Merge branch 'main' into add_how_to_make_a_release_notes

Author: h-mayorquin

.github/scripts/determine_testing_environment.py

@@ -48,7 +48,7 @@
     elif changed_file.name == "nwbextractors.py":
         extractors_changed = True  # There are NWB tests that are not streaming
         stream_extractors_changed = True
-    elif changed_file.name == "iblextractors.py":
+    elif changed_file.name == "iblextractors.py" or changed_file.name == "test_iblextractors.py":
         stream_extractors_changed = True
     elif "core" in changed_file.parts:
         core_changed = True

doc/api.rst

@@ -143,7 +143,9 @@ Non-NEO-based
     .. autofunction:: read_mcsh5
     .. autofunction:: read_mda_recording
     .. autofunction:: read_mda_sorting
-    .. autofunction:: read_nwb
+    .. autofunction:: read_nwb_sorting
+    .. autofunction:: read_nwb_recording
+    .. autofunction:: read_nwb_timeseries
     .. autofunction:: read_phy
     .. autofunction:: read_shybrid_recording
     .. autofunction:: read_shybrid_sorting

doc/how_to/customize_a_plot.rst

@@ -0,0 +1,136 @@
+Customize a plot
+================
+
+The ``SpikeInterface`` widgets are designed to have reasonable default
+plotting options, but sometimes you’ll want to make adjustments to the
+plots. The plotting functions all return a ``Widget`` object. These
+contain and give you access to the underlying matplotlib figure and
+axis, which you can apply any matplotlib machinery to. Let’s see how to
+do this in an example, by first making some synthetic data and computing
+extensions which can be used for plotting.
+
+.. code::
+
+    import spikeinterface.full as si
+    import matplotlib.pyplot as plt
+
+    recording, sorting = si.generate_ground_truth_recording(seed=1205)
+    sorting_analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording)
+    sorting_analyzer.compute({"random_spikes": {'seed': 1205}, "templates": {}, "unit_locations": {}})
+
+    unit_locations = sorting_analyzer.get_extension("unit_locations").get_data()
+
+
+
+.. parsed-literal::
+
+    estimate_sparsity (no parallelization):   0%|          | 0/10 [00:00<?, ?it/s]
+
+
+
+.. parsed-literal::
+
+    estimate_templates_with_accumulator (no parallelization):   0%|          | 0/10 [00:00<?, ?it/s]
+
+
+Now we can plot the ``unit_locations`` and ``unit_templates`` using the
+appropriate widgets (see the `full list of
+widgets <https://spikeinterface.readthedocs.io/en/stable/modules/widgets.html#available-plotting-functions>`__
+for more!). These functions output a ``Widget object``. We’ll assign the
+unit locations widget to ``fig_units``.
+
+.. code::
+
+    fig_units = si.plot_unit_locations(sorting_analyzer)
+
+    # Each widget contains a `matplotlib` figure and axis:
