Efficiency help

hi, i need some help in improving this section of code. it takes over 20 seconds to run. Because i have over 150 samples to run, a 10 second improvement would mean close to 1 hour of time saved. Thanks!

 for p = 1: length(unique_cell(1,:))                                                                     for f = 1:length(ions{1,p})
            max_inloop(f)= (ions{2,p}(1,f))/(ions{1,p}(1,f));
            max_inloop2(f)= (ions{1,p}(1,f))/(ions{2,p}(1,f));
        end
        max_ion_list{p} = max_inloop;
        max_ion_list2{p} = max_inloop2;

    end

[Alex]

One issue you are having with speed is based off of memory, each time through the loop, MATLAb is having to re-allocate memory for a larger cell matrix. Simply defining the size of the cell before you start the loop will save a LOT of time.

Answer 1

[Walter Roberson]

for p = 1 : length(unique_cell(1,:))
  max_inloop = ions{2,p}(1,:) ./ ions{1,p}(1,:);
  max_ion_list{p} = max_inloop;
  max_ion_list2{p} = 1 ./ max_inloop;
end

[Andy]

thanks! works perfectly

Answer 2

[Alex]

This should work. I can't test it out though. Also, note the comment I made on your main post. Always pre-allocate memory if you can. Currently, within your loop, each time, Matlab has to take time to make the matrix larger.

   max_ion_list = cell(length(unique_cell(1,:)), length(ions{1,p}));
   max_ion_list2 = cell(length(unique_cell(1,:)), length(ions{1,p}));

   f = 1:length(ions{1,p});

   for p = 1: length(uniue_cell(1,:))

       max_ion_list{p}  = (ions{2,p}(1,f))/(ions{1,p}(1,f));
       max_ion_list2{p} = (ions{1,p}(1,f))/(ions{2,p}(1,f));
   end

[Andy]

oh i did preallocate, just didnt show it, walter's code works perfect

[Walter Roberson]

Alex, with "f" being a vector, you have vector / vector, and that is going to be the mrdivide operation rather than the rdivide operation which is coded as ./

[Alex]

I was referencing max_ion_list{p} = [];

I thought, that without pre-allocation, on each loop iteration, the size of max_ion_list would grow by one, and thus the Matlab memory manager would need to allocate memory for a larger variable, copy the variable, and then clear the old memory space.

Am I wrong? Is the Matlab memory manager capable to detecting how large the variable will be at runtime?

[Walter Roberson]

In R2011b, MATLAB apparently does better on memory allocation; I do not have access to that version to experiment with.

max_ion_list{p} = []; will not help with pre-allocation, as all of max_ion_list{p} is overwritten.

Anyhow, my earlier comment to you had nothing to do with preallocation, and only had to do with the difference between the "/" operator that you coded and the "./" operator that is needed.

[Alex]

Ahh, I understand now.