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(VERDI): User`s Manual

1. 5 41E 02 SPO ba Pe a l ed o oo 4 74E 02 ee A z Export Scatter Plot Data into a CS File x Z 406E 02 as Sy 3 38E 02 9 C Alllayers 2 71E 02 Time steps 2 03E 02 Current time step 0 Alltime steps Cancel 1 35E 02 6 77E 03 0 00E00 lt 0 00E00 1 25E 02 2 50E 02 3 74E 02 4 99E 02 6 24E 02 7 49E 02 8 73E 02 9 98E 02 1 12E 01 1 25E 01 1 37E NO 1 ppmv February 16 2004 23 00 00 UTC Layer 0 NO 1 NO2 1 Tile Oak_white S NO 1 x NO2 1 Scatter FastTilePlot Tile O3 2 Tile LUFRAC_01 4 9 7 Vector Plot The vector plot shows vector lines representing the vector formed by using two formulas one for each component of the vector across a geographic area one formula represents the horizontal component the other represents the vertical component Figure 9 10 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 9 11 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 p
2. com JTS jts_frame htm log4j 1 2 13 jar http www unidata ucar edu software netcdf java http logging apache org log4j 1 2 license html saf core runtime j r http www eclipse org legal epl http safr sourceforge n et http www eclipse org stp cf sat S AFcore html v10 html vecmath jar http java3d j3d org https vecmath dev java n http www gnu org licenses old et licenses gpl 2 0 html geoapi http geoapi sourceforg http www codeplex com LGPL V2 1 Feb 1999 e net GeoAPI license Gt2 http sourceforge net pr http docs codehaus org d http www gnu org licenses lgpl ojects geotools isplay GEOTDOC 00 So_ 2 1 txt urce License hsqldb http hsqldb org http hsqldb org web hsqlLicens e html jfreechart http sourceforge net pr http developer vrjuggler LGPL V2 1 Feb 1999 ojects jfreechart org browser trunk juggler external jfreechart LICEN SE txt rev 15441 jscience http jscience org http swik net Jean http swik net License BSD BS Marie Dautelle D License Text Piccolo 1 2 http www cs umd edu http www cs umd edu hc http opensource org licenses bs heil jazz il jazz download open d license php source shtml Ucar_ma2 http www unidata ucar http www unidata ucar e http www gnu org copyleft less edu software netcdf du software ne
3. ssssesseseeeseseessesresreeseesstsereeseessessesreseessesereressee 10 2 4 Graphics RSG URNS TICE LS 25525 cad snieni ada E E a E S a a s 10 3 VERDI Installation Instructions e ssessosoessessoesoosoossessoesoosseesessoesoosseesesoossoosoeesessossosssesseesossoe 10 ple VERD Mnst llati on irnir E A EEE R RR O E E E EE 10 3 2 Installation Instructions for Linux and Other non Windows JRE 6 Supported System C nfis rationS saien uia deceased a uae E ONS 10 3 3 Installation Instructions for Windows sssesesssessseseeseesseesseeesseesseesseesseesseeesseesseesseesseee 12 3 4 Setting VERDI Preferences c scicisiscyicccisdccdassnedeas eth seeectina rE e E a EES TEES 16 4 Starting VERDI and Getting Your Data into VERDI esessseoessoossssooesesoceesosccesosoosssoossee 16 a ARo a eiT ANA m ra DI ES A E E E E E A A 16 4I WW MELLOW Sa sei caer coalolionc E E E R A R 16 4 1 2 Linux and Other non Windows JRE 6 Supported System CONMPUTAU ONS ite sa siete a tel r a a E ile ac a ce eS eee Tas 17 4 2 Maim Window Lenssen ea ee a n a a he westside a 17 4 3 Floating the Dataset and Formula Panes seseesseseeseesessessresressessrseresressesesereseessesereeessee 19 5 Navigating VERDPI s Main Menu Options e eeessessseesseessossssssssesssossooseooesssessoossoosssssssssssooee 19 Sd File Menu OptiSeo ea ets d e a pea aE ALEE gaa cence 19 Dell Open Project mietten n E date anaes E KEES O EERS 19 A EA A PT 1S OE EEE E TE E SE AE A E
4. 09 08 1983 04 00 00 09 08 1983 08 00 00 09 08 1983 12 00 00 09 08 1983 16 00 00 09 08 1983 20 00 00 09 09 1983 00 00 00 Time Step Avg Value PPM 40 Institute for the Environment VERDI User s Manual 9 5 Time Series Bar Plot The time series bar plot shows average values over time in a bar plot format Figure 9 6 rather than a line format Figure 9 5 Other than that the description of this plot type is the same as for the time series line plot see Section 9 4 Figure 9 6 Time Series Bar Plot HO 2 HO2 2 File Configure Controls Layer bis HO 2 HO2 2 Layer 0 0 0000275 0 0000250 0 0000225 0 0000200 0 0000175 0 0000150 a 9 0000125 0 0000100 0 0000075 0 0000050 0 0000025 0 0000000 0 0000025 Time Step W Avg Value PPM Time Series Bar HO 2 HO2 2 9 6 Scatter Plot The scatter plot shows the relationship between two formulas using an array of dots Figure 9 7 The user specifies the formulas using the dialog box that comes up before the plot is displayed Figure 9 8 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 9 9 allows users to specify whether they would like the data for the current layer or for all layers and for the cur
5. 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 Vertical Cross Section Vector Plot and Contour Plot An Animate Plot dialog box Figure 10 12 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 UNC Chapel Hill 57 Institute for the Environment VERDI User s Manual Figure 10 15 Animate Plot Dialog Box x Animate Plot Starting Time Step 09 07 1983 00 00 00 Ending Time Step 48 09 09 1983 00 00 00 Make Animated GIF E Make Movie ea Start 10 4 3 Observational data overlays It is useful to visually compare the results contained in model output datasets with the data points in observational datasets You can do this by creating a tile plot of the model output and then overlaying observational data points on the tile plot This capability will be added to the Fast Tile Plot in a future release This capability will not be available in version 1 1 The observational dataset needs to be in I O API format se
6. 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 cpjai 1_1_3 lib libmlib_jai so path to verdi_1 1 jre1 6 0_05 lib i386 ii cp jai 1_1_3 lib jar path to verdi_1 1 jre1 6 0_05 lib ext UNC Chapel Hill 11 Institute for the Environment VERDI User s Manual If JRE 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 3 3 Installation Instructions for Windows To install VERDI for Windows run the installation program VERDI_1 1_Installer exe on your Windows machine Follow the instructions on the installation windows that appear as shown in Figures 3 1 through 3 6 Figure 3 1 VERDI Setup Wizard P VERDI 1 1 Setup Welcome to the VERDI 1 1 Setup Wizard This wizard will guide you through the installation of VERDI It is recommended that you dose all other applications before starting Setup This will make it possible to update relevant system files without having to reboot your computer Click Next to continue UNC Chapel Hill 12 Institute for the Environment VERDI User
