def test_execute_division():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df["vol"] = 1.0
sheet.specs["face"]["prefered_vol"] = 1.0
sheet.face_df["prefered_vol"] = 1.0
sheet.face_df["id"] = sheet.face_df.index.values
manager = EventManager("face")
face_id = 1
event = (division, {
"face_id": face_id,
"growth_rate": 1.2,
"critical_vol": 1.5
})
manager.current.append(event)
V0 = sheet.face_df.loc[1, "prefered_vol"]
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[1, "prefered_vol"] == V0 * 1.2
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[1, "prefered_vol"] == V0 * 1.44
sheet.face_df.loc[1, "vol"] *= 1.6
manager.execute(sheet)
assert sheet.Nf == 4
def test_execute_constriction():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
geom.update_all(sheet)
sheet.settings["constriction"] = {
"contractile_increase": 5,
"critical_area": 5,
"max_traction": 10,
}
sheet.face_df["id"] = sheet.face_df.index.values
init_nb_cells = len(sheet.face_df)
sheet.face_df["is_mesoderm"] = 0
sheet.vert_df["radial_tension"] = 0
manager = EventManager("face")
face_id = 17
sheet.face_df.loc[face_id, "is_mesoderm"] = 1
sheet.settings["constriction"].update({"face_id": face_id})
initial_cell_event = (constriction, sheet.settings["constriction"])
manager.current.append(initial_cell_event)
manager.execute(sheet)
manager.update()
assert len(manager.current) > 0
for i in range(20):
manager.execute(sheet)
manager.update()
if len(sheet.face_df) == init_nb_cells:
assert len(manager.current) > 0
def test_compute_gradient():
h5store = 'small_hexagonal.hf5'
datasets = load_datasets(h5store,
data_names=['face', 'vert', 'edge'])
specs = config.geometry.sheet_spec()
sheet = Sheet('emin', datasets, specs)
nondim_specs = config.dynamics.quasistatic_sheet_spec()
dim_model_specs = model.dimentionalize(nondim_specs)
sheet.update_specs(dim_model_specs)
geom.update_all(sheet)
isotropic_relax(sheet, nondim_specs)
nrj_norm_factor = sheet.specs['settings']['nrj_norm_factor']
(grad_t, grad_c,
grad_v_srce, grad_v_trgt) = model.compute_gradient(sheet,
components=True)
grad_t_norm = np.linalg.norm(grad_t, axis=0).sum() / nrj_norm_factor
assert_almost_equal(grad_t_norm, 0.4497370048, decimal=DECIMAL)
grad_c_norm = np.linalg.norm(grad_c, axis=0).sum() / nrj_norm_factor
assert_almost_equal(grad_c_norm, 0.49692791, decimal=DECIMAL)
grad_vs_norm = np.linalg.norm(grad_v_srce.dropna(),
axis=0).sum() / nrj_norm_factor
assert_almost_equal(grad_vs_norm, 0.3028136725, decimal=DECIMAL)
grad_vt_norm = np.linalg.norm(grad_v_trgt.dropna(),
axis=0).sum() / nrj_norm_factor
assert_almost_equal(grad_vt_norm, 0.277320351, decimal=DECIMAL)
def test_execute_division():
sheet = Sheet('emin', *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df['vol'] = 1.
sheet.specs['face']['prefered_vol'] = 1.
sheet.face_df['prefered_vol'] = 1.
