.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_datasets_plot_volume2D.py>`     to download the full example code
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_datasets_plot_volume2D.py:


===================
Plot 2D Volume Data
===================

This plots example volume data onto an example subject, S1, onto a flatmap
using quickflat. In order for this to run, you have to have a flatmap for
this subject in the pycortex filestore.

The cortex.Volume2D object is instantiated with two numpy arrays of the same
size as the scan for this subject and transform. Here, there are two datasets
that have been generated to look like gradients across the brain, but you can
replace these with any numpy arrays of the correct dimensionality.

The colormap used in the first two flatmaps is

.. image:: ../../../filestore/colormaps/RdBu_covar.png

As with a 1D Volume, you can change vmin and vmax to threshold, but here
they can be manipulated individually for the two arrays.

You can also change the colormap when creating a new 2D volume.  The colormap
used in the last flatmap is

.. image:: ../../../filestore/colormaps/GreenWhiteBlue_2D.png



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


    *

      .. image:: /auto_examples/datasets/images/sphx_glr_plot_volume2D_001.png
          :alt: plot volume2D
          :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/datasets/images/sphx_glr_plot_volume2D_002.png
          :alt: plot volume2D
          :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/datasets/images/sphx_glr_plot_volume2D_003.png
          :alt: plot volume2D
          :class: sphx-glr-multi-img






.. code-block:: default


    import cortex
    import numpy as np
    import matplotlib.pyplot as plt

    subject = "S1"
    xfm = "fullhead"

    # Creating two different test datasets that are both the same shape as this
    # transform with one entry for each voxel
    # The matrices have just been reordered in different ways so that they make
    # gradients across the brain in different directions
    test_data1 = np.arange(31 * 100 * 100).reshape((31, 100, 100), order='C')
    test_data2 = np.arange(31 * 100 * 100).reshape((31, 100, 100), order='F')

    # This creates a 2D Volume object for both of our test datasets for the given
    # subject and transform
    vol_data = cortex.Volume2D(test_data1, test_data2, subject, xfm)
    cortex.quickshow(vol_data, with_colorbar=False)
    plt.show()

    # You can alter the minimum and maximum values shown on the colorbar and this
    # can be done separately for the two different datasets
    vol_data = cortex.Volume2D(test_data1, test_data2, subject, xfm,
                               vmin=np.mean(test_data1), vmax=np.max(test_data1),
                               vmin2=np.min(test_data2), vmax2=np.mean(test_data2))
    cortex.quickshow(vol_data, with_colorbar=False)
    plt.show()

    # To change the colormap, you have to create a new Volume2D object
    vol_color = cortex.Volume2D(test_data1, test_data2, subject, xfm,
                                cmap="GreenWhiteBlue_2D")
    cortex.quickshow(vol_color, with_colorbar=False)
    plt.show()


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

   **Total running time of the script:** ( 0 minutes  6.629 seconds)


.. _sphx_glr_download_auto_examples_datasets_plot_volume2D.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_volume2D.py <plot_volume2D.py>`



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

     :download:`Download Jupyter notebook: plot_volume2D.ipynb <plot_volume2D.ipynb>`


.. only:: html

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

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