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JAS3 – Current Status and Prospects

JAS3 – Current Status and Prospects. by Victor Serbo, SLAC. Contents. Introduction to JAS3 (Java Analysis Studio) Basic: Opening Files, Plots, Printing, etc. Web Browser, Editor, Java Compiler, Scripting Miscellaneous: Spreadsheet, Configuration Save/Restore, Preferences, etc. Analysis

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JAS3 – Current Status and Prospects

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  1. JAS3 – Current Status and Prospects by Victor Serbo, SLAC

  2. Contents • Introduction to JAS3 (Java Analysis Studio) • Basic: Opening Files, Plots, Printing, etc. • Web Browser, Editor, Java Compiler, Scripting • Miscellaneous: Spreadsheet, Configuration Save/Restore, Preferences, etc. • Analysis • AIDA – Abstract Interfaces for Data Analysis • JAIDA – Java Implementation of AIDA • AIDA JNI – using JAIDA from C++ • Analysis with JAIDA and JAS3 • JAS3 Plugins • What is Plugin, examples • Demo: AmbientPlugin and Geant4 Plugin • Demo: JAIDA Web Interface JAS3 – Current Status and Prospects, V. Serbo

  3. JAS3 Overview • A completely new version of JAS • Design based on Application Shell, into which many (optional) modules can be plugged • Highly customizable for different application domains • HEP/Astrophysics/Other • Data analysis/Online Monitoring/GRID analysis • Experiment/User specific modules • Modules can be updated independently of shell • Possible to release bug fixes fast • Includes support for programming in many languages • Scripting: Pnuts, Python, …. • Command prompt • Java (compiled) • Analysis (histograms, tuples, fitting) based on AIDA standard • Not technically backwards compatible with JAS2 • But migration is straightforward. JAS3 – Current Status and Prospects, V. Serbo

  4. JAS3 Lightning Tour • Tour designed to give you an overview of the capabilities of JAS3, you can try them out for yourself: http://jas.freehep.org/jas3 Welcome Page, gives initial info and links to example scripts and programs Memory monitor JAS3 – Current Status and Prospects, V. Serbo

  5. Opening Files Use file menu Drag from explorer JAS3 – Current Status and Prospects, V. Serbo

  6. Plot Manipulation and Printing Or copy/paste into Word, PowerPoint etc. Can send individual plots or full page direct to printer Or save as PS, EPS, PDF, SWF, SVG, PNG, GIF… JAS3 – Current Status and Prospects, V. Serbo

  7. Java Editor, Compiler and Loader Tree shows loaded programs Built-in editor for writing analysis code JAS3 allows any Java program to be loaded. This example “main routine” is taken directly from the AIDA manual Built-in Java compiler JAS3 – Current Status and Prospects, V. Serbo

  8. Miscellaneous Features Save/Restore configuration User Preferences Plugin Manager JAS3 – Current Status and Prospects, V. Serbo

  9. JAS3 Spreadsheet • Simple spreadsheet plugin • for • Displaying results • Calculations • Simple Plots • Supports reading/writing • .csv files • Excel files • Cut/Paste with Excel etc • Coming Soon… • Scripting interface • GUI for building plots • User defined functions • Java, scripting JAS3 – Current Status and Prospects, V. Serbo

  10. JAS3 Scripting • JAS3 has multi-language OO scripting support • Command line, Console, Editor • Major components (e.g. AIDA) have scripting interfaces • Currently have plugins to support • Pnuts – syntax almost identical to Java, fast, well documented and feature complete • Python • Use Jython (the Java implementation of Python) • Limitation: can not call Python libraries written in C • More scripting languages can be added • not restricted to Java implementations (e.g. could use C-Python, JPE) JAS3 – Current Status and Prospects, V. Serbo

  11. Pnuts Language • Currently support Pnuts scripting language • Complete and well documented • http://javacenter.sun.co.jp/pnuts/doc/guide.html • Fast (although not as fast as compiled Java) • Syntax very similar to Java; can compile script into Java bytecode or convert it to Java code • Can easily call compiled Java classes from scripts – best of both worlds JAS3 – Current Status and Prospects, V. Serbo

  12. JAS3 Scripting II Can also write and run scripts Console allows direct interaction with scripting language JAS3 – Current Status and Prospects, V. Serbo

  13. AIDA - Abstract Interfaces for Data Analysis • AIDA is a standard set of interfaces for creating and manipulating histograms, n-tuples and related data analysis objects, like Plotter, Fitter, etc. • AIDA defines storage XML format. • It has been created cooperatively by a group of developers working on high-energy physics data analysis tools. The goal of the AIDA project is to provide the user with a powerful set of interfaces which can be used regardless of which analysis tool they are using. • Only define “protocol” for analysis objects, no internal details • AIDA defines behavior, analysis tool provides implementation • C++ and Java versions of interfaces are generated from the AID files. JAS3 – Current Status and Prospects, V. Serbo

