def test_create_thresholded_conc_fields(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.create_thresholded_conc_fields(
path_conc_field=self.ibo.path_forward_conc,
path_to_reduced_domain=self.ibo.path_to_domain_meshfct_main,
plot=True)
def test_04a_run_forward_sim_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.init_forward_problem(seed_position=self.seed_position_2d,
sim_params=self.params_sim,
model_params_fixed=self.params_fix,
model_params_varying=self.params_target)
self.ibo.run_forward_sim(plot=True)
def test_03b_mesh_domain_3d(self):
self.ibo = ImageBasedOptimizationBase(
self.base_dir_3d,
path_to_labels_atlas=self.path_to_labels_atlas,
path_to_image_atlas=self.path_to_image_atlas,
image_z_slice=None,
plot=False)
self.ibo.path_to_domain_image_3d = self.ibo.path_to_image_atlas_orig
self.ibo.path_to_domain_labels_3d = self.ibo.path_to_labels_atlas_orig
self.ibo.mesh_domain()
def test_01_init_domain(self):
self.ibo = ImageBasedOptimizationBase(
self.base_dir_2d,
path_to_labels_atlas=self.path_to_labels_atlas,
path_to_image_atlas=self.path_to_image_atlas,
image_z_slice=self.image_slice,
plot=False)
self.ibo2 = ImageBasedOptimizationBase(self.base_dir_2d)
self.assertEqual(self.ibo.path_to_image_atlas_orig,
self.ibo2.path_to_image_atlas_orig)
self.assertEqual(self.ibo.dim, self.ibo2.dim)
def test_05a_create_deformed_image_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
path_image_warped = self.ibo.data.create_image_path(
processing=self.ibo.steps_sub_path_map['target_fields'],
datasource='sim',
frame='deformed',
content='T1')
self.ibo._create_deformed_image(
path_image_ref=self.ibo.path_to_domain_image_2d,
output_path=self.ibo.path_target_fields,
path_image_warped=path_image_warped)
def test_reconstruct_deformation_field_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
path_image_warped = self.ibo.data.create_image_path(
processing=self.ibo.steps_sub_path_map['target_fields'],
datasource='sim',
frame='deformed',
content='T1')
path_to_warp_field = os.path.join(
self.ibo.path_target_fields,
'registered_image_deformed_to_reference_warp.nii.gz')
self.ibo._reconstruct_deformation_field(
path_to_reference_image=self.ibo.path_to_domain_image_2d,
path_to_deformed_image=path_image_warped,
path_to_warp_field=path_to_warp_field,
path_to_reduced_domain=self.ibo.path_to_domain_meshfct_main,
plot=True)
def test_02_reload_state(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
class TestImageBasedOptimizationBase(TestCase):
def setUp(self):
self.base_dir_2d = os.path.join(config.output_dir_testing,
'ImageBasedOptimizationBase_2d')
self.base_dir_3d = os.path.join(config.output_dir_testing,
'ImageBasedOptimizationBase_3d')
self.path_to_labels_atlas = os.path.join(config.test_data_dir,
'brain_atlas_image_3d.mha')
self.path_to_image_atlas = os.path.join(config.test_data_dir,
'brain_atlas_image_t1_3d.mha')
self.image_slice = 87
self.params_sim = {
"sim_time": 10,
"sim_time_step": 1,
}
self.params_fix = {
"E_GM": 3000E-6,
"E_WM": 3000E-6,
"E_CSF": 1000E-6,
"E_VENT": 1000E-6,
"nu_GM": 0.45,
"nu_WM": 0.45,
"nu_CSF": 0.45,
"nu_VENT": 0.3
}
self.params_target = {
"D_WM": 0.1,
"D_GM": 0.02,
"rho_WM": 0.1,
"rho_GM": 0.1,
"coupling": 0.15
}
self.params_init = {
"D_WM": 0.001,
"D_GM": 0.001,
"rho_WM": 0.001,
"rho_GM": 0.001,
"coupling": 0.001
}
self.bounds = [[0.001, 0.001, 0.001, 0.001, 0.001],
[0.5, 0.5, 0.5, 0.5, 0.5]]
self.opt_params = {
'bounds': self.bounds,
'method': "L-BFGS-B",
