Ignoring header text when using dlmread or similar function

Hi,

I have some data files in a format called .xvg. These files come from a program called Gromacs, which runs molecular dynamics simulations. A typical .xvg file looks like this:

# This file was created Tue May 31 09:51:38 2011
# by the following command:
# g_energy -f npt-md.edr -o analysis/pressure.xvg 
#
# g_energy is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulations 
#
@    title "Gromacs Energies"
@    xaxis  label "Time (ps)"
@    yaxis  label "(bar)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Pressure"
    0.000000  270.490936
    0.002000  217.628891
    0.004000  246.423630
    0.006000  231.255936
    0.008000  227.903320
    0.010000  170.745224

and the file continues on and on and on with these two columns of data. There is no text footnote, only a text header. Matlab is able to read .xvg files, since they are just files containing ASCII text.

I am able to use Matlab's ImportData function in the graphical user interface to import this data, specifying that there are a certain number of lines of text headers. This works, but importing many such files this way is rather slow, since one has to specify in the ImportData dialog the exact number of lines to ignore, and then one has to wait for Matlab to generate a preview before continuing.

My question is, is there a way to do this from the Command Window or using a script? I found that the function dlmread has one option,

M = dlmread(filename, delimiter, R, C)

where R and C specify the row and column of the upper left corner of the data. They are zero-based, the documentation says. So since my above example file has 19 lines of text header, it seems that I want to ignore rows 0 through 18. So I try:

M = dlmread('pressure.xvg', '', 19, 0)

and this works, and it works great! But, suppose I am lazy and do not wish to always manually count the number of lines of text header. Is there a way to have Matlab automatically ignore the lines of text header? The lines of text header always begin with either # or @ so perhaps there is a way to have Matlab ignore these lines?

Thank you very much for your time!

Andrew DeYoung

Carnegie Mellon University

Answer 1

[Fangjun Jiang]

use textscan(), try the "CommentStyle" parameter. Hopefully, the .xvg file contains fixed number of #lines.

FID=fopen('test.xvg','rt');
a=textscan(FID,'%f%f','Headerlines',8,'CommentStyle','@');
fclose(FID);

a =

    [6x1 double]    [6x1 double]

>> a{1}

ans =

         0
    0.0020
    0.0040
    0.0060
    0.0080
    0.0100

[Walter Roberson]

Unfortunately the user's file has # and @ indicating comments, and textscan() can only handle one comment symbol.

Answer 2

[Sadia Khaf]

I have the same question for a different file format. I have an IONEX file, it can be read as a simple .txt file in MATLAB. You can see the attached file. There doesn't seem to be a specific comment style for this type of file and I can't count number of lines to ignore since I need to read multiple files.