interpolation_time_bin_edges_s : None or np.array
+        If present, interpolation chunks will be the time bins defined by these edges
+        rather than interpolation_time_bin_centers_s or the motion's bins.
     spatial_interpolation_method : "idw" | "kriging", default: "kriging"
         The spatial interpolation method used to interpolate the channel locations:
             * idw : Inverse Distance Weighing

From 28527d2a8bcd03a3c6d9036ac9be180ad4dc6334 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:46:30 +0000
Subject: [PATCH 19/45] Should be centers!

---
 .../sortingcomponents/motion/motion_interpolation.py            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 7c6f0ba71a..f0fff5c039 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -126,7 +126,7 @@ def interpolate_motion_on_traces(
 
     # -- determine the blocks of frames that will land in the same interpolation time bin
     if interpolation_time_bin_centers_s is None and interpolation_time_bin_edges_s is None:
-        bin_centers_s = motion.temporal_bin_edges_s[segment_index]
+        bin_centers_s = motion.temporal_bin_centers_s[segment_index]
         bin_edges_s = motion.temporal_bin_edges_s[segment_index]
     else:
         bin_centers_s, bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)

From b3b3fcf5be7b67451f54cac753844cbb06b8d4a3 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:47:34 +0000
Subject: [PATCH 20/45] Typo

---
 .../sortingcomponents/motion/motion_interpolation.py            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index f0fff5c039..9e32e189d9 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -132,7 +132,7 @@ def interpolate_motion_on_traces(
         bin_centers_s, bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
 
     # nearest interpolation bin:
-    # seachsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
+    # searchsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
     # hence the -1. doing it with "left" is not as nice -- we want t==b[0]
     # to lead to i=1 (rounding down).
     # time_bins are bin centers, but we want to snap to the nearest center.

From b02860e463262a3b9522ebf9badc45c860cf8d29 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:51:11 +0000
Subject: [PATCH 21/45] Clarify comments

---
 .../sortingcomponents/motion/motion_interpolation.py        | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 9e32e189d9..8f96579228 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -131,14 +131,10 @@ def interpolate_motion_on_traces(
     else:
         bin_centers_s, bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
 
-    # nearest interpolation bin:
+    # bin the frame times according to the interpolation time bins.
     # searchsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
     # hence the -1. doing it with "left" is not as nice -- we want t==b[0]
     # to lead to i=1 (rounding down).
-    # time_bins are bin centers, but we want to snap to the nearest center.
-    # idea is to get the left bin edges and bin the interp times.
-    # this is like subtracting bin_dt_s/2, but allows non-equally-spaced bins.
-    # it's fine to use the first bin center for the first left edge
     bin_inds = np.searchsorted(bin_edges_s, times, side="right") - 1
 
     # the time bins may not cover the whole set of times in the recording,

From df2484002b562861f0f64bc053b5da619253e983 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:57:08 +0000
Subject: [PATCH 22/45] Rename variables for clarity

---
 .../motion/motion_interpolation.py            | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 8f96579228..2bd3493650 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -126,30 +126,30 @@ def interpolate_motion_on_traces(
 
     # -- determine the blocks of frames that will land in the same interpolation time bin
     if interpolation_time_bin_centers_s is None and interpolation_time_bin_edges_s is None:
-        bin_centers_s = motion.temporal_bin_centers_s[segment_index]
-        bin_edges_s = motion.temporal_bin_edges_s[segment_index]
+        interpolation_time_bin_centers_s = motion.temporal_bin_centers_s[segment_index]
+        interpolation_time_bin_edges_s = motion.temporal_bin_edges_s[segment_index]
     else:
-        bin_centers_s, bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
+        interpolation_time_bin_centers_s, interpolation_time_bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
 
     # bin the frame times according to the interpolation time bins.
     # searchsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]
     # hence the -1. doing it with "left" is not as nice -- we want t==b[0]
     # to lead to i=1 (rounding down).
-    bin_inds = np.searchsorted(bin_edges_s, times, side="right") - 1
+    interpolation_bin_inds = np.searchsorted(interpolation_time_bin_edges_s, times, side="right") - 1
 
     # the time bins may not cover the whole set of times in the recording,
     # so we need to clip these indices to the valid range
-    n_bins = bin_edges_s.shape[0] - 1
-    np.clip(bin_inds, 0, n_bins - 1, out=bin_inds)
+    n_bins = interpolation_time_bin_edges_s.shape[0] - 1
+    np.clip(interpolation_bin_inds, 0, n_bins - 1, out=interpolation_bin_inds)
 
     # -- what are the possibilities here anyway?
-    bins_here = np.arange(bin_inds[0], bin_inds[-1] + 1)
+    interpolation_bins_here = np.arange(interpolation_bin_inds[0], interpolation_bin_inds[-1] + 1)
 
     # inperpolation kernel will be the same per temporal bin
     interp_times = np.empty(total_num_chans)
     current_start_index = 0
-    for bin_ind in bins_here:
-        bin_time = bin_centers_s[bin_ind]
+    for interp_bin_ind in interpolation_bins_here:
+        bin_time = bin_centers_s[interp_bin_ind]
         interp_times.fill(bin_time)
         channel_motions = motion.get_displacement_at_time_and_depth(
             interp_times,
@@ -177,16 +177,17 @@ def interpolate_motion_on_traces(
         # ax.set_title(f"bin_ind {bin_ind} - {bin_time}s - {spatial_interpolation_method}")
         # plt.show()
 
+        # quick search logic to find frames corresponding to this interpolation bin in the recording
         # quickly find the end of this bin, which is also the start of the next
         next_start_index = current_start_index + np.searchsorted(
-            bin_inds[current_start_index:], bin_ind + 1, side="left"
+            interpolation_bin_inds[current_start_index:], interp_bin_ind + 1, side="left"
         )
-        in_bin = slice(current_start_index, next_start_index)
+        frames_in_bin = slice(current_start_index, next_start_index)
 
         # here we use a simple np.matmul even if dirft_kernel can be super sparse.
         # because the speed for a sparse matmul is not so good when we disable multi threaad (due multi processing
         # in ChunkRecordingExecutor)
-        np.matmul(traces[in_bin], drift_kernel, out=traces_corrected[in_bin])
+        np.matmul(traces[frames_in_bin], drift_kernel, out=traces_corrected[frames_in_bin])
         current_start_index = next_start_index
 
     return traces_corrected

From 91fb7320eafbcdaa8fe728e36cbc7fa686f32ba8 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 20:59:13 +0000
Subject: [PATCH 23/45] Note on clipping behavior

---
 .../sortingcomponents/motion/motion_interpolation.py        | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 2bd3493650..8aed8085bf 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -64,7 +64,11 @@ def interpolate_motion_on_traces(
     """
     Apply inverse motion with spatial interpolation on traces.
 
