From f55a9405040310064f716015f8d9b0c976b97923 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Mon, 28 Oct 2024 14:28:05 +0000
Subject: [PATCH 01/32] Add 'shift start time' function.

---
 src/spikeinterface/core/baserecording.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 5e2e9e4014..b8a0420794 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,6 +509,26 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
+    def shift_start_time(self, shift, segment_index=None):
+        """
+        Shift the starting time of the times.
+
+        shift : int | float
+            The shift to apply to the first time point. If positive,
+            the current start time will be increased by `shift`. If
+            negative, the start time will be decreased.
+
+        segment_index : int | None
+            The segment on which to shift the times.
+        """
+        segment_index = self._check_segment_index(segment_index)
+        rs = self._recording_segments[segment_index]
+
+        if self.has_time_vector():
+            rs.time_vector += shift
+        else:
+            rs.t_start += shift
+
     def sample_index_to_time(self, sample_ind, segment_index=None):
         """
         Transform sample index into time in seconds

From f34da1aff682828dfba78cd17034c0fc2cb40fda Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 1 Nov 2024 14:03:13 +0000
Subject: [PATCH 02/32] Make new index page with hover CSS.

---
 doc/_static/css/custom.css     |  20 +++
 doc/conf.py                    |   6 +-
 doc/index.rst                  |   1 +
 doc/tutorials_custom_index.rst | 254 +++++++++++++++++++++++++++++++++
 4 files changed, 279 insertions(+), 2 deletions(-)
 create mode 100644 doc/_static/css/custom.css
 create mode 100644 doc/tutorials_custom_index.rst

diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css
new file mode 100644
index 0000000000..0c51da539e
--- /dev/null
+++ b/doc/_static/css/custom.css
@@ -0,0 +1,20 @@
+/* Center and make the title bold */
+.gallery-card .grid-item-card-title {
+    text-align: center;
+    font-weight: bold;
+}
+
+/* Default style for hover content (hidden) */
+.gallery-card .hover-content {
+    display: none;
+    text-align: center;
+}
+
+/* Show the hover content when hovering over the card */
+.gallery-card:hover .default-title {
+    display: none;
+}
+
+.gallery-card:hover .hover-content {
+    display: block;
+}
diff --git a/doc/conf.py b/doc/conf.py
index e3d58ca8f2..db16269991 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -109,8 +109,10 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
-
+html_static_path = ['_static']
+html_css_files = [
+    'css/custom.css',
+]
 html_favicon = "images/favicon-32x32.png"
 
 
diff --git a/doc/index.rst b/doc/index.rst
index ed443e4200..57a0c95443 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -51,6 +51,7 @@ SpikeInterface is made of several modules to deal with different aspects of the
 
