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    <p>As noted by <a href="http://blogs.mathworks.com/loren/2007/03/22/in-place-operations-on-data/">Loren on his blog</a>, MATLAB does support <strong>in-line</strong> operations on matrices, which essentially covers passing arrays by reference, modifying them in a function, and returning the result. You seem to know that, but you erroneously state that <em>because the script must contain identical variable names as the calling script</em>. Here is code example that shows this is wrong. When testing, please copy it verbatim and save as a function:</p> <pre><code>function inplace_test y = zeros(1,1e8); x = zeros(1,1e8); tic; x = compute(x); toc tic; y = compute(y); toc tic; x = computeIP(x); toc tic; y = computeIP(y); toc tic; x = x+1; toc end function x=computeIP(x) x = x+1; end function y=compute(x) y = x+1; end </code></pre> <p>Time results on my computer:</p> <pre><code>Elapsed time is 0.243335 seconds. Elapsed time is 0.251495 seconds. Elapsed time is 0.090949 seconds. Elapsed time is 0.088894 seconds. Elapsed time is 0.090638 seconds. </code></pre> <p>As you see, the two last calls that use an <strong>in-place</strong> function are equally fast for both input arrays <code>x</code> and <code>y</code>. Also, they are equally fast as running <code>x = x+1</code> without a function. The only important thing is that <strong>inside the function</strong> input and output parameters are the same. And there is one more thing...</p> <p>If I should guess what is wrong with your code, I'd say you made <strong>nested</strong> functions that you expect to be in-place. And they are not. So the below code will not work:</p> <pre><code>function inplace_test y = zeros(1,1e8); x = zeros(1,1e8); tic; x = compute(x); toc tic; y = compute(y); toc tic; x = computeIP(x); toc tic; y = computeIP(y); toc tic; x = x+1; toc function x=computeIP(x) x = x+1; end function y=compute(x) y = x+1; end end Elapsed time is 0.247798 seconds. Elapsed time is 0.257521 seconds. Elapsed time is 0.229774 seconds. Elapsed time is 0.237215 seconds. Elapsed time is 0.090446 seconds. </code></pre> <p>The bottom line - be careful with those nested functions..</p>
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