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

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

.. _sphx_glr_auto_examples_viz_surfaces.py:


==================
Visualize surfaces
==================

Here is a simple tutorial that shows how to visualize surfaces using DIPY. It
also shows how to load/save, get/set and update ``vtkPolyData`` and show
surfaces.

``vtkPolyData`` is a structure used by VTK to represent surfaces and other data
structures. Here we show how to visualize a simple cube but the same idea
should apply for any surface.


.. code-block:: python


    import numpy as np







Import useful functions from ``dipy.viz.utils``


.. code-block:: python


    import dipy.io.vtk as io_vtk
    import fury.utils as ut_vtk
    from fury import window

    # Conditional import machinery for vtk
    # Allow import, but disable doctests if we don't have vtk
    from dipy.utils.optpkg import optional_package
    vtk, have_vtk, setup_module = optional_package('vtk')







Create an empty ``vtkPolyData``


.. code-block:: python


    my_polydata = vtk.vtkPolyData()







Create a cube with vertices and triangles as numpy arrays


.. code-block:: python


    my_vertices = np.array([[0.0,  0.0,  0.0],
                           [0.0,  0.0,  1.0],
                           [0.0,  1.0,  0.0],
                           [0.0,  1.0,  1.0],
                           [1.0,  0.0,  0.0],
                           [1.0,  0.0,  1.0],
                           [1.0,  1.0,  0.0],
                           [1.0,  1.0,  1.0]])
    # the data type for vtk is needed to mention here, numpy.int64
    my_triangles = np.array([[0,  6,  4],
                             [0,  2,  6],
                             [0,  3,  2],
                             [0,  1,  3],
                             [2,  7,  6],
                             [2,  3,  7],
                             [4,  6,  7],
                             [4,  7,  5],
                             [0,  4,  5],
                             [0,  5,  1],
                             [1,  5,  7],
                             [1,  7,  3]], dtype='i8')








Set vertices and triangles in the ``vtkPolyData``


.. code-block:: python


    ut_vtk.set_polydata_vertices(my_polydata, my_vertices)
    ut_vtk.set_polydata_triangles(my_polydata, my_triangles)







Save the ``vtkPolyData``


.. code-block:: python


    file_name = "my_cube.vtk"
    io_vtk.save_polydata(my_polydata, file_name)
    print("Surface saved in " + file_name)





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

 Out:

 .. code-block:: none

    Surface saved in my_cube.vtk


Load the ``vtkPolyData``


.. code-block:: python


    cube_polydata = io_vtk.load_polydata(file_name)







add color based on vertices position


.. code-block:: python


    cube_vertices = ut_vtk.get_polydata_vertices(cube_polydata)
    colors = cube_vertices * 255
    ut_vtk.set_polydata_colors(cube_polydata, colors)

    print("new surface colors")
    print(ut_vtk.get_polydata_colors(cube_polydata))





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

 Out:

 .. code-block:: none

    new surface colors
    [[  0   0   0]
     [  0   0 255]
     [  0 255   0]
     [  0 255 255]
     [255   0   0]
     [255   0 255]
     [255 255   0]
     [255 255 255]]


Visualize surfaces


.. code-block:: python


    # get vtkActor
    cube_actor = ut_vtk.get_actor_from_polydata(cube_polydata)

    # renderer and scene
    renderer = window.Renderer()
    renderer.add(cube_actor)
    renderer.set_camera(position=(10, 5, 7), focal_point=(0.5, 0.5, 0.5))
    renderer.zoom(3)

    # display
    # window.show(renderer, size=(600, 600), reset_camera=False)
    window.record(renderer, out_path='cube.png', size=(600, 600))



.. image:: /auto_examples/images/sphx_glr_viz_surfaces_001.png
    :class: sphx-glr-single-img




**Total running time of the script:** ( 0 minutes  0.114 seconds)


.. _sphx_glr_download_auto_examples_viz_surfaces.py:


.. only :: html

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



  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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