7. 1 VERDI 1 1 VERDI 1 1 5 VERDI 1 1 5 Training Registration Not regi ed for any upcoming cl Register Now UNC Chapel Hill 4 Institute for the Environment VERDI User s Manual Figure 1 4 Downloading VERDI from the CMAS Web Site Community Modeling and Analysis MAS VERD Version 11 Mozilla Firefox File Edit View History Bookmarks Yahoo Tools Help e S MG 3 http v www cmascenter org download models verdi verdi_1 1 cfm temp_id 74384373456 amp DB TRUE Google m COMMUNITY a PHR MODELING 3 4 amp ANALYSIS me SYSTEM J yy N SearchCMAS __ Search Installation Instructions The files in the table below contain VERDI scripts executables source code and documentation for version 1 1 The installation instructions describe how to unpack the distribution archives for both Linux and Windows The RELEASE NOTES file documents some outstanding issues with the current release The User s Guide has been updated for VERDI Version 1 1 The test documentation demonstrates comparisons of the functionality between PAVE and VERDI The Windows distribution is a windows installer that contains the VERDI scripts Java JRE 6 0 and needed third party libraries The Linux distribution is a gzipped tar file of the VERDI scripts and code archive NOTE Save the files that you download into a common directory File type Download link and file name Right click on link and choose Save Target As Linux inst
8. Actions Home New Search Il Find i Reports My Requests Preferences Log out lizadams email unc edu Edit Parameters User Preferences Sanity Check Users Products Flags z DOuintawen Mialdan Mialo Viahian earna LIZ ams eterna LIM tai ian aa 1 Figure 1 9 Add Attachment Form in Bugzilla Attachment Don t add an attachment Add an attachment File Enter fhe path fo the file on your computer Browse Description Describe fhe attachment bnefly Content Type ifthe attachment is a patch check fhe box below patch Ofherwise choose a method for determining the content type gquto detect select from list plain text text plain z enter manually Depends on Blocks Commit Remember values as bookmarkable template UNC Chapel Hill 8 Institute for the Environment VERDI User s Manual 1 5 Future VERDI Development As stated in Schwede et al 2007 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 contribu
9. 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 8 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 UNC Chapel Hill 35 Institute for the Environment VERDI User s Manual Figure 8 5 Error obtained when incompatible subset domains are created using the Dataset pane Fa VERDI iol x File Plots Window Help Slan Tile Plot Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot vector Plot Contour Plot Selected Formula 03 2 03 1 4 Formulas a Tie O3 1 i F Tile O3 2 x Fi Confit Cont a iste teed File Configure Controls Plot Te ae z step o 06 01 2002 00 00 00 Layer 05 03 2 Layer 0 0 08 0 07 4 fost2 o3 1 J Error while e
10. Formula refers to the formula that has been selected in the Formula pane discussed briefly below and in detail in Section 6 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 two tabbed panes e 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 UNC Chapel Hill 17 Institute for the Environment VERDI User s Manual e 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 Any plots that are created are shown in the plots area
11. Probed Save Configuration Set Data Ranges Cell s Maps Show Lat Lon Time Series of Min Cell s Time Series of Max Cell s Animate Plot Add Overlay 10 1 File Menu Options Options in the File menu include printing a plot and exporting a plot as an image Plots can be saved as a PNG JPG BMP or TIF files 10 2 Configure Menu Option The Configure pull down menu contains the following options Configure Plot Load Configuration Save Configuration and Maps 10 2 1 Configuring plots Figures 10 2 through 10 5 show the dialog boxes for configuring plots that appears when you select Configure Plot The Configure Plot dialog box contains four tabbed options Titles Color Map Labels and Other e The Titles tab allows you to edit and set the font and color for the title and two subtitles of the plot e 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 To change the spacing between the color intervals select Custom from the Interval pull down menu and change the interval start values in the list at the bottom of the dialog box This allows you to set the interval values for each color in
12. Step z V Zoom Probe 0 00 00 Layer 4 Layer 0 v Show Lat Lon 100 90 80 70 60 30 20 10 0 20 40 60 80 1 o0 1 20 1 40 x June 02 2002 00 00 00 UTC Min 79 843 43 707 0 006 Max 76 441 38 514 0 093 35 6084N 78 8953W UNC Chapel Hill 56 Institute for the Environment VERDI User s Manual 10 4 Plot Menu Options The Plot pull down menu 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 10 14 Plot Menu Options Tile O3 1 File Configure Controls Time Step 1 o6 Time Series of Probed Cell s Time Series Bar of Probed Cell s Time Series of Min Cell s 101 Time Series of Max Cell s 96 Animate Plot Add Overlay 91 86 10 4 1 Time series plots The Time Series of Probed Cell s and Time Series Bar of Probed Cell s allows the user to select a set of cells and then produce a time series or time series bar plot of the chosen subset of probed cells The Time Series of Min or Max Cell s option creates a time series plot using data for the currently selected formula at that formula s domain layer range and time step range The minimum or maximum value of that formula over the domain and layer range at that time step is calculated by VERDI and used for each of the time step s data points 10 4 2 Animate plots
13. VERDI When you select VERDI Help Docs the VERDI user s manual is displayed in a VERDI Help window This window is not searchable but it does allow you to navigate via hyperlinks in the Table of Contents and to scroll down and read the user s manual When you select About a pop up window that contains the name of the product the version number and the date the software was built is displayed 6 Working with Datasets 6 1 Input File Formats VERDI currently supports visualizing files that have either the EDSS Models 3 Input Output Applications Programming Interface I O API format or the WRF input output format Version 1 1 currently supports Lambert conformal conic LCC map projection I O API Files Universal Transverse Mercator UTM map projection I O API input files and polar stereographic map projection I O API Files Users are encouraged to provide small input I O API datasets in additional projections as attachments to Bugzilla for testing and to facilitate future development efforts The I O API was designed as a high level interface on top of the netCDF standard see http www baronams com products ioapi for further info It 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 portable across computing platforms This means that the file can be read regardless of what computer type or operating system you are
