: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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Markers
=======

Gallery of examples on using HyperSpy markers.



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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.">

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

  :doc:`/auto_examples/Markers/ragged_points`

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


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

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

  :doc:`/auto_examples/Markers/arrows`

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


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

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

  :doc:`/auto_examples/Markers/vertical_lines`

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


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    <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">

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

  :doc:`/auto_examples/Markers/circles_color_radius`

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


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

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

  :doc:`/auto_examples/Markers/texts`

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


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

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

  :doc:`/auto_examples/Markers/lines`

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      <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">

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

  :doc:`/auto_examples/Markers/arrows_ragged`

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      <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">

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

  :doc:`/auto_examples/Markers/circles`

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


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

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

  :doc:`/auto_examples/Markers/filled_circles`

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


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

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

  :doc:`/auto_examples/Markers/rotation_makers`

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      <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.">

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

  :doc:`/auto_examples/Markers/add_remove_marker`

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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">

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

  :doc:`/auto_examples/Markers/polygons`

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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">

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

  :doc:`/auto_examples/Markers/ellipses`

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      <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:

  :doc:`/auto_examples/Markers/squares`

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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">

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

  :doc:`/auto_examples/Markers/stars`

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


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

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

  :doc:`/auto_examples/Markers/rectangles`

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


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

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

  :doc:`/auto_examples/Markers/arrows_navigation`

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      <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.">

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

  :doc:`/auto_examples/Markers/from_signal`

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      <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 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:

  :doc:`/auto_examples/Markers/transforms_and_units`

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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.">

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

  :doc:`/auto_examples/create_signal/from_tabular_data_file`

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      <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.">

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

  :doc:`/auto_examples/create_signal/line_spectrum`

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      <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).">

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

  :doc:`/auto_examples/create_signal/from_tabular_data`

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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:

  :doc:`/auto_examples/create_signal/1D_image_stack`

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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.">

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

  :doc:`/auto_examples/create_signal/spectrum_image`

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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.">

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

  :doc:`/auto_examples/create_signal/2D_image_stack`

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


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

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



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

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

  :doc:`/auto_examples/io/export_single_spectrum`

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


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    <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.">

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

  :doc:`/auto_examples/io/convert_color_image`

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


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

Below is a gallery of examples on model fitting.



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

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

  :doc:`/auto_examples/model_fitting/plot_residual`

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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:

  :doc:`/auto_examples/model_fitting/simple_arctan_fit`

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

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

  :doc:`/auto_examples/region_of_interest/SpanROI`

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


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

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

  :doc:`/auto_examples/region_of_interest/map_signal`

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


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

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

  :doc:`/auto_examples/region_of_interest/ROI_navigator`

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


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

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

  :doc:`/auto_examples/region_of_interest/map_signal_circleROI`

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


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    <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.">

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

  :doc:`/auto_examples/region_of_interest/ExtractLineProfile`

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


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

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

  :doc:`/auto_examples/region_of_interest/SpanROI_interactive_sum`

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      <div class="sphx-glr-thumbnail-title">Interactive integration of one dimensional signal</div>
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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-thumbcontainer" tooltip="Creates a 2D hyperspectrum consisting of two Gaussians and plots it.">

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

  :doc:`/auto_examples/simple_simulations/two_gaussians`

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


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.. 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


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      :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>`


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