:orphan:

.. _examples-index:

Gallery of Examples
===================

This gallery contains the commented code for short examples illustrating simple
tasks that can be performed with HyperSpy.



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    <div class="sphx-glr-thumbnails">

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Markers
=======

Gallery of examples on using HyperSpy markers.



.. raw:: html

    <div class="sphx-glr-thumbnails">

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    <div class="sphx-glr-thumbcontainer" tooltip="As for ragged signals, the number of markers at each position can vary and this is done by passing a ragged array to the constructor of the markers.">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_ragged_points_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_ragged_points.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Ragged Points</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Arrow markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_arrows_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_arrows.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arrow markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Vertical Line Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_vertical_lines_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_vertical_lines.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Vertical Line Markers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to draw circle with the color of the circle scaling with the radius of the circle">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_circles_color_radius_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_circles_color_radius.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Circle Markers with Radius Dependent Coloring</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Text Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_texts_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_texts.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Text Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Line  Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_lines_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_lines.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Line  Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Varying number of arrows per navigation position">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_arrows_ragged_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_arrows_ragged.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Varying number of arrows per navigation position</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Circle Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_circles_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_circles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Circle Markers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Filled Circle Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_filled_circles_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_filled_circles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Filled Circle Markers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how markers are rotated.">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_rotation_makers_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_rotation_makers.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Rotation of markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to add or remove marker from an existing collection. This is done by setting the parameters (offsets, sizes, etc.) of the collection.">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_add_remove_marker_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_add_remove_marker.py`

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      <div class="sphx-glr-thumbnail-title">Add/Remove items from existing Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Polygon  Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_polygons_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_polygons.py`

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      <div class="sphx-glr-thumbnail-title">Polygon  Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Ellipse markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_ellipses_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_ellipses.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Ellipse markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Square Markers">

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  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_squares_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_squares.py`

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      <div class="sphx-glr-thumbnail-title">Square Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Star Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_stars_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_stars.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Star Markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Rectangle Markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_rectangles_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_rectangles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Rectangle Markers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Arrow markers">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_arrows_navigation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_arrows_navigation.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arrow markers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to create markers from a signal. This is useful for creating lazy markers from some operation such as peak finding on a signal. Here we show how to create markers from a simple map function which finds the maximum value and plots a marker at that position.">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_from_signal_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_from_signal.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creating Markers from a signal</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to make images that overlay the main images.  These can be images overlaid using some king of transparency or make an inset image.  It can also be useful for something like making something like a circular color bar to show orientation.">

.. only:: html

  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_making_inset_images_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_making_inset_images.py`

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      <div class="sphx-glr-thumbnail-title">Making Inset Images</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use both the offset_transform and ```transforms`` parameters for markers">

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  .. image:: /auto_examples/Markers/images/thumb/sphx_glr_transforms_and_units_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_Markers_transforms_and_units.py`

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      <div class="sphx-glr-thumbnail-title">Transforms and Units</div>
    </div>


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Signal Creation
===============

Below is a gallery of examples on creating a signal and plotting.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a signal from tabular data imported from a txt file using numpy.loadtxt. The signal axis and the EELS intensity values are given by the first and second columns, respectively.">

.. only:: html

  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_from_tabular_data_file_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_from_tabular_data_file.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creates a signal1D from a text file</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a line spectrum and plots it.">

.. only:: html

  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_line_spectrum_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_line_spectrum.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creates a line spectrum</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a signal from tabular data, where the signal axis is given by an array of data values (the x column) and the tabular data are ordered in columns with 5 columns containing each 20 values and each column corresponding to a position in the navigation space (linescan).">

.. only:: html

  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_from_tabular_data_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_from_tabular_data.py`

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      <div class="sphx-glr-thumbnail-title">Creates a signal1D from tabular data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates an image stack and plots it.">

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  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_1D_image_stack_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_1D_image_stack.py`

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      <div class="sphx-glr-thumbnail-title">Creates a 3D image</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a spectrum image, i.e. navigation dimension 2 and signal dimension 1, and plots it.">

.. only:: html

  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_spectrum_image_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_spectrum_image.py`

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      <div class="sphx-glr-thumbnail-title">Creates a spectrum image</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a 4D dataset, i.e. 2 navigation dimension and 2 signal dimension and plots it.">

.. only:: html

  .. image:: /auto_examples/create_signal/images/thumb/sphx_glr_2D_image_stack_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_create_signal_2D_image_stack.py`

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      <div class="sphx-glr-thumbnail-title">Creates a 4D image</div>
    </div>


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    </div>

Data Visualization
==================

This gallery shows how to plot data using the convenience functions
:func:`~.api.plot.plot_spectra`, :func:`~.api.plot.plot_images` and
:func:`~.api.plot.plot_signals`.
Unlike the :meth:`~.api.signals.BaseSignal.plot`, these functions
can plot multiple signal together and can be useful to compose figure
comparing signals, etc.




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    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compose a figure using plot_images and plot_spectra">

.. only:: html

  .. image:: /auto_examples/data_visualization/images/thumb/sphx_glr_compose_figure_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_data_visualization_compose_figure.py`

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      <div class="sphx-glr-thumbnail-title">Composing Figure</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Specifying Matplotlib Axis">

.. only:: html

  .. image:: /auto_examples/data_visualization/images/thumb/sphx_glr_specifying_ax_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_data_visualization_specifying_ax.py`

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      <div class="sphx-glr-thumbnail-title">Specifying Matplotlib Axis</div>
    </div>


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    </div>

Loading, saving and exporting
=============================

Below is a gallery of examples on loading, saving and exporting data.