14. 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 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 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 14 Known Bugs 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
15. load any additional datasets or create any additional variables formulas If you load a dataset that is not part of the previously saved project and then try to open a previously saved project you will get a message that says All currently loaded datasets will be unloaded and will be asked if you want to continue 5 1 2 Save Project The Save Project and Save Project As options save dataset lists and associated formulas as a project for later re use Note that plots are not saved with a project only datasets and formulas are saved If you wish to save a plot configuration for later use see Section 10 2 2 Loading and saving configuration UNC Chapel Hill 19 Institute for the Environment VERDI User s Manual 5 2 Plots Menu Options VERDI opens a single window for plots to the right of the Dataset and Formula panes As plots are created each in its own sub window the most recent plot is displayed on top of previously created plots Each plot has a tab beneath it listing the type of plot and the formula used to create it If you want to view a previously created plot select the tab associated with its sub window underneath the current plot and the desired plot will be brought to the front 5 2 1 Undock all plots As with the Dataset and Formula 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
16. on the right hand side of the main window These plots can be placed into their own movable windows using Plots gt Undock all Plots on VERDI s main menu as discussed in Section 5 2 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 fast tile plots are described in Section 9 Creating Plots Figure 4 2 VERDI Main Window 101 x File Plots Window Help eleak Datasets t Fast Tile Plot Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot vector Plot Contour Plot Selected Formula O3 2 Fie Configure Controls Plot Time Step os 06 01 2002 00 00 00 Layer os 1 CAMx_psat 040217_sh nc 2 CCTM46_P16 base0Za 36k REDUCED 200200601 Layer 0 03 2 101 1 00861 5 91 8 822E 2 4 81 71 7 562E 2 4 B 6 302E 2 gt 51 gt E 5 04162 4 i 41 a 31 3 78162 4 m Time Steps 0 24 21 I Use Time Range 252162 Min os 06 01 2002 00 00 00 11 J 2 J 1 2662 4 Max 24 06 02 2002 00 00 00 1 Layers 0 21 1 21 41 61 81 101 121 141 x 2 7967 Use Layer Range June 01 2002 00 00 00 UTC min o Min 124 45 0 005 Max 54 48 0 08 xi Datasets Formulas Tile o32 FastTilePlot Tile O3 2 UNC Chapel Hill 18 Institute for the Environment VERDI User s Manual 4 3 Float
17. sind cosd tand minx miny minz maxx maxy maxz mint maxt mean sum min max power i oS ee Se A A d V V i VERDI also supports the following constants Ls EE 2 7182818284590452354 PN E EE 3 14159265358979323846 3 NROWG Number of rows in the formula s currently selected domain 4 NCOLS 2 200004 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 e The function sqrt 4 will return 2 0 e 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 UNC Chapel Hill 64 Institute for the Environment VERDI User s Manual 2 sqrt Returns the square root of the argument Sane gee Returns the square of the argument 4 log Returns the base 10 logarithm of the argument 5 EXD asi Returns Euler s number raised the power of the argument 6 n Returns the natural logarithm of the argument Tio Saser Returns the sine of the argument The argume
18. that have been written to convert data into this format which are discussed in this section or by starting from one of these routines to write your own 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 postprocessing 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 e The input AIRS AMP350 print format file name e The time zone conversion file provided with the obs2api program tzt dat e Additional hour shift variable The AIRS data are hourly averaged and a 00 time flag represe
19. the color map 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 e g 4 2E the numbers on the legend will then look like 9 49E 2 To reset the range for the values of UNC Chapel Hill 46 Institute for the Environment VERDI User s Manual the legend change the values for the minimum and maximum and then left mouse click on Rebuild Click OK to have your selected changes displayed on the plot that you have configured e The Labels tab contains options to edit the labels of the Domain Axis x axis the Range Axis y axis axis and the Legend e The Other tab allows you to enable or disable showing the grid lines and to edit the vector arrow color and to edit 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 UNC Chapel Hill 47 Institute for the Environment VERDI User s Manual Figure 10 2 Configure Plot Titles Tab Figure 10 3 Configure Plot Color Map Tab S Configure Plot m gt Configure Plot Ex olor Map Labels Other Other Te 8 Palette Type Sequential X Show Tite 7 Palette arer 10311 C1 ight to dark purple Font Dialog plain 12 CEE light
20. 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 VERDiIzilla 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 UNC Chapel Hill 63 Institute for the Environment VERDI User s Manual 15 Mathematical Functions 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 In sin cos tan
