def create(cls, config: 'SimulationConfig'):
"""Generate a new state object from a config."""
shape = (
config.getint('simulation', 'nz'),
config.getint('simulation', 'ny'),
config.getint('simulation', 'nx'),
)
spacing = (
config.getfloat('simulation', 'dz'),
config.getfloat('simulation', 'dy'),
config.getfloat('simulation', 'dx'),
)
grid = RectangularGrid.construct_uniform(shape, spacing)
state = State(time=0.0, grid=grid, config=config)
for module in state.config.modules:
if hasattr(state, module.name):
# prevent modules from overriding existing class attributes
raise ValueError(
f'The name "{module.name}" is a reserved token.')
with validation_context(f'{module.name} (construction)'):
state._extra[module.name] = module.StateClass(
global_state=state)
module.construct(state)
return state
def __init__(self, shape: ShapeType, space: SpacingType, scale: int,
randomness: int):
self.scale = scale
self.randomness = randomness
self.shape = (shape[0] * scale, shape[1] * scale, shape[2] * scale)
self.space = space
self.grid = RectangularGrid.construct_uniform(self.shape, self.space)
self.geo = self.grid.allocate_variable(dtype=np.dtype(np.int8))
self.geo.fill(2)
self.fixed = np.zeros(self.shape)
self.duct_f: List[Union[Sphere, Cylinder]] = []
self.sac_f: List[Union[Sphere, Cylinder]] = []
def create(cls, config: 'SimulationConfig'):
"""Generate a new state object from a config."""
voxel_volume = config.getfloat('simulation', 'voxel_volume')
lung_tissue = get_geometry_file(
config.get('simulation', 'geometry_path'))
# python type checker isn't enough to understand this
assert len(lung_tissue.shape) == 3
# noinspection PyTypeChecker
shape: Tuple[int, int, int] = lung_tissue.shape
space_volume = voxel_volume * np.product(shape)
spacing = (
config.getfloat('simulation', 'dz'),
config.getfloat('simulation', 'dy'),
config.getfloat('simulation', 'dx'),
)
grid = RectangularGrid.construct_uniform(shape, spacing)
state = State(
time=0.0,
grid=grid,
config=config,
lung_tissue=lung_tissue,
voxel_volume=voxel_volume,
space_volume=space_volume,
)
for module in state.config.modules:
if hasattr(state, module.name):
# prevent modules from overriding existing class attributes
raise ValueError(
f'The name "{module.name}" is a reserved token.')
with validation_context(f'{module.name} (construction)'):
state._extra[module.name] = module.StateClass(
global_state=state)
module.construct(state)
return state
def grid():
# a 100 x 100 x 100 unit grid
yield RectangularGrid.construct_uniform((10, 10, 10), (10, 10, 10))
def grid():
shape = [10, 20, 30]
spacing = [1, 1, 1]
yield RectangularGrid.construct_uniform(shape=shape, spacing=spacing)
def grid():
yield RectangularGrid.construct_uniform(shape=(3, 3, 3), spacing=(1, 1, 1))