Question

here is the input data:

  % @param Landmarks:
  %           Landmarks should be 1*m struct. 
  %           m is the number of training set.
  %           Landmark(i).data is a n*2 matrix

old function:

  function Landmarks=CenterOfGravity(Landmarks)
  % align center of gravity

  for i=1 : length(Landmarks)
      Landmarks(i).data=Landmarks(i).data - ones(size(Landmarks(i).data,1),1)...
          *mean(Landmarks(i).data);
  end
  end

new function which use arrayfun:

  function [Landmarks] = center_to_gravity(Landmarks)
  Landmarks = arrayfun(@(struct_data)...
                          struct('data', struct_data.data - repmat(mean(struct_data.data), [size(struct_data.data, 1), 1]))...
                                              ,Landmarks);
  end %function center_to_gravity

when using profiler, I find the usage of time is NOT what I expected:

  Function          Total Time    Self Time*
  CenterOfGravity     0.011s      0.004 s
  center_to_gravity   0.029s      0.001 s

Can someone tell me why?

BTW…I can’t add “arrayfun” as a new tag for my reputation.

Answer 1

Using arrayfun does not count as “vectorizing your code” as described in every Matlab performance blog post ever written.

If your .data field is the same length for all entries of landmark, your could vectorize this code by first placing all of the data into a single DATASIZE-BY-LANDMARKSIZE martix, and then running this command

meanRemovedData = bsxfun(@minus, data, mean(data,1));

But you lose an awful lot of code clarity that way. (I’m pretty sure that bsxfun usually has vectorization-like speed advantages, but I haven’t done any time testing this morning.)

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In terms of why, I’m not really the right guy to ask. But many of the advantages of vectorization are dependent on performing simple operations of contiguous blocks of memory. Data stored in an array of structures is (I believe) stored as an array of pointers to disparate memory locations, which is why you can change the size or class of Landmarks(i).data without reallocating the whole structure array.