21. to dark blue color OM C it to derk orange C ich purple to dark blue E igi CTI ht orange to dark red l oor COE tht to dark red Text light yellow to dark green Font Select LTT ict vellow to oreen to dark blue T Color Select Interval Automatic Number Format 2 3f Subtitle 2 Min 0 006099 Max 0 100828 Rebuild Show Tite F Color Interval Start Text Font ol m E Color E O E ok Cancel ox Cancel Figure 10 4 Configure Plot Labels Tab Figure 10 5 Configure Plot Other Tab L Configure Plot x L Configure Plot xs Titles Color Map Titles Color Map Labels ae Grid Lines Domain Axis Range Axis Legend Show Grid Lines Label Colcr Select Text P Font Vector Arrow Color Color sali Ticks Series Color w W i Show Tick Labels Color UNC Chapel Hill 48 Institute for the Environment VERDI User s Manual 10 2 2 Loading and saving configuration If you have made changes to the configuration of a plot and would like to save the configuration for future use on other plots use the Save Configuration option from the Configure pull down menu on the plot It is important to create a file name that indicates the formula name the dataset and the type of plot along with the cfg extension that indicates that it is a configuration file so that you will know which plot the configuration file was saved for An exam
22. verdi_1 1 tar into a location where you would like to install VERDI UNC Chapel Hill 10 Institute for the Environment VERDI User s Manual 2 Edit verdi_1 1 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 JRE 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 JRE 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 1ib 1386 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
23. 080 ppm you could use the formula O3 1 gt 0 080 O3 1 In the resulting plot each cell where O3 1 exceeds 0 080 will show the value of O3 1 for that cell for all other cells the value shown will be zero The notations that can be used in formulas to represent various mathematical functions and the order of precedence of these functions are listed in Section 16 Mathematical Functions 7 3 Selecting a Formula for Plotting Before creating a plot a formula must be selected Check to see which formula is highlighted in the Formula pane or look to the right of the plot buttons above the plots area of the main window to see the selected formula By default VERDI designates the most recently added formula as the selected formula To change the selected formula to a different one in the list click on a formula in the list on the Formula pane and you will then see it displayed as the selected formula above the plots area 7 4 Saving Formulas Both formulas and datasets can be saved using the Save Project item in the File pull down menu on the VERDI main window Saving new projects and loading existing projects was discussed in Section 5 1 7 5 Time Step Range Layer Range and Edit Domain Instructions for using the Time Steps Layers and Domain panels that you see in Figure 7 2 are discussed in the next section Spatial and Temporal Data Subsetting UNC Chapel Hill 31 Institute for the Environment VERDI User s Ma
24. 10 112 114 116 118 120 122 124 126 128 130 X June 01 2002 00 00 00 UTC Min 98 50 0 022 Max 122 49 0 101 Tile O3 1 EH 10 4 4 Vector overlays Users have two options for overlaying vectors e g wind vectors on a tile plot One option is to do it when working with a vector plot using the procedure described in Section 9 7 The other options is to do it when working with a tile plot which is described here To add a vector overlay to a tile plot select the Add Overlay gt Vectors option from the tile plot s Plot pull down menu This capability is planned to be added to the Fast Tile Plot in a future release these options are currently grayed out for the Fast Tile Plot The Vector Overlay dialog box 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 that 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 UNC Chapel Hill 60 Institute for the Environment VERDI User s Manual A
25. 19 5 2 Ploty Menu OPON S yesir a cea E E eat a ached E aa 20 5 2 1 Upnd ck all Plots en a a a E ETTE 20 UNC Chapel Hill ii Institute for the Environment VERDI User s Manual 5 2 2 Animate tile plots siccccss ccscaccuesecies secdiceasanadedas pagedadeapnteneses saanaatusdacdaunceuscledasngentaaaies 20 53 Wid w Men Options 3 5 cats vs acawleaheasanspagsecg a A e a a A RS 21 5 3 1 Datas tsand Formulasi ssn ee e i E R RRA AE 21 DSS PAR E a E 9 OIA E E A E E AE E TE AE E 21 S4 Help Menu Options oers a ee E E A E RAE E E eee TEE 22 6 Working With Datasets icscicscsicsscasccicsess scnicdassscesaccsdeonssssadonscsisacensdsaeereussedentudahedeasuasseatciaseneasss 22 co DRAE Ent olei AE rO a aa AUS eg sce E ccs cea tsa deg EET E oe ces dnc oe oc onto ow nna gem 22 6 2 Example Datasets Sorosi aa E E TE AET EER RAE RAEE EN Bae Neos 24 6 3 Adding and Removing a Dataset syinccecccwoscvesacdescossaysused cade veteeaydeactsscveceadedandetensese deve teese 2s 24 o S a E10 ED B Fe e E E E eitecussachenseesaseisaegucases 26 6 3 Tame Steps Layers Panels rriar ere ap E E n tale S a ieaeaatiaeacaaten 27 265 Woman Fame lisse sand E E EE T E E E 27 Gd Saving Projects nois oes a E e E E E E A E E a ee RR 28 6 8 Configuring Default Directories s ssssessssssssseseseseessesseesseesssetsseesseesseesseeesseesseeseeesser 28 7 Working with Formulas eeessooesssooesscoesesooesesosccesscoesssoocesooeeesooecessocosssoossesooses
26. 57 VERDI is licensed under the Gnu Public License GPL version 3 and the source code is available through verdi sourceforge net VERDI is supported by the Community Modeling and Analysis System CMAS Center under U S EPA Contract No EP W 05 045 The CMAS Center is located within the Institute for the Environment at the University of North Carolina at Chapel Hill This guide describes VERDI version 1 1 released in May 2009 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 models cfm 3 CMAS SourceForge net website for developers of VERDI http sourceforge net projects verdi 4 To submit bug reports questions and or requests http bugz unc edu enter_bug cgi product VERDI If you do not already have a login and password click the Home link for instructions on how to obtain them 1 2 Where to Obtain VERDI You can download the latest version of VERDI from http www verdi tool org see Figure 1 1 When you click on the link to download VERDI you will be sent to the CMAS Model Download Center To download and install VERDI follow the instructions below skipping UNC Chapel Hill 1 Institute for the Environment VERDI User s Manual step 2 Alternatively you may also begin at the CMAS web site http www cmascenter org and follow the inst
