Visualization Environment for Rich Data Interpretation (VERDI 1.4.1): User’s Manual

 

U.S. 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

                              U.S. 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

 


Contents

 

1     Introduction. 1

1.1     Background. 1

1.2     Where to Obtain VERDI 2

1.3     Where to Obtain VERDI Documentation. 6

1.4     Help Desk Support for VERDI 8

1.5     Future VERDI Development 8

2     Requirements for Using VERDI. 9

2.1     Java Runtime Environment 9

2.2     Memory and CPU Requirements. 9

2.3     Requirements to Run VERDI Remotely. 10

2.4     Graphics Requirements. 10

2.5     Display Properties. 10

3     VERDI Installation Instructions. 10

3.1     VERDI Installation. 10

3.2     Installation Instructions for Linux and Other Non-Windows JRE 6 Supported System Configurations  11

3.3     Installation Instructions for computer that that requires a JRETM 6 other than what was provided in the distribution: 11

3.4     Installation Instructions for Windows. 12

3.5     Setting VERDI Preferences. 16

4     Starting VERDI and Getting Your Data into VERDI. 18

4.1     Starting VERDI 18

4.1.1     Windows. 18

4.1.2     Linux and Other Non-Windows JRETM 6 Supported System Configurations. 18

4.2     Main Window.. 19

4.3     Floating the Dataset and Formula Panes. 20

5     Navigating VERDI’s Main Menu Options. 20

5.1     File Menu Options. 21

5.1.1     Open Project 21

5.1.2     Save Project 21

5.1.3     View Script Editor 21

5.2     Plots Menu Options. 22

5.2.1     Undock All Plots. 22

5.2.2     Animate Tile Plots. 22

5.3     Window Menu Options. 23

5.3.1     Datasets and Formulas. 23

5.3.2     List of Plots. 23

5.4     Help Menu Options. 24

6     Working with Gridded Datasets. 24

6.1     Gridded Input File Formats. 24

6.1.1     Model Formats. 24

6.1.2     Observational Data Formats. 24

6.2     Example Datasets. 25

6.3     Adding and Removing a Dataset from a Local File System.. 26

6.4     Adding and Removing a Dataset from a Remote File System.. 28

6.4.1     Remote File Browser 28

6.4.2     Adding Additional Remote Hosts. 31

6.5     Variables List 32

6.6     Time Steps, Layers Panels. 33

6.7     Domain Panel 33

6.8     Saving Projects. 34

7     Working with Formulas. 34

7.1     Adding and Removing a Formula. 34

7.2     Example Formulas. 37

7.3     Selecting a Formula for Plotting. 37

7.4     Saving Formulas. 37

7.5     Time Step Range, Layer Range, and Edit Domain. 37

8     Working with Area Files. 38

8.1     Area File Formats. 38

8.2     Example Area File. 38

8.3     Adding and Removing an Area File. 38

8.4     Areas List 39

8.5     Areal Interpolation. 39

9     Spatial and Temporal Data Subsetting. 43

9.1     Specify Time Step Range. 44

9.2     Specify Layer Range. 44

9.3     Specify Domain Range. 45

9.4     Rules of Precedence for Subsetting Data. 47

10   Creating Plots. 48

10.1   Fast Tile Plot 49

10.1.1   Time Selection and Animation Controls. 49

10.1.2   Layer Selection. 50

10.1.3   Grid Cell Time Aggregate Statistics. 50

10.2   Areal Interpolation Plot 51

10.2.1   Option Pull-down Menu Item.. 51

10.2.2   Areal Values for Polygon Segment 55

10.2.3   View and Export Areal Plot Data in Spreadsheet Format 56

10.2.4   Export Areal Plot Data to Shapefiles. 57

10.3   Vertical Cross Section Plot 58

10.4   Time Series Plot 60

10.5   Time Series Bar Plot 60

10.6   Scatter Plot 61

10.7   Vector Plot 63

10.8   Contour Plot 65

11   Plot Menu Bar. 65

11.1   File Menu Options. 67

11.2   Configure Menu Option. 67

11.2.1   Configuring Plots. 67

11.2.2   Loading and Saving Configuration. 70

11.3   Controls Menu Options. 71

11.3.1   Zoom Using the Left Mouse Button. 71

11.3.2   Zoom Using the Right Mouse Button. 71

11.3.2.1     Vector Plot 71

11.3.2.2     Fast Tile Plot and Areal Plot 72

11.3.3   Probing Values at Specific Points. 73

11.3.4   Probing a Domain Region of Data. 74

11.3.5   Set Data Ranges. 75

11.3.6   Showing Latitude and Longitude. 77

11.4   Plot Menu Options. 78

11.4.1   Time Series Plots. 79

11.4.2   Animate Plots. 79

11.4.3   Add Overlays. 80

11.4.3.1     Observational Data Overlays. 80

11.4.3.2     Vector Overlays. 82

11.5   GIS Layer Options (Fast Tile Plot) 84

11.5.1   Add Map Layers. 84

11.5.2   Configure GIS Layers (Fast Tile Plot) 87

11.5.3   Set Current Maps as Default Location. 89

12   Supported Grid and Coordinate Systems  (Map Projections) 89

12.1   I/O API-formatted Data. 89

12.2   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

17.1   Specify hour/time step formula in batch script mode. 106

17.2   Mathematical function capability in batch script mode. 108

17.2.1   Batch Script Example: Maximum Ozone – layer 1 (Figure 17-11) 108

17.2.2   Batch Script Example : Minimum Ozone – layer 1 (Figure 17-12) 109

17.2.3   Batch Script Example : Mean of Ozone – layer 1 (Figure 17-13) 110

17.2.4   Batch Script Example : Sum of Ozone – layer 1 (Figure 17-14) 111

18   Command Line Scripting. 112

18.1   Example Command Line Script for Linux Users. 112

18.2   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 v4.1 Library: 120

 


Figures

 

Figure 1‑1. 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. 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 configure.properties 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 Browser 40

Figure 8‑3. Open Area File: Select Name Field. 40

Figure 8‑4. Coordinate System.. 41

Figure 8‑5. Projection Information. 41

Figure 8‑6. 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. Area Information Spreadsheet 57

Figure 10‑9. Export Spreadsheet 57

Figure 10‑10. Name and save spreadsheet 57

Figure 10‑11. Export Shapefile. 58

Figure 10‑12. Name and save shapefile. 58

Figure 10‑13. Vertical Cross Section Plot 59

Figure 10‑14. Vertical Cross Section Dialog Box. 59

Figure 10‑15. Time Series Plot 60

Figure 10‑16. Time Series Bar Plot 61

Figure 10‑17. Scatter Plot 62

Figure 10‑18. Scatter Plot Dialog Box. 62

Figure 10‑19. Scatter Plot Export Data into a CSV file. 63

Figure 10‑20. Vector Plot 64

Figure 10‑21. Vector Plot Dialog Box. 64

Figure 10‑22. Contour Plot 65

Figure 10‑23. Contour Plot Menu Options. 65

Figure 11‑1. Fast Tile and Areal Plot Pull-down Menu Options. 66

Figure 11‑2. Vector Plot Pull-down Menu Options. 66

Figure 11‑3. Configure Plot, Titles Tab. 69

Figure 11‑4. Configure Plot, Color Map Tab. 69

Figure 11‑5. Configure Plot, Labels Tab. 69

Figure 11‑6. Configure Plot, Other Tab. 69

Figure 11‑7. Example Plot with Tick Marks reduced for the Legend and Range Axis. 70

Figure 11‑8. Right Click on Tile Plot to Zoom Out 72

Figure 11‑9. Right Click on Fast Tile Plot to access Zoom Out Option. 73

Figure 11‑10. Click on Plot to Probe: Data Value Shown in Lower Left of VERDI, Grid Values Shown in Lower Right 74

Figure 11‑11. Spreadsheet Showing Probed Values for Region of Interest 75

Figure 11‑12. Select Set Row and Column Ranges. 76

Figure 11‑13. Enter Row and Column Values. 77

Figure 11‑14. Lat/Lon Values Shown in Lower Right of VERDI 78

Figure 11‑15. Plot Menu Options. 79

Figure 11‑16. Animate Plot Dialog Box. 80

Figure 11‑17. Fast Tile Plot Observation Dialog. 81

Figure 11‑18. Fast Tile Plot with Multiple Observational Data Overlays with Grid Lines. 82

Figure 11‑19. Vector Overlay Dialog Box. 83

Figure 11‑20. Wind Vector Overlay on an Ozone Fast Tile Plot 84

Figure 11‑21. Plot Menu Options. 84

Figure 11‑22. Add Map Layers. 85

Figure 11‑23. shape2bin command usage. 86

Figure 11‑24. Manage Layers Dialog Box. 87

Figure 11‑25. Add Layer Pop-up Window.. 88

Figure 11‑26. Edit Layer Pop-up Window.. 89

Figure 12‑1. Lambert Conformal Conic Map Projection Example Plot 90

Figure 12‑2. Polar Stereographic Map Projection Example Plot 91

Figure 12‑3. Mercator Map Projection Example Plot 92

Figure 12‑4. UTM Map Projection Example Plot 93

Figure 12‑5. Example CAMx diagnostic text file. 94

Figure 12‑6. Models-3 I/O API Map Projection Parameters for Lambert 94

Figure 12‑7. Sample Projection File: camxproj.txt 95

Figure 12‑8. CAMx Example Plot 95

Figure 17-1. File: View Script Editor 100

Figure 17-2. Open Pop-up Window.. 101

Figure 17-3. Top of Sample Script File – VERDI_1.4.1/data/scripts/file_patterns.txt 102

Figure 17-4. Bottom of Sample Script File – VERDI_1.4.1/data/scripts/tile_patterns.txt 102

Figure 17-5. Close Dataset(s) Warning Message. 103

Figure 17-6. Highlight Text to Select Task and Click Run. 104

Figure 17-7 Successful Batch Script Run Message. 105

Figure 17-8. Unsuccessful Batch Script Run Message: File not found. 105

Figure 17-9. Plot Image Generated by Task Block. 106

Figure 17-10. Fast Tile Plot of Ozone at Time step 17, Layer 1. 108

Figure 17-11. Fast Tile Plot of Maximum Air Temperature (aggregated over 25 time steps) 109

Figure 17-12. Fast Tile Plot of Minimum Ozone (aggregated over 25 time steps) 110

Figure 17-13. Fast Tile Plot of Mean Ozone (aggregated over 25 time steps) 111

Figure 17-14. Fast Tile Plot of the Sum of Ozone (aggregated over 25 time steps) 112

Figure 18-1. Location of run.bat script in Windows. 114

Figure 18-2. Submit run.bat script from Run command. 115

                                                                                                               

 


1            Introduction

1.1      Background

This manual describes how to use the Visualization Environment for Rich Data Interpretation (VERDI). VERDI is a flexible and modular Java-based visualization software tool that allows users to visualize multivariate gridded environmental datasets created by environmental modeling systems such as the Community Multiscale Air Quality (CMAQ) modeling system and the Weather Research and Forecasting (WRF) modeling system. These systems produce files of gridded concentration and deposition fields that users need to visualize and compare with observational data both spatially and temporally. VERDI can facilitate these types of analyses.

