how to Drawing 3d Voxel data

Question

Itzik Ben Shabat 2012-12-4

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https://ww2.mathworks.cn/matlabcentral/answers/55633-how-to-drawing-3d-voxel-data

评论： M.S. Khan 2020-8-30

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?

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Walter Roberson 2012-12-4

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 2012-12-4

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

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Answer 1

Walter Roberson 2012-12-4

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/55633-how-to-drawing-3d-voxel-data#answer_67439

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.

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Itzik Ben Shabat 2012-12-5

在 MATLAB Online 中打开

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

Mehmet Mutlu 2017-1-19

编辑：Mehmet Mutlu 2017-1-19

在 MATLAB Online 中打开

This single improvement is indeed much faster. Thanks a lot. Drawing only external ones should accelerate further. If someone wants to replace voxel.m from filexchange:

function voxel_improved(i,d,c,alpha)
%VOXEL function to draw a 3-D voxel in a 3-D plot
%Usage
%   voxel_improved(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_improved([2 3 4],[1 2 3],'r',0.7);
%   Based on Suresh Joel Apr 15,2003 and Itzik's answer
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;
FV.vertices=[i(1)+[0 d(1) d(1) 0 0 d(1) d(1) 0]; ...
        i(2)+[0 0 0 0 d(2) d(2) d(2) d(2)]; ...
        i(3)+[0 0 d(3) d(3) 0 0 d(3) d(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',c,'FaceAlpha',alpha);
end

Itzik Ben Shabat 2019-5-10

If I understand correctly, this error usually occure when you assign a functions output to more variables than it actually outputs. So, in this case, voxel_impoved does not return any value so make sure you did not assign it to anything.

Regardless, for plotting voxels I have this file exchange entry that may be usefull:

https://www.mathworks.com/matlabcentral/fileexchange/50802-voxelplotter

Walter Roberson 2019-5-10

Please show the complete error message, showing which line the error is occuring on, and the code for that line.

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Answer 2

Badreddine Alane 2019-5-12

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what im doing exactly is that i I have a matrix(i extracted it from 3d point cloud) with 3 columns (x, y and z coordinates) and 41472 lines. So, each line represents one point in a volume .i want to plot a voxel for this point cloud from this matrix, but i think it's not what i should give as an input for the voxel_impoved.(i have tried to draw a voxel for each point,and also tried it for the fulll matrix ) .it's first time for me working on the voxel form, hope someone will help .

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Walter Roberson 2019-5-12

You can use discretize() on the X, Y, and Z coordinate separately. Then you can accumarray() to generate the volume. (If you were working in 2D you could sparse() instead.)

This presumes that each coordinate triple can be approximated by the cuboid it falls into, which should typically be acceptable for a point cloud.

M.S. Khan 2020-8-30

i have used it but it tell that memory is out range

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Answer 3

Badreddine Alane 2019-5-13

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编辑：Badreddine Alane 2019-5-13

so if i understand your answers, my first task is that i have to voxleize the point cloud ?; and if it's can you please guide me how can i voxleize a point cloud

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Walter Roberson 2019-5-16

在 MATLAB Online 中打开

x_edges_go_here might be something like

dx = 0.01;
minx = min(x);
maxx = max(x);
first_x = floor(minx / dx) * dx;
last_x = ceil(maxx / dx) * dx;
x_edges_go_here = first_x : dx : last_x;

M.S. Khan 2020-8-30

Hi Walter. its good but tell me why you took dx =0.01. how if i took dx=0.0001

please guide me. i also want to use voxel to measure volume.

regards,

M.shafiq

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Answer 4

Badreddine Alane 2019-5-21

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https://ww2.mathworks.cn/matlabcentral/answers/55633-how-to-drawing-3d-voxel-data#answer_376013

thank you so much for your help

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