petab.visualize.cli

Command-line interface for visualization.

class petab.visualize.cli.Path(*args, **kwargs)

Bases: PurePath

PurePath subclass that can make system calls.

Path represents a filesystem path but unlike PurePath, also offers methods to do system calls on path objects. Depending on your system, instantiating a Path will return either a PosixPath or a WindowsPath object. You can also instantiate a PosixPath or WindowsPath directly, but cannot instantiate a WindowsPath on a POSIX system or vice versa.

_raw_open(flags, mode=511)

Open the file pointed by this path and return a file descriptor, as os.open() does.

absolute()

Return an absolute version of this path. This function works even if the path doesn’t point to anything.

No normalization is done, i.e. all ‘.’ and ‘..’ will be kept along. Use resolve() to get the canonical path to a file.

property anchor

The concatenation of the drive and root, or ‘’.

as_posix()

Return the string representation of the path with forward (/) slashes.

as_uri()

Return the path as a ‘file’ URI.

chmod(mode)

Change the permissions of the path, like os.chmod().

classmethod cwd()

Return a new path pointing to the current working directory (as returned by os.getcwd()).

property drive

The drive prefix (letter or UNC path), if any.

exists()

Whether this path exists.

expanduser()

Return a new path with expanded ~ and ~user constructs (as returned by os.path.expanduser)

glob(pattern)

Iterate over this subtree and yield all existing files (of any kind, including directories) matching the given relative pattern.

group()

Return the group name of the file gid.

classmethod home()

Return a new path pointing to the user’s home directory (as returned by os.path.expanduser(‘~’)).

is_absolute()

True if the path is absolute (has both a root and, if applicable, a drive).

is_block_device()

Whether this path is a block device.

is_char_device()

Whether this path is a character device.

is_dir()

Whether this path is a directory.

is_fifo()

Whether this path is a FIFO.

is_file()

Whether this path is a regular file (also True for symlinks pointing to regular files).

is_mount()

Check if this path is a POSIX mount point

is_relative_to(*other)

Return True if the path is relative to another path or False.

is_reserved()

Return True if the path contains one of the special names reserved by the system, if any.

is_socket()

Whether this path is a socket.

is_symlink()

Whether this path is a symbolic link.

iterdir()

Iterate over the files in this directory. Does not yield any result for the special paths ‘.’ and ‘..’.

joinpath(*args)

Combine this path with one or several arguments, and return a new path representing either a subpath (if all arguments are relative paths) or a totally different path (if one of the arguments is anchored).

lchmod(mode)

Like chmod(), except if the path points to a symlink, the symlink’s permissions are changed, rather than its target’s.

link_to(target)

Make the target path a hard link pointing to this path.

Note this function does not make this path a hard link to target, despite the implication of the function and argument names. The order of arguments (target, link) is the reverse of Path.symlink_to, but matches that of os.link.

lstat()

Like stat(), except if the path points to a symlink, the symlink’s status information is returned, rather than its target’s.

match(path_pattern)

Return True if this path matches the given pattern.

mkdir(mode=511, parents=False, exist_ok=False)

Create a new directory at this given path.

property name

The final path component, if any.

open(mode='r', buffering=-1, encoding=None, errors=None, newline=None)

Open the file pointed by this path and return a file object, as the built-in open() function does.

owner()

Return the login name of the file owner.

property parent

The logical parent of the path.

property parents

A sequence of this path’s logical parents.

property parts

An object providing sequence-like access to the components in the filesystem path.

read_bytes()

Open the file in bytes mode, read it, and close the file.

read_text(encoding=None, errors=None)

Open the file in text mode, read it, and close the file.

readlink()

Return the path to which the symbolic link points.

relative_to(*other)

Return the relative path to another path identified by the passed arguments. If the operation is not possible (because this is not a subpath of the other path), raise ValueError.

rename(target)

Rename this path to the target path.

The target path may be absolute or relative. Relative paths are interpreted relative to the current working directory, not the directory of the Path object.

Returns the new Path instance pointing to the target path.

replace(target)

Rename this path to the target path, overwriting if that path exists.