Initial development of VERDI was done by the Argonne National Laboratory for the U.S. Environmental Protection Agency (EPA) and its user community. Argonne National Laboratory's work was supported by the EPA though U.S. Department of Energy contract DE-AC02-06CH11357.  Further development has been performed by the University of North Carolina Institute for the Environment under U.S. EPA Contract No. EP-W-05-045 and EP-W-09-023, by Lockheed Corporation under U.S. EPA contract No. 68-W-04-005, and Argonne National Laboratory.  VERDI is licensed under the Gnu Public License (GPL) version 3, and the source code is available through verdi.sourceforge.net.  Instructions for developers within the community are included in the Developer User Guide (see Section 1.3). VERDI is supported by the Community Modeling and Analysis System (CMAS) Center under U.S. EPA Contract No. EP-W-09-023. The batch script and VERDI Script Editor were developed and documented under U.S. EPA Contract No. EP-D-07-102, through an Office of Air Quality Planning and Standards project managed by Kirk Baker. The CMAS Center is located within the Institute for the Environment at the University of North Carolina at Chapel Hill.

This guide describes VERDI version 1.4.1 released in April 2013.

The following are useful web links for obtaining VERDI downloads and support:

1.      VERDI Visualization Tool web site:

http://www.verdi-tool.org

2.      CMAS download page for users of VERDI:
http://www.cmascenter.org/download/software.cfm

3.      CMAS SourceForge.net website for developers of VERDI:

http://sourceforge.net/projects/verdi/

4.      VERDI Frequently Asked Questions (FAQs):

http://www.verdi-tool.org/VERDI.faq.html

5.      To query M3USER listserv for VERDI related technical support questions and answers: http://lists.unc.edu/read/?forum=m3user

 

6.      To query bugs and submit bug reports, questions, and/or requests: http://bugz.unc.edu/enter_bug.cgi?product=VERDI
(If you do not already have a login and password, click the “Home” link for instructions on how to obtain them.)

1.2       Where to Obtain VERDI

You can download the latest version of VERDI from http://www.verdi-tool.org/ (see Figure 1-1). When you click on the link to download VERDI, you will be sent to the CMAS Model Download Center.  To download and install VERDI, follow the instructions below, skipping step 2.  Alternatively, you may also begin at the CMAS web site http://www.cmascenter.org, and follow the instructions below:

1.      Log in using an existing CMAS account, or create a new CMAS account.

2.      Hover the cursor over the Download Center link on the left-hand side of the web site and choose MODELS from the menu that appears.

3.       Select a model family to download, as shown in Figure 1-2. Use the pull-down list to select VERDI, and then click Submit.

4.      Select the product you wish to download, as shown in Figure 1-3. Also specify the type of computer you are planning to run VERDI on (such as Linux PC, Windows, or Other) from the items in the scroll list. Note that the compilers question is not relevant for VERDI so it can be skipped. Finally, click Submit.

5.      In the table that appears, follow the links to the Linux or Windows installation instructions, the release notes file, the user’s manual, the test documentation, and either a zip archive for Windows or a gzipped tar archive for Linux (see Figure 1-4).

Figure 11. Top of Main VERDI Web Site Page

Figure 12. Downloading VERDI from the CMAS Web Site, Step 1

Figure 13. Downloading VERDI from the CMAS Web Site, Step 2

Figure 14. Downloading VERDI from the CMAS Web Site, Step 3

1.3      Where to Obtain VERDI Documentation

Documentation is available in several locations, described below. Each location provides links to the available documentation for VERDI, which can be viewed in your web browser or downloaded and saved to your computer.    

·        The VERDI download page on the CMAS website (accessed using step 4 in Section 1.2) contains links to all of the available documentation.

·        On the left-hand side of the www.cmascenter.org web site, you can hover the cursor over the Help Desk link and choose DOCUMENTATION from the menu that appears. Select the product documentation that you want from the drop-down list (Figure 1-5) and click Submit. Select the model release from the drop-down list and click Search. The resulting documentation pane shows that the available documentation for the chosen release of VERDI.

·        From the www.verdi-tool.org web site, there are two ways to access the VERDI documentation on the www.cmascenter.org model documentation web page: (1) A link near the top of the www.verdi-tool.org home page sends you to a new page where you choose the model version. When you click submit, you are taken to the www.cmascenter.org VERDI documentation web page. (2) Direct links from a box on the right-hand side of the www.verdi-tool.org home page take you to the documentation available for VERDI.  Figure 1-6 shows the list of documentation that is available for download.

Figure 1‑5. Getting Documentation on VERDI from the CMAS Web Site

Figure 1‑6. VERDI Documentation on the CMAS Web Site

1.4      Help Desk Support for VERDI

You are encouraged to check the VERDI FAQs, search archived support requests using the web-based Bugzilla system, search the M3USER listserv for VERDI-related technical support questions, and report errors and/or requests for enhancement to the m3user forum.  The m3user forum is supported by the community and also by CMAS to help users resolve issues and identify and fix bugs found in supported software products.

1.5      Future VERDI Development

As stated in Schwede et al. (2007),[1] “VERDI is intended to be a community based visualization tool with strong user involvement.” The VERDI source code is available to the public under a GPL license at http://sourceforge.net/projects/verdi/.  This allows users who wish to make improvements to VERDI to download the software, and to develop enhancements and improvements that they feel may be useful to the modeling community. Examples could include user-developed readers for additional file formats and modules for additional plot types. Users may wish to contribute data analysis routines, such as adding the ability to do bilinear interpolation (smoothing), or to contribute other enhancements to the existing plot types. The direction of future development will depend on the resources and the needs of the modeling community.  If you are interested in contributing code to VERDI, please review the information in Chapter 14, “Contributing to VERDI Development.”

2            Requirements for Using VERDI

2.1      Java Runtime Environment

VERDI requires version 6 of the Java Standard Edition Runtime Environment (JRE). The JRETM 6  is provided as part of the VERDI release for Linux 32 bit and Windows. Instructions for how to download JRETM 6 and the additional third-party libraries for Linux 64 bit are provided in section 3.2.  On Windows 32 bit machines, the contour plot requires DirectX SDK.  Download and install this software if you obtain the following error when running the contour plot.

http://www.microsoft.com/en-us/download/details.aspx?id=6812

2.2      Memory and CPU Requirements

VERDI’s memory and CPU requirements largely depend on the size of the datasets to be visualized. Small datasets can be visualized and manipulated using less than 1024 megabytes of RAM, while larger datasets may need considerably more. If you are using datasets that require either more or less than 1024 MB of memory, you can change the default maximum memory setting used by VERDI:

·                    On Windows, edit the Verdi.ini file to specify a different heap size from the default 1024M. 

·                    On Linux or another Unix platform, you can edit verdi.sh and replace the 1024 in –Xmx1024M with a different value; for example, -Xmx2048M will allow VERDI to access up to 2048MB (or 2GB) of RAM.

Note that even slower CPUs can quickly view and animate smaller datasets, whereas larger datasets can take longer. Initially, VERDI’s performance was slow when it was used across the network via ssh. This problem was addressed in version 1.1 with the addition of the Fast Tile Plot. Beginning with version VERDI 1.4, memory was more effectively managed. As a user opens new Fast Tile plots or other plot types, the memory requirements increase. As the user then closes the plots, the memory is correctly released by VERDI.

2.3      Requirements to Run VERDI Remotely

VERDI may be used to run on a remote compute server and have the graphics display locally on your desktop machine (Unix workstation, Mac, or PC) using the Fast Tile Plot.  Your computer needs to be configured to run X-Windows. Typically, you will connect to the remote compute server using secure shell (SSH).  If you are using an X-Server and wish to generate 3-D plots using Open GL, you need to turn on Open GL support within the X-Server.

2.4      Graphics Requirements

Three-dimensional contour plots require a graphics card with OpenGL or DirectX capability.  By default VERDI uses OpenGL for 3D rendering. If you would like to use DirectX instead, add the line: j3d=-Dj3d.rend=d3d to the verdi.ini file. 

2.5      Display Properties

VERDI works best on screen displays that have been set to a high or perhaps the highest screen resolution (1280 ´ 1024 pixels for Windows XP machines or 1440 ´ 900 for Mac or Windows Vista).  To adjust your screen resolution for a Windows XP machine, right click on your desktop and then click on the Settings tab in the pop-up window.  Use the slider under the screen resolution section to set the resolution to 1280 ´ 1024 pixels.  You may need to reboot your computer for this modified screen setting to take effect. For Windows Vista, right click on your desktop and click on Graphics Properties.  In the pop-up window, click on Display Settings. To adjust the screen resolution on a Mac, go to Applications and double click on System Preferences, then under Hardware select Displays.  Select 1440 ´ 900.

3            VERDI Installation Instructions

3.1      VERDI Installation

Installing VERDI on a Windows operating system is accomplished by running a standard installer program. For Linux and other non-Windows platforms, VERDI is distributed as a gzipped tar file that contains the executable application and the third-party libraries needed for VERDI. Currently, the VERDI distributions provide a platform-specific Java Runtime Environment 6.0 (see Section 3.3) for Windows and Linux. Note that the version of Java provided with VERDI includes the JAVA 3D and JAI packages to support the three-dimensional plots used by VERDI’s contour plot. For more information on supporting the contour plot on your non-windows platform of interest, see the Java3D discussion section 3.2 that follows. Instructions on how to download JRETM 6 for other system configurations that run it are also provided.

3.2      Installation Instructions for Linux and Other Non-Windows JRE 6 Supported System Configurations

 

Follow these instructions to install VERDI:

 

1.      tar -xvf verdi_1.4.1.tar into a location where you would like to install VERDI.

2.      Edit verdi_1.4.1/verdi.sh: Change the path for the VERDI_HOME variable to reflect the location where VERDI was installed (e.g., VERDI_HOME=/usr/local/verdi)

3.      VERDI should now run if you execute the verdi.sh executable script (e.g., ./verdi.sh).

3.3      Installation Instructions for computer that that requires a JRETM 6 other than what was provided in the distribution:

1.      Download Java 6 for your platform from http://www.java.com/en/download/manual.jsp.

2.      Download Java3D

a.       For all platforms, go to http://java.sun.com/javase/technologies/desktop/java3d/

b.      Go to download section, click on Download Java 3D 1.5.1 Software, select your platform, agree to license agreement, and continue.

c.       mv java3d-1_5_1-linux-i586.bin to the jre1.6.0_06 directory

d.      chmod a+x  java3d-1_5_1-linux-i586.bin

e.       ./java3d-1_5_1-linux-i586.bin (this will place the lib/ext and lib/i386 files where they are needed)

3.      Download JAI 1.1.3

a.       For all platforms, go to http://download.java.net/media/jai/builds/release/1_1_3/    Select JRE Install (Note JRE is the Java Runtime Environment and needed for running VERDI, JDK is the Java Development Kit, and the JDK is only needed by those who are developing code for VERDI)

b.      Download the .tar.gz package and untar. This will create a directory "jai-1_1_3".

c.       Copy the following files:

                                                               i.      cp jai-1_1_3/lib/libmlib_jai.so /path-to-/verdi_1.4.1/jre1.6.0_13/lib/i386

                                                             ii.      cp jai-1_1_3/lib/*.jar /path-to-/verdi_1.4.1/jre1.6.0_13/lib/ext

4.      Download JAI ImageIO

a.       Download jai_imageio-1_1-lib-{yourplatform}.exe by clicking on it and saying save as.  Run the executable by double clicking on it to start the InstallShield Wizard.  Specify the Destination Folder as the location where the JRE was installed.

