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_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_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 move(self, rec_r, grid, cyto, tissue, fungus: FungusCellList):
for cell_index in self.alive():
cell = self[cell_index]
cell_voxel = grid.get_voxel(cell['point'])
valid_voxel_offsets = []
above_threshold_voxel_offsets = []
# iterate over nearby voxels, recording the cytokine levels
for dx, dy, dz in itertools.product((-1, 0, 1), repeat=3):
zi = cell_voxel.z + dz
yj = cell_voxel.y + dy
xk = cell_voxel.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
if tissue[zi, yj, xk] != TissueTypes.AIR.value:
valid_voxel_offsets.append((dx, dy, dz))
if cyto[zi, yj, xk] >= rec_r:
above_threshold_voxel_offsets.append(
(cyto[zi, yj, xk], (dx, dy, dz)))
# pick a target for the move
if len(above_threshold_voxel_offsets) > 0:
# shuffle + sort (with _only_ 0-key, not lexicographic as tuples) ensures
# randomization when there are equal top cytokine levels
# note that numpy's shuffle will complain about ragged arrays
shuffle(above_threshold_voxel_offsets)
above_threshold_voxel_offsets = sorted(
above_threshold_voxel_offsets,
key=lambda x: x[0],
reverse=True)
_, target_voxel_offset = above_threshold_voxel_offsets[0]
elif len(valid_voxel_offsets) > 0:
target_voxel_offset = choice(valid_voxel_offsets)
else:
raise AssertionError(
'This cell has no valid voxel to move to, including the one that it is in!'
)
# Some nonsense here, b/c jump is happening at the voxel level, not the point level
starting_cell_point = Point(x=cell['point'][2],
y=cell['point'][1],
z=cell['point'][0])
starting_cell_voxel = grid.get_voxel(starting_cell_point)
ending_cell_voxel = grid.get_voxel(
Point(
x=grid.x[cell_voxel.x + target_voxel_offset[0]],
y=grid.y[cell_voxel.y + target_voxel_offset[1]],
z=grid.z[cell_voxel.z + target_voxel_offset[2]],
))
ending_cell_point = (starting_cell_point +
grid.get_voxel_center(ending_cell_voxel) -
grid.get_voxel_center(starting_cell_voxel))
cell['point'] = ending_cell_point
self.update_voxel_index([cell_index])
for i in range(0, self.len_phagosome(cell_index)):
f_index = cell['phagosome'][i]
fungus[f_index]['point'] = ending_cell_point
fungus.update_voxel_index([f_index])
def test_iron_uptake(populated_fungus: FungusCellList, iron):
iron_min = 5
iron_max = 100
iron_absorb = 0.5
assert iron[5, 5, 5] == 10
populated_fungus.iron_uptake(iron, iron_max, iron_min, iron_absorb)
for cell in populated_fungus.cell_data:
assert cell['iron'] == 5
def populated_fungus(fungus_list: FungusCellList):
points = []
for i in range(10, 60, 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 damage_hyphae(self, n_det, n_kill, time, health, grid,
fungus: FungusCellList, iron):
for i in self.alive(self.cell_data['granule_count'] > 0):
cell = self[i]
vox = grid.get_voxel(cell['point'])
# Moore neighborhood, but order partially randomized. Closest to furthest order, but
# the order of any set of points of equal distance is random
neighborhood = list(
itertools.product(tuple(range(-1 * n_det, n_det + 1)),
repeat=3))
shuffle(neighborhood)
neighborhood = sorted(neighborhood,
key=lambda v: v[0]**2 + v[1]**2 + v[2]**2)
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = fungus.get_cells_in_voxel(
Voxel(x=xk, y=yj, z=zi))
if len(index_arr) > 0:
iron[zi, yj, xk] = 0
for index in index_arr:
if (fungus[index]['form'] == FungusCellData.Form.HYPHAE
and cell['granule_count'] > 0):
fungus[index]['health'] -= health * (time / n_kill)
cell['granule_count'] -= 1
cell[
'status'] = NeutrophilCellData.Status.GRANULATING
elif cell['granule_count'] == 0:
cell[
'status'] = NeutrophilCellData.Status.NONGRANULATING
break
def internalize_conidia(self, e_det, max_spores, p_in, grid,
spores: FungusCellList):
for i in self.alive():
cell = self[i]
vox = grid.get_voxel(cell['point'])
# Moore neighborhood, but order partially randomized. Closest to furthest order, but
# the order of any set of points of equal distance is random
neighborhood = list(
itertools.product(tuple(range(-1 * e_det, e_det + 1)),
repeat=3))
shuffle(neighborhood)
neighborhood = sorted(neighborhood,
key=lambda v: v[0]**2 + v[1]**2 + v[2]**2)
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = spores.get_cells_in_voxel(
Voxel(x=xk, y=yj, z=zi))
for index in index_arr:
if (spores[index]['form']
== FungusCellData.Form.CONIDIA
and not spores[index]['internalized']
and p_in > rg.random()):
spores[index]['internalized'] = True
if self.append_to_phagosome(i, index, max_spores):
spores[index]['mobile'] = False
else:
spores[index]['internalized'] = False
def produce_cytokines(self, m_det, m_n, grid, fungus: FungusCellList,
cyto):
for i in self.alive():
vox = grid.get_voxel(self[i]['point'])
hyphae_count = 0
# Moore neighborhood
neighborhood = tuple(
itertools.product(tuple(range(-1 * m_det, m_det + 1)),
repeat=3))
for dx, dy, dz in neighborhood:
zi = vox.z + dz
yj = vox.y + dy
xk = vox.x + dx
if grid.is_valid_voxel(Voxel(x=xk, y=yj, z=zi)):
index_arr = fungus.get_cells_in_voxel(
Voxel(x=xk, y=yj, z=zi))
for index in index_arr:
if fungus[index]['form'] == FungusCellData.Form.HYPHAE:
hyphae_count += 1
cyto[vox.z, vox.y,
vox.x] = cyto[vox.z, vox.y, vox.x] + m_n * hyphae_count
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_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_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_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_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_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 fungus_list(grid: RectangularGrid):
fungus = FungusCellList(grid=grid)
yield fungus
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