hyperspy.component module

class hyperspy.component.Component(parameter_name_list)

Bases: traits.has_traits.HasTraits

active_is_multidimensional

as_dictionary(fullcopy=True)

Returns component as a dictionary For more information on method and conventions, see hyperspy.misc.export_dictionary.export_to_dictionary() :param fullcopy: Copies of objects are stored, not references. If any found,

functions will be pickled and signals converted to dictionaries

Returns:dic – A dictionary, containing at least the following fields: parameters : list

a list of dictionaries of the parameters, one per

_whitelist : dictionary

a dictionary with keys used as references saved attributes, for more information, see hyperspy.misc.export_dictionary.export_to_dictionary()

• any field from _whitelist.keys() *

Return type:dictionary

export(folder=None, format='hspy', save_std=False, only_free=True)

Plot the value of the parameters of the model

Parameters:

• folder (str or None) – The path to the folder where the file will be saved. If None the current folder is used by default.
• format (str) – The extension of the file format, default “hspy”.
• save_std (bool) – If True, also the standard deviation will be saved.
• only_free (bool) –

  If True, only the value of the parameters that are free will

  be

  exported.

Notes

The name of the files will be determined by each the Component and each Parameter name attributes. Therefore, it is possible to customise the file names modify the name attributes.

fetch_stored_values(only_fixed=False)

fetch_values_from_array(p, p_std=None, onlyfree=False)

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

• display (bool) – If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.
• toolkit (str, iterable of strings or None) – If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

init_parameters(parameter_name_list)

plot(only_free=True)

Plot the value of the parameters of the model

Parameters:only_free (bool) –

If True, only the value of the parameters that are free will

be plotted

set_parameters_free(parameter_name_list=None)

Sets parameters in a component to free.

Parameters:parameter_name_list (None or list of strings, optional) – If None, will set all the parameters to free. If list of strings, will set all the parameters with the same name as the strings in parameter_name_list to free.

Examples

>>> v1 = hs.model.components1D.Voigt()
>>> v1.set_parameters_free()
>>> v1.set_parameters_free(parameter_name_list=['area','centre'])

See also

set_parameters_not_free(), hyperspy.model.BaseModel.set_parameters_free(), hyperspy.model.BaseModel.set_parameters_not_free()

set_parameters_not_free(parameter_name_list=None)

Sets parameters in a component to not free.

Parameters:parameter_name_list (None or list of strings, optional) – If None, will set all the parameters to not free. If list of strings, will set all the parameters with the same name as the strings in parameter_name_list to not free.

Examples

>>> v1 = hs.model.components1D.Voigt()
>>> v1.set_parameters_not_free()
>>> v1.set_parameters_not_free(parameter_name_list=['area','centre'])

See also

set_parameters_free(), hyperspy.model.BaseModel.set_parameters_free(), hyperspy.model.BaseModel.set_parameters_not_free()

store_current_parameters_in_map()

summary()

update_number_parameters()

class hyperspy.component.NoneFloat(default_value=<traits.trait_handlers.NoDefaultSpecified object>, **metadata)

Bases: traits.trait_types.CFloat

default_value = None

validate(object, name, value)

Validates that a specified value is valid for this trait.

Note: The ‘fast validator’ version performs this check in C.

class hyperspy.component.Parameter

Bases: traits.has_traits.HasTraits

Model parameter

value

float or array – The value of the parameter for the current location. The value for other locations is stored in map.

bmin, bmax

float – Lower and upper bounds of the parameter value.

twin

{None, Parameter} – If it is not None, the value of the current parameter is a function of the given Parameter. The function is by default the identity function, but it can be defined by twin_function

twin_function_expr

str – Expression of the twin_function that enables setting a functional relationship between the parameter and its twin. If twin is not None, the parameter value is calculated as the output of calling the twin function with the value of the twin parameter. The string is parsed using sympy, so permitted values are any valid sympy expressions of one variable. If the function is invertible the twin inverse function is set automatically.

