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.
This guide describes VERDI version 1.3 released in June 2010.
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.)
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:
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 1‑1. Top of Main VERDI Web Site Page
Figure 1‑2. Downloading VERDI from the CMAS Web Site, Step 1
Figure 1‑3. Downloading VERDI from the CMAS Web Site, Step 2
Figure 1‑4. Downloading VERDI from the CMAS Web Site, Step 3
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 1‑6. Getting Documentation on VERDI from the CMAS
Web Site
Figure 1‑6. VERDI Documentation on the CMAS Web Site
You are encouraged to check the VERDI FAQs, to search the M3USER
listserv for VERDI-related technical support questions, and to report
errors and make requests for enhancements using the web-based Bugzilla system,
which is used by CMAS to track issues with supported products. The Bugzilla
site for VERDI is http://bugz.unc.edu/enter_bug.cgi?product=VERDI.
If you have not used Bugzilla before, first go to http://bugz.unc.edu
and follow the instructions for requesting a new account. Once you are logged in, you can enter
information about your question or bug using the form shown in Figure 1-7. When
filing a report, you will need to choose from among the following components:
Automating VERDI with Scripts, Configuring Plots, Documentation, Exporting
Images and Animations, Formulas, GIS Layers, Importing Model Data, Importing
Observation Data, Projects, Selections of Domains, Layers, and Time-steps, and
Using the GUI.
Bugzilla also allows you to submit software code
improvements for review and testing by others, to submit small test cases, to
submit new GIS background maps, or to make other contributions to VERDI. To
submit attachments to a bug report or request, click on the Add Attachment
button in the bottom half of the form (Figure 1-8) to bring up a form
requesting additional information about the attachment (Figure 1-9). Note that
only minor code updates should be submitted through Bugzilla. If you are doing
a substantial amount of software development on VERDI, please see Section 1.5
for additional information.
Figure 1‑7. Top of Bugzilla Form for VERDI
Figure 1‑8. Bottom of Bugzilla Form for VERDI
Figure 1‑9. Add Attachment Form in Bugzilla
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 adding nonlinear scales (e.g., log) to
the color map. 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.”
2.1 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.
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.
In VERDI version 1.3, the Fast Tile Plot supports most of the
configuration options of the original tile plot including display lat/long,
probing, zooming and adding grid lines.
A future release will add vector overlay capability to the Fast Tile
Plot.
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.
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.
VERDI works best on screen displays
that have been set to a screen resolution of 1280 ´ 1024 pixels. 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 will need to reboot your
computer for this screen setting to take effect.
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 has been customized 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.
VERDI requires the following third party software: JRE™ 6, Java3D, and Java™ Advanced
Imaging (JAI). The Linux 32 bit version
of the required third party software is provided in the VERDI release tar file.
1. tar
-xvf verdi_1.3.tar into a location where you would like to install VERDI.
2.
Edit
verdi_1.3/verdi.sh
a. Change
the path for the VERDI_HOME variable to reflect the location where VERDI was
installed (e.g., VERDI_HOME=/usr/local/verdi)
b. If
you download JRETM 6 for a
version other than Linux 32 bit that is provided with VERDI as described in the
next section, change the path for the JAVA variable to reflect where the java
executable has been installed.
3. If
the settings for the variables in step 5 are correct, VERDI should now run if
you execute the verdi.sh executable script (e.g., ./verdi.sh).
If your non-Windows computer 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 https://jai.dev.java.net/binary-builds.html#Release_builds
b.
Installation
instructions: http://download.java.net/media/jai/builds/release/1_1_3/INSTALL.html
c. Download
the .tar.gz package and untar. This will create a directory
"jai-1_1_3".
d. Copy
the following files:
i.
cp jai-1_1_3/lib/libmlib_jai.so /path-to-/verdi_1.3/jre1.6.0_13/lib/i386
ii.
cp jai-1_1_3/lib/*.jar /path-to-/verdi_1.3/jre1.6.0_13/lib/ext
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 included version of Java 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
For Linux platform with ia64 architecture, please find the
installed jre or jdk library directory (ex. /usr/java/jre1.6.0_13/lib/ext or
/usr/java/jdk1.6.0_11/jre/lib/ext) and copy all missing library files from
$VERDI_HOME/jre1.6.0_13/lib/ext directory. If ia64 jre/jdk package is not
installed, please go to java.sun.com download the install file and install the
package. Then copy the missing library files from
$VERDI_HOME/jre1.6.0_13/lib/ext directory.
To install VERDI for Windows, run
the installation program VERDI_1.3_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 3‑1. VERDI Setup Wizard
Figure 3‑2. License Agreement
Figure
3‑3. Selecting an Installation Directory
Figure 3‑4. Setting the Start Menu Folder
Figure 3‑5. File Extraction
Figure 3‑6. Installation Complete
The VERDI installation package contains a file called
config.properties. On Windows, this file is copied into the verdi subdirectory
of your USERPROFILE directory (e.g., “C:\Documents and Settings\yourusername\verdi”).
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. An example of the
contents of a Windows version of this file is:
verdi.dataset.home=D:\\VERDI
verdi.project.home=C:\\Documents and Settings\\user_a\verdi
verdi.config.home=D:\\Program Files\\VERDI 1.3\\config
On Linux, this file is copied into the $USER_HOME/verdi/
subdirectory. An example of the contents
of a Linux version of this file is:
verdi.dataset.home=/home/user_a/verdi/data
verdi.project.home=/home/user_a/verdi/proj
verdi.config.home=/home/user_a/verdi/conf
The items in the
config.properties 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 dataset.home setting specifies the
default location from which to load datasets.
The project.home setting specifies the default location from which to
load and save projects. The config.home
setting specifies the default location from which to load and save plot
configurations. 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.
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 4‑1. 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.
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. This will replace the
current tile plot, once it is fully operational and configurable. The functions that are currently enabled for tile
plots and fast tile plots are described in Section 10, “Creating Plots.”
Figure 4‑2. VERDI Main Window
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 arrow
pointing out of the upper left corner. You can then click on the pane and move
it to the left 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. To re-dock a window or pane, click on the
icon in the upper right corner. The icon
looks like a circle enclosed in a square.
This will return the floating pane back to where it usually lives within
the main window.
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 5‑1. VERDI Main Menu Options
|
File
|
Plots
|
Window
|
Help
|
|
Open Project
Save Project
View Script Editor
|
Undock All Plots
Animate Tile Plots
|
Areas
Datasets
Formulas
|
VERDI Help Docs
About
|
|
|
|
|
Exit
|
|
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.
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.”
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_1.3. 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.
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.