-    Traces can be full traces, but also waveforms snippets.
+    Traces can be full traces, but also waveforms snippets. Times used for looking up
+    displacements are controlled by interpolation_time_bin_edges_s or 
+    interpolation_time_bin_centers_s, or fall back to the Motion object's time bins
+    by default; times in the recording outside these time bins use the closest edge
+    bin's displacement value during interpolation.
 
     Parameters
     ----------

From b80bad71e2c1ee316048beb79a9169dd8f68c6ff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Nov 2024 21:01:47 +0000
Subject: [PATCH 24/45] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../sortingcomponents/motion/motion_interpolation.py        | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 8aed8085bf..14471f77fc 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -65,7 +65,7 @@ def interpolate_motion_on_traces(
     Apply inverse motion with spatial interpolation on traces.
 
     Traces can be full traces, but also waveforms snippets. Times used for looking up
-    displacements are controlled by interpolation_time_bin_edges_s or 
+    displacements are controlled by interpolation_time_bin_edges_s or
     interpolation_time_bin_centers_s, or fall back to the Motion object's time bins
     by default; times in the recording outside these time bins use the closest edge
     bin's displacement value during interpolation.
@@ -133,7 +133,9 @@ def interpolate_motion_on_traces(
         interpolation_time_bin_centers_s = motion.temporal_bin_centers_s[segment_index]
         interpolation_time_bin_edges_s = motion.temporal_bin_edges_s[segment_index]
     else:
-        interpolation_time_bin_centers_s, interpolation_time_bin_edges_s = ensure_time_bins(interpolation_time_bin_centers_s, interpolation_time_bin_edges_s)
+        interpolation_time_bin_centers_s, interpolation_time_bin_edges_s = ensure_time_bins(
+            interpolation_time_bin_centers_s, interpolation_time_bin_edges_s
+        )
 
     # bin the frame times according to the interpolation time bins.
     # searchsorted(b, t, side="right") == i means that b[i-1] <= t < b[i]

From c89060314e233b89e4e9112e74c7643545806d22 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 16:09:45 -0500
Subject: [PATCH 25/45] Fix variable typo; add docstring

---
 .../motion/motion_interpolation.py               |  5 +++--
 .../sortingcomponents/motion/motion_utils.py     | 16 ++++++++++++++++
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index 14471f77fc..e87f83751c 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -3,7 +3,8 @@
 import numpy as np
 from spikeinterface.core.core_tools import define_function_from_class
 from spikeinterface.preprocessing import get_spatial_interpolation_kernel
-from spikeinterface.preprocessing.basepreprocessor import BasePreprocessor, BasePreprocessorSegment
+from spikeinterface.preprocessing.basepreprocessor import (
+    BasePreprocessor, BasePreprocessorSegment)
 from spikeinterface.preprocessing.filter import fix_dtype
 
 from .motion_utils import ensure_time_bin_edges, ensure_time_bins
@@ -155,7 +156,7 @@ def interpolate_motion_on_traces(
     interp_times = np.empty(total_num_chans)
     current_start_index = 0
     for interp_bin_ind in interpolation_bins_here:
-        bin_time = bin_centers_s[interp_bin_ind]
+        bin_time = interpolation_time_bin_centers_s[interp_bin_ind]
         interp_times.fill(bin_time)
         channel_motions = motion.get_displacement_at_time_and_depth(
             interp_times,
diff --git a/src/spikeinterface/sortingcomponents/motion/motion_utils.py b/src/spikeinterface/sortingcomponents/motion/motion_utils.py
index ec0a55a8f8..680d75f221 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_utils.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_utils.py
@@ -580,6 +580,22 @@ def make_3d_motion_histograms(
 
 
 def ensure_time_bins(time_bin_centers_s=None, time_bin_edges_s=None):
+    """Ensure that both bin edges and bin centers are present
+
+    If either of the inputs are None but not both, the missing is reconstructed
+    from the present. Going from edges to centers is done by taking midpoints.
+    Going from centers to edges is done by taking midpoints and padding with the
+    left and rightmost centers.
+
+    Parameters
+    ----------
+    time_bin_centers_s : None or np.array
+    time_bin_edges_s : None or np.array
+
+    Returns
+    -------
+    time_bin_centers_s, time_bin_edges_s
+    """
     if time_bin_centers_s is None and time_bin_edges_s is None:
         raise ValueError("Need at least one of time_bin_centers_s or time_bin_edges_s.")
 

From 6d2e47911a5e64737f2c98f9cdc199e9f6d306fc Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Thu, 21 Nov 2024 16:14:00 -0500
Subject: [PATCH 26/45] Variable names in tests

---
 .../motion/tests/test_motion_interpolation.py | 45 +++++++++----------
 1 file changed, 21 insertions(+), 24 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
index 8542b62524..c97c8324ba 100644
--- a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
@@ -4,11 +4,8 @@
 import spikeinterface.core as sc
 from spikeinterface.sortingcomponents.motion import Motion
 from spikeinterface.sortingcomponents.motion.motion_interpolation import (
-    InterpolateMotionRecording,
-    correct_motion_on_peaks,
-    interpolate_motion,
-    interpolate_motion_on_traces,
-)
+    InterpolateMotionRecording, correct_motion_on_peaks, interpolate_motion,
+    interpolate_motion_on_traces)
 from spikeinterface.sortingcomponents.tests.common import make_dataset
 
 
@@ -84,26 +81,26 @@ def test_interpolate_motion_on_traces():
 def test_interpolation_simple():
     # a recording where a 1 moves at 1 chan per second. 30 chans 10 frames.
     # there will be 9 chans of drift, so we add 9 chans of padding to the bottom
-    nt = nc0 = 10  # these need to be the same for this test
-    nc1 = nc0 + nc0 - 1
-    traces = np.zeros((nt, nc1), dtype="float32")
-    traces[:, :nc0] = np.eye(nc0)
+    n_samples = num_chans_orig = 10  # these need to be the same for this test
+    num_chans_drifted = num_chans_orig + num_chans_orig - 1
+    traces = np.zeros((n_samples, num_chans_drifted), dtype="float32")
+    traces[:, :num_chans_orig] = np.eye(num_chans_orig)
     rec = sc.NumpyRecording(traces, sampling_frequency=1)
-    rec.set_dummy_probe_from_locations(np.c_[np.zeros(nc1), np.arange(nc1)])
+    rec.set_dummy_probe_from_locations(np.c_[np.zeros(num_chans_drifted), np.arange(num_chans_drifted)])
 
