Indexing errors with my function

Hello, Im trying to implement a morpholigcal hitormiss using erosion(erode_3x3 in the code) and I have a bit of trouble with my indexing, I used the erode function found in this forum post (Link: Erode), Here is my code:

function Imatch = hitormiss_3x3(I,M)

if (ndims(I)==3)
  I=I(:,:,2);
end
if (isa(I,'uint8'))
  I=double(I)/255;
end

% --------------- INSERT YOUR CODE BELOW -----------------
[r, c] = size(M); % initalise the size to iterate over structure element
B1s = zeros(size(M));
B0s = zeros(size(M));
for i = 1:c
    for j = 1:r
        if M(i,j)>0 %swapping out -1 to 0s and assign to B1
            B1s(i,j) = M(i,j); 
        else
            B1s(i,j) = 0;
        end
        
        if M(i,j)<0
            B0s(i,j) = 1; %swapping out -1s to 1s and 1s to 0s and assign to B2 
        else
            B0s(i,j) = 0;
        end
    end
end

imComp = imcomplement(I); %complement of I
Imatch = erode_3x3(I,B1s) & erode_3x3(imComp,B0s); %hitormiss usinng erode

% note use the erode_3x3 function call as part of your solution
return


% erode_3x3(I,S) - apply erosion using the 3x3 structure element S
function E = erode_3x3(I,S)

[p, q]=size(S); 
[rows, columns] = size(I);
halfHeight = floor(p/2);
halfWidth = floor(q/2);
ErodedImage = zeros(size(I));
for col = (halfWidth + 1) : (columns - halfWidth)
  for row = (halfHeight + 1) : (rows - halfHeight)
        row1 = (row-halfHeight);
        row2 = (row+halfHeight);
        col1 = (col-halfWidth);
        col2 = (col+halfWidth);
        neighbourhood = I(row1:row2, col1:col2); %this is the part I think is where the indexing is wrong
        pixelsInSE = neighbourhood(S);
        ErodedImage(row, col) = min(pixelsInSE);
  end
end
E = ErodedImage;
return

The main error I have here is, I tried changing the indexing to integers to but that didnt help either, can someone tell me whats wrong with my code and why the indexing is faulty? Thank you for your time and input.

Array indices must be positive integers or logical values.
Error in hitormiss_3x3>erode_3x3 (line 54)
        pixelsInSE = neighbourhood(S);
Error in hitormiss_3x3 (line 31)
Imatch = erode_3x3(I,B1) & erode_3x3(imComp,B2); %hitormiss usinng erode
Error in hitormiss_test (line 7)
B1 = hitormiss_3x3(I,T1); 

For refrence I have a test script that supplies this function with inputs which is as follows:

I = imread('hitmiss_image.tif');
I = double(I(:,:,1))/255;


T1 = [ -1 1 -1 ; 1 1 1 ; -1 1 -1 ]; % simple cross template
B1 = hitormiss_3x3(I,T1);


T2 = [ -1 0 -1 ; 0 1 0 ; -1 0 -1 ]; % centre set & zero diagonals
B2 = hitormiss_3x3(I,T2);

subplot(2,3,1); imagesc(I); colormap(gray); title('Input Image');

subplot(2,3,2); imagesc(T1); title('Template 1'); caxis([-1 1]);
subplot(2,3,3); imagesc(B1); title('Match 1');

subplot(2,3,5); imagesc(T2); title('Template 2'); caxis([-1 1]);
subplot(2,3,6); imagesc(B2); title('Match 2');

drawnow;

Answer 1

[Jan]

Some of the indices are zeros.

        if M(i,j)>0 %swapping out -1 to 0s and assign to B1
            B1s(i,j) = M(i,j); 
        else
            B1s(i,j) = 0;
        end
        
        ...
erode_3x3(I,B1s)

But indices must be > 0 in Matlab.

[Abdul Rahim Mohammad]

Thank you, Jan. Any ideas on how I can fix this? I mean I need the zeros in the structuring element to perform the Hitormiss in this part of the code.

imComp = imcomplement(I); %complement of I
Imatch = erode_3x3(I,B1s) & erode_3x3(imComp,B0s); %hitormiss usinng erode

How would I workaround this to make the code work?

[Jan]

At first I'd start with cleaning the code. You can replace:

[r, c] = size(M); % initalise the size to iterate over structure element
B1s = zeros(size(M));
B0s = zeros(size(M));
for i = 1:c
    for j = 1:r
        if M(i,j)>0 %swapping out -1 to 0s and assign to B1
            B1s(i,j) = M(i,j); 
        else
            B1s(i,j) = 0;
        end
        
        if M(i,j)<0
            B0s(i,j) = 1; %swapping out -1s to 1s and 1s to 0s and assign to B2 
        else
            B0s(i,j) = 0;
        end
    end
end

by

B1s = max(0, M);
B0s = double(M < 0);

Perhaps all you want to do is to replace:

pixelsInSE = neighbourhood(S);

by

pixelsInSE = neighbourhood(S(S~=0));

But without any meaningful comments in the code, it is impossible to guess this reliably. Remember, that all we see is the failing code. How could we know, what it should do instead?

[Abdul Rahim Mohammad]

Thank you for the help Jan, I solved the indexing issue by using :

pixelsInSE = neighbourhood( logical(S) )

Turns out this alone can fix the issue for my code where indices can be used as logical values

Array indices must be positive integers or logical values.