def test_damage_hyphae_conidia(
neutrophil_list: NeutrophilCellList, grid: RectangularGrid, fungus_list: FungusCellList, iron
):
n_det = 1
n_kill = 2
t = 1
health = 100
point = Point(x=35, y=35, z=35)
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=5
)
)
# conidia
fungus_list.append(
FungusCellData.create_cell(point=point, status=FungusCellData.Status.RESTING)
)
neutrophil_list.damage_hyphae(n_det, n_kill, t, health, grid, fungus_list, iron)
assert fungus_list[0]['health'] == 100
assert neutrophil_list[0]['granule_count'] == 5
assert neutrophil_list[0]['status'] == NeutrophilCellData.Status.NONGRANULATING
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 test_damage_hyphae_0(
neutrophil_list: NeutrophilCellList, grid: RectangularGrid, fungus_list: FungusCellList, iron
):
n_det = 0
n_kill = 2
t = 1
health = 100
point = Point(x=35, y=35, z=35)
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=5
)
)
# hyphae
fungus_list.append(
FungusCellData.create_cell(
point=point, status=FungusCellData.Status.RESTING, form=FungusCellData.Form.HYPHAE
)
)
neutrophil_list.damage_hyphae(n_det, n_kill, t, health, grid, fungus_list, iron)
assert fungus_list[0]['health'] == 50
assert neutrophil_list[0]['granule_count'] == 4
assert neutrophil_list[0]['status'] == NeutrophilCellData.Status.GRANULATING
vox = grid.get_voxel(neutrophil_list[0]['point'])
assert iron[vox.z, vox.y, vox.x] == 0
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 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_damage_hyphae_granuleless(
neutrophil_list: NeutrophilCellList, grid: RectangularGrid, fungus_list: FungusCellList, iron
):
n_det = 1
n_kill = 2
t = 1
health = 100
point = Point(x=35, y=35, z=35)
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=2
)
)
fungus_list.append(
FungusCellData.create_cell(
point=point, status=FungusCellData.Status.RESTING, form=FungusCellData.Form.HYPHAE
)
)
fungus_list.append(
FungusCellData.create_cell(
point=Point(x=45, y=35, z=35),
status=FungusCellData.Status.RESTING,
form=FungusCellData.Form.HYPHAE,
)
)
fungus_list.append(
FungusCellData.create_cell(
point=Point(x=25, y=35, z=35),
status=FungusCellData.Status.RESTING,
form=FungusCellData.Form.HYPHAE,
)
)
neutrophil_list.damage_hyphae(n_det, n_kill, t, health, grid, fungus_list, iron)
assert fungus_list[0]['health'] == 50
# one should be 50, the other 100. It doesn't matter which is which
assert fungus_list[1]['health'] == 100 or fungus_list[2]['health'] == 100
assert fungus_list[1]['health'] == 50 or fungus_list[2]['health'] == 50
assert neutrophil_list[0]['granule_count'] == 0
assert neutrophil_list[0]['status'] == NeutrophilCellData.Status.NONGRANULATING
def test_internalize_conidia_2(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))
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) == 2
assert 0 in epithelium_list[0]['phagosome']
assert 1 in epithelium_list[0]['phagosome']
def test_internalize_and_move(
macrophage_list: MacrophageCellList,
grid: RectangularGrid,
fungus_list: FungusCellList,
cyto,
tissue,
):
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))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
macrophage_list.internalize_conidia(1, 50, 1, grid, fungus_list)
assert fungus_list.cell_data['internalized'][0]
assert fungus_list.cell_data['internalized'][1]
assert macrophage_list.len_phagosome(0) == 2
rec_r = 10
cell = macrophage_list[0]
vox = grid.get_voxel(cell['point'])
assert vox.z == 3 and vox.y == 3 and vox.x == 3
assert cyto.all() == 0
cyto[4, 3, 3] = 10
macrophage_list.move(rec_r, grid, cyto, tissue, fungus_list)
vox = grid.get_voxel(cell['point'])
assert vox.z == 4 and vox.y == 3 and vox.x == 3
for f in fungus_list:
vox = grid.get_voxel(f['point'])
assert vox.z == 4 and vox.y == 3 and vox.x == 3
def test_update(
neutrophil_list: NeutrophilCellList, grid: RectangularGrid, fungus_list: FungusCellList, iron
):
n_det = 1
n_kill = 2
t = 1
health = 100
point = Point(x=35, y=35, z=35)
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=2
)
)
fungus_list.append(
