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.. only:: html

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.. _sphx_glr_auto_examples_04_demos_viz_contour.py:


===================
3D Contour Surfaces
===================

This example demonstrates how to use contour actors to visualize
3D volume data as surface meshes. FURY provides two main functions
for creating contours:

1. ``contour_from_volume``: Creates contours directly from 3D volume data
2. ``contour_from_roi``: Creates contours with affine transformation support

We will start by creating simple geometric shapes and visualizing their
contours. Then, we'll work with real medical imaging data from the
`MNI template <https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009>`_
to demonstrate contours from regions of interest (ROI).

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.. code-block:: Python


    import numpy as np
    from fury import actor, window
    from dipy.data import read_mni_template


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Example 1: Simple Contour from Volume
======================================
Let's create a 3D volume with a simple geometric shape - a sphere inside
a cube. We'll use ``contour_from_volume`` to extract and visualize the
surface of the sphere.

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.. code-block:: Python


    size = 100
    volume = np.zeros((size, size, size), dtype=np.uint8)

    # Create coordinate grids
    x, y, z = np.indices((size, size, size))
    center = (size - 1) / 2

    # Calculate distances from center
    distances = np.sqrt((x - center) ** 2 + (y - center) ** 2 + (z - center) ** 2)

    # Create a sphere by setting voxels within radius to 1
    sphere_radius = size // 3
    volume[distances <= sphere_radius] = 1


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Now we'll create a contour actor from this volume. The contour will
extract the surface where the volume transitions from 0 to 1, creating
a mesh representation of the sphere.

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.. code-block:: Python


    contour_actor = actor.contour_from_volume(
        volume, color=(1, 0, 0), opacity=0.8, material="phong"
    )

    scene = window.Scene()
    scene.add(contour_actor)


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Create the ShowManager that we'll reuse throughout the tutorial

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.. code-block:: Python


    show_m = window.ShowManager(scene=scene, title="FURY Contour Examples")


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Display the first example

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.. code-block:: Python


    show_m.start()


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Example 2: Multiple Contours with Different Objects
====================================================
Let's create a more complex volume with multiple objects and visualize
them with different colors. We'll create a cube with two spheres of
different sizes.

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.. code-block:: Python


    volume_multi = np.zeros((size, size, size), dtype=np.uint8)

    # First sphere (larger)
    sphere1_radius = size // 3
    sphere1_center = (size // 3, size // 2, size // 2)
    distances1 = np.sqrt(
        (x - sphere1_center[0]) ** 2
        + (y - sphere1_center[1]) ** 2
        + (z - sphere1_center[2]) ** 2
    )
    volume_multi[distances1 <= sphere1_radius] = 1

    # Second sphere (smaller)
    sphere2_radius = size // 4
    sphere2_center = (2 * size // 3, size // 2, size // 2)
    distances2 = np.sqrt(
        (x - sphere2_center[0]) ** 2
        + (y - sphere2_center[1]) ** 2
        + (z - sphere2_center[2]) ** 2
    )
    volume_multi[distances2 <= sphere2_radius] = 2


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Create one actor for all contours to identify they are coming from same
volume.

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.. code-block:: Python

    scene.clear()

    contour_actors = actor.contour_from_volume(
        volume_multi, color=(0, 1, 0), opacity=0.5, material="phong"
    )
    scene.add(contour_actors)

    show_m = window.ShowManager(scene=scene, title="FURY Multi Contour Examples")
    show_m.start()


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Create contours for each label directly from the labeled volume using
``contour_from_label``.

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.. code-block:: Python


    scene.clear()

    label_colors = np.array([[1, 0, 0, 0.7], [0, 0, 1, 0.7]])
    multi_contour_actor = actor.contour_from_label(volume_multi, colors=label_colors)
    scene.add(multi_contour_actor)


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Display the scene with multiple contours

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.. code-block:: Python

    show_m = window.ShowManager(scene=scene, title="FURY Multi Contour Examples")
    show_m.start()


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Example 3: Contour from ROI with Affine Transformation
=======================================================
Now let's work with real medical imaging data. We'll read the MNI template
and create an ellipsoid ROI with the same dimensions. The ``contour_from_roi``
function allows us to apply affine transformations to properly position
the contours in world coordinates. We'll display the contour alongside
the actual volume slices.

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.. code-block:: Python


    nifti = read_mni_template()
    data = np.asarray(nifti.dataobj)
    affine = nifti.affine


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Let's examine the data shape and affine matrix

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.. code-block:: Python


    print(f"Data shape: {data.shape}")
    print(f"Affine transformation matrix:\n{affine}")


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Create an ellipsoid ROI with the same dimensions as the MNI template.
The ellipsoid will be centered in the volume.

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.. code-block:: Python


    roi_shape = data.shape
    roi_ellipsoid = np.zeros(roi_shape, dtype=np.uint8)

    # Calculate the center and radii for the ellipsoid
    center_x, center_y, center_z = roi_shape[0] // 2, roi_shape[1] // 2, roi_shape[2] // 2
    radius_x, radius_y, radius_z = roi_shape[0] // 5, roi_shape[1] // 5, roi_shape[2] // 5

    # Create coordinate grids
    x_roi, y_roi, z_roi = np.indices(roi_shape)

    # Create ellipsoid using the equation: (x/a)^2 + (y/b)^2 + (z/c)^2 <= 1
    ellipsoid_eq = (
        ((x_roi - center_x) / radius_x) ** 2
        + ((y_roi - center_y) / radius_y) ** 2
        + ((z_roi - center_z) / radius_z) ** 2
    )

    roi_ellipsoid[ellipsoid_eq <= 1] = 1

    print(f"Created ellipsoid ROI with shape: {roi_ellipsoid.shape}")
    print(f"Number of voxels in ROI: {np.sum(roi_ellipsoid)}")


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Now create a contour from the ellipsoid ROI with affine transformation.
The affine matrix ensures the contour is positioned correctly in
anatomical space alongside the volume slicer.

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.. code-block:: Python


    contour_ellipsoid = actor.contour_from_roi(
        roi_ellipsoid, affine=affine, color=(1, 0.5, 0), opacity=0.6, material="phong"
    )


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Create a volume slicer for the MNI template to display alongside the contour

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.. code-block:: Python


    slicer_actor = actor.volume_slicer(data, affine=affine, interpolation="linear")


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Clear the scene and add both the contour and the slicer

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.. code-block:: Python


    scene.clear()
    scene.add(contour_ellipsoid)
    scene.add(slicer_actor)


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Display the scene with the ellipsoid contour and volume slices

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.. code-block:: Python


    show_m = window.ShowManager(scene=scene, title="FURY Contour from ROI Examples")
    show_m.start()


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