emblsaxs / saxsview Goto Github PK

DAMMIF .fir files contain the chi^2 in the header line. BODIES files give the model parameters. It ought to be possible to read and write these values with libsaxsdocument.

I installed a new version of ATSAS 3.0.1 for win 10 (64x) and saxsdocument cannot be imported in python. Even when I am inside the directory "c/Program Files (x86)/ATSAS 3.0.1/bin/python3.7/site-packages" and there is the saxsdocument.pyd file, it is not visible from python. I am using python 3 64.

There is currently a .out file reader but no writer

e.g. SASDB76.dat
https://www.sasbdb.org/data/SASDB76/

Reported by Al

e.g. "nanometer", "nanometre", "1/nm", "nm-1", "A-1", "Angstrom" etc.

Programs like BUNCH, CORAL, SASREF write the chi^2 value and the subtracted constant (if applicable) to the .fit file. However, these metadata are not read as saxs_properties by libsaxsdocument.

libsaxsdocument doesn't read the properties from a .dat file correctly if "Code" is missing or empty. E.g. from Buffer_0001_00004.dat.txt I get "sample-concentration" and "sample-description" but no properties from the footer. If I add a Code - I get all the properties. This becomes quite a problem for SASFLOW (e.g. at SSRF in Shanghai).

This may happen in libsaxsdocument/src/atsas_dat.c in autosub_dat_parse_footer(), line 751:

  int nscan = sscanf(currline->line_buffer, "Sample: %30s c= %20s mg/ml
Code: %20s", sample_code, conc, code);
  if (nscan != 3) {
    return errno?errno:ENOTSUP;
  }

(Proximate cause: upgraded CMake has better search heuristics, so it finds the libxml2 library and tries to build with canSAS-XML enabled, whereas previously libxml2 was not found and canSAS was disabled.)

Trying to build saxsview gives linker errors saying something like: undefined reference to '__imp_recv'

e.g. when libsaxsdocument.so is already installed in the system, the python saxsdocument module may be available in the system site-packages but will not be in any virtualenv. Having a separate setup.py will allow installing pysaxsdocument in a virtualenv.

https://www.sasbdb.org/media/intensities_files/SASDCH9.dat
This file came in GB 18030 encoding (Chinese government standard), the data can be accessed using libsaxsdocument from C code (autorg, primus) but not from Python code (sasbdb).
If one converts this file to UTF-8 - it is correctly read by all applications.

i.e. merge PR #15

possibly create a legacy-cmake branch for old code to use

All tests fail with SIGSEGV on Windows, the crash happens when lines_read calls fesetenv.

If libxml is not found then libsaxsdocument is not linked with -lm. This is possibly a bug in the add_shared_library CMake macro?

Was PR1443 on ATSAS Bugzilla

Originally reported as a problem in SASREFCV
http://www.saxier.org/forum/viewtopic.php?f=9&t=3140&p=8205

e.g. from GIFT, BioXTAS etc