Standardize actors colors

fury/actor.py

@@ -80,6 +80,7 @@
     set_polydata_triangles,
     set_polydata_vertices,
     shallow_copy,
+    normalize_color,
 )
 
 
@@ -383,6 +384,7 @@ def surface(vertices, faces=None, colors=None, smooth=None, subdivision=3):
     triangle_poly_data.SetPoints(points)
 
     if colors is not None:
+        colors = normalize_color(colors)
         triangle_poly_data.GetPointData().SetScalars(numpy_to_vtk_colors(255 * colors))
 
     if faces is None:
@@ -528,6 +530,9 @@ def contour_from_roi(data, affine=None, color=np.array([1, 0, 0]), opacity=1):
     skin_actor = Actor()
 
     skin_actor.SetMapper(skin_mapper)
+
+    color = normalize_color(color)
+
     skin_actor.GetProperty().SetColor(color[0], color[1], color[2])
     skin_actor.GetProperty().SetOpacity(opacity)
 
@@ -570,6 +575,8 @@ def contour_from_label(data, affine=None, color=None):
     elif color.shape != (nb_surfaces, 3) and color.shape != (nb_surfaces, 4):
         raise ValueError('Incorrect color array shape')
 
+    color = normalize_color(color)
+
     if color.shape == (nb_surfaces, 4):
         opacity = color[:, -1]
         color = color[:, :-1]
@@ -680,6 +687,7 @@ def streamtube(
 
     """
     # Poly data with lines and colors
+    colors = normalize_color(colors)
     poly_data, color_is_scalar = lines_to_vtk_polydata(lines, colors)
     next_input = poly_data
 
@@ -831,6 +839,7 @@ def line(
 
     """
     # Poly data with lines and colors
+    colors = normalize_color(colors)
     poly_data, color_is_scalar = lines_to_vtk_polydata(lines, colors)
     next_input = poly_data
 
@@ -948,6 +957,8 @@ def axes(
     dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
     colors = np.array([colorx + (opacity,), colory + (opacity,), colorz + (opacity,)])
 
+    colors = normalize_color(colors)
+
     scales = np.asarray(scale)
     arrow_actor = arrow(centers, dirs, colors, scales, repeat_primitive=False)
     return arrow_actor
@@ -1690,6 +1701,7 @@ def dot(points, colors=None, opacity=None, dot_size=5):
         vtk_faces.InsertNextCell(1)
         vtk_faces.InsertCellPoint(idd)
 
+    colors = normalize_color(colors)
     color_tuple = color_check(len(points), colors)
     color_array, global_opacity = color_tuple
 
@@ -1757,6 +1769,9 @@ def point(points, colors, point_radius=0.1, phi=8, theta=8, opacity=1.0):
     >>> # window.show(scene)
 
     """
+
+    colors = normalize_color(colors)
+
     return sphere(
         centers=points,
         colors=colors,
@@ -1818,6 +1833,7 @@ def sphere(
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     if not use_primitive:
         src = SphereSource() if faces is None else None
 
@@ -1915,6 +1931,7 @@ def cylinder(
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     if repeat_primitive:
 
         if resolution < 8:
@@ -2030,6 +2047,8 @@ def disk(
         src = None
         rotate = None
 
+    colors = normalize_color(colors)
+
     disk_actor = repeat_sources(
         centers=centers,
         colors=colors,
@@ -2072,6 +2091,7 @@ def square(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_square()
     res = fp.repeat_primitive(
         verts,
@@ -2124,6 +2144,7 @@ def rectangle(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=(1, 2, 0))
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     return square(centers=centers, directions=directions, colors=colors, scales=scales)
 
 
@@ -2157,6 +2178,7 @@ def box(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=(1, 2, 3)):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_box()
     res = fp.repeat_primitive(
         verts,
@@ -2205,6 +2227,7 @@ def cube(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     return box(centers=centers, directions=directions, colors=colors, scales=scales)
 
 
@@ -2265,6 +2288,7 @@ def arrow(
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     if repeat_primitive:
         vertices, faces = fp.prim_arrow()
         res = fp.repeat_primitive(
@@ -2352,6 +2376,7 @@ def cone(
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     if not use_primitive:
         src = ConeSource() if faces is None else None
 