As with the Dataset, Formula, and Area
panes (Section 4.3), plot sub-windows can be undocked so that you can move them
into separate windows. This allows side by side comparisons of plots. Note that
undocking is performed only on previously created plots; any newly created
plots are docked to the VERDI main window.
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 5‑2. Animate Plots Dialog and Tile Plots
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.
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.
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.
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.
VERDI currently supports visualizing files in three
formats: CMAQ Input/Output Applications Programming Interface (I/O API) netCDF,
WRF netCDF, and CAMx (UAM-IV). 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.
Several example
datasets are provided under the $VERDI_HOME/data directory. 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:
- CAMx – contains sample CAMx dataset and camxproj.txt file
- hucRegion – contains Hydrologic Unit (HUC) shapefiles for
region 3 (southeast US)
- Model – contains sample WRF and CMAQ I/O API datasets
- Obs – contains observational dataset created by airs2m3
converter
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 6-1) allows you to select a dataset
for use in VERDI. Support for loading
data from a remote file system has been added in version 1.3. The use of the yellow plus remote button will be discussed in Section 6.4.
After you specify a gridded 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 6-2). (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.
Figure 6‑1. Open Dataset
File Browser
Figure 6‑2. Datasets Pane Displaying Information about a
Dataset
The
VERDI 1.3 release allows the user to select and add variables from datasets on
remote file systems. To do this, press the yellow plus remote button at the top of the Datasets pane. In the Remote File Access Browser (Figure
6-3) that appears, enter your user name, choose a host from a list, and enter
your password, then click Connect.
Figure 6‑3. Available Hosts in the Remote File Access
Browser
The
top panel displays a listing of the home directory on the remote file system,
as shown in Figure 6-4. If the files are
in a different directory than your default home directory, please double click
on the ../ symbol at the top of the list, to navigate back a directory, then
navigate within the remote file system to the directory where your files are
located. When you double click on the file that you would like to use, VERDI
will provide you with a list of variables that are available within the
file. 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 discontinuous variables. Once the variables that you would like VERDI
to read are highlighted, click on the Read
button.
Figure 6‑4. 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 6-5. 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 to your home directory on your local file system, ie. C:\Documents
and Settings\username on a Windows XP machine. 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 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 6‑5. Remote Dataset Labeled with Number at
End of the Filename
The
VERDI 1.3 release contains the RemoteFileUtility and ncvariable programs that enable
VERDI to add your IO/API netCDF or WRF netCDF formatted dataset from a remote file
system. A gzipped tar file is available
in the $VERDI_HOME directory.
- Provide the RemoteFileReader.tgz file
to a System Administrator for the linux server that contains data files
you need to access remotely using VERDI.
- The RemoteFileUtility c-shell script
and ncvariable binary need to be installed in /usr/local/bin by the System
Administrator. (A future release of
VERDI will allow the user to specify the location of these programs,
rather than requiring the use of /usr/local/bin.)
- 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.
- Edit the ui.properties file in your
$VERDI_HOME/plugins/bootstrap/ folder.
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
ui.properties file, as shown in Figure 6-6. You will need to restart VERDI in order
for it to recognize a newly added remote host name.
Figure 6‑6. Edit ui.properties file to add a remote host
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 6-7.
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 6‑7. Right Click on
Variable in Dataset Pane
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
6-4 are discussed in Section 9, “Spatial and Temporal Data Subsetting.”
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 6-8). 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
6‑8. 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.
A
config.properties file (discussed previously in Section 3.4) allows the user to
customize where VERDI will look by default for the location of datasets and
project files. This file is located in
the $USER_HOME/verdi/subdirectory, and can be edited to specify where datasets
and/or project files are saved and stored.
An example is as follows:
# This file should be put in
$USER_HOME/verdi/subdirectory
# Please use double
backslash for windows platform or slash for UNIX like platforms
# Please uncomment the
following lines and modify them to suit your local settings
verdi.dataset.home=D:\\data
verdi.project.home=D:\\programs
verdi.config.home=D:\\config
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.
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.
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]+.001)”.
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.”
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.
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.”
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.
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
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.
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.
When the user
selects the Areal Interpolation Plot, the selected formula is interpolated 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 8‑1. Areas Pane
Figure
8‑2. Open Area File Browser
Figure 8‑3. Open Area
File: Select Name Field
Figure 8‑4. Coordinate System
Figure 8‑5. Projection Information
Figure 8‑6. Additional Data Fields appear
depending on projection selected.
Figure
8‑7. Area Name Fields available for Shapefile
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.
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 9‑1. Specify Time
Step 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 9‑2. Edit
Layer Range
in Formula Pane
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 9‑3. Using the Slider to View the Domain Panel
Figure 9‑4. Edit Domain Dialog Box
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 9‑5. Error obtained when incompatible subset domains
are created using the Dataset pane
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: tile plot, 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.”
Tile plots show a color contour of the selected
formula. The tile plot currently only supports Lambert conformal and UTM
projections. Users are encouraged to use
the Fast Tile Plot to create tile plots.
In the future release, the Tile Plot will be removed as a plot option as
it does not have the functionality of the Fast Tile Plot. Figure 10-1 shows a
tile plot created in VERDI. The legend on the right side of the window shows
the range of values contained in the data displayed. The current time step can
be changed using the Time Step spinner control above the plot. When
you make a change, this is reflected in the information below the x-axis label on the plot. You can use
the Layer spinner control to change the current layer. When you make a change in the layer, the layer
number is automatically updated in the plot title. To zoom in and out, use either
the left mouse button to click and drag, or the right mouse button to right
click on the plot and access a pull-down menu.
Zooming and other plot configuration options are discussed further in
Section 11.3.
Figure 10‑1. Tile Plot
The Fast Tile Plot was developed with
less third-party software, and provides faster rendering of images than the tile
plot. The fast tile plot supports all of
the functionality of the tile plot with the exception of vector overlays. An
example of the Fast Tile Plot window is shown in Figure 10-2. The
motivation for developing the fast tile plot was the slow display speed of the
original tile plot when VERDI was used on a remote compute server. The fast
tile plot draws and animates substantially faster than the original tile plot.
Figure
10‑2. Fast Tile
Plot
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 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. 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. 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.
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.
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 10-3), the Area Totals (Figure 10-4), or the value of the
formula contained in the Gridded Dataset (uninterpolated) (Figure 10-5). 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 10-6).
Figure 10-3. Areal
Plot: Area Average
Figure 10‑4. Areal Plot:
Area Totals
Figure 10‑5. Areal Interpolation Plot:
Show Grid (Gridded Data)
Figure 10‑6. Areal
Interpolation Plot:
Show Selected Areas
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
10-7).
Figure 10‑7. Areal Values
for Polygon Segments
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 10-8). 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 10-9). At the top of the Area
Information tab, the user may select File>Export to export the
data to a spreadsheet file (Figure 10-10).