-    true_motion = Motion(np.arange(nt)[:, None], 0.5 + np.arange(nt), np.zeros(1))
+    true_motion = Motion(np.arange(n_samples)[:, None], 0.5 + np.arange(n_samples), np.zeros(1))
     rec_corrected = interpolate_motion(rec, true_motion, spatial_interpolation_method="nearest")
     traces_corrected = rec_corrected.get_traces()
-    assert traces_corrected.shape == (nc0, nc0)
-    assert np.array_equal(traces_corrected[:, 0], np.ones(nt))
-    assert np.array_equal(traces_corrected[:, 1:], np.zeros((nt, nc0 - 1)))
+    assert traces_corrected.shape == (num_chans_orig, num_chans_orig)
+    assert np.array_equal(traces_corrected[:, 0], np.ones(n_samples))
+    assert np.array_equal(traces_corrected[:, 1:], np.zeros((n_samples, num_chans_orig - 1)))
 
     # let's try a new version where we interpolate too slowly
     rec_corrected = interpolate_motion(
         rec, true_motion, spatial_interpolation_method="nearest", num_closest=2, interpolation_time_bin_size_s=2
     )
     traces_corrected = rec_corrected.get_traces()
-    assert traces_corrected.shape == (nc0, nc0)
+    assert traces_corrected.shape == (num_chans_orig, num_chans_orig)
     # what happens with nearest here?
     # well... due to rounding towards the nearest even number, the motion (which at
     # these time bin centers is 0.5, 2.5, 4.5, ...) flips the signal's nearest
@@ -131,8 +128,8 @@ def test_cross_band_interpolation():
     fs_ap = 300.0
     t_start = 10.0
     total_duration = 5.0
-    nt_lfp = int(fs_lfp * total_duration)
-    nt_ap = int(fs_ap * total_duration)
+    num_samples_lfp = int(fs_lfp * total_duration)
+    num_samples_ap = int(fs_ap * total_duration)
     t_switch = 3
 
     # because interpolation uses bin centers logic, there will be a half
@@ -140,18 +137,18 @@ def test_cross_band_interpolation():
     halfbin_ap_lfp = int(0.5 * (fs_ap / fs_lfp))
 
     # channel geometry
-    nc = 10
-    geom = np.c_[np.zeros(nc), np.arange(nc)]
+    num_chans = 10
+    geom = np.c_[np.zeros(num_chans), np.arange(num_chans)]
 
     # make an LFP recording which drifts a bit
-    traces_lfp = np.zeros((nt_lfp, nc))
+    traces_lfp = np.zeros((num_samples_lfp, num_chans))
     traces_lfp[: int(t_switch * fs_lfp), 5] = 1.0
     traces_lfp[int(t_switch * fs_lfp) :, 6] = 1.0
     rec_lfp = sc.NumpyRecording(traces_lfp, sampling_frequency=fs_lfp)
     rec_lfp.set_dummy_probe_from_locations(geom)
 
     # same for AP
-    traces_ap = np.zeros((nt_ap, nc))
+    traces_ap = np.zeros((num_samples_ap, num_chans))
     traces_ap[: int(t_switch * fs_ap) - halfbin_ap_lfp, 5] = 1.0
     traces_ap[int(t_switch * fs_ap) - halfbin_ap_lfp :, 6] = 1.0
     rec_ap = sc.NumpyRecording(traces_ap, sampling_frequency=fs_ap)
@@ -160,8 +157,8 @@ def test_cross_band_interpolation():
     # set times for both, and silence the warning
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=UserWarning)
-        rec_lfp.set_times(t_start + np.arange(nt_lfp) / fs_lfp)
-        rec_ap.set_times(t_start + np.arange(nt_ap) / fs_ap)
+        rec_lfp.set_times(t_start + np.arange(num_samples_lfp) / fs_lfp)
+        rec_ap.set_times(t_start + np.arange(num_samples_ap) / fs_ap)
 
     # estimate motion
     motion = estimate_motion(rec_lfp, method="dredge_lfp", rigid=True)
@@ -169,7 +166,7 @@ def test_cross_band_interpolation():
     # nearest to keep it simple
     rec_corrected = interpolate_motion(rec_ap, motion, spatial_interpolation_method="nearest", num_closest=2)
     traces_corrected = rec_corrected.get_traces()
-    target = np.zeros((nt_ap, nc - 2))
+    target = np.zeros((num_samples_ap, num_chans - 2))
     target[:, 4] = 1
     ii, jj = np.nonzero(traces_corrected)
     assert np.array_equal(traces_corrected, target)

From b4c91a0d941e97be68908b11974d18f802ec74a5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Nov 2024 21:15:30 +0000
Subject: [PATCH 27/45] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../sortingcomponents/motion/motion_interpolation.py       | 3 +--
 .../motion/tests/test_motion_interpolation.py              | 7 +++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index e87f83751c..b3a4c9a207 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -3,8 +3,7 @@
 import numpy as np
 from spikeinterface.core.core_tools import define_function_from_class
 from spikeinterface.preprocessing import get_spatial_interpolation_kernel
-from spikeinterface.preprocessing.basepreprocessor import (
-    BasePreprocessor, BasePreprocessorSegment)
+from spikeinterface.preprocessing.basepreprocessor import BasePreprocessor, BasePreprocessorSegment
 from spikeinterface.preprocessing.filter import fix_dtype
 
 from .motion_utils import ensure_time_bin_edges, ensure_time_bins
diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
index c97c8324ba..e4ba870325 100644
--- a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_interpolation.py
@@ -4,8 +4,11 @@
 import spikeinterface.core as sc
 from spikeinterface.sortingcomponents.motion import Motion
 from spikeinterface.sortingcomponents.motion.motion_interpolation import (
-    InterpolateMotionRecording, correct_motion_on_peaks, interpolate_motion,
-    interpolate_motion_on_traces)
+    InterpolateMotionRecording,
+    correct_motion_on_peaks,
+    interpolate_motion,
+    interpolate_motion_on_traces,
+)
 from spikeinterface.sortingcomponents.tests.common import make_dataset
 
 

From 38e0adac18c2c862f9193e5a5d643b394a6d3d52 Mon Sep 17 00:00:00 2001
From: Charlie Windolf <charliexwindolf@gmail.com>
Date: Fri, 22 Nov 2024 10:28:34 -0500
Subject: [PATCH 28/45] Typo

---
 .../sortingcomponents/motion/motion_interpolation.py            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
index b3a4c9a207..fc8ccb788b 100644
--- a/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
+++ b/src/spikeinterface/sortingcomponents/motion/motion_interpolation.py
@@ -130,7 +130,7 @@ def interpolate_motion_on_traces(
 
     # -- determine the blocks of frames that will land in the same interpolation time bin
     if interpolation_time_bin_centers_s is None and interpolation_time_bin_edges_s is None:
-        interpolation_time_bin_centers_s = motion.temporal_bin_centers_s[segment_index]
+        interpolation_time_bin_centers_s = motion.temporal_bins_s[segment_index]
         interpolation_time_bin_edges_s = motion.temporal_bin_edges_s[segment_index]
     else:
         interpolation_time_bin_centers_s, interpolation_time_bin_edges_s = ensure_time_bins(

