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_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_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_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_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_face_elimination():
sheet = Sheet('emin', *three_faces_sheet())
sheet.face_df['id'] = sheet.face_df.index
face_id = 0
manager = EventManager('face')
event = (face_elimination, {'face_id': face_id})
manager.current.append(event)
manager.execute(sheet)
manager.update()
assert sheet.Nf == 2
assert sheet.Nv == 8
assert sheet.Ne == 10
def test_face_elimination():
sheet = Sheet("emin", *three_faces_sheet())
sheet.face_df["id"] = sheet.face_df.index
face_id = 0
manager = EventManager("face")
event = (face_elimination, {"face_id": face_id})
manager.current.append(event)
manager.execute(sheet)
manager.update()
assert sheet.Nf == 2
assert sheet.Nv == 8
assert sheet.Ne == 10
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_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_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_check_tri_faces():
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)
initial_nb_cells = len(sheet.face_df)
nb_tri_cells = len(sheet.face_df[(sheet.face_df["num_sides"] < 4)])
geom.update_all(sheet)
sheet.face_df["id"] = sheet.face_df.index.values
manager = EventManager("face")
manager.current.append((check_tri_faces, {}))
manager.execute(sheet)
manager.update()
manager.execute(sheet)
manager.update()
assert len(sheet.face_df) == initial_nb_cells - nb_tri_cells
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_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_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_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_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_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_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_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 run_sim(
dirname,
solver,
solver_kw,
sheet,
geom,
model,
max_contractility_rate,
profile_width,
k,
cable_cut=False,
apical_cut=False,
nb_apical_cut=2,
):
"""
Run simulation according to parameters.
Parameters
----------
dirname: saving directory to hf5 file
solver:
solver_kw: solver arguments
sheet:
geom:
model:
max_contractility_rate: maximal constriction cell for all cell in the tissue.
k: steepness coefficient characterizing the profile decay
profile_width: width of the profile
cable_cut: True/False, define if apico-basal force is exerted
apical_cut: True/False, define if a domain of cell is isolated
nb_apical_cut: Define number of apical cut (1 or 2)
"""
# Initiate manager
manager = EventManager("face")
sheet.face_df["enter_in_process"] = 0
t = 0
stop = 200
sheet.face_df["contract_rate"] = 0
if apical_cut:
if nb_apical_cut == 1:
# posterior apical ablation
apical_cut(sheet, 45.0)
elif nb_apical_cut == 2:
# anterior & posterior apical ablation
apical_cut(sheet, 45.0)
apical_cut(sheet, -45.0)
# Add all cells in constriction process
for f in sheet.face_df[sheet.face_df["is_mesoderm"]].index:
x = sheet.face_df.loc[f, "x"]
c_rate = constriction_rate(x, max_contractility_rate, k, profile_width)
sheet.face_df.loc[f, "contract_rate"] = c_rate
delam_kwargs = sheet.settings["delamination"].copy()
delam_kwargs.update({
"face_id": f,
"contract_rate": c_rate,
"current_traction": 0,
"max_traction": 30,
})
manager.append(constriction, **delam_kwargs)
for f in sheet.face_df[sheet.face_df["is_relaxation"]].index:
delam_kwargs = sheet.settings["delamination"].copy()
delam_kwargs.update({
"face_id": f,
"contract_rate": max_contractility_rate,
"current_traction": 0,
"max_traction": 30,
})
manager.append(constriction, **delam_kwargs)
while manager.current and t < stop:
# Clean radial tension on all vertices
sheet.vert_df["radial_tension"] = 0
manager.execute(sheet)
if cable_cut:
# Mettre ici la mise à 0 de la force AB dans la zone -45 45
sheet.vert_df["radial_tension"] = [
0 if ((z > -45.0) and (z < 45.0)) else rad
for (z, rad) in sheet.vert_df[["z", "radial_tension"]].values
]
res = solver.find_energy_min(sheet, geom, model, **solver_kw)
# add noise on vertex position to avoid local minimal.
sheet.vert_df[["x", "y"]] += np.random.normal(scale=1e-3,
size=(sheet.Nv, 2))
geom.update_all(sheet)
# Save result in each time step.
figname = os.path.join(dirname, "invagination_{:04d}.png".format(t))
hdfname = figname[:-3] + "hf5"
hdf5.save_datasets(hdfname, sheet)
# Add cells with initially 3 neighbourghs to be eliminated.
check_tri_faces(sheet, manager)
manager.update()
t += 1
return sheet
def run_sim(sim_save_dir,
original_tissue,
polarity,
perturbation,
ve,
iteration=0):
time.sleep(np.random.rand())