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    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="Creates a single spectrum image, saves it and plots it:">

.. only:: html

  .. image:: /auto_examples/io/images/thumb/sphx_glr_export_single_spectrum_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_io_export_single_spectrum.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Export single spectrum</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to adjust the contrast and intensities using scikit-image and save it as an RGB image.">

.. only:: html

  .. image:: /auto_examples/io/images/thumb/sphx_glr_convert_color_image_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_io_convert_color_image.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Adjust contrast and save RGB images</div>
    </div>


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.. raw:: html

    </div>

Model fitting
=============

Below is a gallery of examples on model fitting.



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    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="Fit an affine function and plot the residual.">

.. only:: html

  .. image:: /auto_examples/model_fitting/images/thumb/sphx_glr_plot_residual_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_model_fitting_plot_residual.py`

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      <div class="sphx-glr-thumbnail-title">Plot Residual</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Fit an arctan function.">

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  .. image:: /auto_examples/model_fitting/images/thumb/sphx_glr_simple_arctan_fit_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_model_fitting_simple_arctan_fit.py`

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      <div class="sphx-glr-thumbnail-title">Simple arctan fit</div>
    </div>


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    </div>


Making Custom Layouts for Plots
===============================

Below is a gallery of examples on making simple custom layouts for plotting data
using :class:`matplotlib.figure.SubFigure`.

.. Note::
    Plotting data with subfigures is slower than using separates figures.



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    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="Custom layouts for hyperspy figures can be created using the matplotlib.figure.SubFigure class. Passing the fig argument to the plot method of a hyperspy signal object will target that figure instead of creating a new one. This is useful for creating custom layouts with multiple subplots.">

.. only:: html

  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_custom_figure_layout_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_plotting_custom_figure_layout.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creating Custom Layouts</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="ROI&#x27;s can be powerful tools to help visualize data.  In this case we will define ROI&#x27;s in hyperspy, sum the data within the ROI, and then plot the sum as a signal. Using the matplotlib.figure.SubFigure class we can create a custom layout to visualize and interact with the data.">

.. only:: html

  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_ROI_insets_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_plotting_ROI_insets.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">ROI Insets</div>
    </div>


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.. raw:: html

    </div>

Region of Interest
==================

Below is a gallery of examples on using regions of interest with HyperSpy signals.



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    <div class="sphx-glr-thumbcontainer" tooltip="Use a SpanROI interactively on a Signal1D.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_SpanROI_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_SpanROI.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">SpanROI on signal axis</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Use the plot_roi_map function to create interactive maps defined from ROIs in signal space.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_map_signal_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_map_signal.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Create Map from ROI in signal space</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Use a PolygonROI interactively on a Signal2D.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_PolygonROI_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_PolygonROI.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PolygonROI</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Use a RectangularROI to take the sum of an area of the navigation space.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_ROI_navigator_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_ROI_navigator.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Navigator ROI</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Use the plot_roi_map function to create interactive maps defined from a CircleROI in signal space.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_map_signal_circleROI_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_map_signal_circleROI.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Create Map from CircleROI in signal space</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Get interactive fast Fourier transform (FFT) from a subset of a Signal2D using RectangularROI.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_fast_fourier_transform_live_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_fast_fourier_transform_live.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Live FFT</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Combine several PolygonROI.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_combine_PolygonROI_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_combine_PolygonROI.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Combine PolygonROI</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Interactively extract a line profile (with a certain width) from an image using :py~.api.roi.Line2DROI. Use plot_spectra to plot several line profiles on the same figure. Save a profile data as msa file.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_ExtractLineProfile_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_ExtractLineProfile.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Extract line profile from image interactively</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to integrate a signal using an interactive ROI.">

.. only:: html

  .. image:: /auto_examples/region_of_interest/images/thumb/sphx_glr_SpanROI_interactive_sum_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_region_of_interest_SpanROI_interactive_sum.py`

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      <div class="sphx-glr-thumbnail-title">Interactive integration of one dimensional signal</div>
    </div>


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    </div>

Simple simulations
==================

Below is a gallery of examples on simulating signals which can be used to test
HyperSpy functionalities



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    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="Creates a 2D hyperspectrum consisting of two Gaussians and plots it.">

.. only:: html

  .. image:: /auto_examples/simple_simulations/images/thumb/sphx_glr_two_gaussians_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_simple_simulations_two_gaussians.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Simple simulation (2 Gaussians)</div>
    </div>


.. thumbnail-parent-div-close

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    </div>


.. toctree::
   :hidden:
   :includehidden:


   /auto_examples/Markers/index.rst
   /auto_examples/create_signal/index.rst
   /auto_examples/data_visualization/index.rst
   /auto_examples/io/index.rst
   /auto_examples/model_fitting/index.rst
   /auto_examples/plotting/index.rst
   /auto_examples/region_of_interest/index.rst
   /auto_examples/simple_simulations/index.rst


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  .. container:: sphx-glr-footer sphx-glr-footer-gallery

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_