Esempio n. 1
0
	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())
Esempio n. 2
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	def run(self, inp):
		fpath = self.path_format % self._i
		nbsave(inp, os.path.join(self.recording_dir, fpath))
		self._i += 1
Esempio n. 3
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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