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Topic: reduce computation time for using a matrix with nan
Replies: 1   Last Post: Nov 15, 2012 9:29 AM

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 Steven Lord Posts: 18,038 Registered: 12/7/04
Re: reduce computation time for using a matrix with nan
Posted: Nov 15, 2012 9:29 AM
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"Skirt Zhang" <silence_qunzi@hotmail.com> wrote in message
news:k824b5\$civ\$1@newscl01ah.mathworks.com...
> Dear ALL,
>
> I have a matrix x(750,2000) got from a cell r{} with size (1*6)which has
> the following format:
>
> 1 2 nan nan nan 4 5 6....
> 1 nan 2 nan 4 nan5 6....
> 4 5 2 nan 4 nan5 6....
> ...
> 4 5 6 1 2 nan nan nan....
> nan 4 nan5 1 nan 2 6....
> 4 5 2 nan 4 nan5 6....
> I want to calculate a function for the non-nans on each row and then get
> the mean value for the results of the functions (from matrix row
> calculation). Below is my code:
>
> for i=1:length(r)
> x=r{i} ;
>
> x2=nan(750,1);
> for ii=1:size(x,1)
> x1=x(ii,:);
> x1=x1(~isnan(x1));
> if ~isempty(x1)
> x2(ii,1)=(sum(x1)^3-3*sum(x1.^2)*sum(x1)+2*sum(x1.^3));
> end
>
> The problem is the computation time is huge since in one loop I need 1hour
> to do so, but without this step it took me only 4min... Since I have 200
> loops to run reducing this step's computation time will be extremely
> helpful, can anyone help me about this?

Use ISNAN on the whole matrix at once. Using that information for logical
indexing, replace all the NaNs in x with 0's (since those will contribute 0
to the SUMs.) Call SUM on the resulting matrix and specify the dimension
input. You don't need to use a loop at all.

--
Steve Lord
slord@mathworks.com
To contact Technical Support use the Contact Us link on
http://www.mathworks.com

Date Subject Author
11/15/12 Q Zhang
11/15/12 Steven Lord

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