+    print(type(fig_units.figure))
+    print(type(fig_units.ax))
+
+
+.. parsed-literal::
+
+    <class 'matplotlib.figure.Figure'>
+    <class 'matplotlib.axes._axes.Axes'>
+
+
+
+.. image:: customize_a_plot_files/customize_a_plot_4_1.png
+
+
+By gaining access to the matplotlib objects, we are able to utilize the
+full ``matplotlib`` machinery: adding custom titles, axis labels, ticks,
+more plots etc. Let’s customize our unit locations plot. (Note: the
+``SpikeInterface`` Team does not endorse the following style
+conventions):
+
+.. code::
+
+    # Get the widget
+    fig_units = si.plot_unit_locations(sorting_analyzer)
+
+    # Modify the widget's `axis`` to set the title and axes labels
+    fig_units.ax.set_title("My favorite units", fontname = "Comic Sans MS")
+    fig_units.ax.set_xlabel("x probe location (um)")
+    fig_units.ax.set_ylabel("y probe location (um)")
+
+    # You can also set custom ticks
+    fig_units.ax.set_xticks([-60,-30,unit_locations[0,0],30,60])
+    fig_units.ax.set_xticklabels([-60,-30,"unit_0_x",30,60])
+    fig_units.ax.set_yticks([-40,-20,0,unit_locations[0,1],40])
+    fig_units.ax.set_yticklabels([-40,-20,0,"unit_0_y",40])
+
+    # Change the limits of the plot
+    fig_units.ax.set_xlim((-30,50))
+    fig_units.ax.set_ylim((-50,50))
+
+    # And add extra information on the plot
+    fig_units.ax.text(unit_locations[6,0], unit_locations[6,1]+5, s="UNIT 6!!!", fontname="Courier")
+
+    fig_units
+
+
+
+
+.. parsed-literal::
+
+    <spikeinterface.widgets.unit_locations.UnitLocationsWidget at 0x147a81520>
+
+
+
+
+.. image:: customize_a_plot_files/customize_a_plot_6_1.png
+
+
+Beautiful!!!
+
+You can also combine figures into a multi-figure plot. The easiest way
+to do this is to set up your figure and axes first, then tell
+``SpikeInterface`` which axes it should attach the widget plot to.
+Here’s an example of making a unit summary plot.
+
+.. code::
+
+    import matplotlib.pyplot as plt
+    fig, axs = plt.subplots(ncols=2, nrows=1)
+
+    unit_id=8
+    si.plot_unit_locations(sorting_analyzer=sorting_analyzer, ax=axs[0])
+    si.plot_unit_templates(sorting_analyzer, axes=[axs[1]], unit_ids=[f'{unit_id}'])
+
+    axs[0].plot([unit_locations[8,0], unit_locations[8,0]+50], [unit_locations[8,1], unit_locations[8,1]+50])
+    axs[0].text(unit_locations[8,0]+52, unit_locations[8,1]+52, s=f"Unit {unit_id}")
+    axs[0].set_title("Unit location", fontsize=10)
+
+    fig.suptitle(f"Unit {unit_id} summary", fontfamily="Comic Sans MS", fontsize=20)
+
+    fig.tight_layout()
+
+
+
+
+.. image:: customize_a_plot_files/customize_a_plot_8_1.png
+
+
+For more details on what you can do using matplotlib, check out their
+`extensive documentation <https://matplotlib.org/stable/>`__

