GitHub - wojdyr/xylib: library for reading files with x-y data from powder diffraction, spectroscopy, or other experimental methods (original) (raw)

xylib

xylib is a portable library for reading files that contain x-y data from powder diffraction, spectroscopy and other experimental methods.

It comes with two programs that can convert supported formats to plain text: command-line xyconv and graphical xyconvert.

Supported formats:

• plain text, delimiter-separated values (e.g. CSV)
• Crystallographic Information File for Powder Diffraction (pdCIF)
• Siemens/Bruker UXD
• Siemens/Bruker RAW ver. 1/2/3/4
• Philips UDF
• Philips PC-APD RD raw scan V3/V5
• PANalytical XRDML
• Rigaku DAT
• Sietronics Sieray CPI
• DBWS/DMPLOT data file
• Canberra CNF (from Genie-2000 software; aka CAM format)
• Canberra AccuSpec MCA
• XFIT/Koalariet XDD
• RIET7/LHPM/CSRIET/ILL_D1A5/PSI_DMC DAT
• Vamas ISO14976_(only experiment modes: SEM or MAPSV or MAPSVDP are supported; only REGULAR scan_mode is supported)_
• Princeton Instruments WinSpec SPE_(only 1-D data is supported)_
• χPLOT CHI
• Ron Unwin's Spectra XPS format (VGX-900 compatible)
• Freiberg Instruments XSYG (from lexsyg)
• Bruker SPC/PAR

Examples of supported files are collected in sample-urls.

LIBRARY

The library is written in C++11 and has C bindings.

R bindings: rxylib (CRAN)by Sebastian Kreutzer.

Python bindings: pip-installable, generated by SWIG, details below.

Other languages (suggestions): you may access C API through FFI (here is an example), or extend xylib.i to wrap the C++ interface using SWIG.

The API is documented in the xylib/xylib.h file. Adding new formats -- inREADME.dev.

Licence: LGPL 2+

xylib is used by:

• fityk
• qpx-gamma
• GammaSpy
• gamma through rxylib
• ...

xyconv

Converts a file from one of the supported formats to plain text:

xyconv myfile.bin plain.txt

It has a few options, see xyconv -h for details.

xyConvert

The GUI is designed for quick converting of many files at once.

DOWNLOAD

Binary packages:

Source:

To compile the source code you need:

• C++ compiler (all popular ones are tested: GCC, Clang, MSVC, icc)
• Boost libraries >= 1.46.1 (only headers).
• optionally, zlib and bzlib libraries (for reading compressed files)
• optionally, wxWidgets 3.0 (for xyconvert - GUI converter)

Two build systems are provided: either use CMake or, on Unix,./configure && make. To skip building the GUI use option-D GUI=OFF for CMake or --without-gui for configure. If you are using git, autoreconf -i is needed before ./configure.

Python bindings require SWIG, Boost headers and a C++ compiler. It may be enough to just type:

pip install xylib-py --user

If the Boost headers cannot be found, run pip with options--global-option=build_ext --global-option=-I/path/to/boost_1_60_0. See the xyconv.py file for usage examples.

AUTHORS

• Marcin Wojdyr wojdyr@gmail.com (maintainer)
• Peng ZHANG zhangpengcas@gmail.com

CONTACT

Feel free to send e-mail to the authors, or to thefityk-dev mailing list.

CREDITS

• Google - the library was started as Google Summer of Code 2007 project by Peng ZHANG, mentored by Marcin Wojdyr from Fityk organization.
• Michael Richardson provided VAMAS specification and sample files.
• David Hovis provided a WinSpec file format specification and sample files.
• Pablo Bianucci provided his code for reading WinSpec format and sample files.
• Martijn Fransen provided very useful specifications of Philips formats.
• Vincent Favre-Nicolin provided PSI_DMC and ILL_D1A5 samples; reading his ObjCryst library was also helpful.
• Janos Vegh sent us his VAMAS reading routines (long time ago, before this project started).
• Andreas Breslau added Bruker V3 (RAW1.01) support.
• Bjørn Tore Lønstad provided Bruker RAW V3 format specification and samples.
• Hector Zhao patched VAMAS code.
• Jim Fitzgerald (author of FitzPeaks) provided code for reading Canberra (Genie) CNF files.
• Matthias Richter added Ron Unwin's Spectra XPS format and SpecsLab2 xy format.
• Johannes Friedrich added xsyg (lexsyg) format.
• Sebastian Kreutzer added Bruker SPC binary format.

HISTORY

• 1.6 (2020-09-08)
  • added XSYG format from Freiberg Instruments' lexsyg (Johannes Friedrich)
  • added Bruker SPC binary format (Sebastian Kreutzer)
  • added PANalytical XRDML
• 1.5 (2016-12-17)
  • improved CNF reading (thanks to Jim and Miha)
  • changes to reading SpecsLab2 xy
  • support text files with lines terminated by CR only
  • more robust reading of CSV files
• 1.4 (2015-03-31)
  • included xyConvert (GUI converter)
  • support filenames with non-ascii characters
• 1.3 (2014-01-24)
  • bug fixes only
• 1.2 (2013-08-01)
  • added SpecsLab2 xy format (Matthias Richter)
• 1.1 (2012-11-05)
  • added XPS format from Ron Unwin's Spectra program (Matthias Richter)
  • fixed bug in reading energy calibration from Canberra formats
• 1.0 (2012-07-25)
  • added option decimal-comma for text format
  • fixed bug in CSV format
• 0.9 (2012-05-20)
  • added CSV format, or more acurately: delimiter-separated values format. Supports popular delimiters (TAB ,;|:/), quoting (") and escape character (\). Non-numeric fields are read as NaNs.
  • added Canberra CNF format
• 0.8 (2011-01-18)
  • fixed a couple of bugs in pdCIF implementation
• 0.7 (2010-10-09)
  • added χPLOT (CHIPLOT) format (extension .chi)
  • fixed bug in reading VAMAS files with transmission data (Hector Zhao)
• 0.6 (2010-04-29)
  • fixed reading of Bruker v3 files
  • changes in API, added C API
• 0.5 (2010-01-04)
  • added support for compressed files *.gz (requires zlib) and *.bz2 (bzlib)
• 0.4 (2009-06-11)
  • added file caching (for details see xylib/cache.h)
  • changes to parsing text files in which numeric data is mixed with text
• 0.3 (2008-06-03)
  • added Bruker binary RAW1.01 format
  • fixed bug in reading one-column ascii files
• 0.2 (2008-03-09)
  • initial public release