     overview
     get_started/index
+    tutorials_custom_index
     tutorials/index
     how_to/index
     modules/index
diff --git a/doc/tutorials_custom_index.rst b/doc/tutorials_custom_index.rst
new file mode 100644
index 0000000000..46a7bea630
--- /dev/null
+++ b/doc/tutorials_custom_index.rst
@@ -0,0 +1,254 @@
+.. This page provides a custom index to the 'Tutorials' page, rather than the default sphinx-gallery
+.. generated page. The benefits of this are flexibility in design and inclusion of non-sphinx files in the index.
+..
+.. To update this index with a new documentation page
+.. 1) Copy the grid-item-card and associated ".. raw:: html" section.
+.. 2) change :link: to a link to your page. If this is an `.rst` file, point to the rst file directly.
+..    If it is a sphinx-gallery generated file, format the path as separated by underscore and prefix `sphx_glr`,
+..    pointing to the .py file. e.g. `tutorials/my/page.py` -> `sphx_glr_tutorials_my_page.py
+.. 3) Change :img-top: to point to the thumbnail image of your choosing. You can point to images generated
+..    in the sphinx gallery page if you wish.
+.. 4) In the `html` section, change the `default-title` to your pages title and `hover-content` to the subtitle.
+
+:orphan:
+
+TutorialsNew
+============
+
+Longer form tutorials about using SpikeInterface. Many of these are downloadable as notebooks or Python scripts so that you can "code along" with the tutorials.
+
+If you're new to SpikeInterface, we recommend trying out the :ref:`get_started/quickstart:Quickstart tutorial` first.
+
+Updating from legacy
+--------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorials/waveform_extractor_to_sorting_analyzer
+
+Core tutorials
+--------------
+
+These tutorials focus on the :py:mod:`spikeinterface.core` module.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_1_recording_extractor.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
+      :img-alt: Recording objects
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Recording objects</div>
+         <div class="hover-content">Manage loaded recordings in SpikeInterface</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
+      :img-alt: Sorting objects
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Sorting objects</div>
+         <div class="hover-content">Explore sorting extractor features</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
+      :img-alt: Handling probe information
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Handling probe information</div>
+         <div class="hover-content">Handle and visualize probe information</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
+      :img-alt: SortingAnalyzer
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">SortingAnalyzer</div>
+         <div class="hover-content">Analyze sorting results with ease</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
+      :img-alt: Append/Concatenate segments
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Append and/or concatenate segments</div>
+         <div class="hover-content">Combine segments efficiently</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_6_handle_times.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png
+      :img-alt: Handle time information
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Handle time information</div>
+         <div class="hover-content">Manage and analyze time information</div>
+
+Extractors tutorials
+--------------------
+
+The :py:mod:`spikeinterface.extractors` module is designed to load and save recorded and sorted data, and to handle probe information.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py
+      :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
+      :img-alt: Read various formats
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Read various formats</div>
+         <div class="hover-content">Read different recording formats efficiently</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py
+      :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
+      :img-alt: Unscaled traces
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Working with unscaled traces</div>
+         <div class="hover-content">Learn about managing unscaled traces</div>
+
+Quality metrics tutorial
+------------------------
+
+The :code:`spikeinterface.qualitymetrics` module allows users to compute various quality metrics to assess the goodness of a spike sorting output.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py
+      :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
+      :img-alt: Quality Metrics
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Quality Metrics</div>
+         <div class="hover-content">Evaluate sorting quality using metrics</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py
+      :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
+      :img-alt: Curation Tutorial
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Curation Tutorial</div>
+         <div class="hover-content">Learn how to curate spike sorting data</div>
+
+Comparison tutorial
+-------------------
+
+The :code:`spikeinterface.comparison` module allows you to compare sorter outputs or benchmark against ground truth.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py
+      :img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
+      :img-alt: Sorter Comparison
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Sorter Comparison</div>
+         <div class="hover-content">Compare sorter outputs and assess weaknesses</div>
+
+Widgets tutorials
+-----------------
+
+The :code:`widgets` module contains several plotting routines (widgets) for visualizing recordings, sorting data, probe layout, and more.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
+      :img-alt: Recording Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">RecordingExtractor Widgets</div>
+         <div class="hover-content">Visualize recordings with widgets</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
+      :img-alt: Sorting Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">SortingExtractor Widgets</div>
+         <div class="hover-content">Explore sorting data using widgets</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
+      :img-alt: Waveforms Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Waveforms Widgets</div>
+         <div class="hover-content">Display waveforms using SpikeInterface</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
+      :img-alt: Peaks Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Peaks Widgets</div>
+         <div class="hover-content">Visualize detected peaks</div>
+
+Download All Examples
+---------------------
+
+- :download:`Download all examples in Python source code </tutorials/tutorials_python.zip>`
+- :download:`Download all examples in Jupyter notebooks </tutorials/tutorials_jupyter.zip>`

From 7aa93490cca20916338629518800a1cbf976b8ff Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 1 Nov 2024 14:53:22 +0000
Subject: [PATCH 03/32] Remove CSS and update development docs.

