Stitching sub images to reconstruct full image

Question

Jason 2015-1-13

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回答： KHOR WEI KOK 2016-9-2

I have subdivided an image into 4x4 tiles and produced a subimage and obtained a binary imaged. I add each of these binary images to a binary stack using a loop.

After the loop, how do I reconstruct/stitch the sub binary images back to the full image size, so I can create a binary image representing the while raw image so to use as a mask:

My binary sub images are expressed as :

BI(:,:,i) %where i is 1:16 as I'm using 4x4 tiles

This is my approach that isn't working:

%Now combine binary images so to create regions to act as mask on original
%image
size(BI)   %Confirm there are 16 planes of images in the binarystack
Binary=[]; %Create empty Binary Image that will hold reconstructed sub images 
ct=0;  %counter
for jj=1:tiles
  for ii=1:tiles  
      ii
      jj
      ct=ct+1
      startingCols(jj)
      startingRows(ii)
    Binary(startingCols(ii):endingCols(ii), startingRows(jj):endingRows(jj))=BI(:,:,ct);
    figure(2)
    subplot(4,4,ct)
    imshow(BI(:,:,ct),[0,1])
    Binary=BI; 
    end
  end

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Answer 1

Mohammad Abouali 2015-1-14

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编辑：Mohammad Abouali 2015-1-14

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Again, why don't you use blockproc()? :D

what you are asking, i.e. stitching the sub images into one big one, can be done in a single command using blockproc() as follows:

Binary=blockproc( reshape(1:16,4,4)', [1,1], @(x) BI(:,:,x.data) );

where Binary contains all the sub images placed in the order you show in the figure. 16 sub images are not much but if there were more you can even do this in parallel as easily as:

Binary =blockproc( reshape(1:16,4,4)', [1,1], @(x) BI(:,:,x.data), 'UseParallel',true);

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Mohammad Abouali 2015-1-14

编辑：Mohammad Abouali 2015-1-14

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If your sub images, i.e. BI, is of size 25x25x16 then of course when you put them back together in a 4x4 tiles you would get 100x100 pixels and not 101x101. If your original image before processing was 101x101 and after tiling it and processing it you ended up with 16 tiles of 25x25 then pretty much you have dropped one row and column.

I can suggest two approaches:

Approach 1 based on what you have and the codes that you posted I think you are dropping the last raw and column of the original image. Therefore, that row and column is not being processed as part of your tile. then you have two options:

Approach1, Option 1 Let say OrigImage is your original image with size 101x101. Then you tile it into BI with size 25x25x16. You can stitch BI back using the command I gave you above:

Binary=blockproc( reshape(1:16,4,4)', [1,1], @(x) BI(:,:,x.data) );

Binary would be 100x100. Then to compare it with original image resize your original image as follow

OrigImage=OrigImage(1:end-1,1:end=1);

The above command drops the last row and column from your original image and makes it 100x100, now both Binary and OrigImage have the same size.

Approach1, Option 2 This is the same as previous option, but instead you resize the binary to make it 101x101. Here is what you should do:

% stitch the tiles
Binary=blockproc( reshape(1:16,4,4)', [1,1], @(x) BI(:,:,x.data) );
% resize Binary
Binary=imresize(Binary,[101,101],'nearest');

Now both Binary and OrigImage are 101x101.

Approach 2 The second approach is to go back and fix the tiling; so that you don't drop a row and a column from the image. I really suggest that you use blockproc and then you won't have any of these problems.

Let's say you have combined all the processing that you need to do on a tile in a function called myOperation.m. Therefore you have

BI(:,:,1)=myOperation(Tile1);
BI(:,:,2)=myOperation(Tile2);
... 
BI(:,:,16)=myOperation(Tile16); of course you do this in a loop.

This means that you need to divide the original image into Tiles (tile 1 to tile 16. then you need to stitch BI back into one image.

If you have such function then you can use blockprock as follow:

Binary=blockproc(OrigImage,[tileRowSize, tileColSize],@(x) myOperation(x.data));

Note that the above command does not requires the origimage to be divided in tile. and note that you won't get the BIs but you would get directly the stitched image.

In this approach you just have to make sure that myOperation should be able to work on variable sized tiles.

Mohammad Abouali 2015-1-14

编辑：Mohammad Abouali 2015-1-14

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If you are just thresholding using graythresh you can write your blockproc like this

Binary=blockproc(OrigImage,[25,25],@(x) (im2bw(x.data,graythresh(x.data(:)))) )

That would threshold your image using Otsu's method and it is not global, the threshold is decided on each 25x25 tile separately. You don't need to divide the image into tiles, you don't need to spend time stitching them back.

Another approach is to use the function that ImageAnalyst told you.

Jason 2015-1-14

Thankyou very much

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Answer 2

Iain 2015-1-13

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depending how you've done it....

 BInew = permute(BI,[1 3 2]);
 BInew = reshape(BInew,16*size(BI,1),[]);

ought to work.