If JRETM 6 is already installed on your Linux platform, and you would like to use the already installed version, you will need to add Java 3D support. Copy the following files from the version of Java provided in the VERDI release into the JRE_HOME/bin directory used by your version of Java:

j3dcore-d3d.dll
j3dcore-ogl.dll
j3dcore-ogl-cg.dll
j3dcore-ogl-chk.dll
j3dutils.dll

3.4      Installation Instructions for Windows

To install VERDI for Windows, run the installation program VERDI_1.4.1_Installer.exe on your Windows machine. Follow the instructions on the installation windows that appear, as shown in Figures 3-1 through 3-6.  If you are unable to install VERDI on your computer, please check to see whether your user account is authorized to install software. You may need to request that a user with a computer administrator account install VERDI, or provide you with an account that has permission to install software.  For more information about user account types, click Start and select Control Panel and then click on the User Account icon.

Figure 31. VERDI Setup Wizard

Figure 32. License Agreement

Figure 33. Selecting an Installation Directory

Figure 34. Setting the Start Menu Folder

 

Figure 35. File Extraction

Figure 36. Installation Complete

3.5      Setting VERDI Preferences

The VERDI installation package contains a file called config.properties.TEMPLATE. On Windows, this file is copied into the VERDI subdirectory of your USERPROFILE directory (e.g., “C:\Documents and Settings\yourusername\verdi”) and renamed to config.properties.  On Linux, this file is copied into the ~username/verdi/ subdirectory and renamed to config.properties.  Users are encouraged to edit this file to specify default directories for saving files, for placing the location of configuration files, and for saving project files.  Contents of config.properties.TEMPLATE:

 

# This file should be put in $USER_HOME/verdi/ subdirectory

# Please use double backslash for windows platform or slash for UNIX like platforms as file

# Please uncomment the following lines and modify them to suit your local settings

 

# Windows example settings format

# verdi.project.home=C:\\Program Files\\VERDI_1.4.1\\project

# verdi.config.home=C:\\Program Files\\VERDI_1.4.1\\config

 

# Linux example settings format

verdi.project.home=../../data/project

verdi.config.home=../../data/configs

verdi.user.home=../../data/model

 verdi.dataset.home=../../data/model

 verdi.script.home=../../data/scripts

 

# WDT default area file folder

 verdi.hucData=../../data/hucRegion/

 

# For VERDI to access remote big netCDF data files

 verdi.remote.hosts=terrae.nesc.epa.gov,vortex.rtpnc.epa.gov,garnet01.rtpnc.epa.gov,tulip.rtpnc.epa.gov

remote.file.util=/usr/local/bin/RemoteFileUtility

verdi.remote.ssh=/usr/bin/ssh

 

#on local machine where VERDI is running. Used to hold temporary data file downloaded from a remote machine

verdi.temporary.dir=C:\\temp

The items in the config.properties.TEMPLATE file that is installed with VERDI are commented out, and will need to be uncommented by removing the starting ‘#’ sign if you do not want to specify the directories each time a file is loaded or saved. Example settings that are provided in the default file show how to specify the paths to these locations, depending on whether the installation is for a Windows or Linux platform.  The verdi.project.home setting specifies the default location from which to load and save projects.  The verdi.config.home setting specifies the default location from which to load and save plot configurations. The verdi.dataset.home setting specifies the default location from which to load datasets.  The verdi.script.home setting specifies the default location from which to load and save batch scripts.  Note that VERDI stores the most recently used directory for each of these functions and will go to that directory when you repeat the load or save. The verdi.hucData setting specifies the default locations where area shapefiles are located.  VERDI will navigate to this directory when the user selects to add a dataset in the Area pane. The verdi.remote.hosts setting contains a list of machines that the user can select to browse from when adding a remote dataset using VERDI’s Remote File Access capability. The verdi.remote.util setting specifies the location of the RemoteFileUtility script for Linux and Mac installations of VERDI. Starting in VERDI version 1.4, the ui.properties file was removed, and the user configurable settings such as the default directory location that were previously specified in the ui.properties file were moved to the config.properties file.

4            Starting VERDI and Getting Your Data into VERDI

4.1      Starting VERDI

4.1.1 Windows

To start VERDI, open the Start menu, then highlight the Programs directory, followed by the VERDI directory, and then select the VERDI icon, as shown in Figure 4-1.

Figure 41. Starting VERDI in Windows

4.1.2 Linux and Other Non-Windows JRETM 6 Supported System Configurations

To start VERDI from Linux and other non-Windows JRETM 6 Supported System Configurations, find the directory where VERDI was installed, then run the verdi.sh script. On a Mac go to the /Applications/verdi_1.4.1 directory and run the verdi.command script.

4.2      Main Window

After starting VERDI, the main window will come up on the screen (Figure 4-2). At the top of the main window, there is a menu bar with the main window options (File, Plots, Window, and Help). Below the menu bar there are three icons that are shortcuts to some of the options available in the Main Window Menu Bar; the first is an Open Project icon, the second is a Save Project icon, the third is an icon that allows you to Undock All Plots. These shortcuts and the options available in the Main Window Menu Bar are discussed further in Section 5, “Navigating VERDI’s Main Menu Options.” Next to these three shortcut icons are buttons that list all of the available plot types. To the right of all the plot buttons the Selected Formula is listed.  The Selected Formula refers to the formula that has been selected in the Formula pane (discussed briefly below and in detail in Section 7), and that will be used to create plots. Below the icons and plot buttons, the window is divided into two main areas: a parameters area on the left side and a plots area on the right side. The parameters area contains three tabbed panes:

·        The Datasets pane is used to load in the dataset files that you want to work with in this session (this is discussed in Section 6). Once the datasets are loaded, VERDI automatically displays the lists of variables that are in the datasets. To see the variables in a dataset, click on the dataset, and the variables will be displayed in the Variables panel underneath the list of datasets. In Version 1.05 and later, if you double click on the name of a variable listed on the variables panel, the variable will automatically be added as a formula on the Formula pane and will be the default formula for new plots that are created.

·        The Formula pane is used to create a formula that refers to the variable and the dataset that you are interested in plotting (see Section 7 for more information). All plots in VERDI are generated from formulas. A formula can be as simple as a single variable from one dataset or it can be an equation that uses variable(s) from one or more datasets.

·        The Areas pane is used to load area files that are used to create areal interpolation plots (see Section 8 for more information).  Area files are defined as shapefiles that contain area features such as watersheds and counties, or any other shapefile that consists of a set of closed polygons.

Any plots that are created are shown in the plots area on the right-hand side of the main window. These plots can be placed into their own movable windows using Plots>Undock all Plots on VERDI’s main menu, as discussed in Section 5.2.1. The fast tile plot option was added in VERDI version 1.1.  As of VERDI 1.4, the tile plot option was removed, since the functionality has been replaced by the fast tile plot; however, there are derivative plots, such as the vector plot, that still use the tile plot code. In a future release, these derivative plots will be migrated to use the Fast Tile Plot as their base.  The Fast Tile Plot has an option (Plot>Add Overlay> Vectors) to create a Fast Tile Plot of a variable with a vector overlay of wind vectors or other vector types.  The Fast Tile Plot with vector overlay should be used as the preferred alternative to the Vector Plot until the Vector Plot is updated in a future release.  The functions that are currently enabled for fast tile plots are described in Section 10, “Creating Plots.”

Figure 42. VERDI Main Window

4.3      Floating the Dataset and Formula Panes

The Formula, Dataset, and Areas panes can each be configured to float, to allow you to position them alongside one another. To allow a pane to float, click the icon at the top of the pane that looks like a rectangle with an angle bracket above the upper right corner. You can then click on the pane and move it independently of the VERDI main window. This is useful when you are entering a formula in the Formula pane, if you have difficulty remembering the variables that are in a loaded dataset.  Once a pane is unconnected from the frame, the icon changes to be a box with an arrow pointing inward, with the hover over text tip: “Connects this panel to the frame”.  Click on the box with the inward arrow to reconnect the panel with the frame.  This will return the floating pane back to where it usually lives within the main window.

5            Navigating VERDI’s Main Menu Options

Figure 5-1 shows a graphic of the main menu options that are available on the top menu bar in VERDI’s main window (Figure 4-2 above). These options are discussed in detail below.

 

 

Figure 51. VERDI Main Menu Options

VERDI

File

Plots

Window

Help

About VERDI

Open Project

Save Project

Save Project As

View Script Editor

Undock All Plots

Animate Tile Plots

Areas

Datasets

Formulas

VERDI Help Docs

About

Preferences

 

 

Services

Exit

 

 

 

Quit VERDI

 

 

5.1      File Menu Options

5.1.1 Open Project

Open Project retrieves projects that were saved during a previous session (using the two Save Project options described next). Note that when you use a saved project, it is very important to load that project into VERDI before you load any additional datasets or create any additional variables/formulas. If you load a dataset that is not part of the previously saved project and then try to open a previously saved project, you will get a message that says “All currently loaded datasets will be unloaded”, and will be asked if you want to continue.

5.1.2 Save Project

The Save Project and Save Project As options save dataset lists and associated formulas as a “project” for later re-use.

Note that plots are not saved with a project; only datasets and formulas are saved.  If you wish to save a plot configuration for later use, see Section 11.2.2, “Loading and Saving configuration.”

5.1.3 View Script Editor

The View Script Editor allows users to modify and run batch scripts within VERDI.  Three sample script files are provided with the VERDI distribution under the $VERDI_HOME/data/scripts directory.  On a Windows machine the $VERDI_HOME is typically C://Program Files//VERDI_1.4.1.  Use the Open pop-up window to specify eps.txt, one of the sample script files.  The contents of the eps.txt will be displayed in the Script Editor in the right side of the VERDI window.  Modify it to specify the local directory path name for the sample data files, the formulas, the type of plots, and the image format.  The plots are not rendered within VERDI, but may be viewed using an image viewer.  The batch scripting language is described in the sample script files, and will be described in more detail in Section 17: VERDI Script Editor.

5.2      Plots Menu Options

VERDI opens a single window for plots, to the right of the Dataset, Formula, and Area panes. As plots are created (each in its own sub-window), the most recent plot is displayed on top of previously created plots. Each plot has a tab beneath it listing the type of plot and the formula used to create it. If you want to view a previously created plot, select the tab associated with its sub-window underneath the current plot, and the desired plot will be brought to the front.

