Merge pull request #551 from Sassafrass6/glyph_orientation

Fixed #550 : Added necessary allignment between glyph creation and ac…

fury/actor.py

@@ -22,7 +22,7 @@
                       PolyDataNormals, Assembly, LODActor, VTK_UNSIGNED_CHAR,
                       PolyDataMapper2D, ScalarBarActor, PolyVertex, CellArray,
                       UnstructuredGrid, DataSetMapper, ConeSource, ArrowSource,
-                      SphereSource, CylinderSource, TexturedSphereSource,
+                      SphereSource, CylinderSource, DiskSource, TexturedSphereSource,
                       Texture, FloatArray, VTK_TEXT_LEFT, VTK_TEXT_RIGHT,
                       VTK_TEXT_BOTTOM, VTK_TEXT_TOP, VTK_TEXT_CENTERED,
                       TexturedActor2D, TextureMapToPlane, TextActor3D,
@@ -1609,21 +1609,93 @@ def cylinder(centers, directions, colors, radius=0.05, heights=1,
     >>> # window.show(scene)
 
     """
-    src = CylinderSource() if faces is None else None
-
-    if src is not None:
+    if faces is None:
+        src = CylinderSource()
         src.SetCapping(capped)
         src.SetResolution(resolution)
         src.SetRadius(radius)
+        rotate = np.array([[0, 1, 0, 0],
+                           [-1, 0, 0, 0],
+                           [0, 0, 1, 0],
+                           [0, 0, 0, 1]])
+    else:
+        src = None
+        rotate = None
 
     cylinder_actor = repeat_sources(centers=centers, colors=colors,
                                     directions=directions,
                                     active_scalars=heights, source=src,
-                                    vertices=vertices, faces=faces)
+                                    vertices=vertices, faces=faces,
+                                    orientation=rotate)
 
     return cylinder_actor
 
 
+def disk(centers, directions, colors, rinner=0.3,
+         router=0.7, cresolution=6, rresolution=2, vertices=None, faces=None):
+    """Visualize one or many disks with different features.
+
+    Parameters
+    ----------
+    centers : ndarray, shape (N, 3)
+        Disk positions
+    directions : ndarray, shape (N, 3)
+        The orientation vector of the disk.
+    colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
+        RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1]
+    rinner : float
+        disk inner radius, default: 0.3
+    router : float
+        disk outer radius, default: 0.5
+    cresolution: int, optional
+        Number of facets used to define perimeter of disk, default: 6
+    rresolution: int, optional
+        Number of facets used radially, default: 2
+    vertices : ndarray, shape (N, 3)
+        The point cloud defining the disk.
+    faces : ndarray, shape (M, 3)
+        If faces is None then a disk is created based on theta and phi angles
+        If not then a disk is created with the provided vertices and faces.
+
+    Returns
+    -------
+    disk_actor: Actor
+
+    Examples
+    --------
+    >>> from fury import window, actor
+    >>> import numpy as np
+    >>> scene = window.Scene()
+    >>> centers = np.random.rand(5, 3)
+    >>> dirs = np.random.rand(5, 3)
+    >>> colors = np.random.rand(5, 4)
+    >>> actor = actor.disk(centers, dirs, colors,
+    >>>                    rinner=.1, router=.8, cresolution=30)
+    >>> scene.add(actor)
+    >>> window.show(scene)
+    """
+    if faces is None:
+        src = DiskSource()
+        src.SetCircumferentialResolution(cresolution)
+        src.SetRadialResolution(rresolution)
+        src.SetInnerRadius(rinner)
+        src.SetOuterRadius(router)
+        rotate = np.array([[0, 0, -1, 0],
+                           [0, 1, 0, 0],
+                           [1, 0, 0, 0],
+                           [0, 0, 0, 1]])
+    else:
+        src = None
+        rotate = None
+
+    disk_actor = repeat_sources(centers=centers, colors=colors,
+                                directions=directions, source=src,
+                                vertices=vertices, faces=faces,
+                                orientation=rotate)
+
+    return disk_actor
+
+
 def square(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     """Visualize one or many squares with different features.
 

