def setUp(self):
wd = os.path.dirname(os.path.abspath(__file__))
self.data_dir = os.path.join(wd, 'test_data', 'images')
self.mask_dir = os.path.join(wd, 'test_data', 'masks')
self.img = io.open_nii(os.path.join(self.data_dir, 'test.nii.gz'))
self.brain_mask = io.open_nii(
os.path.join(self.mask_dir, 'mask.nii.gz'))
self.template_mask = os.path.join(self.mask_dir, 'mask.nii.gz')
self.wm_mask = fcm.find_wm_mask(self.img, self.brain_mask)
self.norm_val = 1000
def process(image_fn, brain_mask_fn, wm_mask_fn, output_dir, args, logger):
img = io.open_nii(image_fn)
dirname, base, _ = io.split_filename(image_fn)
if output_dir is not None:
dirname = output_dir
if not os.path.exists(dirname):
logger.info('Making output directory: {}'.format(dirname))
os.mkdir(dirname)
if brain_mask_fn is not None:
mask = io.open_nii(brain_mask_fn)
wm_mask = fcm.find_wm_mask(img, mask)
outfile = os.path.join(dirname, base + '_wmmask.nii.gz')
io.save_nii(wm_mask, outfile, is_nii=True)
if wm_mask_fn is not None:
wm_mask = io.open_nii(wm_mask_fn)
normalized = fcm.fcm_normalize(img, wm_mask, args.norm_value)
outfile = os.path.join(dirname, base + '_fcm.nii.gz')
logger.info('Normalized image saved: {}'.format(outfile))
io.save_nii(normalized, outfile, is_nii=True)