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()

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(

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()

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(

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])

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0. Use `RGB_DTYPES` instead
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(

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:
CurrentComponentValues: Lorentzian
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
             A |    True |          1 |          0 |          0 |            |   True
        centre |    True |        220 |          0 |            |            |  False
         gamma |    True |          1 |          0 |            |            |  False

CurrentComponentValues: Offset
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
        offset |    True |         10 |          0 |            |            |   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()

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0. Use `RGB_DTYPES` instead
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(
ConvolvedModel1D:
CurrentComponentValues: Lorentzian
Active: True
Parameter Name |    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

CurrentComponentValues: Offset
Active: True
Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
============== | ======= | ========== | ========== | ========== | ========== | ======
        offset |    True |     9.9982 | 0.00035862 |            |            |   True