:orphan:

.. _examples-index:

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

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



.. raw:: html

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

.. thumbnail-parent-div-open

.. thumbnail-parent-div-close

.. raw:: html

    </div>


Markers
=======

Gallery of examples on using HyperSpy markers.



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

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

.. 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>


.. raw:: html

    <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>


.. raw:: html

    <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 t...">

.. 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>


.. raw:: html

    <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>


.. raw:: html

    <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>


.. raw:: html

    <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>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to add or remove marker from an existing collection. This is done by set...">

.. 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`

.. raw:: html

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


.. raw:: html

    <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`

.. raw:: html

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


.. raw:: html

    <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>


.. raw:: html

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

.. only:: html

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

  :ref:`sphx_glr_auto_examples_Markers_squares.py`

.. raw:: html

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


.. raw:: html

    <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>


.. raw:: html

    <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>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to create markers from a signal. This is useful for creating lazy marker...">

.. 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>


.. raw:: html

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

.. only:: html

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

  :ref:`sphx_glr_auto_examples_Markers_transforms_and_units.py`

.. raw:: html

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


.. thumbnail-parent-div-close

.. raw:: html

    </div>

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

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



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a signal from tabular data imported from a txt file using numpy.loadtxt. T...">

.. 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>


.. raw:: html

    <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>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a signal from tabular data, where the signal axis is given by an array of ...">

.. 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`

.. raw:: html

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


.. raw:: html

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

.. only:: html

  .. 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`

.. raw:: html

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


.. raw:: html

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

.. 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`

.. raw:: html

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


.. raw:: html

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

.. 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`

.. raw:: html

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


.. thumbnail-parent-div-close

.. raw:: html

    </div>

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

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



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <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...">

.. 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>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

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

Below is a gallery of examples on model fitting.



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <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`

.. raw:: html

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


.. raw:: html

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

.. only:: html

  .. 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`

.. raw:: html

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


.. thumbnail-parent-div-close

.. raw:: html

    </div>

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

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



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <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 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 spa...">

.. 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="Interactively extract a line profile (with a certain width) from an image using :py~.api.roi.Li...">

.. 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`

.. raw:: html

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


.. thumbnail-parent-div-close

.. raw:: html

    </div>

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

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



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <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

.. raw:: html

    </div>


.. toctree::
   :hidden:
   :includehidden:


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


.. only:: html

  .. 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>`_