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 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,
_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
