Visualization Environment for Rich Data …

1 Visualization Environment for rich data interpretation (VERDI ): User s Manual EPA Contract No. EP-W-09-023, Operation of the Center for Community Air Quality Modeling and Analysis (CMAS) Prepared for: William Benjey and Donna Schwede EPA, ORD/NERL/AMD/APMB E243-04 USEPA Mailroom Research Triangle Park, NC 27711 Prepared by: Liz Adams and Darin Del Vecchio Institute for the Environment The University of North Carolina at Chapel Hill 137 E. Franklin St., CB 6116 Chapel Hill, NC 27599-6116 Date: April 30, 2013 User s Manual for VERDI UNC Chapel Hill ii Institute for the Environment Contents 1 Introduction ..1 Background ..1 Where to Obtain VERDI ..2 Where to Obtain VERDI Documentation ..6 Help Desk Support for VERDI.

2 8 Future VERDI Development ..8 2 Requirements for Using VERDI ..9 Java Runtime Environment ..9 Memory and CPU Requirements ..9 Requirements to Run VERDI Remotely ..10 Graphics Requirements ..10 Display Properties ..10 3 VERDI Installation Instructions ..10 VERDI Installation ..10 Installation Instructions for Linux and Other Non-Windows JRE 6 Supported System Configurations ..11 Installation Instructions for computer that that requires a JRETM 6 other than what was provided in the distribution:..11 Installation Instructions for Windows ..12 Setting VERDI Preferences ..16 4 Starting VERDI and Getting Your data into VERDI ..18 Starting VERDI ..18 Windows ..18 Linux and Other Non-Windows JRETM 6 Supported System Configurations ..18 Main Window.

3 19 Floating the Dataset and Formula Panes ..20 5 Navigating VERDI s Main Menu Options ..20 File Menu Options ..21 Open User s Manual for VERDI UNC Chapel Hill iii Institute for the Environment Save Project ..21 View Script Editor ..21 Plots Menu Undock All Plots ..22 Animate Tile Plots ..22 Window Menu Options ..23 Datasets and Formulas ..23 List of Plots ..23 Help Menu Options ..24 6 Working with Gridded Datasets ..24 Gridded Input File Formats ..24 Model Formats ..24 Observational data Formats ..24 Example Datasets ..25 Adding and Removing a Dataset from a Local File System ..26 Adding and Removing a Dataset from a Remote File System ..28 Remote File Browser ..28 Adding Additional Remote Hosts ..31 Variables List.

4 32 Time Steps, Layers Panels ..33 Domain Panel ..33 Saving 7 Working with Formulas ..34 Adding and Removing a Formula ..34 Example Formulas ..37 Selecting a Formula for Plotting ..37 Saving Formulas ..37 Time Step Range, Layer Range, and Edit Domain ..37 8 Working with Area Files ..38 Area File Formats ..38 Example Area File ..38 Adding and Removing an Area File ..38 Areas List ..39 Areal Interpolation ..39 9 Spatial and Temporal data Subsetting ..43 User s Manual for VERDI UNC Chapel Hill iv Institute for the Environment Specify Time Step Range ..44 Specify Layer Range ..44 Specify Domain Range ..45 Rules of Precedence for Subsetting data ..47 10 Creating Plots ..48 Fast Tile Plot ..49 Time Selection and Animation Layer Selection.

5 50 Grid Cell Time Aggregate Statistics ..50 Areal Interpolation Option Pull-down Menu Item ..51 Areal Values for Polygon View and Export Areal Plot data in Spreadsheet Format ..56 Export Areal Plot data to Shapefiles ..57 Vertical Cross Section Plot ..58 Time Series Plot ..60 Time Series Bar Plot ..60 Scatter Plot ..61 Vector Plot ..63 Contour Plot ..65 11 Plot Menu Bar ..65 File Menu Options ..67 Configure Menu Option ..67 Configuring Plots ..67 Loading and Saving Configuration ..70 Controls Menu Options ..71 Zoom Using the Left Mouse Button ..71 Zoom Using the Right Mouse Button ..71 Vector 71 Fast Tile Plot and Areal Plot .. 72 Probing Values at Specific Points ..73 Probing a Domain Region of data ..74 Set data Ranges.

