def test_absorb_cytokines(macrophage_list: MacrophageCellList, cyto,
grid: RectangularGrid):
cyto[1, 2, 3] = 64
macrophage_list.append(
MacrophageCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[2],
z=grid.z[1]), ))
assert len(macrophage_list) == 1
assert cyto[1, 2, 3] == 64
m_abs = 0.5
macrophage_list.absorb_cytokines(m_abs, cyto, grid)
assert cyto[1, 2, 3] == 32
macrophage_list.absorb_cytokines(m_abs, cyto, grid)
assert cyto[1, 2, 3] == 16
macrophage_list.append(
MacrophageCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[2],
z=grid.z[1]), ))
macrophage_list.absorb_cytokines(m_abs, cyto, grid)
assert cyto[1, 2, 3] == 4
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 = 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 populated_macrophage(macrophage_list: MacrophageCellList,
grid: RectangularGrid):
macrophage_list.append(
MacrophageCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[3],
z=grid.z[3]), ))
yield macrophage_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_move_1(populated_macrophage: MacrophageCellList,
grid: RectangularGrid, cyto, tissue, fungus_list):
rec_r = 10
cell = populated_macrophage[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_macrophage.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
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
def test_recruit_new_multiple_locations(macrophage_list: MacrophageCellList,
tissue, grid: RectangularGrid, cyto):
rec_r = 2
p_rec_r = 1.0
rec_rate_ph = 50
cyto[1, 2, 3] = 2
cyto[4, 5, 6] = 2
macrophage_list.recruit_new(rec_rate_ph, rec_r, p_rec_r, tissue, grid,
cyto)
assert len(macrophage_list) == 50
for cell in macrophage_list.cell_data:
vox = grid.get_voxel(cell['point'])
assert vox.x in [3, 6] and vox.y in [2, 5] and vox.z in [1, 4]
def test_produce_cytokines_n(
macrophage_list: MacrophageCellList,
grid: RectangularGrid,
populated_fungus: FungusCellList,
cyto,
):
m_n = 10
macrophage_list.append(
MacrophageCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[3],
z=grid.z[3]), ))
vox = grid.get_voxel(macrophage_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
m_det = 1
assert cyto[3, 3, 3] == 0
macrophage_list.produce_cytokines(m_det, m_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 30
# 2
m_det = 2
cyto[3, 3, 3] = 0
macrophage_list.produce_cytokines(m_det, m_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 50
def test_produce_cytokines_0(
macrophage_list: MacrophageCellList,
grid: RectangularGrid,
populated_fungus: FungusCellList,
cyto,
):
m_det = 0
m_n = 10
assert cyto[3, 3, 3] == 0
macrophage_list.append(
MacrophageCellData.create_cell(point=Point(x=grid.x[3],
y=grid.y[3],
z=grid.z[3]), ))
vox = grid.get_voxel(macrophage_list[0]['point'])
assert vox.z == 3 and vox.y == 3 and vox.x == 3
macrophage_list.produce_cytokines(m_det, m_n, grid, populated_fungus, cyto)
assert cyto[3, 3, 3] == 10
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
def test_sporeless0(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']
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_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_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 macrophage_list(grid: RectangularGrid):
macrophage = MacrophageCellList(grid=grid)
yield macrophage