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 10-11).
Figure 10‑8.
Right Click on Area Plot
|
Figure 10‑9. Area
Information Spreadsheet
|
|
Figure 10‑10.
Export Spreadsheet
|
Figure 10‑11. Name and
save spreadsheet
|
|
|
|
|
|
At the top of the Area Information
tab, the user may select File>Export Shape Files to export the data
to a shapefile. 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 10‑12.
Export Shapefile
|
Figure 10‑13. Name and
save shapefile
|
The vertical cross
section plot allows you to show a slice of data (Figure 10-14). A popup
dialog box (Figure 10-15) 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 10‑14. Vertical
Cross Section Plot
Figure
10‑15. Vertical
Cross Section Dialog Box
The time series
plot shows a line graph with the average values over time (Figure 10-16).
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 10‑16. Time Series
Plot
The time series bar
plot shows average values over time in a bar plot format (Figure 10-17)
rather than a line format (Figure 10-16). Other than that, the description of
this plot type is the same as for the time series line plot (see Section 10.5).
Figure 10‑17. Time Series
Bar Plot
The scatter plot
shows the relationship between two formulas using an array of dots (Figure
10-18). The user specifies the formulas using the dialog box that comes up
before the plot is displayed (Figure 10-19). 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 10-18) 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 10‑18. Scatter Plot
Figure 10‑19. Scatter Plot
Dialog Box
Figure 10‑20.
Scatter Plot Export Data into a CSV file
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 10-21). 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 10-22).
After the plot is displayed, the current time step and layer can be adjusted
using the controls above the 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 10-22) 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 10‑21. Vector Plot
Figure 10‑22. Vector Plot
Dialog Box
The contour plot
shows a 3‑D representation of values over a geographic area (Figure 10-23).
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 10-24). 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 10‑23. Contour Plot
Figure 10‑24. Contour Plot Menu Options
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 Tile Plot and the Fast Tile Plot. Currently, the Vector Plot is based on the
Tile Plot. 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 and the Tile Plot will
be removed. 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 the Tile Plot that, for the Fast Tile and Areal
Plots, were moved to a new column labeled GIS Layers that is applicable only
to those two plot types. Configure GIS Layers is supported in the Tile
Plot as an option of Configure>Maps>Configure GIS Layers.
Plot configuration options
that are available in VERDI are discussed in this section.
Figure 11‑1. Fast Tile and Areal Plot Pull-down Menu Options
|
File
|
Configure
|
Controls
|
Plot
|
GIS Layers
|
|
Print
Export as Image
|
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 Tile and Vector Plot is shown in
Figure 11.2. 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.
Tile and 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
|
Options in the File
menu include printing a plot and exporting a plot as an image. Plots can be
saved as a PNG, JPEG, BMP, EPS or TIFF image files.
The Configure
pull-down menu contains the following options: Configure Plot, Load Configuration,
Save Configuration, and Maps.
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 allows you to edit and set the font and color for the title and two
subtitles of the plot.
·
The Color
Map tab allows you to select the number of tiles, the palette type to be
used, the color interval, and the number format to be used. 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”). 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. Once the settings
are finalized, click OK and the Configure Plot dialog will close.
·
The Labels
tab contains options to edit the labels of the Domain Axis (x- axis), the Range
Axis (y-axis axis), and the Legend.
·
The Other
tab 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
|
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; ie. configFile=C:\\Program Files\\VERDI_1.3\\config.txt.
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.
The Controls pull-down
menu contains the following options: Zoom, Probe, Set Data 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.
On a tile plot or 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 11-7).
Figure 11‑7. Right Click on Tile Plot to Zoom Out
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 11-8).
Figure 11‑8. Right Click on Fast Tile Plot to access
Zoom Out Option
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 11-9).
Figure 11‑9. Click on Plot
to Probe: Data Value Shown in Lower Left of VERDI, Grid Values Shown in Lower
Right
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 11-10). 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 11‑10. 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 11-11). Specify the values and then click OK.
Figure
11‑11. Select Set
Row and Column Ranges
Figure 11‑12. Enter Row
and Column Values
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 11‑13). The option to display
the lat/lon coordinates may be selected, and works with either the Zoom or the Probe
option.
Figure 11‑13. Lat/Lon
Values Shown in Lower Right of VERDI
The Plot
pull-down menu (Figure 11-14) 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 11‑14.
Plot Menu Options
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.
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 11-15)
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 11‑15. Animate Plot
Dialog Box
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 tile plot or 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). A future enhancement of the VERDI Fast Tile
Plot will be the ability to support CSV-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
Plots. The User is encouraged to use the
Fast Tile Plot, as improvements have been made to the Observational Overlays,
such as the observational data is plotted at the actual lat/lon rather than in
the middle of the corresponding grid cell, and multiple observational overlays
are supported. The Observational Data
Overlay Dialog is different for the Fast Tile Plot and the Tile 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. Next, create a formula in the Formula pane using a variable from
the model output dataset. Use
this formula to create either a fast tile plot or a 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 tile plot’s Plot pull-down menu (Figure 11-14). An Observation
dialog box (Figure 11-16) will appear containing the variables that are
available in the observational dataset. Select the
observational variable or variables that you would like to overlay on the 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 11-16). 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 IO/API observational data file. Figure
11-16 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 side by side.
Figure 11‑16. Fast Tile
Plot Observation Dialog
Figure
11‑17. Fast Tile
Plot with Observational Data Overlay
To view observational data as an overlay on a fast tile
plot, select Add Overlay>Observations from the tile plot’s Plot pull-down menu (Figure 11-14). An Observation
dialog box (Figure 11-18) will appear containing the variables that are
available in the observational dataset. Select the observational variable or
variables that you would like to overlay on the tile plot from the Observation
Details list. Select the stroke size,
shape size, and symbol and then click OK.
Once the observational data is overlaid on the tile plot, the user is
not able to remove or resize an overlay.
The center of the observational data point is positioned on the center
of the grid for which the observational data point was located, rather than at
the lat/lon location. This is different than the Fast Tile Plot.
Figure 11‑18. Tile Plot Observation Dialog
Note: The Fast Tile Plot does not currently support
vector overlays. This feature is
available only in the Tile Plot. Vector
overlays will be added to the Fast Tile Plot in a future release.
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 tile plot, as described
below.
To add a vector overlay to a tile plot, select the Add
Overlay>Vectors option from the tile plot’s Plot pull-down menu (Figure 11-14). (Because this capability has
not yet been added to VERDI for Fast Tile Plots, these options are currently
grayed out for that plot type) 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 METDOT3D , which are defined at dot
points or cell corners. Plotting the
wind vector at their calculated locations and adjusting the length of the wind vector based on the magnitude of the wind speed will be added to
the Fast Tile Plot in a future release.
