[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
you.
B
--
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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