IntendedFor.py

#!/usr/bin/python
import json
import os
from glob import glob
import numpy
import subprocess

"""
This script is designed to determine which field maps apply to discrete fMRI scans

Author - Timothy J Hendrickson
"""

def setup(subject_path):
	if "ses" in os.listdir(subject_path)[0]:
		for item in (os.listdir(subject_path)):
			session_path = subject_path + '/'+ item
			IntendedFor(session_path)
	IntendedFor(subject_path)

def IntendedFor(data_path):
    for fmap in sorted(glob(data_path+'/fmap/*.json')):
        # change fmap file permissions to allow write access
        os.system("chmod 660 " + fmap)
        with open(fmap, 'r') as f:
            fmap_json = json.load(f)
            f.close()
        if "IntendedFor" in fmap_json:
            del fmap_json["IntendedFor"]
        shim_fmap = fmap_json["ShimSetting"]
        patient_pos_fmap = fmap_json["ImageOrientationPatientDICOM"]
        func_list = []
        for func in sorted(glob(data_path+'/func/*bold.json')):
            with open(func, 'r') as g:
                func_json = json.load(g)
                shim_func = func_json["ShimSetting"]
                patient_pos_func = func_json["ImageOrientationPatientDICOM"]
                g.close()
            if shim_fmap == shim_func:
                func_nii = glob(data_path+'/func/' +func.split('/')[-1].split('.')[0]+".nii*")[0]
                if "ses" in data_path:
                    func_nii = "/".join(func_nii.split("/")[-3:])
                    func_list.append(func_nii)
                else:
                    func_nii = "/".join(func_nii.split("/")[-2:])
                    func_list.append(func_nii)
        entry = {"IntendedFor": func_list}
        fmap_json.update(entry)
        with open(fmap, 'w') as f:
            json.dump(fmap_json, f)
            f.close()
            
        # change file permissions to read only
        os.system("chmod 444 " + fmap)