An example of an ozone concentration tile plot with wind
vector overlays is shown in Figure 11‑20. By default, the vectors are all
given the same length. The thickness of the line width used to draw the vector
indicates the magnitude of the vector; a larger-magnitude vector is drawn with
a thick line, a smaller-magnitude vector with a thinner line. At this time
there is no user control over how the vectors are displayed, and there is no
option to remove the vectors from a tile plot.
Figure 11‑19. Vector Overlay Dialog Box
Figure 11‑20. Wind Vector
Overlay on an Ozone Tile Plot
The GIS Layers pull-down menu (Figure 11-21) contains
the following options: Add Map Layers, Configure GIS Layers, and Set Current Maps
As Plot Default.
Figure 11‑21. Plot Menu Options
The Add Maps Layers
option in the GIS Layers pull-down menu is used to add maps to
a Fast Tile Plot (Figure 11-22). (Tile
plots, fast tile plots, and areal interpolation plots are the only plots that
have maps.)
For the Fast Tile Plot, a selection of default maps—including
World, North America. USA States, USA
Counties, HUCs, Rivers, and Roads—can be selected or deselected by clicking
with the left mouse button on one of these map names. This will cause a check button to appear or
disappear next to the chosen map name, and the selected map to appear on the
plot.
Figure 11‑22. Add Map Layers
The fast tile plot uses a new format for all maps and GIS
layers, called the bin format, to improve the speed of displaying the map
layers. A shape2bin program that runs on
linux platforms has been provided with the VERDI distribution to allow users to
convert new map shapefiles to the bin format for the fast tile plot.
Linux:
o
extract the shape2bin.zip that is located under
$VERDI_HOME/VERDI_1.3/ directory using: unzip shape2bin.zip
o
cd shape2bin
o
Several linux binary executables are provided in
with the code under the bin directory. A
makeit script is provided that documents the compiler flags and options used to
build the executables.
o
Edit the runit script to specify DATA_DIR as the
directory where your shapefiles are located.
Run the script using the syntax: ./runit
The bin files will be written to the same directory as where the
shapefiles are located. After the script has run, copy the new bin file from
the DATA_DIR directory to the bin map directory:
$VERDI_HOME/Verdi_1.3/plugins/bootstrap/data, as this is where VERDI looks for
the bin format files. Several shapefiles and their converted bin files are
provided under the bin map directory.
Windows
o
Extract the win_shape2bin.zip file provided
under the $VERDI_HOME/verdi_1.3 directory by double clicking on the file.
o
Copy the two files cygwin1.dll and shape2bin.exe
to the bin map directory: $VERDI_HOME/VERDI_1.3/data
o
Place the shapefile(s) that you would like to
convert into the bin map directory
o
Start a command line prompt by using Run and
type in cmd
o
cd C:\Program
Files\VERDI_1.3\plugins\bootstrap\data
o
type the command shape2bin, and it will provide
the format that the user should use to convert a shape file to a bin file (see
Figure 11-23)
Figure 11‑23. shape2bin command usage
To show an additional map on the plot, select the Configure GIS Layers option in the GIS Layers pull-down menu. When you click on this item, a dialog box titled
Manage Layers gives you the following options: Add Layer, Move Up, Move Down,
Remove Layer, and Edit Layer (Figure 11-24).
Figure 11‑23. Manage Layers Dialog Box
·
When you select Add Layer, an Add Layer pop-up window (Figure 11-25) prompts
you to select a map file to import into the base map. Navigate to
bootstrap/data directory and select a map file with the .bin extension and
click next. The Edit Style pop-up window to allow you to
edit the layer style (Figure 11-26), or you can use the default line color and
thickness. The outline color of the map layer can be changed to help
distinguish between map layers by clicking on the box next to outline color and
selecting from the color palette (Figure 11-26). The outline transparency or thickness can be
changed by using spin controls to change the values. Once the layer style
editing is done, Click Finish, and
the new map name will appear in the list on the Manage Layer pop-up window. After the layer you have added and
edited is listed in the Manage Layers dialog box, click OK to have the layer
added to the plot. If you add multiple layers to the list in this dialog box,
the one at the top of the list is the top layer shown on the plot.
·
To rearrange the order in which the GIS layers
are displayed on the plot, select a layer in the Manage Layers dialog box, and
then select Move Up or Move Down, and then click OK to reposition the order of
that layer within the list. If the
layers that you are selecting are boundaries and were created to have a
transparent fill, then rearranging the order of the layers will not change the
look of the boundaries on the plot.
·
To remove a GIS layer from the plot, select that
layer in the list, then select Remove Layer, then click OK to remove it.
·
To edit a GIS layer, select the layer from the
list under Manage Layers and then select Edit Layer. The Edit Layer pop-up window will allow you
to select the map outline color, transparency, and thickness (see Figure 11-26).
Figure 11‑25. Add Layer Pop-up Window
Figure 11‑26. Edit Layer Pop-up Window
This option is currently greyed
out. It will be supported in a future
release to allow a user specify and save the maps loaded by default to a configuration
file.
VERDI makes calls to the netCDF Java library to obtain the
grid and coordinate system information about the data directly from the model
data input files when the input data files are self-describing (CMAQ, SMOKE,
WRF netCDF format files).
For IO/API files, support for Lambert conformal conic
(LCC) map projection, Universal Transverse Mercator (UTM) map projection, and
polar stereographic map projection was added in VERDI 1.1., and Mercator
projection in VERDI 1.2. The grid
projections listed on the following website are supported, although not all
have been tested: http://www.baronams.com/products/ioapi/GRIDS.html
Users are encouraged to provide small input datasets as
attachments to Bugzilla, for testing and to facilitate future development
efforts. Figures 12-1-12-3 shows example
plots generated for a dataset with an LCC, polar stereographic, and Mercator
map projections, respectively.
Figure 12‑1. Lambert Conformal Conic
Map Projection Example Plot
Figure 12‑2. Polar Stereographic Map
Projection Example Plot
Figure 12‑3. Mercator Map
Projection Example Plot
The netCDF-java v4.1 library used in the VERDI 1.3 release
includes support for CAMx UAM‑IV binary files, using a pre-set default
projection. CAMx or UAM binary files
contain information about the x and y offsets from the center of the projection
in meters, but do not contain information about the projection. The projection information is available in
separate diagnostic files, which are part of the CAMx output along with the UAM
binaries (Figure 12-4)
Figure 12‑4. Example CAMx
diagnostic text file
The netCDF-java
v4.1 library writes the default projection information to a text file in the
directory where the CAMx binary (UAM-IV) file is located. This allows the user to review and edit the
projection information to make it consistent with the projection specified in
the CAMx diagnostic text files. The definitions
of the projection parameters used in the camxproj.txt file are defined using
Models-3 IO/API format, http://www.baronams.com/products/ioapi/GRIDS.html. The user must edit the camxproj.txt file to match the grid description information
provided in the corresponding camx.diag file. Figure 12-5 shows the definition
for the grid projection parameters for a Lambert projection.
