Get a suitable color scale in Image3D?

Questions
1

I’m attempting to do some image processing on electron beam simulation results. Specifically I’m trying to visualize the dose profile from a 100x100x100 rectangular mesh.

Creating contour plots for any slice of the cube was simple, but when I try to use Image3D on the data I get one solid color for nearly every non-zero data point no matter how much I fiddle with the opacity and color function options.

Any suggestions on what to do? I’ve attached a contour slice and my image 3d attempt (temperature map color scheme).

dose_slice_2.png
dose_slice_2.png482×477 77.6 KB

dose_3d.jpg
dose_3d.jpg447×487 30.6 KB

2

Hi,

to answer your question, people might need some additional info. What is the data like and what code did you use. I can easily create 3D data and plot it in more than one colour:

data = RandomReal[1, {10, 10, 10}];
Image3D[data, ColorFunction -> "TemperatureMap"]

ScreenShot2016-06-19at20.32.43.png
ScreenShot2016-06-19at20.32.43.png760×732 22.2 KB

What function did you use? I am quite sure you did not use Image3D which in fact appears to be quite useless in the context you describe, but it would be helpful to get some more info on what you’ve tried.

Cheers,

M.

3

I’m using the MCNP transport code to create the data. I’m using mathematica to analyze it.
In my case I used MCNP to track 100 keV electrons through a material and score the energy deposited in each cell. My primary goal was to find the isodose curves at any slice of the data set, which I was able to do. I was hoping to find some interesting results with image3d and was greeted with a red blob.

As far as what the data is like? I’m not sure if I understand your question. Could you be specific? The data is pretty much equivalent to any study on electron beams, so I can only refer you to those. Here’s one that shows electron tracks.
https://www.researchgate.net/publication/269112923_YW-PolymerPhysics-2013/figures?lo=1

My exact mathematica code I used to create the plots are:

Manipulate[
ListContourPlot[totaldose[[1 ;; 100, 1 ;; 100, m]], PlotRange → All,
Contours → 40, ColorFunction → “TemperatureMap”], {m, 1, 100, 1}]

logged = Table[Table[Table[
If[
totaldose[[i, j, k]] == 0,
0,
Log10[totaldose[[i, j, k]]]
]
, {i, 1, 100}], {j, 1, 100}], {k, 1, 100}]

Image3D[logged]

“totaldose” is my data set. I created the “logged” term because I wasn’t sure if the issue was the huge difference in minimum and maximum values (from 10 to 10^7). It didn’t seem to matter because the results were essentially identical as if I had just used “totaldose” with image3d. I tried using the slider options on the image to adjust my output. I’m not familiar with image3d.

4

Hi,

without data it is hard to tell what the problem is - so Marcos answer has some background. To have a hopefully appropriate example at hand I created a 3D array of data describing a 3D dose distribution of a 15MeV electron beam in water. Then I get:

9269dose3D.jpg
9269dose3D.jpg576×1442 117 KB

(Code and data come as an attachment.) I basically want to communicate that if Image3D does not work for you, then you can use the nice functions ListSliceDensityPlot3D, ListSliceContourPlot3D and friends.

BTW: A simple way to apply a function to the values of a multidimensional array is e.g.:

Attributes[logScale] = Listable;
logScale[dose_] := Piecewise[{{0, dose < 0.001}}, Log[1. + dose]]

logDose3D = logScale[dose3D];

Regards – Henrik

5

Dear Henrik
I have a one .txt file with 4 columns (not .mx file) i want to plot my data same as your plotting. with Image3D and ListSliceCountorPlot3D. can you help me more. the files size is more than 20 MB and i could not attached it.( my mesh cells are 100 (x) *100 (y) * 200 (z) ). The data with 4 columns and 2000,000 rows.

Best regards

Saeid

6

Dear Saeid,

to give an unspecific answer to your unspecific question: To begin with I would try to create a 3D array from your data. To be able to give more help, one needs at least a small but representative sample of your data.

Regards – Henrik

7

Dear Saeid,

to give an unspecific answer to your unspecific question: To begin with I would try to create a 3D array from your data. To be able to give more help, one needs at least a small but representative sample of your data.

Regards – Henrik

8

Dear Henrik, Thank you very much

yes, I attached the example data with 5050200 pixels.

Best regards

9

Dear Saeid,

the first three rows of your data appear to be the coordinates and are Integers - excellent! (This is why I wished to see a sample!) Try this:

ClearAll["Global`*"]

textData = Import[" < your file > ", "Table"];
(* dimenstions taken from the last row: *)
dims = Most[Last@textData] + 1
(* generate empty array: *)
data3D = ConstantArray[0, dims];
(* values are filled in: *)    
Set[data3D[[#1 + 1, #2 + 1, #3 + 1]], #4] & @@@ textData;

Attributes[logScale] = Listable;
logScale[data_] := Piecewise[{{0, data < 0.001}}, Log[1. + data]];

logData3D = logScale[data3D];

Now you can do e.g.:

Saeid.png
Saeid.png638×687 62.6 KB

Regards – Henrik
[1]: http://community.wolfram.com//c/portal/getImageAttachment?filename=Saeid.png&userId=32203

10

Dear Henrik

Thanks a lot for your fast reply and very useful help!

Best wishes