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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_plot_segment_sphinx_macaque_ants_based.py:


.. _plot_segment_sphinx_macaque_ants_based:

==============================================================================
Plot the results of a segmentation with ANTS-based pipeline in sphinx position
==============================================================================

.. GENERATED FROM PYTHON SOURCE LINES 8-19

.. code-block:: default


    # Authors: David Meunier, Bastien Cagna

    # License: BSD (3-clause)
    # sphinx_gallery_thumbnail_number = 2

    import os
    import os.path as op

    from macapype.utils.utils_tests import load_test_data








.. GENERATED FROM PYTHON SOURCE LINES 20-22

Testing plot in local
#############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 22-38

.. code-block:: default


    orig_data_path = load_test_data("data_test_sphinx_macaque")

    data_path = load_test_data("data_test_sphinx_macaque_processed")

    wf_path = os.path.join(data_path, "example_segment_sphinx_macaque_ants_based")

    graph = os.path.join(wf_path, "graph.png")

    import matplotlib.pyplot as plt  # noqa
    img = plt.imread(graph)
    plt.figure(figsize=(36, 72))
    plt.imshow(img)
    plt.axis('off')
    plt.show()




.. image-sg:: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_001.png
   :alt: plot segment sphinx macaque ants based
   :srcset: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_001.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    data_dirpath /home/meunier.d/data_macapype already exists
    /home/meunier.d/data_macapype/data_test_sphinx_macaque Already exists, skipping download
    data_dirpath /home/meunier.d/data_macapype already exists
    /home/meunier.d/data_macapype/data_test_sphinx_macaque_processed Already exists, skipping download




.. GENERATED FROM PYTHON SOURCE LINES 39-41

Data preparation
#############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 44-46

# Reorient
#==========================

.. GENERATED FROM PYTHON SOURCE LINES 46-72

.. code-block:: default



    orig_T1_file = op.join(orig_data_path, "sub-ziggy_T1w.nii")

    reoriented_T1_file = op.join(wf_path, "old_data_preparation_pipe", "reorient_T1_pipe", "swap_dim", "sub-ziggy_T1w_newdims.nii.gz")

    # displaying results
    orig_T1 = os.path.join(wf_path, "orig_T1.png")
    cmd = "fsleyes render --outfile {} --size 1800 600 {}".format(orig_T1, orig_T1_file)
    os.system(cmd)

    reoriented_T1 = os.path.join(wf_path, "reoriented_T1.png")
    cmd = "fsleyes render --outfile {} --size 1800 600 {}".format(reoriented_T1, reoriented_T1_file)
    os.system(cmd)

    import matplotlib.pyplot as plt  # noqa

    fig, axs = plt.subplots(2, 1, figsize=(36, 24))
    axs[0].imshow(plt.imread(orig_T1))
    axs[0].axis('off')

    axs[1].imshow(plt.imread(reoriented_T1))
    axs[1].axis('off')

    plt.show()




.. image-sg:: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_002.png
   :alt: plot segment sphinx macaque ants based
   :srcset: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 73-75

# Cropping and denoise
#==========================

.. GENERATED FROM PYTHON SOURCE LINES 75-102

.. code-block:: default


    cropped_T1_file = op.join(wf_path, "old_data_preparation_pipe", "bet_crop", "sub-ziggy_T1w_newdims_cropped.nii.gz")
    assert os.path.exists(cropped_T1_file), "Error with {}".format(cropped_T1_file)

    cropped_T1 = os.path.join(wf_path, "cropped_T1.png")
    cmd = "fsleyes render --outfile {} --size 1800 600 {}".format(cropped_T1, cropped_T1_file)
    os.system(cmd)


    denoised_T1_file = op.join(wf_path, "old_data_preparation_pipe", "denoise_T1", "sub-ziggy_T1w_newdims_cropped_noise_corrected.nii.gz")

    denoised_T1 = os.path.join(wf_path, "denoised_T1.png")
    cmd = "fsleyes render --outfile {} --size 1800 600 {}".format(denoised_T1, denoised_T1_file)
    os.system(cmd)

    import matplotlib.pyplot as plt  # noqa

    fig, axs = plt.subplots(2, 1, figsize=(36, 24))
    axs[0].imshow(plt.imread(cropped_T1))
    axs[0].axis('off')

    axs[1].imshow(plt.imread(denoised_T1))
    axs[1].axis('off')

    plt.show()





.. image-sg:: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_003.png
   :alt: plot segment sphinx macaque ants based
   :srcset: /auto_examples/images/sphx_glr_plot_segment_sphinx_macaque_ants_based_003.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** ( 0 minutes  37.341 seconds)


.. _sphx_glr_download_auto_examples_plot_segment_sphinx_macaque_ants_based.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_segment_sphinx_macaque_ants_based.py <plot_segment_sphinx_macaque_ants_based.py>`



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

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


.. only:: html

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

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