The target path may be absolute or relative. Relative paths are interpreted relative to the current working directory, not the directory of the Path object.

Returns the new Path instance pointing to the target path.

resolve(strict=False)

Make the path absolute, resolving all symlinks on the way and also normalizing it (for example turning slashes into backslashes under Windows).

rglob(pattern)

Recursively yield all existing files (of any kind, including directories) matching the given relative pattern, anywhere in this subtree.

rmdir()

Remove this directory. The directory must be empty.

property root

The root of the path, if any.

samefile(other_path)

Return whether other_path is the same or not as this file (as returned by os.path.samefile()).

stat()

Return the result of the stat() system call on this path, like os.stat() does.

property stem

The final path component, minus its last suffix.

property suffix

The final component’s last suffix, if any.

This includes the leading period. For example: ‘.txt’

property suffixes

A list of the final component’s suffixes, if any.

These include the leading periods. For example: [‘.tar’, ‘.gz’]

symlink_to(target, target_is_directory=False)

Make this path a symlink pointing to the target path. Note the order of arguments (link, target) is the reverse of os.symlink.

touch(mode=438, exist_ok=True)

Create this file with the given access mode, if it doesn’t exist.

unlink(missing_ok=False)

Remove this file or link. If the path is a directory, use rmdir() instead.

with_name(name)

Return a new path with the file name changed.

with_stem(stem)

Return a new path with the stem changed.

with_suffix(suffix)

Return a new path with the file suffix changed. If the path has no suffix, add given suffix. If the given suffix is an empty string, remove the suffix from the path.

write_bytes(data)

Open the file in bytes mode, write to it, and close the file.

write_text(data, encoding=None, errors=None)

Open the file in text mode, write to it, and close the file.

class petab.visualize.cli.Problem(sbml_model: libsbml.Model = None, sbml_reader: libsbml.SBMLReader = None, sbml_document: libsbml.SBMLDocument = None, model: Model = None, model_id: str = 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, mapping_df: pd.DataFrame = None, extensions_config: Dict = None)

Bases: object

PEtab parameter estimation problem as defined by

• model

• condition table

• measurement table

• parameter table

• observables table

• mapping 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

mapping_df

PEtab mapping 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)

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.

create_parameter_df(*args, **kwargs)

Create a new PEtab parameter table

See create_parameter_df().

static from_combine(filename: Path | str) → Problem

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: Path | str | None = None, condition_file: str | Path | Iterable[str | Path] | None = None, measurement_file: str | Path | Iterable[str | Path] | None = None, parameter_file: str | Path | Iterable[str | Path] | None = None, visualization_files: str | Path | Iterable[str | Path] | None = None, observable_files: str | Path | Iterable[str | Path] | None = None, model_id: str | None = None, extensions_config: Dict | None = None) → Problem

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

• model_id – PEtab ID of the model

• extensions_config – Information on the extensions used

static from_yaml(yaml_config: Dict | Path | str) → Problem

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)

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_model_parameters()

See petab.sbml.get_model_parameters()

get_observable_ids()

Returns dictionary of observable ids.

get_optimization_parameter_scales()

Return list of optimization parameter scaling strings.

See petab.parameters.get_optimization_parameters().

get_optimization_parameters()

Return list of optimization parameter IDs.

See petab.parameters.get_optimization_parameters().

get_optimization_to_simulation_parameter_mapping(**kwargs)

See petab.parameter_mapping.get_optimization_to_simulation_parameter_mapping(), to which all keyword arguments are forwarded.

get_simulation_conditions_from_measurement_df()

See petab.get_simulation_conditions

get_ub(free: bool = True, fixed: bool = True, scaled: bool = False)

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)

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)

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.

property lb: List

Parameter table lower bounds.

property lb_scaled: List

Parameter table lower bounds with applied parameter scaling

property n_estimated: int

The number of estimated parameters.

property n_measurements: int

Number of measurements.

property n_priors: int

Number of priors.

sample_parameter_startpoints(n_starts: int = 100, **kwargs)

Create 2D array with starting points for optimization

See petab.sample_parameter_startpoints().

sample_parameter_startpoints_dict(n_starts: int = 100) → List[Dict[str, float]]

Create dictionaries with starting points for optimization

See also petab.sample_parameter_startpoints().