27. 6_P16 base 36k 200200601 107 1 00861 amt 1 00861 4 81 8 823E 2 81 8 82262 5i 7 56362 i 7 50262 4 gt 6 30262 gt gt 6 30262 4 a 5 04262 G E 504162 21 2 3 78162 21 e 378162 4 1 2 52162 i 2 52162 4 1 2662 1 2A A 6 81 10 12114 1 2662 4 x 2 7967 x 2 7067 June 01 2002 01 00 00 UTC June 01 2002 00 00 00 UTC Min 124 45 0 002 Max 16 54 0 08 Min 124 45 0 005 Max 54 48 0 08 E EEEN 5 3 Window Menu Options The Window menu provides an alternate way to select windows panes to be brought to the front and provides the same function as clicking on the tabs at the bottom of the windows panes 5 3 1 Datasets and Formulas Select from the Window pull down menu to bring to the front either the Datasets pane or the Formulas pane when those panes are docked 5 3 2 List of plots The Window pull down menu is automatically updated each time a plot is created in a VERDI session each entry in the plot list indicates the type of plot and the formula used Clicking on a given plot entry brings that plot to the front for viewing Alternatively you can bring a plot to the front by selecting the desired plot tab underneath the plots area of the main window As in the menu entries each plot tab is labeled with the plot type and the formula used UNC Chapel Hill 21 Institute for the Environment VERDI User s Manual 5 4 Help Menu Options The Help pull down menu contains two items that you can use to learn more about
28. 75 0 05654102 0 05057155 0 05704820 0 06014926 0 05772105 0 05688525 0 05 0 06C 0 05157429 0 05155760 0 05378941 0 05655036 0 05715896 0 06C 0 05146443 0 05165763 0 05354829 0 05437502 0 05 0 05822665 0 05127602 0 05187001 0 05041530 0 05405997 0 05748555 0 062 0 05134670 0 05083859 0 05285481 0 05435295 0 05 0 05611136 fosb_ 1 0 04938178 0 05310810 0 04434832 0 05448048 0 05496275 0 04 Time Steps 0 48 0 05112159 0 05288953 0 04726538 0 04970066 0 05371705 0 04 J Use Time Range 0 05302355 0 05153894 0 05075091 0 04897014 0 04923818 0 05019323 0 05200012 0 04785371 0 05153491 0 05399327 0 051 J Use Layer Range zi Datasets Formulas j Tile O3b_ 1 Tile Probe O3b_ 1 0 0 7 21 12 31 min o5 09 07 0 04960227 0 04913480 0 04879814 0 05043450 0 04925504 0 03 max 48 09 09 23 0 04967739 0 04986827 0 04897213 0 04967715 0 04733799 0 044 24 0 04838874 0 05027971 0 04
29. 81E 2 2 521E 2 1 260E 2 2 7 90E 1 25 49 73 97 121 145 June 1 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 To show an additional map on the plot select the Configure GIS Layers option When you click on this item a dialog box titled Manage Layers gives you the following options Add Layer Move Up Move Down and Remove Layer Figure 10 7 When you select Add Layer a window prompts you to select a shapefile for a tile plot or a shapefile that has been converted into a binary format for a fast tile plot VERDI looks for files with the shp or bin extension After selecting a shapefile or a bin file you are asked to edit the layer style for the shape Figure 10 7 Edit the layer title to specify what type of shapefile you are adding If the shapefile contains a fill and you intend to have the map layer to be on top of other map layers you will need to change the fill to be transparent so that you can see the other map layers Change the fill transparency value from 1 1 opaque to 0 O transparent and select the Finish button After the layer you have added is listed under Manage Layers 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 M
30. 984380 0 04890250 0 04611914 0 05 Layers 0 5 25 0 04867472 0 05022133 0 04972808 0 04784472 0 04667569 0 04 0 0 7 23 0 04967739060521126 10 3 4 Set Rows and Columns The fast tile plot has one option that is not currently available in the any other plot This option is briefly discussed here rather than in section 10 due to the fact that this option is only available for the Fast Tile Plot Controls gt Set Data Ranges menu item will bring up a pop up window that allows the user to configure the minimum and maximum values used in the x axis range and y axis range Figure 10 12 Configure Min and Max Range Values UNC Chapel Hill 55 Institute for the Environment VERDI User s Manual File Configure Plot Timestep 9 V Zoom Probe Set Data Ranges Show Lat Lon 97 89 81 73 65 10 3 5 Showing latitude and longitude To view the latitude and longitude values for a point on the plot select the Show Lat Lon option on the Controls menu then hover your cursor over the location for which you would like to know those values The lat lon coordinates will be displayed in the lower right hand side of the window Figure 10 11 The option to display the lat lon coordinates may be selected and works with either the Zoom or the Probe option Figure 10 11 Lat Lon Values Shown in Lower Right of VERDI Tile O3 1 File Configure Controls Plot Time
31. CMAS Web Site seseeeeeeeseesesesrisresresersresrerrreseese 3 Figure 1 3 Downloading VERDI from the CMAS Web Site ssseseeeeeseseesesressisrereresersrrsrrrresseese 4 Figure 1 4 Downloading VERDI from the CMAS Web Site sseseeseseseeesesressesrisriesersresrerresseese 5 Figure 1 5 Getting Documentation on VERDI from the CMAS Web Site 6 Figure 1 6 VERDI Documentation on the CMAS Web Site sesssesessssesessesessesresrreseeseesresreeseese 6 Figure 1 7 Top of Bugzilla Form for VERDLI sssessessesssesessessessesrresressesresresseesrenresreeseesresreereeseese 7 Figure 1 8 Bottom of Bugzilla Form for VERDI 20 66 OGG OS 8 Figure 1 9 Add Attachment Form in Bugzilla ee ceeeeescecnseceseesseeceaeceseesseecnaecnseesseeenaeens 8 Preure 3 1 VERDI Set p Wizard yc50250 cc ucys cles as sees ee mec nice es cy peel a a a a engines 12 Figure 3 2 License Agreement iciveses civics secede seus ceke issia EE EEEE EE EAE ens a ESSES 13 Figure 3 3 Selecting an Installation Directory esesesseseseesessesseseresressesrserssressesseseresresseserseresre 13 Figure 3 4 Setting the Start Menu Folder ssessesseesesseesesesesressesstserssressesseserssresestseresresseseeseresee 14 Figure 3 3 File P xia tt OM tase pated ee calc E oat aan A A EATA E E e 15 Fig re 3 6 Installation Completes erect en er aaa aces ea oe EEEa a Sa RE edness 15 Figure 4 1 Starting VERDI in Windows sssessssesseesessesseseresressesseseresressesseserssresesteeresees
