Implementation of a model supporting convolution of components

This example illustrates how to implement a model supporting convolution.

Note

Model convolution has only been tested for 1D signals.

import hyperspy.api as hs
import numpy as np

Model class implementation

Create a model class subclassing hyperspy.models.model1d.Model1D. The subclass needs to implement the following API:

• _convolution_axis

• _signal_to_convolve

• convolved

The steps of how the convolution is implemented are explained in component convolution example.

from hyperspy.models.model1d import Model1D
from hyperspy.misc.axis_tools import calculate_convolution1D_axis

class ConvolvedModel1D(Model1D):

    def __init__(self, signal1D, detector_response=None, **kwargs):
        super().__init__(signal1D, **kwargs)
        self._convolved = False
        self._detector_response = None
        self._convolution_axis = None
        self.detector_response = detector_response
        self._whitelist.update(
            {
                "_convolved": None,
                "detector_response": ("sig", None),
            }
        )


    def _set_convolution_axis(self):
        """
        Set the convolution axis used to add padding before taking
        the convolution.
        """
        # Used during model fitting
        self._convolution_axis = calculate_convolution1D_axis(
            self.signal.axes_manager.signal_axes[0],
            self.detector_response.axes_manager.signal_axes[0]
        )

    @property
    def detector_response(self):
        return self._detector_response

    @detector_response.setter
    def detector_response(self, signal):
        if signal is not None:
            self._detector_response = signal
            self._set_convolution_axis()
            self._convolved = True
        else:
            self._detector_response = None
            self._convolution_axis = None
            self._convolved = False

    @property
    def _signal_to_convolve(self):
        # Used during model fitting
        return self.detector_response

    @property
    def convolved(self):
        # Used during model fitting
        return self._convolved

Example signal

We create a signal of a Lorentzian convolved with a Gaussian function, where the Lorentzian function is the measurement of interest and the Gaussian function a model for a detector response.

Generate a signal of the detector response:

g = hs.model.components1D.Gaussian(sigma=3)
g_signal = hs.signals.Signal1D(g.function(np.arange(-20, 20)))
g_signal.axes_manager.signal_axes.set(offset=-20)
g_signal.plot()

Generate an example signal using the same approach as in the implementation of a convolution for model fitting (see component convolution):

f = hs.model.components1D.Lorentzian(centre=220)
f_signal = hs.signals.Signal1D(f.function(np.arange(200, 300)))
f_signal.axes_manager.signal_axes.set(offset=200)
convolution_axis = calculate_convolution1D_axis(
    f_signal.axes_manager.signal_axes[0], g_signal.axes_manager.signal_axes[0]
    )
f_padded_data = f.function(convolution_axis)
f_signal.data = np.convolve(f_padded_data, g_signal.data, mode="valid") + 10

Plot signal composed of the convolution of a Lorentzian and a Gaussian function:

f_signal.plot()

Fit model with convolution

m = ConvolvedModel1D(f_signal, detector_response=g_signal)
lorentzian_component = hs.model.components1D.Lorentzian()
lorentzian_component.estimate_parameters(f_signal, 200, 300)
offset_component = hs.model.components1D.Offset()
m.extend([lorentzian_component, offset_component])

The component of the model can be set to be convolved or not during model fitting. Specify that the Lorentzian is convolved:

lorentzian_component.convolved = True
offset_component.convolved = False

Show the results

m.fit()
m.print_current_values()

m.plot()

ConvolvedModel1D:
Lorentzian: Lorentzian
Active: True
+----------------+---------+------------+------------+------------+------------+--------+
|      Parameter |    Free |      Value |        Std |        Min |        Max | Linear |
+----------------+---------+------------+------------+------------+------------+--------+
|              A |    True |          1 | 2.5244e-15 |          0 |            |   True |
|         centre |    True |        220 | 6.3587e-15 |            |            |  False |
|          gamma |    True |          1 | 1.0635e-14 |            |            |  False |
+----------------+---------+------------+------------+------------+------------+--------+
Offset: Offset
Active: True
+----------------+---------+------------+------------+------------+------------+--------+
|      Parameter |    Free |      Value |        Std |        Min |        Max | Linear |
+----------------+---------+------------+------------+------------+------------+--------+
|         offset |    True |         10 | 3.7789e-17 |            |            |   True |
+----------------+---------+------------+------------+------------+------------+--------+

Fit model without convolution

m2 = ConvolvedModel1D(f_signal)
lorentzian_component2 = hs.model.components1D.Lorentzian()
lorentzian_component2.estimate_parameters(f_signal, 200, 300)
offset_component2 = hs.model.components1D.Offset()
m2.extend([lorentzian_component2, offset_component2])

m2.fit()
m2.print_current_values()

m2.plot()

ConvolvedModel1D:
Lorentzian: Lorentzian
Active: True
+----------------+---------+------------+------------+------------+------------+--------+
|      Parameter |    Free |      Value |        Std |        Min |        Max | Linear |
+----------------+---------+------------+------------+------------+------------+--------+
|              A |    True |     1.2522 |   0.023949 |          0 |            |   True |
|         centre |    True |        220 |   0.054812 |            |            |  False |
|          gamma |    True |      3.527 |   0.085845 |            |            |  False |
+----------------+---------+------------+------------+------------+------------+--------+
Offset: Offset
Active: True
+----------------+---------+------------+------------+------------+------------+--------+
|      Parameter |    Free |      Value |        Std |        Min |        Max | Linear |
+----------------+---------+------------+------------+------------+------------+--------+
|         offset |    True |     9.9982 | 0.00035862 |            |            |   True |
+----------------+---------+------------+------------+------------+------------+--------+