doc/how_to/customize_a_plot_files/customize_a_plot_4_1.png

@@ -17,3 +17,4 @@ Guides on how to solve specific, short problems in SpikeInterface. Learn how to.
     drift_with_lfp
     auto_curation_training
     auto_curation_prediction
+    customize_a_plot

doc/how_to/customize_a_plot_files/customize_a_plot_6_1.png

@@ -0,0 +1,120 @@
+.. _release0.102.2:
+
+SpikeInterface 0.102.2 release notes
+------------------------------------
+
+2nd April 2025
+
+Minor release with bug fixes
+
+core:
+
+* Add check that `remove_channel_ids` are in parent recording (#3822)
+* Print zarr exception if `super_zarr_open` fails (#3803)
+* Add `_precomputable_kwarg_names` to `BaseExtractor` (#3781)
+* Fix dict representation in aggregation (numpy 2.0) (#3744)
+* Explicit sparsity mask for SparseWaveform (#3742)
+* Renaming: `from_time_labels` -> `from_samples_and_labels` (#3724)
+* New sparsity (to add Ks clustering in components) (#3717)
+
+extractors:
+
+* Add nwb extractors to API docs (#3810)
+* Make sure to use the latest ibllib version - ONE will come along (#3802)
+* Better naming for SI units  (#3788)
+* Add Intan port groups by default (#3753)
+* Fix stream names and ids representation in numpy 2.0 (#3751)
+* Add warning message for streams with mixed units (#3739)
+* Fix: get_streams call in OpenEphysBinaryRecordingExtractor completed (#3738)
+* Fix gain inference for "Volts" unit in Plexon2 files (#3728)
+* Fix IBL streaming tests (#3718)
+* Set max_channel property of MdaSortingExtractor (#3701)
+
+preprocessing:
+
+* Allow preprocessing on dicts of recordings (again) (#3773)
+* Update `load_motion_info` to load legacy motion folders (#3772)
+* Allow `aggregate_channels` to accept a dict of recordings (#3767)
+
+sorters:
+
+* Add job kwargs to KS4 (#3786)
+* Fix KS4 tests (#3768)
+* Patch for merging (#3749)
+
+postprocessing:
+
+* Warn instead of print in solve_monopolar (#3736)
+
+curation:
+
+* Support new sortingview and kachery (#3762)
+* Improve merging and iterative merging (#3487)
+
+widgets:
+
+* In sorting_summary: `rp_violation` -> `rp_violations` (#3770)
+* Support new sortingview and kachery (#3762)
+* Pin sortingview version (#3757)
+* Fitting scaling factors in waveform/template plots for irregular probe layouts (#3748)
+* Fix `extra_properties` propagation in sorting summary and SV string properties (#3716)
+* Enhance the CC plots (#3713)
+* Add `BaseRasterWidget` (#3661)
+* Add LocationsWidget and plot_locations (#3649)
+* Adding colorbar support to peak activity widget (#3646)
+
+sortingcomponents:
+
+* Prevent error of trying to delete non-existent variable in sorting components (#3820)
+* Ks clustering (#3712)
+* Peak SVD motion extraction (#3693)
+* Implement motion_aware option in tdc-peeler (#3682)
+* Improve peak detection benchmark (#3662)
+* improve tdc clustering options (#3658)
+* Improve merging and iterative merging (#3487)
+
+motion correction:
+
+* Wrap medicine motion estimation (#3552)
+
+documentation:
+
+* Switch `print` to `warnings.warn` (#3811)
+* Add nwb extractors to API docs (#3810)
+* Fixed typo in import statement (#3791)
+* Clean up all docs warnings (#3746)
+* Remove commented-out study classes from comparison (#3743)
+
+continuous integration:
+
+* Update tj-actions changes-files for security (#3787)
+* Add torch to test installation (#3706)
+
+packaging:
+
+* Update floor of `setuptools` for metadata (#3800)
+* Switch `numba` check to `importlib.util.find_spec` (#3797)
+* Cleanup imports and use `importlib.util.find_spec` rather than try-except (#3795)
+* Replace deep relative imports with absolute imports (#3766)
+* Add psutil to [test] (#3759)
+
+testing:
+
+* Fix KS4 tests (#3768)
+
+Contributors:
+
+* @FrancescoNegri
+* @OleBialas
+* @abhinavsns
+* @alejoe91
+* @chrishalcrow
+* @guptadivyansh
+* @h-mayorquin
+* @oliche
+* @remi-pr
+* @rly
+* @samuelgarcia
+* @yger
+* @zm711
+* @zzhmark

doc/how_to/customize_a_plot_files/customize_a_plot_8_1.png

@@ -14,7 +14,7 @@ with `nbconvert`. Here are the steps (in this example for the `get_started`):
 
 ```
 >>>  jupytext --to notebook get_started.py
->>>  jupytext --set-formats ipynb,py get_started.ipynb
+>>>  jupytext --set-formats ipynb.py get_started.ipynb
 ```
 