From b0e7b1c60086fd818759b8df0f617d5441f4ff40 Mon Sep 17 00:00:00 2001
From: Pierre Yger <pierre.yger@gmail.com>
Date: Fri, 29 Nov 2024 06:04:48 +0100
Subject: [PATCH 29/45] Fix kwargs in silence periods

---
 src/spikeinterface/preprocessing/silence_periods.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py
index 85169011d8..a188f5d8db 100644
--- a/src/spikeinterface/preprocessing/silence_periods.py
+++ b/src/spikeinterface/preprocessing/silence_periods.py
@@ -97,7 +97,12 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see
             rec_segment = SilencedPeriodsRecordingSegment(parent_segment, periods, mode, noise_generator, seg_index)
             self.add_recording_segment(rec_segment)
 
-        self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, noise_generator=noise_generator)
+        self._kwargs = dict(recording=recording,
+                            list_periods=list_periods,
+                            mode=mode,
+                            noise_levels=noise_levels,
+                            seed=seed,
+                            random_chunk_kwargs=random_chunk_kwargs)
 
 
 class SilencedPeriodsRecordingSegment(BasePreprocessorSegment):

From 60d7ad53b59fac5b47bd976905d64efc62b3daeb Mon Sep 17 00:00:00 2001
From: Pierre Yger <pierre.yger@gmail.com>
Date: Fri, 29 Nov 2024 06:10:02 +0100
Subject: [PATCH 30/45] Fix

---
 src/spikeinterface/preprocessing/silence_periods.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py
index a188f5d8db..5e410d51d5 100644
--- a/src/spikeinterface/preprocessing/silence_periods.py
+++ b/src/spikeinterface/preprocessing/silence_periods.py
@@ -100,7 +100,6 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see
         self._kwargs = dict(recording=recording,
                             list_periods=list_periods,
                             mode=mode,
-                            noise_levels=noise_levels,
                             seed=seed,
                             random_chunk_kwargs=random_chunk_kwargs)
 

From 01ae85cbb3ebcfd6f9e20eb191d92a278bbcb5e4 Mon Sep 17 00:00:00 2001
From: Pierre Yger <pierre.yger@gmail.com>
Date: Fri, 29 Nov 2024 06:14:16 +0100
Subject: [PATCH 31/45] WIP

---
 src/spikeinterface/preprocessing/silence_periods.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py
index 5e410d51d5..7c518d02a0 100644
--- a/src/spikeinterface/preprocessing/silence_periods.py
+++ b/src/spikeinterface/preprocessing/silence_periods.py
@@ -100,8 +100,8 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see
         self._kwargs = dict(recording=recording,
                             list_periods=list_periods,
                             mode=mode,
-                            seed=seed,
-                            random_chunk_kwargs=random_chunk_kwargs)
+                            seed=seed)
+        self._kwargs.update(random_chunk_kwargs)
 
 
 class SilencedPeriodsRecordingSegment(BasePreprocessorSegment):

From db2b4d5130a095500637c06f9d74aa2f03d41b73 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 29 Nov 2024 05:15:54 +0000
Subject: [PATCH 32/45] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/preprocessing/silence_periods.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/spikeinterface/preprocessing/silence_periods.py b/src/spikeinterface/preprocessing/silence_periods.py
index 7c518d02a0..00d9a1a407 100644
--- a/src/spikeinterface/preprocessing/silence_periods.py
+++ b/src/spikeinterface/preprocessing/silence_periods.py
@@ -97,10 +97,7 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see
             rec_segment = SilencedPeriodsRecordingSegment(parent_segment, periods, mode, noise_generator, seg_index)
             self.add_recording_segment(rec_segment)
 
-        self._kwargs = dict(recording=recording,
-                            list_periods=list_periods,
-                            mode=mode,
-                            seed=seed)
+        self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, seed=seed)
         self._kwargs.update(random_chunk_kwargs)
 
 

From 5af4f858268c18421c8d1e7a3cbaca3c9957491e Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Mon, 2 Dec 2024 09:19:15 +0000
Subject: [PATCH 33/45] Hard code synchony_size for users, but leave flexible
 code underneathe

---
 doc/get_started/quickstart.rst                |  2 +-
 doc/modules/qualitymetrics/synchrony.rst      |  4 +-
 .../qualitymetrics/misc_metrics.py            | 27 ++++++-------
 .../tests/test_metrics_functions.py           | 39 ++++++++-----------
 4 files changed, 30 insertions(+), 42 deletions(-)

diff --git a/doc/get_started/quickstart.rst b/doc/get_started/quickstart.rst
index 3d45606a78..1349802ce5 100644
--- a/doc/get_started/quickstart.rst
+++ b/doc/get_started/quickstart.rst
@@ -673,7 +673,7 @@ compute quality metrics (some quality metrics require certain extensions
                               'min_spikes': 0,
                               'window_size_s': 1},
      'snr': {'peak_mode': 'extremum', 'peak_sign': 'neg'},
-     'synchrony': {'synchrony_sizes': (2, 4, 8)}}
+     'synchrony': {}
 
 
 Since the recording is very short, let’s change some parameters to
diff --git a/doc/modules/qualitymetrics/synchrony.rst b/doc/modules/qualitymetrics/synchrony.rst
index d244fd0c0f..696dacbd3c 100644
--- a/doc/modules/qualitymetrics/synchrony.rst
+++ b/doc/modules/qualitymetrics/synchrony.rst
@@ -12,7 +12,7 @@ trains. This way synchronous events can be found both in multi-unit and single-u
 Complexity is calculated by counting the number of spikes (i.e. non-empty bins) that occur at the same sample index,
 within and across spike trains.
 
-Synchrony metrics can be computed for different synchrony sizes (>1), defining the number of simultaneous spikes to count.
+Synchrony metrics are computed for 2, 4 and 8 synchronous spikes.
 
 
 
@@ -29,7 +29,7 @@ Example code
 
     import spikeinterface.qualitymetrics as sqm
     # Combine a sorting and recording into a sorting_analyzer
-    synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer synchrony_sizes=(2, 4, 8))
+    synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer)
     # synchrony is a tuple of dicts with the synchrony metrics for each unit
 
 
diff --git a/src/spikeinterface/qualitymetrics/misc_metrics.py b/src/spikeinterface/qualitymetrics/misc_metrics.py
index 8dfd41cf88..b0e0a0ad19 100644
--- a/src/spikeinterface/qualitymetrics/misc_metrics.py
+++ b/src/spikeinterface/qualitymetrics/misc_metrics.py
@@ -520,7 +520,7 @@ def compute_sliding_rp_violations(
 )
 
 
-def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
+def _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=np.array([2, 4, 8])):
     """
     Compute synchrony counts, the number of simultaneous spikes with sizes `synchrony_sizes`.
 
@@ -528,10 +528,10 @@ def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
     ----------
     spikes : np.array
         Structured numpy array with fields ("sample_index", "unit_index", "segment_index").
-    synchrony_sizes : numpy array
-        The synchrony sizes to compute. Should be pre-sorted.
     all_unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. Expecting all units.
+    synchrony_sizes : numpy array
+        The synchrony sizes to compute. Should be pre-sorted.
 
