APPIAN/civet2bids.py at master · llevitis/APPIAN · GitHub

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import os
from sys import exit, argv
from glob import glob
from shutil import copy
from ntpath import basename

def old_paths(files, attributes):
    l=[]
    for f in files:
        d={}
        file_paths, ext = os.path.splitext(f)
        filename = basename(file_paths)
        f_split = filename.split('_')
        for var  in attributes:
            d[var]=None
            for x in f_split:
                if var in x :
                    d[var]=x
        d['ext'] = ext
        l.append(d)
    return(l)

def new_paths(files,attributes, out_dir, image_type, folder_name, l):
    for d,f in zip(l,files):
        print d, files
        new_pet = out_dir + os.sep + d['sub'] + os.sep
        if not os.path.exists(new_pet) : os.mkdir(new_pet)
        if d['ses'] != None:
            new_pet = new_pet + '_' + d['ses'] +  os.sep
        if not os.path.exists(new_pet) : os.mkdir(new_pet)
        new_pet +=  folder_name + os.sep
        if not os.path.exists(new_pet) : os.mkdir(new_pet)
        for var in  attributes:
            if d[var] != None:
                new_pet +=  d[var] + '_'

        new_pet = new_pet + image_type + d['ext']
        print f, new_pet
        if not os.path.exists(new_pet):
            copy(f, new_pet)

def copy_paths(file_dir, out_dir, attributes, input_image_type, image_type, folder_name):
    files = glob(file_dir+"*"+ input_image_type + ".*")
    new_paths(files, attributes, out_dir, image_type, folder_name, old_paths(files, attributes))

def civet2bids(pet_dir, civet_dir, out_dir):
    pet_attributes = ['sub', 'ses', 'task', 'acq', 'rec']
    t1_attributes = [ 'sub', 'ses', 'task']
    input_image_suffixes = ['pet', 't1', 't1_nuc',  't1_tal', 'brain_mask', 'skull_mask', 't1_tal', 'nlfit_It', 'classify', 'labels_masked', 'gray_surface_*', 'white_surface_*', 'mid_surface_*'  ]
    output_image_suffixes=['pet', 'T1w', 'T1w_nuc', 'T1w_space-mni', 'T1w_space-mni_brainmask', 'T1w_space-mni_skullmask', 'target-MNI_affine', 'target-MNI_warp', 'space-mni_variant-cls_dtissue', 'space-mni_variant-seg_dtissue', 'pial', 'wmsmooth', 'midthickness' ]
    input_dirs = [ pet_dir, civet_dir+'*/native/', civet_dir+'*/native/', civet_dir+'*/final/', civet_dir+'*/mask/', civet_dir+'*/mask/', civet_dir+'*/transforms/linear/', civet_dir+'*/transforms/nonlinear/', civet_dir+'*/classify/' , civet_dir+'*/segment/', civet_dir+'*/surfaces/', civet_dir+'*/surfaces/', civet_dir+'*/surfaces/'  ]
    folder_names = ['pet', 'anat', 'anat', 'anat', 'anat', 'anat', 'transforms', 'transforms', 'anat', 'anat' ]
    n = len(input_image_suffixes) - 1
    attributes_list = [ pet_attributes ] + [ t1_attributes ] * n

    if not os.path.exists(out_dir) : os.mkdir(out_dir)
    for input_dir, attributes, input_image_suffix, output_image_suffix, folder_name in zip(input_dirs, attributes_list, input_image_suffixes, output_image_suffixes, folder_names ):
        print input_dir, input_image_suffix, attributes, folder_name
        copy_paths(input_dir, out_dir, attributes, input_image_suffix, output_image_suffix, folder_name)


if __name__ == "__main__":
    if len(argv) != 4:
        print "Useage: civet2bids <PET Directory> <CIVET Directory> <Out Directory>"
        exit(1)
    elif argv[1] in ["-help", "--help"]:
        print "Useage: civet2bids <PET Directory> <CIVET Directory> <Out Directory>"
        exit(1)
    pet_dir = argv[1] + os.sep
    civet_dir = argv[2] + os.sep
    out_dir = argv[3] + os.sep
    civet2bids(pet_dir, civet_dir, out_dir)