5.2.1 Undock All Plots

As with the Dataset, Formula, and Area panes (Section 4.3), plot sub-windows can be undocked or externalized so that you can move them into separate, floating windows. This allows side by side comparisons of plots. Note that undocking is performed only on previously created plots; any newly created plots are created within the VERDI main window.

5.2.2  Animate Tile Plots

This option opens an Animate Plots dialog box (Figure 5-2) that allows you to select one or more plots, select a subset of the time range, and create an animated GIF file. There is also a separate way to create a Quicktime movie instead of a GIF, if desired.

Within the Animate Plots dialog box, you can select plot(s) to animate by clicking the check box beside each plot name.

You can choose to animate a single plot, or animate multiple plots synchronously. To view multiple animated plots synchronously, undock the plots (see Section 5.2.1) and move them so that they are located side by side for visual comparison during the animation.

Once a plot has been selected, you can select the time range by specifying both the starting time step and ending time step of the animation.

To create an animated GIF, check the Make Animated GIF(s) option in the Animate Plots dialog box. In the Save dialog box that appears, select the directory in which to store the file and the name to use for the animated GIF, then click the save button. When saving as an animated GIF, when multiple plots are selected, each animated plot will be saved to a separate animated GIF file.  For example, if three plots were selected, the animated plots would be saved as <filename>-1.gif, <filename>-2.gif, <filename>-3.gif. You can view the animated GIF by opening the file in a web browser. 

Creating a Quicktime movie is also an option, but this is not done through the Plots>Animate Tile Plots main menu option.  Instead, use the Plot menu option found at the top of each individual plot to make a Quicktime movie.

Figure 52. Animate Plots Dialog and Fast Tile Plots

5.3      Window Menu Options

The Window menu provides an alternate way to select windows/panes to be brought to the front, and provides the same function as clicking on the tabs at the bottom of the windows/panes.

5.3.1 Datasets and Formulas

Select from the Window pull-down menu to bring to the front either the Areas pane, Datasets pane or Formulas pane when those panes are docked.

5.3.2 List of Plots

The Window pull-down menu is automatically updated each time a plot is created in a VERDI session; each entry in the plot list indicates the type of plot and the formula used. Clicking on a given plot entry brings that plot to the front for viewing. Alternatively, you can bring a plot to the front by selecting the desired plot tab underneath the plots area of the main window. As in the menu entries, each plot tab is labeled with the plot type and the formula used.

5.4      Help Menu Options

The Help pull-down menu contains two items that you can use to learn more about VERDI. When you select VERDI Help Docs, the VERDI user’s manual is displayed in a VERDI Help window. This window is not searchable, but it does allow you to navigate via hyperlinks in the Table of Contents, and to scroll down and read the user’s manual. When you select About a pop-up window that contains the name of the product, the version number, and the date the software was built is displayed.

6            Working with Gridded Datasets

6.1      Gridded Input File Formats

6.1.1  Model Formats

VERDI currently supports visualizing files in the following formats: CMAQ Input/Output Applications Programming Interface (I/O API) netCDF, WRF netCDF, and CAMx (UAM-IV), and ASCII format (for observational data). VERDI uses version 4.1 of the netCDF java I/O library (http://www.unidata.ucar.edu/software/netcdf-java).

The CMAQ I/O API was designed as a high-level interface on top of the netCDF Java library. (see http://www.baronams.com/products/ioapi and http://www.unidata.ucar.edu/software/netcdf/ for further info).  The I/O API library provides a comprehensive programming interface to files for the air quality model developer and model-related tool developer, in both FORTRAN and C/C++.  I/O API files are self-describing and include projection information within the gridded dataset.  See section 12 for additional information on what projections and gridded data formats are supported by VERDI.

netCDF and I/O API files are portable across computing platforms. This means that these files can be read regardless of what computer type or operating system you are using. There are routines available to convert data to these formats or new code can be written and contributed to VERDI for use by the community.  Discussion of the I/O API conversion programs and how to use them can be found in Section 13, “I/O API Utilities, Data Conversion Programs, and Libraries.”  If you write a routine for VERDI to read gridded data from other formats, please consider contributing your code to the user community using sourceforge.net, as described in Section 14.

6.1.2  Observational Data Formats

Observational data in ASCII format can be obtained from EPA’s Remote Sensing Information Gateway - RSIG (http://badger.epa.gov/rsig).  To use a consistent set of units, between the model data and the observational data, the user may need to import the ASCII data into an Excel spreadsheet to do a unit conversion.  VERDI doesn’t allow the user to use an observational variable to create a formula, so conversions to different units should be done within an Excel spreadsheet.  Import the file ASCII file that is generated by RSIG into Excel, change the units to match the units found in the gridded model data file and then save using a tab delimited ASCII file format.

The observational data ASCII format recognized by VERDI is an ASCII file with tab-separated columns where the first four columns are provided in the order shown in Figure 6-1 and one or more additional columns are arbitrary but must have the header format 'name(units)' as shown in Figure 6-1.  Spreadsheet programs can be used to edit and write the files by choosing ASCII output and tab as the delimiting character (instead of comma). Data within a column must be complete, as empty fields within a column will cause VERDI to be unable to read the observational data. VERDI 1.4.1 allows the user to specify an alphanumeric value (either numbers and/or letters) for the fourth column (Station ID).

Figure 6-1. Observational File ASCII Format

Timestamp(UTC)    LONGITUDE(deg)    LATITUDE(deg)     STATION(-)  pm25(ug/m3)
2005-08-26T00:00:00-0000      -121.7842   37.6875     060010007   11.0000
2005-08-26T00:00:00-0000      -122.3991   37.7660     060750005   12.0000
2005-08-26T00:00:00-0000      -122.2034   37.4829     060811001   21.0000
2005-08-26T00:00:00-0000      -121.8950   37.3485     060850005   16.0000
2005-08-26T01:00:00-0000      -121.7842   37.6875     060010007   21.0000
2005-08-26T01:00:00-0000      -122.3991   37.7660     060750005   22.0000
2005-08-26T01:00:00-0000      -122.2034   37.4829     060811001   19.0000
2005-08-26T01:00:00-0000      -121.8950   37.3485     060850005   20.0000
2005-08-26T02:00:00-0000      -121.7842   37.6875     060010007   28.0000

Alternatively, users may use a converter such as AIRS2M3 (see Chapter 13) to convert ASCII observational data into I/O API "observational-data" files.

6.2      Example Datasets

Several example datasets are provided under the $VERDI_HOME/data directory. For example:

Windows: C:\\Program Files\\VERDI 1.4.1\\data

Mac: /Applications/verdi_1.4.1/data/

Linux: $VERDI_HOME/verdi_1.4.1/data

These datasets may be used to re-create example plots that are provided in this user guide, including a tile plot with observational data overlay in Section 11.4.3, and the example datasets for the various dataset projections that VERDI supports including LCC, polar stereographic, UTM and Mercator.  The data directory currently contains four subdirectories:

  1. CAMx – contains sample CAMx dataset and camxproj.txt file
  2. hucRegion – contains Hydrologic Unit (HUC) shapefiles for region 3 (southeast US)
  3. Model – contains sample WRF and CMAQ I/O API datasets
  4. Obs – contains an ASCII formatted observational dataset (Chapter 6-1), and an observational dataset created by airs2m3 converter (Chapter 13).

6.3      Adding and Removing a Dataset from a Local File System

To load a data set from a local file system, press the yellow plus button at the top of the Datasets pane. A file browser (Figure 6-2) allows you to select a dataset for use in VERDI.  Support for loading data from a remote file system has been added beginning in version 1.4.  The use of the yellow plus remote button will be discussed in Section 6.4.

After you select a  dataset, VERDI will load header information and display the available variables, time steps, layers, and domain used by the file in the Datasets pane (Figure 6-3). (The actual model data are not loaded until later, when plots are created.) To view the variables for a particular dataset that has been loaded, click on the dataset name in the list to highlight it, and the variables will be listed in the panel below.

Datasets can be removed by highlighting the name of the dataset in the dataset list and pressing the yellow minus button. Note that although the dataset will be removed, the number that was assigned to that dataset will not be reused by VERDI during the current session (unless there had been only one dataset loaded, and it was removed; in that case the next dataset that is loaded will be labeled number 1).

Figure 6‑2. Open Dataset File Browser

 

Figure 6‑3. Datasets Pane Displaying Information about a Dataset

6.4      Adding and Removing a Dataset from a Remote File System

VERDI provides users with the ability to select and add variables from datasets on remote file systems. To do this, press the yellow plus remote (plus with a diagonal arrow) button at the top of the Datasets pane.  In the Remote File Access Browser (Figure 6-4) that appears, enter your user name, choose a host from the list, and enter your password, then click Connect.

Figure 6‑4. Available Hosts in the Remote File Access Browser

 

6.4.1 Remote File Browser

The top panel displays a listing of the home directory on the remote file system, as shown in Figure 6-5.  The current path is displayed in the text box and users can edit this information to change to another directory. An alternate way to navigate between directories is using the middle panel. In the middle panel, double click on a directory name to go into that directory, or click on the “../” at the top of the middle panel to navigate up a directory.  As you enter a directory, the contents of the directory will be displayed as a list in the middle panel.  Directory names are followed by a “/” symbol, while filenames do not have a “/” symbol after them.  View the variables within each file of interest by double clicking on the netCDF filename listed in the middle panel.  Note: if the selected file has a format that is not supported by VERDI then the following message will be displayed in the bottom panel: “Not a valid NetCDF file”. For supported netCDF files, VERDI will provide a list of variables that are available within the file in the bottom panel labeled “Select one or more variables”.  To select variables from the list, use your mouse to click on a single variable, or use either the Shift key with the mouse to select a contiguous list of variables, or the Control key with the mouse to select a set of individual variables.  Once the variables that you would like VERDI to read are highlighted, click on the Read button.

Figure 6‑5. Select one or more variables from Remote Dataset

 

The variables read from the remote dataset will be displayed in the dataset and variable browser in the same way that variables from a local dataset are added and displayed within VERDI.  The subsetted local dataset names are identical to the file names on the remote host, except for an additional extension that enumerates how many times the remote files were read and saved locally by VERDI (i.e., filename1, filename2, filename3, etc.), as shown in Figure 6-6.  To add additional variables from the same remote dataset, click on the plus remote button, and repeat the above procedure.  The Remote File Browser retains the login session and the directory that was last accessed by the user, to facilitate ease of accessing remote datasets. VERDI will increment the numerical extension to the dataset name, to allow the user to know that this subset file was created using the same remote dataset, but that the subset file with the new numerical extension may contain a different subset of variables.  Note that VERDI does not check to see if the same variable from the same remote dataset has already been read.  Also note that subset files read in by VERDI will be saved either to your home directory on your local file system (e.g., C:\Documents and Settings\username on a Windows XP machine), or to the location that is specified in the config.properties file using the verdi.temporary.dir setting. Refer to Section 6.4.2 on how to edit and save the config.properties file.  The files are saved on your local machine to facilitate project management.  To be able to save and then load a project for future use, the files need to be saved on the local machine. To avoid filling up your local file system, regularly inspect the file list in the home or verdi.temporary.dir directory and manually delete unneeded subset files. 

