.. 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:: default
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'])
Store fractional anisotropy.
.. code-block:: default
fa = dix['fa']
Store grid to world transformation matrix.
.. code-block:: default
affine = dix['affine']
Store the cingulum bundle. A bundle is a list of streamlines.
.. code-block:: default
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:: default
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:: default
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:: default
scene.camera_info()
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
# Active Camera
Position (-237.76, 115.97, 138.55)
Focal Point (112.80, 127.81, 76.06)
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:: default
scene.clear()
stream_actor2 = actor.line(bundle_native, fa, linewidth=0.1)
We can also show the scalar bar.
.. code-block:: default
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:: default
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:: default
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:: default
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:: default
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
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
/Users/koudoro/miniconda3/envs/fury-env-37/lib/python3.7/site-packages/numpy/core/_asarray.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
return array(a, dtype, copy=False, order=order)
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:: default
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:: default
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:: default
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:: default
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.
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 7.562 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.github.io>`_