FungusCellData.create_cell(
point=point, status=FungusCellData.Status.RESTING, form=FungusCellData.Form.HYPHAE
)
)
fungus_list.append(
FungusCellData.create_cell(
point=Point(x=45, y=35, z=35),
status=FungusCellData.Status.RESTING,
form=FungusCellData.Form.HYPHAE,
)
)
neutrophil_list.damage_hyphae(n_det, n_kill, t, health, grid, fungus_list, iron)
assert fungus_list[0]['health'] == 50
assert fungus_list[1]['health'] == 50
assert neutrophil_list[0]['granule_count'] == 0
assert neutrophil_list[0]['status'] == NeutrophilCellData.Status.GRANULATING
neutrophil_list.update()
assert neutrophil_list[0]['status'] == NeutrophilCellData.Status.NONGRANULATING
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 populated_fungus(fungus_list: FungusCellList, grid: RectangularGrid):
points = []
for i in range(int(grid.x[1]), int(grid.x[6]), 10):
points.append(Point(x=i, y=i, z=i))
for point in points:
fungus_list.append(
FungusCellData.create_cell(
point=point,
status=FungusCellData.Status.GROWABLE,
form=FungusCellData.Form.HYPHAE,
iron=0,
mobile=False,
))
yield fungus_list
def test_sporeless30(macrophage_list: MacrophageCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
# should release all conidia
point = Point(x=35, y=35, z=35)
for _ in range(0, 30):
macrophage_list.append(MacrophageCellData.create_cell(point=point))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING,
form=FungusCellData.Form.HYPHAE))
macrophage_list.remove_if_sporeless(0.3)
assert len(macrophage_list.alive()) < 30
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_kill_macrophage(macrophage_list: MacrophageCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
# should release all conidia
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))
macrophage_list.internalize_conidia(1, 50, 1, grid, fungus_list)
assert fungus_list.cell_data['internalized'][0]
# simulate death
macrophage_list.clear_all_phagosome(0, fungus_list)
assert not fungus_list.cell_data['internalized'][0]
assert macrophage_list.len_phagosome(0) == 0
def test_sporeless1(macrophage_list: MacrophageCellList, grid: RectangularGrid,
fungus_list: FungusCellList):
# should release all conidia
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))
if len(
fungus_list.alive(fungus_list.cell_data['form'] ==
FungusCellData.Form.CONIDIA)) == 0:
macrophage_list.remove_if_sporeless(0.1)
assert not macrophage_list.cell_data[0]['dead']
macrophage_list.remove_if_sporeless(0.1)
assert macrophage_list.cell_data[0]['dead']
def test_damage_conidia(macrophage_list: MacrophageCellList,
grid: RectangularGrid, fungus_list: FungusCellList):
kill = 2
t = 1
health = 100
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))
macrophage_list.internalize_conidia(1, 50, 1, grid, fungus_list)
macrophage_list.damage_conidia(kill, t, health, fungus_list)
assert fungus_list.cell_data['health'][0] == 50
macrophage_list.damage_conidia(kill, t, health, fungus_list)
assert fungus_list.cell_data['health'][0] == 0
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_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 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_internalize_conidia_n(macrophage_list: MacrophageCellList,
grid: RectangularGrid,
fungus_list: FungusCellList):
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))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
point = Point(x=45, y=35, z=35)
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
point = Point(x=55, y=35, z=35)
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
fungus_list.append(
FungusCellData.create_cell(point=point,
status=FungusCellData.Status.RESTING))
# internalize some not all
macrophage_list.internalize_conidia(1, 50, 1, grid, fungus_list)
assert fungus_list.cell_data['internalized'][0]
assert fungus_list.cell_data['internalized'][2]
assert macrophage_list.len_phagosome(0) == 4
# internalize all
macrophage_list.internalize_conidia(2, 50, 1, grid, fungus_list)
assert fungus_list.cell_data['internalized'][5]
assert macrophage_list.len_phagosome(0) == 6