Wrong results while accessing matrix

Hello there. I try to implement my own version of SLIC method to work on both an RGB or a Hyperspectral image. After clustering process I need to apply a second step to correct faulty labeling and remove redundant labels. I find the connected components using MATLAB's "bwconncomp" function. Checking connected components sizes and neighbour labels. I want to modify label of some element's label to their nearest neighbour cluster center's label. To achieve this I need to find an average vector [L a b x y] of given connected component. Labxy is a vector that I created for this purpose. But the values those are stored in Labxy vector are not correct. What am I doing wrong?

clc,clear, close all;

Image = imread('anyrgbimage.jpg');

Superpixels = 512;

tic
[LabelMatrix,ClusterCenters] = slic(Image, Superpixels,10);
toc

ImageLab = rgb2lab(Image);

[Height, Width] = size(LabelMatrix);

SuperPixelSize = (Height * Width)/ Superpixels;

MinimumSegmentSize = round(SuperPixelSize/4);

LabelMatrix2 = LabelMatrix;

for label = 1:size(ClusterCenters,1)

%     fprintf('Calculations for Label %d\n\n', label');

      ConnectedComponentsL = bwconncomp(LabelMatrix == label);
      numPixels = cellfun(@numel,ConnectedComponentsL.PixelIdxList);

      [BiggestSegment,idx] = max(numPixels); 

      for i = 1:length(numPixels)

          if(BiggestSegment > MinimumSegmentSize)

              if(i ~= idx )

%                 fprintf( 'numPixels(%d) = %d\n\n', i,numPixels(i));

                  Segment = ConnectedComponentsL.PixelIdxList{i};

                  S = [Height , Width];

                  AdjacentLabelCount = zeros(1,size(ClusterCenters,1));

                  Labxy = uint8(zeros(length(Segment),size(ClusterCenters,2)));

                  for j = 1:length(Segment)

                      [X, Y] = ind2sub(S, Segment(j));

                      Labxy(j,:) = [(squeeze(ImageLab(X,Y,:)))' X Y];
                      fprintf('[%d %d %d %d %d]\n\n', Labxy(1),Labxy(2),Labxy(3), X, Y);

                      fprintf('%d) Segment Index = %d, Subscript = [%d %d], Size of Segment = %d elements \n\n', j, Segment(j), X, Y, numPixels(i));

                      NLoc = [X, Y]  + [-1 , 0];
                      %                 fprintf('NLoc = [%d %d] ', NLoc(1), NLoc(2));
                      NELoc = [X, Y] + [-1 , 1];
                      %                 fprintf('NELoc = [%d %d] ', NELoc(1), NELoc(2));
                      NWLoc = [X, Y] + [-1 , -1];
                      %                 fprintf('NWLoc = [%d %d] ', NWLoc(1), NWLoc(2));
                      SLoc = [X, Y]  + [ 1 , 0];
                      %                 fprintf('SLoc = [%d %d] ', SLoc(1), SLoc(2));
                      SELoc = [X, Y] + [1 , 1];
                      %                 fprintf('SELoc = [%d %d] ', SELoc(1), SELoc(2));
                      SWLoc = [X, Y] + [1 , -1];
                      %                 fprintf('SWLoc = [%d %d] ', SWLoc(1), SWLoc(2));
                      WLoc = [X, Y]  + [0 ,-1];
                      %                 fprintf('WLoc = [%d %d] ', WLoc(1), WLoc(2));
                      ELoc = [X, Y]  + [0 , 1];
                      %                 fprintf('ELoc = [%d %d] \n\n', ELoc(1), ELoc(2));

                      [AdjacentLabelCount, NorthLabel] = checknorth(NLoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, NorthWestLabel] = checknorthwest(NWLoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, NorthEastLabel] = checknortheast(NELoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, SouthLabel] = checksouth(SLoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, SouthWestLabel] = checksouthwest(SWLoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, SouthEastLabel] = checksoutheast(SELoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, EastLabel]  = checkeast(ELoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);
                      [AdjacentLabelCount, WestLabel]  = checkwest(WLoc, Height, Width, label, LabelMatrix, AdjacentLabelCount);

                      %MaxMat = find(AdjacentLabelCount == max(AdjacentLabelCount));

                  end

                  MaxMat = find(AdjacentLabelCount == max(AdjacentLabelCount));

                  if(length(MaxMat) == 1)

%                     fprintf('Biggest adjacent of Label %d is Label %d\n\n', label, MaxMat);

                      LabelMatrix2(Segment) = MaxMat;

                  else

%                     fprintf('There are more than one adjacent labels at same quantity\n\n');

                      for t = 1 : length(MaxMat)

%                         fprintf('%d. Biggest adjacent of Label %d is Label %d\n\n', t, label, MaxMat(t))

                          %                     LabelMatrix2(Segment) = MaxMat;

                      end

                  end

              end

          else

              fprintf('Segment size of Label %d is equal to %d and it is smaller than Minimum Segment Size which is %d\n\n', ...
                  label, numPixels(i) , MinimumSegmentSize);

          end

      end
  end

Answer 1

[Walter Roberson]

You have

                      [X, Y] = ind2sub(S, Segment(j));
                      Labxy(j,:) = [(squeeze(ImageLab(X,Y,:)))' X Y];

You have made the fairly common mistake of thinking that rows correspond to X and that columns correspond to Y. Instead, rows correspond to Y and columns correspond to X. So,

                        [Y, X] = ind2sub(S, Segment(j));
                        Labxy(j,:) = [(squeeze(ImageLab(Y,X,:)))' X Y];   %you need to rethink here whether you want X Y or Y X at the end

[Batuhan Hangun]

Actually my indexing was right I guess because I did not get any error about matrix dimensions. I think source of wrong results was uint8( ) at

                 Labxy=uint8(zeros(length(Segment),size(ClusterCenters,2)));

I removed that conversion and everything seems fine. Now I try to access ImageLab(X,Y,:) with [X Y] given by ind2sub(S, Segment(j)); and it looks like that it does fine. I think while displaying it(imagesc, image, imshow), MATLAB converts ImageLab(X,Y,:) to ImageLab(Y,X,:) right? Since I do not display anything

[X, Y] = ind2sub(S, Segment(j));
Labxy(j,:) = [(squeeze(ImageLab(X,Y,:)))' X Y];

this usage is okay. Am I right?

[Walter Roberson]

MATLAB always uses rows for Y and columns for X for image display. The only question for MATLAB is whether location (1,1) should represent the top left of the image or the bottom left of the image.