MATLAB Array Pre-allocation help

[hoffmann]

Hi everyone. I'm working on a piece of code and I'm having a bit of trouble with array pre-allocation. Here it is:

function [react_in1 react_in2 react_out1 react_out2]=oneVtwoXone(masses,prec);

prec = 1e-4;
N=length(masses);
masses=[0;masses]; % adding dummy metabolite with zero mass
masses=masses(:);

%mass2=masses*ones(size(masses))'+ones(size(masses))*masses';
%mass2=mass2(:);

mass2=zeros(N*(N+1)/2,1); % list of mass pairs
met1=mass2; % list of the first metabolite in a pair
met2=mass2; % same for the second metabolite
k=0;
for i=1:N
for j=i:N
k=k+1;
met1(k)=i;
met2(k)=j;
mass2(k)=masses(i)+masses(j);
end
end

disp(['Number of distinct pairs is' length(mass2) ])

[mass2, ord]=sort(mass2); % sorted mass pairs
met1=met1(ord); % metabolites in the same order as sorted mass pairs
met2=met2(ord);

dm=diff(mass2);

while(length(find(dm <= mass2(1:length(dm))*prec)) > 0) % while have metabolite pairs that have about the same mass
ind=find(dm<mass2(length(mass2)-length(dm)+1:end)*prec);




react_in1=[react_in1 met1(ind)];
react_in2=[react_in2 met2(ind)];
react_out1=[react_out1 met1(ind+1)];
react_out2=[react_out2 met2(ind+1)];


dm = dm(1:end-1) + dm(2:end);

end

disp(['Number of conforming reactions is' length(react_in1) ])

The source of my trouble is in the second while loop. The react_in1 etc. takes up too much memory and I need to figure out how to preallocate a matrix to hold values approximately 10000, and how to delete the excess zeros if there is any unused space.

Can anyone help?

 

[chroot]

To preallocate a large matrix, just use the zeros() function. Why do you think your matrices are taking up too much memory? Preallocating them will make your code faster, but won't make them take up any less memory.

- Warren

 

[hoffmann]

well actually I've found that preallocating takes up a significantly less amount of time. i have such a huge data set of 10000 values so my code runs faster. here's what I'm doing now:

while(length(find(dm <= mass2(1:length(dm))*prec)) > 0) % while have metabolite pairs that have about the same mass
ind=find(dm<mass2(length(mass2)-length(dm)+1:end)*prec);


react_in1=zeros(10000, 1); % preallocate a new array for all four reactants
react_in2=zeros(10000, 1);
react_out1=zeros(10000, 1);
react_out2=zeros(10000, 1);
count = 0;

for ind=1:10000

react_in1(ind)=met1(ind);
react_in2(ind)=met2(ind);
react_out1(ind)=met1(ind+1);
react_out2(ind)=met2(ind+1);
end


dm = dm(1:end-1) + dm(2:end);

end

how do i truncate the unused zeros?

 

[chroot]

An array of 10,000 values is actually quite SMALL.

You can use the slice operators (like dm(1:10)) to "truncate" an array to whatever size you want.

- Warren

 

[imanius]

how can I preallocate long strings? in other words, How can I rapidly create a string of a certain length and then fill it in a loop?