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Iain 2015-1-13

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You'd need to change the reshapes, not the permute. You've got 16 tiles though.... (4 x 4)

 BInew = reshape(BI,[25 25 tileshigh tileswide]);
 BInew = permute(BInew,[1 3 2 4]);
 BInew = reshape(BInew, 25*tileshigh, [])

Jason 2015-1-14

Thankyou

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Answer 3

Image Analyst 2015-1-13

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Why bother saying this:

Binary(startingCols(ii):endingCols(ii), startingRows(jj):endingRows(jj))=BI(:,:,ct);

if you're just going to say this

Binary=BI;

three lines later? Not only that, but you switched rows and columns. The first index should be rows, not columns as you have it, and the second index should be columns, not rows as you have it.

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Image Analyst 2015-1-13

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Jason's reply moved from an Answer to here:

I think I have identified the problem (not sur ehow to fix it): the definition of the start and end points for the grid to split up the image (in this case into 4x4 subimages , as per I.A help is:

[rows,cols]=size(ROI) % ROI is my Image
tiles = 4  % Number of tiles or chunks you want it divide up into.
% Find out where the dividing lines are.  This may be a fractional value.
startingRows = linspace(1, rows, tiles+1);
startingCols = linspace(1, cols, tiles+1);
% Now get the starting integer rows / cols.
startingRows = int32(startingRows(1:end-1))
startingCols = int32(startingCols(1:end-1))
% Get the ending rows.
endingRows = [startingRows(2:end)-1, rows]
endingCols = [startingCols(2:end)-1, cols]
%Determine number of pixels in each tile;
nx=endingRows(1)-startingRows(1);
ny=endingCols(1)-startingCols(1);

If I look at the output of the end points, the last entry should be 100 and not 101? (My raw image size is 101 x 101.

endingRows =
            25          50          75         101
endingCols =
            25          50          75         101

Jason 2015-1-13

编辑：Jason 2015-1-13

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This is my code for stacking the subimages into the 3rd dimension (i.e. an image stack)

tiles=4;    %image chunks
nimages=tiles*tiles
%Determine number of pixels in each tile;
nx=endingRows(1)-startingRows(1);
ny=endingCols(1)-startingCols(1);
 %Initialise Image and binary stack (IM)
IM=[]; %Initialise Image stack array 
BI=[]; %Initialise Binary array
subplot(2,4,[1,2,5,6])
hold on
ct=0;    %counter
for j=1:tiles
   for i=1:tiles 
    ct=ct+1;
    %Plot tile boundary lines on raw image
    plot([startingRows(i),startingRows(i)],[0,cols],'y-');  %plot tile lines
    plot([0,rows],[startingCols(i),startingCols(i)],'y-');  %plot tile lines
      %Add region number
      xr=double(floor(endingCols(i)-ny/2));
      yr=double(floor(endingRows(j)-nx/2));
      text(xr,yr,num2str(ct),'FontSize', 20, 'Color', [0 1 0]);
      %Divide Image into tiles
      IM1=imcrop(ROI,[startingRows(i) startingCols(j) nx ny ]);
      [thresh1, thresh2] = Threshold(hObject, eventdata, handles,IM1);
      %Create Binary Image
      ix=IM1;
      level=thresh2;
      ix(ix<level)=0;
      ix(ix>level+1)=1;
      BI1=ix;
      %Concatenate to image stack
      IM=cat(3,IM,IM1);   %add along 3rd dimension
      BI=cat(3,BI,BI1);   %create binary image stack
     end; 
  end
  hold off;

Image Analyst 2015-1-14

See attached blockproc demos. And don't forget to look at Mohammad's last comment under his answer.

Jason 2015-1-14

Thankyou

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Answer 4

Jason 2015-1-13

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Why does this approach not work:

ct=0;
for ii=1:4
 for jj=1:4
   ct=ct+1
   Binary(startingCols(jj):endingCols(jj), startingRows(ii):endingRows(ii))=BI(:,:,ct);
 end
end

imshow(Binary,[0,1])

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Iain 2015-1-13

That should work provided you calculate startingcols etc. correctly.

Image Analyst 2015-1-13

The first index should be rows, not columns as you have it, and the second index should be columns, not rows as you have it.

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Answer 5

Alessandro Masullo 2015-1-13

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What about using mat2cell and cell2mat? It should be much easier.

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Jason 2015-1-13

Hi, I don't see how this can reconstruct a full image from the subimages

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Answer 6

Jason 2015-1-14

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I've managed to get a solution where I first have to crop the image to ensure there number of pixels corresponding to integer tiling: (100 in my case). its not ideal, but it seems a big struggle to get the non integer tiles as well.

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Jason 2015-1-14

local thresholding worked a lot better than global!

Image Analyst 2015-1-14

OK but you don't need to split apart your image to do that. You can get a better local thresholding using adapthisteq() to flatten your image and then use a global threshold, or use blockproc like Mohammad suggested. adapthisteq is like splitting your image apart into tons of tiles that are only a pixel apart and will be much better and more accurate than splitting your image into 4 tiles and then computing the threshold for the whole tile. You should really look into these methods.

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