Remote datasets can be removed from the dataset list in VERDI using the same procedure as for removing local datasets: highlight the name of the dataset in the dataset list and press the yellow minus button. Note that although the dataset will be removed from the dataset list, the number that was assigned to that dataset will not be reused by VERDI during the current session.

 

Figure 6‑6. Remote Dataset Labeled with Number at End of the Filename

 

6.4.2 Adding Additional Remote Hosts

VERDI contains the RemoteFileUtility and ncvariable programs that enable VERDI to add your I/O API netCDF or WRF netCDF formatted dataset from a remote file system.  A gzipped tar file is available in the $VERDI_HOME directory.

  1. The RemoteFileUtility c-shell script and ncvariable binary need to be installed either in /usr/local/bin by the System Administrator, or you can place it in a different location, and specify that location in the configure.properties file located in your $USER_HOME/verdi/ directory (see section 3.4 for the specific directory location that is used for each platform [Linux, Windows, Mac]).  A template for the configure.properties file called configure.properties.TEMPLATE is provided in the distribution under the $VERDI_HOME directory (see section 3.4 for information on how to edit the settings).
  2. A README file provided with the software contains instructions on how to compile the source code if the binaries provided do not match your operating system.
  3. Copy the file configure.properties.TEMPLATE to configure.properties. Edit the configure.properties file in the $USER_HOME/verdi directory.  Add the name or IP address of the Linux server, preceded by a comma, at the end of the list of machines defined as remote hosts in the configure.properties file, as shown in Figure 6-7.  You will need to restart VERDI in order for it to recognize a newly added remote host name.

Figure 6‑7. Edit configure.properties file to add a remote host

6.5      Variables List

The variables list shows all of the variables contained in a loaded dataset (see the example in Figure 6-7). To display a variables list, select the name of the dataset of interest in the Datasets pane. Each of the variables in the list can be used to create a formula in the Formula pane that can then be used to create plots.  VERDI allows the user to automatically add a formula by double clicking on the name of a variable.  Double clicking on a variable will automatically create a formula that contains the variable for the loaded dataset and it will become the default formula for making plots. In addition, you may right click on the name of the variable to show a popup menu as shown in Figure 6-8.  From this menu you can either add the variable as a formula, or you can to add it into the formula editor so that it can be used to compose more complex formulas. Formulas are described in more detail in Section 7.

Figure 6‑8. Right Click on Variable in Dataset Pane

6.6      Time Steps, Layers Panels

The range that is available for the dataset is listed in the Time Steps or Layers Panel in parenthesis next to the label for the panel, e.g. for a dataset that has 5 time steps, the range would be displayed as: Time Steps (1-5). The user can select to use a subset of the full time step range by clicking on the Use Time Range checkbox, and then using the Min and Max spinner controls to set a new minimum or maximum values, for example choosing time step 2 as the minimum time step, and time step 4 as the maximum.  When a tile plot is created, it will only display time steps 2-4. Detailed instructions for using the Time Steps, Layers, and Domain panels that you see in Figure 6-7 are discussed in Section 9, “Spatial and Temporal Data Subsetting.”

6.7      Domain Panel

The domain panel contains an Edit button and a Metadata button. Detailed instructions for using the Edit button are provided in Section 9, “Spatial and Temporal Data Subsetting”.

To display the metadata information about a dataset, click on the Metadata button in the Domain panel. A window containing the metadata will appear (Figure 6-9).  Each dataset includes metadata information that is part of the file header. The metadata provided include the map projection information, the number of time steps in the file, the number of columns and rows, and other information.

Figure 6‑9. Dataset Metadata Information

6.8      Saving Projects

As noted in Section 5.1.2, lists of datasets and formulas can be saved as “projects” using the Save Project option in the File pull-down menu on the VERDI main window. Refer back to that section for discussion on saving new projects and loading existing projects. Note again that the plots created in VERDI are not saved with the project.

7            Working with Formulas

All plots in VERDI are generated from formulas. A formula is used to compare or manipulate variables in one or more gridded datasets. A formula can be as simple as a single variable from one gridded dataset or it can be an equation that uses variable(s) from one or more gridded datasets. Formulas are used to create visualizations that can assist with model performance evaluations, for example, or that help in comparing model results with observations.

7.1      Adding and Removing a Formula

After loading the desired gridded datasets, you can use the variables in them to create formulas.  To use a variable to create a simple formula, double click on the name of the variable.  This will add the formula <Variable Name>[<Dataset Number>] to the formula list in the Formulas pane—for example, O3[1]. To add a variable to the formula editor window, highlight the variable, right click on the variable name in the Datasets pane, and select Add Variable(s) to Formula Editor. To add all or a subset of variables from the Dataset pane to the formula editor window, click on the first variable to highlight it, hold the Shift key down and click at the last variable that you want to include, then right click and select Add Variables(s). The formulas that are highlighted using this method will be added to the formula editor (Figure 7-1).

Figure 7‑1. Adding Multiple Variables to Formula Editor

After the variable names are added to the Formula Editor, click on the formula pane and use the cursor and the keyboard to type in the mathematical functions and operators where needed to create a valid formula (see Section 7.2 and Section 16).  After the formula has been created in the Formula Editor, click the Add button, to place it in the list of formulas available in the Formula pane. 

To remove a formula from the formulas list, highlight the name in the list and press the yellow minus button.  Note that removing a formula from the formula list does not remove plots that were created prior to the deletion of the formula.

7.2      Example Formulas

To examine the values of ozone in dataset 1, the formula would be “O3[1]”.

To examine the difference in ozone between datasets 1 and 2, the formula would be “O3[1]-O3[2]”.

To calculate the percent difference in ozone between datasets 1 and 2, the formula would be “(O3[1]-O3[2])*100/(O3[2])”.To identify all cells where the ozone concentration exceeds a certain value, you can use the Boolean operators to “screen out” ranges of your data that are of particular interest. A Boolean expression will evaluate to either True = 1 or False = 0. For example, to plot the cells in which the ozone values in dataset 1 exceed 0.080 ppm, you could use the formula “(O3[1]>0.080)*O3[1]”. In the resulting plot, each cell where O3[1] exceeds 0.080 will show the value of O3[1] for that cell; for all other cells the value shown will be zero.

The notations that can be used in formulas to represent various mathematical functions, and the order of precedence of these functions, are listed in Section 16, “Mathematical Functions.”

7.3      Selecting a Formula for Plotting

Before creating a plot, a formula must be selected. Check to see which formula is highlighted in the Formula pane, or look to the right of the plot buttons above the plots area of the main window to see the selected formula. By default, VERDI designates the most recently added formula as the selected formula. To change the selected formula to a different one in the list, click on a formula in the list on the Formula pane, and you will then see it displayed as the selected formula above the plots area.

7.4      Saving Formulas

Both formulas and datasets can be saved using the Save Project item in the File pull-down menu on the VERDI main window. Saving new projects and loading existing projects was discussed in Section 5.1.

7.5      Time Step Range, Layer Range, and Edit Domain

Instructions for using the Time Steps, Layers, and Domain panels that you see in Figure 7-1 are discussed in the next section, “Spatial and Temporal Data Subsetting.”

8            Working with Area Files

8.1      Area File Formats

Area files are defined as shapefiles that contain area features such as watersheds and counties, or any other shapefile that consists of a set of closed polygons.

The shapefile format (ESRI, 1998) consists of four files.

1.      The *.shp file contains the actual shape vertices.

2.      The *.shx file contains the index data pointing to the structures in the .shp file.

3.      The *.dbf file contains the attributes (e.g., gridded concentrations).

4.      The *.prj file contains the map projection information used for the gridded concentrations.

8.2      Example Area File

Shapefiles that contain closed polygons are used by VERDI to interpolate gridded data to geographic boundary regions to create Areal Interpolation Plots.  Shapefiles containing state, county, or census block, for example, or any other shapefile containing polygon areas may be used in VERDI to calculate and map formulas to the user-selected geographic regions. An example shapefile containing the 8-digit HUC watershed boundary map for the Southeast (Region 3) is provided in the VERDI release under the $VERDI_HOME/data/HucRegion directory.

Example on-line data archives for these shapefiles include:

http://datagateway.nrcs.usda.gov

http://www2.census.gov/cgi-bin/shapefiles/national-files

8.3      Adding and Removing an Area File

To load a shapefile, press the yellow plus button at the top left corner of the Areas pane (Figure 8-1). A file browser (Figure 8-2) allows you to change directories and select a shapefile file for use in VERDI.  Click on the shapefile name and click Next.  The Open Area pop-up window will be displayed next which allows you to select the name of the field to read from the file and supply projection information if needed.  Use the pull-down menu and click on the Name Field (Figure 8‑3) to be used.  If a *.prj file is not provided with the dataset, the user is required to specify the projection information.  A pull-down menu will prompt the user to select the coordinate system used in the file: either the Geographic (lat/lon) coordinate system or a Projected (x/y) coordinate system (Figure 8-4).  If the user selects Projected, an additional pull-down menu asks what type of projection, and a text box allows users to provide the required information to do the projection (Figures 8-5 and 8-6).  After the Name Field and the Coordinate System have been specified, select Finish.  The resulting plot will be in the same projection as the gridded information used in the plot.

8.4      Areas List

The shapefile name(s) will be listed in the top panel of the Areas pane, and the name fields for the polygons provided in the shapefile(s) will be listed in the panel underneath (Figure 8-7). The actual model data are not loaded until later, when the Areal Interpolation plots are created.  As additional shapefiles are added, the name fields associated with each shapefile are appended to the bottom of the Areas list.  Use the scrollbar on the right side of the Areas pane to view the additional name fields that are available.  To remove a shapefile, click on the name of the shapefile and press the yellow minus button at the top left corner of the Areas pane. 

8.5      Areal Interpolation

When the user selects the Areal Interpolation Plot, the selected formula is remapped over the polygon areas that are listed in the Areas pane.  To select a subset of the polygon areas, and view the average and total values for selected formulas, see Section 10.3: Areal Interpolation Plot.

 

Figure 81. Areas Pane

 

Figure 82. Open Area File Browser

 

Figure 83. Open Area File: Select Name Field

 

Figure 84. Coordinate System

Figure 85. Projection Information

 

Figure 86. Additional Data Fields appear depending on projection selected.

 

Figure 87. Area Name Fields available for Shapefile

 

 

 

9            Spatial and Temporal Data Subsetting

Both the Dataset pane and the Formula pane include the three panels discussed in Sections 9.1 through 9.3: Time Steps, Layers, and Domain. Section 9.4 then discusses the precedence rules for subsetting data that determine which pane’s subsettings (Dataset or Formula) take priority.

9.1      Specify Time Step Range

Information about the range of time-step values included in a dataset is displayed in the Time Steps panel (Figure 9-1). The maximum time-step range that can be used for a dataset or formula is specified in the Min and Max spinner controls. You can use these controls to select a subset of the available time-step range for plotting. Check the Use Time Range box above the spinner controls to tell VERDI to use the time-step range values you have specified when it creates a plot. By default, a plot will initially display data for the minimum time step that was specified in the Time Steps panel. The range of the time steps available in the Time Step spinner control at the top of the plot will reflect the subset of time steps specified when the Use Time Range box is checked. The date and time of that time step are shown below the plot. Subsetting (also called cropping) a dataset’s or formula’s time-step range will affect any plots made; see Section 9.4 to learn the precedence rules.

