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par_opt_ids = self.petab_problem.get_optimization_parameters()
# take sim parameter vector from model to ensure correct order
par_sim_ids = list(model.getParameterIds())
parameter_mapping = \
petab.core.get_optimization_to_simulation_parameter_mapping(
condition_df=self.petab_problem.condition_df,
measurement_df=self.petab_problem.measurement_df,
parameter_df=self.petab_problem.parameter_df,
sbml_model=self.petab_problem.sbml_model,
par_opt_ids=par_opt_ids,
par_sim_ids=par_sim_ids
)
scale_mapping = \
petab.core.get_optimization_to_simulation_scale_mapping(
parameter_df=self.petab_problem.parameter_df,
mapping_par_opt_to_par_sim=parameter_mapping
)
# create objective
obj = PetabAmiciObjective(
petab_importer=self,
amici_model=model, amici_solver=solver, edatas=edatas,
x_ids=par_opt_ids, x_names=par_opt_ids,
mapping_par_opt_to_par_sim=parameter_mapping,
mapping_scale_opt_to_scale_sim=scale_mapping
)
return obj