def test_jacobian_1DN3():
force = ff.Linear()
force_prime = force.derive()
y = np.array([1.0, 0.7, 2.5])[:, np.newaxis]
model = cbmos.CBModel(force, ef.solve_ivp, 1)
A = model.jacobian(y, {})
# calculate manually
y1 = y[0]
y2 = y[1]
y3 = y[2]
A12 = (y2-y1)**2/abs(y2-y1)**2\
*(force_prime(abs(y2-y1)) - force(abs(y2-y1))/abs(y2-y1))\
+ force(abs(y2-y1))/abs(y2-y1)
A13 = (y3-y1)**2/abs(y3-y1)**2\
*(force_prime(abs(y3-y1)) - force(abs(y3-y1))/abs(y3-y1))\
+ force(abs(y3-y1))/abs(y3-y1)
A23 = (y3-y2)**2/abs(y3-y2)**2\
*(force_prime(abs(y3-y2)) - force(abs(y3-y2))/abs(y3-y2))\
+ force(abs(y3-y2))/abs(y3-y2)
A2 = np.squeeze(
np.array([[-(A12 + A13), A12, A13], [A12, -(A12 + A23), A23],
[A13, A23, -(A13 + A23)]]))
assert (np.all(A == A2))
def test_jacobian_3DN3():
g = ff.Linear()
g_prime = g.derive()
y = np.array([[0., 0., 0.], [0.7, 0.1, -0.6], [0.3, -1., -2.0]])
model = cbmos.CBModel(g, ef.solve_ivp, 3)
A = model.jacobian(y, {})
# calculate manually
y1 = y[0, :][:, np.newaxis]
y2 = y[1, :][:, np.newaxis]
y3 = y[2, :][:, np.newaxis]
r12 = y2 - y1
norm_12 = np.linalg.norm(r12)
r13 = y3 - y1
norm_13 = np.linalg.norm(r13)
r23 = y3 - y2
norm_23 = np.linalg.norm(r23)
A12 = r12 @ r12.transpose() / norm_12**2 * (g_prime(
norm_12) - g(norm_12) / norm_12) + g(norm_12) / norm_12 * np.eye(3)
A13 = r13 @ r13.transpose() / norm_13**2 * (g_prime(
norm_13) - g(norm_13) / norm_13) + g(norm_13) / norm_13 * np.eye(3)
A23 = r23 @ r23.transpose() / norm_23**2 * (g_prime(
norm_23) - g(norm_23) / norm_23) + g(norm_23) / norm_23 * np.eye(3)
A2 = np.block([[-(A12 + A13), A12, A13], [A12, -(A12 + A23), A23],
[A13, A23, -(A13 + A23)]])
assert (np.all(A == A2))
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_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_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_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_calculate_positions(two_cells):
for dim in [1, 2, 3]:
cbm_solver = cbmos.CBModel(ff.Linear(), ef.solve_ivp, dim)
T = np.linspace(0, 10, num=10)
# Check cells end up at the resting length
for s in [1., 2., 3.]:
sol = cbm_solver._calculate_positions(
T,
two_cells.reshape(-1, 3)[:, :dim].reshape(-1), {
's': s,
'mu': 1.0
}, {
'dt': 0.1
}).y.reshape(-1, 2 * dim)
assert np.abs(sol[-1][:dim] - sol[-1][dim:]).sum() - s < 0.01
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)
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