def test_03a_run_forward_sim_2d(self):
self.ibo = ImageBasedOptimizationAtlas(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_06a_run_inverse_problem_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.init_inverse_problem(seed_position=self.seed_position_2d,
sim_params=self.params_sim,
model_params_varying=self.params_init,
optimization_type=3)
self.ibo.run_inverse_problem(self.opt_params)
def test_02a_prepare_domain_2d(self):
self.ibo = ImageBasedOptimizationAtlas(
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.prepare_domain(plot=True)
def test_01_init_domain(self):
self.ibo = ImageBasedOptimizationAtlas(
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 = ImageBasedOptimizationAtlas(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)
class TestImageBasedOptimizationAtlas(TestCase):
def setUp(self):
self.base_dir_2d = os.path.join(config.output_dir_testing,
'ImageBasedOptimizationAtlas_2d')
self.base_dir_3d = os.path.join(config.output_dir_testing,
'ImageBasedOptimizationAtlas_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], [0.5, 0.5, 0.5]]
# large tolerance for quick tests
self.opt_params = {
'bounds': self.bounds,
'method': "L-BFGS-B",
'tol': 1,
'options': {
'disp': True,
'gtol': 1
}
}
self.seed_position_2d = [148, -67]
self.seed_position_3d = [118, -109, 72]
def test_01_init_domain(self):
self.ibo = ImageBasedOptimizationAtlas(
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 = ImageBasedOptimizationAtlas(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_02a_prepare_domain_2d(self):
self.ibo = ImageBasedOptimizationAtlas(
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.prepare_domain(plot=True)
#
# def test_02b_prepare_domain_3d(self):
# self.ibo = ImageBasedOptimizationAtlas(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.prepare_domain(plot=True)
def test_03a_run_forward_sim_2d(self):
self.ibo = ImageBasedOptimizationAtlas(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_run_forward_sim_3d(self):
# self.ibo = ImageBasedOptimizationAtlas(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_04a_create_target_fields_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.create_target_fields()
def test_05a_plotting_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.plot_all()
def test_06a_run_inverse_problem_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.init_inverse_problem(seed_position=self.seed_position_2d,
sim_params=self.params_sim,
model_params_varying=self.params_init,
optimization_type=3)
self.ibo.run_inverse_problem(self.opt_params)
def test_07a_run_optimized_sim_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
print(self.ibo.params_inverse)
self.ibo.init_optimized_problem()
self.ibo.run_optimized_sim()
def test_08_compare_original_optimized(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.compare_original_optimized(plot=True)
def test_09_postprocess(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.post_process()
self.ibo.write_analysis_summary()
def test_09_postprocess(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.post_process()
self.ibo.write_analysis_summary()
def test_08_compare_original_optimized(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.compare_original_optimized(plot=True)
def test_07a_run_optimized_sim_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
print(self.ibo.params_inverse)
self.ibo.init_optimized_problem()
self.ibo.run_optimized_sim()
def test_05a_plotting_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.plot_all()
def test_04a_create_target_fields_2d(self):
self.ibo = ImageBasedOptimizationAtlas(self.base_dir_2d)
self.ibo.reload_state()
self.ibo.create_target_fields()