review_images.py

""" Test we can correctly import example PARREC files
"""
from __future__ import print_function, absolute_import

from glob import glob
from os.path import join as pjoin, basename, splitext, exists, dirname

import numpy as np

from nibabel import load as top_load, Nifti1Image
from nibabel.processing import resample_to_output

from nibabel.tests.nibabel_data import get_nibabel_data, needs_nibabel_data

def to_real_3d(img):
    if len(img.shape) == 4:
        img = Nifti1Image(img.get_data()[..., 0], img.affine, img.header)
    return resample_to_output(img)


def view_pair(pair):
    img0, img1 = pair
    viewer0 = img0.plot()
    viewer1 = img1.plot()
    viewer0.link_to(viewer1)
    viewer0.show()


NIBABEL_DATA = get_nibabel_data()
ROSETTA = pjoin(NIBABEL_DATA, 'rosetta-samples', 'philips')

def get_pairs():
    pairs = []
    for par in glob(pjoin(ROSETTA, '*', '*', 'PARREC', '*.PAR')):
        par_root, ext = splitext(basename(par))
        # Check we can load the image
        pimg = top_load(par)
        # Compare against NIFTI if present
        nifti_glob = pjoin(dirname(par), '..', 'NIFTI', '4D', '*.nii')
        niftis = glob(nifti_glob)
        if len(niftis) == 0:
            raise ValueError("Missing nifti for " + par)
        if len(niftis) > 1:
            raise ValueError("Too many niftis for " + par)
        nifti_fname = niftis.pop()
        nimg = top_load(nifti_fname)
        pairs.append((to_real_3d(pimg), to_real_3d(nimg)))
    return pairs