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The State of NeXus

The State of NeXus. P.F. Peterson and F.A. Akeroyd on behalf of the NeXus International Advisory Committee. 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008. NIAC Berkeley, CA. NIAC Villigen, Switzerland. NIAC Berlin, Germany. NIAC Sydney, Australia.

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The State of NeXus

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  1. The State of NeXus P.F. Peterson and F.A. Akeroyd on behalf of the NeXus International Advisory Committee

  2. 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 NIAC Berkeley, CA NIAC Villigen, Switzerland NIAC Berlin, Germany NIAC Sydney, Australia NIAC Santa Fe, NM v1.1.0, v1.2.0, v1.2.1, v1.3.0 NIAC Grenoble, France v1.3.1, v1.3.2, v1.3.3 NIAC Pasadena, CA SoftNeSS’94 SoftNeSS’95 SoftNeSS’96 v2.0.0 v2.1.0 v3.0.0 v4.0.0 NeSSI: Collaborative Software and Other Mythical Creatures

  3. NeSSI: Collaborative Software and Other Mythical Creatures

  4. NIAC Members • Frederick Akeroyd, Rutherford Appleton Laboratory, UK (ISIS, Executive Secretary) • Stephen Cottrell, Rutherford Appleton Laboratory, UK (Muon Representative) • Matthias Drochner, Forschungzentrum Jülich, Germany • Emmanuel Farhi, Institut Laue Langevin • Andrew Götz, European Synchrotron Radiation Facility, France • Nick Hauser, Australian Nuclear Science and Technology Organisation, Australia (Documentation Release Manager, netCDF contact) • Jens-Uwe Hoffmann, Helmholtz Zentrum Berlin (renamed HMI), Germany • Pete Jemian, Advanced Photon Source, USA • Paul Kienzle, DANSE, USA • Mark Könnecke, Paul Scherrer Institut, Switzerland (Technical Committee Chair) • Nick Maliszewskyj - NIST Center for Neutron Research, USA • Raymond Osborn, Argonne National Laboratory, USA • Peter Peterson, Spallation Neutron Source, USA (Chair) • Stephane Poirier, Synchrotron Soleil, France • Thomas Proffen, Los Alamos National Laboratory, USA • Jiro Suzuki, KEK, Japan

  5. Principles of NeXus Mission: NeXus enables comprehension of data amongst the neutron, x-ray, and muon science communities through a standard data format.

  6. Reduced need for local expertise • nexus@nexusformat.org • nexus-developers@nexusformat.org • http://www.nexusformat.org • http://svn.nexusformat.org • http://trac.nexusformat.org

  7. Simple Plotting NXdata

  8. Reduced need for conversion

  9. Is it based on anything? • Hierarchical Data Format (4 and 5) • NXopen(filename,NXACC_CREATE4,handle) • NXopen(filename,NXACC_CREATE5,handle) • eXtensible Markup Language • NXopen(filename,NXACC_CREATEX,handle) • NXopen(filename,NXACC_RDWR,handle) • NXopen(filename,NXACC_READ,handle)

  10. Who is committed to NeXus SNS at ORNL NCNR at NIST ISIS at RAL (neutrons and muons) DIAMOND at RAL BI at ANSTO FRM2 at TUM KENS at KEK J-PARC APS at ANL HMI in Berlin MLNSC at LANL SINQ at PSI ILL in Grenoble LLB at Saclay

  11. Existing HDF4/5 tools • HDFLook – HDF based plotter (???) • Java HDF Viewer (NCSA) • Scientific Data Browser – view data over the web (NCSA) • Any web browser • Eclipse with WTP plugin Existing XML tools

  12. NeXus Utilities • NXbrowse – CLI tool to interactively explore NeXus files • NXdir – CLI tool that lists contents of NeXus file and convert selected portions to ASCII • NXextract • NXtoDTD – Creates a definition file from an existing NeXus file • NXtoXML – Writes an XML version of an existing NeXus file • NXtranslate – anything to NeXus converter NXvalid – GUI tool to interactively explore, plot, and validate NeXus files • NXtree – Create a html based tree view of NeXus files • NXvalid – GUI tool to view and validate NeXus files • NXvalidate – command line tool for validating structure of NeXus files

