Merge branch 'main' into extended-template-metrics

.gitignore

@@ -188,3 +188,4 @@ test_folder/
 
 # Mac OS
 .DS_Store
+test_data.json

README.md

@@ -59,15 +59,17 @@ With SpikeInterface, users can:
 - post-process sorted datasets.
 - compare and benchmark spike sorting outputs.
 - compute quality metrics to validate and curate spike sorting outputs.
-- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, in jupyter)
-- export report and export to phy
-- offer a powerful Qt-based viewer in separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)
-- have some powerful sorting components to build your own sorter.
+- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
+- export a report and/or export to phy
+- offer a powerful Qt-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)
+- have powerful sorting components to build your own sorter.
 
 
 ## Documentation
 
-Detailed documentation for spikeinterface can be found [here](https://spikeinterface.readthedocs.io/en/latest).
+Detailed documentation of the latest PyPI release of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/0.98.2).
+
+Detailed documentation of the development version of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/latest).
 
 Several tutorials to get started can be found in [spiketutorials](https://github.com/SpikeInterface/spiketutorials).
 
@@ -77,9 +79,9 @@ and sorting components.
 You can also have a look at the [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui).
 
 
-## How to install spikeinteface
+## How to install spikeinterface
 
-You can install the new `spikeinterface` version with pip:
+You can install the latest version of `spikeinterface` version with pip:
 
 ```bash
 pip install spikeinterface[full]
@@ -94,7 +96,7 @@ To install all interactive widget backends, you can use:
 ```
 