---
 doc/_static/css/custom.css      |  20 -----
 doc/conf.py                     |   6 +-
 doc/development/development.rst |  19 +++++
 doc/index.rst                   |   1 -
 doc/tutorials_custom_index.rst  | 128 +++++++++-----------------------
 5 files changed, 56 insertions(+), 118 deletions(-)
 delete mode 100644 doc/_static/css/custom.css

diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css
deleted file mode 100644
index 0c51da539e..0000000000
--- a/doc/_static/css/custom.css
+++ /dev/null
@@ -1,20 +0,0 @@
-/* Center and make the title bold */
-.gallery-card .grid-item-card-title {
-    text-align: center;
-    font-weight: bold;
-}
-
-/* Default style for hover content (hidden) */
-.gallery-card .hover-content {
-    display: none;
-    text-align: center;
-}
-
-/* Show the hover content when hovering over the card */
-.gallery-card:hover .default-title {
-    display: none;
-}
-
-.gallery-card:hover .hover-content {
-    display: block;
-}
diff --git a/doc/conf.py b/doc/conf.py
index db16269991..e3d58ca8f2 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -109,10 +109,8 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-html_css_files = [
-    'css/custom.css',
-]
+# html_static_path = ['_static']
+
 html_favicon = "images/favicon-32x32.png"
 
 
diff --git a/doc/development/development.rst b/doc/development/development.rst
index a91818a271..1638c41243 100644
--- a/doc/development/development.rst
+++ b/doc/development/development.rst
@@ -213,6 +213,25 @@ We use Sphinx to build the documentation. To build the documentation locally, yo
 
 This will build the documentation in the :code:`doc/_build/html` folder. You can open the :code:`index.html` file in your browser to see the documentation.
 
+Adding new documentation
+------------------------
+
+Documentation can be added as a
+`sphinx-gallery <https://sphinx-gallery.github.io/stable/index.html>`_
+python file ('tutorials')
+or a
+`sphinx rst <https://sphinx-tutorial.readthedocs.io/step-1/>`_
+file (all other sections).
+
+To add a new tutorial, add your ``.py`` file to ``spikeinterface/examples``.
+Then, update the ``spikeinterface/doc/tutorials_custom_index.rst`` file
+to make a new card linking to the page and an optional image. See
+``tutorials_custom_index.rst`` header for more information.
+
+For other sections, write your documentation in ``.rst`` format and add
+the page to the appropriate ``index.rst`` file found in the relevant
+folder (e.g. ``how_to/index.rst``).
+
 How to run code coverage locally
 --------------------------------
 To run code coverage locally, you can use the following command:
diff --git a/doc/index.rst b/doc/index.rst
index 57a0c95443..e6d8aa3fea 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -52,7 +52,6 @@ SpikeInterface is made of several modules to deal with different aspects of the
     overview
     get_started/index
     tutorials_custom_index
-    tutorials/index
     how_to/index
     modules/index
     api
diff --git a/doc/tutorials_custom_index.rst b/doc/tutorials_custom_index.rst
index 46a7bea630..4c7625d811 100644
--- a/doc/tutorials_custom_index.rst
+++ b/doc/tutorials_custom_index.rst
@@ -12,12 +12,14 @@
 
 :orphan:
 
-TutorialsNew
+Tutorials
 ============
 
-Longer form tutorials about using SpikeInterface. Many of these are downloadable as notebooks or Python scripts so that you can "code along" with the tutorials.
+Longer form tutorials about using SpikeInterface. Many of these are downloadable
+as notebooks or Python scripts so that you can "code along" with the tutorials.
 
-If you're new to SpikeInterface, we recommend trying out the :ref:`get_started/quickstart:Quickstart tutorial` first.
+If you're new to SpikeInterface, we recommend trying out the
+:ref:`get_started/quickstart:Quickstart tutorial` first.
 