Figure 12‑5. Models-3
IO/API Map Projection Parameters for Lambert
Figure 12-6 shows the values of the camxproj.txt once it
was edited to match the values of the camx.diag file (Figure 12-4) using the
definitions of the Models-3 grid parameters (Figure 12-5). Figure 12-7 shows the resulting Fast Tile
Plot of the CAMx sample dataset.
Figure 12‑6. Sample
Projection File: camxproj.txt
Figure 12‑7. CAMx Example
Plot
As discussed in Section 6.1, there are routines available
to convert gridded input data to I/O API
format or new code can be written and contributed to VERDI for use by
the community. The I/O API routines that have been written to convert data into
this format are discussed in this section. If you are unable to use the
available routines to convert your data and have a gridded dataset that VERDI
is unable to read, please submit a bugzilla bug or enhancement request with a
description of the dataset, and attach a small example dataset for use in
development and testing.
The I/O API Interface contains an extensive set of utility
routines. There are example conversion programs to convert data from different
data formats into the I/O API format. The I/O API Utilities are command line
programs that are easy to script for automating analysis and post processing.
An example of an I/O API Utility that may be useful to VERDI users is m3merge.
This utility merges selected variables from a set of input files for a
specified time period, and writes them to a single output file, with optional
variable-renaming in the process. Another utility that you may find useful is m3xtract.
This program allows you to extract a few species from a large file and save
them to a smaller file on your local computer so you can explore them using
VERDI. The I/O API Related Programs and Examples can be found at the following
web site: http://www.baronams.com/products/ioapi/AA.html#tools.
Airs2m3 is an example of a data conversion program that
converts the standard AIRS AMP350 observational data format to the I/O API format.
The airs2m3 program requires the following inputs:
·
The input AIRS AMP350 print format file name.
·
The time zone conversion file (provided with the
obs2api program - tzt.dat).
·
Additional hour shift variable. The AIRS data are
hourly averaged, and a 00 time flag represents the hour 00-01. You may wish to
represent that data segment by the ending hour. In that case, a 1 should be
entered here.
·
Starting year, month, day, hour (GMT) (e.g., 1997 07
10 12).
·
Ending year, month, day, hour (GMT) (e.g., 1997 07 16
12).
·
Name of output variable (8 characters
max) (e.g., O3_OBS).
If you have made an improvement to the development of VERDI source code,
documentation, or anything else, please consider contributing it back to the community.
Instructions on how to set up the Eclipse Development
Environment on Windows, and for running and building VERDI within Eclipse are
available on www.verdi-tool.org. If you are doing a substantial amount of
software development on VERDI, you should become a member of the VERDI project
on SourceForge and submit your code updates through the VERDI subversion
repository. You may submit a request to
become a member of the VERDI project by submitting a Bugzilla request (see
below). The
SourceForge web site for VERDI is http://sourceforge.net/projects/verdi/.
Once your code has been reviewed by the existing team of developers for
VERDI, you will be added to the developer list.
Contributions to the code will be tested by the VERDI developers and
will be included along the documentation about these contributions in future
VERDI releases. Note that
anything you contribute must have the same license as the rest of VERDI, i.e.
GPL.
Bugzilla can be used to report bugs, check the status of bugs, suggest
enhancements, or submit code contributions using the following website: http://bugz.unc.edu/enter_bug.cgi?product=VERDI. First, check to see if your issue is already
listed as a bug or request for enhancement If you do not see an entry that
matches please submit a new request or bug using Bugzilla. Please use the Bugzilla comment section to
inquire if the feature or bug is already under development. Use Bugzilla to notify the VERDI community
about improvements to VERDI that you would like to contribute.
As discussed in Section 1.4, you are encouraged to use
Bugzilla for submitting bug reports, suggestions, and questions http://bugz.unc.edu/enter_bug.cgi?product=VERDI.
To enter information on a bug, you must first register with Bugzilla http://bugz.unc.edu. If you have already registered, you can
search for all bugs that reference VERDI by using the website http://bugz.unc.edu/query.cgi and
entering the word VERDI then pressing search.
If you would like to be notified of any change of status
for a bug that was submitted by another user, you can add your e-mail address
to the CC list by clicking on the bug ID, then entering your e-mail address to
the Add CC text box.
For a complete list of bugs and enhancement requests that
have been submitted for VERDI, and the status of each one, visit the www.verdi-tool.org web site and click on
the Query VERDIzilla Tickets link under the Support Quick Links section. The html query that is used to create this
list of bugs is extensive, and therefore is not listed here.
All VERDI visualizations are the result of a formula
evaluation. Formulas operate on the variables provided by the datasets. The
simplest valid formula consists of a single variable; for example, “O3[1].”
Using infix notation, more complicated formulas can be constructed using the
following mathematical operators and functions. (Note that the documentation
below derives from the equivalent documentation for the Package for Analysis
and Visualization of
Environmental data [PAVE], which is available at http://www.ie.unc.edu/cempd/EDSS/pave_doc/EntirePaveManual.html.)
Listed in order of precedence, the functions and operators
are:
1. abs, sqr, sqrt, exp, log, ln, sin, cos, tan, sind, cosd, tand, minx, miny, minz, maxx, maxy, maxz, mint, maxt, mean, sum, min, max
2. ** (power)
3. /, *
4. +, -
5. <, <=, >, >=
6. ==, !=
7. &&
8. ||
VERDI also supports the following constants:
1. E..................... 2.7182818284590452354
2. PI................... 3.14159265358979323846
3. NROWS........ Number of rows in the formula’s currently selected domain
4. NCOLS.......... Number of columns in the formula’s currently selected domain
5. NLEVELS..... Number of levels in the formula’s currently selected domain
Unary Functions
Unary functions are passed a single argument. Depending on the argument and the function type, the function will return a single value or a matrix of data by performing the function on each cell of the arguments array. For example:
· The function sqrt(4) will return 2.0.
· The function sqrt(O3[1]) will return a matrix containing the square root of each value in the O3[1] variable’s array.
The following functions will return a matrix when passed a dataset variable:
1. abs......... Returns the absolute value of the argument
2. sqrt........ Returns the square root of the argument.
3. sqr.......... Returns the square of the argument.
4. log.......... Returns the base 10 logarithm of the argument.
5. exp......... Returns Euler’s number raised the power of the argument.
6. ln............ Returns the natural logarithm of the argument.