sheet.face_df['id'] = sheet.face_df.index.values
manager = EventManager('face')
face_id = 1
event = (division, {
'face_id': face_id,
'growth_rate': 0.2,
'critical_vol': 1.5
})
manager.current.append(event)
V0 = sheet.face_df.loc[1, 'prefered_vol']
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[1, 'prefered_vol'] == V0 * 1.2
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[1, 'prefered_vol'] == V0 * 1.44
sheet.face_df.loc[1, 'vol'] *= 1.6
manager.execute(sheet)
assert sheet.Nf == 4
def test_execute_constriction():
h5store = os.path.join(stores_dir, 'small_hexagonal.hf5')
datasets = load_datasets(h5store, data_names=['face', 'vert', 'edge'])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet('emin', datasets, specs)
geom.update_all(sheet)
sheet.settings['constriction'] = {
'contractile_increase': 5,
'critical_area': 5,
'max_traction': 10
}
sheet.face_df['id'] = sheet.face_df.index.values
init_nb_cells = len(sheet.face_df)
sheet.face_df['is_mesoderm'] = 0
sheet.vert_df['radial_tension'] = 0
manager = EventManager('face')
face_id = 17
sheet.face_df.loc[face_id, 'is_mesoderm'] = 1
sheet.settings['constriction'].update({'face_id': face_id})
initial_cell_event = (constriction, sheet.settings['constriction'])
manager.current.append(initial_cell_event)
manager.execute(sheet)
manager.update()
assert len(manager.current) > 0
for i in range(20):
manager.execute(sheet)
manager.update()
if len(sheet.face_df) == init_nb_cells:
assert len(manager.current) > 0
def test_split_vert():
datasets, specs = three_faces_sheet()
sheet = Sheet("3cells_2D", datasets, specs)
geom.update_all(sheet)
split_vert(sheet, 0, multiplier=10)
geom.update_all(sheet)
assert sheet.Nv == 14
assert sheet.Ne == 20
def test_execute_apoptosis():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
geom.update_all(sheet)
sheet.settings["apoptosis"] = {
"contractile_increase": 2.0,
"critical_area": 0.1
}
sheet.face_df["id"] = sheet.face_df.index.values
init_nb_faces = len(sheet.face_df)
manager = EventManager("face")
face_id = 17
face_area = sheet.face_df.loc[face_id, "area"]
initial_nbsides = sheet.face_df.loc[face_id, "num_sides"]
sheet.settings["apoptosis"].update({"face_id": face_id})
initial_cell_event = (apoptosis, sheet.settings["apoptosis"])
manager.current.append(initial_cell_event)
manager.execute(sheet)
manager.update()
assert len(manager.current) > 0
manager.execute(sheet)
manager.update()
sheet.settings["apoptosis"] = {
"contractile_increase": 2.0,
"critical_area": 2 * face_area,
}
manager.current.clear()
sheet.settings["apoptosis"].update({"face_id": face_id})
modified_cell_event = (apoptosis, sheet.settings["apoptosis"])
manager.current.append(modified_cell_event)
manager.execute(sheet)
manager.update()
next_nbsides = sheet.face_df.loc[sheet.idx_lookup(face_id, "face"),
"num_sides"]
i = 1
while next_nbsides > 4:
assert next_nbsides == initial_nbsides - i
assert len(manager.current) > 0
i = i + 1
manager.execute(sheet)
manager.update()
next_nbsides = sheet.face_df.loc[sheet.idx_lookup(face_id, "face"),
"num_sides"]
if i > 20:
raise RecursionError
manager.execute(sheet)
manager.update()
assert len(sheet.face_df) < init_nb_faces
def test_execute_apoptosis():
h5store = os.path.join(stores_dir, 'small_hexagonal.hf5')
datasets = load_datasets(h5store, data_names=['face', 'vert', 'edge'])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet('emin', datasets, specs)
geom.update_all(sheet)
sheet.settings['apoptosis'] = {
'contractile_increase': 2.0,
'critical_area': 0.1
}
sheet.face_df['id'] = sheet.face_df.index.values
init_nb_faces = len(sheet.face_df)
manager = EventManager('face')
face_id = 17
face_area = sheet.face_df.loc[face_id, 'area']
initial_nbsides = sheet.face_df.loc[face_id, 'num_sides']
sheet.settings['apoptosis'].update({'face_id': face_id})
initial_cell_event = (apoptosis, sheet.settings['apoptosis'])
manager.current.append(initial_cell_event)
manager.execute(sheet)
manager.update()
assert len(manager.current) > 0
manager.execute(sheet)
manager.update()
sheet.settings['apoptosis'] = {
'contractile_increase': 2.0,
'critical_area': 2 * face_area
}
manager.current.clear()
sheet.settings['apoptosis'].update({'face_id': face_id})
modified_cell_event = (apoptosis, sheet.settings['apoptosis'])
manager.current.append(modified_cell_event)
manager.execute(sheet)
manager.update()
next_nbsides = sheet.face_df.loc[sheet.idx_lookup(face_id, 'face'),
'num_sides']
i = 1
while next_nbsides > 4:
assert next_nbsides == initial_nbsides - i
assert len(manager.current) > 0
i = i + 1
manager.execute(sheet)
manager.update()
next_nbsides = sheet.face_df.loc[sheet.idx_lookup(face_id, 'face'),
