cortex-lab / cortex-lab/phylib

Single template

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Python
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Description

Hi,

I used spyking-circus to "sort" a single unit which gave me a single template.
I was having trouble to load this dataset into phy and I tracked down the problem to this line
https://github.com/cortex-lab/phylib/blob/3e4dfb9be8caead2d82b38c842b3fddbc84cf59a/phylib/io/model.py#L476

The problem arise because read_array returns an array of shape (1,91,4) and then the squeeze method changes it to just (91,4).
And then this line gives the error
https://github.com/cortex-lab/phylib/blob/3e4dfb9be8caead2d82b38c842b3fddbc84cf59a/phylib/io/model.py#L710
just after 'Loading templates' and 'Templates are sparse'

I tried exportingfrom spyking-circus to phy without sparse matrices and now it fails in this line
https://github.com/cortex-lab/phylib/blob/3e4dfb9be8caead2d82b38c842b3fddbc84cf59a/phylib/io/model.py#L434
after 'Loading the inverse of the whitening matrix.'

If I remove the 'squeze' I can load this dataset of only one template, and also I didn't have problems with any other dataset sorted with spyking-circus, but I can not load anymore datasets sorted with kilosort2.5.
With kilosort output it fails in this line, just after 'Start capturing exceptions'
https://github.com/cortex-lab/phylib/blob/3e4dfb9be8caead2d82b38c842b3fddbc84cf59a/phylib/io/model.py#L647

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the single-template and kilosort loading failures in phylib/io/model.py at the referenced lines 434, 476, 647, and 710. Compare the array shapes and loading paths for sparse and non-sparse exports; done means the reported datasets load successfully without breaking the existing template-loading cases.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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