Protect unit summary and unit locations plots against NaNs #4128
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alejoe91
added
exporters
eabhorrocks
reviewed
Sep 4, 2025
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I ran into this error
Traceback (most recent call last):
File "/home/saleem_lab/si_edd/SI_processing/runSpikeSorting.py", line 123, in <module>
export_report(sorting_analyzer=probe_we_ks4, output_folder=save_folder +'probe'+str(probe)+'/sorters/kilosort4/report/')
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/exporters/report.py", line 144, in export_report
sw.plot_unit_summary(sorting_analyzer, unit_id, figure=fig)
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/unit_summary.py", line 82, in __init__
BaseWidget.__init__(self, plot_data, backend=backend, **backend_kwargs)
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/base.py", line 87, in __init__
self.do_plot()
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/base.py", line 108, in do_plot
func(self.data_plot, **self.backend_kwargs)
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/unit_summary.py", line 172, in plot_matplotlib
UnitWaveformDensityMapWidget(
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/unit_waveforms_density_map.py", line 87, in __init__
bins = np.arange(bin_min, bin_max, bin_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: arange: cannot compute length
replacing (lines 85, 86) didn't solve the issue.
#bin_min = np.min(templates) * 1.3
#bin_max = np.max(templates) * 1.3
bin_min = np.nanmin(templates) * 1.3
bin_max = np.nanmax(templates) * 1.3
bin_size = (bin_max - bin_min) / 100
bins = np.arange(bin_min, bin_max, bin_size)
but gave:
File "/home/saleem_lab/anaconda3/envs/siedd_env/lib/python3.11/site-packages/spikeinterface/widgets/unit_waveforms_density_map.py", line 90, in __init__
bin_size = (bin_max - bin_min) / 100
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: arange: cannot compute length
I saw there are some empty entries in the templates metrics csv, not sure if this is linked
Unfortunately, the way my code is factored makes this a bit painful to debug quickly
| extremum_channel_indices = get_template_extremum_channel(sorting_analyzer, outputs="index") | ||
| for unit_id in unit_ids: | ||
| if np.any(np.isnan(unit_locations[unit_id])): | ||
| unit_locations[unit_id] = channel_locations[extremum_channel_indices[unit_id]] |
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We should make a copy of unit_locaions in this case to avoid inplace replacement in the analyzer
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It's already a copy since we use the by_unit: https://github.com/SpikeInterface/spikeinterface/blob/main/src/spikeinterface/postprocessing/unit_locations.py#L126-L133
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Fixes #2844
@eabhorrocks @meszena could you test this out when you get the chance?