     Returns
     -------
@@ -565,17 +565,15 @@ def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
     return synchrony_counts
 
 
-def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_ids=None):
+def compute_synchrony_metrics(sorting_analyzer, unit_ids=None):
     """
     Compute synchrony metrics. Synchrony metrics represent the rate of occurrences of
-    "synchrony_size" spikes at the exact same sample index.
+    spikes at the exact same sample index, with synchrony sizes 2, 4 and 8.
 
     Parameters
     ----------
     sorting_analyzer : SortingAnalyzer
         A SortingAnalyzer object.
-    synchrony_sizes : list or tuple, default: (2, 4, 8)
-        The synchrony sizes to compute.
     unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. If None, all units are used.
 
@@ -583,19 +581,16 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_
     -------
     sync_spike_{X} : dict
         The synchrony metric for synchrony size X.
-        Returns are as many as synchrony_sizes.
 
     References
     ----------
     Based on concepts described in [Grün]_
     This code was adapted from `Elephant - Electrophysiology Analysis Toolkit <https://github.com/NeuralEnsemble/elephant/blob/master/elephant/spike_train_synchrony.py#L245>`_
     """
-    assert min(synchrony_sizes) > 1, "Synchrony sizes must be greater than 1"
-    # Sort the synchrony times so we can slice numpy arrays, instead of using dicts
-    synchrony_sizes_np = np.array(synchrony_sizes, dtype=np.int16)
-    synchrony_sizes_np.sort()
 
-    res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes_np])
+    synchrony_sizes = np.array([2, 4, 8])
+
+    res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes])
 
     sorting = sorting_analyzer.sorting
 
@@ -606,10 +601,10 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_
 
     spikes = sorting.to_spike_vector()
     all_unit_ids = sorting.unit_ids
-    synchrony_counts = get_synchrony_counts(spikes, synchrony_sizes_np, all_unit_ids)
+    synchrony_counts = _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=synchrony_sizes)
 
     synchrony_metrics_dict = {}
-    for sync_idx, synchrony_size in enumerate(synchrony_sizes_np):
+    for sync_idx, synchrony_size in enumerate(synchrony_sizes):
         sync_id_metrics_dict = {}
         for i, unit_id in enumerate(all_unit_ids):
             if unit_id not in unit_ids:
@@ -623,7 +618,7 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_
     return res(**synchrony_metrics_dict)
 
 
-_default_params["synchrony"] = dict(synchrony_sizes=(2, 4, 8))
+_default_params["synchrony"] = dict()
 
 
 def compute_firing_ranges(sorting_analyzer, bin_size_s=5, percentiles=(5, 95), unit_ids=None):
diff --git a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
index 4c0890b62b..f51dc3e884 100644
--- a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
+++ b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
@@ -39,7 +39,7 @@
     compute_firing_ranges,
     compute_amplitude_cv_metrics,
     compute_sd_ratio,
-    get_synchrony_counts,
+    _get_synchrony_counts,
     compute_quality_metrics,
 )
 
@@ -352,7 +352,7 @@ def test_synchrony_counts_no_sync():
     one_spike["sample_index"] = spike_times
     one_spike["unit_index"] = spike_units
 
-    sync_count = get_synchrony_counts(one_spike, np.array((2)), [0])
+    sync_count = _get_synchrony_counts(one_spike, [0])
 
     assert np.all(sync_count[0] == np.array([0]))
 
@@ -372,7 +372,7 @@ def test_synchrony_counts_one_sync():
     two_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     two_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(two_spikes, np.array((2)), [0, 1])
+    sync_count = _get_synchrony_counts(two_spikes, [0, 1])
 
     assert np.all(sync_count[0] == np.array([1, 1]))
 
@@ -392,7 +392,7 @@ def test_synchrony_counts_one_quad_sync():
     four_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     four_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(four_spikes, np.array((2, 4)), [0, 1, 2, 3])
+    sync_count = _get_synchrony_counts(four_spikes, [0, 1, 2, 3])
 
     assert np.all(sync_count[0] == np.array([1, 1, 1, 1]))
     assert np.all(sync_count[1] == np.array([1, 1, 1, 1]))
@@ -409,7 +409,7 @@ def test_synchrony_counts_not_all_units():
     three_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     three_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(three_spikes, np.array((2)), [0, 1, 2])
+    sync_count = _get_synchrony_counts(three_spikes, [0, 1, 2])
 
     assert np.all(sync_count[0] == np.array([0, 1, 1]))
 
@@ -610,9 +610,9 @@ def test_calculate_rp_violations(sorting_analyzer_violations):
 def test_synchrony_metrics(sorting_analyzer_simple):
     sorting_analyzer = sorting_analyzer_simple
     sorting = sorting_analyzer.sorting
-    synchrony_sizes = (2, 3, 4)
-    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=synchrony_sizes)
-    print(synchrony_metrics)
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer)
+
+    synchrony_sizes = np.array([2, 4, 8])
 
     # check returns
     for size in synchrony_sizes:
@@ -625,10 +625,8 @@ def test_synchrony_metrics(sorting_analyzer_simple):
         sorting_sync = add_synchrony_to_sorting(sorting, sync_event_ratio=sync_level)
         sorting_analyzer_sync = create_sorting_analyzer(sorting_sync, sorting_analyzer.recording, format="memory")
 
-        previous_synchrony_metrics = compute_synchrony_metrics(
-            previous_sorting_analyzer, synchrony_sizes=synchrony_sizes
-        )
-        current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync, synchrony_sizes=synchrony_sizes)
+        previous_synchrony_metrics = compute_synchrony_metrics(previous_sorting_analyzer)
+        current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync)
         print(current_synchrony_metrics)
         # check that all values increased
         for i, col in enumerate(previous_synchrony_metrics._fields):
@@ -647,22 +645,17 @@ def test_synchrony_metrics_unit_id_subset(sorting_analyzer_simple):
 
     unit_ids_subset = [3, 7]
 
-    synchrony_sizes = (2,)
-    (synchrony_metrics,) = compute_synchrony_metrics(
-        sorting_analyzer_simple, synchrony_sizes=synchrony_sizes, unit_ids=unit_ids_subset
-    )
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple, unit_ids=unit_ids_subset)
 
-    assert list(synchrony_metrics.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_2.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_4.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_8.keys()) == [3, 7]
 
 
 def test_synchrony_metrics_no_unit_ids(sorting_analyzer_simple):
 
-    # all_unit_ids = sorting_analyzer_simple.sorting.unit_ids
-
-    synchrony_sizes = (2,)
-    (synchrony_metrics,) = compute_synchrony_metrics(sorting_analyzer_simple, synchrony_sizes=synchrony_sizes)
-
-    assert np.all(list(synchrony_metrics.keys()) == sorting_analyzer_simple.unit_ids)
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple)
+    assert np.all(list(synchrony_metrics.sync_spike_2.keys()) == sorting_analyzer_simple.unit_ids)
 