'num_sides']
manager.execute(sheet)
manager.update()
assert len(sheet.face_df) < init_nb_faces
def test_face_rotation():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
sgeom.update_all(sheet)
face = 17
normal = sheet.edge_df[sheet.edge_df["face"] == face][sheet.ncoords].mean()
rot = sgeom.face_rotation(sheet, face, 0)
rotated = np.dot(rot, normal)
np.testing.assert_allclose(rotated[:2], np.zeros(2), atol=1e-7)
def test_execute_contraction():
sheet = Sheet('emin', *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df['contractility'] = 1.12
sheet.face_df['id'] = sheet.face_df.index.values
manager = EventManager('face')
face_id = 1
event = (contraction, {
'face_id': face_id,
'contractile_increase': 0.2,
'critical_area': 1e-2
})
manager.current.append(event)
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[face_id, 'contractility'] == 1.32
def test_type1_transition():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df["id"] = sheet.face_df.index.values
manager = EventManager("face")
face_id = 1
nb_neighbors_start = len(sheet.edge_df[sheet.edge_df["face"] == face_id])
edge_to_modify = sheet.edge_df[sheet.edge_df["face"] == face_id].index[0]
sheet.edge_df.loc[edge_to_modify, "length"] = 0.2
event = (type1_transition, {"face_id": face_id, "critical_length": 0.3})
manager.current.append(event)
manager.execute(sheet)
manager.update()
nb_neighbors_end = len(sheet.edge_df[sheet.edge_df["face"] == face_id])
assert nb_neighbors_end == nb_neighbors_start - 1
def test_rotations():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
sgeom.update_all(sheet)
sheet.sanitize()
sgeom.update_all(sheet)
sgeom.center(sheet)
assert sgeom.face_rotations(sheet, method='normal',
output_as='edge').shape[0] == sheet.Ne
assert sgeom.face_rotations(sheet, method='normal',
output_as='face').shape[0] == sheet.Nf
assert sgeom.face_rotations(sheet, method='svd',
output_as='edge').shape[0] == sheet.Ne
assert sgeom.face_rotations(sheet, method='svd',
output_as='face').shape[0] == sheet.Nf
def test_type1_transition():
sheet = Sheet('emin', *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df['id'] = sheet.face_df.index.values
manager = EventManager('face')
face_id = 1
nb_neighbors_start = len(sheet.edge_df[sheet.edge_df['face'] == face_id])
edge_to_modify = sheet.edge_df[sheet.edge_df['face'] == face_id].index[0]
sheet.edge_df.loc[edge_to_modify, 'length'] = 0.2
event = (type1_transition, {'face_id': face_id, 'critical_length': 0.3})
manager.current.append(event)
manager.execute(sheet)
manager.update()
nb_neighbors_end = len(sheet.edge_df[sheet.edge_df['face'] == face_id])
assert nb_neighbors_end == nb_neighbors_start - 1
def test_compute_energy():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
nondim_specs = config.dynamics.quasistatic_sheet_spec()
dim_model_specs = model.dimensionalize(nondim_specs)
sheet.update_specs(dim_model_specs, reset=True)
geom.update_all(sheet)
Et, Ec, Ev = model.compute_energy(sheet, full_output=True)
assert_almost_equal(Et.mean(), 0.02458566846202479, decimal=DECIMAL)
assert_almost_equal(Ec.mean(), 0.08638339061549484, decimal=DECIMAL)
assert_almost_equal(Ev.mean(), 0.06277441190064434, decimal=DECIMAL)
energy = model.compute_energy(sheet, full_output=False)
assert_almost_equal(energy, 15.040138762574534, decimal=DECIMAL)
def test_execute_contraction():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.face_df["contractility"] = 1.12
sheet.face_df["id"] = sheet.face_df.index.values
manager = EventManager("face")
face_id = 1
event = (
contraction,
{
"face_id": face_id,
"contractile_increase": 0.2,
"critical_area": 1e-2
},
)
manager.current.append(event)
manager.execute(sheet)
manager.update()
assert sheet.face_df.loc[face_id, "contractility"] == 1.32
def test_compute_energy():
h5store = 'small_hexagonal.hf5'
datasets = load_datasets(h5store,
data_names=['face', 'vert', 'edge'])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet('emin', datasets, specs)
nondim_specs = config.dynamics.quasistatic_sheet_spec()
dim_model_specs = model.dimentionalize(nondim_specs)
sheet.update_specs(dim_model_specs)
geom.update_all(sheet)
isotropic_relax(sheet, nondim_specs)
Et, Ec, Ev = model.compute_energy(sheet, full_output=True)
assert_almost_equal(Et.mean(), 0.02301937, decimal=DECIMAL)
assert_almost_equal(Ec.mean(), 0.15260879, decimal=DECIMAL)
assert_almost_equal(Ev.mean(), 0.03189850, decimal=DECIMAL)
energy = model.compute_energy(sheet, full_output=False)
assert_almost_equal(energy, 12.9049416411, decimal=DECIMAL)
assert_almost_equal(energy/sheet.face_df.is_alive.sum(),
0.3226, decimal=2)