def setUp(self):
# Domain
nx = ny = nz = 10
self.mesh = fenics.RectangleMesh(fenics.Point(-2, -2),
fenics.Point(2, 2), nx, ny)
self.sim = TumorGrowth(self.mesh)
label_funspace = fenics.FunctionSpace(self.mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0.5) ? (1.0) : (2.0)', degree=1)
self.labels = fenics.project(label_expr, label_funspace)
self.tissue_map = {0: 'outside', 1: 'tissue', 2: 'tumor'}
boundary = Boundary()
self.boundary_dict = {'boundary_1': boundary, 'boundary_2': boundary}
self.dirichlet_bcs = {
'clamped_0': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary': Boundary(),
'subspace_id': 0
},
'clamped_1': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_id': 0,
'subspace_id': 0
},
'clamped_2': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_name': 'boundary_1',
'subspace_id': 0
}
}
self.von_neuman_bcs = {
'no_flux': {
'bc_value': fenics.Constant(0.0),
'boundary_id': 0,
'subspace_id': 1
},
'no_flux_2': {
'bc_value': fenics.Constant(0.0),
'boundary_name': 'boundary_1',
'subspace_id': 1
},
}
self.u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
self.u_0_disp_expr = fenics.Constant((0.0, 0.0))
self.youngmod = {'outside': 10E6, 'tissue': 1, 'tumor': 1000}
self.poisson = {'outside': 0.4, 'tissue': 0.4, 'tumor': 0.49}
self.diffusion = {'outside': 0.0, 'tissue': 1.0, 'tumor': 0.1}
self.prolif = {'outside': 0.0, 'tissue': 0.1, 'tumor': 1.0}
self.coupling = {'outside': 0.0, 'tissue': 0.0, 'tumor': 0.5}
u_0_disp_expr = fenics.Constant((0.0, 0.0))
# model parameters
youngmod = {'outside': 10E6, 'A': 0.001, 'B': 0.001}
poisson = {'outside': 0.49, 'A': 0.40, 'B': 0.10}
diffusion = {'outside': 0.0, 'A': 0.1, 'B': 0.0}
prolif = {'outside': 0.0, 'A': 0.1, 'B': 0.0}
coupling = {'outside': 0.0, 'A': 0.2, 'B': 0.0}
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 5
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters(label_function=labels,
domain_names=tissue_map,
boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
ivs = {0: u_0_disp_expr, 1: u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=diffusion,
coupling=coupling,
proliferation=prolif,
E=youngmod,
poisson=poisson,
sim_time=sim_time,
u_0_conc_expr = fenics.Expression(
('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'),
degree=1,
a=1,
x0=0.0,
y0=0.0)
u_0_disp_expr = fenics.Expression(('0', '0'), degree=1)
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 10
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters(boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
ivs = {0: u_0_disp_expr, 1: u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=0.1,
coupling=1,
proliferation=0.1,
E=0.001,
poisson=0.4,
sim_time=sim_time,
sim_time_step=sim_time_step)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
# model parameters
youngmod = {'outside': 10E6, 'A': 0.001, 'B': 0.001}
poisson = {'outside': 0.49, 'A': 0.40, 'B': 0.10}
diffusion = {'outside': 0.0, 'A': 0.1, 'B': 0.0}
prolif = {'outside': 0.0, 'A': 0.1, 'B': 0.0}
coupling = {'outside': 0.0, 'A': 0.2, 'B': 0.0}
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 10
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters(label_function=labels,
domain_names=tissue_map,
boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
ivs = {0: u_0_disp_expr, 1: u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=diffusion,
coupling=coupling,
proliferation=prolif,
E=youngmod,
poisson=poisson,
sim_time=sim_time,
a=0.5,
x0=118,
y0=-109,
z0=72)
# u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)+pow(x[2]-z0,2)) < 15 ? (1.0) : (0.0)',
# degree=1, x0=118, y0=-109, z0=72)
u_0_disp_expr = fenics.Expression(('0.0', '0.0', '0.0'), degree=1)
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 5
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.projection_parameters = {'solver_type': 'cg', 'preconditioner_type': 'amg'}
sim.setup_global_parameters(subdomains=subdomains,
domain_names=tissue_id_name_map,
boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
youngmod = {
'WM': 3000E-6,
'GM': 3000E-6,
'CSF': 1000E-6,
'Ventricles': 1000E-6
}
}
# Initial Values
# u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
# degree=1, x0=0.0, y0=0.0)
u_0_conc_expr = fenics.Expression( ('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'), degree=1, a=1, x0=0.0, y0=0.0)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 20
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters( boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs )
ivs = {0:u_0_disp_expr, 1:u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=0.1,
coupling=1,
proliferation=0.1,
E=0.001,
poisson=0.45,
sim_time=sim_time, sim_time_step=sim_time_step)
# ==============================================================================
a=0.5,
x0=118,
y0=-109,
z0=72)
# u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)+pow(x[2]-z0,2)) < 15 ? (1.0) : (0.0)',
# degree=1, x0=118, y0=-109, z0=72)
u_0_disp_expr = fenics.Expression(('0.0', '0.0', '0.0'), degree=1)
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 50
