def test_filter_out_dead(grid: RectangularGrid):
cells = CellList(grid=grid)
cells.extend([CellData.create_cell(dead=bool(i % 2)) for i in range(10)])
assert_array_equal(cells.alive(), [0, 2, 4, 6, 8])
assert_array_equal(cells.alive([1, 2, 3, 6]), [2, 6])
mask = np.arange(10) < 5
assert_array_equal(cells.alive(mask), [0, 2, 4])
def create_cell_tuple(
cls,
**kwargs,
) -> Tuple:
iteration = 0
phagosome = np.empty(MAX_CONIDIA)
phagosome.fill(-1)
return CellData.create_cell_tuple(**kwargs) + (
iteration,
phagosome,
)
def test_get_neighboring_cells(grid: RectangularGrid):
point = Point(x=4.5, y=4.5, z=4.5)
raw_cells = [CellData.create_cell(point=point) for _ in range(5)]
raw_cells[1]['point'] = Point(x=-1, y=4.5, z=4.5)
raw_cells[4]['point'] = Point(x=4.5, y=4.5, z=-1)
cells = CellList(grid=grid)
cells.extend(raw_cells)
assert_array_equal(cells.get_neighboring_cells(cells[0]), [0, 2, 3])
assert_array_equal(cells.get_cells_in_voxel(Voxel(x=0, y=0, z=0)),
[0, 2, 3])
def create_cell_tuple(
cls,
**kwargs,
) -> Tuple:
initializer = {
'phagosome':
kwargs.get('phagosome', -1 * np.ones(MAX_CONIDIA, dtype=np.int64)),
}
# ensure that these come in the correct order
return CellData.create_cell_tuple(**kwargs) + tuple([
initializer[key] for key, *_ in PhagocyteCellData.PHAGOCYTE_FIELDS
])
def create_cell_tuple(
cls,
*,
status=Status.NONGRANULATING,
granule_count=0,
**kwargs,
) -> Tuple:
iteration = 0
return CellData.create_cell_tuple(**kwargs) + (
status,
iteration,
granule_count,
)
def create_cell_tuple(
cls,
*,
iron_pool: float = 0,
status: Status = Status.RESTING,
**kwargs,
) -> np.record:
iteration = 0
phagosome = np.empty(MAX_PHAGOSOME_LENGTH)
phagosome.fill(-1)
return CellData.create_cell_tuple(**kwargs) + (
status,
iron_pool,
iteration,
phagosome,
)
def create_cell_tuple(cls, **kwargs) -> Tuple:
initializer = {
'iron_pool': kwargs.get('iron_pool', 0),
'state': kwargs.get('state', AfumigatusCellState.FREE),
'status': kwargs.get('status', AfumigatusCellStatus.RESTING_CONIDIA),
'is_root': kwargs.get('is_root', True),
'vec': kwargs.get('vec', random_sphere_point()), # dz, dy, dx
'activation_iteration': kwargs.get('activation_iteration', 0),
'growth_iteration': kwargs.get('growth_iteration', 0),
'boolean_network': kwargs.get('boolean_network', cls.initial_boolean_network()),
'bn_iteration': kwargs.get('bn_iteration', 0),
'next_branch': kwargs.get('next_branch', -1),
'next_septa': kwargs.get('next_septa', -1),
'previous_septa': kwargs.get('previous_septa', -1),
}
# ensure that these come in the correct order
return CellData.create_cell_tuple(**kwargs) + tuple(
[initializer[key] for key, *_ in AfumigatusCellData.AFUMIGATUS_FIELDS]
)
def create_cell_tuple(
cls,
*,
iron: float = 0,
status: Status = Status.RESTING,
form: Form = Form.CONIDIA,
iteration=0,
mobile=False,
internalized=False,
health=100,
**kwargs,
) -> Tuple:
return CellData.create_cell_tuple(**kwargs) + (
form,
status,
iteration,
mobile,
internalized,
iron,
health,
)
def test_move_cell(grid: RectangularGrid):
point = Point(x=4.5, y=4.5, z=4.5)
raw_cells = [CellData.create_cell(point=point) for _ in range(5)]
raw_cells[1]['point'] = Point(x=-1, y=4.5, z=4.5)
raw_cells[4]['point'] = Point(x=4.5, y=4.5, z=-1)
cells = CellList(grid=grid)
cells.extend(raw_cells)
cells[0]['point'] = Point(x=50, y=50, z=50)
# updating an incorrect index will not update the cell at index 0
cells.update_voxel_index([1, 3])
assert_array_equal(cells.get_neighboring_cells(cells[2]), [0, 2, 3])
assert cells._reverse_voxel_index[0] == grid.get_voxel(point)
# this should correctly update the voxel index
cells.update_voxel_index([0])
assert_array_equal(cells.get_neighboring_cells(cells[0]), [0])
assert cells._reverse_voxel_index[0] == grid.get_voxel(cells[0]['point'])
def cell(grid: RectangularGrid, point: Point):
# a single cell in the middle of the domain
cell = CellData.create_cell(point=point)
cells = CellData([cell])
yield cells