Figure 91. Specify Time Step Range

9.2      Specify Layer Range

Information on the range of vertical model layers included in a dataset is displayed in the Layers panel (Figure 9-2). You can use the Min and Max spinner controls to select a subset of the available layer data for plotting. Check the Use Layer Range box above the spinner controls to tell VERDI to use the layers you have specified. By default, a plot will initially display data for the minimum layer chosen in the Layers panel. The range of the layers available in the Layer spinner control at the top of the plot will reflect the subset of layers specified when the Use Layer Range box is checked. Subsetting a dataset’s or formula’s layer range will affect any plots made; see Section 9.4 to learn the precedence rules.

Figure 92. Edit Layer Range in Formula Pane

9.3      Specify Domain Range

Datasets contain data for cells over a particular geographic area. In the VERDI program this area is referred to as a “domain.” By default, the entire domain contained in a dataset is used in creating plots. The Edit Domain dialog box can be used to select a subset of this domain for plotting. To access the Edit Domain dialog box, first use the vertical slide bar to bring the Domain panel (located below the Layers panel) into view if it is not already visible (Figure 9-3).  To select a subset of the domain, press the Edit button. The Edit Domain dialog box will appear (Figure 9-4). If the area of interest is large, background data such as state and county outlines will be shown on the map. The magnifying glass buttons above the map can be used to zoom in and out on the map. Use the pan icon to drag the map to a position where the desired area is displayed. To select the desired cells, first press the Select Region button. You can then drag a box around the area of interest; selected cells will appear in blue. To clear out the selected area, use the Clear Region button. When you are satisfied with the domain subset you have chosen, click the OK button. Subsetting a dataset’s or formula’s domain range will affect any plots made; see Section 8.4 to learn the precedence rules.

Figure 93. Using the Slider to View the Domain Panel

Figure 94. Edit Domain Dialog Box

9.4      Rules of Precedence for Subsetting Data

The subsetting feature allows the user to combine variables from two or more datasets that may have originally contained differing layer, time step or domain ranges, when a sub-portion of the datasets contains an identical set of layers, time steps and domain range. The user may select a subset of the data available in the dataset so that the range selected is for an identical time step, layer and domain range so that they may be used to create a formula and be displayed in a plot. Because both the Dataset pane and the Formula pane have the Time Steps, Layers, and Domain panels described above, precedence rules were established that determine which pane’s subsettings take priority. It is important to understand these rules.

·                    A subset of data specified in the Dataset pane takes precedence over any subset specified in the Formula pane. At the time of this release, the range displayed in the Formula pane does not get updated when a subset range is selected on the Datasets pane.  For example, if a dataset has a full time-step range of 0-48, and a time-step range of 2-40 is selected on the Dataset pane, then the 0-48 time-step range that is listed for the formula in the Formula pane is not applicable. When a plot is then created, the time-step range subset you chose in the Dataset pane (2-40) is displayed.

If no subsetting has been done for a particular data type (time steps, layers, or domain) in the Dataset pane, then any subsetting done for that parameter in the Formula pane will take effect.

·                    When a subset of data is requested in the Dataset pane, this deactivates the ability to further subset the data for this range in the Formula pane. For example, if the data are subset in the Dataset pane to a layer range of 2-7, and then in the Formula pane you attempt to further subset the layer range to 4-5, the further subsetting will be ignored and the plot will be created with a layer range of 2-7.

·                    When the user wants to create formulas using variables from multiple datasets, it is important to use the Formula pane to subset the domain range (if such subsetting is needed). The user should not try to create matching subset domain ranges for multiple datasets using the Dataset pane for each dataset, because if all of the subsetted domains do not match exactly, an error will occur when the user attempts to create a formula using variables from those datasets (Figure 9-5). Using the Formula pane instead to do the domain subsetting allows the user to select a subset of the domain to be applied for all dataset variables used in the selected formula.

Figure 95. Error obtained when incompatible subset domains
are created using the Dataset pane

10        Creating Plots

After creating a formula, you are ready to create and view some plots. The available plot types are shown on the buttons at the top of the VERDI main window: fast tile plot, vertical cross section plot, time series plot, time series bar plot, scatter plot, vector plot, and contour plot. All of these are described in this section. Once you have selected (highlighted) a formula in the list of formulas you have created in the Formula pane, you generate each plot type by clicking on the appropriate button using your left mouse button. You can also see the selected formula to the right of all of the plot buttons. If additional information is required in order to generate the plot you have requested, a dialog box appears to prompt you for that information.

Each plot contains its own menu bar at the top that has options for configuring and exploring the plot; the four pull-down menus there are File, Configure, Controls, and Plot. The options for each of these menus are described in more detail in Section 11, “Configuring Plots Using the Plot Menu Bar.”

 

10.1   Fast Tile Plot

The Fast Tile Plot allows the user to display the time steps and vertical layers contained in a gridded dataset and to display grid cell time aggregate statistics.  An example of the Fast Tile Plot window is shown in Figure 10-1.

Figure 10‑1. Fast Tile Plot

10.1.1   Time Selection and Animation Controls

At the top left of the fast tile plot, the spin control can be used to incrementally change the time step by clicking on the up or down arrow.  The top right corner of the plot contains buttons that allow the user to use play, reverse, forward, and pause options to control the animation of the plot.  A text box labeled Slow allows the user to add a delay between frames by entering a number (delay is in milliseconds); the default delay is 0 milliseconds. (If the text box is not visible, expand the width by clicking with the left mouse button on the edge of the window and dragging to the right.) Enter a number for the delay in the box and then hit Enter. A larger plot with multiple map layers would not require the user to add a delay between frames, but a small zoomed-in plot with few map layers will require the user to add at least a 200-millisecond delay between frames, to comfortably view the data. Putting in a larger number will further slow the animation.

10.1.2   Layer Selection

The Layer displayed for the plot can be controlled by clicking on the up or down arrow for the Layer spin control in the top center of the plot.

10.1.3   Grid Cell Time Aggregate Statistics

The pull down menu option labeled Stats provides the user the option to display grid cell time-aggregate statistics (e.g., per-cell minimum, maximum, mean, geometric mean, median, first quartile, third quartile, variance, standard deviation, coefficient of variance, range, interquartile range, sum, time step of minimum, time step of maximum, maximum 8-hour average, and hours of noncompliance).

VERDI calculates the grid cell time aggregate statistics as follows: For each cell (i,j,k) in the currently selected domain (independent of neighboring cells), the aggregated statistical value is calculated over the currently selected time steps. In other words, the aggregated statistical value is calculated for a variable for cells (i,j,k,tmin...tmax), with the number of time steps n, where n=(tmax-tmin+1).

·        MINIMUM: min (var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax))

·        MAXIMUM: max (var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax))

·        MEAN: SUM / n

·        GEOMETRIC_MEAN: ((var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax)))(1/n)

·        MEDIAN: middle_value_of (sorted {var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax)})

·        FIRST_QUARTILE: value_in_first_quarter_of( sorted (var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax)))

·        THIRD_QUARTILE: value_in_third_quarter_of( sorted (var(i,j,k,tmin), var(i,j,k,tmin+1), ..., var(i,j,k,tmax)))

·        VARIANCE: ((var(i,j,k,tmin)-MEAN)2 + (var(i,j,k,tmin+1)-MEAN)2 + ... + (var(i,j,k,tmax)-MEAN)2) / (n - 1)

·        STANDARD_DEVIATION: VARIANCE0.5

·        COEFFICIENT_OF_VARIANCE: STANDARD_DEVIATION / |MEAN|

·        RANGE: MAXIMUM - MINIMUM

·        INTERQUARTILE_RANGE: THIRD_QUARTILE - FIRST_QUARTILE

·        SUM: var(i,j,k,tmin) + var(i,j,k,tmin+1) + ... + var(i,j,k,tmax)

·        TIMESTEP_OF_MINIMUM: 0-based time step when cell contains its minimum value

·        TIMESTEP_OF_MAXIMUM: 0-based time step when cell contains its maximum value

·        HOURS_OF_NON_COMPLIANCE: number of time steps that the cell value exceeds a given threshold

|{Var(I,j,k,t(i))>threshold}|

·        MAXIMUM_8HOUR_MEAN: Max (M1, M2, ..., Mn-8) where Mi = mean(var(i,j,k,t(i)), var(i,j,k,t(i)+1), var(i,j,k,t(i+2)), ...,var(i,j,k,t(i+8)), for i = 1..n-8

10.2   Areal Interpolation Plot

The areal interpolation plot displays the interpolated value of the selected formula for each polygon in the selected area file.  By comparing the colors of the polygons to those shown in the legend, users can see the relative values of the formula for each polygon area.  The Areal Interpolation Plot includes several capabilities that are not available for other plot types, so these are described below, rather than in Section 11: Plot Menu Bar.

10.2.1   Option Pull-down Menu Item

The Areal Interpolation Plot Menu contains an Options pull-down menu to allow the user to change the map to display either the Area Averages (Figure 10-2), the Area Totals (Figure 10-3), or the value of the formula contained in the Gridded Dataset (uninterpolated) (Figure 10-4).  The Options pull-down menu may also be used to display All area segments that are loaded in the area list, or to display only the area segments that are selected by highlighting the name field from the area list (Figure 10-5).

 

Figure 10-2. Areal Plot: Area Average

 

 

Figure 10‑3. Areal Plot: Area Totals

 

 

Figure 10‑4. Areal Interpolation Plot:
Show Grid (Gridded Data)

 

Figure 10‑5. Areal Interpolation Plot:
Show Selected Areas

 

 

10.2.2   Areal Values for Polygon Segment

To view the area, total value, and average value for a selected polygon segment use the mouse cursor to hover over a polygon on the map.  The values are shown at the bottom left of the information panel (Figure 10-6).

Figure 10‑6. Areal Values for Polygon Segments

10.2.3   View and Export Areal Plot Data in Spreadsheet Format

To view the average and total interpolation values for selected formulas in a spreadsheet format, right click on the Areal Interpolation Plot and select Area Information (Figure 10-7). The Area Information Spreadsheet contains four columns: the identification number from the name field for the polygon, the total area, average interpolated value, and total interpolated value (Figure 10-8). At the top of the Area Information tab, the user may select File>Export to export the data to a spreadsheet file (Figure 10-9).  The save pop-up window allows the user to specify with either a text (.txt) or comma-separated-values (*.csv) format, also known as a comma-delimited file (Figure 10-10).

