def test_syn_registration_flow():
moving_data, static_data = get_synthetic_warped_circle(40)
moving_data[..., :10] = 0
moving_data[..., -1:-11:-1] = 0
static_data[..., :10] = 0
static_data[..., -1:-11:-1] = 0
syn_flow = SynRegistrationFlow()
with TemporaryDirectory() as out_dir:
static_img = nib.Nifti1Image(static_data.astype(np.float), np.eye(4))
fname_static = pjoin(out_dir, 'tmp_static.nii.gz')
nib.save(static_img, fname_static)
moving_img = nib.Nifti1Image(moving_data.astype(np.float), np.eye(4))
fname_moving = pjoin(out_dir, 'tmp_moving.nii.gz')
nib.save(moving_img, fname_moving)
positional_args = [fname_static, fname_moving]
metric_optional_args = {'metric': 'ssd',
'mopt_smooth': 4.0,
'mopt_inner_iter': 5,
'mopt_step_type': 'demons',
}
optimizer_optional_args = {'level_iters': [200, 100, 50, 25],
'step_length': 0.5,
'opt_tol': 1e-4,
'inv_iter': 40,
'inv_tol': 1e-3,
'ss_sigma_factor': 0.2
}
all_args = dict(metric_optional_args, **optimizer_optional_args)
syn_flow.run(*positional_args,
out_dir=out_dir,
**all_args
)
warped_path = syn_flow.last_generated_outputs['out_warped']
npt.assert_equal(os.path.isfile(warped_path), True)
warped_map_path = syn_flow.last_generated_outputs['out_field']
npt.assert_equal(os.path.isfile(warped_map_path), True)
def test_syn_registration_flow():
moving_data, static_data = get_synthetic_warped_circle(40)
moving_data[..., :10] = 0
moving_data[..., -1:-11:-1] = 0
static_data[..., :10] = 0
static_data[..., -1:-11:-1] = 0
syn_flow = SynRegistrationFlow()
with TemporaryDirectory() as out_dir:
static_img = nib.Nifti1Image(static_data.astype(np.float), np.eye(4))
fname_static = pjoin(out_dir, 'tmp_static.nii.gz')
nib.save(static_img, fname_static)
moving_img = nib.Nifti1Image(moving_data.astype(np.float), np.eye(4))
fname_moving = pjoin(out_dir, 'tmp_moving.nii.gz')
nib.save(moving_img, fname_moving)
positional_args = [fname_static, fname_moving]
metric_optional_args = {
'metric': 'ssd',
'mopt_smooth': 4.0,
'mopt_inner_iter': 5,
'mopt_step_type': 'demons',
}
optimizer_optional_args = {
'level_iters': [200, 100, 50, 25],
'step_length': 0.5,
'opt_tol': 1e-4,
'inv_iter': 40,
'inv_tol': 1e-3,
'ss_sigma_factor': 0.2
}
all_args = dict(metric_optional_args, **optimizer_optional_args)
syn_flow.run(*positional_args, out_dir=out_dir, **all_args)
warped_path = syn_flow.last_generated_outputs['out_warped']
npt.assert_equal(os.path.isfile(warped_path), True)
warped_map_path = syn_flow.last_generated_outputs['out_field']
npt.assert_equal(os.path.isfile(warped_map_path), True)