[Ifeffit] Binary SSRL Files crash upon import.

Logan Giles gileslo at slac.stanford.edu
Thu Sep 17 12:13:00 CDT 2015

Thanks Bruce. I'll speak to the beam-line scientists here and see what they


On Thu, Sep 17, 2015 at 9:54 AM, Bruce Ravel <bravel at bnl.gov> wrote:

> On 09/16/2015 06:26 PM, Logan Giles wrote:
>> I am running Demeter 0.9.22 and trying import recent SSRL Binary files.
>> I have the SSRL plugins enabled as well. The problem is when I try to
>> import binary files, the program crashes.
>> It seems that something might have changed recently in SSRL BL 7-3 files
>> because I can import July 2013 files but not July 2015. I have attached
>> a NaMoO4 sweep at the Mo K-edge from each run for your testing.
>> Immediately after trying to import the binary July 2015 files, the
>> program immediately crashes and exits. The July 2013 binary opens right
>> up.
>> When I look at the dathena.log file for the "2015 crash", everything
>> looks normal until the end:
>> "Demeter version 0.9.22
>> At line 316 of file iff_rddata.fFortran runtime error: End of record"
>> Also, when I try to import the ascii files of the July 2013 or July 2015
>> data, I get an error as well, but the same error. I can fix this by
>> changing two of the blank rows, which are the column labels for the
>> data, to "BLANK" or something. I have attached these unedited ascii
>> files as well, but I am more concerned with my binary problem. The
>> reason for this is that I was recently sent some other SSRL binary files
>> without their corresponding ascii files that also crash.
> Logan,
> The fundamental problem here is that the SSRL binary and ascii files
> are not well documented.  And, they both suck really hard as file
> formats.
> When I made the SSRLA and SSRLB plugins, I was working from examples
> that people had provided to me.  (It has been something like 22 years
> since I was last at SSRL for an experiment, so I have no direct
> experience with these files.)  To interpret the wacky binary formats,
> I followed the example that Sam had programed into sixpack.  The only
> sense in which the plugins ever worked was in the sense that "they
> worked on the examples in front of me".
> On the computer I am sitting at, I am able to read the 2015 binary file.
> The 2013 binary file fails.  I am guessing that is because there are a
> lot of ^M characters in that file that are not in my example data or
> in the 2015 file.
> Both ascii files fail.  Your explanation appears to be correct.  The
> plugin expects all of the columns to be named.  It expects that the
> list of column labels ends in a blank line, with the data to follow.
> Your files have blank lines in the middle of the column labels.  That
> breaks the plugin.
> I am not clear that any of this is my problem.  I don't actually know
> the specification for either format.  Three of your four examples fail
> to meet my expectation based off of examples I was given some years
> back.  I don't think I should be expected to meet an ill-defined and
> moving target.
> If you or someone else wants to update the SSRLA or SSRLB filetype
> plugins to work better with actual files from SSRL, I would be very
> happy to accept that contribution.
> But fixing them myself on the basis of this small sample set is very
> low on my to-do list.  If you intend to use Athena, your best bet
> would be to write yourself a little conversion program that leaves the
> data in a state that Athena can interpret.  Another option is to use
> sixpack.
> 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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Logan Giles, PhD
Postdoctoral Scholar
Stanford University
Cell: (406) 600-6883
Work: (650) 926-5033
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