@@ -2416,6 +2441,7 @@ def triangularprism(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_triangularprism()
     res = fp.repeat_primitive(
         verts,
@@ -2464,6 +2490,7 @@ def rhombicuboctahedron(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_rhombicuboctahedron()
     res = fp.repeat_primitive(
         verts,
@@ -2513,6 +2540,7 @@ def pentagonalprism(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_pentagonalprism()
     res = fp.repeat_primitive(
         verts,
@@ -2562,6 +2590,7 @@ def octagonalprism(centers, directions=(1, 0, 0), colors=(1, 0, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_octagonalprism()
     res = fp.repeat_primitive(
         verts,
@@ -2611,6 +2640,7 @@ def frustum(centers, directions=(1, 0, 0), colors=(0, 1, 0), scales=1):
     >>> # window.show(scene)
 
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_frustum()
     res = fp.repeat_primitive(
         verts,
@@ -2682,6 +2712,8 @@ def have_2_dimensions(arr):
     else:
         roundness = np.array(roundness)
 
+    colors = normalize_color(colors)
+
     res = fp.repeat_primitive_function(
         func=fp.prim_superquadric,
         centers=centers,
@@ -2744,6 +2776,7 @@ def billboard(
     -------
     billboard_actor: Actor
     """
+    colors = normalize_color(colors)
     verts, faces = fp.prim_square()
     res = fp.repeat_primitive(
         verts, faces, centers=centers, colors=colors, scales=scales
@@ -2954,6 +2987,7 @@ def add_to_scene(scene):
 
     texta.SetMapper(textm)
 
+    color = normalize_color(color)
     texta.GetProperty().SetColor(color)
 
     # Set ser rotation origin to the center of the text is following the camera
@@ -3076,6 +3110,8 @@ def get_position(self):
     text_actor.set_position(position)
     text_actor.font_family(font_family)
     text_actor.font_style(bold, italic, shadow)
+
+    color = normalize_color(color)
     text_actor.color(color)
     text_actor.justification(justification)
     text_actor.vertical_justification(vertical_justification)
@@ -3377,7 +3413,7 @@ def texture(rgb, interp=True):
     act: Actor
 
     """
-    arr = rgb
+    arr = normalize_color(rgb)
     grid = rgb_to_vtk(np.ascontiguousarray(arr))
 
     Y, X = arr.shape[:2]
@@ -3558,6 +3594,7 @@ def sdf(centers, directions=(1, 0, 0), colors=(1, 0, 0), primitives='torus', sca
     """
     prims = {'sphere': 1, 'torus': 2, 'ellipsoid': 3, 'capsule': 4}
 
+    colors = normalize_color(colors)
     verts, faces = fp.prim_box()
     repeated = fp.repeat_primitive(
         verts,
@@ -3670,6 +3707,7 @@ def markers(
     >>> # window.show(scene, size=(600, 600))
 
     """
+    colors = normalize_color(colors)
     n_markers = centers.shape[0]
     verts, faces = fp.prim_square()
     res = fp.repeat_primitive(

fury/tests/test_utils.py

@@ -839,7 +839,7 @@ def test_color_check():
     npt.assert_equal(global_opacity, 1)
 
     points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
-    colors = (1, 1, 1, 0.5)
+    colors = np.array([1, 1, 1, 0.5])
 
     color_tuple = color_check(len(points), colors)
     color_array, global_opacity = color_tuple
@@ -848,7 +848,7 @@ def test_color_check():
     npt.assert_equal(global_opacity, 0.5)
 
     points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
-    colors = (1, 0, 0)
+    colors = np.array([1, 0, 0])
 
     color_tuple = color_check(len(points), colors)
     color_array, global_opacity = color_tuple
@@ -865,6 +865,44 @@ def test_color_check():
     npt.assert_equal(global_opacity, 1)
 
