ParameterGroup

class glotaran.parameter.parameter_group.ParameterGroup(label: Optional[str] = None, root_group: Optional[glotaran.parameter.parameter_group.ParameterGroup] = None)[source]

Bases: dict

Represents are group of parameters.

Can contain other groups, creating a tree-like hierarchy.

Initialize a ParameterGroup instance with label.

Parameters

label (str) – The label of the group.
root_group (ParameterGroup) – The root group

Raises

ValueError – Raised if the an invalid label is given.

Attributes Summary

`label`	Label of the group.
`root_group`	Root of the group.

Methods Summary

`add_group`	Add a `ParameterGroup` to the group.
`add_parameter`	Add a `Parameter` to the group.
`all`	Iterate over all parameter in the group and it's subgroups together with their labels.
`clear`
`copy`	Create a copy of the `ParameterGroup`.
`from_dataframe`	Create a `ParameterGroup` from a `pandas.DataFrame`.
`from_dict`	Create a `ParameterGroup` from a dictionary.
`from_list`	Create a `ParameterGroup` from a list.
`from_parameter_dict_list`	Create a `ParameterGroup` from a list of parameter dictionaries.
`fromkeys`	Create a new dictionary with keys from iterable and values set to value.
`get`	Get a `Parameter` by its label.
`get_group_for_parameter_by_label`	Get the group for a parameter by it's label.
`get_label_value_and_bounds_arrays`	Return a arrays of all parameter labels, values and bounds.
`get_nr_roots`	Return the number of roots of the group.
`groups`	Return a generator over all groups and their subgroups.
`has`	Check if a parameter with the given label is in the group or in a subgroup.
`items`
`keys`
`loader`	Create a `ParameterGroup` instance from the specs defined in a file.
`markdown`	Format the `ParameterGroup` as markdown string.
`pop`	If key is not found, d is returned if given, otherwise KeyError is raised
`popitem`	Remove and return a (key, value) pair as a 2-tuple.
`set_from_history`	Update the `ParameterGroup` with values from a parameter history.
`set_from_label_and_value_arrays`	Update the parameter values from a list of labels and values.
`setdefault`	Insert key with a value of default if key is not in the dictionary.
`to_csv`	Save a `ParameterGroup` to a CSV file.
`to_dataframe`	Create a pandas data frame from the group.
`to_parameter_dict_list`	Create list of parameter dictionaries from the group.
`update`	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
`update_parameter_expression`	Update all parameters which have an expression.
`values`

Methods Documentation

add_group(group: glotaran.parameter.parameter_group.ParameterGroup)[source]

Add a ParameterGroup to the group.

Parameters: group (ParameterGroup) – The group to add.
Raises: TypeError – Raised if the group is not an instance of ParameterGroup.

add_parameter(parameter: Parameter | list[Parameter])[source]

Add a Parameter to the group.

Parameters: parameter (Parameter | list[Parameter]) – The parameter to add.
Raises: TypeError – If parameter or any item of it is not an instance of Parameter.

all(root: str | None = None, separator: str = '.') → Generator[tuple[str, Parameter], None, None][source]

Iterate over all parameter in the group and it’s subgroups together with their labels.

Parameters

root (str) – The label of the root group
separator (str) – The separator for the parameter labels.

Yields

tuple[str, Parameter] – A tuple containing the full label of the parameter and the parameter itself.

clear() → None. Remove all items from D.

copy() → glotaran.parameter.parameter_group.ParameterGroup[source]

Create a copy of the ParameterGroup.

Returns: A copy of the ParameterGroup.
Return type: ParameterGroup

classmethod from_dataframe(df: pandas.core.frame.DataFrame, source: str = 'DataFrame') → glotaran.parameter.parameter_group.ParameterGroup[source]

Create a ParameterGroup from a pandas.DataFrame.

Parameters

df (pd.DataFrame) – The source data frame.
source (str) – Optional name of the source file, used for error messages.

Returns

The created parameter group.

Return type

ParameterGroup

Raises

ValueError – Raised if the columns ‘label’ or ‘value’ doesn’t exist. Also raised if the columns ‘minimum’, ‘maximum’ or ‘values’ contain non numeric values or if the columns ‘non-negative’ or ‘vary’ are no boolean.

classmethod from_dict(parameter_dict: dict[str, dict[str, Any] | list[float | list[Any]]], label: str = None, root_group: ParameterGroup = None) → ParameterGroup[source]

Create a ParameterGroup from a dictionary.

Parameters

parameter_dict (dict[str, dict | list]) – A parameter dictionary containing parameters.
label (str) – The label of the group.
root_group (ParameterGroup) – The root group

Returns

The created ParameterGroup

Return type

ParameterGroup

classmethod from_list(parameter_list: list[float | list[Any]], label: str = None, root_group: ParameterGroup = None) → ParameterGroup[source]

Create a ParameterGroup from a list.

Parameters

parameter_list (list[float | list[Any]]) – A parameter list containing parameters
label (str) – The label of the group.
root_group (ParameterGroup) – The root group

Returns

The created ParameterGroup.

