solved conflicts

fury/actor.py

@@ -10,7 +10,8 @@
 from fury import layout
 from fury.actors.odf_slicer import OdfSlicerActor
 from fury.actors.peak import PeakActor
-from fury.actors.tensor import double_cone, main_dir_uncertainty
+from fury.actors.tensor import double_cone, main_dir_uncertainty, \
+    tensor_ellipsoid
 from fury.colormap import colormap_lookup_table
 from fury.deprecator import deprecate_with_version, deprecated_params
 from fury.io import load_image
@@ -3798,6 +3799,77 @@ def callback(
     return sq_actor
 
 
+def ellipsoid(
+    centers,
+    axes,
+    lengths,
+    colors=(1, 0, 0),
+    scales=1.0,
+    opacity=1.0
+):
+    """
+    VTK actor for visualizing ellipsoids.
+
+    Parameters
+    ----------
+    centers : ndarray(N, 3)
+        Ellipsoid positions.
+    axes : ndarray (3, 3) or (N, 3, 3)
+        Axes of the ellipsoid.
+    lengths : ndarray (3, ) or (N, 3)
+        Axes lengths.
+    colors : ndarray (N,3) or tuple (3,), optional
+        Default red color. R, G and B should be in the range [0, 1].
+    scales : float or ndarray (N, ), optional
+        Ellipsoid size, default(1.0).
+    opacity : float, optional
+        Takes values from 0 (fully transparent) to 1 (opaque), default(1.0).
+
+    Returns
+    -------
+    tensor_ellipsoid: Actor
+
+    """
+
+    if not isinstance(centers, np.ndarray):
+        centers = np.array(centers)
+    if centers.ndim == 1:
+        centers = np.array([centers])
+
+    if not isinstance(axes, np.ndarray):
+        axes = np.array(axes)
+    if axes.ndim == 2:
+        axes = np.array([axes])
+    if axes.shape[0] != centers.shape[0]:
+        raise ValueError('number of axes defined does not match with number of'
+                         'centers')
+
+    if not isinstance(lengths, np.ndarray):
+        lengths = np.array(lengths)
+    if lengths.ndim == 1:
+        lengths = np.array([lengths])
+    if lengths.shape[0] != centers.shape[0]:
+        raise ValueError('number of lengths defined does not match with number'
+                         'of centers')
+
+    if not isinstance(scales, np.ndarray):
+        scales = np.array(scales)
+    if scales.size == 1:
+        scales = np.repeat(scales, centers.shape[0])
+    elif scales.size != centers.shape[0]:
+        scales = np.concatenate(
+            (scales, np.ones(centers.shape[0] - scales.shape[0])), axis=None)
+
+    if isinstance(colors, tuple):
+        colors = np.array([colors])
+    elif not isinstance(colors, np.ndarray):
+        colors = np.array(colors)
+    if colors.shape[1] == 4:
+        colors = colors[:, :-1]
+
+    return tensor_ellipsoid(centers, axes, lengths, colors, scales, opacity)
+
+
 def uncertainty_cone(
     evals,
     evecs,