32. ES a ee A e SINE A n r R 57 10 4 3 Observational data overlays sssssesesesesesesseessesssereseeesseesseesseesseeesseesseesseesseee 58 10 44 Vect r oyerla yssen a R EEE A 60 11 Supported Grid and Coordinate Systems Map Projections sssesesooessecssccssocesocesoesssee 61 12 I O API Utilities Data Conversion Programs and Libraries cccccccccssssssscssseeees 62 13 Contributing to VERDI Development csssssscssssscccsssssecscssseccccssescccsssssecsscsssseees 63 14 Known BS scsi sisas es isass Sass ta seid svien ec oibucaeea vc data ce sdacatssnusawtute seas Sehsewseaauacs waphadesne i sssi oseta s raS 63 15 Mathematical Functions sicscciicctectsceccsecetetascecesccevesvenecebndeseoscensoxveccecstdccupnseteosvacessinevecvenscsbnaeses 64 16 Command Line Scripting nck 2 5 5 oa scape ca cena sh ces pacha ns seamed eet ceo eee IE 66 16 1 Example Script for Linux Users i s4ccnecceeh 4 eed ai visohiativites ey deed eens 67 16 2 Example Script for Windows Users ctcad ication vine ania tee adn 67 16 3 Commands that can be used listed in alphabetical order 0 eee eesceeeeeceesteeeeneeeeees 68 17 Licenses for JAVA Libraries used by VERDI cscsscccssssssccccssscccsscscccsssssessssssecseees 71 UNC Chapel Hill iv Institute for the Environment VERDI User s Manual Figures Figure 1 1 Top of Main VERDI Web Site Page icc ceric iid Site nile eek 2 Figure 1 2 Downloading VERDI from the
33. HOME gt DOWNLOAD gt STEP 1 Model Download Step 1 Periodically check the release notes for each model to find out about patches or bugs Please select a model family to download associated with each version of the models in the Model Documentation section of the site Join the model listserv services to stay informed about updates releases and news about all CMAS supported software User Details are logged in as Recent Download VERDI 1 0 VERDI 1 1 VERDI 1 1 VERDI 1 1 VERDI 1 1 Training Registration Not ered for any upcoming cl Register Now UNC Chapel Hill 3 Institute for the Environment VERDI User s Manual Figure 1 3 Downloading VERDI from the CMAS Web Site File Edit View History Bookmarks Yahoo Tools Help RAY http www cmascenter org download forms step_2 cfm temp_id 74384373456 COMMUNITY Uels 8 te amp ANALYSIS SYSTEM Welcome Elizabeth Adams Search CMAS OUT CMAS HOME gt DOWNLOAD gt STEP 2 Model Download Step 2 Please select a particular model from the list and provide information about your platform and compiler Select the product you wish to download VERDI 1 1 x Please Make a Selection On which types of computers do you run or anticipate running Linux PC this product Other x Please Make a Selection a Which compilers do you anticipate using GNU Compilers IRIX Fortran 90 x Submit VERDI 1
34. Script for Linux Users 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 SVERDI HOME data CCTM46 P16 03MAX s O3 1 gtype tile 16 2Example Script for Windows Users Edit the run bat script in the VERDI_1 1 directory by right clicking on the file and selecting edit Figure 16 1 Location of run bat script in Windows Oa gt Computer OS C Program Files VERDI 11 gt v i T 5 By Organize z Views v g Burn Fona lni Name s Date modified Type Size E Docent dJ jrel 6 0 5 25 2009 11 53 AM File Folder i p licenses 5 25 2009 11 54 AM File Folder E Pictures Di plugins 5 25 2009 11 54 AM File Folder E Music E run bat 5 21 2009 11 39 AM Windows Batch File 1KB 4 Recently Changed J shape2bin zip 5 21 2009 11 39 AM Compressed zipp 2 944 KB B Searches Uninstall exe 5 25 2009 12 33 PM Application 49 KB I Public SE VERDLexe 5 21 2009 11 39 AM Application 34 KB verdi ini 5 21 2009 11 39 AM Configuration Sett 1KB 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
35. allation instructions Vie 05 22 09 Windows installation instructions Vie 05 22 09 VERDI version 1 1 RELEASE NOTES Vie 05 22 09 ESS Users Guide PDF Download 05 22 09 ne User s Guide HTML View 05 22 09 ERDI 1 1 Test Documentation Download 05 22 09 ERDI 1 1 Zip archive for Windows Download 05 22 09 sah Gzipped tar archive for Linux Download 05 22 09 Training Registration Example Data Files Example Data is provided in the release archive 05 22 09 Developer Instructions View 05 22 09 1 3 Where to Obtain VERDI Documentation Documentation is available in several locations described below Each location provides links to the available documentation for VERDI which can be viewed in your web browser or downloaded and saved to your computer e The VERDI download page on the CMAS website accessed using step 4 in Section 1 2 contains links to all of the available documentation e 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 e From the www verdi tool org web site there are two ways to access the VERDI documentation
36. alysis System CMAS Center at the University of North Carolina at Chapel Hill Windows Linux 512 Mb RAM VERDI version 1 1 ear components are onnstaee contained in the installation package Visualize gridded netCDF data with this easy to use Java program Download VERDI version 1 1 VERDI version 1 1 Release Notes VERDIzilla email support Vi i Query VERDIzilla tickets VERDI User s Manual uery VERDIzilla tickets EEEEEADNDE ED GING Click on image to zoom VERDI is a Java program for visualizing meteorology emissions and air quality modeling data With options for overlaying GIS Shapefiles and observational data onto model output VERDI offers a range of options for viewing atmospheric modeling data VERDI scripting provides a powerful interface for automating the production of graphics for analyzing your data Features of VERDI VERDI News a UNC Chapel Hill 2 Institute for the Environment VERDI User s Manual Figure 1 2 Downloading VERDI from the CMAS Web Site Community Modeling and Analysis CMAS File Edit View History Bookmarks Yahoo Tools Help lt hd e x a B http www cmascenter org download forms step_1 cfm temp_id 74384373456 E Community Modeling and Analysi E COMMUNITY MODELING amp ANALYSIS SYSTEM Welcome Elizabeth Adams Search CMAS Search HOME UT CMAS QUARTERLY CONTACT EAC SITEMAP USER SURVEY
37. aset name in the list to highlight it 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 3 Open Dataset File Browser Look in E data x amp ime E Ozone_2 ncf E RADM_CONC_1 Fe My Recent Documents E Desktop My Documents PE My Computer EC File name Open My Network Places Files of type fa Files X Cancel UNC Chapel Hill 25 Institute for the Environment VERDI User s Manual Figure 6 4 Datasets Pane Displaying Information about a Dataset Datasets 2 RADM_CONC_1 Variables Time Steps 0 48 JV Use Time Range min 2 09 07 1983 02 00 00 Max 48 09 09 1983 00 00 00 Layers 0 5 Use Layer Range 6 4 Variables List The variables list shows all of the variables contained in a loaded dataset see the example in Figure 6 4 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 1 1 allows the user to automatically add a formula by double clicking on the name of a variable Double clicking on a variable will automatica
