Gumnix Lab

1. 10-11 m 10-9 m 10-7 m 10-5 m 10-3 m Viruses Proteins Bacteria GumTree Scientific Workbench UI Parts (Views, Wizards, Preference Pages, etc.) NeXus DANSE Data Adapter Instrument / Device Control System Visualisation Tool Data Analyser HDF MATLAB XML LAMP GumTree Platform SICS TANGO EPICS ISAW Ptplot VTK UI VIS DRA Control Sequencer Device Servers • SICS, EPICS Hardware • TANGO, CIMA Drivers Integrated Scientific Workbench Batch Run Server Database • MySql, Derby Data Visualisation ESRF ANSTO • ISAW, Ptplot Gumnix Lab Analysis Sequencer Data Files Analysis Servers • HDF, NeXus • DANSE GumTree Platform GumNIX Games HIPD Simulation Device HRPD Clock TAS Environment Control Device (Ancillary) SANS Other Eclipse Plug-ins REFL REST Core Data Data Analysis Algorithm MRPD Your Plug-ins Device ACC Instrument Operation Procedure CS Multimedia Eclipse RCP Runtime Their Plug-ins Accessaries SDK Testing Framework GumTree Project The GumTree Project An Eclipse Based GUI Framework for Scientific Experiments T. Lam, A. Götz, F. Franceschini, P. Hathaway, N. Hauser, H. Rayner Bragg Institute, ANSTO, Lucas Heights Sydney, Australia Open Source Technologies Introduction Architecture Design Open Source Technology encourages code reusability, reducing code maintenance, and leveraging other developers’ effort at no cost. The following technologies have been embedded to enhance the functionality of GumTree: Eclipse Project:Eclipse has been used extensively throughout the Neutron Beam Instrument Project at ANSTO. It serves as an IDE (both Java and C), testing platform, database modelling, and the foundation of the GumTree Platform. Various Eclipse technologies such as Hyades, GEF and automated testing framework are also being examined in the development process. IBM Cloudscape (Derby):Derby is a pure java based database with extremely small code size footprint. It has been embedded into GumTree to provide data storage for data transactions across the network. ISAW:Integrated Spectral Analysis Workbench software (ISAW) was designed specifically for visualising neutron scattering data. TANGO:TANGO is a CORBA based network protocol for controlling various instrument devices in a distributed environment. More than 100 device servers have been wrapped by TANGO. It is the result of multi institute collaborative effort between ESRF (France), Soleil (France) and Elettra (Italy). SICS:SINQ Instrument Control Software (SICS) is an UNIX based instrument control system developed by Mark Könnecke from the Paul Scherrer Institute (PSI), Switzerland. SICS is currently being adapted by ANSTO to control beamline instruments in conjunction with GumTree. VTK: The Visualization ToolKit (VTK) is an API for 3D computer graphics, image processing, and visualization used in different areas such as medical imaging and molecule modelling. FreeTTS:A free Java Text-To-Speech component to improve the accessibility of GumTree. HDF / NeXus:Hierarchical Data Format (HDF) is an effective file format for managing scientific data. This is developed by the National Center for Supercomputing Applications (NCSA) and the University of Illinois. NeXus is an implementation of HDF, which is now widely accepted by the Neutron and X-ray Scattering community as the data storage format. GumTree is an open source Eclipse Rich Client Application for running scientific experiments under a distributed environment. It provides an intuitive graphical front end (scientific workbench) for instrument data acquisition, data visualisation and analysis, allowing a complete experiment cycle to be performed under a single application. The foundation of GumTree is based on a GUI framework named the GumTree Platform. It contains the infrastructure for control system, data format handling, visualisation tool adaptation, and other GUI components as extensions of the Eclipse Platform. Software developers can rapidly customise and extend GumTree to any client-server based scientific instrument. GumTree is being adapted to several instrument control server system protocols including TANGO, EPICS, CIMA and SICS. The Eclipse RCP version of GumTree begun at ANSTO in the middle of 2004, to serve as the multi-platform solution for remotely controlling six neutron beam instruments at the Open Pool Australian Light-water (OPAL) reactor. At the end of 2004, GumTree became an open source project, encouraging ongoing development for other scientific areas, like telescope control and sensor networks. The GumTree Platform is designed to be highly adaptable with other building blocks in a dynamic instrument system. For example, developers can choose to adapt a different plotting package without refactoring any code for the graphical user interface. Components within the framework allow exchange of data to achieve tight integration between building blocks in the system. The design also leverage from many