feedsRun

#!/usr/bin/env fslpython

import os
import sys
import subprocess as sp

import numpy   as np
import nibabel as nib


def create_image(shape, pixdim):
    pixdim = list(pixdim)
    data   = np.random.random(shape).astype(np.float32)
    hdr    = nib.Nifti1Header()

    hdr.set_data_dtype(np.float32)
    hdr.set_data_shape(shape)
    hdr.set_zooms(pixdim[:len(shape)])

    return nib.Nifti1Image(data, np.eye(4), hdr)


def check_image(origimg, changedimg, exppixdim):

    gotshape  = changedimg.shape
    gotpixdim = list(changedimg.header.get_zooms())
    gotdata   = changedimg.get_fdata()

    assert origimg.shape == gotshape
    assert gotpixdim     == exppixdim
    assert np.all(origimg.get_fdata() == gotdata)


def run_tests():
    # (image shape, command, exppixdims)
    tests = [
        ((5, 5, 5),    '2 2 2',   (2, 2, 2)),
        ((5, 5, 5),    '2 2 2 2', (2, 2, 2)),
        ((5, 5, 5, 5), '2 2 2',   (2, 2, 2, 1)),
        ((5, 5, 5, 5), '2 2 2 2', (2, 2, 2, 2)),
    ]

    for shape, cmd, exppixdim in tests:

        imgfile = 'image.nii.gz'
        img     = create_image(shape, [1] * len(shape))
        img.to_filename(imgfile)

        try:
            sp.run(['fslchpixdim', imgfile] + list(cmd.split()))
            check_image(img, nib.load(imgfile), list(exppixdim))

        finally:
            os.remove(imgfile)


if __name__ == '__main__':
    sys.exit(run_tests())