7. sin.......... Returns the sine of the argument. The argument is in radians.
8. cos.......... Returns the cosine of the argument. The argument is in radians.
9. tan.......... Returns the tangent of the argument. The argument is in radians.
10. sind........ Returns the sine of the argument. The argument is in degrees.
11. cosd........ Returns the cosine of the argument. The argument is in degrees.
12. tand....... Returns the tangent of the argument. The argument is in degrees.
The following functions will return a single number in all
cases when passed a dataset variable:
1. mean....... Average cell value for all cells in currently selected domain.
2. sum......... Sum of all cell values in currently selected domain.
3. mint........ Time step index with minimum value in currently selected domain.
4. maxt....... Time step index with maximum value in currently selected domain.
5. minx....... x index with minimum value in currently selected domain.
6. maxx....... x index with maximum value in currently selected domain.
7. miny....... y index with minimum value in currently selected domain.
8. maxy....... y index with maximum value in currently selected domain.
9. minz........ z index with minimum value in currently selected domain.
10. maxz....... z index with maximum value in currently selected domain.
11. min......... For each cell (i,j,k) in the currently selected domain, this calculates the
minimum value for that cell over the currently selected time steps. In other
words, the minimum value in cells (i,j,k,tmin..tmax).
12. max......... For each cell (i,j,k) in the currently selected domain, this calculates
the maximum value for that cell over the currently selected time steps. In
other words, the maximum value in cells (i,j,k,tmin..tmax).
Binary Operators
Binary operators are not passed a value but operate on the
operands to their left and right. Typically, they will return a matrix of data
by performing the operation on each cell of the operand’s arrays. If both of
the operands are single numbers then these binary operators will return a
single number. For example:
·
O3[1] * 2 multiplies each item in the O3[1]
array by 2 and returns the result.
·
O3[1] * O3[3] multiplies each item in the O3[1]
array by the corresponding item in the O3[3] array and returns the result.
(Note that this assumes that the arrays are of equivalent shape.)
·
3 * 2 simply multiplies 3 by 2.
The binary operators:
1. + ............ Returns the sum of the operands
2. - ............. Returns the difference of the operands
3. * ............ Returns the product of the operands
4. / ............. Returns the ratio of the operands
5. ** .......... Returns the left operand raised to the power of the right operand.
Boolean
binary operators return either 1 or 0 in each cell of the resulting matrix. If
the operands are single numbers, then a single 1 or 0 is returned. The Boolean
binary operators:
1. < ............ Returns 1 if the left operand is less than the right operand, else 0.
2. <= .......... Returns 1 if the left operand is less than or equal to the right operand, else 0.
3. > ............ Returns 1 if the left operand is greater than the right operand, else 0.
4. >= .......... Returns 1 if the left operand is greater than or equal to the right operand, else 0.
5. != ........... Returns 1 if the left operand is not equal to the right operand, else 0.
6. == .......... Returns 1 if the left operand is equal to the right operand, else 0.
7. && ........ Returns 1 if both operands are non-zero, else 0.
8. || ............. Returns 1 if either operand is non-zero, else 0.
Time Step Index
A time step index can be specified after a variable name.
For example, “O3[1]:0” is the value of the O3[1] variable at the first time
step.
To open the Script
Editor, use File>View Script Editor, as shown in Figure 17.1 Prior running a batch script, remove all
datasets from the dataset list. To remove a dataset, click on each dataset in
the dataset panel and press the yellow minus button.
Figure 17-1. File: View Script Editor
An Open
pop-up window will be displayed, click on a sample script file in the
VERDI_1.3/data/scripts directory (Figure 17.2).
Figure 17-2. Open Pop-up Window
After you select a
script file and click Open in the Open pop-up window, the Script Editor window
(Figures 17-3 and 17-4) will appear in the right hand side of VERDI. The Script Editor allows you to edit, save,
and run batch scripts within VERDI. The
Batch Scripting Language used for the VERDI Script Editor is described in the
header of the sample text format script files (Figure 17-3).
Figure 17-3. Top of Sample Script File –
VERDI_1.3/data/scripts/file_patterns.txt
Figure 17-4. Bottom of Sample Script File –
VERDI_1.3/data/scripts/tile_patterns.txt
As
shown in Figure 17-4, the Batch Script File format consists of two blocks, a
Global block and a Task Block. The
Global block allows a user to specify a set of parameters (such as the file and
directory names) on which all other tasks will be performed. In this block, the user can specify any
parameters that will be used to run any other tasks. If in any other Task block, the same
parameters are specified with different values, these values will over-write
the values specified in the Global block. One Global Block is used to specify
the common parameters shared by all Task blocks, and multiple task blocks can
be defined, to specify the type of batch operations that will be performed,
such as defining formulas and creating plots
Prior
to running a batch script within the Script Editor, all datasets must be
unloaded. If they are not, a pop-up
warning message will appear (Figure 17-5) requesting that all datasets be
unloaded prior to running a batch script in the script editor.
Figure 17-5. Close Dataset(s) Warning Message
The
multifiles.txt sample script that is provided as part of the VERDI 1.3 release demonstrates
how to create a tile plot that uses a mathematical combination of variables, an
excerpt of which is shown here:
<Task>
dir=D:\\verdi-dist2\\data\\model
f=copy.36k.O3MAX
f=CCTM46_P16.baseO2a.36k.O3MAX
f=another.36k.O3MAX
s=O3[1]-O3[2]+O3[3]*2
gtype=tile
saveImage=jpeg
imageDir=D:\\verdi-dist2
imageFile=three_components_36k.O3MAX
</Task>
The above task
specifies the name of three input files.
The input files are assigned a number based on the order that they are
specified.
[1]=Copy.36k.O3MAX
[2]=CCTM46_P16.baseO2a.36k.O3MAX
[3]=another.36k.O3MAX
s=O3[1]-O3[2]+O3[3]*2’
defines a formula that uses variables from the three filenames
This formula takes
ozone in file 1 and subtracts the ozone in file 2 and adds two times the ozone
in file 3.
The type of plot is
specified as a tile plot by setting the parameter gype to tile; ie. gtype=tile.
The image file
format is specified by setting the parameter saveImage to jpeg; ie.
saveImage=jpeg.
The output
directory where the images will be stored is specified by setting the parameter
imageDir; ie. imageDir=D:\\verdi-dis2.
The image file name
is specified by setting the parameter imageFile; imageFile=three_components_36k.O3MAX.
Use the left mouse
button to highlight the task that you would like to run and then click Run
in the Script Editor window, a pop-up window will appear that indicates the
task ran successfully (Figure 17-6). In
the example shown in Figure 17-6, the title and sub-title were obtained from
the definition in the global block.
