def test_historyHDF5_from_archive():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet, hf5file="test.hf5")
history.record()
history.record()
history.record()
retrieved = HistoryHdf5.from_archive("test.hf5")
try:
assert isinstance(retrieved.sheet, type(sheet))
finally:
os.remove("test.hf5")
def test_historyHDF5_path_warning():
sheet = Sheet("3", *three_faces_sheet())
with pytest.warns(UserWarning):
history = HistoryHdf5(sheet)
history.record(time_stamp=0)
with pytest.warns(UserWarning):
history = HistoryHdf5(sheet, hf5file="out.hf5")
history.record(time_stamp=0)
for p in Path(".").glob("out*.hf5"):
p.unlink()
def test_historyHDF5_path_warning():
"""
"""
sheet = Sheet("3", *three_faces_sheet())
with pytest.warns(UserWarning):
history = HistoryHdf5(sheet, extra_cols={"edge": ["dx"]})
history.record(time_stamp=0)
with pytest.warns(UserWarning):
history = HistoryHdf5(sheet,
extra_cols={"edge": ["dx"]},
hf5file="out.hf5")
history.record(time_stamp=0)
os.remove("out.hf5")
os.remove("out0.hf5")
def test_historyHDF5_itemsize():
sheet = Sheet("3", *three_faces_sheet())
sheet.vert_df["segment"] = "apical"
history = HistoryHdf5(
sheet,
hf5file="out.hf5",
)
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
sheet.vert_df.loc[0, "segment"] = ""
history.record(time_stamp=1)
sheet.vert_df.loc[0, "segment"] = "lateral"
history.record(time_stamp=2)
sheet.face_df.loc[0, "area"] = 12.0
history.record(time_stamp=3, sheet=sheet)
sheet1_ = history.retrieve(1)
assert sheet1_.vert_df.loc[0, "segment"] == ""
sheet2_ = history.retrieve(2)
assert sheet2_.vert_df.loc[0, "segment"] == "lateral"
sheet3_ = history.retrieve(3)
assert sheet3_.face_df.loc[0, "area"] == 12.0
for p in Path(".").glob("out*.hf5"):
p.unlink()
def test_historyHDF5_save_other_sheet():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
save_only={
"edge": ["dx"],
"face": ["area"],
"vert": ["segment"]
},
hf5file="out.hf5",
)
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
sheet.face_df.loc[0, "area"] = 1.0
history.record(time_stamp=1)
sheet.face_df.loc[0, "area"] = 12.0
history.record(time_stamp=2, sheet=sheet)
sheet1_ = history.retrieve(1)
assert sheet1_.face_df.loc[0, "area"] == 1.0
sheet2_ = history.retrieve(2)
assert sheet2_.face_df.loc[0, "area"] == 12.0
for p in Path(".").glob("out*.hf5"):
p.unlink()
def test_historyHDF5_itemsize():
sheet = Sheet("3", *three_faces_sheet())
sheet.vert_df["segment"] = "apical"
history = HistoryHdf5(sheet,
extra_cols={
"edge": ["dx"],
"face": ["area"],
"vert": ["segment"]
})
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
sheet.vert_df.loc[0, "segment"] = ""
history.record(time_stamp=1)
sheet.vert_df.loc[0, "segment"] = "lateral"
history.record(time_stamp=2)
sheet.face_df.loc[0, "area"] = 12.0
history.record(time_stamp=3, sheet=sheet)
sheet1_ = history.retrieve(1)
assert sheet1_.vert_df.loc[0, "segment"] == ""
sheet2_ = history.retrieve(2)
assert sheet2_.vert_df.loc[0, "segment"] == "lateral"
sheet3_ = history.retrieve(3)
assert sheet3_.face_df.loc[0, "area"] == 12.0
os.remove("out.hf5")
def test_historyHDF5_save_every():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet,
extra_cols={"edge": ["dx"]},
save_every=2,
dt=1)
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
for i in range(6):
history.record(time_stamp=i)
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(2)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 2
os.remove("out.hf5")
def test_historyHDF5_save_every():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
save_every=2,
dt=1,
hf5file="out.hf5",
)
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
for i in range(6):
history.record(time_stamp=i)
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(2)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 2
for p in Path(".").glob("out*.hf5"):
p.unlink()
def test_overwrite_tim_hdf5e():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet, hf5file="out.hf5")
history.record(time_stamp=1)
history.record(time_stamp=1)
sheet_ = history.retrieve(1)
os.remove("out.hf5")
assert sheet_.Nv == sheet.Nv
def test_unsaved_col():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
hf5file="test.hf5",
)
history.record()
history.record()
sheet.face_df["new_col"] = 0
with pytest.warns(UserWarning):
history.record()
os.remove("test.hf5")
def test_change_col_types():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
hf5file="test.hf5",
)
history.record()
history.record()
sheet.face_df["z"] = "abc"
with pytest.raises(ValueError):
history.record()
os.remove("test.hf5")
def test_to_and_from_archive():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
history.record()
history.record()
history.record()
history.to_archive("test.hf5")
history_h = HistoryHdf5.from_archive("test.hf5")
sheet_ = history_h.retrieve(2)
try:
assert sheet_.Nv == sheet.Nv
finally:
os.remove("test.hf5")
def test_unsaved_col():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
extra_cols={
"face": sheet.face_df.columns,
"edge": list(sheet.edge_df.columns),
"vert": list(sheet.vert_df.columns),
},
hf5file="test.hf5",
)
history.record()
history.record()
sheet.face_df["new_col"] = 0
with pytest.warns(UserWarning):
history.record()
os.remove("test.hf5")
def test_change_col_types():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(
sheet,
extra_cols={
"face": sheet.face_df.columns,
"edge": list(sheet.edge_df.columns),
"vert": list(sheet.vert_df.columns),
},
hf5file="test.hf5",
)
history.record()
history.record()
sheet.face_df["z"] = "abc"
with pytest.raises(ValueError):
history.record()
os.remove("test.hf5")
def test_historyHDF5_save_other_sheet():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet, extra_cols={"edge": ["dx"], "face": ["area"]})
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
sheet.face_df.loc[0, "area"] = 1.0
history.record(time_stamp=1)
sheet.face_df.loc[0, "area"] = 12.0
history.record(time_stamp=2, sheet=sheet)
sheet1_ = history.retrieve(1)
assert sheet1_.face_df.loc[0, "area"] == 1.0
sheet2_ = history.retrieve(2)
assert sheet2_.face_df.loc[0, "area"] == 12.0
os.remove("out.hf5")
def test_historyHDF5_retrieve():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet, extra_cols={"edge": ["dx"]})
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
history.record(time_stamp=0)
history.record(time_stamp=1)
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 1
os.remove("out.hf5")
def test_historyHDF5_retrieve():
sheet = Sheet("3", *three_faces_sheet())
history = HistoryHdf5(sheet, hf5file="out.hf5")
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
history.record(time_stamp=0)
history.record(time_stamp=1)
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 0
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert dset.time.unique()[0] == 1
for p in Path(".").glob("out*.hf5"):
p.unlink()
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
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')
