def test_kill_epithelium_n(epithelium_list: EpitheliumCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
# should release all conidia
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
for _ in range(0, 10):
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
epithelium_list.internalize_conidia(0, 10, 1, grid, fungus_list)
epithelium_list.die_by_germination(fungus_list)
for i in range(0, 10):
assert fungus_list.cell_data['internalized'][i]
assert epithelium_list.len_phagosome(0) == 10
fungus_list.cell_data['status'][6] = FungusCellData.Status.GERMINATED
epithelium_list.die_by_germination(fungus_list)
for i in range(0, 10):
assert not fungus_list.cell_data['internalized'][i]
assert epithelium_list.len_phagosome(0) == 0
def populated_epithelium(epithelium_list: EpitheliumCellList,
grid: RectangularGrid):
epithelium_list.append(
EpitheliumCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[3],
z=grid.z[3]), ))
yield epithelium_list
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_1(epithelium_list: EpitheliumCellList,
grid: RectangularGrid,
fungus_list: FungusCellList):
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
vox = grid.get_voxel(epithelium_list[0]['point'])
epithelium_list.internalize_conidia(0, 10, 1, grid, fungus_list)
assert grid.get_voxel(fungus_list[0]['point']) == vox
assert epithelium_list.len_phagosome(0) == 1
assert 0 in epithelium_list[0]['phagosome']
def test_internalize_conidia_max(epithelium_list: EpitheliumCellList,
grid: RectangularGrid,
fungus_list: FungusCellList):
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
max_spores = 10
epithelium_list[0]['phagosome'][:max_spores] = 99 # artificially fill
epithelium_list.internalize_conidia(0, max_spores, 1, grid, fungus_list)
assert epithelium_list.len_phagosome(0) == max_spores
assert 0 not in epithelium_list[0]['phagosome']
assert not fungus_list[0]['internalized']
def test_dead_conidia_1(epithelium_list: EpitheliumCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
epithelium_list.internalize_conidia(0, 10, 1, grid, fungus_list)
fungus_list[0]['dead'] = True # simulate killing
epithelium_list.remove_dead_fungus(fungus_list)
assert epithelium_list.len_phagosome(0) == 0
assert 0 not in epithelium_list[0]['phagosome']
def test_damage_conidia(epithelium_list: EpitheliumCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
kill = 2
t = 1
health = 100
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
epithelium_list.internalize_conidia(0, 10, 1, grid, fungus_list)
epithelium_list.damage(kill, t, health, fungus_list)
assert fungus_list.cell_data['health'][0] == 50
epithelium_list.damage(kill, t, health, fungus_list)
assert fungus_list.cell_data['health'][0] == 0
def test_kill_epithelium(epithelium_list: EpitheliumCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
# should release all conidia
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
fungus_list.cell_data['internalized'][0] = True
epithelium_list[0]['phagosome'][0] = 0 # internalized
epithelium_list.die_by_germination(fungus_list)
assert fungus_list.cell_data['internalized'][0]
assert epithelium_list.len_phagosome(0) == 1
fungus_list.cell_data['status'][0] = FungusCellData.Status.GERMINATED
epithelium_list.die_by_germination(fungus_list)
assert not fungus_list.cell_data['internalized'][0]
assert epithelium_list.len_phagosome(0) == 0
def test_produce_cytokines_2(
epithelium_list: EpitheliumCellList,
grid: RectangularGrid,
fungus_list: FungusCellList,
m_cyto,
n_cyto,
):
s_det = 1
h_det = 2
cyto_rate = 10
assert m_cyto[3, 3, 3] == 0
assert n_cyto[3, 3, 3] == 0
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
spoint = Point(x=15, y=35, z=35)
fungus_list.append(
FungusCellData.create_cell(
point=spoint,
status=FungusCellData.Status.SWOLLEN,
form=FungusCellData.Form.CONIDIA,
iron=0,
mobile=False,
))
epithelium_list.cytokine_update(s_det, h_det, cyto_rate, m_cyto, n_cyto,
fungus_list, grid)
assert m_cyto[3, 3, 3] == 0
assert n_cyto[3, 3, 3] == 0
fungus_list.append(
FungusCellData.create_cell(
point=spoint,
status=FungusCellData.Status.GROWABLE,
form=FungusCellData.Form.HYPHAE,
iron=0,
mobile=False,
))
epithelium_list.cytokine_update(s_det, h_det, cyto_rate, m_cyto, n_cyto,
fungus_list, grid)
assert m_cyto[3, 3, 3] == 0
assert n_cyto[3, 3, 3] == 10
def test_produce_cytokines_0(
epithelium_list: EpitheliumCellList,
grid: RectangularGrid,
fungus_list: FungusCellList,
m_cyto,
n_cyto,
):
s_det = 0
h_det = 0
cyto_rate = 10
assert m_cyto[3, 3, 3] == 0
assert n_cyto[3, 3, 3] == 0
point = Point(x=35, y=35, z=35)
epithelium_list.append(EpitheliumCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(
point=point,
status=FungusCellData.Status.RESTING,
form=FungusCellData.Form.CONIDIA,
iron=0,
mobile=False,
))
# fungus is not swollen or germinated
epithelium_list.cytokine_update(s_det, h_det, cyto_rate, m_cyto, n_cyto,
fungus_list, grid)
assert m_cyto[3, 3, 3] == 0
assert n_cyto[3, 3, 3] == 0
fungus_list[0]['status'] = FungusCellData.Status.SWOLLEN
epithelium_list.cytokine_update(s_det, h_det, cyto_rate, m_cyto, n_cyto,
fungus_list, grid)
assert m_cyto[3, 3, 3] == 10
assert n_cyto[3, 3, 3] == 10
def epithelium_list(grid: RectangularGrid):
epithelium = EpitheliumCellList(grid=grid)
yield epithelium