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.projection_parameters = {'solver_type': 'cg', 'preconditioner_type': 'amg'}
sim.setup_global_parameters(subdomains=subdomains,
domain_names=tissue_id_name_map,
boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
youngmod = {
'WM': 3000E-6,
'GM': 3000E-6,
'CSF': 1000E-6,
'Ventricles': 1000E-6
}
prolif = {
'outside': 0.0,
'CSF': 0.0,
'WM': rho_WM,
'GM': rho_GM,
'Ventricles': 0.0
}
coupling = 0.1
# ==============================================================================
# TumorGrowth
# ==============================================================================
sim_TG = TumorGrowth(mesh)
sim_TG.setup_global_parameters(label_function=labelfunction,
domain_names=tissue_id_name_map,
boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
sim_TG.setup_model_parameters(iv_expression=ivs,
diffusion=diffusion,
coupling=coupling,
proliferation=prolif,
E=youngmod,
poisson=poisson,
sim_time=sim_time,
sim_time_step=sim_time_step)
u_0_conc_expr = fenics.Expression(
('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'),
degree=1,
a=1,
x0=0.0,
y0=0.0)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 5
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters(boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
ivs = {0: u_0_disp_expr, 1: u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=0.1,
coupling=1,
proliferation=0.1,
E=0.001,
poisson=0.45,
sim_time=sim_time,
sim_time_step=sim_time_step)
}
# Initial Values
# u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
# degree=1, x0=0.0, y0=0.0)
u_0_conc_expr = fenics.Expression( ('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'), degree=1, a=1, x0=0.0, y0=0.0)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 20
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters( boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs )
ivs = {0:u_0_disp_expr, 1:u_0_conc_expr}
sim.setup_model_parameters(iv_expression=ivs,
diffusion=0.1,
coupling=1,
proliferation=0.1,
E=0.001,
poisson=0.45,
sim_time=sim_time, sim_time_step=sim_time_step)
# ==============================================================================
class TestBaseImplementation(TestCase):
def setUp(self):
# Domain
nx = ny = nz = 10
self.mesh = fenics.RectangleMesh(fenics.Point(-2, -2),
fenics.Point(2, 2), nx, ny)
self.sim = TumorGrowth(self.mesh)
label_funspace = fenics.FunctionSpace(self.mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0.5) ? (1.0) : (2.0)', degree=1)
self.labels = fenics.project(label_expr, label_funspace)
self.tissue_map = {0: 'outside', 1: 'tissue', 2: 'tumor'}
boundary = Boundary()
self.boundary_dict = {'boundary_1': boundary, 'boundary_2': boundary}
self.dirichlet_bcs = {
'clamped_0': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary': Boundary(),
'subspace_id': 0
},
'clamped_1': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_id': 0,
'subspace_id': 0
},
'clamped_2': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_name': 'boundary_1',
'subspace_id': 0
}
}
self.von_neuman_bcs = {
'no_flux': {
'bc_value': fenics.Constant(0.0),
'boundary_id': 0,
'subspace_id': 1
},
'no_flux_2': {
'bc_value': fenics.Constant(0.0),
'boundary_name': 'boundary_1',
'subspace_id': 1
},
}
self.u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
self.u_0_disp_expr = fenics.Constant((0.0, 0.0))
self.youngmod = {'outside': 10E6, 'tissue': 1, 'tumor': 1000}
self.poisson = {'outside': 0.4, 'tissue': 0.4, 'tumor': 0.49}
self.diffusion = {'outside': 0.0, 'tissue': 1.0, 'tumor': 0.1}
self.prolif = {'outside': 0.0, 'tissue': 0.1, 'tumor': 1.0}
self.coupling = {'outside': 0.0, 'tissue': 0.0, 'tumor': 0.5}
def test_setup_global_parameters(self):
# subdomains from labels
self.sim.setup_global_parameters(label_function=self.labels,
domain_names=self.tissue_map,
boundaries=self.boundary_dict,
dirichlet_bcs=self.dirichlet_bcs,
von_neumann_bcs=self.von_neuman_bcs)
# subdomains
self.assertTrue(hasattr(self.sim, 'subdomains'))
self.assertTrue(hasattr(self.sim.subdomains, 'subdomain_boundaries'))
# functionspaces
self.assertTrue(hasattr(self.sim.functionspace, 'element'))
self.assertTrue(hasattr(self.sim.functionspace, 'subspaces'))
# boundary conditions
self.assertTrue(hasattr(self.sim.bcs, 'dirichlet_bcs'))
self.assertEqual(len(self.sim.bcs.dirichlet_bcs), 3)
self.assertTrue(hasattr(self.sim.bcs, 'von_neumann_bcs'))
self.assertEqual(len(self.sim.bcs.von_neumann_bcs), 2)
def test_setup_model_parameters(self):
self.sim.setup_global_parameters(label_function=self.labels,
domain_names=self.tissue_map,
boundaries=self.boundary_dict,
dirichlet_bcs=self.dirichlet_bcs,
von_neumann_bcs=self.von_neuman_bcs)
ivs = {0: self.u_0_disp_expr, 1: self.u_0_conc_expr}
self.sim.setup_model_parameters(iv_expression=ivs,
diffusion=1,
coupling=1,
proliferation=1,
E=self.params,
poisson=self.params,
otherparam=1,
sim_time=10,
sim_time_step=1)
self.assertTrue(self.sim.params.get_iv(0), self.u_0_disp_expr)
self.assertTrue(hasattr(self.sim.params, 'E'))
self.assertFalse(hasattr(self.sim.params, 'otherparam'))