twin_inverse_function

str – Expression of the twin_inverse_function that enables setting the value of the twin parameter. If twin is not None, its value is set to the output of calling the twin inverse function with the value provided. The string is parsed using sympy, so permitted values are any valid sympy expressions of one variable.

twin_function

function – Setting this attribute manually is deprecated in HyperSpy newer than 1.1.2. It will become private in HyperSpy 2.0. Please use ``twin_function_expr`` instead.

twin_inverse_function

function – Setting this attribute manually is deprecated in HyperSpy newer than 1.1.2. It will become private in HyperSpy 2.0. Please use ``twin_inverse_function_expr`` instead.

ext_force_positive

bool – If True, the parameter value is set to be the absolute value of the input value i.e. if we set Parameter.value = -3, the value stored is 3 instead. This is useful to bound a value to be positive in an optimization without actually using an optimizer that supports bounding.

ext_bounded

bool – Similar to ext_force_positive, but in this case the bounds are defined by bmin and bmax. It is a better idea to use an optimizer that supports bounding though.

as_signal(field = 'values')

Get a parameter map as a signal object

plot()

Plots the value of the Parameter at all locations.

export(folder=None, name=None, format=None, save_std=False)

Saves the value of the parameter map to the specified format

connect, disconnect(function)

Call the functions connected when the value attribute changes.

as_dictionary(fullcopy=True)

Returns parameter as a dictionary, saving all attributes from self._whitelist.keys() For more information see hyperspy.misc.export_dictionary.export_to_dictionary()

Parameters:fullcopy (Bool (optional, False)) – Copies of objects are stored, not references. If any found, functions will be pickled and signals converted to dictionaries Returns:dic –

_id_name : string

_id_name of the original parameter, used to create the dictionary. Has to match with the self._id_name

_twins : list

a list of ids of the twins of the parameter

_whitelist : dictionary

a dictionary, which keys are used as keywords to match with the parameter attributes. For more information see hyperspy.misc.export_dictionary.export_to_dictionary()

• any field from _whitelist.keys() *

Return type:dictionary with the following keys:

as_signal(field='values')

Get a parameter map as a signal object.

Please note that this method only works when the navigation dimension is greater than 0.

Parameters:field ({'values', 'std', 'is_set'}) – Raises:NavigationDimensionError : if the navigation dimension is 0

assign_current_value_to_all(mask=None)

Assign the current value attribute to all the indices

Parameters:mask ({None, boolean numpy array}) – Set only the indices that are not masked i.e. where mask is False.

See also

store_current_value_in_array(), fetch()

default_traits_view()

Returns the name of the default traits view for the object’s class.

export(folder=None, name=None, format='hspy', save_std=False)

Save the data to a file.

All the arguments are optional.

Parameters:

• folder (str or None) –

  The path to the folder where the file will be saved.

  If None the current folder is used by default.

• name (str or None) –

  The name of the file. If None the Components name followed

  by the Parameter name attributes will be used by default.

  If a file with the same name exists the name will be modified by appending a number to the file path.

• save_std (bool) – If True, also the standard deviation will be saved
• format (str) – The extension of any file format supported by HyperSpy, default hspy

ext_bounded

ext_force_positive

fetch()

Fetch the stored value and std attributes.

See also

store_current_value_in_array(), assign_current_value_to_all()

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

• display (bool) – If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.
• toolkit (str, iterable of strings or None) – If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

plot(**kwargs)

Plot parameter signal.

Parameters:**kwargs – Any extra keyword arguments are passed to the signal plot.

Example

>>> parameter.plot() 

Set the minimum and maximum displayed values

>>> parameter.plot(vmin=0, vmax=1) 

store_current_value_in_array()

Store the value and std attributes.

See also

fetch(), assign_current_value_to_all()

twin

twin_function = None

twin_function_expr

twin_inverse_function

twin_inverse_function_expr