def test_apply_mask(self): mask = np.zeros((3,4,5)) ix = [[0,1],[1,2],[2,3]] mask[ix] = 1 mask_path = os.path.join(test_data_directory, 'mask.nii') nbsave(Nifti1Image(mask, np.eye(4)), mask_path) apply_mask = ApplyMask() apply_mask.load_mask(mask_path) self.assertTrue(apply_mask.mask.shape==(3,4,5)) data = np.random.randn(2) voxels = np.zeros_like(mask) voxels[ix] = data volume = Nifti1Image(voxels, np.eye(4)) data_out = apply_mask.run(volume) self.assertTrue((data==data_out).all())
def run(self, inp): fpath = self.path_format % self._i nbsave(inp, os.path.join(self.recording_dir, fpath)) self._i += 1
def transform(inp, base, output_transform=False):
if type(base)==str:
base_path = base
else:
base_path = str(uuid4())+'.nii'
nbsave(base, base_path)
if type(inp)==str:
inp_path = inp
else:
inp_path = str(uuid4())+'.nii'
nbsave(inp, inp_path)
out_path = str(uuid4())+'.nii'
params = [
{
'name': 'input file path',
'position': 'last',
'value': inp_path
},
{
'name': 'reference path',
'flag': 'base',
'value': base_path
},
{
'name': 'output file path',
'flag': 'prefix',
'value': out_path
}
]
if output_transform:
transform_path = str(uuid4())+'.aff12.1D'
params.append({
'name': 'transform path',
'flag': '1Dmatrix_save',
'value': transform_path
})
cmd = generate_command('3dvolreg', params)
devnull = open(os.devnull, 'w')
ret = call(cmd, stdout=devnull, stderr=STDOUT, close_fds=True)
if ret>0:
print ' '.join(cmd)
out_img = nbload(out_path)
out_img.get_data()
os.remove(out_path)
if inp is not inp_path:
os.remove(inp_path)
if base is not base_path:
os.remove(base_path)
if output_transform:
xfm = load_afni_xfm(transform_path)
os.remove(transform_path)
return out_img, xfm
else:
return out_img