 

 


Figure 10‑7. Right Click on Area Plot

Figure 10‑8. Area Information Spreadsheet

 

 

 

 

 

 

 

Figure 10‑9. Export Spreadsheet

Figure 10‑10. Name and save spreadsheet

 

 

10.2.4   Export Areal Plot Data to Shapefiles

At the top of the Area Information tab (Figure 10-11), the user may select File>Export Shape Files to export the data to a shapefile. In the Save pop-up window (Figure 10-12), input the name in the File Name field, and select file type: Shapefile (*.shp).  The data provided in the spreadsheet—name field, total area, average value, total value—are exported to the shapefile.  A GIS program such as User-friendly Desktop Internet GIS (uDig; http://udig.refractions.net/), an open-source Java program, may be used to view the shapefiles generated by VERDI.  The shapefiles are saved as five separate files that must be kept together as part of the ESRI format (*.shp, *.dbf, *.prj, *.shx, and *.fix).  There are no units assigned to the data that are saved in the shapefile, so it is important for the user to keep a copy of the comma-delimited text file, or to keep some alternative text file that specifies the units for each data field.

 


Figure 10‑11. Export Shapefile

Figure 10‑12. Name and save shapefile

10.3    Vertical Cross Section Plot

The vertical cross section plot allows you to show a slice of data (Figure 10-13). A popup dialog box (Figure 10-14) prompts you for information needed to create the plot. You will need to enter either the column to be used (for an x-axis cross section) or the row to be used (for a y-axis cross section) in the plot. The current time step on the plot can be changed using the Time Step spinner control above the plot. There is also a Column spinner control to change the column number (or row number). The cross-section column number (or row number) is included in the title of the plot.

Figure 10‑13. Vertical Cross Section Plot

Figure 10‑14. Vertical Cross Section Dialog Box

10.4   Time Series Plot

The time series plot shows a line graph with the average values over time (Figure 10-15). The plot is made for the formula’s selected domain, layer range, and time-step range.  Each time step’s data are averaged linearly to produce that time step’s data point.  The current layer can be changed using the Layer spinner control above the plot. The layer value listed in the title is updated when you change the layer.

                                                     Figure 10‑15. Time Series Plot              

10.5   Time Series Bar Plot

The time series bar plot shows average values over time in a bar plot format (Figure 10-16) rather than a line format (Figure 10-15). Other than that, the description of this plot type is the same as for the time series line plot (see Section 10.4).

Figure 10‑16. Time Series Bar Plot

10.6   Scatter Plot

The scatter plot shows the relationship between two formulas using an array of dots (Figure 10-17). The user specifies the formulas using the dialog box that comes up before the plot is displayed (Figure 10-18). The current time step and layer can be adjusted using the spinner controls above the plot. The data from a scatter plot may be exported by selecting the File menu option and then selecting Export data.  A pop-up window (see Figure 10-19) allows users to specify whether they would like the data for the current layer, or for all layers, and for the current time step, or for all time steps.  Specify the time and layer ranges, and then click the OK button.  A Save pop-up dialog box will appear.  Fill in a file name of your choice with a .csv extension, and specify the directory in which you would like to save this file.  The CSV file will be comma delimited, and will contain the following columns of data: layer, time, x-axis formula, y-axis formula.

Figure 10‑17. Scatter Plot

Figure 10‑18. Scatter Plot Dialog Box

 

Figure 10‑19. Scatter Plot Export Data into a CSV file

 

10.7   Vector Plot

The vector plot shows vector lines representing the vector formed by using two formulas (one for each component of the vector) across a geographic area; one formula represents the horizontal component, the other represents the vertical component (Figure 10-20). The formulas selected as components of the vector must match in domain, layer range, and time-step range.  You specify the components of the vector using the dialog box that comes up before the plot is displayed (Figure 10-21). After the plot is displayed, the current time step and layer can be adjusted using the controls above the plot. Note: the Vector Plot currently uses the old Tile Plot option.  In a future release, this plot will be updated to use the Fast Tile Plot.

It is also possible to overlay vectors (e.g., wind vectors) on a tile plot. This can be done either from within the vector plot option (discussed here) or from within the tile plot option (discussed in Section 10.4.4). To do this overlay from within the vector plot option, you select a formula for the Tile option in the vector plot dialog box (Figure 10-21) in addition to specifying the formulas to be used for the horizontal and vertical vector components. See Section 11.4.4 for more information on vector overlays. 

Figure 10‑20. Vector Plot

Figure 10‑21. Vector Plot Dialog Box

10.8   Contour Plot

The contour plot shows a 3‑D representation of values over a geographic area (Figure 10-22). The current time step and layer can be adjusted using controls above the plot. You can also animate the plot over time using an option in the Plot pull-down menu (Figure 10-23). In addition, the contour plots can be rotated in three dimensions to achieve different viewing angles by using the left mouse button to grab and rotate the plot.

Figure 10‑22. Contour Plot

Figure 10‑23. Contour Plot Menu Options

11         Plot Menu Bar

Each VERDI plot contains its own menu bar that has options specific to that type of plot. As an example, the menu options at the top of a Fast Tile plot include those shown in Figure 11-1.   Most options are common to all plots, and function in the same way (unless the option is grayed out) for all plot types, so it is easier to describe the function of these configuration menu options once, rather than repeat the same information for each type of plot. Only options that are applicable to a particular plot type are enabled; others are grayed out and cannot be selected.  Menu options were rearranged and/or added in VERDI 1.3, which resulted in the Plot Menu Bar being significantly different for the Vector Plot and the Fast Tile Plot.  Currently, the Vector Plot is based on the original Tile Plot (which was removed in VERDI 1.4). The Areal Plot is based on the Fast Tile Plot. In a future release the vector plot will also be based on the Fast Tile Plot. The Plot menu bars options will be discussed separately. 

The items listed in red font in Figure 11-1 are new options supported in the Fast Tile Plot and Areal Plot; the items listed in blue font are features of Vector Plot that, for the Fast Tile and Areal Plots, were moved to a new column labeled GIS Layers.

Plot configuration options that are available in VERDI are discussed in this section.

Figure 111. Fast Tile and Areal Plot Pull-down Menu Options

File

Configure

Controls

Plot

GIS Layers

Print

Export as Image/GIS

Configure Plot

Load Configuration

Save Configuration

Zoom

Probe

 

Time Series of Probed Cell(s)

Time Series Bar of Probed Cell(s)

Time Series of Min. Cell(s)

Time Series of Max. Cell(s)

Add Map Layers

 

 

Set Row and Column Ranges

Configure GIS Layers

 

 

Show Grid Lines

Animate Plot

Set Current Maps as Plot Default

 

Show Lat/Lon

Add Overlay

 

 

The Plot Menu Bar for the Vector Plot is shown in Figure 11.2.  Configure GIS Layers is supported in the Vector Plot as an option of Configure>Maps>Configure GIS Layers. The map option is highlighted in blue font.  When the user selects the map menu option, a pull-down menu allows the user to select map layers, configure GIS layers and set current maps as plot default.

Figure 11‑2. Vector Plot Pull-down Menu Options

File

Configure

Controls

Plot

Print

Export as Image

Configure Plot

Load Configuration

Save Configuration

Maps

Zoom

Probe

 

Time Series of Probed Cell(s)

Time Series Bar of Probed Cell(s)

Time Series of Min. Cell(s)

Time Series of Max. Cell(s)

 

 

Show Lat/Lon

 

 

 

Animate Plot

 

 

Add Overlay

 

11.1   File Menu Options

Options in the File menu include printing a plot and exporting a plot as an image. Plots can be saved as PNG, JPEG, BMP, EPS, or TIFF image file formats; SHP, SHX, DBF Shapefile formats (the shapefiles are saved as five separate files that must be kept together (*.shp, *.dbf, *.prj, *.shx, and *.fix); and ASCII grid (*.asc) formats.

11.2    Configure Menu Option

The Configure pull-down menu contains the following options: Configure Plot, Load Configuration, Save Configuration, and Maps.

11.2.1   Configuring Plots

Figures 11-3 through 11-6 show the dialog boxes that appear when you select Configure Plot. The Configure Plot dialog box contains four tabbed options: Titles, Color Map, Labels, and Other.

·        The Titles tab (Figure 11-3) allows you to edit title text and select the font type, size, and color for the title and two subtitles of the plot. Titles may be turned on or off by selecting or deselecting the check box for each title.  If a check box is unselected, the title text box, font type and size box, and color box are grayed out.

·        The Color Map tab (Figure 11-4) allows you to select the number of tiles, the palette type to be used, the color interval, the number format, and the option to have a linear or logarithmic scale. As you vary the number of tiles, the palette types that are available to choose from are automatically updated. The palette type options include sequential (similar to what users typically use for PAVE plots), qualitative, and diverging. The Interval pull-down menu is set to Automatic by default.  The color intervals are automatically calculated based on the Min and Max values of the dataset and the number of tiles.  To change the Min or Max value, type a new value into the text box, and then click Rebuild. To specify the number format used in the map legend, enter the format in the entry box using the C language's printf() routine's format syntax, and then click Rebuild (e.g., for %1.2E, a zero in the legend would be printed with the format “0.00E0”; for %1.2F the format would be 0.00).  To choose a logarithmic scale, select the pull-down menu option and select Logarithmic. The start values for each legend bin will be automatically adjusted when the user changes the scale.  Click Apply to review changes made to the map while the Configure Plot dialog is open.  Use the Apply button as needed to make additional adjustments to the color map, legend range, and/or number of tiles in the range.  To use an irregular spacing or to change the spacing between the color tiles, select Custom from the Interval pull-down menu and change the interval start values in the list at the bottom of the dialog box. Specify the interval start values for each color in the legend and then click Apply.  If you try to enter a value for an interval that does not fall between the interval start values that are above and below the value that you are changing, then the value will not be accepted and the number will revert back to the previous value.  When you have chosen to create custom intervals, the Min and Max text boxes and the Rebuild button are disabled and grayed out, because you are choosing to override automatic calculation of the color interval spacing and instead define the min, max, and number of tiles manually. Note: values above the maximum specified will be colored the same as the color for the maximum range, and similarly, values less than the minimum specified will be colored the same as the color for the minimum range. Once the settings are finalized, click OK and the Configure Plot dialog will close.

·        The Labels tab (Figure 11-5) contains options to edit the labels of the Domain Axis (x-axis), the Range Axis (y-axis), Legend, and Footer. VERDI allows the user to select the number of discreet numerical labels shown on plots.  For example, it can be difficult to read the numbers when there are more than 13 different colors on a scale. The legend can be improved by reducing the number of tick marks that are labeled (see Figure 11-5).  From the Plot menu option, select Configure> Configure Plot.  When the Configure Plot window appears, select the Labels Tab, as shown in Figure 11-5.  At the top of the Labels Tab are four additional tabs that can be selected: Domain Axis, Range Axis, Legend, and Footer.  To edit the number of tick marks that are labeled on the Legend of the plot, select the Legend tab, and there will be a check box labeled Show Tick Labels, and a text box where you can change the number of tick labels that are placed on the plot.  After you change the number of tick labels and click on the Apply button, the density of the labels on the plot is increased or decreased accordingly.  Once you are satisfied with the number of Tick Labels on the Legend of your plot, then click Apply.  If you would like to change the number of tick marks on the Domain Axis, click on the Domain Axis Tab, and you will see the check box labeled Show Tick Labels, and a text box.  Change the number in the text box, then Click OK, and repeat this for the Range Axis Tab.  Once you are finished customizing the number of Tick Labels for the three different regions of the Plot, click OK, and the Configure Plot Window will close. Figure 11-7 shows an example plot where the number of Tick Labels has been reduced in both the Range Axis and the Legend, but the number of tick labels has not been reduced in the Domain Axis.

