.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/aimsvolumetest.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_aimsvolumetest.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_aimsvolumetest.py:


AIMS / Anatomist volume manipulation
====================================

Loading, handling and viewing a Volume with aims and anatomist

.. GENERATED FROM PYTHON SOURCE LINES 39-109



.. image-sg:: /auto_examples/images/sphx_glr_aimsvolumetest_001.png
   :alt: aimsvolumetest
   :srcset: /auto_examples/images/sphx_glr_aimsvolumetest_001.png
   :class: sphx-glr-single-img





.. code-block:: default


    from __future__ import absolute_import
    import anatomist.direct.api as anatomist
    from soma import aims
    from soma.qt_gui.qt_backend import Qt
    import sys

    # load any volume as a aims.Volume_* object
    vol = aims.read('irm.ima')

    runloop = False
    if Qt.QApplication.instance() is None:
        runloop = True

    # initialize Anatomist
    a = anatomist.Anatomist()

    # convert the carto volume to Anatomist API
    avol = a.toAObject(vol)
    avol.releaseAppRef()

    win = a.createWindow('Axial')

    # put volume in window
    win.addObjects(avol)

    # volume change and update test

    # using Numeric API
    arr = vol.arraydata()
    # we're just printing a white square in the middle of the volume
    arr[0, 50:70, 100:130, 100:130] = 255

    # update Anatomist object and its views
    avol.setChanged()
    avol.notifyObservers()


    # fusion test

    # have a second volume. We could have loaded another one
    # (and it would have been nicer on screen). This example also
    # shows the ability to share the volume data with multiple anatomist/aims
    # objects
    avol2 = a.toAObject(vol)
    avol2.releaseAppRef()

    # set a different palette on the second object so we can see something
    a.setObjectPalette(avol2, 'Blue-Red-fusion')

    # another view
    win2 = a.createWindow('Axial')

    a.addObjects(avol2, win2)

    # create the fusion object
    fus = a.fusionObjects([avol, avol2], 'Fusion2DMethod')

    # show it
    win3 = a.createWindow('Sagittal')

    a.addObjects(fus, win3)


    # display in matplotlib for sphinx_gallery
    win3.sphinx_gallery_snapshot()
    if runloop and 'sphinx_gallery' not in sys.modules:
        Qt.QApplication.instance().exec_()
    if runloop or 'sphinx_gallery' in sys.modules:
        del win, win2, win3, fus, avol, arr, avol2


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

   **Total running time of the script:** ( 0 minutes  0.996 seconds)


.. _sphx_glr_download_auto_examples_aimsvolumetest.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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