 
-To get the latest updates, you can install `spikeinterface` from sources:
+To get the latest updates, you can install `spikeinterface` from source:
 
 ```bash
 git clone https://github.com/SpikeInterface/spikeinterface.git

doc/how_to/load_matlab_data.rst

@@ -54,7 +54,7 @@ Use the following Python script to load the binary data into SpikeInterface:
    dtype = "float64"  # MATLAB's double corresponds to Python's float64
 
    # Load data using SpikeInterface
-   recording = si.read_binary(file_path, sampling_frequency=sampling_frequency,
+   recording = si.read_binary(file_paths=file_path, sampling_frequency=sampling_frequency,
                               num_channels=num_channels, dtype=dtype)
 
    # Confirm that the data was loaded correctly by comparing the data shapes and see they match the MATLAB data
@@ -86,7 +86,7 @@ If your data in MATLAB is stored as :code:`int16`, and you know the gain and off
    gain_to_uV = 0.195  # Adjust according to your MATLAB dataset
    offset_to_uV = 0   # Adjust according to your MATLAB dataset
 
-   recording = si.read_binary(file_path, sampling_frequency=sampling_frequency,
+   recording = si.read_binary(file_paths=file_path, sampling_frequency=sampling_frequency,
                               num_channels=num_channels, dtype=dtype_int,
                               gain_to_uV=gain_to_uV, offset_to_uV=offset_to_uV)
 

doc/modules/curation.rst

@@ -24,21 +24,21 @@ The merging and splitting operations are handled by the :py:class:`~spikeinterfa
 
     from spikeinterface.curation import CurationSorting
 
-    sorting = run_sorter('kilosort2', recording)
+    sorting = run_sorter(sorter_name='kilosort2', recording=recording)
 
-    cs = CurationSorting(sorting)
+    cs = CurationSorting(parent_sorting=sorting)
 
     # make a first merge
-    cs.merge(['#1', '#5', '#15'])
+    cs.merge(units_to_merge=['#1', '#5', '#15'])
 
     # make a second merge
-    cs.merge(['#11', '#21'])
+    cs.merge(units_to_merge=['#11', '#21'])
 
     # make a split
     split_index = ... # some criteria on spikes
-    cs.split('#20', split_index)
+    cs.split(split_unit_id='#20', indices_list=split_index)
 
-    # here the final clean sorting
+    # here is the final clean sorting
     clean_sorting = cs.sorting
 
 
@@ -60,20 +60,20 @@ merges. Therefore, it has many parameters and options.
 
     from spikeinterface.curation import MergeUnitsSorting, get_potential_auto_merge
 
-    sorting = run_sorter('kilosort', recording)
+    sorting = run_sorter(sorter_name='kilosort', recording=recording)
 
-    we = extract_waveforms(recording, sorting, folder='wf_folder')
+    we = extract_waveforms(recording=recording, sorting=sorting, folder='wf_folder')
 
     # merges is a list of lists, with unit_ids to be merged.
-    merges = get_potential_auto_merge(we, minimum_spikes=1000,  maximum_distance_um=150.,
+    merges = get_potential_auto_merge(waveform_extractor=we, minimum_spikes=1000,  maximum_distance_um=150.,
                                       peak_sign="neg", bin_ms=0.25, window_ms=100.,
                                       corr_diff_thresh=0.16, template_diff_thresh=0.25,
                                       censored_period_ms=0., refractory_period_ms=1.0,
                                       contamination_threshold=0.2, num_channels=5, num_shift=5,
                                       firing_contamination_balance=1.5)
 
     # here we apply the merges
-    clean_sorting = MergeUnitsSorting(sorting, merges)
+    clean_sorting = MergeUnitsSorting(parent_sorting=sorting, units_to_merge=merges)
 
 
 Manual curation with sorting view
@@ -98,24 +98,24 @@ The manual curation (including merges and labels) can be applied to a SpikeInter
     from spikeinterface.widgets import plot_sorting_summary
 
     # run a sorter and export waveforms
-    sorting = run_sorter('kilosort2', recording)
-    we = extract_waveforms(recording, sorting, folder='wf_folder')
+    sorting = run_sorter(sorter_name'kilosort2', recording=recording)
+    we = extract_waveforms(recording=recording, sorting=sorting, folder='wf_folder')
 
     # some postprocessing is required
-    _ = compute_spike_amplitudes(we)
-    _ = compute_unit_locations(we)
-    _ = compute_template_similarity(we)
-    _ = compute_correlograms(we)
+    _ = compute_spike_amplitudes(waveform_extractor=we)
+    _ = compute_unit_locations(waveform_extractor=we)
+    _ = compute_template_similarity(waveform_extractor=we)
+    _ = compute_correlograms(waveform_extractor=we)
 
     # This loads the data to the cloud for web-based plotting and sharing
-    plot_sorting_summary(we, curation=True, backend='sortingview')
+    plot_sorting_summary(waveform_extractor=we, curation=True, backend='sortingview')
     # we open the printed link URL in a browswe
     # - make manual merges and labeling
     # - from the curation box, click on "Save as snapshot (sha1://)"
 
     # copy the uri
     sha_uri = "sha1://59feb326204cf61356f1a2eb31f04d8e0177c4f1"
-    clean_sorting = apply_sortingview_curation(sorting, uri_or_json=sha_uri)
+    clean_sorting = apply_sortingview_curation(sorting=sorting, uri_or_json=sha_uri)
 
 Note that you can also "Export as JSON" and pass the json file as :code:`uri_or_json` parameter.
 