 Updating from legacy
 --------------------
@@ -35,77 +37,53 @@ These tutorials focus on the :py:mod:`spikeinterface.core` module.
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Recording objects
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_1_recording_extractor.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
       :img-alt: Recording objects
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Recording objects</div>
-         <div class="hover-content">Manage loaded recordings in SpikeInterface</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Sorting objects
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
       :img-alt: Sorting objects
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Sorting objects</div>
-         <div class="hover-content">Explore sorting extractor features</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Handling probe information
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
       :img-alt: Handling probe information
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Handling probe information</div>
-         <div class="hover-content">Handle and visualize probe information</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: SortingAnalyzer
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
       :img-alt: SortingAnalyzer
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">SortingAnalyzer</div>
-         <div class="hover-content">Analyze sorting results with ease</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Append and/or concatenate segments
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
       :img-alt: Append/Concatenate segments
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Append and/or concatenate segments</div>
-         <div class="hover-content">Combine segments efficiently</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Handle time information
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_6_handle_times.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png
       :img-alt: Handle time information
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Handle time information</div>
-         <div class="hover-content">Manage and analyze time information</div>
+      :text-align: center
 
 Extractors tutorials
 --------------------
@@ -115,29 +93,21 @@ The :py:mod:`spikeinterface.extractors` module is designed to load and save reco
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Read various formats
       :link-type: ref
       :link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py
       :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
       :img-alt: Read various formats
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Read various formats</div>
-         <div class="hover-content">Read different recording formats efficiently</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Working with unscaled traces
       :link-type: ref
       :link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py
       :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
       :img-alt: Unscaled traces
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Working with unscaled traces</div>
-         <div class="hover-content">Learn about managing unscaled traces</div>
+      :text-align: center
 
 Quality metrics tutorial
 ------------------------
@@ -147,29 +117,21 @@ The :code:`spikeinterface.qualitymetrics` module allows users to compute various
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Quality Metrics
       :link-type: ref
       :link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py
       :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
       :img-alt: Quality Metrics
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Quality Metrics</div>
-         <div class="hover-content">Evaluate sorting quality using metrics</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Curation Tutorial
       :link-type: ref
       :link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py
       :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
       :img-alt: Curation Tutorial
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Curation Tutorial</div>
-         <div class="hover-content">Learn how to curate spike sorting data</div>
+      :text-align: center
 
 Comparison tutorial
 -------------------
@@ -179,17 +141,13 @@ The :code:`spikeinterface.comparison` module allows you to compare sorter output
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Sorter Comparison
       :link-type: ref
       :link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py
       :img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
       :img-alt: Sorter Comparison
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Sorter Comparison</div>
-         <div class="hover-content">Compare sorter outputs and assess weaknesses</div>
+      :text-align: center
 
 Widgets tutorials
 -----------------
@@ -199,53 +157,37 @@ The :code:`widgets` module contains several plotting routines (widgets) for visu
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: RecordingExtractor Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
       :img-alt: Recording Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">RecordingExtractor Widgets</div>
-         <div class="hover-content">Visualize recordings with widgets</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: SortingExtractor Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
       :img-alt: Sorting Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">SortingExtractor Widgets</div>
-         <div class="hover-content">Explore sorting data using widgets</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Waveforms Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
       :img-alt: Waveforms Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Waveforms Widgets</div>
-         <div class="hover-content">Display waveforms using SpikeInterface</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Peaks Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
       :img-alt: Peaks Widgets
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Peaks Widgets</div>
-         <div class="hover-content">Visualize detected peaks</div>
+      :text-align: center
 
 Download All Examples
 ---------------------

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 04/32] 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 05/32] 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 06/32] [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 d6b4c1e7474c372c6d9f71787ddbe707854bd11f Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 7 Nov 2024 11:44:13 +0100
Subject: [PATCH 07/32] Fix cbin_file_path

---
 src/spikeinterface/extractors/cbin_ibl.py | 30 +++++++++++++++--------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index d7e5b58e11..88e1029ab0 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
+import warnings
 import numpy as np
 
 import probeinterface
@@ -30,8 +31,10 @@ class CompressedBinaryIblExtractor(BaseRecording):
     stream_name : {"ap", "lp"}, default: "ap".
         Whether to load AP or LFP band, one
         of "ap" or "lp".
-    cbin_file : str or None, default None
+    cbin_file_path : str or None, default None
         The cbin file of the recording. If None, searches in `folder_path` for file.
+    cbin_file : str or None, default None
+        (deprecated) The cbin file of the recording. If None, searches in `folder_path` for file.
 