fury/lib.py

@@ -124,6 +124,7 @@
 ##############################################################
 #  vtkFiltersGeneral Module
 SplineFilter = fgvtk.vtkSplineFilter
+TransformPolyDataFilter = fgvtk.vtkTransformPolyDataFilter
 
 ##############################################################
 #  vtkFiltersHybrid Module

fury/tests/test_actors.py

@@ -919,20 +919,22 @@ def test_basic_geometry_actor(interactive=False):
 
 def test_advanced_geometry_actor(interactive=False):
     xyz = np.array([[0, 0, 0], [50, 0, 0], [100, 0, 0]])
-    dirs = np.array([[0, 1, 0], [1, 0, 0], [0, 0.5, 0.5]])
+    dirs = np.array([[0.5, 0.5, 0.5], [0.5, 0, 0.5], [0, 0.5, 0.5]])
 
-    actor_list = [[actor.cone, {'directions': dirs, 'resolution': 8}],
-                  [actor.arrow, {'directions': dirs, 'resolution': 9}],
-                  [actor.cylinder, {'directions': dirs}]]
+    heights = np.array([5, 7, 10])
+
+    actor_list = [[actor.cone, {'heights': heights, 'resolution': 8}],
+                  [actor.arrow, {'heights': heights, 'resolution': 9}],
+                  [actor.cylinder, {'heights': heights, 'resolution': 10}],
+                  [actor.disk, {'rinner': 4, 'router': 8, 'rresolution': 2,
+                                'cresolution': 2}]]
 
     scene = window.Scene()
 
     for act_func, extra_args in actor_list:
         colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [1, 1, 0, 1]])
-        heights = np.array([5, 7, 10])
 
-        geom_actor = act_func(centers=xyz, heights=heights, colors=colors[:],
-                              **extra_args)
+        geom_actor = act_func(xyz, dirs, colors, **extra_args)
         scene.add(geom_actor)
 
         if interactive:
@@ -941,12 +943,11 @@ def test_advanced_geometry_actor(interactive=False):
         report = window.analyze_snapshot(arr, colors=colors)
         npt.assert_equal(report.objects, 3)
 
+        scene.clear()
+
         colors = np.array([1.0, 1.0, 1.0, 1.0])
-        heights = 10
 
-        scene.clear()
-        geom_actor = act_func(centers=xyz[:, :3], heights=10, colors=colors[:],
-                              **extra_args)
+        geom_actor = act_func(xyz, dirs, colors, **extra_args)
         scene.add(geom_actor)
 
         if interactive:

fury/utils.py

@@ -6,7 +6,7 @@
                       CellArray, PolyDataNormals, Actor, PolyDataMapper,
                       Matrix4x4, Matrix3x3, Glyph3D, VTK_DOUBLE, VTK_FLOAT,
                       Transform, AlgorithmOutput, VTK_INT, VTK_UNSIGNED_CHAR,
-                      IdTypeArray)
+                      TransformPolyDataFilter, IdTypeArray)
 
 
 def remove_observer_from_actor(actor, id):
@@ -706,7 +706,7 @@ def get_actor_from_primitive(vertices, triangles, colors=None,
 
 
 def repeat_sources(centers, colors, active_scalars=1., directions=None,
-                   source=None, vertices=None, faces=None):
+                   source=None, vertices=None, faces=None, orientation=None):
     """Transform a vtksource to glyph."""
     if source is None and faces is None:
         raise IOError("A source or faces should be defined")
@@ -749,10 +749,16 @@ def repeat_sources(centers, colors, active_scalars=1., directions=None,
 
     glyph = Glyph3D()
     if faces is None:
+        if orientation is not None:
+            transform = Transform()
+            transform.SetMatrix(numpy_to_vtk_matrix(orientation))
+            rtrans = TransformPolyDataFilter()
+            rtrans.SetInputConnection(source.GetOutputPort())
+            rtrans.SetTransform(transform)
+            source = rtrans
         glyph.SetSourceConnection(source.GetOutputPort())
     else:
         glyph.SetSourceData(polydata_geom)
-
     glyph.SetInputData(polydata_centers)
     glyph.SetOrient(True)
     glyph.SetScaleModeToScaleByScalar()