 
 @pytest.mark.sortingcomponents

From 45eb5b74e58061ee04dcb2a4bba10dbcf2a2c892 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Mon, 2 Dec 2024 09:31:23 +0000
Subject: [PATCH 34/45] Add warning and ability to pass synchrony_sizes

---
 src/spikeinterface/qualitymetrics/__init__.py     | 2 +-
 src/spikeinterface/qualitymetrics/misc_metrics.py | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/qualitymetrics/__init__.py b/src/spikeinterface/qualitymetrics/__init__.py
index 9d604f6ae2..754c82d8e3 100644
--- a/src/spikeinterface/qualitymetrics/__init__.py
+++ b/src/spikeinterface/qualitymetrics/__init__.py
@@ -6,4 +6,4 @@
     get_default_qm_params,
 )
 from .pca_metrics import get_quality_pca_metric_list
-from .misc_metrics import get_synchrony_counts
+from .misc_metrics import _get_synchrony_counts
diff --git a/src/spikeinterface/qualitymetrics/misc_metrics.py b/src/spikeinterface/qualitymetrics/misc_metrics.py
index b0e0a0ad19..2f178c46f3 100644
--- a/src/spikeinterface/qualitymetrics/misc_metrics.py
+++ b/src/spikeinterface/qualitymetrics/misc_metrics.py
@@ -565,7 +565,7 @@ def _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=np.array([2, 4,
     return synchrony_counts
 
 
-def compute_synchrony_metrics(sorting_analyzer, unit_ids=None):
+def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=None):
     """
     Compute synchrony metrics. Synchrony metrics represent the rate of occurrences of
     spikes at the exact same sample index, with synchrony sizes 2, 4 and 8.
@@ -588,6 +588,10 @@ def compute_synchrony_metrics(sorting_analyzer, unit_ids=None):
     This code was adapted from `Elephant - Electrophysiology Analysis Toolkit <https://github.com/NeuralEnsemble/elephant/blob/master/elephant/spike_train_synchrony.py#L245>`_
     """
 
+    if synchrony_sizes is not None:
+        warning_message = "Custom `synchrony_sizes` is deprecated; the `synchrony_metrics` will be computed using `synchrony_sizes = [2,4,8]`"
+        warnings.warn(warning_message)
+
     synchrony_sizes = np.array([2, 4, 8])
 
     res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes])

From 039b408a59ce965b91908de82d0bc55114f8655e Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Mon, 2 Dec 2024 13:43:39 +0000
Subject: [PATCH 35/45] move backwards compat to
 `_handle_backward_compatibility_on_load`

---
 .../postprocessing/template_metrics.py        | 25 ++++++++++---------
 .../quality_metric_calculator.py              | 14 +++++------
 2 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 477ad04440..7de6e8766a 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -88,9 +88,22 @@ class ComputeTemplateMetrics(AnalyzerExtension):
     need_recording = False
     use_nodepipeline = False
     need_job_kwargs = False
+    need_backward_compatibility_on_load = True
 
     min_channels_for_multi_channel_warning = 10
 
+    def _handle_backward_compatibility_on_load(self):
+
+        # For backwards compatibility - this reformats metrics_kwargs as metric_params
+        if (metrics_kwargs := self.params.get("metrics_kwargs")) is not None:
+
+            metric_params = {}
+            for metric_name in self.params["metric_names"]:
+                metric_params[metric_name] = deepcopy(metrics_kwargs)
+            self.params["metric_params"] = metric_params
+
+            del self.params["metrics_kwargs"]
+
     def _set_params(
         self,
         metric_names=None,
@@ -344,18 +357,6 @@ def _run(self, verbose=False):
     def _get_data(self):
         return self.data["metrics"]
 
-    def load_params(self):
-        AnalyzerExtension.load_params(self)
-        # For backwards compatibility - this reformats metrics_kwargs as metric_params
-        if (metrics_kwargs := self.params.get("metrics_kwargs")) is not None:
-
-            metric_params = {}
-            for metric_name in self.params["metric_names"]:
-                metric_params[metric_name] = deepcopy(metrics_kwargs)
-            self.params["metric_params"] = metric_params
-
-            del self.params["metrics_kwargs"]
-
 
 register_result_extension(ComputeTemplateMetrics)
 compute_template_metrics = ComputeTemplateMetrics.function_factory()
diff --git a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
index e7e7c244ea..d71450853f 100644
--- a/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
+++ b/src/spikeinterface/qualitymetrics/quality_metric_calculator.py
@@ -55,6 +55,13 @@ class ComputeQualityMetrics(AnalyzerExtension):
     need_recording = False
     use_nodepipeline = False
     need_job_kwargs = True
+    need_backward_compatibility_on_load = True
+
+    def _handle_backward_compatibility_on_load(self):
+        # For backwards compatibility - this renames qm_params as metric_params
+        if (qm_params := self.params.get("qm_params")) is not None:
+            self.params["metric_params"] = qm_params
+            del self.params["qm_params"]
 
     def _set_params(
         self,
@@ -262,13 +269,6 @@ def _run(self, verbose=False, **job_kwargs):
     def _get_data(self):
         return self.data["metrics"]
 
-    def load_params(self):
-        AnalyzerExtension.load_params(self)
-        # For backwards compatibility - this renames qm_params as metric_params
-        if (qm_params := self.params.get("qm_params")) is not None:
-            self.params["metric_params"] = qm_params
-            del self.params["qm_params"]
-
 
 register_result_extension(ComputeQualityMetrics)
 compute_quality_metrics = ComputeQualityMetrics.function_factory()

From 771de98c6ddd07e064cb28d6e2450e599d54d2a6 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Tue, 3 Dec 2024 09:51:28 +0000
Subject: [PATCH 36/45] Respond to z-man

---
 src/spikeinterface/postprocessing/template_metrics.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 7de6e8766a..da917e673c 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -64,8 +64,7 @@ class ComputeTemplateMetrics(AnalyzerExtension):
         Whether to compute multi-channel metrics
     delete_existing_metrics : bool, default: False
         If True, any template metrics attached to the `sorting_analyzer` are deleted. If False, any metrics which were previously calculated but are not included in `metric_names` are kept, provided the `metric_params` are unchanged.
-    metric_params : dict of dicts
-        metric_params : dict of dicts or None
+    metric_params : dict of dicts or None, default: None
         Dictionary with parameters for template metrics calculation.
         Default parameters can be obtained with: `si.postprocessing.template_metrics.get_default_tm_params()`
 
