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how to Drawing 3d Voxel data

Asked by Itzik Ben Shabat on 4 Dec 2012

I want to draw voxels in 3d space (I have them stored in a 3d matrix). i used patch to do this (or voxel function from file exchange, draws every face of each voxel). here is my code

        function  PlotVoxelinput()
        clear all;
        clc;
      %PlotVoxelInput Summary of this function goes here
      %   Detailed explanation goes here
    voxel_init_loc=[0,0,0];
    voxel_loc=voxel_init_loc;
    voxel_size=[1,1,1];
    file='Other inputs/nucleon.raw';
    %file='Lev input/Model 128/bone_model_3061.raw';
    fileID=fopen(file);
    [A, count] = fread(fileID);
    m_hight=nthroot(count,3);
    m_width=nthroot(count,3);
    m_depth=nthroot(count,3);
    %set figure parameters
    xlim([0 m_hight]);
    ylim([0 m_width]);
    zlim([0 m_depth]);
    view(45,45);
    daspect([1 1 1])
    %get 3d data
    VoxelMat= multibandread(file,[m_hight,m_width,m_depth],'uint8',0,'bip','ieee-le');
    for i=1:m_hight
        for j=1:m_width
            for k=1:m_depth
                if VoxelMat(i,j,k)==1
                voxel(voxel_loc,voxel_size,'b',1)
                end
                voxel_loc=[voxel_loc(1),voxel_loc(2),voxel_loc(3)+1];
            end
            voxel_loc=[voxel_loc(1),voxel_loc(2)+1,voxel_init_loc(3)];
        end
        voxel_loc=[voxel_loc(1)+1,voxel_init_loc(2),voxel_init_loc(3)];
    end
    fclose(fileID);
    end

here is voxel function from file exchange

     function voxel(i,d,c,alpha);
      %VOXEL function to draw a 3-D voxel in a 3-D plot
      %
      %Usage
      %   voxel(start,size,color,alpha);
      %
      %   will draw a voxel at 'start' of size 'size' of color 'color' and
      %   transparency alpha (1 for opaque, 0 for transparent)
      %   Default size is 1
      %   Default color is blue
      %   Default alpha value is 1
      %
      %   start is a three element vector [x,y,z]
      %   size the a three element vector [dx,dy,dz]
      %   color is a character string to specify color 
      %       (type 'help plot' to see list of valid colors)
      %   
      %
      %   voxel([2 3 4],[1 2 3],'r',0.7);
      %   axis([0 10 0 10 0 10]);
      %
      %   Suresh Joel Apr 15,2003
      %           Updated Feb 25, 2004
      switch(nargin),
      case 0
          disp('Too few arguements for voxel');
          return;
      case 1
          l=1;    %default length of side of voxel is 1
          c='b';  %default color of voxel is blue
      case 2,
          c='b';
      case 3,
          alpha=1;
      case 4,
          %do nothing
      otherwise
          disp('Too many arguements for voxel');
      end;
      x=[i(1)+[0 0 0 0 d(1) d(1) d(1) d(1)]; ...
              i(2)+[0 0 d(2) d(2) 0 0 d(2) d(2)]; ...
              i(3)+[0 d(3) 0 d(3) 0 d(3) 0 d(3)]]';
      for n=1:3,
          if n==3,
              x=sortrows(x,[n,1]);
          else
              x=sortrows(x,[n n+1]);
          end;
          temp=x(3,:);
          x(3,:)=x(4,:);
          x(4,:)=temp;
          h=patch(x(1:4,1),x(1:4,2),x(1:4,3),c);
          set(h,'FaceAlpha',alpha);
          temp=x(7,:);
          x(7,:)=x(8,:);
          x(8,:)=temp;
          h=patch(x(5:8,1),x(5:8,2),x(5:8,3),c);
          set(h,'FaceAlpha',alpha);
      end;

The problem is that matlab crashes if i try to plot a 128X128X128 voxel file (only 2Mb). when i say crashes i mean its simply stuck. nothing happens and it seems most of my computer resources are trying to plot this I am pretty sure its not my pc thats the problem (i7, 8Gb RAM, bench results: 0.2806 0.2195 0.1979 0.2687 0.6053 0.6086). anyone know how can i plot these voxels?

2 Comments

Walter Roberson on 4 Dec 2012

How much of the matrix is occupied? e.g., what is sum(VoxelMat(:)) ?

If everything was occupied you would be trying to draw two million patches, which would drag down MATLAB graphics for sure.

Itzik Ben Shabat on 4 Dec 2012

well its not sparse, pretty dense actually. so is there a way to overcome this? a different function maybe?

