MATLAB: Fprintf to txt too slow, anyway to accelerate it

fprintf slow

hi:
I have data with different column, such as
 a=ones(100,2), b=ones(50,2);
but I want to append them and export to a .txt file, so what I did is:
  1. construct a new matrix that has the size (max row of a&b, sum of the column of a&b), here is with the size: (100,4).
  2. for each row, find the data that equal to '1', and build a new row that set all the element '1' to ' ,', and save to .txt file using fprinf. however, I found that it is too slow.
below is my test code, and I also attatched the test file A.
load A
tic
fid = fopen('test.txt','w');    
for i=1:1:length(A(:,1))
    str={''};
    for j=1:1:length(A(1,:))
        if A(i,j)==1e5;
            str=strcat(str,{' ,'});
        else
            str=strcat(str,sprintf('%0.5e',A(i,j)),',');
        end
      end
      fprintf(fid,'%s\n',str{1});
  end
  fclose(fid);
toc
tic
dlmwrite('test_dlm.txt',A)
toc
here the 1e5 is the identifier that need to be set to ' ,'. the result shows that fprintf will cost about 129 seconds, while the dlmwrite cost only 12 seconds.
thanks!
Li

Best Answer

A=[a;b];              % append to one array for convenience
A(A==badValue)=nan;   % replace the bum values with NaN
csvwrite('FixedUpCombined.csv',A)  % write to csv file with missing value indicator
Much simpler than creating the specific format to write an empty field; let NaN serve as the placeholder instead. This will also be unequivocal as to what is bum data; "csvread fills empty delimited fields with zero." from the documentation.
Note, however, if you're adamant about using empty delimited fields, the way to go about it is to find the locations in the row and use those locations to build the proper format string with the appropriate number of fields of given type, then write the record using that format string. repmat is exceedingly useful in these machinations since unfortunately the C-like formatting strings cannot accept a repeat count.
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