Return type

ParameterGroup

classmethod from_parameter_dict_list(parameter_dict_list: list[dict[str, Any]]) → ParameterGroup[source]

Create a ParameterGroup from a list of parameter dictionaries.

Parameters: parameter_dict_list (list[dict[str, Any]]) – A list of parameter dictionaries.
Returns: The created ParameterGroup.
Return type: ParameterGroup

fromkeys(iterable, value=None, /): Create a new dictionary with keys from iterable and values set to value.

get(label: str) → glotaran.parameter.parameter.Parameter[source]

Get a Parameter by its label.

Parameters: label (str) – The label of the parameter, with its path in a ParameterGroup prepended.
Returns: The parameter.
Return type: Parameter
Raises: ParameterNotFoundException – Raised if no parameter with the given label exists.

get_group_for_parameter_by_label(parameter_label: str, create_if_not_exist: bool = False) → glotaran.parameter.parameter_group.ParameterGroup[source]

Get the group for a parameter by it’s label.

Parameters

parameter_label (str) – The parameter label.
create_if_not_exist (bool) – Create the parameter group if not existent.

Returns

The group of the parameter.

Return type

ParameterGroup

Raises

KeyError – Raised if the group does not exist and create_if_not_exist is False.

get_label_value_and_bounds_arrays(exclude_non_vary: bool = False) → tuple[list[str], np.ndarray, np.ndarray, np.ndarray][source]

Return a arrays of all parameter labels, values and bounds.

Parameters: exclude_non_vary (bool) – If true, parameters with vary=False are excluded.
Returns: A tuple containing a list of parameter labels and an array of the values, lower and upper bounds.
Return type: tuple[list[str], np.ndarray, np.ndarray, np.ndarray]

get_nr_roots() → int[source]

Return the number of roots of the group.

Returns: The number of roots.
Return type: int

groups() → Generator[glotaran.parameter.parameter_group.ParameterGroup, None, None][source]

Return a generator over all groups and their subgroups.

Yields: ParameterGroup – A subgroup of ParameterGroup.

has(label: str) → bool[source]

Check if a parameter with the given label is in the group or in a subgroup.

Parameters: label (str) – The label of the parameter, with its path in a ParameterGroup prepended.
Returns: Whether a parameter with the given label exists in the group.
Return type: bool

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

property label: str | None

Label of the group.

Returns: The label of the group.
Return type: str

loader(format_name: str = None, **kwargs) → ParameterGroup

Create a ParameterGroup instance from the specs defined in a file.

Parameters

file_name (StrOrPath) – File containing the parameter specs.
format_name (str) – Format the file is in, if not provided it will be inferred from the file extension.
**kwargs (Any) – Additional keyword arguments passes to the load_parameters implementation of the project io plugin.

Returns

ParameterGroup instance created from the file.

Return type

ParameterGroup

markdown(float_format: str = '.3e') → glotaran.utils.ipython.MarkdownStr[source]

Format the ParameterGroup as markdown string.

This is done by recursing the nested ParameterGroup tree.

Parameters: float_format (str) – Format string for floating point numbers, by default “.3e”
Returns: The markdown representation as string.
Return type: MarkdownStr

pop(k[, d]) → v, remove specified key and return the corresponding value.: If key is not found, d is returned if given, otherwise KeyError is raised

popitem(/)

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

property root_group: ParameterGroup | None

Root of the group.

Returns: The root group.
Return type: ParameterGroup

set_from_history(history: ParameterHistory, index: int)[source]

Update the ParameterGroup with values from a parameter history.

Parameters

history (ParameterHistory) – The parameter history.
index (int) – The history index.

set_from_label_and_value_arrays(labels: list[str], values: np.ndarray)[source]

Update the parameter values from a list of labels and values.

Parameters

labels (list[str]) – A list of parameter labels.
values (np.ndarray) – An array of parameter values.

Raises

ValueError – Raised if the size of the labels does not match the stize of values.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

to_csv(filename: str, delimiter: str = ',') → None[source]

Save a ParameterGroup to a CSV file.

Warning

Deprecated use glotaran.io.save_parameters(parameters, file_name=<parameters.csv>, format_name="csv") instead.

Parameters

filename (str) – File to write the parameter specs to.
delimiter (str) – Character to separate columns., by default “,”

to_dataframe(as_optimized: bool = True) → pandas.core.frame.DataFrame[source]

Create a pandas data frame from the group.

Parameters: as_optimized (bool) – Whether to include properties which are the result of optimization.
Returns: The created data frame.
Return type: pd.DataFrame

to_parameter_dict_list(as_optimized: bool = True) → list[dict[str, Any]][source]

Create list of parameter dictionaries from the group.

Parameters: as_optimized (bool) – Whether to include properties which are the result of optimization.
Returns: Alist of parameter dictionaries.
Return type: list[dict[str, Any]]

update([E, ]**F) → None. Update D from dict/iterable E and F.: If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

update_parameter_expression()[source]

Update all parameters which have an expression.

Raises: ValueError – Raised if an expression evaluates to a non-numeric value.

values() → an object providing a view on D's values