[Ifeffit] Importing data to Athena

Bruce Ravel bravel at bnl.gov
Mon Oct 20 10:28:54 CDT 2014

On 10/20/2014 11:08 AM, Samson Vallerie Ann wrote:
> Hi Bruce, I have some trouble importing data to Athena even if it's
> just ordinary column text file. I have attached two sample data.
> These are processed data from full-field XANES images. Basically I
> select a region in the image then write/output the total intensity of
> that region in a text file and I just iterate over several images. I
> have tried deleting out the headers, putting back the headers,
> padding some 0's in the energy column, checking some plugins, but to
> no avail. Your tips, advice is badly needed.
> Many thanks, Vallerie

Hi Vallerie,

2 problems.

1. Ifeffit and Athena presume that the data table is composed entirely
    of numbers.  The file Area2.dat has a column of filenames.  You
    would either need to export these data without columns that cannot
    be interpreted as numbers or you would need to write one of
    Athena's filetype plugins to strip the non-numerical columns of the
    data table before importing.

2. Your examples are very short, only 12 data points.  Athena's
    algorithms make some assumptions about your data (for example, that
    you have a pre-edge region, that your data look like a wiggly step
    function, and so on).  One of these is that the data are of a
    certain length.  That length is set by the file-->minlength
    configuration parameter.  The default for that is 20 and the
    description of the parameter explains that data files shorter than
    that will be rejected, which is in fact what you are seeing.

    You can set that to a smaller number, but I would not have great
    confidence that all the algorithms in Athena will work as expected
    with only 12 points of data.  You can try, but don't be surprised
    if funny things happen, such as difficulty finding E0, wonky
    determinations of the pre- and post-edge lines, and so on.  That
    said, if you take care to set all the parameters of the
    normalization carefully and by hand, Athena might do OK with such
    short data.

I think the moral of the story is that while Athena is a decent tool
for a lot of XAS jobs, it's not the right tool for every job.  If your
stacks are only 12 images deep, Athena may not be the right tool for


  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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