doc/modules/exporters.rst

@@ -28,15 +28,14 @@ The input of the :py:func:`~spikeinterface.exporters.export_to_phy` is a :code:`
     from spikeinterface.exporters import export_to_phy
 
     # the waveforms are sparse so it is faster to export to phy
-    folder = 'waveforms'
-    we = extract_waveforms(recording, sorting, folder, sparse=True)
+    we = extract_waveforms(recording=recording, sorting=sorting, folder='waveforms', sparse=True)
 
     # some computations are done before to control all options
-    compute_spike_amplitudes(we)
-    compute_principal_components(we, n_components=3, mode='by_channel_global')
+    compute_spike_amplitudes(waveform_extractor=we)
+    compute_principal_components(waveform_extractor=we, n_components=3, mode='by_channel_global')
 
     # the export process is fast because everything is pre-computed
-    export_to_phy(we, output_folder='path/to/phy_folder')
+    export_to_phy(wavefor_extractor=we, output_folder='path/to/phy_folder')
 
 
 
@@ -72,12 +71,12 @@ with many units!
 
 
     # the waveforms are sparse for more interpretable figures
-    we = extract_waveforms(recording, sorting, folder='path/to/wf', sparse=True)
+    we = extract_waveforms(recording=recording, sorting=sorting, folder='path/to/wf', sparse=True)
 
     # some computations are done before to control all options
-    compute_spike_amplitudes(we)
-    compute_correlograms(we)
-    compute_quality_metrics(we, metric_names=['snr', 'isi_violation', 'presence_ratio'])
+    compute_spike_amplitudes(waveform_extractor=we)
+    compute_correlograms(waveform_extractor=we)
+    compute_quality_metrics(waveform_extractor=we, metric_names=['snr', 'isi_violation', 'presence_ratio'])
 
     # the export process
-    export_report(we, output_folder='path/to/spikeinterface-report-folder')
+    export_report(waveform_extractor=we, output_folder='path/to/spikeinterface-report-folder')

doc/modules/extractors.rst

@@ -13,11 +13,12 @@ Most of the :code:`Recording` classes are implemented by wrapping the
 
 Most of the :code:`Sorting` classes are instead directly implemented in SpikeInterface.
 
-
 Although SpikeInterface is object-oriented (class-based), each object can also be loaded with a convenient
 :code:`read_XXXXX()` function.
 
+.. code-block:: python
 
+    import spikeinterface.extractors as se
 
 
 Read one Recording
@@ -27,40 +28,42 @@ Every format can be read with a simple function:
 
 .. code-block:: python
 
-    recording_oe = read_openephys("open-ephys-folder")
+    recording_oe = read_openephys(folder_path="open-ephys-folder")
 
-    recording_spikeglx = read_spikeglx("spikeglx-folder")
+    recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")
 
-    recording_blackrock = read_blackrock("blackrock-folder")
+    recording_blackrock = read_blackrock(folder_path="blackrock-folder")
 
-    recording_mearec = read_mearec("mearec_file.h5")
+    recording_mearec = read_mearec(file_path="mearec_file.h5")
 
 
 Importantly, some formats directly handle the probe information:
 
 .. code-block:: python
 
-    recording_spikeglx = read_spikeglx("spikeglx-folder")
+    recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")
     print(recording_spikeglx.get_probe())
 
-    recording_mearec = read_mearec("mearec_file.h5")
+    recording_mearec = read_mearec(file_path="mearec_file.h5")
     print(recording_mearec.get_probe())
 
 
+
+
 Read one Sorting
 ----------------
 
 .. code-block:: python
 
-    sorting_KS = read_kilosort("kilosort-folder")
+    sorting_KS = read_kilosort(folder_path="kilosort-folder")
 
 
 Read one Event
 --------------
 
 .. code-block:: python
 
-    events_OE = read_openephys_event("open-ephys-folder")
+    events_OE = read_openephys_event(folder_path="open-ephys-folder")
 
 
 For a comprehensive list of compatible technologies, see :ref:`compatible_formats`.
@@ -77,7 +80,7 @@ The actual reading will be done on demand using the :py:meth:`~spikeinterface.co
 .. code-block:: python
 
     # opening a 40GB SpikeGLX dataset is fast
-    recording_spikeglx = read_spikeglx("spikeglx-folder")
+    recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")
 
     # this really does load the full 40GB into memory : not recommended!!!!!
     traces = recording_spikeglx.get_traces(start_frame=None, end_frame=None, return_scaled=False)

doc/modules/motion_correction.rst

@@ -77,12 +77,12 @@ We currently have 3 presets:
 .. code-block:: python
 
   # read and preprocess
-  rec = read_spikeglx('/my/Neuropixel/recording')
-  rec = bandpass_filter(rec)
-  rec = common_reference(rec)
+  rec = read_spikeglx(folder_path='/my/Neuropixel/recording')
+  rec = bandpass_filter(recording=rec)
+  rec = common_reference(recording=rec)
 
   # then correction is one line of code
-  rec_corrected = correct_motion(rec, preset="nonrigid_accurate")
+  rec_corrected = correct_motion(recording=rec, preset="nonrigid_accurate")
 
 The process is quite long due the two first steps (activity profile + motion inference)
 But the return :code:`rec_corrected` is a lazy recording object that will interpolate traces on the
@@ -94,20 +94,20 @@ If you want to user other presets, this is as easy as:
 .. code-block:: python
 
   # mimic kilosort motion
-  rec_corrected = correct_motion(rec, preset="kilosort_like")
