I'm trying to render a simple spherical distribution where the opacity varies with radius using Image3D. Unfortunately, the outcome is not very appealing, with discrete colors showing up in the rendering:

enter image description here

You can see that not only are the colors discrete, they are not even in order, with some darker bands appearing in the image in the lighter regions, whereas the image should have the appearance of a smooth radial gradient.

The code I used to generate the above image is:

res = 100;
coords = Table[{i, j, k} - 0.5, {i, Range@res}, {j, Range@res}, {k, Range@res}];
dists = Map[N@Norm[# - res/2.] &, coords, {3}];
opa = 1/(dists + 0.1);
opa /= Max@opa;
ImageAdjust@Image3D[opa, ColorFunction -> "GrayOpacity"]

My question is if there are limitations for opacity in Image3D, and if so, are there ways around it?

  • $\begingroup$ In V9 I don't see the "alternating" effect $\endgroup$ – Dr. belisarius Oct 1 '14 at 16:13
  • $\begingroup$ This is what I get $\endgroup$ – Dr. belisarius Oct 1 '14 at 16:18
  • $\begingroup$ @belisarius I'm using V9 on OS X. Even if the banding is absent, the discrete color levels are undesirable, which I still see in your output. $\endgroup$ – Guillochon Oct 1 '14 at 17:14
  • $\begingroup$ There is a question somewhere about Opacity having a sharp cutoff (ie not being able to represent low gray values). Probably a hint that it's working with discrete values. $\endgroup$ – Dr. belisarius Oct 1 '14 at 17:25
  • $\begingroup$ I know that some volume renderers do only 256 discrete levels (IDL being an ancient example). I was hoping it was a global rendering option that perhaps was causing this. $\endgroup$ – Guillochon Oct 1 '14 at 17:33

Your understandig is not appropriate. You use cartesian coordinate and wonder why the result is not spherical. You remain on the cartesion grid and only assign each cube a spherical calculated value of a combined gray level with opacity.

The problem is not changed by

res = 10;
coords = Table[{Sqrt[i^2 + j^2 + k^2], ArcTan[k, Sqrt[i^2 + j^2]], 
    ArcTan[i, j]}, {i, -res, res}, {j, -res, res}, {k, -res, res}];
dists = Map[N@Norm[# - .5] &, coords[[All, All, All, 1]], {3}];
opa = 1/(dists + 0.3);
opa /= Max@opa;
ImageAdjust@Image3D[opa, ColorFunction -> "GrayOpacity"]

more spherical result

Some small turn and You see the cubes much clearer:

after a small turn.

res is not the right parameter to get the desired shading! The very same is in Your solution at work.

The documentation page for DelaunayMesh shows an example how to avoid cubic volume grids in Mathematica:

pts = RandomReal[{-1, 1}, {25, 3}];
Rsc = DelaunayMesh[pts];
HighlightMesh[Rsc, {Style[0, 
   Directive[PointSize[Medium], Black]], Style[2, Opacity[0.1]]}]

enter image description here

Your procedure path may be Delauney mesh spheres stacked in each other and assign the volumes of this mesh elements gray levels and opactiy. Then increase res again.

This guide list Solid Geometry what is in Mathematica. Cone has some samples how this looks on the basis of Cone and Circle in color.

Sphere show some example: Place Sphere instead of Cube. The main problem is that Mathematica visualizes surfaces instead of volumes by primitives. A volume is represented by the boundary and that is in 3D a surface. The professional term is tessalation. Boundaries are reprensented at most by Polygons. The shadings are achieved if desires by Your res parameter alike parameters. This relies on a scene graph like structure and that is it.

But as shown in Volume Mathematica has both MeshRegion and MeshBoundaryRegion. The built-in MeshPrimitives should suit Your question real hidden intent, but it does not of-the-shelf. Sphere meshing is problematic in Mathematica, surface-mesh-of-a-hemisphere. Have a look at this: draw-a-triangulated-sphere This answer how-to-discretize-a-sphere suggests

G = Geodesate[PolyhedronData["Icosahedron", "Faces"], 5] // N;

enter image description here as discrete closed accurate approximation of the Sphere. It is suitable for Your intent. Or more random: voronoi grid on a sphere.

Or use my full example and increase $res$ and optimize the left over parameters. So chose a different distribution with a sharper upper drop. For example Fermi or piecewise, step function and alike.

This is a counterexample:

 Graphics3D[{Opacity[a], Black, Specularity[White, 5], Sphere[]}, 
  Lighting -> "Neutral"], {a, 0, 1, 0.1}]

Opacity in action

This shows up clearly the concept of Mathematica Graphics3D and color and lighting and opacity. And it works. The Sphere is special and somewhat cheating the critical human eye. That is all. No second level or higher. The documentation of Specularity clearly state that Specularity does not work with flat 3D surface. You are making use of flat 3D surfaces.

Another example:

 Graphics3D[{Opacity[a], GrayLevel[.25], Specularity[White, 10], 
   Sphere[]}, Lighting -> "Neutral"], {a, 0, 1, 0.1}]

enter image description here

 Graphics3D[{Opacity[a], Glow[Black], White, Sphere[]}, 
  Lighting -> "Neutral"], {a, 0, 1, 0.1}]

enter image description here

DensityPlot[Exp[-.15/(x^2 + y^2)], {x, -1, 1}, {y, -1, 1}, 
 ColorFunction -> GrayLevel, Frame -> None]

enter image description here

  Exp[-.5/(x^2 + y^2 + z^2)], {x, y, z} \[Element] Ball[], 
  ColorFunction -> GrayLevel, 
  OpacityFunction -> Function[f, (1 - f)^2], Boxed -> False, 
  PlotPoints -> pp], {pp, {50, 75, 100}}]

enter image description here

The more plotpoints the smoother.

Or make use of the DensityPlot as a texture on the Sphere.

enter image description here

enter image description here

Make use of the image dimensions in the parameter set for ImageSize.

The great trick with Raster will help it further the last step.

  • 1
    $\begingroup$ The issue of discrete opacity still persists even without spherical elements. Try DensityPlot3D[Exp[-Abs[Max[x, y, z]]], {x, 0, 5}, {y, 0, 5}, {z, 0, 5}, OpacityFunction -> Function[f, f]] $\endgroup$ – Vsevolod A. Nov 29 '20 at 10:01
  • $\begingroup$ The first part was to answer the question as tight as possible and to go into details. DensitiyPlot make use of a rectangular grid too there is no real change. But that is for sure not the limit in Mathematica. $\endgroup$ – Steffen Jaeschke Dec 7 '20 at 21:16

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.