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ElVis Developments for Simulation and Analysis Programs

This project focuses on developing enhancements for ElVis, a Java-based visualization software used to graph outputs of scientific experiments and simulations. The goal is to improve the netCDF panel in ElVis and add new capabilities such as data selection, data interpolation, and logarithmic surface plots. The project also aims to implement graph window templates, allowing users to format graphs without programming.

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ElVis Developments for Simulation and Analysis Programs

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  1. ElVis Developmentsfor Simulation and Analysis Programs Tarun Pondicherry Summer 2006 Science Ed High School Intern Eliot Feibush, Mentor 8/16/2006

  2. MSE – Motional Stark Effect • Local Magnetic Field Measurements by Motional Stark Splitting – JET • Determine direction of magnetic field lines inside plasma • MSE diagnostic measures current profiles in plasma Source: JET Website - jet.efda.org

  3. MSE Simulation • Simulate MSE diagnostic for ITER design • Source code from JET • Required GHOST graphics package – impractical to distribute • Modified by Tina Ludescher to output results to netCDF file instead of using GHOST • Separated Simulation from Visualization • Display graphs of netCDF variables in ElVis

  4. ElVis Developmentsfor Simulation and Analysis Programs Tarun Pondicherry Summer 2006 Science Ed High School Intern Eliot Feibush, Mentor 8/16/2006

  5. Overview Background My Topics: 1. MSE (Motional Stark Effect) 2. Monitoring Simulations 3. Interactive Techniques Demo

  6. Background • ElVis – Java based Visualization Software which graphs outputs of scientific experiments and simulations • Accepts input from a variety of sources including Data Files, Sockets, Simulations, etc. • Graphs 1D and 2D data in several forms (Animated, Surface, Contour, etc.) • Reads variables from netCDF Files; User composes graphs

  7. NetCDF File Format • File format and interface for scientific data storage • Machine Independent and accessible through URL • Consist of a collection of dimensions, variables and attributes • Variable • Single Value • Array of one or more Dimensions • Variables and Dimensions can have attributes specifying units, alternate names or other information • Unidata provides NetCDF API’s in C, Java and Fortran

  8. NetCDF File Elements • convention = elvis • elvis_template = mytemplate.xml • time = 50 • long_name = time_of_capture • unit = seconds • x_coordinate = 200 • time [time] • sine [x_coordinate X time] • amplitude = 1 • time = {0,2,6,17,…} • sine = {-1, -0.5, 0, 0.5,…} {-1, -0.75, -0.5, -0.25,…} … • Global Attributes • … • Dimensions • Attributes • … • … • Coordinate Variables [dim name] • Attributes • … • … • Variables (definition) [dim0 x dim1 x …] • Attributes • … • … • Variables (data) • …

  9. 1. ElVis Enhancements for netCDF Data • Motivation • MSE display requirements • Generalize monitoring of Fusion Simulations & Analysis programs

  10. My Goals Improve netCDF Panel in ElVis • Insert in first cell of GraphWindow (previously separate frame, confusing when many files open) • List all variables (previously listed only 1D and 2D) • Read files with large number of variables (TRANSP) Add New Capabilities to ElVis • Select 2D subset of 3D+ variable • Transpose 2D variable • Save/Load GW presentation templates • Progress pop-up • Monitor output files from long-running programs

  11. Data Selection • Allows variables with more than 2 dimensions to be plotted in ElVis • Users specify a 2D “slice” by selecting the index for the fixed dimensions • Result is ordinary 2D data • Can be presented as Animated, Surface, Contour or Multiplot • 2D slices can be plotted with normal 2D variables, other 2D slices or a combination of both – multiple 2D variables

  12. Data Selection and Display

  13. 2D Presentation Styles • Allow ElVis to convert between all types of 2D plots (Animated, f(x,i), Contour, Surface) • Original 2D data stored in memory • When presentation changes, data is read from memory to create the desired plot Added multi-plot – requested by MSE physicists

  14. Logarithmic Surface Plots • Applied logarithmic scaling functions to Surface plots • (Log functions developed by Steve Krenzel) • All axes (X, Y, Z) can be independently scaled as linear or logarithmic

  15. Transpose Data • Transposes data within the 2D array prior to plotting • Once transposed, data remains that way for any presentation option • Animated swaps X Axis and Index • Contour swaps X and Y • Surface swaps X and Z • Multiplot swaps X Axis and Index

  16. Data Interpolation • Allows Variables of Different Lengths to be plotted against each other • Adds or removes x values to match number f(x) values • Values added created by linear interpolation • Values removed by periodic sampling • Works for both 1D and 2D data • Performed automatically when dataset sizes vary

  17. Data Interpolation Example

  18. Graph Window Templates • Suggested by Steve Scott for MSE • Allow ElVis to show NetCDF Files with a user specified view • Enables author of the data to format graphs (without programming!) for collaborators to view over the Internet

  19. Graph Window Templates • Stored in XML under the user home directory • ElVis automatically finds templates in 3 ways: • .cdft file with the same name as the NetCDF File in the same directory • elvis_template attribute specified in NetCDF File • default template stored in settings.props in user home • Users can choose a different template from the drop down in the template panel • ElVis stores the most recently used template as the default

  20. 2. NetCDF File Monitoring • Allows Elvis to monitor simulations which periodically update a NetCDF File • Polls the file on the server, checks for dimension length change; user specifies rate • Starts and stops automatically if “running” attribute set to true or false in the NetCDF File • When the file is updated, ElVis loads new file and replots with the current template

  21. File Monitoring – Solution • Generalized way to monitor simulations • Overcomes the need for custom programming for monitoring • Can be combined with templates to compose the graphs without programming • Fusion Simulation Projects

  22. 3. Interactive Techniques • Resize graphs when frame is resized - warm-up exercise • Legend display options • Interactive Positioning • Graph width • Dataset editor • Edit set names • Color, style, thickness • Points, Lines • Access Greek Letters in Unicode Font • Save/Load to ElVis convention netCDF file

  23. Unicode Font Character Chooser • Unicode –16 bit font overcomes limit of ASCII’s 8 bits • Enables storing 1000s of characters organized by function, e.g. Greek Letters, Math Symbols • Java uses Unicode Fonts  Developed Character Chooser • Displays selected section in a grid • Displays recently selected characters at the bottom • User clicks on letter to add it to label

  24. Summary – How I spent my summer vacation • ElVis enhancements for MSE display requirements • Generalized solution for monitoring simulations • Interactive techniques

  25. Acknowledgements • Eliot Feibush • Jill Foley for MSE background info • James Morgan, Andrew Post-Zwicker and the PPPL Science Education Department • Princeton Plasma Physics Lab

  26. Demo • ElVis • http://w3.pppl.gov/elvis/

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