38. atasets are referenced in a formula using the format lt VariableName gt lt DatasetNumber gt For example the ozone variable from dataset 2 would be referenced as 03 2 The dataset number in the brackets corresponds to the sequential number assigned to the dataset as it was loaded into VERDI this number is shown on the Dataset panel to the left of the dataset name Figure 7 2 Formula Pane Add Time Steps 0 24 Use Time Range Min m 06 01 2002 00 00 00 Max 24 06 02 2002 00 00 00 Layers 0 21 J Use Layer Range zi Datasets Formulas To remove a formula from the formulas list highlight the name in the list and press the yellow minus button 7 2 Example Formulas To examine the values of ozone in dataset 1 the formula would be O3 1 UNC Chapel Hill 30 Institute for the Environment VERDI User s Manual 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 03 2 100 03 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
39. 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 lt level gt sets the level range of all formulas to the single level specified levelRange lt levelMax gt lt levelMin gt sets the level range of all formulas to the range specified openProject lt VERDIProjectName gt 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 lt windowid gt raises the window with the specified plot ID i e brings it to the front UNC Chapel Hill 69 Institute for the Environment VERDI User s Manual s lt formula gt loads the specified formula into VERDI s memory and makes it the currently selected formula save2ascii lt filename gt export data to a tab delimited data file suitable for reading into a spreadsheet application such as Excel saveImage lt image type gt lt file name gt saves the most recently created plot This command works for all plot types Supported formats include PNG BMP TIF and JPG scatter lt formulal gt lt formula2 gt 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 cas
40. d for saving project files An example of the contents of a Windows version of this file is verdi dataset home D VERD verdi project home C Documents and Settings lizadams verdi verdi config home D Program Files VERDI 1 1 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 vex 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 4 Starting VERDI and Getting Your Data into VERDI 4 1 Starting VERDI 4 1 1 Wi
41. data directory to C VERDI data or some other similar location Enter the following in the Run command C Program Files WERDI_1 1 run bat f C VERDI data cctm 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 WERDI_1 1 data CCTM46_P16 baseO2a 36k O3MAX select O3 1 as the formula and create a fast tile plot UNC Chapel Hill 67 Institute for the Environment VERDI User s Manual run bat cd plugins bootstrap SET JAVA jre1 6 0 bin java JAV A 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 WERDI_1 1 data CCTM46_P16 baseO2a 36k O3MAX s O3 1 gtype fasttile The changes to the run bat are highlighted in red Run the run bat script by clicking on Start then select Run then use Browse to find the run bat or type it in as follows Figure 16 2 Submit run bat script from Run command LS t Type the name of a program Folder document or Internet resource and Windows will open it For you Cancel Browse 16 3 Commands that can be used lis
42. e LUFRAC_01 4 HE Fie Configure Controls Plot Time Step 4 03 16 2006 00 00 00 Layer 4 Layer 0 LUFRAC_01 4 GRIDCRO2D_2006075_polar_stereographic Polar Stereographic 614 56 4 514 z 5 O oF u 41 51 61 71 81 91 101 X March 16 2006 00 00 00 UTC Min 127 51 0 Max 88 27 0 611 FastTilePlot Tile O3 2 Tile LUFRAC_01 4 6 2 Example Datasets 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 10 4 3 and the example datasets for the various dataset projections that VERDI supports including LCC polar stereographic and UTM 6 3 Adding and Removing a Dataset The first step after starting VERDI is to load a dataset To do this press the yellow plus button at the top of the Datasets pane A file browser Figure 6 3 allows you to select an I O API or WRF file for use in VERDI UNC Chapel Hill 24 Institute for the Environment VERDI User s Manual After you specify a dataset VERDI will load header information and display the available variables time steps layers and domain used by the file in the Datasets pane Figure 6 4 The actual model data are not loaded until later when plots are created To view the header information for a particular dataset that has been loaded click on the dat
43. e A aaelcee 59 Figure 10 17 Tile Plot with Observational Data Overlay eeseeseseeseesessisesesressessererssressesseseresre 60 Figure 10 18 Wind Vector Overlay on an Ozone Tile Plot eeseseeeeeeseseseeressrssrseresressessrseresre 61 Figure 16 1 Location of run bat script in Windows cee ceeeeseceseceseeesseeceeeeeeeeaeeseeeseeesaeenaeenees 67 Figure 16 2 Submit run bat script from Run cOMMANA ee eee ceeeeeseceeeceeeeeeseenseeeseeeeaeenaeenees 68 UNC Chapel Hill Vi Institute for the Environment VERDI User s Manual 1 Introduction 1 1 Background This manual describes how to use the Visualization Environment for Rich Data Interpretation VERDI VERDI is a flexible and modular Java based visualization software tool that allows users to visualize multivariate gridded environmental datasets created by environmental modeling systems such as the Community Multiscale Air Quality CMAQ modeling system and the Weather Research and Forecasting WRF modeling system These systems produce files of gridded concentration and deposition fields that users need to visualize and compare with observational data both spatially and temporally VERDI can facilitate these types of analyses VERDI was developed by the Argonne National Laboratory for the U S Environmental Protection Agency EPA and its user community Argonne National Laboratory s work was supported by the EPA though U S Department of Energy contract DE AC02 06CH113
44. e Chapter 12 for more information about how to convert observational data into this format To begin load both a model output dataset and an observational dataset using the yellow plus button in the Dataset pane 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 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 will be invalid and cannot be used to create a plot To view observational data as an overlay on a tile plot select Add Overlay gt Observations from the tile plot s Plot pull down menu An Observation dialog box will appear containing the variables that are available in the observational dataset The time step range for the dataset used in the tile plot must match the time step range for the observational dataset If this condition is not met then the following message will appear in the dialog box Observational variable must be compatible with tile plot Figure 10 13 and you will not be able to add an overlay UNC Chapel Hill 58 Institute for the Environment VERDI User s Manual Figure 10 16 Observational Dialog Box Observation Dialog x Observation variable must be compatible with tile plot Observation Details S
