[Ifeffit] Importing 100 element Ge data into Larch

Matt Newville newville at cars.uchicago.edu
Fri Jul 13 14:08:22 CDT 2018

On Fri, Jul 13, 2018 at 1:27 PM Macon Abernathy <maber001 at ucr.edu> wrote:

> Hey all,
> Has anyone had success loading data from larger pixel arrays into Larch? I
> have data collected on a 100 element Ge detector that results in Athena
> crashing upon import (running on Mac OS 10.13.4, Demeter v9.25). I figure
> this is a good task for Larch, but am having a difficult time figuring out
> how to import all 100 channels for each data set simultaneously.
> Thanks in advance for any tips,

What format is the data in?  ​Larch can read very large files, including
HDF5 and netCDF files. I don't know anyone using those formats for XAFS
data, but I use them all the time for fluorescence maps, where the files
can easily get to be 10s of Gb.

But most XAFS data can be held in ASCII files, even for 100 element
detectors.  If the data is in an ASCII file, something like

    fdata = read_ascii('MyDataFile.txt')

might just work, and will give you a 2D array in 'fdata.data' that has a
shape of  (ncolumns, n_energy_points).  Read_ascii() will also try to parse
the column labels, which may work for some data files, but might not work
great for all data files. With the full 2D data table you might be able to
do something like (totally making up the array indices):
    fdata.energy  = fdata.data[0, :]
    fdata.i0  = fdata[2, :]
    fdata.fluor = fdata.data[4:104, :].sum(axis=0)  # sum columns 5 to 104
    fdata.mu = fdata.fluor / fdata.i0

If something like that doesn't work, send a data file and we'll figure it

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