fury/actors/tensor.py

@@ -3,8 +3,214 @@
 import numpy as np
 
 from fury import actor
-from fury.shaders import (attribute_to_actor, import_fury_shader,
-                          shader_to_actor, compose_shader)
+from fury.shaders import (attribute_to_actor, compose_shader,
+                          import_fury_shader, shader_to_actor)
+
+def tensor_ellipsoid(centers, axes, lengths, colors, scales, opacity):
+    """
+    Visualize one or many Tensor Ellipsoids with different features.
+
+    Parameters
+    ----------
+    centers : ndarray(N, 3)
+        Tensor ellipsoid positions.
+    axes : ndarray (3, 3) or (N, 3, 3)
+        Axes of the tensor ellipsoid.
+    lengths : ndarray (3, ) or (N, 3)
+        Axes lengths.
+    colors : ndarray (N,3) or tuple (3,)
+        R, G and B should be in the range [0, 1].
+    scales : float or ndarray (N, )
+        Tensor ellipsoid size.
+    opacity : float
+        Takes values from 0 (fully transparent) to 1 (opaque).
+
+    Returns
+    -------
+    box_actor: Actor
+
+    """
+
+    box_actor = actor.box(centers, colors=colors, scales=scales)
+    box_actor.GetMapper().SetVBOShiftScaleMethod(False)
+    box_actor.GetProperty().SetOpacity(opacity)
+
+    # Number of vertices that make up the box
+    n_verts = 8
+
+    big_centers = np.repeat(centers, n_verts, axis=0)
+    attribute_to_actor(box_actor, big_centers, 'center')
+
+    big_scales = np.repeat(scales, n_verts, axis=0)
+    attribute_to_actor(box_actor, big_scales, 'scale')
+
+    big_values = np.repeat(np.array(lengths, dtype=float), n_verts, axis=0)
+    attribute_to_actor(box_actor, big_values, 'evals')
+
+    evec1 = np.array([item[0] for item in axes])
+    evec2 = np.array([item[1] for item in axes])
+    evec3 = np.array([item[2] for item in axes])
+
+    big_vectors_1 = np.repeat(evec1, n_verts, axis=0)
+    attribute_to_actor(box_actor, big_vectors_1, 'evec1')
+    big_vectors_2 = np.repeat(evec2, n_verts, axis=0)
+    attribute_to_actor(box_actor, big_vectors_2, 'evec2')
+    big_vectors_3 = np.repeat(evec3, n_verts, axis=0)
+    attribute_to_actor(box_actor, big_vectors_3, 'evec3')
+
+    # Start of shader implementation
+
+    vs_dec = \
+        """
+        in vec3 center;
+        in float scale;
+        in vec3 evals;
+        in vec3 evec1;
+        in vec3 evec2;
+        in vec3 evec3;
+
+        out vec4 vertexMCVSOutput;
+        out vec3 centerMCVSOutput;
+        out float scaleVSOutput;
+        out vec3 evalsVSOutput;
+        out mat3 tensorMatrix;
+        """
+
+    # Variables assignment
+    v_assign = \
+        """
+        vertexMCVSOutput = vertexMC;
+        centerMCVSOutput = center;
+        scaleVSOutput = scale;
+        """
+
+    # Normalization
+    n_evals = "evalsVSOutput = evals/(max(evals.x, max(evals.y, evals.z)));"
+
+    # Values constraint to avoid incorrect visualizations
+    evals = "evalsVSOutput = clamp(evalsVSOutput,0.05,1);"
+
+    # Scaling matrix
+    sc_matrix = \
+        """
+        mat3 S = mat3(1/evalsVSOutput.x, 0.0, 0.0,
+                      0.0, 1/evalsVSOutput.y, 0.0,
+                      0.0, 0.0, 1/evalsVSOutput.z);
+        """
+
+    # Rotation matrix
+    rot_matrix = "mat3 R = mat3(evec1, evec2, evec3);"
+
+    # Tensor matrix
+    t_matrix = "tensorMatrix = inverse(R) * S * R;"
+
+    vs_impl = compose_shader([v_assign, n_evals, evals, sc_matrix, rot_matrix,
+                              t_matrix])
+
+    # Adding shader implementation to actor
+    shader_to_actor(box_actor, 'vertex', decl_code=vs_dec, impl_code=vs_impl)
+
+    fs_vars_dec = \
+        """
+        in vec4 vertexMCVSOutput;
+        in vec3 centerMCVSOutput;
+        in float scaleVSOutput;
+        in vec3 evalsVSOutput;
+        in mat3 tensorMatrix;
+
+        uniform mat4 MCVCMatrix;
+        """
+
+    # Importing the sphere SDF
+    sd_sphere = import_fury_shader(os.path.join('sdf', 'sd_sphere.frag'))
+
+    # SDF definition
+    sdf_map = \
+        """
+        float map(in vec3 position)
+        {
+            /*
+            As the scaling is not a rigid body transformation, we multiply
+            by a factor to compensate for distortion and not overestimate
+            the distance.
+            */
+            float scFactor = min(evalsVSOutput.x, min(evalsVSOutput.y,
+                                     evalsVSOutput.z));
+                                     
+            /*
+            The approximation of distance is calculated by stretching the
+            space such that the ellipsoid becomes a sphere (multiplying by
+            the transformation matrix) and then computing the distance to
+            a sphere in that space (using the sphere SDF).
+            */
+            return sdSphere(tensorMatrix * (position - centerMCVSOutput),
+                scaleVSOutput*0.48) * scFactor;
+        }
+        """
+
+    # Importing central differences function for computing surface normals
+    central_diffs_normal = import_fury_shader(os.path.join(
+        'sdf', 'central_diffs.frag'))
+
+    # Importing raymarching function
+    cast_ray = import_fury_shader(os.path.join(
+        'ray_marching', 'cast_ray.frag'))
+
+    # Importing Blinn-Phong model for lighting
+    blinn_phong_model = import_fury_shader(os.path.join(
+        'lighting', 'blinn_phong_model.frag'))
+
+    # Full fragment shader declaration
+    fs_dec = compose_shader([fs_vars_dec, sd_sphere, sdf_map,
+                             central_diffs_normal, cast_ray,
+                             blinn_phong_model])
+
+    shader_to_actor(box_actor, 'fragment', decl_code=fs_dec)
+
+    # Vertex in Model Coordinates.
+    point = "vec3 point = vertexMCVSOutput.xyz;"
+
+    # Camera position in world space
+    ray_origin = "vec3 ro = (-MCVCMatrix[3] * MCVCMatrix).xyz;"
+
+    ray_direction = "vec3 rd = normalize(point - ro);"
+
+    light_direction = "vec3 ld = normalize(ro - point);"
+
+    ray_origin_update = "ro += point - ro;"
+
+    # Total distance traversed along the ray
+    distance = "float t = castRay(ro, rd);"
+
+    # Fragment shader output definition
+    # If surface is detected, color is assigned, otherwise, nothing is painted
+    frag_output_def = \
+        """
+        if(t < 20)
+        {
+            vec3 pos = ro + t * rd;
+            vec3 normal = centralDiffsNormals(pos, .0001);
+            // Light Attenuation
+            float la = dot(ld, normal);
+            vec3 color = blinnPhongIllumModel(la, lightColor0, 
+                diffuseColor, specularPower, specularColor, ambientColor);
+            fragOutput0 = vec4(color, opacity);
+        }
+        else
+        {
+            discard;
+        }
+        """
+
+    # Full fragment shader implementation
+    sdf_frag_impl = compose_shader([point, ray_origin, ray_direction,
+                                    light_direction, ray_origin_update,
+                                    distance, frag_output_def])
+
+    shader_to_actor(box_actor, 'fragment', impl_code=sdf_frag_impl,
+                    block='light')
+
+    return box_actor
 