     Returns
     -------
@@ -41,14 +44,21 @@ class CompressedBinaryIblExtractor(BaseRecording):
 
     installation_mesg = "To use the CompressedBinaryIblExtractor, install mtscomp: \n\n pip install mtscomp\n\n"
 
-    def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap", cbin_file=None):
+    def __init__(
+        self, folder_path=None, load_sync_channel=False, stream_name="ap", cbin_file_path=None, cbin_file=None
+    ):
         from neo.rawio.spikeglxrawio import read_meta_file
 
         try:
             import mtscomp
         except ImportError:
             raise ImportError(self.installation_mesg)
-        if cbin_file is None:
+        if cbin_file is not None:
+            warnings.warn(
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning
+            )
+            cbin_file_path = cbin_file
+        if cbin_file_path is None:
             folder_path = Path(folder_path)
             # check bands
             assert stream_name in ["ap", "lp"], "stream_name must be one of: 'ap', 'lp'"
@@ -60,17 +70,17 @@ def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap",
             assert (
                 len(curr_cbin_files) == 1
             ), f"There should only be one `*.cbin` file in the folder, but {print(curr_cbin_files)} have been found"
-            cbin_file = curr_cbin_files[0]
+            cbin_file_path = curr_cbin_files[0]
         else:
-            cbin_file = Path(cbin_file)
-            folder_path = cbin_file.parent
+            cbin_file_path = Path(cbin_file_path)
+            folder_path = cbin_file_path.parent
 
-        ch_file = cbin_file.with_suffix(".ch")
-        meta_file = cbin_file.with_suffix(".meta")
+        ch_file = cbin_file_path.with_suffix(".ch")
+        meta_file = cbin_file_path.with_suffix(".meta")
 
         # reader
         cbuffer = mtscomp.Reader()
-        cbuffer.open(cbin_file, ch_file)
+        cbuffer.open(cbin_file_path, ch_file)
 
         # meta data
         meta = read_meta_file(meta_file)
@@ -119,7 +129,7 @@ def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap",
         self._kwargs = {
             "folder_path": str(Path(folder_path).resolve()),
             "load_sync_channel": load_sync_channel,
-            "cbin_file": str(Path(cbin_file).resolve()),
+            "cbin_file_path": str(Path(cbin_file_path).resolve()),
         }
 
 

From e6f45056852e181fb8d6909c8a3365a08cb2c8f5 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 7 Nov 2024 15:56:48 +0100
Subject: [PATCH 08/32] Update src/spikeinterface/extractors/cbin_ibl.py

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

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 88e1029ab0..357afde04e 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -55,7 +55,7 @@ def __init__(
             raise ImportError(self.installation_mesg)
         if cbin_file is not None:
             warnings.warn(
-                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning, stacklevel=2
             )
             cbin_file_path = cbin_file
         if cbin_file_path is None:

From 471ce724faac7245766538880b7fcd196f49fa30 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Nov 2024 14:57:14 +0000
Subject: [PATCH 09/32] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/extractors/cbin_ibl.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 357afde04e..8fe19f3d7e 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -55,7 +55,9 @@ def __init__(
             raise ImportError(self.installation_mesg)
         if cbin_file is not None:
             warnings.warn(
-                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning, stacklevel=2
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead",
+                DeprecationWarning,
+                stacklevel=2,
             )
             cbin_file_path = cbin_file
         if cbin_file_path is None:

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 10/32] 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 11/32] 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 12/32] [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 620f8013b8bf4f1332a7802dd3f6804ce068493c Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:37:50 +0000
Subject: [PATCH 13/32] Apply to all segments if 'segment_index' is 'None'.

