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@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/