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HyperSpy API is changing in version 2.0, see the release notes!

Getting and setting parameter values and attributes#

Getting parameter values#

print_current_values() prints the properties of the parameters of the components in the current coordinates. In the Jupyter Notebook, the default view is HTML-formatted, which allows for formatted copying into other software, such as Excel. One can also filter for only active components and only showing component with free parameters with the arguments only_active and only_free, respectively.

The current values of a particular component can be printed using the print_current_values() method.

>>> s = exspy.data.EDS_SEM_TM002() 
>>> m = s.create_model() 
>>> m.fit() 
>>> G = m[1] 
>>> G.print_current_values() 
Gaussian: Al_Ka
Active: True
Parameter Name |  Free |      Value |        Std |        Min
============== | ===== | ========== | ========== | ==========
             A |  True | 62894.6824 | 1039.40944 |        0.0
         sigma | False | 0.03253440 |       None |       None
        centre | False |     1.4865 |       None |       None

The current coordinates can be either set by navigating the plot(), or specified by pixel indices in m.axes_manager.indices or as calibrated coordinates in m.axes_manager.coordinates.

parameters contains a list of the parameters of a component and free_parameters lists only the free parameters.

The value of a particular parameter in the current coordinates can be accessed by component.Parameter.value (e.g. Gaussian.A.value). To access an array of the value of the parameter across all navigation pixels, component.Parameter.map['values'] (e.g. Gaussian.A.map["values"]) can be used. On its own, component.Parameter.map returns a NumPy array with three elements: 'values', 'std' and 'is_set'. The first two give the value and standard error for each index. The last element shows whether the value has been set in a given index, either by a fitting procedure or manually.

If a model contains several components with the same parameters, it is possible to change them all by using set_parameters_value():

>>> s = hs.signals.Signal1D(np.arange(100).reshape(10,10))
>>> m = s.create_model()
>>> g1 = hs.model.components1D.Gaussian()
>>> g2 = hs.model.components1D.Gaussian()
>>> m.extend([g1,g2])
>>> m.set_parameters_value('A', 20)
>>> g1.A.map['values']
array([20., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> g2.A.map['values']
array([20., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> m.set_parameters_value('A', 40, only_current=True)
>>> g1.A.map['values']
array([40., 20., 20., 20., 20., 20., 20., 20., 20., 20.])
>>> m.set_parameters_value('A',30, component_list=[g2])
>>> g2.A.map['values']
array([30., 30., 30., 30., 30., 30., 30., 30., 30., 30.])
>>> g1.A.map['values']
array([40., 20., 20., 20., 20., 20., 20., 20., 20., 20.])

Setting Parameters free / not free#

To set the free state of a parameter change the free attribute. To change the free state of all parameters in a component to True use set_parameters_free(), and set_parameters_not_free() for setting them to False. Specific parameter-names can also be specified by using parameter_name_list, shown in the example:

>>> g = hs.model.components1D.Gaussian()
>>> g.free_parameters
(<Parameter A of Gaussian component>, <Parameter centre of Gaussian component>, <Parameter sigma of Gaussian component>)
>>> g.set_parameters_not_free()
>>> g.set_parameters_free(parameter_name_list=['A','centre'])
>>> g.free_parameters
(<Parameter A of Gaussian component>, <Parameter centre of Gaussian component>)

Similar functions exist for BaseModel: set_parameters_free() and set_parameters_not_free(). Which sets the free states for the parameters in components in a model. Specific components and parameter-names can also be specified. For example:

>>> g1 = hs.model.components1D.Gaussian()
>>> g2 = hs.model.components1D.Gaussian()
>>> m.extend([g1,g2])
>>> m.set_parameters_not_free()
>>> g1.free_parameters
()
>>> g2.free_parameters
()
>>> m.set_parameters_free(parameter_name_list=['A'])
>>> g1.free_parameters
(<Parameter A of Gaussian_1 component>,)
>>> g2.free_parameters
(<Parameter A of Gaussian_2 component>,)
>>> m.set_parameters_free([g1], parameter_name_list=['sigma'])
>>> g1.free_parameters
(<Parameter A of Gaussian_1 component>, <Parameter sigma of Gaussian_1 component>)
>>> g2.free_parameters
(<Parameter A of Gaussian_2 component>,)

Setting twin parameters#

The value of a parameter can be coupled to the value of another by setting the twin attribute:

>>> s = hs.signals.Signal1D(np.arange(100))
>>> m = s.create_model()

>>> gaussian = hs.model.components1D.Gaussian()
>>> gaussian2 = hs.model.components1D.Gaussian() # Create another gaussian
>>> gaussian3 = hs.model.components1D.Gaussian() # Create a third gaussian
>>> gaussian.name = 'Carbon'
>>> gaussian2.name = 'Long Hydrogen name'
>>> gaussian3.name = 'Nitrogen'
>>> m.extend((gaussian, gaussian2, gaussian3))

>>> gaussian.parameters # Print the parameters of the Gaussian components
(<Parameter A of Carbon component>, <Parameter centre of Carbon component>, <Parameter sigma of Carbon component>)
>>> gaussian.centre.free = False # Fix the centre
>>> gaussian.free_parameters  # Print the free parameters
(<Parameter A of Carbon component>, <Parameter sigma of Carbon component>)
>>> m.print_current_values(only_free=True) # Print the values of all free parameters.
Model1D:
CurrentComponentValues: Carbon
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |        1.0 |       None |        0.0 |       None |   True
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

CurrentComponentValues: Long Hydrogen name
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |        1.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

CurrentComponentValues: Nitrogen
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |        1.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

>>> # Couple the A parameter of gaussian2 to the A parameter of gaussian 3:
>>> gaussian2.A.twin = gaussian3.A
>>> gaussian2.A.value = 10 # Set the gaussian2 A value to 10
>>> gaussian3.print_current_values()
CurrentComponentValues: Nitrogen
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |       10.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False
>>> gaussian3.A.value = 5 # Set the gaussian1 centre value to 5
>>> gaussian2.print_current_values()
CurrentComponentValues: Long Hydrogen name
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A | Twinned |        5.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

Deprecated since version 1.2.0: Setting the twin_function and twin_inverse_function attributes, set the twin_function_expr and twin_inverse_function_expr attributes instead.

New in version 1.2.0: twin_function_expr and twin_inverse_function_expr.

By default the coupling function is the identity function. However it is possible to set a different coupling function by setting the twin_function_expr and twin_inverse_function_expr attributes. For example:

>>> gaussian2.A.twin_function_expr = "x**2"
>>> gaussian2.A.twin_inverse_function_expr = "sqrt(abs(x))"
>>> gaussian2.A.value = 4
>>> gaussian3.print_current_values()
CurrentComponentValues: Nitrogen
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |        2.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

>>> gaussian3.A.value = 4
>>> gaussian2.print_current_values()
CurrentComponentValues: Long Hydrogen name
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A | Twinned |       16.0 |       None |        0.0 |       None |   True
        centre |    True |        0.0 |       None |       None |       None |  False
         sigma |    True |        1.0 |       None |        0.0 |       None |  False

Batch setting of parameter attributes#

The following model methods can be used to ease the task of setting some important parameter attributes. These can also be used on a per-component basis, by calling them on individual components.

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