---
 src/spikeinterface/core/baserecording.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index b8a0420794..7392caa69b 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -521,13 +521,20 @@ def shift_start_time(self, shift, segment_index=None):
         segment_index : int | None
             The segment on which to shift the times.
         """
-        segment_index = self._check_segment_index(segment_index)
-        rs = self._recording_segments[segment_index]
+        self._check_segment_index(segment_index)
 
-        if self.has_time_vector():
-            rs.time_vector += shift
+        if segment_index is None:
+            segments_to_shift = range(self.get_num_segments())
         else:
-            rs.t_start += shift
+            segments_to_shift = (segment_index,)
+
+        for idx in segments_to_shift:
+            rs = self._recording_segments[idx]
+
+            if self.has_time_vector():
+                rs.time_vector += shift
+            else:
+                rs.t_start += shift
 
     def sample_index_to_time(self, sample_ind, segment_index=None):
         """

From 22d5dfc2a552e00d7b55d7c28681e25a1f51a711 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:39:34 +0000
Subject: [PATCH 14/32] Add type hints.

---
 src/spikeinterface/core/baserecording.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 7392caa69b..0af9c4bb6a 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,7 +509,7 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
-    def shift_start_time(self, shift, segment_index=None):
+    def shift_start_time(self, shift: int | float, segment_index: int | None = None) -> None:
         """
         Shift the starting time of the times.
 
@@ -536,15 +536,14 @@ def shift_start_time(self, shift, segment_index=None):
             else:
                 rs.t_start += shift
 
-    def sample_index_to_time(self, sample_ind, segment_index=None):
-        """
-        Transform sample index into time in seconds
-        """
+    def sample_index_to_time(self, sample_ind: int, segment_index: int | None = None):
+        """ """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.sample_index_to_time(sample_ind)
 
-    def time_to_sample_index(self, time_s, segment_index=None):
+    def time_to_sample_index(self, time_s: float, segment_index: int | None = None):
+        """ """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.time_to_sample_index(time_s)

From 458a3dcc201380740583ef1f075951e83ee77ed8 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:43:45 +0000
Subject: [PATCH 15/32] Update name and docstring.

---
 src/spikeinterface/core/baserecording.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 0af9c4bb6a..91f99f17b0 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,19 +509,24 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
-    def shift_start_time(self, shift: int | float, segment_index: int | None = None) -> None:
+    def shift_times(self, shift: int | float, segment_index: int | None = None) -> None:
         """
-        Shift the starting time of the times.
+        Shift all times by a scalar value. The default behaviour is to
+        shift all segments uniformly.
 
+        Parameters
+        ----------
         shift : int | float
-            The shift to apply to the first time point. If positive,
-            the current start time will be increased by `shift`. If
-            negative, the start time will be decreased.
+            The shift to apply. If positive, times will be increased by `shift`.
+            e.g. shifting by 1 will be like the recording started 1 second later.
+            If negative, the start time will be decreased i.e. as if the recording
+            started earlier.
 
         segment_index : int | None
-            The segment on which to shift the times.
+            The segment on which to shift the times. if `None`, all
+            segments will be shifted.
         """
-        self._check_segment_index(segment_index)
+        self._check_segment_index(segment_index)  # Check the segment index is valid only
 
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())

From 8845d3d7eb6caad8c6a5f0c12842f480766d3a26 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Wed, 13 Nov 2024 14:40:16 +0000
Subject: [PATCH 16/32] Add verbose kwarg to mda write_recording

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

diff --git a/src/spikeinterface/extractors/mdaextractors.py b/src/spikeinterface/extractors/mdaextractors.py
index f055e1d7c9..d2886d9e79 100644
--- a/src/spikeinterface/extractors/mdaextractors.py
+++ b/src/spikeinterface/extractors/mdaextractors.py
@@ -72,6 +72,7 @@ def write_recording(
         params_fname="params.json",
         geom_fname="geom.csv",
         dtype=None,
+        verbose=False,
         **job_kwargs,
     ):
         """Write a recording to file in MDA format.
@@ -93,6 +94,8 @@ def write_recording(
             File name of geom file
         dtype : dtype or None, default: None
             Data type to be used. If None dtype is same as recording traces.
+        verbose : bool
+            If True, shows progress bar when saving recording.
         **job_kwargs:
             Use by job_tools modules to set:
 
@@ -130,6 +133,7 @@ def write_recording(
             dtype=dtype,
             byte_offset=header_size,
             add_file_extension=False,
+            verbose=verbose,
             **job_kwargs,
         )
 

From 3e98c670a27671590613b7c1c4118780a8c47ce8 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:32:48 +0000
Subject: [PATCH 17/32] Add tests.

