.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/extensions/model_convolution.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_extensions_model_convolution.py: ============================================================== 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. .. GENERATED FROM PYTHON SOURCE LINES 12-16 .. code-block:: Python import hyperspy.api as hs import numpy as np .. GENERATED FROM PYTHON SOURCE LINES 17-30 Model class implementation -------------------------- Create a model class subclassing :class:`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 :ref:`component convolution example `. .. GENERATED FROM PYTHON SOURCE LINES 30-85 .. code-block:: Python 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 .. GENERATED FROM PYTHON SOURCE LINES 86-94 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: .. GENERATED FROM PYTHON SOURCE LINES 94-100 .. code-block:: Python 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() .. image-sg:: /auto_examples/extensions/images/sphx_glr_model_convolution_001.png :alt: Signal :srcset: /auto_examples/extensions/images/sphx_glr_model_convolution_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 101-103 Generate an example signal using the same approach as in the implementation of a convolution for model fitting (see :ref:`component convolution `): .. GENERATED FROM PYTHON SOURCE LINES 103-113 .. code-block:: Python 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 .. GENERATED FROM PYTHON SOURCE LINES 114-116 Plot signal composed of the convolution of a Lorentzian and a Gaussian function: .. GENERATED FROM PYTHON SOURCE LINES 116-118 .. code-block:: Python f_signal.plot() .. image-sg:: /auto_examples/extensions/images/sphx_glr_model_convolution_002.png :alt: Signal :srcset: /auto_examples/extensions/images/sphx_glr_model_convolution_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 119-122 Fit model with convolution -------------------------- .. GENERATED FROM PYTHON SOURCE LINES 122-128 .. code-block:: Python 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]) .. GENERATED FROM PYTHON SOURCE LINES 129-132 The component of the model can be set to be convolved or not during model fitting. Specify that the Lorentzian is convolved: .. GENERATED FROM PYTHON SOURCE LINES 132-136 .. code-block:: Python lorentzian_component.convolved = True offset_component.convolved = False .. GENERATED FROM PYTHON SOURCE LINES 137-138 Show the results .. GENERATED FROM PYTHON SOURCE LINES 138-144 .. code-block:: Python m.fit() m.print_current_values() m.plot() .. image-sg:: /auto_examples/extensions/images/sphx_glr_model_convolution_003.png :alt: Signal :srcset: /auto_examples/extensions/images/sphx_glr_model_convolution_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none ConvolvedModel1D: CurrentComponentValues: Lorentzian Active: True Parameter Name | Free | Value | Std | Min | Max | Linear ============== | ======= | ========== | ========== | ========== | ========== | ====== A | True | 1.00000000 | 0.0 | 0.0 | None | True centre | True | 220.0 | 0.0 | None | None | False gamma | True | 1.00000000 | 0.0 | None | None | False CurrentComponentValues: Offset Active: True Parameter Name | Free | Value | Std | Min | Max | Linear ============== | ======= | ========== | ========== | ========== | ========== | ====== offset | True | 10.0 | 0.0 | None | None | True .. GENERATED FROM PYTHON SOURCE LINES 145-148 Fit model without convolution ----------------------------- .. GENERATED FROM PYTHON SOURCE LINES 148-157 .. code-block:: Python 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() .. image-sg:: /auto_examples/extensions/images/sphx_glr_model_convolution_004.png :alt: Signal :srcset: /auto_examples/extensions/images/sphx_glr_model_convolution_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none ConvolvedModel1D: CurrentComponentValues: Lorentzian Active: True Parameter Name | Free | Value | Std | Min | Max | Linear ============== | ======= | ========== | ========== | ========== | ========== | ====== A | True | 1.25223037 | 0.02394923 | 0.0 | None | True centre | True | 220.000597 | 0.05481208 | None | None | False gamma | True | 3.52697303 | 0.08584538 | None | None | False CurrentComponentValues: Offset Active: True Parameter Name | Free | Value | Std | Min | Max | Linear ============== | ======= | ========== | ========== | ========== | ========== | ====== offset | True | 9.99817205 | 0.00035862 | None | None | True .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 1.646 seconds) .. _sphx_glr_download_auto_examples_extensions_model_convolution.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: model_convolution.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: model_convolution.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: model_convolution.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_