PEtab¶
pyPESTO support for the PEtab data format.
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class
pypesto.petab.
PetabImporter
(petab_problem: petab.Problem, output_folder: str = None, model_name: str = None)¶ Bases:
pypesto.objective.amici.AmiciObjectBuilder
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MODEL_BASE_DIR
= 'amici_models'¶
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__init__
(petab_problem: petab.Problem, output_folder: str = None, model_name: str = None)¶ - petab_problem:
Managing access to the model and data.
- output_folder:
Folder to contain the amici model. Defaults to ‘./amici_models/{model_name}’.
- model_name:
Name of the model, which will in particular be the name of the compiled model python module.
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compile_model
(**kwargs)¶ Compile the model. If the output folder exists already, it is first deleted.
- Parameters
kwargs (Extra arguments passed to amici.SbmlImporter.sbml2amici.) –
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create_edatas
(model: amici.Model = None, simulation_conditions=None) → List[amici.ExpData]¶ Create list of amici.ExpData objects.
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create_model
(force_compile: bool = False, **kwargs) → amici.Model¶ Import amici model. If necessary or force_compile is True, compile first.
- Parameters
force_compile –
If False, the model is compiled only if the output folder does not exist yet. If True, the output folder is deleted and the model (re-)compiled in either case.
Warning
If force_compile, then an existing folder of that name will be deleted.
kwargs (Extra arguments passed to amici.SbmlImporter.sbml2amici) –
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create_objective
(model: amici.Model = None, solver: amici.Solver = None, edatas: Sequence[amici.ExpData] = None, force_compile: bool = False, **kwargs) → pypesto.objective.amici.AmiciObjective¶ Create a
pypesto.AmiciObjective
.- Parameters
model – The AMICI model.
solver – The AMICI solver.
edatas – The experimental data in AMICI format.
force_compile – Whether to force-compile the model if not passed.
**kwargs – Additional arguments passed on to the objective.
- Returns
A
pypesto.AmiciObjective
for the model and the data.- Return type
objective
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create_prior
() → pypesto.objective.priors.NegLogParameterPriors¶ Creates a prior from the parameter table. Returns None, if no priors are defined.
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create_problem
(objective: pypesto.objective.amici.AmiciObjective = None, **kwargs) → pypesto.problem.Problem¶ Create a
pypesto.Problem
.- Parameters
objective – Objective as created by create_objective.
**kwargs – Additional key word arguments passed on to the objective, if not provided.
- Returns
A
pypesto.Problem
for the objective.- Return type
problem
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create_solver
(model: amici.Model = None) → amici.Solver¶ Return model solver.
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static
from_yaml
(yaml_config: Union[dict, str], output_folder: str = None, model_name: str = None) → pypesto.petab.importer.PetabImporter¶ Simplified constructor using a petab yaml file.
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rdatas_to_measurement_df
(rdatas: Sequence[amici.ReturnData], model: amici.Model = None) → pandas.core.frame.DataFrame¶ Create a measurement dataframe in the petab format from the passed rdatas and own information.
- Parameters
rdatas – A list of rdatas as produced by pypesto.AmiciObjective.__call__(x, return_dict=True)[‘rdatas’].
model – The amici model.
- Returns
A dataframe built from the rdatas in the format as in self.petab_problem.measurement_df.
- Return type
measurement_df
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rdatas_to_simulation_df
(rdatas: Sequence[amici.ReturnData], model: amici.Model = None) → pandas.core.frame.DataFrame¶ Same as rdatas_to_measurement_df, execpt a petab simulation dataframe is created, i.e. the measurement column label is adjusted.
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