---
 .../core/tests/test_time_handling.py          | 92 ++++++++++++++++++-
 1 file changed, 89 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/core/tests/test_time_handling.py b/src/spikeinterface/core/tests/test_time_handling.py
index a129316ee7..9b7ed11bbb 100644
--- a/src/spikeinterface/core/tests/test_time_handling.py
+++ b/src/spikeinterface/core/tests/test_time_handling.py
@@ -15,7 +15,10 @@ class TestTimeHandling:
     is generated on the fly. Both time representations are tested here.
     """
 
-    # Fixtures #####
+    # #########################################################################
+    # Fixtures
+    # #########################################################################
+
     @pytest.fixture(scope="session")
     def time_vector_recording(self):
         """
@@ -95,7 +98,10 @@ def _get_fixture_data(self, request, fixture_name):
         raw_recording, times_recording, all_times = time_recording_fixture
         return (raw_recording, times_recording, all_times)
 
-    # Tests #####
+    # #########################################################################
+    # Tests
+    # #########################################################################
+
     def test_has_time_vector(self, time_vector_recording):
         """
         Test the `has_time_vector` function returns `False` before
@@ -305,7 +311,87 @@ def test_sorting_analyzer_get_durations_no_recording(self, time_vector_recording
 
         assert np.array_equal(sorting_analyzer.get_total_duration(), raw_recording.get_total_duration())
 
-    # Helpers ####
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    @pytest.mark.parametrize("shift", [-123.456, 123.456])
+    def test_shift_time_all_segments(self, request, fixture_name, shift):
+        """
+        Shift the times in every segment using the `None` default, then
+        check that every segment of the recording is shifted as expected.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        num_segments, orig_seg_data = self._store_all_times(times_recording)
+
+        times_recording.shift_times(shift)  # use default `segment_index=None`
+
+        for idx in range(num_segments):
+            assert np.allclose(
+                orig_seg_data[idx], times_recording.get_times(segment_index=idx) - shift, rtol=0, atol=1e-8
+            )
+
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    @pytest.mark.parametrize("shift", [-123.456, 123.456])
+    def test_shift_times_different_segments(self, request, fixture_name, shift):
+        """
+        Shift each segment separately, and check the shifted segment only
+        is shifted as expected.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        num_segments, orig_seg_data = self._store_all_times(times_recording)
+
+        # For each segment, shift the segment only and check the
+        # times are updated as expected.
+        for idx in range(num_segments):
+
+            scaler = idx + 2
+            times_recording.shift_times(shift * scaler, segment_index=idx)
+
+            assert np.allclose(
+                orig_seg_data[idx], times_recording.get_times(segment_index=idx) - shift * scaler, rtol=0, atol=1e-8
+            )
+
+            # Just do a little check that we are not
+            # accidentally changing some other segments,
+            # which should remain unchanged at this point in the loop.
+            if idx != num_segments - 1:
+                assert np.array_equal(orig_seg_data[idx + 1], times_recording.get_times(segment_index=idx + 1))
+
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    def test_save_and_load_time_shift(self, request, fixture_name, tmp_path):
+        """
+        Save the shifted data and check the shift is propagated correctly.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        shift = 100
+        times_recording.shift_times(shift=shift)
+
+        times_recording.save(folder=tmp_path / "my_file")
+
+        loaded_recording = si.load_extractor(tmp_path / "my_file")
+
+        for idx in range(times_recording.get_num_segments()):
+            assert np.array_equal(
+                times_recording.get_times(segment_index=idx), loaded_recording.get_times(segment_index=idx)
+            )
+
+    def _store_all_times(self, recording):
+        """
+        Convenience function to store original times of all segments to a dict.
+        """
+        num_segments = recording.get_num_segments()
+        seg_data = {}
+
+        for idx in range(num_segments):
+            seg_data[idx] = copy.deepcopy(recording.get_times(segment_index=idx))
+
+        return num_segments, seg_data
+
+    # #########################################################################
+    # Helpers
+    # #########################################################################
+
     def _check_times_match(self, recording, all_times):
         """
         For every segment in a recording, check the `get_times()`

