def test_simulate():
dim = 1
cbm_solver = cbmos.CBModel(ff.Cubic(), scpi.solve_ivp, dim)
cell_list = [cl.Cell(0, [0]), cl.Cell(1, [1.0], 0.0, True)]
cell_list[1].division_time = 1.05 # make sure not to divide at t_data
N = 100
t_data = np.linspace(0, 10, N) # stay away from 24 hours
t_data_sol, history = cbm_solver.simulate(cell_list,
t_data, {}, {},
raw_t=False)
assert len(history) == N
assert t_data_sol.tolist() == t_data.tolist()
assert len(history[10]) == 2
assert np.isclose(abs(history[10][0].position - history[10][1].position),
1)
assert len(history[-1]) == 3
scells = sorted(history[-1], key=lambda c: c.position)
assert np.isclose(abs(scells[0].position - scells[1].position),
1,
atol=1e-03)
assert np.isclose(abs(scells[1].position - scells[2].position),
1,
atol=1e-03)
def test_no_division_skipped():
dim = 1
cbm_solver = cbmos.CBModel(ff.Linear(), scpi.solve_ivp, dim)
cell_list = [
cl.Cell(0, [0], proliferating=True),
cl.Cell(1, [1.0], 0.0, True)
]
cell_list[0].division_time = 1.0
cell_list[1].division_time = 1.0
t_data = np.linspace(0, 30, 101)
_, history = cbm_solver.simulate(cell_list, t_data, {}, {}, raw_t=False)
eq = [
hq.heappop(cbm_solver._queue._events)
for i in range(len(cbm_solver._queue._events))
]
assert eq == sorted(eq)
assert len(eq) == len(history[-1]) - 1
for t, cells in zip(t_data, history):
for c in cells:
assert c.birthtime <= t
assert c.division_time > t
def test_event_at_t_data():
dim = 1
cbm_solver = cbmos.CBModel(ff.Linear(), scpi.solve_ivp, dim)
cell_list = [
cl.Cell(0, [0], proliferating=True),
cl.Cell(1, [1.0], 0.0, True)
]
cell_list[0].division_time = 1.0
cell_list[1].division_time = 1.0
t_data = np.linspace(0, 10, 101)
_, history = cbm_solver.simulate(cell_list, t_data, {}, {}, raw_t=False)
assert len(history) == len(t_data)
def test_push():
cell = cl.Cell(0, [0, 0])
queue = eventqueue.EventQueue([])
queue.push(1, cell)
assert len(queue._events) == 1
assert (1, cell) == queue._events[0]
cell2 = cl.Cell(1, [0.25, 0.25])
queue.push(2, cell2)
assert len(queue._events) == 2
assert queue._events[0][0] <= queue._events[1][0]
def test_cell_list_order():
# 2D honeycomb mesh
n_x = 5
n_y = 5
xcrds = [(2 * i + (j % 2)) * 0.5 for j in range(n_y) for i in range(n_x)]
ycrds = [np.sqrt(3) * j * 0.5 for j in range(n_y) for i in range(n_x)]
# make cell_list for the sheet
sheet = [
cl.Cell(i, [x, y], -6.0, True, lambda t: 6 + t)
for i, x, y in zip(range(n_x * n_y), xcrds, ycrds)
]
# delete cells to make it circular
del sheet[24]
del sheet[20]
del sheet[19]
del sheet[9]
del sheet[4]
del sheet[0]
solver = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, 2)
dt = 0.01
t_data = np.arange(0, 3, dt)
_, history = solver.simulate(sheet,
t_data, {"mu": 6.91}, {'dt': dt},
seed=17)
history = history[1:] # delete initial data because that's less cells
ids = [cell.ID for cell in history[0]]
assert np.all([ids == [cell.ID for cell in clt] for clt in history[1:]])
def test_cell_list_copied():
dim = 1
cbm_solver_one = cbmos.CBModel(ff.Linear(), scpi.solve_ivp, dim)
cbm_solver_two = cbmos.CBModel(ff.Linear(), scpi.solve_ivp, dim)
cell_list = [
cl.Cell(0, [0], proliferating=True),
cl.Cell(1, [0.3], proliferating=True)
]
t_data = np.linspace(0, 1, 101)
_, history_one = cbm_solver_one.simulate(cell_list, t_data, {}, {})