  14. AIDA Examples • IHistogram1D • IAxis axis() • void fill(double x) • void fill(double x, double w) • double mean() • double rms() • double binEntries(int index) • double binError(int index) • …. • For more details on AIDA, see: http://aida.freehep.org • IAxis • int bins() • double lowerEdge() • double upperEdge() • double binLowerEdge(int index) • double binUpperEdge(int index) • double binWidth(int index) • int coordinateToIndex(double x) • …. JAS3 – Current Status and Prospects, V. Serbo

  15. JAIDA • JAIDA = Java implementation of AIDA • Complete implementation of AIDA interfaces • With a few exceptions • Support for plot styles is somewhat limited • Some missing features in ITree, like cp, mv • Uses Java “service provider mechanism” for dynamic loading of services at Runtime • Can be used to add support for new fitters, stores etc. • Have defined “developer level” interfaces for IOptimizer, IStore etc • Uses Java Expression Library (JEL) for runtime compilation of expressions (for tuple evaluators and functions) JAS3 – Current Status and Prospects, V. Serbo

  16. JAIDA – Features continued… • Fitting • support for multiple fitting engines (optimizers) • UNCMIN (pure Java) • Minuit (needs minuitAdapter native library) • Support for multiple fitting methods • LeastSquares, Chi2, BinnedMaximumLikelihood and UnbinnedMaximumLikelihood • Stores • Read/Write support for AIDA XML format (with built-in gzip) • Read support for HBOOK/PAW files (needs hbookAdapter native library) • Read support for Root files (write support hopefully coming soon) • Future plans to add: • SQL interface, binary store format, text file support … • Plotting • Two implementations of IAnalysisFactory • BatchAnalysisFactory – dummy plotter, ignore calls to IPlotter • AnalysisFactory – Full plotter functionality • Multi-Threaded – plots update in real-time as they are filled • No need to call interact() or refresh() • Support for embedding plotter • In other Java GUI’s • In Java servlets for web based applications. • Graphics export in many formats including: • PDF, EPS, SVG, SWF, PNG, GIF, JPG JAS3 – Current Status and Prospects, V. Serbo

  17. C++ program AIDA- JNI AIDA AIDA AIDA-JNI • C++ interface uses AIDA-JNI JAIDA (Java) • AIDA-JNI partially generated by AID, partly by hand • Does support full AIDA functionality JAS3 – Current Status and Prospects, V. Serbo

  18. Using JAIDA with Java JAS3 – Current Status and Prospects, V. Serbo

  19. Using JAIDA with Python JAS3 – Current Status and Prospects, V. Serbo

  20. Using JAIDA with C++ JAS3 – Current Status and Prospects, V. Serbo

  21. Future Plans for JAIDA • Complete implementation of missing features • Continue to track improvements to AIDA standard • Add support for function arithmetic • Web Interface • Support for “Remote AIDA” • Support for more storage formats • Need good binary IO format .. either AIDA standard or roll our own • Future AIDA developers’ meetings JAS3 – Current Status and Prospects, V. Serbo

  22. JAS3 and AIDA • JAS3 uses JAIDA - supports all AIDA functionality, including • Histograms (includes arithmetic, projections, etc.) • Clouds (unbinned histograms, scatterplots) • Plotter • Tuples • Fitting – AIDA interfaces allow for multiple fitters • Uncmin -- pure java minimizer • Minuit -- Fortran called by Java Native Interface (JNI) • IO • AIDA XML, PAW, Root • JAS3 supports user interaction with AIDA in three ways • Scripting (Pnuts, Python etc) • Compiled (Java) code • GUI – Plotting, Fitting, Cuts etc. JAS3 – Current Status and Prospects, V. Serbo

  23. Graphical Interface to AIDA Histograms, Clouds, Tuples all presented in AIDA tree .aida files, .hbook files, .root files all presented as AIDA objects Drag items onto page, or use (popup) menus JAS3 – Current Status and Prospects, V. Serbo

  24. Tuple Explorer - Plots Histogram Profile Works with any tuple, read from file or dynamically created ScatterPlot XY Data (More appropriate for smaller data sets) JAS3 – Current Status and Prospects, V. Serbo

  25. Tuple Explorer – Define Columns JAS3 – Current Status and Prospects, V. Serbo

  26. Tuple Explorer - Cuts JAS3 – Current Status and Prospects, V. Serbo

  27. Tuple Explorer - Tabulate JAS3 – Current Status and Prospects, V. Serbo

  28. Tuple Explorer – Record Source To be used with record loop JAS3 – Current Status and Prospects, V. Serbo

  29. Record Sources Opening record (or event) based files causes the run control toolbar to appear Supports random access and “tagged” data sets (mainly for event displays) JAS3 – Current Status and Prospects, V. Serbo

