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

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

.. _sphx_glr_auto_examples_viz_bundles.py:


========================================
Visualize bundles and metrics on bundles
========================================

First, let's download some available datasets. Here we are using a dataset
which provides metrics and bundles.


.. code-block:: python


    import numpy as np
    from fury import window, actor
    from dipy.data import fetch_bundles_2_subjects, read_bundles_2_subjects
    from dipy.tracking.streamline import transform_streamlines, length

    interactive = False  # set to True to show the interactive display window

    fetch_bundles_2_subjects()
    dix = read_bundles_2_subjects(subj_id='subj_1', metrics=['fa'],
                                  bundles=['cg.left', 'cst.right'])





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

 Out:

 .. code-block:: none

    Data size is approximately 234MB
    Dataset is already in place. If you want to fetch it again please first remove the folder /Users/koudoro/.dipy/exp_bundles_and_maps


Store fractional anisotropy.


.. code-block:: python


    fa = dix['fa']







Store grid to world transformation matrix.


.. code-block:: python


    affine = dix['affine']







Store the cingulum bundle. A bundle is a list of streamlines.


.. code-block:: python


    bundle = dix['cg.left']







It happened that this bundle is in world coordinates and therefore we need to
transform it into native image coordinates so that it is in the same
coordinate space as the ``fa`` image.


.. code-block:: python


    bundle_native = transform_streamlines(bundle, np.linalg.inv(affine))







Show every streamline with an orientation color
===============================================

This is the default option when you are using ``line`` or ``streamtube``.


.. code-block:: python


    scene = window.Scene()

    stream_actor = actor.line(bundle_native)

    scene.set_camera(position=(-176.42, 118.52, 128.20),
                     focal_point=(113.30, 128.31, 76.56),
                     view_up=(0.18, 0.00, 0.98))

    scene.add(stream_actor)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle1.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_001.png
    :class: sphx-glr-single-img




You may wonder how we knew how to set the camera. This is very easy. You just
need to run ``window.show`` once see how you want to see the object and then
close the window and call the ``camera_info`` method which prints the
position, focal point and view up vectors of the camera.


.. code-block:: python


    scene.camera_info()





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

 Out:

 .. code-block:: none

    # Active Camera
       Position (-237.26, 116.47, 139.05)
       Focal Point (113.30, 128.31, 76.56)
       View Up (0.18, 0.00, 0.98)


Show every point with a value from a volume with default colormap
=================================================================

Here we will need to input the ``fa`` map in ``streamtube`` or ``line``.


.. code-block:: python


    scene.clear()
    stream_actor2 = actor.line(bundle_native, fa, linewidth=0.1)







We can also show the scalar bar.


.. code-block:: python


    bar = actor.scalar_bar()

    scene.add(stream_actor2)
    scene.add(bar)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle2.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_002.png
    :class: sphx-glr-single-img




Show every point with a value from a volume with your colormap
==============================================================

Here we will need to input the ``fa`` map in ``streamtube``


.. code-block:: python


    scene.clear()

    hue = (0.0, 0.0)  # red only
    saturation = (0.0, 1.0)  # white to red

    lut_cmap = actor.colormap_lookup_table(hue_range=hue,
                                           saturation_range=saturation)

    stream_actor3 = actor.line(bundle_native, fa, linewidth=0.1,
                               lookup_colormap=lut_cmap)
    bar2 = actor.scalar_bar(lut_cmap)

    scene.add(stream_actor3)
    scene.add(bar2)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle3.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_003.png
    :class: sphx-glr-single-img




Show every bundle with a specific color
========================================

You can have a bundle with a specific color. In this example, we are chosing
orange.


.. code-block:: python


    scene.clear()
    stream_actor4 = actor.line(bundle_native, (1., 0.5, 0), linewidth=0.1)

    scene.add(stream_actor4)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle4.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_004.png
    :class: sphx-glr-single-img




Show every streamline of a bundle with a different color
========================================================

Let's make a colormap where every streamline of the bundle is colored by its
length.


.. code-block:: python


    scene.clear()

    lengths = length(bundle_native)

    hue = (0.5, 0.5)  # blue only
    saturation = (0.0, 1.0)  # black to white

    lut_cmap = actor.colormap_lookup_table(
        scale_range=(lengths.min(), lengths.max()),
        hue_range=hue,
        saturation_range=saturation)

    stream_actor5 = actor.line(bundle_native, lengths, linewidth=0.1,
                               lookup_colormap=lut_cmap)

    scene.add(stream_actor5)
    bar3 = actor.scalar_bar(lut_cmap)

    scene.add(bar3)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle5.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_005.png
    :class: sphx-glr-single-img




Show every point of every streamline with a different color
============================================================

In this case in which we want to have a color per point and per streamline,
we can create a list of the colors to correspond to the list of streamlines
(bundles). Here in ``colors`` we will insert some random RGB colors.


.. code-block:: python


    scene.clear()

    colors = [np.random.rand(*streamline.shape) for streamline in bundle_native]

    stream_actor6 = actor.line(bundle_native, colors, linewidth=0.2)

    scene.add(stream_actor6)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle6.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_006.png
    :class: sphx-glr-single-img




Add depth cues to streamline rendering
============================================================

By default, lines are drawn with the same width on the screen, regardless of
their distance from the camera. To increase realism, we can enable
``depth_cue`` to make the lines shrink with distance from the camera. We
will return to the default color scheme from the first example. Note that
``depth_cue`` works best for ``linewidth`` <= 1.


.. code-block:: python


    scene.clear()

    stream_actor7 = actor.line(bundle_native, linewidth=0.5, depth_cue=True)

    scene.add(stream_actor7)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle7.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_007.png
    :class: sphx-glr-single-img




Render streamlines as fake tubes
============================================================

We can simulate the look of streamtubes by adding shading to streamlines with
``fake_tube``. Note that ``fake_tube`` requires ``linewidth`` > 1.


.. code-block:: python


    scene.clear()

    stream_actor8 = actor.line(bundle_native, linewidth=3, fake_tube=True)

    scene.add(stream_actor8)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle8.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_008.png
    :class: sphx-glr-single-img




Combine depth cues with fake tubes
============================================================

It is possible to fully simulate streamtubes by enabling both ``depth_cue``
and ``fake_tube``. However, it can be challenging to choose a ``linewidth``
that demonstrates both techniques well.


.. code-block:: python


    scene.clear()

    stream_actor9 = actor.line(bundle_native, linewidth=3,
                               depth_cue=True, fake_tube=True)

    scene.add(stream_actor9)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle9.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_009.png
    :class: sphx-glr-single-img




Render streamlines as tubes
============================================================

For yet more realism, we can use ``streamtube``. Note that this actor
generates much more geometry than ``line``, so it is more computationally
expensive. For large datasets, it may be better to approximate tubes using
the methods described above.


.. code-block:: python


    scene.clear()

    stream_actor10 = actor.streamtube(bundle_native, linewidth=0.5)

    scene.add(stream_actor10)

    if interactive:
        window.show(scene, size=(600, 600), reset_camera=False)

    window.record(scene, out_path='bundle10.png', size=(600, 600))




.. image:: /auto_examples/images/sphx_glr_viz_bundles_010.png
    :class: sphx-glr-single-img




In summary, we showed that there are many useful ways for visualizing maps
on bundles.

**Total running time of the script:** ( 0 minutes  7.217 seconds)


.. _sphx_glr_download_auto_examples_viz_bundles.py:


.. only :: html

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



  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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