Returns:

A list of dictionaries with parameter IDs mapping to samples parameter values.

scale_parameters(x_dict: Dict[str, float]) → Dict[str, float]

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: None | str | Path = None, condition_file: None | str | Path = None, measurement_file: None | str | Path = None, parameter_file: None | str | Path = None, visualization_file: None | str | Path = None, observable_file: None | str | Path = None, yaml_file: None | str | Path = None, prefix_path: None | str | Path = None, relative_paths: bool = True, model_file: None | str | Path = None, mapping_file: None | str | Path = None) → None

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 (deprecated)

• 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

• mapping_file – Mapping 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: str | Path) → str

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.

property ub: List

Parameter table upper bounds

property ub_scaled: List

Parameter table upper bounds with applied parameter scaling

unscale_parameters(x_dict: Dict[str, float]) → Dict[str, float]

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_fixed_ids: List[str]

Parameter table parameter IDs, for fixed parameters.

property x_fixed_indices: List[int]

Parameter table non-estimated parameter indices.

property x_free_ids: List[str]

Parameter table parameter IDs, for free parameters.

property x_free_indices: List[int]

Parameter table estimated parameter indices.

property x_ids: List[str]

Parameter table parameter IDs

property x_nominal: List

Parameter table nominal values

property x_nominal_fixed: List

Parameter table nominal values, for fixed parameters.

property x_nominal_fixed_scaled: List

Parameter table nominal values with applied parameter scaling, for fixed parameters.

property x_nominal_free: List

Parameter table nominal values, for free parameters.

property x_nominal_free_scaled: List

Parameter table nominal values with applied parameter scaling, for free parameters.

property x_nominal_scaled: List

Parameter table nominal values with applied parameter scaling

petab.visualize.cli._parse_cli_args()

Parse command-line arguments.

petab.visualize.cli._petab_visualize_main()

Entrypoint for visualization command-line interface.

petab.visualize.cli.get_simulation_df(simulation_file: str | Path) → DataFrame

Read PEtab simulation table

Parameters:

simulation_file – URL or filename of PEtab simulation table

Returns:

Simulation DataFrame

petab.visualize.cli.get_visualization_df(visualization_file: str | Path | DataFrame | None) → DataFrame | None

Read PEtab visualization table

Parameters:

visualization_file – URL or filename of PEtab visualization table to read from, or a DataFrame or None that will be returned as is.

Returns:

Visualization DataFrame

petab.visualize.cli.plot_problem(petab_problem: Problem, simulations_df: str | DataFrame | None = None, grouping_list: List[List[str]] | None = None, group_by: str = 'observable', plotted_noise: str = 'MeanAndSD', subplot_dir: str | None = None, plotter_type: str = 'mpl') → Dict[str, Axes] | None

Visualization using petab problem. If Visualization table is part of the petab_problem, it will be used for visualization. Otherwise, grouping_list will be used. If neither Visualization table nor grouping_list are available, measurements (simulations) will be grouped by observable, i.e. all measurements for each observable will be visualized on one plot.

Parameters:

• petab_problem – A PEtab problem.

• simulations_df – A simulation DataFrame in the PEtab format or path to the simulation output data file.

• grouping_list – A list of lists. Each sublist corresponds to a plot, each subplot contains the Ids of datasets or observables or simulation conditions for this plot.

• group_by – Possible values: ‘dataset’, ‘observable’, ‘simulation’.

• plotted_noise – A string indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’].

• subplot_dir – A string which is taken as path to the folder where single subplots should be saved. PlotIDs will be taken as file names.

• plotter_type – Specifies which library should be used for plot generation. Currently, only matplotlib is supported.

Returns:

• ax (Axis object of the created plot.)

• None (In case subplots are saved to a file.)