Please help to vectorize this code.

    tic;
    load 'CCA_result.mat';
    CleanData1= CleanData1';
    rows = size(CleanData1);
    Result_cpei = zeros(1,rows(1)); 
    for N = 1:1:rows
        tmp=CPEI(CleanData1(N,:),0);
        Result_cpei = [Result_cpei tmp];
        save ('CPEI','Result_cpei');
    end

The output is not a matter since I got the right output. The issue is can this code to be vectorized?

[per isakson]

• looks wrong: &nbsp rows = size(CleanData1). &nbsp Is rows supposed to be scalar?
• what's &nbsp CPEI ?

[M O]

Thanks for your comment and answer. Yup 'rows' supposed to be scalar and I got nothing error for this.

CPEI is a function in matlab for Qeeg feature extraction. The long term is Composite Permutation Entropy Index (CPEI).

[Jan]

@M O: Yes, you do not get an error for for N=1:1:[a,b], but most likely this will not do what you expect. Please specify, if you want:

rows = size(CleanData1, 1)
% or
rows = size(CleanData1, 2)
% or
rows = numel(CleanData1, 1)

The created file "CPEI.mat" is overwritten in each iteration. This is not useful. Please write a clean code, which does exactly, what you want, before starting to optimize the speed by a vectorization.

[M O]

Ohh..thank you..so because of that my code getting slow..?

Really thanks.

Answer 1

[Jan]

Start with avoiding to re-create the formerly pre-allocated output and do not overwrite the output file in each iteration:

   Data = load('CCA_result.mat');  % Avoid dynamic creation of variables
   CleanData1 = Data.CleanData1';
   rows = size(CleanData1, 1);   % Guessed, perhaps you want NUMEL or the 2nd dim
   Result_cpei = zeros(1, rows); % Pre-allocation
   for N = 1:rows
     Result_cpei(N) = CPEI(CleanData1(N,:),0);  % Write ionto pre-allocated array
   end
   save('CPEI.mat', 'Result_cpei');

If this can be vectorized depends on the contents of the function CPEI. If this function accepts a array as input, the code can be simplified to:

   Data = load('CCA_result.mat');
   CleanData1 = Data.CleanData1';
   Result_cpei = CPEI(CleanData1,0);
   save('CPEI.mat', 'Result_cpei');

[M O]

Here I attached the output of the code that you gave it to me. I want this. But its already vectorized or not? Because this code is running faster than mine previously.

But if I run this code, Its only show 1 value only.

   Data = load('CCA_result.mat');
   CleanData1 = Data.CleanData1';
   Result_cpei = CPEI(CleanData1,0);
   save('CPEI.mat', 'Result_cpei');

Anyway thanks for the code, and need some more clarification on this.

Thank you.