  30. JAS3 Plugins • JAS3 is based on the Freehep Application Framework, which provides a basic application framework into which extension modules, or "plugins" can be loaded. • The application framework provides general purpose functionality, such as top level GUI (windows, menus etc.), help system, storing and retrieving user preferences etc. • All of the data analysis specific functionality of JAS3 is provided by a set of extension modules. • Modules communicate with each other via service interfaces and notification events. JAS3 comes with a standard set of service interfaces and notification events, but new plugins can also define their own interfaces and events. JAS3 – Current Status and Prospects, V. Serbo

  31. JAS3 Plugin II • Plugin functionality: • Do some plugin-specific task • Use services provided by other plugins • Provide services to other plugins • Modify JAS3 menus and pop-up menus • “Core” Plugins – provide basic services • Simple: File Opener, Memory Status, Status Bar, … • More Complex: Web Browser, Plotter, Console, XMLIO, … • “Extensions” – separate packages • Included with JAS3 distribution • AIDA, TupleExplorer, JAVA Compiler and Editor, Spreadsheet, … • Specific to particular Experiment • BaBar Ambient DB Browser: AmbientPlugin, Geant4 Plugin, etc. • Partial Tutorial on writing a plugin: http://jas.freehep.org/jas3/developers/tutorial.jsp JAS3 – Current Status and Prospects, V. Serbo

  32. JAS3 Plugin Demo I • AmbientPlugin: • Access BaBar Ambient DB via CORBA • Present Time History as an AIDA object (DataPointSet) CORBA Server (C++) BaBar Ambient DB JAS3 (Java) AmbientPlugin (Java CORBA Client) JAS3 – Current Status and Prospects, V. Serbo

  33. JAS3 Plugin Demo II • Gean4 Plugin Geant4 Application (C++) Java RMI Server JNI Layer JAS3 (Java) Geant4 Plugin (Java RMI Client) JAS3 – Current Status and Prospects, V. Serbo

  34. AIDA Web Interface

  35. Goals • Provide access to Histogram plots without requiring any software installation • Putting results on to the web for collaborators etc. • For example for viewing results of “quality control” plots • Viewing “live” histograms on the web for • Online monitoring • Monitoring progress of batch jobs • Add as much functionality as possible in a “generic” way so that it can be used by others (with minimal work) • Complete “out-of-the-box” web application • Packaged as a .war file for use with any J2EE app server • (e.g. Tomcat) • Configurable via a simple .ini file (or better via a web interface) JAS3 – Current Status and Prospects, V. Serbo

  36. Application Server (Tomcat) Web Application JAIDA AIDA Servlet SQL C++ App Remote AIDA … Java App Architecture .root .paw .aida JAS3 – Current Status and Prospects, V. Serbo

  37. Features • Current Feature set • Display of “AIDA Tree” for selection of histograms • Displays plots as .png or .gif images in browser • Allows (limited) control of image properties • Allows (limited) control over plot properties • Allows comparison to reference plots (including Kolmagorov test) • Allows export of plots to PDF, EPS, SVG, SWF, GIF, PNG, etc. • Planned features • Extend to support n-tuples as well as histograms • Dynamic definition of new columns and cuts (evaluators, filters) • Web based fitting (including function definition) • Support multiple plots per page • Thumbnail browser • Extend which plot options can be configured through web • Allow users to retain settings via cookies JAS3 – Current Status and Prospects, V. Serbo

  38. Current Interface Can try from the web: http://glast02.slac.stanford.edu:8080/aida/welcome.html JAS3 – Current Status and Prospects, V. Serbo

  39. Status • Currently released JAS3 version 0.7.3 (0.7.4 next week) • AIDA functionality is quite solid • Compiler, Loader, Record Loop all quite recently added, • Certainly still some rough edges • Documentation limited but available • Built-in example scripts and programs • Tutorial on web • If you used JAS2 you will find some functionality not yet ported to JAS3 • Remote (client/server) access to data. • 3D Lego/Surface plots JAS3 – Current Status and Prospects, V. Serbo

  40. JAS3 Conclusion • JAS3 is a powerful and flexible Analysis Tool • JAS3 uses Plugin Architecture • Easy to add new functionality • Easy to fix problems with existing modules – do not have to wait for new release of all libraries • JAS3 release 0.7.3 is out – try it! • It is still a beta version, so bugs happen • We need your input to make JAS3 better! • Report bugs, problems, suggestions at http://bugs.freehep.org • Do not have to be on JAS team to be JAS developer – ideas/code for general-purpose plugins are always welcome • Try writing JAS3 plugins for your own needs: for Experiment and Home  JAS3 – Current Status and Prospects, V. Serbo

  41. JAS3 Links, More Info • Report Issues – http://bugs.freehep.org/ • JAS – Java Analysis Studio - http://jas.freehep.org • JAS3 – http://jas.freehep.org/jas3 • JAIDA – http://java.freehep.org/jaida/ • AIDA – http://aida.freehep.org • FreeHEP - http://www.freehep.org • FreeHEP Java Libraries - http://java.freehep.org • WIRED – http://wired.freehep.org JAS3 – Current Status and Prospects, V. Serbo

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