@@ -138,7 +137,7 @@ def _set_params(
 
         if metrics_kwargs is not None and metric_params is None:
             deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use metric_params instead"
-            warnings.warn(deprecation_msg, category=DeprecationWarning)
+            deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use `metric_params` instead"
 
             metric_params = {}
             for metric_name in metric_names:

From de7210a43135c1164ee2f214e117543441935375 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Tue, 3 Dec 2024 09:52:16 +0000
Subject: [PATCH 37/45] oups

---
 src/spikeinterface/postprocessing/template_metrics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index da917e673c..1969480503 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -136,7 +136,7 @@ def _set_params(
             metric_names += get_multi_channel_template_metric_names()
 
         if metrics_kwargs is not None and metric_params is None:
-            deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use metric_params instead"
+            deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use `metric_params` instead"
             deprecation_msg = "`metrics_kwargs` is deprecated and will be removed in version 0.104.0. Please use `metric_params` instead"
 
             metric_params = {}

From 2081916e33d467145223a7c3099aca556f6e3864 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Tue, 3 Dec 2024 14:18:15 +0000
Subject: [PATCH 38/45] respond to review

---
 src/spikeinterface/qualitymetrics/misc_metrics.py      | 10 ++++++----
 .../qualitymetrics/tests/test_metrics_functions.py     |  8 ++++----
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/spikeinterface/qualitymetrics/misc_metrics.py b/src/spikeinterface/qualitymetrics/misc_metrics.py
index 2f178c46f3..6007de379c 100644
--- a/src/spikeinterface/qualitymetrics/misc_metrics.py
+++ b/src/spikeinterface/qualitymetrics/misc_metrics.py
@@ -520,7 +520,7 @@ def compute_sliding_rp_violations(
 )
 
 
-def _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=np.array([2, 4, 8])):
+def _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
     """
     Compute synchrony counts, the number of simultaneous spikes with sizes `synchrony_sizes`.
 
@@ -530,7 +530,7 @@ def _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=np.array([2, 4,
         Structured numpy array with fields ("sample_index", "unit_index", "segment_index").
     all_unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. Expecting all units.
-    synchrony_sizes : numpy array
+    synchrony_sizes : None or np.array, default: None
         The synchrony sizes to compute. Should be pre-sorted.
 
     Returns
@@ -576,6 +576,8 @@ def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=N
         A SortingAnalyzer object.
     unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. If None, all units are used.
+    synchrony_sizes: None, default: None
+        Deprecated argument. Please use private `_get_synchrony_counts` if you need finer control over number of synchronous spikes.
 
     Returns
     -------
@@ -590,7 +592,7 @@ def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=N
 
     if synchrony_sizes is not None:
         warning_message = "Custom `synchrony_sizes` is deprecated; the `synchrony_metrics` will be computed using `synchrony_sizes = [2,4,8]`"
-        warnings.warn(warning_message)
+        warnings.warn(warning_message, DeprecationWarning, stacklevel=2)
 
     synchrony_sizes = np.array([2, 4, 8])
 
@@ -605,7 +607,7 @@ def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=N
 
     spikes = sorting.to_spike_vector()
     all_unit_ids = sorting.unit_ids
-    synchrony_counts = _get_synchrony_counts(spikes, all_unit_ids, synchrony_sizes=synchrony_sizes)
+    synchrony_counts = _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids)
 
     synchrony_metrics_dict = {}
     for sync_idx, synchrony_size in enumerate(synchrony_sizes):
diff --git a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
index f51dc3e884..ae4c7ab62d 100644
--- a/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
+++ b/src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
@@ -352,7 +352,7 @@ def test_synchrony_counts_no_sync():
     one_spike["sample_index"] = spike_times
     one_spike["unit_index"] = spike_units
 
-    sync_count = _get_synchrony_counts(one_spike, [0])
+    sync_count = _get_synchrony_counts(one_spike, np.array([2, 4, 8]), [0])
 
     assert np.all(sync_count[0] == np.array([0]))
 
@@ -372,7 +372,7 @@ def test_synchrony_counts_one_sync():
     two_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     two_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = _get_synchrony_counts(two_spikes, [0, 1])
+    sync_count = _get_synchrony_counts(two_spikes, np.array([2, 4, 8]), [0, 1])
 
     assert np.all(sync_count[0] == np.array([1, 1]))
 
@@ -392,7 +392,7 @@ def test_synchrony_counts_one_quad_sync():
     four_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     four_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = _get_synchrony_counts(four_spikes, [0, 1, 2, 3])
+    sync_count = _get_synchrony_counts(four_spikes, np.array([2, 4, 8]), [0, 1, 2, 3])
 
     assert np.all(sync_count[0] == np.array([1, 1, 1, 1]))
     assert np.all(sync_count[1] == np.array([1, 1, 1, 1]))
@@ -409,7 +409,7 @@ def test_synchrony_counts_not_all_units():
     three_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     three_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = _get_synchrony_counts(three_spikes, [0, 1, 2])
+    sync_count = _get_synchrony_counts(three_spikes, np.array([2, 4, 8]), [0, 1, 2])
 
     assert np.all(sync_count[0] == np.array([0, 1, 1]))
 

From 09ff624817b53d30d35f1e4f9060edabab45a308 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Wed, 4 Dec 2024 10:33:40 +0100
Subject: [PATCH 39/45] Remove venv in full-tests-with-codecov

---
 .../actions/build-test-environment/action.yml | 36 +++++++------------
 .github/workflows/all-tests.yml               |  2 +-
 2 files changed, 14 insertions(+), 24 deletions(-)

diff --git a/.github/actions/build-test-environment/action.yml b/.github/actions/build-test-environment/action.yml
index 723e8a702f..a212bd64d5 100644
--- a/.github/actions/build-test-environment/action.yml
+++ b/.github/actions/build-test-environment/action.yml
@@ -1,41 +1,20 @@
 name: Install packages
 description: This action installs the package and its dependencies for testing
 