Itzik Ben Shabat

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1 Answer

Answer by Walter Roberson on 4 Dec 2012
Accepted answer

See the Faces and Vertices properties of patch() at http://www.mathworks.com/help/matlab/ref/patch_props.html

That is, instead of creating one patch per voxel, create one (or more) patches that has face and vertex information appropriate for a number of voxels. The voxels do not need to be adjacent to each other. You do not need to construct a left-face if the left voxel is set, not create a bottom face if the bottom voxel is set, not create a front face if the voxel in front is set.

It might be a bit much to create a single patch with all of the voxel information. One patch per slice might be better.

Are you sure you want to create all of this at once?? You are using alpha = 1 for all patches, so it is not possible to see through any face to any detail below, so usually for graphics purpose it is only worth creating the voxels that would be on the "outside" from the line of sight. You might want to set all of the "outside" at once so that you can rotate without recalculating. If your thought was to allow zooming in to the object to see interior detail, then instead of calculating everything at once, please consider using the zoom PreAction or PostAction callback to determine what the new coordinates will be, and calculate what will be visible from the new view and create the patches for that. It is perfectly acceptable for zoom (or pan) callbacks to change the graphics object that are visible, adding or removing, so as to provide only the relevant information.

5 Comments

Itzik Ben Shabat on 4 Dec 2012

i think you are mistaken regarding voxel(). it plots 6 faces for each filled pixel (2 at a time - top&bottom, front&back, right&left). i dont understand what you meant regarding plotting only 1 patch per voxel (what if the voxel is in the corner of the volume ? i have to plot a minimum of 3 patches).

regardless your answer has pointed me in the right direction. i have already written a code to identify which voxels are external (no big improvement), now im writing a code to detect which faces are external and i will only plot them. if this still fails to work, i guess i cant avoid moving to c and opengl which should be faster. thanks for all the help.

Walter Roberson on 5 Dec 2012

You are right, voxel() does use 6 patches per voxel, even worse than the 2 I had noticed before.

When you patch(), even if you use the simple call which lists only vertices in order, you can create more than one visual area. You can insert NaN to indicate a discontinuous jump. So for example, you could have the x coordinates

[x000 x001 x001 x000 x000 nan x225 x226 x226 x225 x225]

to define two disconnected squares.

When you define a patch() object in terms of vertices and faces, you can work even more directly, defining a list of vertices and then using their index numbers to define the faces, any reasonable number of faces at a time. This should translate pretty directly into opengl calls in the graphics driver.

Itzik Ben Shabat on 5 Dec 2012

got it. i improved the code like you said (attached below for anyone who will ever search for this), calling patch() only once for each voxel(but still drawing 6 faces). this improved the speed tremendously! now im working on drawing only the external faces. Thanks for all the help! :)

function  [ExternalIndexes]=PlotVoxelinput()
clear all;
clc;
%PlotVoxelInput opens a RAW voxel file and plots it. 
%   
voxel_init_loc=[0,0,0];
voxel_loc=voxel_init_loc;
voxel_size=[1,1,1];
%file='Other inputs/nucleon.raw';
file='Lev input/Model 128/bone_model_3061.raw';
fileID=fopen(file);
[A, count] = fread(fileID);
m_hight=nthroot(count,3);
m_width=nthroot(count,3);
m_depth=nthroot(count,3);
%set figure parameters
xlim([0 m_hight]);
ylim([0 m_width]);
zlim([0 m_depth]);
view(45,45);
daspect([1 1 1])
%get 3d data
VoxelMat= multibandread(file,[m_hight,m_width,m_depth],'uint8',0,'bip','ieee-be');
%detect the external voxels
[ExternalIndexes,ExtenalNum]=FindExternalVoxels(VoxelMat);
%plot only external voxels
for i=1:ExtenalNum
    FV.vertices=[ExternalIndexes(i,1)+[0 voxel_size(1) voxel_size(1) 0 0 voxel_size(1) voxel_size(1) 0]; ...
       ExternalIndexes(i,2)+[0 0 0 0 voxel_size(2) voxel_size(2) voxel_size(2) voxel_size(2)]; ...
        ExternalIndexes(i,3)+[0 0 voxel_size(3) voxel_size(3) 0 0 voxel_size(3) voxel_size(3)]]';
    FV.faces=[1 2 3 4; 2 6 7 3 ; 6 5 8 7; 5 1 4 8; 4 3 7 8 ; 1 2 6 5];
   patch(FV,'FaceColor','r');
end
fclose(fileID);
end
Walter Roberson

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