  13. NXvalid

  14. NXtranslate • Anything to NeXus converter • Binary dump • FRM2 • IPNS run • NeXus • Spec • XML • Uses an XML-based translation file to determine where to get information from • Additional information can be supplied in the translation file directly • CLI to encourage batch usage • Simple macro language to allow translating several files using one translation file

  15. addit, subi – programs to add or subtract powder data and write files suitable for Rietveld programs (SINQ) Amortool – simple CLI tool for Reflectometer data analysis (SINQ) anatric, cami4pcd – four circle diffractometer data analysis (SINQ) BerSANS – data analysis for SANS through adapter (SINQ) DANSE – Data Analysis Architecture for Neutron Scattering Experiments (CalTech) DAVE (future) - Data Analysis and Visualization Environment (NCNR) FABLE (ESRF) fit – home grown fitting program (SINQ) GumTree – scientific workbench for instrument control (BI) hdfb.sav and h5b.sav – browser for any 1D/2D/3D data saved in HDF (APS) ISAW – Integrated Spectral Analysis Workbench (IPNS) KUPLOT – General purpose plotting program (MLNSC) LAMP – Large Array Manipulation Program (ILL) MANTID – Manipulation Toolkit for ISIS Data (ISIS) McStas – instrument modeling program (SINQ/ILL) Nathan – TOF data analysis for FOCUS (IDL based) (SINQ) NDS – NeXus data server, publish NeXus files on TCP/IP, read only (SINQ) ninx – inx (ILL) adapted to read FOCUS TOF files (SINQ) NNDB – Java program to browse NeXus files published through NDS (SINQ) NXviewer – OpenDave based viewer (FRM2) OpenGenie – General purpose neutron and muon scattering data reduction and analysis tool (ISIS) Redas – data analysis for Reflectometer, based on Scilab (SINQ) ReflPak – data analysis for Reflectometer (future) (NCNR) Scilab – general matlab like data analysis tool - with a NeXus interface for that (SINQ) SNS Portal (SNS) UDA and WIMDA – General purpose muon scattering analysis packages (ISIS) Tools and Utilities

  16. nexusformat.org

  17. NeXus API v4.2

  18. NeXus Definition Language

  19. Validation of NeXus files using XMl Schema Freddie Akeroyd NIAC

  20. Why Validation? • Standardised definitions make sharing files and analysis programs easier • However, developers need a way to confirm their files comply to the standard

  21. NeXus Meta-DTD Format Not really a true DTD, more a template XML file However there are a few issues: • Syntax is a little “cryptic” – required training to read • Not easily machine parsable • Validated by humans

  22. Base classes / dictionaries schema Application definitions Validation form Documentation

  23. New Definition Format <definition name="NXfermi_chopper" type=“group” extends="NXchopper"> <field name="type" type="NX_CHAR"> <doc>fchopper type</doc> </field> <field name="radius" type="NX_LENGTH"> <doc>radius of chopper</doc> <attribute name=“colour” /> </field> <group type="NXgeometry"> <doc>geometry of the fermi chopper</doc> </group> …

  24. NXDL post XSLT transform

  25. NeXus Schema (XSD) File

  26. Advantages of XML schema • Have built-in data types and allow new types • Support extension and restriction of types • Many tools exist for using schema to validate XML files • Tools exist for generating language bindings and data reading libraries from schema • Possible to add constraints on values via enumerations, patterns and ranges • Supports keys and uniqueness constraints

  27. How are definitions built? • Each NX* base class is defined in a separate file • This separation will make life easier for future base class editors • Instrument definitions restrict NXentryType by marking required items as mandatory • Inheritance used to ensure consistency and avoid duplication: • “object”, “component”, “chopper base” • Enumerations created for chopper types, units, shapes, etc. • Special “Types with units” defined, such as floatAngleDataType and floatLengthDataType

  28. NXVALIDATE NeXus file XML file Validation (xmllint) NXD Definition file XML schema

  29. NeXus homepage http://www.nexusformat.org Feature requests http://trac.nexusformat.org Questions?

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