Skip to content

Commit

Permalink
Merge 146cb07 into ae27c19
Browse files Browse the repository at this point in the history
  • Loading branch information
@AlonDaks
AlonDaks committed Nov 24, 2015
2 parents ae27c19 + 146cb07 commit 2e71587
Show file tree
Hide file tree
Showing 2 changed files with 179 additions and 36 deletions.
46 changes: 46 additions & 0 deletions code/reproduction/preprocess.py
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
from __future__ import print_function
from __future__ import division
import json
import nibabel as nib
import numpy as np
import sys
from os.path import exists

DATA_PATHS = json.load(open('../../data/data_path.json'))

CONCATENATE_RUNS_ARG_ERROR_MESSAGE = 'Invalid argument: alignment in concatenate_runs'
PREPROCESS_ARG_ERROR_MESSAGE = 'preprocess.py must be provided with alignment argument'


def concatenate_runs(alignment='linear'):
if alignment == 'linear':
pass
elif alignment == 'non_linear':
pass
elif alignment == 'rcds':
for i, subject in enumerate(DATA_PATHS['subjects']):
nii_file_name = 'sub{0}_{1}'.format(i + 1, alignment)
if not exists(nii_file_name):
run_data = []
for j, run in enumerate(subject['runs']):
task_path = run['rcds']['path']
img = nib.load('../../' + task_path)
data = img.get_data()
if j == 0:
run_data.append(data[..., :-4])
elif j >= 1 and j <= 6:
run_data.append(data[..., 4:-4])
else:
run_data.append(data[..., 4:])
concatenated_run_data = np.concatenate(run_data, axis=3)
concatenated_img = nib.Nifti1Image(concatenated_run_data,
np.eye(4))
nib.save(concatenated_img, nii_file_name)
else:
raise ValueError(CONCATENATE_RUNS_ARG_ERROR_MESSAGE)


if __name__ == '__main__':
if len(sys.argv) != 2:
raise ValueError(PREPROCESS_ARG_ERROR_MESSAGE)
concatenate_runs(sys.argv[1])
169 changes: 133 additions & 36 deletions data/data_path.json
View file
Original file line number Diff line number Diff line change
@@ -1,40 +1,137 @@
{
"bold_dico_7Tad2grpbold7Tad": {
"sub1" : {
"runs" : [
{
"path": "data/raw/sub001/BOLD/task001_run001/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "b4350e69fdbb5c62e4c8be66e71c2d86"
},
{
"path": "data/raw/sub001/BOLD/task001_run002/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "ec625fd0de6433cfecbfb542a6598683"
},
{
"path": "data/raw/sub001/BOLD/task001_run003/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "9b92dc4fb03bc5080f7eae904782424a"
},
{
"path": "data/raw/sub001/BOLD/task001_run004/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "658cb0bcbfe28286af1514a232d1d79d"
},
{
"path": "data/raw/sub001/BOLD/task001_run005/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "3d299ebfc9aa9e4419d3f185068fd5a2"
},
{
"path": "data/raw/sub001/BOLD/task001_run006/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "e381354cf8fcb8dcd50d711e0cd24d92"
},
{
"path": "data/raw/sub001/BOLD/task001_run007/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "814090d79f447671ae483ec2ea9dde3c"
},
{
"path": "data/raw/sub001/BOLD/task001_run008/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "4fc0745cb64f76cd9cf43d6351de5848"
}
]
"subjects" :
[
{
"runs" : [
{
"linear" : {
"path": "data/raw/sub001/task001_run001/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "b4350e69fdbb5c62e4c8be66e71c2d86"
},
"rcds" : {
"path": "data/raw/sub001/task001_run001/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run002/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "ec625fd0de6433cfecbfb542a6598683"
},
"rcds" : {
"path": "data/raw/sub001/task001_run002/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run003/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "9b92dc4fb03bc5080f7eae904782424a"
},
"rcds" : {
"path": "data/raw/sub001/task001_run003/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run004/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "658cb0bcbfe28286af1514a232d1d79d"
},
"rcds" : {
"path": "data/raw/sub001/task001_run004/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run005/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "3d299ebfc9aa9e4419d3f185068fd5a2"
},
"rcds" : {
"path": "data/raw/sub001/task001_run005/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run006/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "e381354cf8fcb8dcd50d711e0cd24d92"
},
"rcds" : {
"path": "data/raw/sub001/task001_run006/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run007/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "814090d79f447671ae483ec2ea9dde3c"
},
"rcds" : {
"path": "data/raw/sub001/task001_run007/bold_dico_dico_rcds_nl.nii"
}
},
{
"linear" : {
"path": "data/raw/sub001/task001_run008/bold_dico_dico7Tad2grpbold7Tad.nii",
"hash": "4fc0745cb64f76cd9cf43d6351de5848"
},
"rcds" : {
"path": "data/raw/sub001/task001_run008/bold_dico_dico_rcds_nl.nii"
}
}
]
},
{
"runs" : [
{
"rcds" : {
"path": "data/raw/sub002/task001_run001/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run002/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run003/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run004/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run005/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run006/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run007/bold_dico_dico_rcds_nl.nii"
}
},
{
"rcds" : {
"path": "data/raw/sub002/task001_run008/bold_dico_dico_rcds_nl.nii"
}
}
]
}
],
"templates": {
"brain_mask_intersection": {
"linear": {
"path": "data/raw/templates/linear_brain_mask_intersection.nii",
"hash": "77ba439c5681570be853be33475e6c98"
},
"nonlinear": {
"path": "data/raw/templates/non_linear_brain_mask_intersection.nii",
"hash": "0daaed45e7f26dca2269be91afcd067e"
}
}
}
}

0 comments on commit 2e71587

Please sign in to comment.