two for loops problem

Hi everyone,

here i want to get pixel intensity out of a 512*512 image.

i wrote two for loops, but in the end in matrix 'intensityValue', l got only the last set of data.

the background is to get the coordinates from x and y. corx and cory are 41*75 matrices.

Thanks !

fluo = imread('fluo0020.tif');
% imshow(fluo);

corx=[];
cory=[];

intensityValue=[];
    
for i=1:length(coordinate)
   
    A = [coordinate ; coordinate(1,:)] ;   
  if mod(i, 2) == 1 
      x= int16(A(:,i));
      y= int16(A(:,(i+1)));
      
      corx=[corx,x];
      cory=[cory,y]; 
  end
  
%      scatter(x,y); 
%      line(x,y); 
%      hold all
  
end


for ttt=1:length(x)
    
    xc=x(ttt,:);
    xy=y(ttt,:);
    
   
      inten=fluo(xc,yc);
      
      intensityValue =[intensityValue;inten];  
  

      
end

[Ameer Hamza]

I don't fully understand the logic of this code, however, shouldn't the last part be,

for ttt=1:length(corx)
    xc=corx(ttt,:);
    xy=cory(ttt,:);
    
    inten=fluo(xc,yc); 
    intensityValue =[intensityValue;inten]; 
end

[yunwei hu]

i am still new to write the code.... it's true there not so much logic..

what l tried to get is the same corresponding values(the same row and column) from corx and cory, which l have uploaded. They are actually the x and y coordinates.

And from the two vuales, i get the intensity from the image.

the final intensityValue i expected is a 42*75 matrix

Thank you for your reply!

[Ameer Hamza]

Please check the one-liner in the answer to directly extract the value instead of writing a for loop.

Answer 1

[Ameer Hamza]

You are directly use corx and cory variables to extract values from the matrix instead of the second for loop in your code.

intensityValue = fluo(sub2ind(size(fluo), cory, corx)); % cory is the row number and corx is the column number 

[yunwei hu]

Hi Ameer,

there is an error "Out of range subscript."

you are right about that l am extracting values form two matrices.

but l am not sure about the row number and column number, since both corx and cory are the matrix have the same number of rows and columns, as l uppolded before.

[Ameer Hamza]

But the corx and cory are extracting the values from fluo. Do the elements of corx denotes the row number of the pixel in flou or the column number?

I suspect that, if you got out of bound error, the following might be the correct.

intensityValue = fluo(sub2ind(size(fluo), corx, cory));

[yunwei hu]

corx is the row number.

but l tried this code as well.

the same error occured.

Could be that the number in corx or cory exceed 512?

Since i turned to all into int16, maybe this could be the problem?

[Ameer Hamza]

This depends on the resolution of you image file. The number in corx and cory should not exceed the image dimensions.

If possible share the image file and the value of variable coordinate in a mat file.

[yunwei hu]

i share the files

they should not exceed l suppose.

[Ameer Hamza]

As you can see, the image dimension is 512x512, and some elements of corx and cory are higher than 512. Therefore it is throwing an error. I guess that there is some issue in the calculation of the corx and cory in the first loop.

[yunwei hu]

Now i see.

i would check the data again.

thank you so much for your help!