Extract contents from cell array - matlab

Question

I have a series of Images, stored into an array A. So every entry of A contains an Image (matrix). All matrices are equally sized.
Now I want to extract the value of a specific position (pixel), but my current approach seems to be slow and I think there may be a better way to do it.
% Create data that resembles my problem
N = 5
for i = 1:N
A{i} = rand(5,5);
end
% my current approach
I = size(A{1},1);
J = size(A{1},2);
val = zeros(N,1);
for i = 1:I
for j = 1:J
for k = 1:N
B(k) = A{k}(i,j);
end
% do further operations on B for current i,j, don't save B
end
end
I was thinking there should be some way along the lines of A{:}(i,j) or vertcat(A{:}(i,j)) but both lead to
??? Bad cell reference operation.
I'm using Matlab2008b.
For further information, I use fft on B afterwards.
Here are the results of the answer by Cris
| Code | # images | Extracting Values | FFT | Overall |
|--------------|----------|-------------------|----------|-----------|
| Original | 16 | 12.809 s | 19.728 s | 62.884 s |
| Original | 128 | 105.974 s | 23.242 s | 177.280 s |
| ------------ | -------- | ----------------- | ------- | --------- |
| Answer | 16 | 42.122 s | 27.382 s | 104.565 s |
| Answer | 128 | 36.807 s | 26.623 s | 102.601 s |
| ------------ | -------- | ----------------- | ------- | --------- |
| Answer (mod) | 16 | 14.772 s | 27.797 s | 77.784 s |
| Answer (mod) | 128 | 13.637 s | 28.095 s | 83.839 s |
The answer codes was modded to double(squeeze(A(i,j,:))); because without double the FFT took much longer.
Answer (mod) uses double(A(i,j,:));
So the improvement seems to really kick in for larger sets of images, however I currently plan with processing ~ 500 images per run.
Update
Measured with the profile function, the result of using/omitting squeeze
| Code | # Calls | Time |
|--------------------------------|---------|----------|
| B = double(squeeze(A(i,j,:))); | 1431040 | 36.325 s |
| B= double(A(i,j,:)); | 1431040 | 14.289 s |

Answer 1

A{:}(i,j) does not work because A{:} is a comma-separated list of elements, equivalent to A{1},A{2},A{3},...A{end}. It makes no sense to index into such an array.
To speed up your operation, I recommend that you create a 3D matrix out of your data, like this:
A3 = cat(3,A{:});
Of course, this will only work if all elements of A have the same size (as was originally specified in the question).
Now you can quickly access the data like so:
for i = 1:I
for j = 1:J
B = squeeze(A3(i,j,:));
% do further operations on B for current i,j, don't save B
end
end
Depending on the operations you apply to each B, you could vectorize those operations as well.
Edit: Since you apply fft to each B, you can obtain that also without looping:
B_fft = fft(A3,[],3); % 3 is the dimension along which to apply the FFT