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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_utils_plot_mosaic.py:


===============================
Mosaic plot
===============================

The function `mosaic` plots all of the slices in a volume in a matplotlib figure. Good for quick visualization or testing of volumes.

.. GENERATED FROM PYTHON SOURCE LINES 11-37



.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /auto_examples/utils/images/sphx_glr_plot_mosaic_001.png
         :alt: plot mosaic
         :srcset: /auto_examples/utils/images/sphx_glr_plot_mosaic_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/utils/images/sphx_glr_plot_mosaic_002.png
         :alt: plot mosaic
         :srcset: /auto_examples/utils/images/sphx_glr_plot_mosaic_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/utils/images/sphx_glr_plot_mosaic_003.png
         :alt: plot mosaic
         :srcset: /auto_examples/utils/images/sphx_glr_plot_mosaic_003.png
         :class: sphx-glr-multi-img


.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    /home/runner/work/pycortex/pycortex/examples/utils/plot_mosaic.py:17: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

    * deprecated from version: 3.0
    * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
      volume_arr = cortex.db.get_xfm('S1', 'fullhead').reference.get_data().T






|

.. code-block:: default

    # sphinx_gallery_thumbnail_number = 3

    import cortex
    import matplotlib.pyplot as plt

    # load reference functional image for test purposes
    volume_arr = cortex.db.get_xfm('S1', 'fullhead').reference.get_data().T
    # volume_arr is a (31,100,100) ndarray


    # with no args mosaic slices this volume in the first dimension
    plt.figure()
    cortex.mosaic(volume_arr)

    # slices along a different dimension can be plotted using the dim param
    # here coronal
    plt.figure()
    cortex.mosaic(volume_arr, dim=1)

    # kwargs are passed through to imshow
    plt.figure()
    cortex.mosaic(volume_arr, cmap=plt.cm.gray, vmin=0, vmax=1500)

    # mosaic always returns the mosaic image along with info about its shape
    # here show=False so we don't generate another plot
    mosaic_arr, (nwide, ntall) = cortex.mosaic(volume_arr, show=False)
    # mosaic_arr is 607 x 607, with nwide = 6, ntall = 6

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

   **Total running time of the script:** ( 0 minutes  0.272 seconds)


.. _sphx_glr_download_auto_examples_utils_plot_mosaic.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: plot_mosaic.py <plot_mosaic.py>`



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

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


.. only:: html

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

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