'tol': 1e-6,
'options': {
'disp': True,
'gtol': 1e-6
}
}
self.seed_position_2d = [148, -67]
self.seed_position_3d = [118, -109, 72]
def test_01_init_domain(self):
self.ibo = ImageBasedOptimizationBase(
self.base_dir_2d,
path_to_labels_atlas=self.path_to_labels_atlas,
path_to_image_atlas=self.path_to_image_atlas,
image_z_slice=self.image_slice,
plot=False)
self.ibo2 = ImageBasedOptimizationBase(self.base_dir_2d)
self.assertEqual(self.ibo.path_to_image_atlas_orig,
self.ibo2.path_to_image_atlas_orig)
self.assertEqual(self.ibo.dim, self.ibo2.dim)
def test_02_reload_state(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
def test_03a_mesh_domain_2d(self):
self.ibo = ImageBasedOptimizationBase(
self.base_dir_2d,
path_to_labels_atlas=self.path_to_labels_atlas,
path_to_image_atlas=self.path_to_image_atlas,
image_z_slice=self.image_slice,
plot=False)
self.ibo.path_to_domain_image_3d = self.ibo.path_to_image_atlas_orig
self.ibo.path_to_domain_labels_3d = self.ibo.path_to_labels_atlas_orig
self.ibo.mesh_domain()
def test_03b_mesh_domain_3d(self):
self.ibo = ImageBasedOptimizationBase(
self.base_dir_3d,
path_to_labels_atlas=self.path_to_labels_atlas,
path_to_image_atlas=self.path_to_image_atlas,
image_z_slice=None,
plot=False)
self.ibo.path_to_domain_image_3d = self.ibo.path_to_image_atlas_orig
self.ibo.path_to_domain_labels_3d = self.ibo.path_to_labels_atlas_orig
self.ibo.mesh_domain()
def test_04a_run_forward_sim_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.init_forward_problem(seed_position=self.seed_position_2d,
sim_params=self.params_sim,
model_params_fixed=self.params_fix,
model_params_varying=self.params_target)
self.ibo.run_forward_sim(plot=True)
# def test_04b_run_forward_sim_3d(self):
# self.ibo = ImageBasedOptimizationBase(self.base_dir_3d)
# self.ibo.reload_state()
# self.ibo.init_forward_problem(seed_position=self.seed_position_3d,
# sim_params=self.params_sim,
# model_params_fixed=self.params_fix,
# model_params_varying=self.params_target)
# self.ibo.run_forward_sim(plot=True)
def test_05a_create_deformed_image_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
path_image_warped = self.ibo.data.create_image_path(
processing=self.ibo.steps_sub_path_map['target_fields'],
datasource='sim',
frame='deformed',
content='T1')
self.ibo._create_deformed_image(
path_image_ref=self.ibo.path_to_domain_image_2d,
output_path=self.ibo.path_target_fields,
path_image_warped=path_image_warped)
def test_reconstruct_deformation_field_2d(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
path_image_warped = self.ibo.data.create_image_path(
processing=self.ibo.steps_sub_path_map['target_fields'],
datasource='sim',
frame='deformed',
content='T1')
path_to_warp_field = os.path.join(
self.ibo.path_target_fields,
'registered_image_deformed_to_reference_warp.nii.gz')
self.ibo._reconstruct_deformation_field(
path_to_reference_image=self.ibo.path_to_domain_image_2d,
path_to_deformed_image=path_image_warped,
path_to_warp_field=path_to_warp_field,
path_to_reduced_domain=self.ibo.path_to_domain_meshfct_main,
plot=True)
def test_create_thresholded_conc_fields(self):
self.ibo = ImageBasedOptimizationBase(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.create_thresholded_conc_fields(
path_conc_field=self.ibo.path_forward_conc,
path_to_reduced_domain=self.ibo.path_to_domain_meshfct_main,
plot=True)
def test_run_inverse_sim(self):
self.fail()
def test_run_optimized_sim(self):
self.fail()