_, history_two = cbm_solver_two.simulate(cell_list, t_data, {}, {})
assert history_two[0][0].position == np.array([0])
assert history_two[0][1].position == np.array([0.3])
def test_sparse_tdata():
dim = 3
solver_cubic = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, dim)
ancestor = [cl.Cell(0, np.zeros((dim, )), -5, True)]
dt = 0.1
t_f = 50
t_data = np.linspace(0, t_f, 2)
_, tumor_cubic = solver_cubic.simulate(ancestor, t_data, {"mu": 6.91},
{"dt": dt})
def test_cell_dimension_exception():
dim = 3
cbm_solver = cbmos.CBModel(ff.Logarithmic(), ef.solve_ivp, dim)
cell_list = [cl.Cell(0, [0, 0], proliferating=True)]
t_data = np.linspace(0, 100, 10)
with pytest.raises(AssertionError):
cbm_solver.simulate(cell_list, t_data, {}, {})
def test_tdata_raw():
n = 100
s = 1.0 # rest length
tf = 1.0 # final time
rA = 1.5 # maximum interaction distance
params_cubic = {"mu": 6.91, "s": s, "rA": rA}
solver_ef = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, 1)
t_data = np.linspace(0, 1, n)
cell_list = [
cl.Cell(0, [0], proliferating=False),
cl.Cell(1, [0.3], proliferating=False)
]
t_data_sol, sols = solver_ef.simulate(cell_list,
t_data,
params_cubic, {'dt': 0.03},
raw_t=True)
assert len(t_data_sol) == len(sols)
def test_tdata():
n = 100
s = 1.0 # rest length
tf = 1.0 # final time
rA = 1.5 # maximum interaction distance
params_cubic = {"mu": 6.91, "s": s, "rA": rA}
solver_ef = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, 1)
t_data = np.linspace(0, 1, n)
cell_list = [
cl.Cell(0, [0], proliferating=False),
cl.Cell(1, [0.3], proliferating=False)
]
_, sols = solver_ef.simulate(cell_list,
t_data,
params_cubic, {'dt': 0.03},
raw_t=False)
y = np.array(
[np.squeeze([clt[0].position, clt[1].position]) for clt in sols])
assert y.shape == (n, 2)
def test_tdata_raw_division():
n = 100
s = 1.0 # rest length
tf = 1.0 # final time
rA = 1.5 # maximum interaction distance
params_cubic = {"mu": 6.91, "s": s, "rA": rA}
solver_ef = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, 1)
t_data = np.linspace(0, 50, n)
cell_list = [
cl.Cell(0, [0], proliferating=True),
cl.Cell(1, [0.3], proliferating=True)
]
t_data_sol, sols = solver_ef.simulate(cell_list,
t_data,
params_cubic, {'dt': 0.03},
raw_t=True)
assert len(sols[-1]) > len(cell_list) # Make sure some cells multiplied
assert len(t_data_sol) == len(sols)
assert all([t[0] < t[1] for t in zip(t_data_sol, t_data_sol[1:])])
def test_update_positions():
dim = 3
cbm_solver = cbmos.CBModel(ff.Linear(), ef.solve_ivp, dim)
cell_list = [cl.Cell(i, [0, 0, i]) for i in range(5)]
for i, cell in enumerate(cell_list):
cell.division_time = cell.ID
cbm_solver.cell_list = cell_list
new_positions = [[0, i, i] for i in range(5)]
cbm_solver._update_positions(new_positions)
for i, cell in enumerate(cbm_solver.cell_list):
print(cell.position)
assert cell.position.tolist() == [0, i, i]
def test_seed():
dim = 3
cbm_solver = cbmos.CBModel(ff.Logarithmic(), ef.solve_ivp, dim)
cell_list = [cl.Cell(0, [0, 0, 0], proliferating=True)]
t_data = np.linspace(0, 100, 10)
histories = [
cbm_solver.simulate(cell_list, t_data, {}, {}, seed=seed)[1]
for seed in [0, 0, 1, None, None]
]
for cells in zip(*[history[-1] for history in histories]):