 
 def double_cone(centers, axes, angles, colors, scales, opacity):

fury/tests/test_actors.py

@@ -1734,6 +1734,45 @@ def test_marker_actor(interactive=False):
     npt.assert_equal(report.objects, 12)
 
 
+def test_ellipsoid_actor(interactive=False):
+    # number of axes does not match with number of centers
+    centers = [-1, 1, 0]
+    axes = [[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
+            [[1, 2, -2], [2, 1, 2], [2, -2, -1]]]
+    lengths = [[1, 1, 1]]
+    npt.assert_raises(ValueError, actor.ellipsoid, centers, axes, lengths)
+
+    # number of lengths does not match with number of centers
+    lengths = [[1, 1, 1], [1, 1, .5]]
+    npt.assert_raises(ValueError, actor.ellipsoid, centers, axes, lengths)
+
+    scene = window.Scene()
+    scene.background((0, 0, 0))
+
+    axes = np.array([[[-.6, .5, -.6], [-.8, -.4, .5], [-.1, -.7, -.7]],
+                     [[.1, .6, -.8], [.6, .5, .5], [-.8, .6, .3]],
+                     [[.7, .5, -.5], [0, -.7, -.7], [-.7, .6, -.5]],
+                     [[.7, -.3, -.6], [.2, -.8, .6], [.7, .6, .5]],
+                     [[1, 2, -2], [2, 1, 2], [2, -2, -1]],
+                     [[1, 0, 0], [0, 1, 0], [0, 0, 1]]])
+    lengths = np.array([[1, 1, 1], [1, 1, .5], [1, .5, .5],
+                        [1, .5, .25], [1, 1, .3], [1, .3, .3]])
+    centers = np.array([[-1, 1, 0], [0, 1, 0], [1, 1, 0],
+                        [-1, 0, 0], [0, 0, 0], [1, 0, 0]])
+    colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1],
+                       [1, 1, 0], [1, 0, 1], [0, 1, 1]])
+
+    ellipsoids = actor.ellipsoid(axes=axes, lengths=lengths, centers=centers,
+                              scales=1.0, colors=colors)
+    scene.add(ellipsoids)
+
+    if interactive:
+        window.show(scene)
+
+    report = window.analyze_scene(scene)
+    npt.assert_equal(report.actors, 1)
+
+
 def test_uncertainty_cone_actor(interactive=False):
     scene = window.Scene()