.. note:: :class: sphx-glr-download-link-note Click :ref:`here ` 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 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 renderer = window.Renderer() stream_actor = actor.line(bundle_native) renderer.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)) renderer.add(stream_actor) # Uncomment the line below to show to display the window # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, 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 renderer.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 renderer.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() renderer.add(stream_actor2) renderer.add(bar) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, 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 renderer.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) renderer.add(stream_actor3) renderer.add(bar2) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, 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 renderer.clear() stream_actor4 = actor.line(bundle_native, (1., 0.5, 0), linewidth=0.1) renderer.add(stream_actor4) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, 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 renderer.clear() from dipy.tracking.streamline import length 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) renderer.add(stream_actor5) bar3 = actor.scalar_bar(lut_cmap) renderer.add(bar3) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, 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 renderer.clear() colors = [np.random.rand(*streamline.shape) for streamline in bundle_native] stream_actor6 = actor.line(bundle_native, colors, linewidth=0.2) renderer.add(stream_actor6) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, out_path='bundle6.png', size=(600, 600)) .. image:: /auto_examples/images/sphx_glr_viz_bundles_006.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 4.604 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 ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: viz_bundles.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_