How to pre-allocate changeable size arrays in a for-loop?
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I have a quite large script, where I deal with different particle size classes (or intervals) depending on given input. Each of the size classes (i=1:NrInt) will result in a cell array with a certain size (nr rows depends on nr of particles, nr columns depends on nr of chemical elements present). These arrays are then submitted to a number of operations in order to produce correspondent pie charts (1 pie per particle size interval).
I received part of this script from a previous colleague, which I then tried to adapt to my specific problem. After lots of error and trial, the script seems to be working just fine, but I still need to improve speed. As several variables are changing size inside the loop, I'm getting the warning preallocate messages all over the place.
The code for that part is in attachment. Can someone help me out?
Guillaume 2017년 3월 23일
편집: Guillaume 님. 2017년 3월 24일
I'm with Adam and Dhruvesh, your code is very difficult to parse. Better indentation (select all code and press CTRL+I), more white spaces and comments would greatly help.
At a quick glance, I fail to see which variable cannot be pre-allocated. They all seem to be indexed by i which you know will have NrInt steps.
Like Adam, I wonder if all these cell arrays are necessary. There are also several number to string conversions. That's never going to be fast.
I also noticed several instances of
somevar = find(someexpression)
othervar(somevar) = ...
which can be replaced by
othervar(someexpression) = ...
There's no point in using find to convert the logical array returned by someexpression into explicit indices when you can use that logical array directly for indexing. The find call just slow things down.
Note that if you cannot preallocate (which is perfectly fine) you can get rid of the warning either by right clicking on the squigly line and selecting Suppress ... on ..., or adding %#ok<AGROW> at the end of the line.
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Dhruvesh Patel 2017년 3월 23일
Your code indeed is difficult to read. However here are some general pointers which might help you undersatnd what is going on under the hood when MATLAB resizes an array. The way MATLAB works while resizing an array when more elements are asked for by the for-loop is nicely explained in the following answer. It talks about both, the normal arrays as well as cell arrays.
So, it is always a good idea to take an estimate for the size and pre-allocate using that as this would mean that MATLAB will not have to resize atleast till the size reaches this estimated value. This would improve execution time as well as reduce memory fragmentation. Ideally if you have an upper bound for your loop iterations (looks like its 'NrInt' in your case) you can pre-allocate using that.