tolias-lab-to-nwb 0.1.1

tool to convert Tolias Lab matlab intracellular electrophysiology data into NWB:N format

tolias-lab-to-nwb

Code for converting Tolias Lab data to NWB. The text metadata is stored in a YAML file, and must be edited with the correct fields to be added to the NWB file.

Installation

pip install git+https://github.com/ben-dichter-consulting/tolias-lab-to-nwb.git

Usage

in python:

import os

from dateutil import parser
from ruamel import yaml
from scipy.io import loadmat

from tolias_lab_to_nwb.convert import ToliasNWBConverter
from tolias_lab_to_nwb.data_prep import data_preparation

input_fpath = '/path/to/08 01 2019 sample 1.mat'
output_fpath = 'path/to/dest.nwb'
metafile_fpath = 'path/to/metafile.yml'

fpath_base, fname = os.path.split(input_fpath)
session_id = os.path.splitext(fname)[0]

with open(metafile_fpath) as f:
    metadata = yaml.safe_load(f)

metadata['NWBFile']['session_start_time'] = parser.parse(session_id[:10])
metadata['NWBFile']['session_id'] = session_id

tolias_converter = ToliasNWBConverter(metadata)

data = loadmat(input_fpath)
time, current, voltage, curr_index_0 = data_preparation(data)

tolias_converter.add_icephys_data(current, voltage, rate=25e3)

tolias_converter.save(output_fpath)

in command line:

usage: convert.py [-h] [-o OUTPUT_FPATH] [-m METAFILE] input_fpath

convert .mat file to NWB

positional arguments:
  input_fpath           path of .mat file to convert

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT_FPATH, --output_fpath OUTPUT_FPATH
                        path to save NWB file. If not provided, file will
                        output as input_fname.nwb in the same directory 
                        as the input data.
  -m METAFILE, --metafile METAFILE
                        YAML file that contains metadata for experiment. 
                        If not provided, will look for metafile.yml in the
                        same directory as the input data.

example usage:
  python -m tolias_lab_to_nwb.convert '/path/to/08 01 2019 sample 1.mat'
  python -m tolias_lab_to_nwb.convert '/path/to/08 01 2019 sample 1.mat' -m path/to/metafile.yml
  python -m tolias_lab_to_nwb.convert '/path/to/08 01 2019 sample 1.mat' -m path/to/metafile.yml -o path/to/dest.nwb