·        The Other tab (Figure 11-6) allows you to enable or disable showing the grid lines, and to edit the vector arrow color and the series color.  The edit series color allows the user to specify the colors used to shade the bars for the time series bar plot, or the colors of the lines on the Time Series Plot.


Figure 11‑3. Configure Plot, Titles Tab

Figure 11‑4. Configure Plot, Color Map Tab

Figure 11‑5. Configure Plot, Labels Tab

Figure 11‑6. Configure Plot, Other Tab


Figure 11‑7. Example Plot with Tick Marks reduced for the Legend and Range Axis

11.2.2    Loading and Saving Configuration

If you have made changes to the configuration of a plot, and would like to save the configuration for future use on other plots, use the Save Configuration option from the Configure pull-down menu on the plot. It is important to create a file name that indicates the formula name, the dataset, and the type of plot, along with the .cfg extension that indicates that it is a configuration file, so that you will know which plot the configuration file was saved for. An example file name is <FormulaName>_<DatasetFilename>_<PlotType>.cfg, or “O3_CCTM_base_tile.cfg”.  This is only an example name; you may use your own naming convention. What is important is not how you name the files, or how you organize the files into directories, but that you remember the datasets and variables to which a specific configuration may be applied.  Saved configuration files may also be invoked in batch or command line scripts by setting the parameter configFile; i.e., configFile=C:\\Program Files\\VERDI_1.4.1\\data\configs\o3_10bin.cfg.

To load a previously saved plot configuration, first create a plot that is of the same type, and uses the same formula that is used within the configuration file. Then select the Load Configuration option from the Configure pull-down menu on the plot.  An Open File Dialog window will allow you to look for the directory in which you saved the configuration file, and to open that file.  The plot title, color map, and other plot configuration features will be applied to the plot.  Note that it is possible to load a saved configuration file that does not apply to the selected plot, so before loading a saved plot configuration check carefully to be sure the plot type and formula of the configuration file match those of the plot.

11.3   Controls Menu Options

The Controls pull-down menu contains the following options: Zoom, Probe, Set Row and Column Ranges, and Show Lat/Lon.

11.3.1   Zoom Using the Left Mouse Button

To zoom in and enlarge a subdomain of the data, select the Zoom option. Then hold down the left mouse button and use the mouse to click on a region of the map and then draw a rectangle around the region of interest. To zoom out click on the map in the right bottom corner using the left mouse button, and while holding down the left mouse button, move the mouse to the upper left corner and then release the left mouse button.

11.3.2   Zoom Using the Right Mouse Button

11.3.2.1    Vector Plot

On a vector plot, right click on the map to see a pop-up window that will allow you to select Zoom In or Zoom Out on either Both Axes, the Domain Axis, or the Range Axis. Select Auto Range>Both Axes to recover the plot of the full domain, or select Auto Range> Domain Axis or Range Axis to zoom out fully along only the domain axis or only the range axis (Figure 11-8).

Figure 11‑8. Right Click on Tile Plot to Zoom Out

11.3.2.2    Fast Tile Plot and Areal Plot

To zoom on a fast tile plot or areal plot, use your mouse button to right click on the map in the area of interest. A pop-up window will appear, allowing you to select Zoom In, Zoom Out, or Max Zoom Out to recover the plot of the full domain (Figure 11-9).

Figure 11‑9. Right Click on Fast Tile Plot to access Zoom Out Option

11.3.3   Probing Values at Specific Points

To determine the data value at a specific point, select the Probe option under the Controls pull-down menu. To probe a single data point, use the mouse to hover the cursor over that grid point on the map; the coordinates of the grid points are shown in the lower right-hand side of the plot in the format (column, row). Once you click on the grid point of interest, the value of the datum at that grid point is displayed in the lower left-hand area of VERDI main window (Figure 11-10).

Figure 11‑10. Click on Plot to Probe: Data Value Shown in Lower Left of VERDI, Grid Values Shown in Lower Right

11.3.4   Probing a Domain Region of Data

To probe the values of a selected region of grid points, select the Probe option under the Controls pull-down menu, then draw a rectangle by clicking on a point on the map, holding down the left mouse button, and then releasing the mouse button once the rectangle encloses the region of interest. VERDI will create a spreadsheet displaying the grid values and will place it in the plot area of the VERDI main window as a tabbed window (Figure 11-11).  The File>Export menu option at the top of the spreadsheet allows you to save probed data as a comma-delimited text file (*.csv).

Figure 11‑11. Spreadsheet Showing Probed Values for Region of Interest

11.3.5   Set Data Ranges

 

The Controls>Set Row and Column Ranges menu item will bring up a pop-up window that allows the user to configure the minimum and maximum values used in the row (x-axis range) and column (y-axis range) (Figure 11-12 and 11-13).  Specify the values and then click OK.

Figure 11‑12. Select Set Row and Column Ranges

 

Figure 11‑13. Enter Row and Column Values

11.3.6   Showing Latitude and Longitude

To view the latitude and longitude values for a point on the plot, select the Show Lat/Lon option on the Controls menu, then hover your cursor over the location for which you would like to know those values. The lat/lon coordinates will be displayed in the lower right-hand side of the window (Figure 11‑14). The option to display the lat/lon coordinates may be selected, and works with either the Zoom or the Probe option. 

Figure 11‑14. Lat/Lon Values Shown in Lower Right of VERDI

 

11.4    Plot Menu Options

The Plot pull-down menu (Figure 11-15) contains the following options: Time Series of Probed Cell(s), Time Series Bar of Probed Cell(s), Time Series of Min. Cell(s), Time Series of Max Cell(s), Animate Plot, and Add Overlay.

 

Figure 11‑15. Plot Menu Options

11.4.1   Time Series Plots

The Time Series of Probed Cell(s) and Time Series Bar of Probed Cell(s) allows the user to select a set of cells, and then produce a time series or time series bar plot of the chosen subset of probed cells. The Time Series of Min.[or Max.] Cell(s) option creates a time series plot using data for the currently selected formula at that formula’s domain, layer range, and time step range. The minimum [or maximum] value of that formula over the domain and layer range at that time step is calculated by VERDI and used for each of the time step’s data points.

11.4.2   Animate Plots

You can create an animated plot by selecting the Animate Plot option. The Time Series and Time Series Bar Plots do not have an Animate Plot option. The plots that may be animated include: Tile, Fast Tile, Vertical Cross Section, Vector Plot, and Contour Plot. An Animate Plot dialog box (Figure 11-16) will appear, allowing you to save animations either as an animated GIF with a file extension of .gif or as a Quicktime movie with a file extension of .mov.  This Plot menu option is plot-specific and so does not allow you to animate more than one plot at a time.  To animate multiple plots, you will need to use the Plots pull-down menu at the top of the VERDI main window; see Section 5.2.2, “Animate Tile Plots.”

Figure 11‑16. Animate Plot Dialog Box

11.4.3   Add Overlays

11.4.3.1    Observational Data Overlays

 

It is useful to visually compare the results contained in model output datasets with the data points in observational datasets. You can do this by creating a fast tile plot of the model output and then overlaying observational data points on the plot. The observational dataset needs to be in an I/O API observational data format (see Chapter 13 for more information about how to convert AIRS observational data into this format) or CSV-or tab delimited format observational data. 

Sample observational data are provided under the directory $VERDI_HOME/data/obs to allow the user to create a sample Observational Data Overlay Plot.  To begin, load both a model output dataset and an observational dataset. Note that when the observational dataset is loaded in the Dataset pane an (obs) label appears to the right of the dataset name in the Dataset pane. When the user double clicks on a variable available from an observational dataset and adds it to the Variable pane, an (obs) label appears to the right of the dataset name in the Variable pane. Next, create a formula in the Formula pane using a variable from the model output dataset. Use this formula to create a fast tile plot. (Note: If you create a formula referencing a variable from an observational dataset, this formula will appear in the formula list but it cannot be used to create a plot. If you try to use a formula that contains a variable from an observational dataset, the following error will occur:  “Error while evaluating formula: Selected dataset is observational.”)

To view observational data as an overlay on a fast tile plot, select Add Overlay>Observations from the fast tile plot’s Plot pull-down menu (Figure 11-15). An Observation dialog box (Figure 11-17) will appear containing the variables that are available in the observational dataset. Multiple observational dataset variables can be overlaid on a fast tile plot.  Select the observational variable or variables that you would like to overlay on the fast tile plot from the Observation Details list. You then have the option to control the appearance of the symbols that represent the observational data. The stroke size controls the thickness of the line used to draw the symbols, while the shape size controls their diameter. You can use up to six different open-area shapes—circle, diamond, square, star, sun, and triangle—to distinguish among multiple observational datasets. After you select the variable, and optionally set the stroke size, shape size, and symbol, select Add Variable and then OK to overlay the observational data on the fast tile plot (Figure 11-17). If you do not specify the size, shape, or symbol, VERDI will use default values.  The symbol shape is set by default to a circle. Repeat the process to add multiple variables. To remove the symbols for a variable on an observational data overlay, or to reset their size or shape or stroke thickness, re-open the Observation dialog by using Add Overlay>Observations and then click on the observational variable you wish to adjust and then change the stroke size, shape size, or symbol, and/or move it up or down, or remove it, and then click OK.  The center of the observational data point corresponds to the lat/lon value that is provided in the I/O API observational data file. Figure 11-18 shows a fast tile plot with grid lines drawn illustrating that when more than one observational data point are located at the same location, they are placed on top of one another, so the user may wish to select different symbols for each dataset, with the largest symbol on the bottom, and the smallest symbol on the top.

Figure 11‑17. Fast Tile Plot Observation Dialog

 

Figure 11‑18. Fast Tile Plot with Multiple Observational Data Overlays with Grid Lines

11.4.3.2    Vector Overlays

Users have two options to display vectors (e.g., wind vectors) on a plot. One option is to select the vector plot type, using the procedure described in Section 9.7 to display the vectors on a map. The other option is to display the vectors as an overlay on a fast tile plot, as described below.

To add a vector overlay to a fast tile plot, select the Add Overlay>Vectors option from the fast tile plot’s Plot pull-down menu (Figure 11-14). The Vector Overlay dialog box (Figure 11-19) asks you to select the formula for the horizontal component and the formula for the vertical component. The formulas listed in the Vector Overlay dialog box are obtained from the formula list in the Formula pane. If the formula you would like to use is not listed in the Vector Overlay dialog box, check to be sure that you have loaded the dataset that contains the variable of interest (for example, UWIND), and that you have created a formula UWIND[x], where x is the dataset number associated with the dataset that contains UWIND. Once you have selected the two components, click OK, and the vector overlays will be displayed on the plot. Currently, vectors are plotted in the center of the grid cell.  UWIND and VWIND are typically obtained from