From 4d7246a529e3d17747cf5a496a0a04bd97f4eb09 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:33:17 +0000
Subject: [PATCH 18/32] Fixes on shift function.

---
 src/spikeinterface/core/baserecording.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 91f99f17b0..4b545dc7c7 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -526,8 +526,6 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             The segment on which to shift the times. if `None`, all
             segments will be shifted.
         """
-        self._check_segment_index(segment_index)  # Check the segment index is valid only
-
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())
         else:
@@ -536,7 +534,7 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
         for idx in segments_to_shift:
             rs = self._recording_segments[idx]
 
-            if self.has_time_vector():
+            if self.has_time_vector(segment_index=idx):
                 rs.time_vector += shift
             else:
                 rs.t_start += shift

From a1cf3367d18a549281208b25c622f2a1ee773226 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:35:32 +0000
Subject: [PATCH 19/32] Undo out of scope changes.

---
 src/spikeinterface/core/baserecording.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 4b545dc7c7..886f7db79f 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -539,14 +539,15 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             else:
                 rs.t_start += shift
 
-    def sample_index_to_time(self, sample_ind: int, segment_index: int | None = None):
-        """ """
+    def sample_index_to_time(self, sample_ind, segment_index=None):
+        """
+        Transform sample index into time in seconds
+        """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.sample_index_to_time(sample_ind)
 
-    def time_to_sample_index(self, time_s: float, segment_index: int | None = None):
-        """ """
+    def time_to_sample_index(self, time_s, segment_index=None):
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.time_to_sample_index(time_s)

From 469b3b0e36fdbc0571d37e100d99d6c741af1377 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:37:20 +0000
Subject: [PATCH 20/32] Fix docstring.

---
 src/spikeinterface/core/baserecording.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 886f7db79f..6d9d2a827f 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -511,8 +511,7 @@ def reset_times(self):
 
     def shift_times(self, shift: int | float, segment_index: int | None = None) -> None:
         """
-        Shift all times by a scalar value. The default behaviour is to
-        shift all segments uniformly.
+        Shift all times by a scalar value.
 
         Parameters
         ----------
@@ -523,8 +522,8 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             started earlier.
 
         segment_index : int | None
-            The segment on which to shift the times. if `None`, all
-            segments will be shifted.
+            The segment on which to shift the times.
+            If `None`, all segments will be shifted.
         """
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())

From 1e53a5e06b2a90956d72150826a8f590d673b5ce Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 19 Nov 2024 17:45:40 +0100
Subject: [PATCH 21/32] Update src/spikeinterface/extractors/cbin_ibl.py

Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
---
 src/spikeinterface/extractors/cbin_ibl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 8fe19f3d7e..728d352973 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -31,7 +31,7 @@ class CompressedBinaryIblExtractor(BaseRecording):
     stream_name : {"ap", "lp"}, default: "ap".
         Whether to load AP or LFP band, one
         of "ap" or "lp".
-    cbin_file_path : str or None, default None
+    cbin_file_path : str, Path or None, default None
         The cbin file of the recording. If None, searches in `folder_path` for file.
     cbin_file : str or None, default None
         (deprecated) The cbin file of the recording. If None, searches in `folder_path` for file.

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 22/32] 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 23/32] 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 24/32] 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 25/32] 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 26/32] 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 27/32] 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 28/32] [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 29/32] 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 30/32] 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 31/32] [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 32/32] 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(