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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
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IndexError: index 41 is out of bounds for axis 0 with size 36 #1275

Closed asheff794 closed 5 months ago

asheff794 commented 6 months ago

I'm trying to curate the results of kilosort4 using phy2, but on some sessions I am getting index out of bound errors when I try to open the gui. The index numbers provided relate to the number of clusters identified. In the example session I'm posting about here, 36 refers to the number of sorted clusters in spike_clusters.npy (haven't identified where the 41 comes from yet).

I've tried sorting both with the kilosort4 api and spikeinterface's wrapper and both experience the same issue. I've also tried installing phy2 from the environment.yml file and this doesn't change anything either compared to the README instructions. So far I haven't identified anything consistent about which sessions fail to load, it feels random so far. Here is the full error, let me know if any other kilosort output files would be helpful in debugging.

(phy2)[kilosort4]$ phy template-gui params.py 08:38:21.107 [E] init:62 An error has occurred (IndexError): index 41 is out of bounds for axis 0 with size 36 Traceback (most recent call last): File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/bin/phy", line 8, in sys.exit(phycli()) ^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phy/apps/init.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phy/apps/template/gui.py", line 209, in template_gui model = load_model(params_path) ^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 1433, in load_model return TemplateModel(**get_template_params(params_path)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 339, in init self._load_data() File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 419, in _load_data self.sparse_clusters = self.cluster_waveforms() ^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 1319, in cluster_waveforms mean_waveform = self.get_cluster_mean_waveforms(clust, unwhiten=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 1215, in get_cluster_mean_waveforms template = self.get_template(best_template, unwhiten=unwhiten) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 959, in get_template return self._get_template_dense( ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/phylib/io/model.py", line 881, in _get_template_dense template_w = self.sparse_templates.data[template_id, ...]


File "/gpfs/gibbs/project/jadi/ags72/anaconda/conda_envs/phy2/lib/python3.11/site-packages/numpy/core/memmap.py", line 335, in __getitem__
res = super().__getitem__(index)
^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 41 is out of bounds for axis 0 with size 36
zm711 commented 6 months ago

I would recommend bringing this up on Kilosort repo. On the SpikeInterface side we have seen multiple cases of Kilosort return spikes both before and after the recording time which can lead errors like this, but I'm not sure if this is the cause. You could try scur.remove_excessive_spikes(sorting, recording) followed by export_to_phy and see if that fixes it. Otherwise this seems more like a problem with the KS output that they would need to know about.

Just wanted to point out I had a typo in the curation function. You need to give it the recording too for it to know which spikes are excessive :)

asheff794 commented 6 months ago

Thanks @zm711, running remove_excessive_spikes did solve the problem! For me it was the spike times occuring after the recording period, as I had other sessions with negative spike times and those didn't seem to cause any issues.

I raised the issue on the Kilosort repo so they're aware of the problem. Thanks again!