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_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_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_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