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coganlab / IEEG_Pipelines

A repo of current preprocessing methods for the Cogan Lab
https://ieeg-pipelines.readthedocs.io/en/latest/
MIT License
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get_bad_chans in ieeg/io.py has outdated file paths #73

Closed jimzhang629 closed 1 year ago

jimzhang629 commented 1 year ago

get_bad_chans currently looks for sub-D0057_task-GlobalLocal_acq-01_run-01_channels.tsv

However, this file doesn't exist, the only file that ends in channels.tsv is sub-D0057_task-GlobalLocal_channels.tsv

21 all_bad = get_bad_chans(info_file)
     22 spec.info.update(bads=[b for b in all_bad if b in spec.ch_names])

File [c:\Users\jz421\Desktop\GlobalLocal\ieeg\io.py:229](file:///C:/Users/jz421/Desktop/GlobalLocal/ieeg/io.py:229), in get_bad_chans(fname)
    216 def get_bad_chans(fname: str):
    217     """Gets the bad channels corresponding to a file.
    218 
    219     Parameters
   (...)
    227         The bad channels.
    228     """
--> 229     data = _from_tsv(fname.replace("_ieeg.edf", "_channels.tsv"))
    230     bads = [n for n, s in zip(data['name'], data['status']) if s == 'bad']
    231     return bads

FileNotFoundError: [C:\Users\jz421\Box\CoganLab\BIDS-1.0_GlobalLocal\BIDS\sub-D0057\ieeg\sub-D0057_task-GlobalLocal_acq-01_run-01_channels.tsv](file:///C:/Users/jz421/Box/CoganLab/BIDS-1.0_GlobalLocal/BIDS/sub-D0057/ieeg/sub-D0057_task-GlobalLocal_acq-01_run-01_channels.tsv) not found.