6 75 Showing Latitude and Longitude ..77 Plot Menu Options ..78 Time Series Plots ..79 User s Manual for VERDI UNC Chapel Hill v Institute for the Environment Animate Plots ..79 Add Overlays ..80 Observational data Overlays .. 80 Vector 82 GIS Layer Options (Fast Tile Plot) ..84 Add Map Layers ..84 Configure GIS Layers (Fast Tile Plot) ..87 Set Current Maps as Default Location ..89 12 Supported Grid and Coordinate Systems (Map Projections) ..89 I/O API-formatted data ..89 CAMx Gridded data ..93 13 I/O API Utilities, data Conversion Programs, and Libraries ..96 14 Contributing to VERDI Development ..96 15 Known Bugs ..97 16 Mathematical Functions ..97 17 VERDI Batch Script Editor ..100 Specify hour/time step formula in batch script mode.

7 106 Mathematical function capability in batch script mode ..108 Batch Script Example: Maximum Ozone layer 1 (Figure 17-11) ..108 Batch Script Example : Minimum Ozone layer 1 (Figure 17-12) ..109 Batch Script Example : Mean of Ozone layer 1 (Figure 17-13) ..110 Batch Script Example : Sum of Ozone layer 1 (Figure 17-14) ..111 18 Command Line Scripting ..112 Example Command Line Script for Linux Users ..112 Example Command Line Script for Windows Users ..113 19 Areal Interpolation Calculations ..118 20 Licenses for JAVA Libraries used by VERDI ..119 Acknowledgments ..120 data Contributions ..120 data Reader Contributions ..120 I/O Service Provider (IOSP) Interface for CAMx: ..120 Incorporating the IOSP into netCDF netcdf-java Library: ..120 User s Manual for VERDI UNC Chapel Hill vi Institute for the Environment User s Manual for VERDI UNC Chapel Hill vii Institute for the Environment Figures Figure 1-1.

8 Top of Main VERDI Web Site Page ..3 Figure 1-2. Downloading VERDI from the CMAS Web Site, Step 1 ..4 Figure 1-3. Downloading VERDI from the CMAS Web Site, Step 2 ..5 Figure 1-4. Downloading VERDI from the CMAS Web Site, Step 3 ..6 Figure 1-5. Getting Documentation on VERDI from the CMAS Web Site ..7 Figure 1-6. VERDI Documentation on the CMAS Web Site ..8 Figure 3-1. VERDI Setup Wizard ..13 Figure 3-2. License Agreement ..13 Figure 3-3. Selecting an Installation Directory ..14 Figure 3-4. Setting the Start Menu Folder ..14 Figure 3-5. File Extraction ..15 Figure 3-6. Installation Complete ..16 Figure 4-1. Starting VERDI in Windows ..18 Figure 4-2. VERDI Main Window ..20 Figure 5-1. VERDI Main Menu Options ..21 Figure 5-2. Animate Plots Dialog and Fast Tile Plots.

9 23 Figure 6-1. Observational File ASCII Format ..25 Figure 6-2. Open Dataset File Browser ..26 Figure 6-3. Datasets Pane Displaying Information about a Dataset ..27 Figure 6-4. Available Hosts in the Remote File Access Browser ..28 Figure 6-5. Select one or more variables from Remote Dataset ..29 Figure 6-6. Remote Dataset Labeled with Number at End of the Filename ..31 Figure 6-7. Edit file to add a remote host ..32 Figure 6-8. Right Click on Variable in Dataset Pane ..33 Figure 6-9. Dataset Metadata Information ..34 Figure 7-1. Adding Multiple Variables to Formula Editor ..36 Figure 8-1. Areas Pane ..39 Figure 8-2. Open Area File Figure 8-3. Open Area File: Select Name Field ..40 Figure 8-4. Coordinate System ..41 Figure 8-5. Projection Information ..41 User s Manual for VERDI UNC Chapel Hill viii Institute for the Environment Figure 8-6.

10 Additional data Fields appear depending on projection selected..41 Figure 8-7. Area Name Fields available for Shapefile ..43 Figure 9-1. Specify Time Step Range ..44 Figure 9-2. Edit Layer Range in Formula Pane ..45 Figure 9-3. Using the Slider to View the Domain Panel ..46 Figure 9-4. Edit Domain Dialog Box ..46 Figure 9-5. Error obtained when incompatible subset domains are created using the Dataset pane ..48 Figure 10-1. Fast Tile Plot ..49 Figure 10-2. Areal Plot: Area Average ..52 Figure 10-3. Areal Plot: Area Totals ..53 Figure 10-4. Areal Interpolation Plot: Show Grid (Gridded data ) ..54 Figure 10-5. Areal Interpolation Plot: Show Selected Areas ..55 Figure 10-6. Areal Values for Polygon Segments ..56 Figure 10-7. Right Click on Area Plot ..57 Figure 10-8.