+  rec_corrected = correct_motion(recording=rec, preset="kilosort_like")
 
   # super but less accurate and rigid
-  rec_corrected = correct_motion(rec, preset="rigid_fast")
+  rec_corrected = correct_motion(recording=rec, preset="rigid_fast")
 
 
 Optionally any parameter from the preset can be overwritten:
 
 .. code-block:: python
 
-    rec_corrected = correct_motion(rec, preset="nonrigid_accurate",
+    rec_corrected = correct_motion(recording=rec, preset="nonrigid_accurate",
                                    detect_kwargs=dict(
                                        detect_threshold=10.),
-                                   estimate_motion_kwargs=dic(
+                                   estimate_motion_kwargs=dict(
                                        histogram_depth_smooth_um=8.,
                                        time_horizon_s=120.,
                                    ),
@@ -123,7 +123,7 @@ and checking. The folder will contain the motion vector itself of course but als
 .. code-block:: python
 
     motion_folder = '/somewhere/to/save/the/motion'
-    rec_corrected = correct_motion(rec, preset="nonrigid_accurate", folder=motion_folder)
+    rec_corrected = correct_motion(recording=rec, preset="nonrigid_accurate", folder=motion_folder)
 
     # and then
     motion_info = load_motion_info(motion_folder)
@@ -156,14 +156,16 @@ The high-level :py:func:`~spikeinterface.preprocessing.correct_motion()` is inte
 
     job_kwargs = dict(chunk_duration="1s", n_jobs=20, progress_bar=True)
     # Step 1 : activity profile
-    peaks = detect_peaks(rec, method="locally_exclusive", detect_threshold=8.0, **job_kwargs)
+    peaks = detect_peaks(recording=rec, method="locally_exclusive", detect_threshold=8.0, **job_kwargs)
     # (optional) sub-select some peaks to speed up the localization
-    peaks = select_peaks(peaks, ...)
-    peak_locations = localize_peaks(rec, peaks, method="monopolar_triangulation",radius_um=75.0,
+    peaks = select_peaks(peaks=peaks, ...)
+    peak_locations = localize_peaks(recording=rec, peaks=peaks, method="monopolar_triangulation",radius_um=75.0,
                                     max_distance_um=150.0, **job_kwargs)
 
     # Step 2: motion inference
-    motion, temporal_bins, spatial_bins = estimate_motion(rec, peaks, peak_locations,
+    motion, temporal_bins, spatial_bins = estimate_motion(recording=rec,
+                                                          peaks=peaks,
+                                                          peak_locations=peak_locations,
                                                           method="decentralized",
                                                           direction="y",
                                                           bin_duration_s=2.0,
@@ -173,7 +175,9 @@ The high-level :py:func:`~spikeinterface.preprocessing.correct_motion()` is inte
 
     # Step 3: motion interpolation
     # this step is lazy
-    rec_corrected = interpolate_motion(rec, motion, temporal_bins, spatial_bins,
+    rec_corrected = interpolate_motion(recording=rec, motion=motion,
+                                       temporal_bins=temporal_bins,
+                                       spatial_bins=spatial_bins,
                                        border_mode="remove_channels",
                                        spatial_interpolation_method="kriging",
                                        sigma_um=30.)
@@ -196,20 +200,20 @@ different preprocessing chains: one for motion correction and one for spike sort
 
 .. code-block:: python
 
-    raw_rec = read_spikeglx(...)
+    raw_rec = read_spikeglx(folder_path='/spikeglx_folder')
 
     # preprocessing 1 : bandpass (this is smoother) + cmr
-    rec1 = si.bandpass_filter(raw_rec, freq_min=300., freq_max=5000.)
-    rec1 = si.common_reference(rec1, reference='global', operator='median')
+    rec1 = si.bandpass_filter(recording=raw_rec, freq_min=300., freq_max=5000.)
+    rec1 = si.common_reference(recording=rec1, reference='global', operator='median')
 
     # here the corrected recording is done on the preprocessing 1
     # rec_corrected1 will not be used for sorting!
     motion_folder = '/my/folder'
-    rec_corrected1 = correct_motion(rec1, preset="nonrigid_accurate", folder=motion_folder)
+    rec_corrected1 = correct_motion(recording=rec1, preset="nonrigid_accurate", folder=motion_folder)
 
     # preprocessing 2 : highpass + cmr
-    rec2 = si.highpass_filter(raw_rec, freq_min=300.)
-    rec2 = si.common_reference(rec2, reference='global', operator='median')
+    rec2 = si.highpass_filter(recording=raw_rec, freq_min=300.)
+    rec2 = si.common_reference(recording=rec2, reference='global', operator='median')
 
     # we use another preprocessing for the final interpolation
     motion_info = load_motion_info(motion_folder)
@@ -220,7 +224,7 @@ different preprocessing chains: one for motion correction and one for spike sort
                       spatial_bins=motion_info['spatial_bins'],
                       **motion_info['parameters']['interpolate_motion_kwargs'])
 
-    sorting = run_sorter("montainsort5", rec_corrected2)
+    sorting = run_sorter(sorter_name="montainsort5", recording=rec_corrected2)
 
 
 References