 2. Run the notebook

doc/how_to/index.rst

@@ -0,0 +1,100 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: -all
+#     formats: py:light,ipynb
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.17.0
+#   kernelspec:
+#     display_name: .venv
+#     language: python
+#     name: python3
+# ---
+
+# # Customize a plot
+
+# The `SpikeInterface` widgets are designed to have reasonable default plotting options, but
+# sometimes you'll want to make adjustments to the plots. The plotting functions all return
+# a `Widget` object. These contain and give you access to the underlying matplotlib figure
+# and axis, which you can apply any matplotlib machinery to. Let's see how to do this in an
+# example, by first making some synthetic data and computing extensions which can be used for plotting.
+
+# +
+import spikeinterface.full as si
+import matplotlib.pyplot as plt
+
+recording, sorting = si.generate_ground_truth_recording(seed=1205)
+sorting_analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording)
+sorting_analyzer.compute({"random_spikes": {'seed': 1205}, "templates": {}, "unit_locations": {}})
+
+unit_locations = sorting_analyzer.get_extension("unit_locations").get_data()
+# -
+
+# Now we can plot the `unit_locations` and `unit_templates` using the appropriate widgets
+# (see the  [full list of widgets](https://spikeinterface.readthedocs.io/en/stable/modules/widgets.html#available-plotting-functions)
+# for more!). These functions output a `Widget object`.  We'll assign the unit locations widget to `fig_units`.
+
+# +
+fig_units = si.plot_unit_locations(sorting_analyzer)
+
+# Each widget contains a `matplotlib` figure and axis:
+print(type(fig_units.figure))
+print(type(fig_units.ax))
+# -
+
+# By gaining access to the matplotlib objects, we are able to utilize the full `matplotlib`
+# machinery: adding custom titles, axis labels, ticks, more plots etc. Let's customize
+# our unit locations plot. (Note: the `SpikeInterface` Team does not endorse the following style conventions):
+
+# +
+# Get the widget
+fig_units = si.plot_unit_locations(sorting_analyzer)
+
+# Modify the widget's `axis`` to set the title and axes labels
+fig_units.ax.set_title("My favorite units", fontname = "Comic Sans MS")
+fig_units.ax.set_xlabel("x probe location (um)")
+fig_units.ax.set_ylabel("y probe location (um)")
+
+# You can also set custom ticks
+fig_units.ax.set_xticks([-60,-30,unit_locations[0,0],30,60])
+fig_units.ax.set_xticklabels([-60,-30,"unit_0_x",30,60])
+fig_units.ax.set_yticks([-40,-20,0,unit_locations[0,1],40])
+fig_units.ax.set_yticklabels([-40,-20,0,"unit_0_y",40])
+
+# Change the limits of the plot
+fig_units.ax.set_xlim((-30,50))
+fig_units.ax.set_ylim((-50,50))
+
+# And add extra information on the plot
+fig_units.ax.text(unit_locations[6,0], unit_locations[6,1]+5, s="UNIT 6!!!", fontname="Courier")
+
+fig_units
+# -
+
+# Beautiful!!!
+#
+# You can also combine figures into a multi-figure plot. The easiest way to do this is to set up your
+# figure and axes first, then tell `SpikeInterface` which axes it should attach the widget plot to.
+# Here's an example of making a unit summary plot.
+
+# +
+import matplotlib.pyplot as plt
+fig, axs = plt.subplots(ncols=2, nrows=1)
+
+unit_id=8
+si.plot_unit_locations(sorting_analyzer=sorting_analyzer, ax=axs[0])
+si.plot_unit_templates(sorting_analyzer, axes=[axs[1]], unit_ids=[f'{unit_id}'])
+
+axs[0].plot([unit_locations[8,0], unit_locations[8,0]+50], [unit_locations[8,1], unit_locations[8,1]+50])
+axs[0].text(unit_locations[8,0]+52, unit_locations[8,1]+52, s=f"Unit {unit_id}")
+axs[0].set_title("Unit location", fontsize=10)
+
+fig.suptitle(f"Unit {unit_id} summary", fontfamily="Comic Sans MS", fontsize=20)
+
+fig.tight_layout()
+# -
+
+# For more details on what you can do using matplotlib, check out their [extensive documentation](https://matplotlib.org/stable/)