def test_apoptosis():
specs = config.geometry.bulk_spec()
sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
mono = Monolayer("mono", datasets, specs)
mono.face_df["id"] = mono.face_df.index.values
geom.center(mono)
geom.update_all(mono)
mono.face_df["contractility"] = 1.0
manager = EventManager("face")
cell_id = 0
apical_face = mono.face_df[
(mono.face_df.index.isin(mono.get_orbits("cell", "face")[cell_id]))
& (mono.face_df.segment == "apical")].index[0]
sheet.settings["apoptosis"] = {"cell_id": cell_id}
initial_cell_event = [(apoptosis, sheet.settings["apoptosis"])]
manager.extend(initial_cell_event)
manager.execute(mono)
manager.update()
assert len(manager.current) == 1
i = 0
while i < 5:
manager.execute(mono)
manager.update()
i = i + 1
assert mono.face_df.loc[apical_face, "contractility"] > 1.0
def test_find_transitions():
sheet = Sheet.planar_sheet_3d("sheet", 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
eptm = Monolayer("test_IHt", datasets, bulk_spec())
BulkGeometry.update_all(eptm)
eptm.settings["threshold_length"] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
eptm.settings["threshold_length"] = 1e-2
ih, hi = find_rearangements(eptm)
assert len(ih) == 0
assert len(hi) == 2
assert len(find_HIs(eptm))
face = eptm.face_df.index[-1]
HI_transition(eptm, face)
BulkGeometry.update_all(eptm)
eptm.settings["threshold_length"] = 2e-1
ih, hi = find_rearangements(eptm)
assert len(ih) == 1
assert len(hi) == 0
assert len(find_IHs(eptm))
def test_ab_pull_edge():
specs = config.geometry.bulk_spec()
sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
mono = Monolayer("mono", datasets, specs)
geom.center(mono)
geom.update_all(mono)
mono.edge_df["line_tension"] = 1.0
mono.specs["edge"]["line_tension"] = 1.0
assert len(mono.edge_df.line_tension.unique()) == 1
ab_pull_edge(mono, 1, 2, False)
assert len(mono.edge_df.line_tension.unique()) == 2
def test_shrink():
specs = config.geometry.bulk_spec()
sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
mono = Monolayer("mono", datasets, specs)
geom.center(mono)
geom.update_all(mono)
mono.cell_df["prefered_vol"] = 1.0
mono.cell_df["prefered_area"] = 1.0
shrink(mono, 0, 0.2)
assert round(mono.cell_df.loc[0, "prefered_vol"], 4) == 0.8333
assert round(mono.cell_df.loc[0, "prefered_area"], 4) == 0.8855
def test_contract():
specs = config.geometry.bulk_spec()
sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
mono = Monolayer("mono", datasets, specs)
geom.center(mono)
geom.update_all(mono)
mono.face_df["contractility"] = 1.0
assert len(mono.face_df.contractility.unique()) == 1
faces = mono.edge_df[mono.edge_df["cell"] == 0]["face"].unique()
for f in faces:
contract(mono, f, 0.2)
assert len(mono.face_df.contractility.unique()) == 2
for f in faces:
assert mono.face_df.loc[f, "contractility"] == 1.2
def test_IH_transition():
sheet = Sheet.planar_sheet_3d('sheet', 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method='translation')
eptm = Epithelium('test_IHt', datasets, bulk_spec())
BulkGeometry.update_all(eptm)
Nc, Nf, Ne, Nv = eptm.Nc, eptm.Nf, eptm.Ne, eptm.Nv
eptm.settings['threshold_length'] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
assert eptm.Nc == Nc
assert eptm.Nf == Nf + 2
assert eptm.Ne == Ne + 12
assert eptm.Nv == Nv + 1
invalid = eptm.get_invalid()
assert np.alltrue(1 - invalid)
assert np.alltrue(eptm.edge_df['sub_vol'] > 0)
def test_HI_transition():
sheet = Sheet.planar_sheet_3d("sheet", 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
eptm = Monolayer("test_HIt", datasets, bulk_spec())
BulkGeometry.update_all(eptm)
Nc, Nf, Ne, Nv = eptm.Nc, eptm.Nf, eptm.Ne, eptm.Nv
eptm.settings["threshold_length"] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
face = eptm.face_df.index[-1]
HI_transition(eptm, face)
assert eptm.Nc == Nc
assert eptm.Nf == Nf
assert eptm.Ne == Ne
assert eptm.Nv == Nv
invalid = eptm.get_invalid()
assert np.alltrue(1 - invalid)
assert np.alltrue(eptm.edge_df["sub_vol"] > 0)
def test_IH_transition():
sheet = Sheet.planar_sheet_3d("sheet", 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
eptm = Monolayer("test_IHt", datasets, bulk_spec())
BulkGeometry.update_all(eptm)
Nc, Nf, Ne, Nv = eptm.Nc, eptm.Nf, eptm.Ne, eptm.Nv
eptm.settings["threshold_length"] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
assert eptm.Nc == Nc
assert eptm.Nf == Nf + 2
assert eptm.Ne == Ne + 12
assert eptm.Nv == Nv + 1
invalid = eptm.get_invalid()
assert np.alltrue(1 - invalid)
assert np.alltrue(eptm.edge_df["sub_vol"] > 0)
assert (eptm.face_df[eptm.face_df.segment == "apical"].shape[0] ==
eptm.cell_df.shape[0])
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