features provided by Eclipse and other open source technologies (see “Open Source Technologies” section for details). Rich Client Application ANSTO and The Neutron Beam Instrument Project GumTree demonstrates the power of Eclipse Rich Client Platform in scientific computing. The following screenshots show the latest development of the GumTree Project: The Australian Nuclear Science and Technology Organisation (ANSTO) is Australia’s national nuclear research and development organisation and the centre of Australian nuclear expertise. ANSTO has a salaried staff of approximately 850. Its main site is located at Lucas Heights, 40 km south west of Sydney’s Central Business District. ANSTO is currently constructing a new 20 megawatt replacement reactor, the Open Pool Australian Light-water(OPAL) reactor, for research purposes. The OPAL reactor will facilitate radioisotope production, irradiation services and neutron beam research. It is designed to achieve high performance in the production of neutrons. Collaborators In addition to the current development of GumTree at ANSTO, GumTree is also being proposed as the scientific workbench for different scientific institutions around the World. ESRF at Grenoble (France) is proposing GumTree as the data analysis front end for their X-ray scattering. PSI (Switzerland) is also considering to use GumTree for their spallation base neutron scattering instruments after GumTree completes its first development cycle. Blood cells, plastic, paper, magnets, chocolate, aircraft components - if it has an atomic structure, our understanding of it can be improved by scientists using neutrons. Thermal neutrons generated in research reactors are scattered by atoms in the material being probed. The scattering pattern reveals the sample's molecular structure. This technique is called neutron scattering, the subject of the 1994 Nobel Prize for Physics. Eight neutron beam instruments are planned for the OPAL reactor under the Neutron Beam Instrument Project (NBIP) by the Bragg Institute. Instruments will be located in a neutron guide hall next to the reactor. A suite of equipment will enable studies at different temperatures, pressures and magnetic fields. Motor Control View, Scientific data browser and 3D visualisation with VTK (Windows / XP) GumTree as a Data Analysis Workbench for neutron scattering data Crystallography Microstructure Structure Polymers Micelles Atomic Structures Precipitates Grain Structures Porous Media X-ray, Neutron Diffraction SANS/ SAXS NR/ XRR 1-100nm Optical Microscopy Grand Unified Model (GUM) Instrument Status and Scan View, Temperature Controller View, 2D Detector Visualisation, and simple 1D Data Fitting Plot (SWT/AWT) Instrument Device Navigator and Command Line Terminal for the Control System (Linux /GTK) “GUM ”Building Blocks References • GumTree / GumNIX Project Homepage, http://www.ansto.gov.au/ansto/bragg/2005/comp/gui.html • ANSTO, http://www.ansto.gov.au • NBIP Homepage, http://home.ansto.gov.au/ansto/bragg/2005/nsrrr.html • GumTree Platform Homepage (SourceForge), https://sourceforge.net/projects/gumtree • Andy Goetz and Nick Hauser, Grand Unified Model for Control and Analysis Systems, NOBUGS 2004 • Eclipse RCP Community, http://www.eclipse.org/community/rcp.html • SICS Homepage, http://lns00.psi.ch • TANGO Homepage, http://www.esrf.fr/computing/cs/tango/tango.html • ISAW Homepage, http://www.pns.anl.gov/computing/isaw These days a complex scientific instrument can have multiple GUIs to control different aspects of the system. Many of the GUIs are ad-hoc and difficult to port into another instrument of its type. In order to reduce development and the user learning curve, GumTree closely follows an instrument control philosophy called the “Grand Unified Model” (or simply GUM). Extending GumTree Extending GumTree becomes easy with the help of the Eclipse plug-in architecture and extension point framework. Many non-IDE Eclipse plug-ins can be integrated into the workbench as usual. The GumTree Platform also defines an API that allows developers to adapt new control system, device, and data format support in GumTree. GumNIX, which stands for GumTree Neutron Beam Instrument Extension, contributes a set of instrument specific plug-ins to the GumTree application. GumTree may soon be extended to provide a transparent GRID enabled service for data analysis and global file storage of scientific data. Grand Unified Model States: The control and analysis parts of a scientific experiment must be treated as part of one system with input and output being readily exchanged between all parts of the system. There must be a single integrated graphical user interface from which all aspects of the control and analysis system can be accessed. There is a basic set of building blocks that all control and analysis systems should have. All building blocks should have a well defined interface.