Aspects of the plot defined in the global block are used for multiple
tasks and are applied even if only a highlighted task is run.
Figure 17-6. Highlight Text to Select Task and Click Run
If the user selects
Run without highlighting a Text Block, then the entire batch script will be
run, and the plots generated. To edit the batch script, highlight a segment
that you would like to copy and use ^C
to copy the text and then click in an area where you want to paste the text and
use ^V to insert the copied text. Test
your changes to the script by highlighting the text block and click run, but
remember to click Save or Save As… to save the edits that you have made prior
to exiting the Script Editor. A
successful script run will result in a pop-up window reporting that the run was
completed, as shown in Figure 17-7.
After saving the
script file (ex. C:\verdi-script\myscript.txt), one can run the batch script
directly from command lines without invoking the VERDI GUI windows. On Windows
system, bring up a command line window and run this command after change
directory to where the run.bat file locates:
>run.bat –batch
C:\verdi-script\myscript.txt
On Linux/Mac
platforms, change directory to where the Verdi.sh locates and run this command
(assuming your script file myscript.txt is saved in /home/user/verdi-script
directory):
$./verdi.sh –batch /home/user/verdi-script/myscript.txt
The batch script
usage (see Figure 17-3) will also be displayed from the command line after
typing the following command:
(Windows)
>run.bat –batch
(Linux/Mac)
$./verdi.sh –batch
Figure 17-7 Successful Batch Script Run Message
If the user has specified
an incorrect path, or incorrect filename for the input dataset, then a series
of error messages will appear, starting with the message shown in Figure 17-8.
Figure 17-8. Unsuccessful Batch Script Run Message: File
not found
The VERDI Batch
Editor does not currently check to see if the path specified by the user in
either the imageDir or ImageFile exists, and instead will send a message that
the script was successfully run, even if it was not. If you are unable to find the images in the
directory locations that you specified, check to see if the directory that you
specified as imageDir in the batch script exists, and then re-run the script. Double
click on the file in the imageDir directory to load and view the image file in
your default visualization software.
Figure 17-9 illustrates the tile plot image that was generated by
running the highlighted text block.
Figure 17-9. Plot Image Generated by Task Block
Currently, the VERDI Script Editor creates plots
for layer 1 and timestep 1 for the
formula and dataset that are specified.
A future release of VERDI will allow the user to specify the range of
layers and timesteps, set the column and row ranges, to create zoomed plots,
and support additional command line scripting options.
The commands described in this section can be executed
from the command line through either command line arguments or Windows batch
files. In Linux, you can edit the verdi.sh script, adding the command options
at the end of the last line of the script. If you are using Windows, edit the
run.bat script, again adding the command options at the end of the last line,
and submitting the script at the windows command line. An example syntax for
all commands follows the format
<command>
<command options> \
where the “\” at the end of the command is optional.
Set an environment variable $VERDI_HOME by using
Setenv VERDI_HOME /home/a_username/VERDI_1.3
Where a_username is your username.
The following script options will read in the file as the
first dataset, select O3[1] as the formula from dataset 1, and create a tile
plot of the O3[1].
./verdi.sh -f “$VERDI_HOME/data/model/CCTM46_P16.baseO2a.36k.O3MAX -s O3[1] -gtype tile
Example script file (Note that quotes (as shown highlighted
in red) may be needed around the entire list of parameters” :
#! /bin/csh -f
#### 8hO3 Daily Max Plot
setenv DIR /home/training/verdi_1.3/data/OBS
../../verdi.sh \
"-f $DIR/ACONC_O3_8hr.dmax \
-f $DIR/AQS_overlay_2002_07.ncf \
-configFile /home/training/config.txt \
-s O3[1] \
-s O38[2]*1000"
Edit the run.bat script in the VERDI_1.3 directory by right
clicking on the file and selecting edit.
Figure 18-1. Location of run.bat script in
Windows
The current run.bat in notepad contains a “%1” at the end
that allows it to accept input following the run.bat script using the Windows
run command. Unfortunately, this command
does not accept directory names that have a space them, such as the “Program Files”. If you would like to enter the script command
line options after run.bat, please move the data directory to C:\VERDI\data or
some other similar location.
Enter the following in the Run
command: cmd
When a command line window opens
do the following:
cd C:\Program Files\VERDI_1.3\
run.bat "-f C:\\VERDI\\data\\CCTM46_P16.baseO2a.36k.O3MAX
-s O3[1] -gtype tile"
The other option is to place the script commands within the
run.bat itself. Remove the “%1”
statement at the end of the run.bat that is provided in the distribution, and
add the script options that you would like to use. The following run.bat contains script options
that will read in the file C:\Program Files\VERDI_1.3\data\CCTM46_P16.baseO2a.36k.O3MAX,
select O3[1] as the formula, and create a fast tile plot. The changes that you
need to make to the run.bat are highlighted in red.
cd .\plugins\bootstrap
SET
JAVA=..\..\jre1.6.0\bin\java
%JAVA% -Xmx512M -classpath
"./bootstrap.jar;./lib/saf.core.runtime.jar;./lib/commons-logging.jar;./lib/jpf-boot.jar;./lib/jpf.jar;./lib\log4j-1.2.13.jar"
saf.core.runtime.Boot -f C:\Program
Files\VERDI_1.3\data\CCTM46_P16.baseO2a.36k.O3MAX -s O3[1] -gtype fasttile
Figure 18-2. Submit run.bat script from Run
command
Script commands that can be used for command line scripting
(listed in alphabetical order) are described below. Adding support for these script commands in
the Script Editor is planned for a future VERDI release.
[-alias <aliasname=definition>] defines an
alias. You can define an alias by creating a definition using variable names
and derived variables that are calculated using the mathematical operators
described in Section 15: Mathematical Functions. The alias definition does not
include the dataset name. The alias is treated like any other formula once the
alias definition and the dataset to which it should be applied are specified.
If you need to redefine an alias definition, you must first use the -unalias command. The alias definitions are saved to
a .verdi.alias file in your home directory. VERDI uses this type of optional
file in your home directory to maintain a snapshot of the current aliases being
used. The following warning will be reported if an alias is defined more than
once: “WARNING: Alias <aliasname>
already defined, new definition ignored.” You are also responsible for
not making circular references. Use the ‑printAlias
command to view what aliases are already defined.
[-animatedGIF<filename>] creates an animated GIF by doing an X Window Dump (XWD) of
each of the time steps in the tile plot, then converting them to GIF images. If
there are many time steps in the dataset, there will be a slight delay before
you are again given control of the GUI.
[-closeWindow
“<windowid>”] closes the window with
the specified window ID.
[-configFile
<configFileName>] specifies a
configuration file for VERDI to use for configuring subsequent tile plots.
