label2rgb problem: 4D to avi cdata

Hello Matlab, I am now working on presenting bwlabeled stacks (image sequences)as avi movies. I have some code which converts the series into a format which is usable. I am using the label2rgb3d function from the exchange in my code, since I want to label every labeled object in 3d (using bwlabeln) as its own color. Normally, label2rgb only works on 2d images or arrays, and I have objects which are living in Z as well as X and Y.

When I try to send to images to frame (im2frame) I get this error returned:

im2frame
Movie cdata must have 2 or 3 dimensions.

I understand matlabs's shortcomings to 4d data handling,yet is there a way to take labeled, colored objects into a movie?

Is there a way label2rgb can be told that objects in 3d are to be labeled the same color?

Thanks

Here is a link to the label2rgb3d function: http://www.mathworks.com/matlabcentral/fileexchange/8355-label2rgb3d

Answer 1

[Sean de Wolski]

I'm able to get an RGB movie of a labeled rgb image volume using this:

movie2avi(immovie(V),'Test1'); %to write the movie (V is the volume)

The function I just wrote to get V is below. It accepts a CC struct, not a label image. If you want to get your label image into a CC struct you can either call bwconncomp directly or use my FEX:label2CC

function X = CC2RGB3(CC,cdata)
%Function to take a three dimensional CC struct and turn it into a 4D rgb volume
%SCd - 07/07/2011
%
%Usage: CC2RGB3(CC)
%       CC2RGB3(CC,cdata)
%
%Input Arguments:
%   -CC: output from bwconncomp of a 3d binary image
%   -cdata: optional nx3 colormap where each row is the uint8 RGB color to be used
%
%Output Arguments:
%   X: 4-dimensional RGB image
%
%See Also: bwconncomp bwlabeln colormap
%

    %Error checking:
    assert(nargin==1||nargin==2,'One or Two input arguments expected');
    assert(isstruct(CC),'The first input argument, CC, is expected to be a struct');
assert(all(ismember({'ImageSize','NumObjects','Connectivity','PixelIdxList'},fieldnames(CC))),'CC is expected to be the output of bwconncomp');
    assert(length(CC.ImageSize)==3,'The volume creating CC was expected to by 3-d');

    %Take care of cdata:
    if nargin == 1;
        cdata = makeCdata(CC.NumObjects);
    elseif size(cdata,2)~=3
        warning('Not:nx3','cdata is expected to be nx3; random will be used');
        cdata = makeCdata(CC.NumObjects);
    elseif size(cdata,1)<CC.NumObjects
        warning('Too:Short','cdata not big enough; random will be used');
        cdata = makeCdata(CC.NumObjects);
    end

    %Make Volume:
    szX = [CC.ImageSize(1),CC.ImageSize(2),3,CC.ImageSize(3)];
    X = zeros(szX,'uint8');

    %Engine:
    for ii = 1:CC.NumObjects
        [r c p2] = ind2sub(CC.ImageSize,CC.PixelIdxList{ii}); %probably could be vectorized
        rgb_idx = repmat(1:3,size(r,1),1);
        idxr = sub2ind(szX, r, c, rgb_idx(:,1), p2);
        X(idxr) = cdata(ii,1);
        idxg = sub2ind(szX, r, c, rgb_idx(:,2), p2);
        X(idxg) = cdata(ii,2);
        idxb = sub2ind(szX, r, c, rgb_idx(:,3), p2);
        X(idxb) = cdata(ii,3);
    end  
end    
function cdata = makeCdata(n)
    for ii = 1:10 %try 10x then accept duplicates
        cdata = uint8(rand(n,3)*255);
        if size(unique(cdata,'rows'),1) == n
            break;
        end 
    end
end

[D]

Thanks, I tried running it, but I get this error returned:

?? Error using ==> checkDisplayRange at 22

HIGH must be greater than LOW.

Error in ==> imageDisplayParseInputs at 215

common_args.DisplayRange =

checkDisplayRange(common_args.DisplayRange,mfilename);

Error in ==> imshow at 173

[common_args,specific_args] = ...

Error in ==> immovie at 56

imshow(X(:,:,:,k),map);

That data converts fine, using bwlableln->label2CC->CC2RGB3 or bwlabeln->label2RGB3. Either way I end up with a 4D double or 4D struct. I just cant get it to an avi. (Which might actually be impossible).

[Sean de Wolski]

It's not impossible seeing as how I did it yesterday with a sample volume.

Does this work?

I = rand(100,100,100)>.8;

CC = bwconncomp(I);

V = CC2RGB3(CC);

movie2avi(immovie(V),'Test1');

?

[D]

Yes, I get a single frame.

[Sean de Wolski]

if you open the avi file outside of MATLAB - it's a single frame? What version of ML are you using and what OS? Is the single frame color?

[D]

It works outside of Matlab. I have ML 7.5.0 (R2007b). WindowsXP-64.

[D]

It is in color as well.

[Sean de Wolski]

Then what is the issue?

[D]

I resolved the issue, it was the data structured from previous operations, thank you again. I owe you a beer.