def single_step_move(self, state: State, cell: PhagocyteCellData,
cell_index: int, cell_list: CellList) -> None:
"""
Move the phagocyte one 1 µm, probabilistically.
depending on single_step_probabilistic_drift
Parameters
----------
state : State
the global simulation state
cell : PhagocyteCellData
the cell to move
cell_index : int
index of cell in cell_list
cell_list : CellList
the CellList for the cell-type (macrophage/neutrophil/etc) of cell
Returns
-------
nothing
"""
grid: RectangularGrid = state.grid
# At this moment, there is no inter-voxel geometry.
cell_voxel: Voxel = grid.get_voxel(cell['point'])
new_point: Point = self.single_step_probabilistic_drift(
state, cell, cell_voxel)
cell['point'] = new_point
cell_list.update_voxel_index([cell_index])
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 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 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 convert_cells_to_vtk(cells: CellList) -> vtkPolyData:
cell_data: CellData = cells.cell_data
live_cells = cells.alive()
cell_data = cell_data[live_cells]
fields = dict(cell_data.dtype.fields) # type: ignore
fields.pop('point')
points = vtkPoints()
poly = vtkPolyData()
poly.SetPoints(points)
if not len(cell_data):
return poly
# vtk uses coordinate ordering x, y, z while we use z, y, x.
points.SetData(numpy_to_vtk(np.flip(cell_data['point'], axis=1)))
point_data = poly.GetPointData()
for field, (dtype, *_) in fields.items():
data = cell_data[field]
# numpy_to_vtk doesn't handle bool for some reason
if dtype == np.dtype('bool'):
data = data.astype(np.dtype('uint8'))
# noinspection PyBroadException
try:
scalar = numpy_to_vtk(data)
except Exception:
print(f'Unhandled data type in field {field}')
continue
scalar.SetName(field)
point_data.AddArray(scalar)
return poly
def test_out_of_memory_error(grid: RectangularGrid, cell: CellData):
cell_list = CellList(grid=grid, max_cells=1)
cell_list.append(cell)
with raises(Exception):
cell_list.append(cell)
def test_serialize(cell_list: CellList, hdf5_group: Group):
cell_list_group = cell_list.save(hdf5_group, 'test', {})
assert cell_list_group['cell_data'].shape == (len(cell_list), )
assert cell_list_group['cell_data'].dtype == cell_list.cell_data.dtype
def cell_list(grid: RectangularGrid, point: Point):
cells = CellList.create_from_seed(grid=grid, point=point)
yield cells
def interact_with_aspergillus(
*,
phagocyte_cell: PhagocyteCellData,
phagocyte_cell_index: int,
phagocyte_cells: CellList,
aspergillus_cell: 'AfumigatusCellData',
aspergillus_cell_index: int,
phagocyte: PhagocyteModuleState,
phagocytize: bool = False,
) -> None:
"""
Possibly have a phagocyte phagocytize a fungal cell.
Parameters
----------
phagocyte_cell : PhagocyteCellData
phagocyte_cell_index: int
aspergillus_cell : AfumigatusCellData
aspergillus_cell_index : int
phagocyte : PhagocyteState
phagocytize : bool
"""
from nlisim.modules.afumigatus import AfumigatusCellState, AfumigatusCellStatus
# We cannot internalize an already internalized fungal cell
if aspergillus_cell['state'] != AfumigatusCellState.FREE:
return
# internalize conidia
if phagocytize or aspergillus_cell['status'] in {
AfumigatusCellStatus.RESTING_CONIDIA,
AfumigatusCellStatus.SWELLING_CONIDIA,
AfumigatusCellStatus.STERILE_CONIDIA,
}:
if phagocyte_cell['status'] not in {
PhagocyteStatus.NECROTIC,
PhagocyteStatus.APOPTOTIC,
PhagocyteStatus.DEAD,
}:
# check to see if we have room before we add in another cell to the phagosome
num_cells_in_phagosome = np.sum(phagocyte_cell['phagosome'] >= 0)
if num_cells_in_phagosome < phagocyte.max_conidia:
aspergillus_cell['state'] = AfumigatusCellState.INTERNALIZING
# place the fungal cell in the phagosome,
# sorting makes sure that an 'empty' i.e. -1 slot is first
phagocyte_cell['phagosome'].sort()
phagocyte_cell['phagosome'][0] = aspergillus_cell_index
# move the phagocyte to the location of the aspergillus
phagocyte_cell['point'] = aspergillus_cell['point']
phagocyte_cells.update_voxel_index([phagocyte_cell_index])
# All phagocytes are activated by their interaction, except with resting conidia
if aspergillus_cell['status'] == AfumigatusCellStatus.RESTING_CONIDIA:
return
phagocyte_cell['state'] = PhagocyteStatus.INTERACTING
if phagocyte_cell['status'] != PhagocyteStatus.ACTIVE:
# non-active phagocytes begin the activation stage
if phagocyte_cell['status'] != PhagocyteStatus.ACTIVATING:
# reset the counter, first time only
phagocyte_cell['status_iteration'] = 0
phagocyte_cell['status'] = PhagocyteStatus.ACTIVATING
else:
# active phagocytes are kept active by resetting their iteration counter
phagocyte_cell['status_iteration'] = 0