# without copy, dataframe is on read only...
sheet = original_tissue.copy()
sheet.settings['lumen_prefered_vol'] = ve
if perturbation != -1:
for p in perturbation:
sheet.face_df.loc[int(p), 'is_mesoderm'] = 1
define_polarity_old(sheet, 1, polarity)
geom.normalize_weights(sheet)
res = solver.find_energy_min(sheet, geom, model, options={"gtol": 1e-8})
filename = '{}_polarity_{}_perturbation_{}_ve_{}'.format(
polarity, perturbation, ve, iteration)
dirname = os.path.join(sim_save_dir, filename)
print('starting {}'.format(dirname))
try:
os.mkdir(dirname)
except IOError:
pass
# Add some information to the sheet and copy initial sheet
sheet.face_df['id'] = sheet.face_df.index.values
# Initiate history
history = HistoryHdf5(sheet,
extra_cols={
"face": sheet.face_df.columns,
"edge": list(sheet.edge_df.columns),
"vert": list(sheet.vert_df.columns)
},
hf5file=os.path.join(dirname, filename + '.hf5'))
# Initiate manager
manager = EventManager('face')
# Update kwargs...
sheet.settings['apoptosis'].update({
'contract_rate': 1.08,
'radial_tension': 50,
})
# save settings
pd.Series(sheet.settings).to_csv(os.path.join(dirname, 'settings.csv'))
manager.append(reconnect, **sheet.settings['rosette_kwargs'])
manager.append(apoptosis_patterning,
**sheet.settings['apopto_pattern_kwargs'])
t = 0.
stop = 150.
# Run simulation
while t < stop:
if t == 5:
for i in sheet.face_df[sheet.face_df.is_mesoderm == 1].index:
delamination_kwargs = sheet.settings[
'delaminate_setting'].copy()
delamination_kwargs.update({
"face_id": i,
#"radial_tension": radial_tension,
"radial_tension": 50,
"contract_rate": 1.08,
"max_traction": 90,
"current_traction": 0,
})
manager.append(delamination, **delamination_kwargs)
# Reset radial tension at each time step
sheet.vert_df.radial_tension = 0.
manager.execute(sheet)
res = solver.find_energy_min(sheet,
geom,
model,
options={"gtol": 1e-8})
# add noise on vertex position to avoid local minimal.
sheet.vert_df[['x', 'y']] += np.random.normal(scale=1e-3,
size=(sheet.Nv, 2))
geom.update_all(sheet)
# Save result in each time step.
"""figname = os.path.join(
dirname, 'invagination_{:04.0f}.png'.format(t))
hdfname = figname[:-3] + 'hf5'
hdf5.save_datasets(hdfname, sheet)
"""
history.record(time_stamp=float(t))
manager.update()
t += 1.
print('{} done'.format(dirname))
print('~~~~~~~~~~~~~~~~~~~~~\n')
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
def run_sim(
sim_save_dir,
_sheet,
polarity,
perturbation=-1,
stop=150.,
iteration=0,
):
# Define solver
solver = QSSolver(with_t1=False, with_t3=False, with_collisions=False)
filename = '{}_polarity{}_perturbation.hf5'.format(polarity, perturbation)
try:
os.mkdir(sim_save_dir)
except IOError:
pass
# without copy, dataframe is on read only...
sheet = _sheet.copy()
sheet.face_df['is_mesoderm'] = 0
if perturbation != -1:
for p in perturbation:
sheet.face_df.loc[int(p), 'is_mesoderm'] = 1
define_polarity(sheet, 1, polarity)
geom.normalize_weights(sheet)
# Add some information to the sheet
sheet.face_df['id'] = sheet.face_df.index.values
# Initiate history
history = HistoryHdf5(sheet,
extra_cols={
"face": sheet.face_df.columns,
"edge": list(sheet.edge_df.columns),
"vert": list(sheet.vert_df.columns)
},
hf5file=os.path.join(sim_save_dir, filename))
# Initiate manager
manager = EventManager('face')
# save settings
pd.Series(sheet.settings).to_csv(
os.path.join(sim_save_dir, (filename[:-4] + '_settings.csv')))
manager.append(reconnect, **sheet.settings['rosette_kwargs'])
manager.append(apoptosis_patterning,
**sheet.settings['apopto_pattern_kwargs'])
t = 0.
stop = 150.
# Run simulation
while t < stop:
if t == 5:
for i in sheet.face_df[sheet.face_df.is_mesoderm == 1].index:
delamination_kwargs = sheet.settings[
'delaminate_setting'].copy()
delamination_kwargs.update({
"face_id": i,
})
manager.append(delamination, **delamination_kwargs)
# Reset radial tension at each time step
sheet.vert_df.radial_tension = 0.
manager.execute(sheet)
res = solver.find_energy_min(sheet,
geom,
model,
options={"gtol": 1e-8})
if res.success is False:
raise ('Stop because solver didn'
't succeed at time t ' + str(t), res)
# add noise on vertex position to avoid local minimal.
sheet.vert_df[['x', 'y']] += np.random.normal(scale=1e-3,
size=(sheet.Nv, 2))
geom.update_all(sheet)
history.record(time_stamp=float(t))
manager.update()
t += 1.
return sheet