lorenfranklab / rec_to_binaries Goto Github PK

User may not want to extract all possible days.

Trodes is planning to move to one function to call for extracting binaries

Hi here,
I made a reader in pure python in neo and spikeextractors see:

NeuralEnsemble/python-neo#954
SpikeInterface/spikeextractors#592

not yet merge and finsh but can be usefull to be awre of.

I use the example code in the README to convert a rec file and receive this error:

PermissionError: [Errno 13] Permission denied: 'exportanalog'

permission_error.txt

test_py.txt

Any ideas on what is happening here?

Summary

I am trying to convert the preprocessed binaries to HDF5 files (related: PR #7 ). But nothing happens for LFP and spike conversion.

The immediate cause of this, I think, is that the preproc_LFP_paths and preproc_spike_path` are empty tables.

Prerequisite

After preprocessing, I would do:

data_path = '/my/data/path'
animal_name = 'kf19'
out_dir = 'my/preprocessing/path'
dates = ['20170901']

anim = td.TrodesAnimalInfo(data_path, animal_name,
                           out_dir=out_path, dates=dates)

Current behavior

I get an empty table for the LFP (or spike) paths:

anim.preproc_LFP_paths

Expected behavior

The table for the DIO paths (as well as pos) looks all right.

anim.preproc_dio_paths

I am copying from my Jupyter notebook output cell.

When running rec to nwb conversions on virga-05, I get the following error, which seems to lead to subsequent fatal errors: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory

This error seems to occur when running via jupyter, but not bash. Possibly related to Trodes versions. This error was avoided by swapping to another computer for the time being.

Not sure who to tag - potentially @edeno, though don't think he has sudo powers, so perhaps @lfrank? Virga-05 may need some general clean-up as well. Thank you!

Trodes is planning to move to one function to call for extracting binaries