[-copyright]
prints out copyright information for VERDI.
[-drawDomainTicks
ON|OFF] turns the domain axis ticks
on and off.
[-drawGridLines
ON|OFF] turns the plot grid lines on and off.
[-drawLegendTicks
ON|OFF] turns the ticks in the
legend on and off.
[-drawRangeTicks
ON|OFF] turns the range axis ticks
on and off.
[-f
<filename>] tells VERDI to load in this
dataset and make it the currently selected dataset. All datasets will stay in
memory.
[-fulldomain] sets the VERDI domain matching the currently selected
dataset to be completely selected. The currently selected dataset is usually
the most recently added dataset.
[-g
<tile|line|bar|contour>] instructs VERDI to create a plot
using the specified type and the currently selected formula’s data.
[-gtype <tile|line|bar|contour>]
instructs VERDI to create a plot using the specified type and the
currently selected formula’s data.
[-help|fullhelp|usage]
display the information on all the command line arguments available. Each of
these three versions performs the identical function.
[-legendBins
"<bin0,bin1,...,bin_n>"] causes VERDI
to use the specified numbers as breaks between colors on subsequent plots. The
value of this argument is a comma-separated list of numbers. For example, -legendBins
“1,10,100,1000” will cause plots to be
created with three colors that correspond to values of 1-10, 10-100, and
100-1000. To go back to the default method for determining breaks between bins,
enter -legendBins DEFAULT.
[-level
<level>] sets the level range of all
formulas to the single level specified.
[-levelRange
<levelMax> <levelMin>] sets the level range of all
formulas to the range specified.
[-openProject
<VERDIProjectName>] opens a previously save
VERDI project.
[-printAlias] prints existing alias definitions.
[-quicktime (NEW)] creates a Quicktime movie of the currently selected plot.
[-quit|exit] ends the VERDI session.
[-raiseWindow
<windowid>] raises the window with the specified plot ID
(i.e., brings it to the front).
[-s
"<formula>"] loads the specified formula
into VERDI’s memory, and makes it the currently selected formula.
[-save2ascii
"<filename>"] export data to a
tab-delimited data file suitable for reading into a spreadsheet application
such as Excel.
[-saveImage
"<image type>" <file name>] saves the most recently created plot. This command works
for all plot types. Supported formats include PNG, BMP, TIF, and JPG.
[-scatter "<formula1>"
"<formula2>"] creates a scatter plot using
the two formulas specified. Note that the formulas for the two components
should already have been loaded into VERDI, and they are case sensitive.
[-showWindow
<windowId> <timestep>] sets the time step of the window
with the specified window ID to the specified time step. The time step must be
within the allowable range for the dataset.
[-subDomain <xmin>
<ymin> <xmax> <ymax>] sets the VERDI domain
matching the currently selected dataset to the bounding box specified by its
arguments. The currently selected dataset is the most recently added dataset.
It is often handy to type -subdomain commands
into VERDI’s standard input if you are trying to select a very precise
subdomain (such as that needed for a vertical cross-section plot).
[-subTitle1 "<sub
title 1 string>"] allow you to control a plot’s subtitles if
desired. Subsequent plots will use the default subtitles, unless these
arguments are used again.
[-subTitle2"<sub
title 2 string>"] allow you to control a
plot’s subtitles if desired. Subsequent plots will use the default subtitles,
unless these arguments are used again.
[-subTitleFont
<fontSize>] allow you to control the font size of the subtitle
of a plot.
[-system "<system
command>"] sends the specified command to the operating
system’s command line.
[-tfinal <final time
step>] sets the last time step for each formula’s time-step range
to the specified step number, where the first step number is denoted by 0.
[-tinit <initial time
step>] sets the first time step for each formula’s time-step
range to the specified step number, where the first step number is denoted by
0.
[-titleFont
<fontSize>] allows you to control the
font size of the title of a plot.
[-titleString
"<title string>"] sets the title
for the next plot made to the specified title. Subsequent plots will use the
default VERDI title, unless this argument is used again.
[-ts <time step>] sets
the selected time step for each formula in VERDI’s memory to the specified step
number, where the first step number is denoted by 0. This will remain the
selected time step until you change it. It affects only tile plots and vertical
cross-section plots.
[-unalias <aliasname>]
is used to undefine an alias.
[-unitString "<unit
string>"] can be used to override the default unit label
used for plots. The default value comes from the dataset(s) themselves.
[-vector
"<U>" "<V>"] creates a
vector plot with U as the left-to-right vector component and V as the
down-to-up vector component. There are no background colors used for this type
of plot. Note that the formulas for the two components should already have been
loaded into VERDI, and they are case sensitive.
[-vectorTile
"<formula>" "<U>" "<V>"] creates a vector plot with the result of "formula" as the background tiles, U as the left-to-right vector
component, and V as the down-to-up vector component. Note that the formulas for
the three components should already have been loaded into VERDI, and they are
case sensitive.
[-version] prints out information about the VERDI version being used
on the standard output stream.
[-verticalCrossPlot
X|Y <row/column> (NEW)] creates a vertical cross-section
plot. You indicate whether this will be an x
or y cross-section plot and what row
or column to use as the base.
[-windowid] prints the
window ID of the currently selected plot.
Before
calculating the average value for a polygon segment, the area for each polygon
is calculated using the projection of the grid system loaded. The system then calculates the area of
overlay between each grid cell and the polygon segment.
The total contribution of a value
(concentration, deposition, rainfall, etc) from each cell for a given polygon segment
is calculated using the following equation:
TV
i = sum (Orci * Vrc) where
Orci = Area of overlay of cell at row r and column
c with segment i,
Vrc = value
of cell at row r and column c, and
r and c iterate across the rows and
columns of the grid.
The Average Value is calculated by dividing the total value by
the area of the polygon segment:
AverageVi = TVi
/ Ai where
Ai
= Area of the polygon segment i
VERDI has been developed using a number of open source
Java libraries. Table 21-1 contains a
list of the jar files or Java libraries that are used by VERDI, a link to where
each library may be acquired, a link to the location where the license is
referenced by the documentation for each library, as well as a link to each
license. The distribution for VERDI
contains a sub-directory called licenses.
This directory contains a copy of the licenses for the open source Java
libraries used by VERDI.
Table 20‑1. JAVA Libraries used by VERDI
Contributions to VERDI from the community are greatly
appreciated.
Marco Rodriguez, CIRA at Colorado State University http://www.cira.colostate.edu/
Tanya Otte, Atmospheric Modeling and Analysis Division, http://www.epa.gov/amad/index.html
Barron Henderson, ORISE Fellow, EPA, Ph.D. student UNC
Chapel Hill
John Carron, Unidata, http://www.unidata.ucar.edu/software/netcdf/index.html
