def test_modify():
datasets, _ = three_faces_sheet()
extruded = extrude(datasets, method="translation")
mono = Monolayer("test", extruded, config.geometry.bulk_spec())
mono.update_specs(config.dynamics.quasistatic_bulk_spec(), reset=True)
modifiers = {
"apical": {
"edge": {
"line_tension": 1.0
},
"face": {
"contractility": 0.2
}
},
"basal": {
"edge": {
"line_tension": 3.0
},
"face": {
"contractility": 0.1
}
},
}
utils.modify_segments(mono, modifiers)
assert mono.edge_df.loc[mono.apical_edges,
"line_tension"].unique()[0] == 1.0
assert mono.edge_df.loc[mono.basal_edges,
"line_tension"].unique()[0] == 3.0
def get_initial_follicle(specs, recreate=False, Nc=200):
"""Retrieves or recreates a spherical epithelium"""
if recreate:
## Lloy_relax=True takes time but should give more spherical epithelium
follicle = spherical_monolayer(9.0, 12.0, Nc, apical="in", Lloyd_relax=True)
geom.update_all(follicle)
geom.scale(follicle, follicle.cell_df.vol.mean() ** (-1 / 3), list("xyz"))
geom.update_all(follicle)
else:
follicle = Monolayer("follicle", hdf5.load_datasets("initial_follicle.hf5"))
follicle.settings["lumen_side"] = "apical"
geom.update_all(follicle)
follicle.update_specs(specs, reset=True)
follicle.cell_df["id"] = follicle.cell_df.index
wgeom = WAMonolayerGeometry
model = model_factory(
[
effectors.LumenVolumeElasticity,
WeightedCellAreaElasticity,
effectors.CellVolumeElasticity,
]
)
print("Finding static equilibrium")
follicle.face_df.loc[follicle.apical_faces, "weight"] = specs["settings"][
"apical_weight"
]
wgeom.update_all(follicle)
solver = QSSolver()
res = solver.find_energy_min(follicle, wgeom, model)
return follicle, model
def test_constriction():
specs = config.geometry.bulk_spec()
sheet = Sheet.planar_sheet_3d("flat", 6, 8, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
mono = Monolayer("mono", datasets, specs)
geom.center(mono)
geom.update_all(mono)
dyn_specs = config.dynamics.quasistatic_bulk_spec()
dyn_specs["cell"]["area_elasticity"] = 0.05
dyn_specs["cell"]["prefered_area"] = 6.0
dyn_specs["cell"]["vol_elasticity"] = 1.0
dyn_specs["cell"]["prefered_vol"] = 1.2
dyn_specs["face"]["contractility"] = 0.0
dyn_specs["edge"]["line_tension"] = 0.0
mono.update_specs(dyn_specs, reset=True)
mono.face_df.loc[mono.apical_faces, "contractility"] = 1.12
mono.face_df.loc[mono.basal_faces, "contractility"] = 1.12
manager = EventManager("face")
sheet.face_df["enter_in_process"] = 0
mono.settings["constriction"] = {}
mono.cell_df["is_mesoderm"] = False
mono.face_df["is_mesoderm"] = False
cell_to_constrict = [12]
apical_face = mono.face_df[(mono.face_df.index.isin(
mono.get_orbits("cell", "face")[cell_to_constrict[0]]))
& (mono.face_df.segment == "apical")].index[0]
mono.cell_df.loc[cell_to_constrict, "is_mesoderm"] = True
mono.cell_df["id"] = mono.cell_df.index.values
mono.face_df["id"] = mono.face_df.index.values
list_face_in_cell = mono.get_orbits("cell", "face")
cell_in_mesoderm = mono.cell_df[mono.cell_df.is_mesoderm].index.values
for i in cell_in_mesoderm:
faces_in_cell = mono.face_df.loc[list_face_in_cell[i].unique()]
for f in faces_in_cell.index.values:
mono.face_df.loc[f, "is_mesoderm"] = True
for i in cell_to_constrict:
delam_kwargs = mono.settings["constriction"].copy()
delam_kwargs.update({
"cell_id": i,
"contract_rate": 2,
"critical_area": 0.02,
"shrink_rate": 0.4,
"critical_volume": 0.1,
"radial_tension": 3,
"max_traction": 35,
"contract_neighbors": True,
"contract_span": 1,
"with_rearrangement": True,
"critical_area_reduction": 5,
})
initial_cell_event = [(constriction, delam_kwargs)]
manager.extend(initial_cell_event)
manager.execute(mono)
manager.update()
assert len(manager.current) == 1
i = 0
while i < 10:
manager.execute(mono)
manager.update()
i = i + 1
assert mono.face_df.loc[apical_face, "contractility"] > 1.0
for c in cell_to_constrict:
assert mono.cell_df.loc[c, "num_faces"] <= 4