3d patches from a 3d matrix

Question

I have a 3d matrix (3x3x3) and I need to extract a 3d patch (2x2x2) and convert them to vectors.

In 2d, just:

I=randi(5,3,3);

2d_patches=im2col(I,[2 2],'sliding');

How about 3d?

I=randi(5,3,3,3);

3d_patches= ???

im2col only works in 2d. In 3d I have to recombine vectors 1 and 7 , 2 and 8 , ... Is there any quick function for this task?

Answer 1

I do not think there is a built-in way to do this. If you need this to be fast, it should be pretty simple to write your own mex function in c and call it from Matlab.

Here is my (quick and dirty) solution:

im3col.c:

 #include <mex.h> void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) { const mxArray *I = prhs[0]; double *indata = mxGetPr(I); double *patchSize = mxGetPr(prhs[1]); const int *size = mxGetDimensions(I); int J = (int)patchSize[0], K = (int)patchSize[1], H = (int)patchSize[2]; int M = size[0], N = size[1], P = size[2]; int numPatches = (M - J + 1)*(N - K + 1)*(P - H + 1); int out_rows = J*K*H, out_cols = numPatches; mxArray *out = mxCreateDoubleMatrix( out_rows, out_cols, mxREAL ); double *outdata = mxGetPr(out); int patch = 0; for( int h_offset = 0; h_offset < P-H+1; h_offset++ ){ for( int k_offset = 0; k_offset < N-K+1; k_offset++ ){ for( int j_offset = 0; j_offset < M-J+1; j_offset++ ){ int row = 0; for( int h = 0; h < H; h++ ){ for( int k = 0; k < K; k++ ){ for( int j = 0; j < J; j++ ){ outdata[patch*out_rows + row] = indata[ (j_offset+j) + (k_offset+k)*M + (h_offset+h)*M*N ]; ++row; }}} ++patch; }}} plhs[0] = out; } 

Compile:

 >> mex -O CFLAGS="\$CFLAGS -std=c99 -Wall" im3col.c 

Test:

 >> A(:,:,1) = [1,4,7;2,5,8;3,6,9]; A(:,:,2) = [10,13,16;11,14,17;12,15,18]; >> B = im3col(A, [2,2,1]) B = 1 2 4 5 10 11 13 14 2 3 5 6 11 12 14 15 4 5 7 8 13 14 16 17 5 6 8 9 14 15 17 18 >> A(:,:,1),A(:,:,2) ans = 1 4 7 2 5 8 3 6 9 ans = 10 13 16 11 14 17 12 15 18 

Answer 2

Here's another direction: (This is a pretty slow and definitely faster way)

 function [img] = patch2im_2d_time(patch, size_img, size_patch, size_skip, border) Nx = size_img(1); Ny = size_img(2); Nt = size_img(5); psz1 = size_patch(1); psz2 = size_patch(2); psz3 = size_patch(3); %Extract blocks. One could save a lot here. patches = reshape(patch, [psz1 psz2 psz3 size(patch,2)]); c = 1; img2 = zeros(squeeze(size_img)); %Count for each pixel how many times we added smth to it. add_count = zeros(size_img); %The first three loops, loop through all the pixels in the image for d=1:Nt-psz3+1 for j=1:Nx-psz2+1 for i=1:Ny-psz1+1 %Here we get the next patch. The next patch is always %the patch that has the pixel at i,j,d at its top front corner. current_patch = patches(:,:,:,c); %counter for the next patch c = c + 1; %In this loop we add the patch values of each pixel in the %patch to the image. i,j,d is the base. We add the offset %ii jj and dd to it. This iteration takes psz^3 many %iterations. for dd=1:psz3 for ii=1:psz2 for jj=1:psz1 img2(i+ii-1,j+jj-1,d+dd-1) = img2(i+ii-1,j+jj-1,d+dd-1) + current_patch(ii,jj,dd); add_count(i+ii-1,j+jj-1,d+dd-1) = add_count(i+ii-1,j+jj-1,d+dd-1) + 1; end end end end end end img = flipud(rot90(img2 ./ add_count,1)); end 

Remember that MATLAB uses col major.

Answer 3

 %One possible way to use matlab to call im2col and reshape twice %N = [row, col, num_frames] [x_height, ~, num_frames] = size(N); patchSize = 16; patchTemporal = 10; N = reshape(N, x_height, []); N = im2col(N, [patchSize, patchSize], 'distinct'); N = reshape(N, [], num_frames); N = im2col(N, [patchSize^2, patchTemporal], 'distinct'); % N = [patchSize^2 *patchTemporal x numPatches] 

Answer 4

Hi guys, how about this solution. To get a 3x3x3 profitability, I suggest:

 blkSize=3; % should be a odd value like 3,5,7,etc r=floor(blkSize/2); k=1; for sliceNo=(r+1):(size(I,3)-r) img= I(:,:,sliceNo-r:sliceNo+r); noPix=(size(img,1)-2*r)*(size(img,2)-2*r); neiblk=zeros(blkSize^3,noPix); for blk=1:blkSize neiblk(blkSize^2*(blk-1)+1:blkSize^2*blk,:)=im2col(img(:,:,blk),... [blkSize,blkSize],'sliding'); end ROIs(:,noPix*(k-1)+1:noPix*k)=neiblk; k=k+1; end