Proof of Concept

In this notebook we will test out some proofs of concept for our package.

First step: going through a directory to read the files in it

[1]:

import glob

root_dir = '/Users/ttapera/BBL/Projects/CuBIDS/'

bids_dir = 'data/'

[2]:

root_dir + bids_dir

[2]:

'/Users/ttapera/BBL/Projects/CuBIDS/data/'

[6]:

# use glob to list all of the files recursively

all_files = glob.glob(root_dir + bids_dir + '**/**/**/*')

[6]:

['/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_magnitude2.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_phase2.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_magnitude2.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_phase2.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_magnitude1.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_magnitude1.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_phase1.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/fmap/sub-1832999514_ses-PNC2_phase1.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/anat/sub-1832999514_ses-PNC2_T1w.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/anat/sub-1832999514_ses-PNC2_rec-refaced_T1w.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/anat/sub-1832999514_ses-PNC2_rec-refaced_T1w.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/anat/sub-1832999514_ses-PNC2_T1w.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-idemo.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-frac2back.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-idemo.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-rest_acq-singleband_bold.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-frac2back.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC2/func/sub-1832999514_ses-PNC2_task-rest_acq-singleband_bold.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-02_dwi.bval',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-01_dwi.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-02_dwi.bvec',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-01_dwi.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-02_dwi.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-02_dwi.json',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-01_dwi.bval',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/dwi/sub-1832999514_ses-PNC1_run-01_dwi.bvec',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/func/sub-1832999514_ses-PNC1_task-rest_acq-singleband_task-rest_bold.nii.gz',
 '/Users/ttapera/BBL/Projects/CuBIDS/data/sub-1832999514/ses-PNC1/func/sub-1832999514_ses-PNC1_task-rest_acq-singleband_task-rest_bold.json']

This is how we use glob to list all of the files

[ ]: