how to divide a 3D figure in matlab in to cubes and getting the cubes's addresses

Hi,

I need to write a code to divide a 3D figure in matlab in to cubes and getting the cubes's addresses, who can help me in this regard?

Best

[KSSV]

What the 3D figure is?

[nasim mirzavand]

sth like this figure

[Walter Roberson]

https://www.mathworks.com/matlabcentral/fileexchange/21044-3d-voxelizer

There are additional contributions if the input is a mesh or obj file

[nasim mirzavand]

Here is your suggested code but I am not sure how can I load my 3D matlab figure in this code, can anybody help me in this regard?

function importAOIJava(package)
% IMPORTAOIJAVA  imports Art of Illusion java functionalities.
%    IMPORTAOIJAVA Checks the java class path for the ArtoOfIllusion.jar file.
%       If the file is not included, it is added to the class path. This jar
%       file is required for all functions which use AOI java objects
%    IMPORTAOIJAVA(PACKAGE) Checks that the specified jar file is in the
%       class path. Package options are:
% 
%          base        ArtOfIllusion.jar
%          voxelizer   voxelizer.jar
% 
% See also JAVACLASSPATH, JAVAADDPATH
  % Set default value
  if nargin<1
    package = 'base';
  end
  % Select package
  if strcmpi(package, 'base')
    jarfile = 'ArtOfIllusion.jar';
  elseif strcmpi(package, 'voxelizer')
    jarfile = 'voxelizer.jar';
  end
  % Do import
  if ~ismember(jarfile, javaclasspath)
    javaaddpath(jarfile);
  end

[Walter Roberson]

Looking again, it appears that FEX contribution works on Wavefront .obj files.

What is the source of your data?

[nasim mirzavand]

I have a matlab 3Dfigure in a 3Dplot and I want to voxelize it.

[Walter Roberson]

It appears that https://github.com/alecjacobson/gptoolbox/blob/master/mesh/voxelize.m takes two parameters that would correspond to the Faces and Vertices of a patch() object.

Which plotting commands are you using to create the 3D plot? Are they patch objects?

[nasim mirzavand]

No, they are some 3D points.

[Walter Roberson]

How are you managing to draw the edges around the red layers if you are using scatter3() to draw the red points?

[nasim mirzavand]

This is my code to generate my 3 D plot of a dicmo file (radiation data), I just create the 3D contours and then fill them ( so I have a bunch of 3D slices) and I want to voxelize them.

% Step 1: Open the regions of interest file
B= dicominfo('C:\Users\mij\Music\RS.1.3.6.1.4.1.2452.6.3144839235.1145246484.2165573795.1001182548.dcm');

% Step 2: Start display
figure(1);
clf;
hold on;

% Step 3: Load number of regions of interest
roi = fieldnames(B.ROIContourSequence);
nroi= size(roi,1);

% Step 4: Loop over all regions of interest
for i=1:nroi
    % Step 4.1: Read the color of region of interest i
    color=(B.ROIContourSequence.(roi{i}).ROIDisplayColor)/255;
    
    % Step 4.2: Read the number of slices for region of interest i
    slices=fieldnames(B.ROIContourSequence.(roi{i}).ContourSequence);
    nslices=size(slices,1);
    
    % Step 4.3: Run over all the slices
    for j=1:nslices
        
        % Step 4.3.1: Find the number of points and their coordinates in
        % the current slice
        npoints=B.ROIContourSequence.(roi{i}).ContourSequence.(slices{j}).NumberOfContourPoints;
        points=B.ROIContourSequence.(roi{i}).ContourSequence.(slices{j}).ContourData;

        % Step 4.3.2: Convert single vector into 3D vector
        x=points(1:3:3*npoints);
        y=points(2:3:3*npoints);
        z=points(3:3:3*npoints);

      % Step 4.3.3: Plot the curve
       H=fill3([x',x(1)],[y',y(1)],[z',z(1)],'r');
        get(H)
        [o1, o2] = find(H(1,:,:) >0);
        set(H,'FaceColor',color)  
        axis off ;
   
    end

D=[x,y,z];
end

[Image Analyst]

Edit yoiur post and highlight the code and press the Code icon so we can copy and paste it into MATLAB.

[Walter Roberson]

fill3 creates patch objects. With a bit of preprocessing for efficiency, the Face and Vertex properties could be extracted and used as input to the github code.

[nasim mirzavand]

Thanks for your helps, would you mind please let me know how can I extract them , is there any kind of prewritten code for that purpose.

[Walter Roberson]

What is the purpose of that find() call?

Answer 1

[KSSV]

How about using this function? https://in.mathworks.com/matlabcentral/fileexchange/15161-plotcube

You can draw cubes by providing vertices and have index for each cube.

Answer 2

[Walter Roberson]

% Step 1: Open the regions of interest file
B= dicominfo('C:\Users\mij\Music\RS.1.3.6.1.4.1.2452.6.3144839235.1145246484.2165573795.1001182548.dcm');
% Step 2: Start display
figure(1);
clf;
hold on;
% Step 3: Load number of regions of interest
roi = fieldnames(B.ROIContourSequence);
nroi= size(roi,1);
roi_cell = cell(nroi, 1);

% Step 4: Loop over all regions of interest
for i=1:nroi
    % Step 4.1: Read the color of region of interest i
    color=(B.ROIContourSequence.(roi{i}).ROIDisplayColor)/255;
    
    % Step 4.2: Read the number of slices for region of interest i
    slices=fieldnames(B.ROIContourSequence.(roi{i}).ContourSequence);
    nslices=size(slices,1);
    patches_info_cell = cell(nslices, 3);
    % Step 4.3: Run over all the slices
    for j=1:nslices
        
        % Step 4.3.1: Find the number of points and their coordinates in
        % the current slice
        npoints=B.ROIContourSequence.(roi{i}).ContourSequence.(slices{j}).NumberOfContourPoints;
        points=B.ROIContourSequence.(roi{i}).ContourSequence.(slices{j}).ContourData;
        % Step 4.3.2: Convert single vector into 3D vector
        x=points(1:3:3*npoints);
        y=points(2:3:3*npoints);
        z=points(3:3:3*npoints);
      % Step 4.3.3: Plot the curve
       H = fill3([x',x(1)],[y',y(1)],[z',z(1)],'r');
       set(H,'FaceColor',color)  
       axis off ;
       patches_info_cell(j,:) = {length(H.Faces), H.Faces, H.Vertices};
    end
    roi_cell{i} = patches_cell;
end

all_roi = vertcat(roi_cell{:});

At this point, if I have written the code correctly, then all_roi will be a something-by-3 cell array of information about contours for slices. Column 1 of the cell will be a scalar indicating the number of vertices, N, in the line. Column 2 of the cell will contain a row vector of face information, and it appears likely that it will be 1 : number of vertices, but if there are duplicate points in your contours that might not hold. Column 3 of the cell will contain an N x 3 2D array of vertex locations.

In preparing the vertex information for the github function, you should unique-ify the vertex coordinates as failure to do so could prevent some of the loops from closing properly; you will need to keep track of the original order (third output of unique)

You cannot just slam all of the face information together into one face array

1. You need to renumber from local vertex numbers to over-all vertex numbers
2. The number of vertices might not be the same for all faces. To create a proper face array in which each row describes one face, the shorter arrays must be padded with nan. The length information I stored saves some post-processing to find that information in order to figure out how wide the final face array will have to be.