assert cells[0].position.tolist() == cells[1].position.tolist()
assert cells[0].position.tolist() != cells[2].position.tolist()
assert cells[3].position.tolist() != cells[4].position.tolist()
def test_min_event_resolution():
dim = 1
cbm_solver = cbmos.CBModel(ff.Linear(), scpi.solve_ivp, dim)
cell_list = [
cl.Cell(0, [0], proliferating=True),
cl.Cell(1, [1.0], 0.0, True)
]
cell_list[0].division_time = 0.25
cell_list[1].division_time = 0.25
t_data = [0, 0.4, 0.6, 1]
_, history = cbm_solver.simulate(
cell_list,
t_data,
{},
{},
raw_t=False,
min_event_resolution=0.5,
)
assert len(history[0]) == 2
assert len(history[1]) == 2
assert len(history[2]) == 4
assert len(history[3]) == 4
def test_constructor():
cells = [cl.Cell(i, [0, 0, i]) for i in range(5)]
for i, cell in enumerate(cells):
cell.division_time = cell.ID
event_list = [(i, cells[i]) for i in reversed(range(5))]
queue = eventqueue.EventQueue(event_list)
assert len(queue._events) == 5
for i in range(5):
t, cell = queue.pop()
assert t == i
assert len(cell) == 1
assert cell[0].ID == i
def test_parameters():
ID = 17
position = [17.4]
birthtime = 0.45
proliferating = True
division_time_generator = lambda t: 3
parent_ID = 5
cell = cl.Cell(ID, position, birthtime, proliferating, division_time_generator,
None, parent_ID)
assert cell.ID == ID
assert cell.position == position
assert cell.birthtime == birthtime
assert cell.proliferating == proliferating
assert cell.division_time == division_time_generator(birthtime)
assert cell.parent_ID == parent_ID
def test_cell_birth(caplog):
logger = logging.getLogger()
logs = io.StringIO()
logger.addHandler(logging.StreamHandler(logs))
caplog.set_level(logging.DEBUG)
dim = 2
cbm_solver = cbmos.CBModel(ff.Cubic(), ef.solve_ivp, dim)
cell_list = [
cl.Cell(0, [0, 0], -5.5, True, division_time_generator=lambda t: 6 + t)
]
t_data = np.linspace(0, 1, 10)
cbm_solver.simulate(cell_list, t_data, {}, {})
division_times = logs.getvalue()
assert parse.search("Division event: t={:f}", division_times)[0] == 0.5
def test_seed_division_time(caplog):
logger = logging.getLogger()
logs = io.StringIO()
logger.addHandler(logging.StreamHandler(logs))
caplog.set_level(logging.DEBUG)
dim = 3
cbm_solver = cbmos.CBModel(ff.Logarithmic(), ef.solve_ivp, dim)
cell_list = [cl.Cell(0, [0, 0, 0], proliferating=True)]
t_data = np.linspace(0, 100, 10)
history = [
cbm_solver.simulate(cell_list, t_data, {}, {}, seed=seed)[1]
for seed in [0, 0, 1]
]
division_times = logs.getvalue().split("Starting new simulation\n")[1:]
assert division_times[0] == division_times[1]
assert division_times[0] != division_times[2]
def test_apply_division():
from cbmos.cbmodel._eventqueue import EventQueue
dim = 3
cbm_solver = cbmos.CBModel(ff.Linear(), ef.solve_ivp, dim)
cell_list = [cl.Cell(i, [0, 0, i], proliferating=True) for i in range(5)]
for i, cell in enumerate(cell_list):
cell.division_time = cell.ID
cbm_solver.cell_list = cell_list
cbm_solver.next_cell_index = 5
cbm_solver._queue = EventQueue([])
cbm_solver._apply_division(cell_list[0], 1)
assert len(cbm_solver.cell_list) == 6
assert cbm_solver.cell_list[5].ID == 5
assert cbm_solver.next_cell_index == 6
assert cell_list[0].division_time != 0
assert np.isclose(
np.linalg.norm(cell_list[0].position - cell_list[5].position),
cbm_solver.separation)