def test_add_several_time_same_events():
manager = EventManager("face")
initial_cell_event = [
(division, {
"face_id": 1,
"geom": geom
}),
(contraction, {
"face_id": 2,
"unique": False
}),
(contraction, {
"face_id": 3,
"unique": False
}),
(apoptosis, {
"face_id": 3,
"shrink_rate": 4
}),
(contraction, {
"face_id": 2,
"unique": False
}),
]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 5
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_logging():
tf = tempfile.mktemp()
manager = EventManager("face", tf)
initial_cell_event = [
(division, {
"face_id": 1,
"geom": geom
}),
(apoptosis, {
"face_id": 3,
"shrink_rate": 4
}),
(apoptosis, {
"face_id": 3
}),
]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
with open(tf, "r") as fh:
l0, l1, l2 = fh.readlines()
assert l2 == "0, -1, wait\n"
def test_add_only_once():
manager = EventManager('face')
initial_cell_event = [(division, {
'face_id': 1,
'geom': geom
}), (apoptosis, {
'face_id': 3,
'shrink_rate': 4
}), (apoptosis, {
'face_id': 3
})]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 2
def test_add_events():
manager = EventManager('face')
initial_cell_event = [(division, {
'face_id': 1,
'geom': geom
}), (wait, {
'face_id': 3,
'n_steps': 4
}), (apoptosis, {
'face_id': 5
}), (constriction, {
'face_id': 2
})]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 4
def test_add_only_once():
manager = EventManager("face")
initial_cell_event = [
(division, {
"face_id": 1,
"geom": geom
}),
(apoptosis, {
"face_id": 3,
"shrink_rate": 4
}),
(apoptosis, {
"face_id": 3
}),
]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 2
def test_logging():
tf = tempfile.mktemp()
manager = EventManager('face', tf)
initial_cell_event = [(division, {
'face_id': 1,
'geom': geom
}), (apoptosis, {
'face_id': 3,
'shrink_rate': 4
}), (apoptosis, {
'face_id': 3
})]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
with open(tf, 'r') as fh:
l0, l1, l2 = fh.readlines()
assert l2 == '0, -1, wait\n'
def test_add_events():
manager = EventManager("face")
initial_cell_event = [
(division, {
"face_id": 1,
"geom": geom
}),
(wait, {
"face_id": 3,
"n_steps": 4
}),
(apoptosis, {
"face_id": 5
}),
(constriction, {
"face_id": 2
}),
]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 4
def test_add_several_time_same_events():
manager = EventManager('face')
initial_cell_event = [(division, {
'face_id': 1,
'geom': geom
}), (contraction, {
'face_id': 2,
'unique': False
}), (contraction, {
'face_id': 3,
'unique': False
}), (apoptosis, {
'face_id': 3,
'shrink_rate': 4
}), (contraction, {
'face_id': 2,
'unique': False
})]
manager.extend(initial_cell_event)
manager.execute(None)
manager.update()
assert len(manager.current) == 5
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
