Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
verify_simulation_results(
rdata, expected_results[subTest][case]['results'],
assert_fun, **verify_simulation_opts
)
if model_name == 'model_steadystate' and \
case == 'sensiforwarderrorint':
edata = amici.amici.ExpData(self.model.get())
if edata and model_name != 'model_neuron_o2' and not (
model_name == 'model_robertson' and
case == 'sensiforwardSPBCG'
):
# Test runAmiciSimulations: ensure running twice
# with same ExpData yields same results
if isinstance(edata, amici.amici.ExpData):
edatas = [edata, edata]
else:
edatas = [edata.get(), edata.get()]
rdatas = amici.runAmiciSimulations(
self.model, self.solver, edatas, num_threads=2,
failfast=False
)
verify_simulation_results(
rdatas[0],
expected_results[subTest][case]['results'],
assert_fun, **verify_simulation_opts
)
verify_simulation_results(
rdatas[1],
expected_results[subTest][case]['results'],
model: Model instance.
edata_list: list of ExpData instances with experimental data.
May also be a single ExpData instance.
rdata_list: list of ReturnData instances corresponding to ExpData.
May also be a single ReturnData instance.
by_id: bool, optional (default = False)
If True, ids are used as identifiers, otherwise the possibly more
descriptive names.
Returns:
pandas DataFrame with conditions and observables.
Raises:
"""
if isinstance(edata_list, (amici.amici.ExpData, amici.amici.ExpDataPtr)):
edata_list = [edata_list]
if isinstance(rdata_list, (amici.amici.ReturnData, amici.amici.ReturnDataPtr)):
rdata_list = [rdata_list]
# list of all column names using either names or ids
cols = _get_extended_observable_cols(model, by_id=by_id)
# initialize dataframe with columns
df_rdata = pd.DataFrame(columns=cols)
# append all converted rdatas
for edata, rdata in zip(edata_list, rdata_list):
for i_time, timepoint in enumerate(rdata['t']):
datadict = {
'time': timepoint,
'datatype': 'simulation',
May also be a single ExpData instance.
rdata_list: list of ReturnData instances corresponding to ExpData.
May also be a single ReturnData instance.
by_id: bool, optional (default = False)
If True, ids are used as identifiers, otherwise the possibly more
descriptive names.
Returns:
pandas DataFrame with conditions and observables.
Raises:
"""
if isinstance(edata_list, (amici.amici.ExpData, amici.amici.ExpDataPtr)):
edata_list = [edata_list]
if isinstance(rdata_list, (amici.amici.ReturnData, amici.amici.ReturnDataPtr)):
rdata_list = [rdata_list]
# list of all column names using either names or ids
cols = _get_extended_observable_cols(model, by_id=by_id)
# initialize dataframe with columns
df_rdata = pd.DataFrame(columns=cols)
# append all converted rdatas
for edata, rdata in zip(edata_list, rdata_list):
for i_time, timepoint in enumerate(rdata['t']):
datadict = {
'time': timepoint,
'datatype': 'simulation',
}
# append simulations
Arguments:
model: Model instance.
edata_list: list of ExpData instances with experimental data.
May also be a single ExpData instance.
by_id: bool (optional, default = False)
If True, uses observable ids as identifiers in dataframe,
otherwise the possibly more descriptive observable names
are used.
Returns:
pandas DataFrame with conditions and observables.
Raises:
"""
if isinstance(edata_list, (amici.amici.ExpData, amici.amici.ExpDataPtr)):
edata_list = [edata_list]
# list of all column names using either ids or names
cols = _get_extended_observable_cols(model, by_id=by_id)
# initialize dataframe with columns
df_edata = pd.DataFrame(columns=cols)
# append all converted edatas
for edata in edata_list:
npdata = ExpDataView(edata)
for i_time, timepoint in enumerate(edata.getTimepoints()):
datadict = {
'time': timepoint,
'datatype': 'data'
}