The readRawData() function now automatically checks if nwb files are present in each data folder, and if so reads them and writes to hdf5 in a format identical to the other read functions. To perform this operation, two additional fields have been added to the GuPPyParametersUsed.json file: nwb_response_series_names and nwb_response_series_indices. Both need to be the same length as folderNames.
Note: the primary conda environment defined by spec_file_mac.txt does not work for .nwb read since pynwb requires python>=3.8, but the existing guppy environment is in python 3.6. To solve this problem, I defined a new guppy_read_env, which uses python>=3.8. The best long-term solution to this problem would be to update the main guppy environment to a newer python version, but since I don't have a solid grasp on all the dependencies I will leave that to @venus-sherathiya.
pauladkisson
commented
1 month ago
This PR adds read support for .nwb files.
The
readRawData()function now automatically checks if nwb files are present in each data folder, and if so reads them and writes to hdf5 in a format identical to the other read functions. To perform this operation, two additional fields have been added to the GuPPyParametersUsed.json file:nwb_response_series_namesandnwb_response_series_indices. Both need to be the same length asfolderNames.Note: the primary conda environment defined by
spec_file_mac.txtdoes not work for .nwb read since pynwb requires python>=3.8, but the existing guppy environment is in python 3.6. To solve this problem, I defined a newguppy_read_env, which uses python>=3.8. The best long-term solution to this problem would be to update the main guppy environment to a newer python version, but since I don't have a solid grasp on all the dependencies I will leave that to @venus-sherathiya.