creating 3d array from images

Hello, I am trying to read and copy a series of 5 images into a 3d array, where each image should have a 'thickness' of 13 pixels. When run I get this error:

Undefined function or variable 'B2'.
Error in U (line 20)
I=cat(3,B1,B2,B3,B4,B5);

Why B1 image is copied, but not B2 (and I suppose the rest)? Here is the code. Thanks!

I=zeros(256,256,100);
n=13;
for i=1:5
   x=[int2str(i) '.png'];
   if exist(x, 'file')
       A{i}=imread(x);
       B{i}=A{i}(:,:,1);
       B{i}=repmat(B{i},[1 1 n]);
   else
       fprintf('File %s does not exist.\n', x);
   end
end
I=cat(3,B1,B2,C3,B4,B5);

Answer 1

[Geoff Hayes]

Xenios - I think that you mean to use B{2} in place of B2 (though I'm not sure how B1 passed - could you have defined it elsewhere?). Try replacing your line

 I=cat(3,B1,B2,C3,B4,B5);

with

 I=cat(3,B{1},B{2},B{3},B{4},B{5});

Note how the above line also uses B{3} rather than C3.

Answer 2

[David Young]

B2 is the name of a variable, which has not been given a value. It appears that B1 was given a value in some code that isn't shown in your question. Anyway, these variables aren't used - instead you need to use the elements of the cell array B.

Assuming that C3 is just a typo, it looks like you mean, for the final line

I = cat(3, B{1}, B{2}, B{3}, B{4}, B{5});

[David Young]

You may also want to consider putting something in the else part of the condition, for when a file is missing - e.g. B{i} = []. For generality and conciseness, you could also replace the final line with

I = cat(3, B{:});

Answer 3

[Xen]

Thanks for the help guys! It solved the problem. Yes, C3 was a typo. It really is strange though, because B1 was not defined anywhere else, and this code works for

I=cat(3,A1,A2,A3,A4,A5);

or

I=cat(3,B1,A2,A3,A4,A5);

but not for the rest of any other Bi values. So I didn't assume that brackets are needed.

(Geoff got the accepted answer as he replied first)

Answer 4

[Xen]

By the way, what's the best way for including the I=cat(...) into the loop?

Thanks.

[Image Analyst]

Xenios, this is not an "Answer" so please respond to whomever you're responding to. I thought the whole reason you were dealing with the complications of cell arrays was that the images aren't the same size. Otherwise there is no reason to mess around with cell arrays. If that's not right, and they are all the same size, don't use cells to store your images and just tack them onto a 3D array immediately after reading in.

I=zeros(256,256,100);
n=13;
for i=1:5
   baseFileName = [int2str(i) '.png'];
   if exist(baseFileName, 'file')
       rgbImage = imread(baseFileName);
       redChannel = rgbImage(:,:,1); % Take red channel
       volumetricImage = repmat(redChannel,[1 1 n]); % Replicate 13 times.
       if i == 1
           I = volumetricImage;
       else
           I = cat(3, I, volumetricImage);
       end
   else
       fprintf('File %s does not exist.\n', baseFileName);
   end
end

There's more wrong with the code - I didn't fix everything for you. For example you should not cat() when you've preallocated - what's the point? And you should use dir() to get the filenames known to exist in advance. If you don't do that, and use exist() to check, then at least have a separate counter for inserting into the preallocated array, which would be better than using cat if you preallocate knowing how many files there are (because you used dir()). The separate counter will make sure you don't have gaps in (the very badly-named) I if a file is missing. And so on. Please read the FAQ: http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

[Xen]

Hi. Thanks for that, it really works. This is not part of a huge code, so naming the variables is not too important! I will also pass the comments to the people who had suggested the use of these functions... Anyway, I apologise as I just started using MATLAB. This code is the only one that works as expected, so I am currently Ok with it! Hopefully all images are perfectly orderly named in their folder.