PEtab

pyPESTO support for the PEtab data format.

class pypesto.petab.PetabImporter(petab_problem: petab.Problem, output_folder: str = None, model_name: str = None)

Bases: pypesto.objective.amici.AmiciObjectBuilder

MODEL_BASE_DIR = 'amici_models'
__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.

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.) –

create_edatas(model: amici.Model = None, simulation_conditions=None) → List[amici.ExpData]

Create list of amici.ExpData objects.

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) –

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

create_prior() → pypesto.objective.priors.NegLogParameterPriors

Creates a prior from the parameter table. Returns None, if no priors are defined.

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

create_solver(model: amici.Model = None) → amici.Solver

Return model solver.

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.

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

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.