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_produce_cytokines_0(
neutrophil_list: NeutrophilCellList,
grid: RectangularGrid,
populated_fungus: FungusCellList,
cyto,
):
n_det = 0
n_n = 10
assert cyto[3, 3, 3] == 0
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=Point(x=grid.x[3], y=grid.y[3], z=grid.z[3]),
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=5,
)
)
vox = grid.get_voxel(neutrophil_list[0]['point'])
assert vox.z == 3 and vox.y == 3 and vox.x == 3
neutrophil_list.produce_cytokines(n_det, n_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 10
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_absorb_cytokines(neutrophil_list: NeutrophilCellList, cyto, grid: RectangularGrid):
cyto[1, 2, 3] = 64
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=Point(x=grid.x[3], y=grid.y[2], z=grid.z[1]),
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=5,
)
)
assert len(neutrophil_list) == 1
assert cyto[1, 2, 3] == 64
n_abs = 0.5
neutrophil_list.absorb_cytokines(n_abs, cyto, grid)
assert cyto[1, 2, 3] == 32
neutrophil_list.absorb_cytokines(n_abs, cyto, grid)
assert cyto[1, 2, 3] == 16
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=Point(x=grid.x[3], y=grid.y[2], z=grid.z[1]),
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=5,
)
)
neutrophil_list.absorb_cytokines(n_abs, cyto, grid)
assert cyto[1, 2, 3] == 4
def populated_neutrophil(neutrophil_list: NeutrophilCellList, grid: RectangularGrid):
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=Point(x=grid.x[3], y=grid.y[3], z=grid.z[3]),
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=5,
)
)
yield neutrophil_list
def test_move_1(populated_neutrophil: NeutrophilCellList, grid: RectangularGrid, cyto, tissue):
rec_r = 10
cell = populated_neutrophil[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
populated_neutrophil.move(rec_r, grid, cyto, tissue)
cell = populated_neutrophil[0]
vox = grid.get_voxel(cell['point'])
assert vox.z == 4 and vox.y == 3 and vox.x == 3
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_recruit_new_multiple_locations(
neutrophil_list: NeutrophilCellList, tissue, grid: RectangularGrid, cyto
):
rec_r = 2
rec_rate_ph = 50
granule_count = 5
neutropenic = False
previous_time = 1
cyto[5, 5, 5] = 2
cyto[4, 5, 5] = 2
neutrophil_list.recruit_new(
rec_rate_ph, rec_r, granule_count, neutropenic, previous_time, grid, tissue, cyto
)
assert len(neutrophil_list) == 50
for cell in neutrophil_list.cell_data:
vox = grid.get_voxel(cell['point'])
assert vox.x == 5 and vox.y == 5 and vox.z in [4, 5]
def test_produce_cytokines_n(
neutrophil_list: NeutrophilCellList,
grid: RectangularGrid,
populated_fungus: FungusCellList,
cyto,
):
n_n = 10
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=Point(x=grid.x[3], y=grid.y[3], z=grid.z[3]),
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=5,
)
)
vox = grid.get_voxel(neutrophil_list[0]['point'])
assert vox.z == 3 and vox.y == 3 and vox.x == 3
for cell in populated_fungus.cell_data:
vox = grid.get_voxel(cell['point'])
assert vox.z in [1, 2, 3, 4, 5] and vox.y in [1, 2, 3, 4, 5] and vox.x in [1, 2, 3, 4, 5]
# 1
n_det = 1
assert cyto[3, 3, 3] == 0
neutrophil_list.produce_cytokines(n_det, n_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 30
# 2
n_det = 2
cyto[3, 3, 3] = 0
neutrophil_list.produce_cytokines(n_det, n_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 50
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_age(
neutrophil_list: NeutrophilCellList,
):
age_limit = 2
point = Point(x=35, y=35, z=35)
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=2
)
)
# age = 0
neutrophil_list.age()
neutrophil_list.kill_by_age(age_limit)
assert len(neutrophil_list.alive()) == 1
assert neutrophil_list[0]['iteration'] == 1
neutrophil_list.append(
NeutrophilCellData.create_cell(
point=point, status=NeutrophilCellData.Status.NONGRANULATING, granule_count=2
)
)
# age = 1, 0
neutrophil_list.age()
neutrophil_list.kill_by_age(age_limit)
assert len(neutrophil_list.alive()) == 2
assert neutrophil_list[0]['iteration'] == 2
# age = 2, 1
neutrophil_list.age()
neutrophil_list.kill_by_age(age_limit)
assert len(neutrophil_list.alive()) == 1
assert neutrophil_list[0]['dead']
assert neutrophil_list[0]['iteration'] == 3
assert neutrophil_list[1]['iteration'] == 2
# age = 2
neutrophil_list.age()
neutrophil_list.kill_by_age(age_limit)
assert len(neutrophil_list.alive()) == 0
def neutrophil_list(grid: RectangularGrid):
neutrophil = NeutrophilCellList(grid=grid)
yield neutrophil