7. NeXus Utilities
There are many utilities available to read, browse, write, and use NeXus data files. Some
are provided by the NeXus technical group while others are provided by the community. Still,
other tools listed here can read or write one of the low-level file formats used by NeXus (HDF4,
HDF5, or XML).
7.1. Utilities supplied with NeXus
Most of these utility programs are run from the command line. It will be noted if a
program provides a graphical user interface (GUI). Short descriptions are provided here with
links to further information, as available.
- nxbrowse
- NeXus Browser
- nxconvert
- Utility to convert a NeXus file into HDF4/HDF5/XML/...
- nxdir
nxdir is a utility for querying
a NeXus file about its contents. Full
documentation can be found by running this command:
- nxingest
- nxingest extracts the metadata from a NeXus file to create an
XML file according to a mapping file. The mapping file defines the structure
(names and hierarchy) and content (from either the
NeXus file, the mapping file or the current time) of the output file. See
the man page for a description of the mapping file. This tool uses the
NAPI. Thus, any of the supported formats (HDF4, HDF5 and XML)
can be read.
- nxsummary
- Use nxsummary to generate summary of a NeXus file.
This program relies heavily on a configuration file. Each item tag
in the file describes a node to print from the NeXus file. The path
attribute describes where in the NeXus file to get information from. The
label attribute will be printed when showing the value of the
specified field. The optional operation attribute provides for certain
operations to be performed on the data before printing out the result.
See the source code documentation for more details.
- nxtranslate
nxtranslate is
an anything to NeXus converter. This is accomplished by
using translation files and a plugin style of architecture where
nxtranslate can read from new formats as plugins become available. The
documentation for nxtranslate describes its usage by three types of
individuals:
- the person using existing translation files to create NeXus files
- the person creating translation files
- the person writing new retrievers
All of these concepts are discussed in detail in the documentation
provided with the source code.
- nxvalidate
From the source code documentation:
“Utility to convert a NeXus file into HDF4/HDF5/XML/...”
Note: this command-line tool is
different than the newer Java GUI program: NXvalidate.
- NXplot
- An extendable utility for plotting any NeXus file. NXplot is
an Eclipse-based GUI project in Java to plot data in NeXus files. (The project was
started at the first NeXus Code Camp in 2009.)
7.2. Data Analysis
The list of applications below are some of the utilities that have been developed (or modified) to read/write NeXus files
as a data format. It is not intended to be a complete list of all available packages.
- DAVE (http://www.ncnr.nist.gov/dave/)
- DAVE is an integrated environment for the reduction, visualization and
analysis of inelastic neutron scattering data. It is built using IDL (Interactive Data
Language) from ITT Visual Information Solutions.
- DAWN (http://www.dawnsci.org)
- The Data Analysis WorkbeNch (DAWN) project is an eclipse based workbench
for doing scientific data anaylsis. It offers generic visualisation,
and domain specific processing.
- GDA (http://www.opengda.org)
- The GDA project is an open-source framework for creating customised
data acquisition software for science facilities such
as neutron and X-ray sources. It has elements of the DAWN analysis
workbench built in.
- Gumtree (http://docs.codehaus.org/display/GUMTREE)
- Gumtree is an open source project, providing a graphical user
interface for instrument status and control, data acquisition
and data reduction.
- IDL (http://www.ittvis.com/)
- IDL is a high-level technical computing language and interactive
environment for algorithm development, data visualization,
data analysis, and numeric computation.
- IgorPro (http://www.wavemetrics.com/)
- IGOR Pro is an extraordinarily powerful and extensible scientific
graphing, data analysis, image processing and programming software
tool for scientists and engineers.
- ISAW (ftp://ftp.sns.gov/ISAW/)
- The Integrated Spectral Analysis Workbench software project (ISAW)
is a Platform-Independent system Data Reduction/Visualization.
ISAW can be used to read, manipulate, view, and save neutron
scattering data. It reads data from IPNS run files or NeXus files
and can merge and sort data from separate measurements.
- LAMP (http://www.ill.eu/data_treat/lamp/>)
- LAMP (Large Array Manipulation Program) is designed for the treatment of
data obtained from neutron scattering experiments at the Institut Laue-Langevin. However,
LAMP is now a more general purpose application which can be seen as
a GUI-laboratory for data analysis based on the IDL language.
- Mantid (http://www.mantidproject.org/)
- The Mantid project
provides a platform that supports high-performance
computing on neutron and muon data. It is being developed as a collaboration between
Rutherford Appleton Laboratory and Oak Ridge National Laboratory.
- MATLAB (http://www.mathworks.com/)
- MATLAB is a high-level technical computing language and interactive
environment for algorithm development, data visualization,
data analysis, and numeric computation.
- NeXpy (http://nexpy.github.io/nexpy/)
- The goal of NeXpy is to provide a simple graphical environment,
coupled with Python scripting capabilities, for the analysis of X-Ray and
neutron scattering data.
(It was decided at the NIAC 2010 meeting that a large portion of this code
would be adopted in the future by NeXus and be part of the distribution)
- OpenGENIE (http://www.opengenie.org/)
- A general purpose data analysis and visualisation package primarily
developed at the ISIS Facility, Rutherford Appleton Laboratory.
- PyMCA (http://pymca.sourceforge.net/)
- PyMca is a ready-to-use, and in many aspects state-of-the-art,
set of applications implementing most of the needs
of X-ray fluorescence data analysis. It also provides a
Python toolkit for visualization and analysis of energy-dispersive
X-ray fluorescence data.
Reads, browses, and plots data from NeXus HDF5 files.
- spec2nexus (http://spec2nexus.readthedocs.org/)
(Python code) Converts SPEC data files and scans into NeXus HDF5 files.
Provides h5toText utility program to inspect HDF5 file content.
Provides libraries:
- spec2nexus.prjPySpec: python binding to read SPEC [#] data files
- spec2nexus.eznx: (Easy NeXus) supports writing NeXus HDF5 files using h5py