-inputs:
-  python-version:
-    description: 'Python version to set up'
-    required: false
-  os:
-    description: 'Operating system to set up'
-    required: false
-
 runs:
   using: "composite"
   steps:
     - name: Install dependencies
       run: |
-        sudo apt install git
         git config --global user.email "CI@example.com"
         git config --global user.name "CI Almighty"
-        python -m venv ${{ github.workspace }}/test_env # Environment used in the caching step
-        python -m pip install -U pip  # Official recommended way
-        source ${{ github.workspace }}/test_env/bin/activate
         pip install tabulate  # This produces summaries at the end
         pip install -e .[test,extractors,streaming_extractors,test_extractors,full]
       shell: bash
-    - name: Force installation of latest dev from key-packages when running dev (not release)
-      run: |
-        source ${{ github.workspace }}/test_env/bin/activate
-        spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
-        if [ $spikeinterface_is_dev_version = "True" ]; then
-          echo "Running spikeinterface dev version"
-          pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo
-          pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface
-        fi
-          echo "Running tests for release, using pyproject.toml versions of neo and probeinterface"
+    - name: Install git-annex
       shell: bash
-    - name: git-annex install
       run: |
+        pip install datalad-installer
         wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
         mkdir /home/runner/work/installation
         mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/
@@ -44,4 +23,15 @@ runs:
         tar xvzf git-annex-standalone-amd64.tar.gz
         echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
         cd $workdir
+        git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
+    - name: Force installation of latest dev from key-packages when running dev (not release)
+      run: |
+        source ${{ github.workspace }}/test_env/bin/activate
+        spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
+        if [ $spikeinterface_is_dev_version = "True" ]; then
+          echo "Running spikeinterface dev version"
+          pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo
+          pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface
+        fi
+          echo "Running tests for release, using pyproject.toml versions of neo and probeinterface"
       shell: bash
diff --git a/.github/workflows/all-tests.yml b/.github/workflows/all-tests.yml
index dcaec8b272..a9c840d5d5 100644
--- a/.github/workflows/all-tests.yml
+++ b/.github/workflows/all-tests.yml
@@ -47,7 +47,7 @@ jobs:
             echo "$file was changed"
           done
 
-      - name: Set testing environment  # This decides which tests are run and whether to install especial dependencies
+      - name: Set testing environment  # This decides which tests are run and whether to install special dependencies
         shell: bash
         run: |
           changed_files="${{ steps.changed-files.outputs.all_changed_files }}"

From 8500b9d0f4488794dcc6d6b71afec2ebf4697b1d Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Wed, 4 Dec 2024 10:48:11 +0100
Subject: [PATCH 40/45] Oups

---
 .github/actions/build-test-environment/action.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/actions/build-test-environment/action.yml b/.github/actions/build-test-environment/action.yml
index a212bd64d5..c2524d2c16 100644
--- a/.github/actions/build-test-environment/action.yml
+++ b/.github/actions/build-test-environment/action.yml
@@ -26,7 +26,6 @@ runs:
         git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
     - name: Force installation of latest dev from key-packages when running dev (not release)
       run: |
-        source ${{ github.workspace }}/test_env/bin/activate
         spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
         if [ $spikeinterface_is_dev_version = "True" ]; then
           echo "Running spikeinterface dev version"

From 922606b6d4d279da103b7e7edde3ecb79a76e3c8 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Wed, 4 Dec 2024 11:16:01 +0100
Subject: [PATCH 41/45] Oups 2

---
 .github/workflows/full-test-with-codecov.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/full-test-with-codecov.yml b/.github/workflows/full-test-with-codecov.yml
index 407c614ebf..f8ed2aa7a9 100644
--- a/.github/workflows/full-test-with-codecov.yml
+++ b/.github/workflows/full-test-with-codecov.yml
@@ -45,7 +45,6 @@ jobs:
         env:
           HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell
         run: |
-          source ${{ github.workspace }}/test_env/bin/activate
           pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
           echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY
           python ./.github/scripts/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY

From 986a74a30c94a49ed2a2dd6183e8ddc078105b85 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 5 Dec 2024 09:02:31 +0100
Subject: [PATCH 42/45] Pin ONE-API version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index fc09ad9198..22fbdc7f22 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,7 +73,7 @@ extractors = [
 ]
 
 streaming_extractors = [
-    "ONE-api>=2.7.0", # alf sorter and streaming IBL
+    "ONE-api>=2.7.0,<2.10.0", # alf sorter and streaming IBL
     "ibllib>=2.36.0", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",

From 96da22f7ac509bfc83a2a90eed06d58e3f71f990 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 5 Dec 2024 10:00:30 +0000
Subject: [PATCH 43/45] Correct method default in docstring

---
 src/spikeinterface/postprocessing/unit_locations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/postprocessing/unit_locations.py b/src/spikeinterface/postprocessing/unit_locations.py
index 3f6dd47eec..bea06fd8f5 100644
--- a/src/spikeinterface/postprocessing/unit_locations.py
+++ b/src/spikeinterface/postprocessing/unit_locations.py
@@ -26,7 +26,7 @@ class ComputeUnitLocations(AnalyzerExtension):
     ----------
     sorting_analyzer : SortingAnalyzer
         A SortingAnalyzer object
-    method : "center_of_mass" | "monopolar_triangulation" | "grid_convolution", default: "center_of_mass"
+    method : "monopolar_triangulation" or  "center_of_mass" or "grid_convolution", default: "monopolar_triangulation"
         The method to use for localization
     **method_kwargs : dict, default: {}
         Kwargs which are passed to the method function. These can be found in the docstrings of `compute_center_of_mass`, `compute_grid_convolution` and `compute_monopolar_triangulation`.

From 10d459f3d45315cee3079e3b14428222487ef9c6 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Thu, 5 Dec 2024 15:18:59 +0000
Subject: [PATCH 44/45] change or to | in docstring

---
 src/spikeinterface/postprocessing/unit_locations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/postprocessing/unit_locations.py b/src/spikeinterface/postprocessing/unit_locations.py
index bea06fd8f5..df19458316 100644
--- a/src/spikeinterface/postprocessing/unit_locations.py
+++ b/src/spikeinterface/postprocessing/unit_locations.py
@@ -26,7 +26,7 @@ class ComputeUnitLocations(AnalyzerExtension):
     ----------
     sorting_analyzer : SortingAnalyzer
         A SortingAnalyzer object
-    method : "monopolar_triangulation" or  "center_of_mass" or "grid_convolution", default: "monopolar_triangulation"
+    method : "monopolar_triangulation" |  "center_of_mass" | "grid_convolution", default: "monopolar_triangulation"
         The method to use for localization
     **method_kwargs : dict, default: {}
         Kwargs which are passed to the method function. These can be found in the docstrings of `compute_center_of_mass`, `compute_grid_convolution` and `compute_monopolar_triangulation`.

From 4c7b6a5be65af4aa4ce6461e84956455f970942f Mon Sep 17 00:00:00 2001
From: Pierre Yger <pierre.yger@gmail.com>
Date: Wed, 11 Dec 2024 09:53:59 +0100
Subject: [PATCH 45/45] Patch

---
 src/spikeinterface/widgets/unit_waveforms.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/widgets/unit_waveforms.py b/src/spikeinterface/widgets/unit_waveforms.py
index c593836061..3b31eacee5 100644
--- a/src/spikeinterface/widgets/unit_waveforms.py
+++ b/src/spikeinterface/widgets/unit_waveforms.py
@@ -565,7 +565,7 @@ def _update_plot(self, change):
             channel_locations = self.sorting_analyzer.get_channel_locations()
         else:
             unit_indices = [list(self.templates.unit_ids).index(unit_id) for unit_id in unit_ids]
-            templates = self.templates.templates_array[unit_indices]
+            templates = self.templates.get_dense_templates()[unit_indices]
             templates_shadings = None
             channel_locations = self.templates.get_channel_locations()