.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "generated\examples\transform\plot_rotate_and_translate.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_generated_examples_transform_plot_rotate_and_translate.py>`
        to download the full example code. or to run this example in your browser via Binder

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_generated_examples_transform_plot_rotate_and_translate.py:


====================
Rotate and translate
====================

Rotating and translating a 3D volume.

This example illustrates the use of the function `.rotate()` from the dbdicom extension :ref:`extension-vreg`. We use an ellipsoid digital reference object as test data and `.plot_surface()` from extension :ref:`extension-matplotlib` to visualise the results.

.. GENERATED FROM PYTHON SOURCE LINES 10-19

.. code-block:: Python

    import numpy as np

    from dbdicom.dro import double_ellipsoid
    from dbdicom.extensions.vreg import rotate
    from dbdicom.extensions.matplotlib import plot_surface, plot_mosaic

    # Choose image 1 as a thumbnail for the gallery
    # sphinx_gallery_thumbnail_number = 2








.. GENERATED FROM PYTHON SOURCE LINES 20-21

Generate and display an ellipsoid test object

.. GENERATED FROM PYTHON SOURCE LINES 21-25

.. code-block:: Python


    ellipsoid_orig = double_ellipsoid(12, 40, 32, spacing=(2,3,1), levelset=True)
    plot_surface(ellipsoid_orig)




.. image-sg:: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_001.png
   :alt: plot rotate and translate
   :srcset: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 26-27

Define a rotation vector, apply it and display the result again.

.. GENERATED FROM PYTHON SOURCE LINES 27-37

.. code-block:: Python


    # Define an anticlockwise rotation of 30 degrees around the y-axis
    rotation = -30*(np.pi/180)*np.array([0,1,0])

    # Perform the rotation and return a rotated series
    ellipsoid_rot = rotate(ellipsoid_orig, rotation, reshape=True, mode='nearest')

    # Display the surface of the rotated shape
    plot_surface(ellipsoid_rot)




.. image-sg:: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_002.png
   :alt: plot rotate and translate
   :srcset: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 38-39

Display the rotated shape as a mosaic

.. GENERATED FROM PYTHON SOURCE LINES 39-42

.. code-block:: Python


    plot_mosaic(ellipsoid_rot) 




.. image-sg:: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_003.png
   :alt: plot rotate and translate
   :srcset: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_003.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 43-44

When applying the rotation we used the `mode='nearest'` so that the values outside the boundaries of the volume are filled by nearest neighbour sampling. The default setting would fill these with a `constant=0` value, producing an additional surface at the edge of the volume:

.. GENERATED FROM PYTHON SOURCE LINES 44-49

.. code-block:: Python


    ellipsoid_rot = rotate(ellipsoid_orig, rotation, reshape=True)
    plot_surface(ellipsoid_rot)





.. image-sg:: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_004.png
   :alt: plot rotate and translate
   :srcset: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_004.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 50-51

We used `reshape=True` so the new volume would encompass the entire shape. Running this with the default setting of `reshape=False` retains the original image shape and therefore misses part of the rotated volume:

.. GENERATED FROM PYTHON SOURCE LINES 51-53

.. code-block:: Python


    ellipsoid_rot = rotate(ellipsoid_orig, rotation, reshape=False, mode='nearest')
    plot_surface(ellipsoid_rot)


.. image-sg:: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_005.png
   :alt: plot rotate and translate
   :srcset: /generated/examples/transform/images/sphx_glr_plot_rotate_and_translate_005.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 24.695 seconds)


.. _sphx_glr_download_generated_examples_transform_plot_rotate_and_translate.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/QIB-Sheffield/dbdicom/main?urlpath=lab/tree/notebooks/generated/examples/transform/plot_rotate_and_translate.ipynb
        :alt: Launch binder
        :width: 150 px

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

      :download:`Download Jupyter notebook: plot_rotate_and_translate.ipynb <plot_rotate_and_translate.ipynb>`

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

      :download:`Download Python source code: plot_rotate_and_translate.py <plot_rotate_and_translate.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_rotate_and_translate.zip <plot_rotate_and_translate.zip>`


.. only:: html

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

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