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handejong / post-kilosort

Python-based toolkit to import and analyse Neuropixel probes data that was previously processed using Kilosort 3.0.
MIT License
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Index Error #1

Open areebaqureshi opened 1 month ago

areebaqureshi commented 1 month ago

Hi, I am very new to coding in Python and this might be a naive problem but I keep getting this error when I try to run pks on my folder:

Screen Shot 2024-06-03 at 12 45 18 PM

Any advice is appreciated. Thank you!

handejong commented 1 month ago

This happens if you run PKS from the command line without an input argument. Presumably you are running it like so:

$ python -i pks.py

However, you should be appending the path to the dataset that you want to look at, like so:

$ python -i pks.py path/to/folder_with_data

If that is not the case. Would you mind sharing the command that you are using to run the script?

areebaqureshi commented 1 month ago

Thank you for your response! This is the command I am using: % python -i pks.py /Users/areebaqureshi/Desktop/MscVisualization/P19-ChR2-Kilosort-Output

Actually now when I run this I get this error: File "/Users/areebaqureshi/Desktop/MscVisualization/KS3_2/pks_processing.py", line 1158, in _find_files_with_extension for file_name in os.listdir(folder_path): ^^^^^^^^^^^^^^^^^^^^^^^ NotADirectoryError: [Errno 20] Not a directory: 'pks.py/'

Is having the 'temp_wh.dat' file necessary to run this the pks.py file?

handejong commented 1 month ago

It depends on which version of Kilosort you used. If you used the Matlab version (Kilosort 3.0) a temp.wh file is necessary. Possibly try navigating (in your terminal) to the "P19-ChR2-Kilosort-Output" folder and run the file pks.py from there using "." as the input folder. I also want to point you towards Phy2 (https://github.com/cortex-lab/phy) which is GUI based, so no Python experience necessary.