How to read large matrix from a csv efficiently in Octave

There are many reports of开发者_JAVA百科 slow performance of Octave's dlmread. I was hoping that this was fixed in 3.2.4, but when I tried to load a csv file that has a size of ca. 8 * 4 mil (32 mil in total), it also took very, very long time. I searched the web but could not find a workaround for this. Does anybody know a good workaround?

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I experienced the same problem and had R handy, so my solution was to use "read.csv" in R, and then use the R package "R.matlab" to write a ".mat" file, and then load that in Octave.

"read.csv" can be pretty slow too, but this worked very well in my case.

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The reason is that Octave has a bug that adding data to a very large matrix takes more time then adding the same amount of data to a small matrix.

Below is my try. I choose to save data each 50000 lines, so meanwhile I could already take a look instead of being forced to wait. It is slower for small files, but much faster for larger files.

function alldata = load_data(filename)
    fid = fopen(filename,'r');
    s=0;
    data=[];
    alldata=[];
    save "temp.mat" alldata;
    if fid == -1
        disp("Couldn't find file mydata");
    else
        while (~feof(fid))
            line = fgetl(fid);
            [t1,t2,t3,t4,d] = sscanf(line,'%i:%i:%i:%i %f', "C"); #reading time as hh:mm:ss:ms and data as float
            s++;
            t = (t1 * 3600000 + t2 * 60000 + t3 * 1000 + t4);
            data = [data; t, d];
            if (mod(s,10000) == 0)
                #disp(s), disp("  "), disp(t), disp("  "), disp(d), disp("\n");
                disp(s);
                fflush(stdout);
            end
            if (mod(s,50000) == 0)
                load "temp.mat";
                alldata=[alldata; data];
                data=[];
                save "temp.mat" alldata;
                disp("data saved");
                fflush(stdout);
            end
        end
        disp(s);
        load "temp.mat";
        alldata=[alldata; data];
        save "temp.mat" alldata;
        disp("data saved");
        fflush(stdout); 
    end
    fclose(fid);

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Here is a workaround that I am using.

I did not find that sscanf will parse input lines as indicated above. Also, I didn't use the temp file.

My .csv file has a large number of rows. They begin with a header of 18 lines and are followed by a data block, each of which has 135 columns. The following code has been tested. My file also begins each row with a dd/mm/yyyy hh:mm field. This will also catch poor lines and indicate where they are by using try/catch.

My .csv file came from a customer who dumped his PARCView load in an Excel file.

function [tags,descr,alldata] = fbcsvread(filename)
  fid = fopen(filename,'r');
  s = 0;
  data=[];
  alldata=zeros(1,135);
  if fid==-1
    disp("Couldn't find file %s\n",filename);
  else
    linecount = 1;
    while (~feof(fid))
      line = fgetl(fid);
      data2 = zeros(1,135);
      if linecount == 1
    tags = strsplit(line,",");
      elseif linecount == 2
    descr = strsplit(line,",");
      elseif linecount >= 19
    data = strsplit(line,",");
    datetime = strsplit(char(data(1))," ");
    modyyr = strsplit(char(datetime(1)),"/");
    hrmin = strsplit(char(datetime(2)),":");
    year1 = sscanf(char(modyyr(3)),"%d","C");
    day1 = sscanf(char(modyyr(2)),"%d","C");
    month1 = sscanf(char(modyyr(1)),"%d","C");
    hour1 = sscanf(char(hrmin(1)),"%d","C");
    minute1 = sscanf(char(hrmin(2)),"%d","C");
    realtime = datenum(year1,month1,day1,hour1,minute1);
    data2(1) = realtime;
    for location = 2:134
      try
        data2(location) = sscanf(char(data(location)),"%f","C");
      catch
        printf("Error at %s %s\n",char(datetime(1)),char(datetime(2)) );
        fflush(stdout);
      end_try_catch
    endfor
    alldata(linecount-18,:) = data2;
    if mod(linecount,50) == 0
      printf(".");
      fflush(stdout);
    endif
      endif
      linecount = linecount + 1;
    endwhile
    fclose(fid);
  endif
endfunction