MATLAB: How can i get specific rows of a matrix without using loops

no loopsrows

My question is, how can I get matrix c in an efficient way?(no loops)

c represents the rows of a, given b.

a=[10 14 12 15
     12 11 12 18
     11 14 28 15
     18 11 15 18
     20 11 45 85] 
b=[1
     4 
     2]  
c=[10 14 12 15
     18 11 15 18
     12 12 12 18]

Thank you in advance

Best Answer

c = a(b,:);

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MATLAB: Dynamic for loops

Create a cell array of the variables. Create a vector of order indices according to user input.

paramcell = {a, b, c, d};
paramlengths = cellfun(@length, paramcell);
order = randperm(4);     %except use user input to decide the order
vals = cell(1,4);
for idx1 = 1 : paramlengths(order(1))
 vals{order(1)} = paramcell{order(1)}(idx1);
 for idx2 = 1 : paramlengths(order(2))
   vals{order(2)} = paramcell{order(2)}(idx2);
   CASE = 0;
   for idx3 = 1 : paramlengths(order(3))
     vals{order(3)} = paramcell{order(3)}(idx3);
     for idx4 = 1 : paramlengths(order(4))
       vals{order(4)} = paramcell{order(4)}(idx4);
       CASE = CASE+1;
       [x, y] = myfunction( vals{:} );
       ...
     end
   end
 end
end

A small time-drain will be the fact that inside the loop, the overlap variable gets constantly resized. In the MATLAB editor, these variables will have a little orange line under them. If you hover over that line, it will warn you about this potential problem.

Here's a first attempt that will reduce the time needed. Note I've also replaced "isempty(x)==0" with "~isempty(x)" (for simplicity) and replaced some of the nested if statements with continue statements, just to have less nesting (which can get confusing).

overlap = cell(2, length(starts));
nonEmptyStarts = find(~cellfun(@isempty,starts));
for i=nonEmptyStarts
    counter = 0;
    thisStart = starts{i};
    thisStop = stops{i};
    for j = 1: length(thisStart)
        for k = nonEmptyStarts
            if isempty(peak_loc3{k}), continue; end
            thatStart = starts{k};
            thatStop = stops{k};
            thisMask = thisStop(j)>=thatStart & thisStop(j)<thatStop & peak_loc3{i}(j)~=peak_loc3{k}(1:length(thatStart))';
            for m = find(thisMask);
                    counter = counter +1;
                    overlap{1,i}(counter) = peak_loc3{k}(m);
                    overlap{2,i}(counter) = peak_loc3{i}(j);
            end
        end
    end
end

Unfortunately there is still a big culprit of "variable size adjustment" sitting inside a loop, which will really slow down the code. If you see the line starting with overlap{1,i}(counter) =, you'll notice that every time this line is run, the variable sitting in the cell at overlap{1,i} grows by one. If this happens a lot, MATLAB has to work really hard to find new space in memory fitting this new size.

This updated code currently has an approximately 10-fold reduction in running time to the original.

UPDATE

overlap = cell(2, length(starts));
nonEmptyStarts = find(~cellfun(@isempty,starts));
for i=nonEmptyStarts
    counter = 0;
    % Get column vectors of the first start/stop pairs
    startA = starts{i}';    stopA = stops{i}';
    for k = nonEmptyStarts
        % Get row vectors of the second start/stop pairs
        startB = starts{k};    stopB = stops{k};
        % Get a mask of all A-B pairs that match requirements
        ABMask = bsxfun(@ge,stopA,startB) & ...
            bsxfun(@lt,stopA,stopB) & ...
            bsxfun(@ne,peak_loc3{i}(1:numel(startA)), peak_loc3{k}(1:numel(startB))');
        [j,m] = find(ABMask);
        numToAdd = length(m);
        if ~numToAdd, continue; end
        % Append them to "overlap"
        indsToInsert = (1:numToAdd) + counter;
        counter = counter + numToAdd;
        overlap{1,i}(indsToInsert) = peak_loc3{k}(m);
        overlap{2,i}(indsToInsert) = peak_loc3{i}(j);
    end
end

This update should make significant improvements on a large dataset. There is still room for improvement, depending on the type and sizes of data you have. You can actually get a good view of what parts of the code take the most time by replacing tic and toc with profile on and profile viewer.

I have a feeling that the assignment into overlap will still be the biggest area for possible improvement.

Best Answer

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MATLAB: Replace nested loops

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