def splice_dir(dirnames, save, nifti, thresh, check, alldirs, mat):
from pycorr.pietools import splice_dir, copy_nii_hdr, load_nii_or_npy
import numpy as np
if alldirs:
dirs = []
for dname in dirnames:
subdirs = os.walk(dname).next()[1]
print subdirs
dirs.extend([os.path.join(dname, fname) for fname in subdirs])
else:
dirs = dirnames
for dirname in dirs:
if 'thresh_fail' in dirname and alldirs: continue
print dirname
if check:
vols = [int(fname.split('.')[0]) for fname in os.listdir(dirname)]
print set(range(max(vols))) - set(vols)
print 'max volume:\t', max(vols)
continue
M = splice_dir(dirname, save=False, mmap='r')
print M.shape
if thresh:
thresh = load_nii_or_npy(thresh)
M[thresh] = np.nan
if save: np.save(dirname, M)
if nifti:
nii = copy_nii_hdr(nifti, M, save=dirname + ".nii.gz")
#WRITE SAVING LINE HERE
if mat:
import scipy.io as sio
sio.savemat(dirname, {'data': M})
if nifti:
nii = copy_nii_hdr(nifti, M, save=dirname + ".nii.gz")
#WRITE SAVING LINE HERE
if mat:
import scipy.io as sio
sio.savemat(dirname, {'data': M})
if __name__ == '__main__':
import sys, os, argparse
basedir = os.path.dirname(__file__)
sys.path.append(os.path.abspath(basedir + '/../..'))
parser = argparse.ArgumentParser()
parser.add_argument('dirnames', nargs='+', help='directory to reconstruct from parallel analyses')
parser.add_argument('-s', '--save', action='store_true', help='save output as {directory_name}.npy')
parser.add_argument('-n', '--nifti', type=str, help='save as nifti, using header from file provided')
parser.add_argument('-t', '--thresh', type=str, help='threshold mask')
parser.add_argument('-c', '--check', action='store_true', help='check for missing volumes in folder')
parser.add_argument('-a', '--alldirs', action='store_true', help='reconstruct all subdirectories')
parser.add_argument('-m', '--mat', action='store_true', help='save as .mat (in addition to others)')
args = parser.parse_args()
splice_dir(**args.__dict__)