def test_internalize_conidia_0(macrophage_list: MacrophageCellList,
grid: RectangularGrid,
fungus_list: FungusCellList):
m_det = 0
point = Point(x=35, y=35, z=35)
macrophage_list.append(MacrophageCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
vox = grid.get_voxel(macrophage_list[0]['point'])
assert len(fungus_list.get_cells_in_voxel(vox)) == 1
f_index = int(fungus_list.get_cells_in_voxel(vox)) # 0
assert f_index == 0
fungus_list[f_index]['form'] = FungusCellData.Form.CONIDIA
fungus_list[f_index]['status'] = FungusCellData.Status.RESTING
macrophage_list.internalize_conidia(m_det, 50, 1, grid, fungus_list)
assert grid.get_voxel(fungus_list[f_index]['point']) == vox
assert fungus_list.cell_data['internalized'][f_index]
assert macrophage_list.len_phagosome(0) == 1
def internalize_conidia(self, m_det, max_spores, p_in, grid,
fungus: FungusCellList):
for i in self.alive():
cell = self[i]
vox = grid.get_voxel(cell['point'])
# Moore neighborhood, but order partially randomized. Closest to furthest order, but
# the order of any set of points of equal distance is random
neighborhood = list(
itertools.product(tuple(range(-1 * m_det, m_det + 1)),
repeat=3))
shuffle(neighborhood)
neighborhood = sorted(neighborhood,
key=lambda v: v[0]**2 + v[1]**2 + v[2]**2)
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = fungus.get_cells_in_voxel(
Voxel(x=xk, y=yj, z=zi))
for index in index_arr:
if (fungus[index]['form']
== FungusCellData.Form.CONIDIA
and not fungus[index]['internalized']
and p_in > rg.random()):
fungus[index]['internalized'] = True
self.append_to_phagosome(i, index, max_spores)
def produce_cytokines(self, m_det, m_n, grid, fungus: FungusCellList,
cyto):
for i in self.alive():
vox = grid.get_voxel(self[i]['point'])
hyphae_count = 0
# Moore neighborhood
neighborhood = tuple(
itertools.product(tuple(range(-1 * m_det, m_det + 1)),
repeat=3))
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = fungus.get_cells_in_voxel(
Voxel(x=xk, y=yj, z=zi))
for index in index_arr:
if fungus[index]['form'] == FungusCellData.Form.HYPHAE:
hyphae_count += 1
cyto[vox.z, vox.y,
vox.x] = cyto[vox.z, vox.y, vox.x] + m_n * hyphae_count
def damage_hyphae(self, n_det, n_kill, time, health, grid, fungus: FungusCellList, iron):
for i in self.alive(self.cell_data['granule_count'] > 0):
cell = self[i]
vox = grid.get_voxel(cell['point'])
# Moore neighborhood, but order partially randomized. Closest to furthest order, but
# the order of any set of points of equal distance is random
neighborhood = list(itertools.product(tuple(range(-1 * n_det, n_det + 1)), repeat=3))
shuffle(neighborhood)
neighborhood = sorted(neighborhood, key=lambda v: v[0] ** 2 + v[1] ** 2 + v[2] ** 2)
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = fungus.get_cells_in_voxel(Voxel(x=xk, y=yj, z=zi))
if len(index_arr) > 0:
iron[zi, yj, xk] = 0
for index in index_arr:
if (
fungus[index]['form'] == FungusCellData.Form.HYPHAE
and cell['granule_count'] > 0
):
fungus[index]['health'] -= health * (time / n_kill)
cell['granule_count'] -= 1
cell['status'] = NeutrophilCellData.Status.GRANULATING
elif cell['granule_count'] == 0:
cell['status'] = NeutrophilCellData.Status.NONGRANULATING
break
def test_internalize_conidia_none(
populated_epithelium: EpitheliumCellList,
grid: RectangularGrid,
fungus_list: FungusCellList,
):
cell = populated_epithelium[0]
vox = grid.get_voxel(cell['point'])
assert len(fungus_list.get_cells_in_voxel(vox)) == 0
populated_epithelium.internalize_conidia(0, 10, 1, grid, fungus_list)
assert populated_epithelium.len_phagosome(0) == 0
for v in cell['phagosome']:
assert v == -1
def test_internalize_conidia_none(
populated_macrophage: MacrophageCellList,
grid: RectangularGrid,
populated_fungus: FungusCellList,
):
m_det = 0
cell = populated_macrophage[0]
vox = grid.get_voxel(cell['point'])
assert len(populated_fungus.get_cells_in_voxel(vox)) == 1
populated_macrophage.internalize_conidia(m_det, 50, 1, grid,
populated_fungus)
assert populated_macrophage.len_phagosome(0) == 0
for v in cell['phagosome']:
assert v == -1