Depth color coding using Volumeviewer/ Volshow

Hi,

I am uisng the below script to display focal stacks in 3D. May I know how to include colormap for depth?

filePattern = fullfile(fileFolder, '*.png');
all_images = dir(filePattern);
I = imread(all_images(1).name);
I= rgb2ind(I,256);
W=365;
H=365;
D = numel(all_tiff);
stack = zeros(W,H,D);
stack(:,:,1) = first_image;
for i = 2:D
   II =  imread(all_tiff(i).name);
   II = rgb2ind(II,256);
   stack(:,:,i) = II;
end
volumeViewer(stack);

I also tried below tutorial which involves Volshow(), However I got the below shown graphics error while running

Error using images.ui.graphics3d.Volume/validateData
Expected input to be finite.

Error in images.ui.graphics3d.Volume/setData

Error in images.ui.graphics3d.GraphicsContainer/set.Data

Error in images.ui.graphics3d.internal.AbstractContainer/set

Error in images.ui.graphics3d.GraphicsContainer

Error in images.ui.graphics3d.Volume

Error in volshow (line 32)
        hVolume = images.ui.graphics3d.Volume(viewer, 'Data', V, remainingInputs{:});

Error in depthVolumeColorCoder (line 83)
V = volshow(arr,...

clear; close all; clc;
%% Display Grayscale Spiral
%set colormap to use for depth coding
colormap = hsv;
%load data from MATLAB
load('spiralVol.mat');
vol = spiralVol;
%display grayscale volume
volshow(vol)
%snap pic of the grayscale volume for publishing 
snapnow
close;
%% Display Color Coded Spiral 
%colorcode the spiral
depthVolumeColorCoder(vol,colormap)

[Walter Roberson]

Test with

nnz(isnan(vol))
nnz(vol == inf)
nnz(vol == -inf)

[MechenG]

Hi @Walter Roberson,

Thanks for the suggestion. Unfortunately, it didn't solve the issue. I am getting the same error.. Here is the tutorial (https://uk.mathworks.com/matlabcentral/fileexchange/92208-depth-volume-color-coder) I have tried out.

[Walter Roberson]

Did all three lines return 0?

Answer 1

[Gayathri]

Hi @MechenG,

To view the volume with the colormap, please use the following lines of code

clear; close all; clc;
%% Display Grayscale Spiral
%set colormap to use for depth coding
colormap = hsv;
%load data from MATLAB
load('spiralVol.mat');
vol = spiralVol;
%display grayscale volume
volshow(vol,Colormap=colormap)

I hope this is your expectation. Let me know if you need something more!

Please refer to the below example, which illustrates the usage of 'volshow' funtion with 'Colormap' argument.

openExample('images/VisualizeVolumeOfMRIDataExample')

[MechenG]

Thank you very much! It's working now.