petab.problem
PEtab Problem class
Classes
|
PEtab parameter estimation problem as defined by |
- class petab.problem.Problem(sbml_model: libsbml.Model = None, sbml_reader: libsbml.SBMLReader = None, sbml_document: libsbml.SBMLDocument = None, model: Model = None, condition_df: pd.DataFrame = None, measurement_df: pd.DataFrame = None, parameter_df: pd.DataFrame = None, visualization_df: pd.DataFrame = None, observable_df: pd.DataFrame = None, extensions_config: Dict = None)[source]
Bases:
object
PEtab parameter estimation problem as defined by
model
condition table
measurement table
parameter table
observables table
Optionally it may contain visualization tables.
- condition_df
PEtab condition table
- measurement_df
PEtab measurement table
- parameter_df
PEtab parameter table
- observable_df
PEtab observable table
- visualization_df
PEtab visualization table
- model
The underlying model
- sbml_reader
Stored to keep object alive (deprecated).
- sbml_document
Stored to keep object alive (deprecated).
- sbml_model
PEtab SBML model (deprecated)
- extensions_config
Information on the extensions used
- _apply_mask(v: List, free: bool = True, fixed: bool = True)[source]
Apply mask of only free or only fixed values.
- Parameters
v – The full vector the mask is to be applied to.
free – Whether to return free parameters, i.e. parameters to estimate.
fixed – Whether to return fixed parameters, i.e. parameters not to estimate.
- Return type
The reduced vector with applied mask.
- static from_combine(filename: Union[Path, str]) Problem [source]
Read PEtab COMBINE archive (http://co.mbine.org/documents/archive).
See also
petab.create_combine_archive()
.- Parameters
filename – Path to the PEtab-COMBINE archive
- Returns
A
petab.Problem
instance.
- static from_files(sbml_file: Optional[Union[Path, str]] = None, condition_file: Optional[Union[str, Path, Iterable[Union[str, Path]]]] = None, measurement_file: Optional[Union[str, Path, Iterable[Union[str, Path]]]] = None, parameter_file: Optional[Union[str, Path, Iterable[Union[str, Path]]]] = None, visualization_files: Optional[Union[str, Path, Iterable[Union[str, Path]]]] = None, observable_files: Optional[Union[str, Path, Iterable[Union[str, Path]]]] = None, extensions_config: Optional[Dict] = None) Problem [source]
Factory method to load model and tables from files.
- Parameters
sbml_file – PEtab SBML model
condition_file – PEtab condition table
measurement_file – PEtab measurement table
parameter_file – PEtab parameter table
visualization_files – PEtab visualization tables
observable_files – PEtab observables tables
extensions_config – Information on the extensions used
- static from_yaml(yaml_config: Union[Dict, Path, str]) Problem [source]
Factory method to load model and tables as specified by YAML file.
- Parameters
yaml_config – PEtab configuration as dictionary or YAML file name
- get_lb(free: bool = True, fixed: bool = True, scaled: bool = False)[source]
Generic function to get lower parameter bounds.
- Parameters
free – Whether to return free parameters, i.e. parameters to estimate.
fixed – Whether to return fixed parameters, i.e. parameters not to estimate.
scaled – Whether to scale the values according to the parameter scale, or return them on linear scale.
- Return type
The lower parameter bounds.
- get_optimization_to_simulation_parameter_mapping(**kwargs)[source]
See
petab.parameter_mapping.get_optimization_to_simulation_parameter_mapping()
, to which all keyword arguments are forwarded.
- get_ub(free: bool = True, fixed: bool = True, scaled: bool = False)[source]
Generic function to get upper parameter bounds.
- Parameters
free – Whether to return free parameters, i.e. parameters to estimate.
fixed – Whether to return fixed parameters, i.e. parameters not to estimate.
scaled – Whether to scale the values according to the parameter scale, or return them on linear scale.
- Return type
The upper parameter bounds.
- get_x_ids(free: bool = True, fixed: bool = True)[source]
Generic function to get parameter ids.
- Parameters
free – Whether to return free parameters, i.e. parameters to estimate.
fixed – Whether to return fixed parameters, i.e. parameters not to estimate.
- Return type
The parameter IDs.
- get_x_nominal(free: bool = True, fixed: bool = True, scaled: bool = False)[source]
Generic function to get parameter nominal values.
- Parameters
free – Whether to return free parameters, i.e. parameters to estimate.
fixed – Whether to return fixed parameters, i.e. parameters not to estimate.
scaled – Whether to scale the values according to the parameter scale, or return them on linear scale.
- Return type
The parameter nominal values.
- scale_parameters(x_dict: Dict[str, float]) Dict[str, float] [source]
Scale parameter values.
- Parameters
x_dict – Keys are parameter IDs in the PEtab problem, values are unscaled parameter values.
- Return type
The scaled parameter values.
- to_files(sbml_file: Union[None, str, Path] = None, condition_file: Union[None, str, Path] = None, measurement_file: Union[None, str, Path] = None, parameter_file: Union[None, str, Path] = None, visualization_file: Union[None, str, Path] = None, observable_file: Union[None, str, Path] = None, yaml_file: Union[None, str, Path] = None, prefix_path: Union[None, str, Path] = None, relative_paths: bool = True, model_file: Union[None, str, Path] = None) None [source]
Write PEtab tables to files for this problem
Writes PEtab files for those entities for which a destination was passed.
NOTE: If this instance was created from multiple measurement or visualization tables, they will be merged and written to a single file.
- Parameters
sbml_file – SBML model destination
model_file – Model destination
condition_file – Condition table destination
measurement_file – Measurement table destination
parameter_file – Parameter table destination
visualization_file – Visualization table destination
observable_file – Observables table destination
yaml_file – YAML file destination
prefix_path – Specify a prefix to all paths, to avoid specifying the prefix for all paths individually. NB: the prefix is added to paths before relative_paths is handled.
relative_paths – whether all paths in the YAML file should be relative to the location of the YAML file. If False, then paths are left unchanged.
- Raises
ValueError – If a destination was provided for a non-existing entity.
- to_files_generic(prefix_path: Union[str, Path]) str [source]
Save a PEtab problem to generic file names.
The PEtab problem YAML file is always created. PEtab data files are only created if the PEtab problem contains corresponding data (e.g. a PEtab visualization TSV file is only created if the PEtab problem has one).
- Parameters
prefix_path – Specify a prefix to all paths, to avoid specifying the prefix for all paths individually. NB: the prefix is added to paths before relative_paths is handled downstream in petab.yaml.create_problem_yaml.
- Returns
The path to the PEtab problem YAML file.
- unscale_parameters(x_dict: Dict[str, float]) Dict[str, float] [source]
Unscale parameter values.
- Parameters
x_dict – Keys are parameter IDs in the PEtab problem, values are scaled parameter values.
- Return type
The unscaled parameter values.
- property x_nominal_fixed_scaled: List
Parameter table nominal values with applied parameter scaling, for fixed parameters.