.. only:: html

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

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

    .. _sphx_glr_auto_examples_quickflat_plot_thickness_nanmean.py:


===================================
Ignore NaN (not-a-number) values in thickness mapping
===================================

By default, pycortex quickshow averages across the thickness of the cortex
for each pixel in the resulting flatmap. If any of these layers contain a value
of NaN (not-a-number), then the result of the average will also be Nan. This
behavior might be undesirable. To avoid it, pass the argument `nanmean=True` to
`cortex.quickshow` (or `cortex.quickflat.make_figure`). This will only take the
mean of the non-NaN values when averaging across the thickness of cortex. A
pixel will only have the value NaN if every voxel between pia and white matter 
has the value NaN.



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


    *

      .. image:: /auto_examples/quickflat/images/sphx_glr_plot_thickness_nanmean_001.png
          :alt: plot thickness nanmean
          :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/quickflat/images/sphx_glr_plot_thickness_nanmean_002.png
          :alt: plot thickness nanmean
          :class: sphx-glr-multi-img


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

 Out:

 .. code-block:: none

    /home/travis/build/gallantlab/pycortex/cortex/quickflat/utils.py:93: RuntimeWarning: invalid value encountered in true_divide
      nanmean_data = nonnan_sum / weights_on_nonnan






|


.. code-block:: default


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

    # create dataset with volume of all 1's
    vol = cortex.Volume.empty('S1', 'fullhead', vmin=0, vmax=2) + 1

    # set 20% of the values in the dataset to NaN
    vol.data[np.random.rand(*vol.data.shape) > 0.8] = np.nan


    # plot the volume with nanmean=False
    # here a nan in ANY layer of the thickness mapping will result in a nan
    # in the final image
    # so this image should have many, many holes that show curvature
    # and all the non-hole points should have value of 1
    _ = cortex.quickshow(vol, nanmean=False, with_curvature=True)

    plt.show()

    # plot the volume with nanmean=True
    # here there should only be a nan in the final image if EVERY layer of the
    # thickness mapping has a nan for the given pixel
    # so this image should have many fewer holes that show curvature
    # and, again, all the non-hole points should have value of 1
    _ = cortex.quickshow(vol, nanmean=True, with_curvature=True)

    plt.show()

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

   **Total running time of the script:** ( 0 minutes  4.669 seconds)


.. _sphx_glr_download_auto_examples_quickflat_plot_thickness_nanmean.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_thickness_nanmean.py <plot_thickness_nanmean.py>`



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

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


.. only:: html

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

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