 
+def test_normalize_color():
+    # Test input None in color
+    none_color = None
+    assert utils.normalize_color(none_color) == None
+
+    # Test 2d input data
+    valid_color_array = np.array([[0.1, 0.2, 0.3, 0.4], [0.4, 0.5, 0.6, 0.7]])
+    outbound_color_array = [[0.1, 0.2, 1.0, 0.3], [255, 255, 255, 0.7]]
+    outbound_color_array_expected = np.array(
+        [[0.1, 0.2, 1.0, 0.3], [1.0, 1.0, 1.0, 0.7]])
+
+    # Test for valid 2d input
+    npt.assert_array_equal(utils.normalize_color(
+        valid_color_array), valid_color_array)
+
+    # Test for invalid 2d input
+    npt.assert_array_equal(utils.normalize_color(
+        outbound_color_array), outbound_color_array_expected)
+
+    # Test for input of type tuple
+    color_tuple = (0.1, 0.2, 0.3)
+    color_tuple_expected = np.array([0.1, 0.2, 0.3])
+    npt.assert_array_equal(utils.normalize_color(color_tuple), color_tuple_expected)
+
+    # Test for input of type list
+    color_list = [100, 150, 200, 0.4]
+    color_list_expected = np.array(color_list)
+    color_list_expected[:3] = color_list_expected[:3]/255.0
+    npt.assert_array_equal(
+        utils.normalize_color(color_list), color_list_expected)
+
+    # Test for input of type 1d np.array
+    color_1d = np.array([0.1, 0.5, 0.9, 0.3])
+    color_1d_expected = np.array([0.1, 0.5, 0.9, 0.3])
+    npt.assert_array_equal(
+        utils.normalize_color(color_1d), color_1d_expected)
+
+
 def test_is_ui():
     panel = Panel2D(position=(0, 0), size=(100, 100))
     valid_ui = DummyUI(act=[])
@@ -885,7 +923,7 @@ def test_empty_array_to_polydata():
     npt.assert_raises(ValueError, utils.lines_to_vtk_polydata, lines)
 
 
-@pytest.mark.skipif(not have_dipy, reason='Requires DIPY')
+@ pytest.mark.skipif(not have_dipy, reason='Requires DIPY')
 def test_empty_array_sequence_to_polydata():
     from dipy.tracking.streamline import Streamlines
 

fury/utils.py

@@ -1,4 +1,5 @@
 import numpy as np
+import warnings
 from scipy.ndimage import map_coordinates
 
 from fury.colormap import line_colors
@@ -1532,7 +1533,7 @@ def color_check(pts_len, colors=None):
         # Automatic RGB colors
         colors = np.asarray((1, 1, 1))
         color_array = numpy_to_vtk_colors(np.tile(255 * colors, (pts_len, 1)))
-    elif type(colors) is tuple:
+    elif colors.shape in [(3,), (4,)]:
         global_opacity = 1 if len(colors) == 3 else colors[3]
         colors = np.asarray(colors)
         color_array = numpy_to_vtk_colors(np.tile(255 * colors, (pts_len, 1)))
@@ -1547,6 +1548,55 @@ def color_check(pts_len, colors=None):
     return color_array, global_opacity
 
 
+def normalize_color(color_array):
+    """
+    Normalize an array of RGB or RGBA color values to be within the range 
+    [0, 1].
+
+    If any values are out of bounds, normalize the color array by scaling all
+    color values to fit within the valid range.
+
+    Parameters
+    ----------
+    color_array : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
+        An array of RGB or RGBA color values, where each row represents 
+        a single color as an array of shape (3,) or (4,). Alternatively,
+        a tuple of length 3 or 4 can be passed to represent a single color.
+
+    Returns
+    -------
+    color_array : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
+        The original array if all values are within the range [0,1]. 
+        If any values in the input array were out of bounds, a new array
+        or tuple is returned with the colors normalized to fit within the
+        valid range.
+
+    """
+    # Keep the option for color = None for some actors
+    if color_array is None:
+        return color_array
+
+    # Convert tuple or list to ndarray
+    if isinstance(color_array, (tuple, list)):
+        color_array = np.asarray(color_array)
+
+    # Normalize the out of bounds array
+    if color_array.ndim == 1 and np.any(color_array > 1):
+        print(
+            f"{color_array} in the color array are outside the valid range [0, 1]")
+        color_array[:3] = color_array[:3] / 255.0
+        print("It has been normalized to fit the range.")
+
+    elif color_array.ndim == 2:
+        for i, row in enumerate(color_array):
+            if np.any(row > 1):
+                print(f"{row} in the color array are outside the valid range [0, 1]")
+                color_array[i, :3] = color_array[i, :3] / 255.0
+                print("It has been normalized to fit the range.")
+
+    return color_array
+
+
 def is_ui(actor):
     """Method to check if the passed actor is `UI` or `vtkProp3D`