45. e sensitive showWindow lt windowId gt lt timestep gt 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 lt xmin gt lt ymin gt lt xmax gt lt ymax gt 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 subTitlel lt sub title 1 string gt allow you to control a plot s subtitles if desired Subsequent plots will use the default subtitles unless these arguments are used again subTitle2 lt sub title 2 string gt allow you to control a plot s subtitles if desired Subsequent plots will use the default subtitles unless these arguments are used again subTitleFont lt fontSize gt allow you to control the font size of the subtitle of a plot system lt system command gt sends the specified command to the operating system s command line tfinal lt final time step gt 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 lt initial time step gt sets the first time step for each formula s tim
46. e step range to the specified step number where the first step number is denoted by 0 titleFont lt fontSize gt allows you to control the font size of the title of a plot titleString lt title string gt 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 lt time step gt 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 lt aliasname gt is used to undefine an alias UNC Chapel Hill 70 Institute for the Environment VERDI User s Manual unitString lt unit string gt can be used to override the default unit label used for plots The default value comes from the dataset s themselves vector lt U gt lt v gt 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 lt formula gt lt U gt lt v gt 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 co
47. eated using the Dataset pahenee nnn cannes seccaes sdawaanea sta chawee RE 36 UNC Chapel Hill Vv Institute for the Environment VERDI User s Manual Figure 9 1 Tile Plot cscessesetssaesiets eset eA eee eee 37 Pioure 9 2 Fast TUEPlOtsninnaiii enn a cele E E uss tes a a STE E a 38 Figure 9 3 Vertical Cross Section Plots icii ei a ei E E ee R e 39 Figure 9 4 Vertical Cross Section Dialog BOX sseesssssssesssessessesseseresressesstserssresessereresressesereeresre 40 Figure 9 5 Time Series Plot sisi fets ad oces adscte eee gait ied etd ca eee cad ee ae EES as 40 Fig te 9 6 Time Series Bat Plot lecateg tc ira neys Gees teeta cace i fe vt Lees ta Seti ae at eet 41 Figure 9 7 Scatter Plots canons eis dia aah nee et nae 42 Figure 9 8 Scatter Plot Dialog BOX to 5 5 6 Seca ce stele sate Socata tee Ri e ed ah e si iE to A suerte 42 Figure 9 9 Scatter Plot Export Data into a CSV file ete sas cc Foss eeeaca ec cca sades ehsinetecesabatecedlonscs tess 43 Pieure 9 10 Vector Plots aioe ail eh Rae ee Ie eh A ORE ec a eee Aiea 44 Fis r 9 11 Vector Plot Dialog BOK iene ciao dass E AE R ees RG ERER E 44 Figure 9 12 Contour Plotesssssnseisiieasnen innii iaasa 45 Figure 9 13 Contour Plot Menu Options seessesssessessesseseresresstsstseresreseseeseresressesresreseesseseseresre 45 Figure 10 1 Tile Plot Pull down Menu Options iis ccccseseecede eee eee nies eect 46 Fig rte 10 2 Comfisure Plot Titles Tab ssisscsiisirerinai sevice ates iinit
48. eft operand is less than the right operand else 0 Di elas Returns 1 if the left operand is less than or equal to the right operand else 0 Do Peed Returns 1 if the left operand is greater than the right operand else 0 Be PS teed Returns 1 if the left operand is greater than or equal to the right operand else 0 Jo Set acacia Returns 1 if the left operand is not equal to the right operand else 0 6 SS Returns 1 if the left operand is equal to the right operand else 0 7 amp amp Returns 1 if both operands are non zero else 0 ARE OS EEA 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 16 Command Line Scripting 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 lt command gt lt command options gt where the at the end of the command is optional UNC Chapel Hill 66 Institute for the Environment VERDI User s Manual 16 1 Example
49. ese 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 UNC Chapel Hill 49 Institute for the Environment VERDI User s Manual Figure 10 6 Configure Maps for a Tile Plot File Configure Controls Plot Times Configure Plot 2002 00 00 00 Layer 04 Load Configuration Save Configuration Layer 0 03 1 World v North America USA Counties Configure GIS Layers Maps gt 1 00861 4 8 822E 2 4 81 71 7 56262 4 Set Current Maps As Plot Default or 6 302E 2 41 041E 2 31 3 78162 4 21 2 52162 4 11 1 2662 4 1 21 4 61 81 101 121 141 x 2 7067 4 June 01 2002 00 00 00 UTC Min 124 45 0 005 Max 54 48 0 08 The fast tile plot has different maps that can be selected as was described in Section 9 2 Also the fast tile plot automatically loads the counties map as you zoom in to a region of the United States UNC Chapel Hill 50 Institute for the Environment VERDI User s Manual Figure 10 7 Fast Tile Plot Map Options e 3 File Controls Plot Tim Configure Plot lt gt gt Slow 50 Layer amp Load Configuration Save Configuration ss awer 1 O31 Maps World ppmv 1 008E 1 97 4 North America a9 4 USA States 8 822E 2 USA Counties Hace 562E 2 Rivers De 6 302E 2 Configure GIS Layers 041E 2 4 Set Current Maps As Plot Default 1 Se E aie ona 3 7
50. ests Preferences Log out lizadams email unc edu Before reporting a bug please read the bug writing quidelines please look at the list of most frequently reported bugs and please search for the bug Reporter lizadams email unc edu Product VERDI Version Component Automating VERDI with Scripts Configuring Plots Documentation Exporting Images and Animations Ea Formulas x Severity question z Platform PC x Priority P3 gt OS Linux gt Initial State NEW gt AssignTo o QA Contact A Ce Default CC Estimated Hours Deadline YYYY MM DD Done IS UNC Chapel Hill 7 Institute for the Environment VERDI User s Manual Figure 1 8 Bottom of Bugzilla Form for VERDI 2101 File Edit View History Bookmarks Tools Help b gt z wy ft O http bugz unc edufenter_bug cai le E Latest Headlines 7s Adobe Studio Docu _ VERDI Visualization _ CMAS Bugzilla Main P _ CMAQ Community _ VERDI Visualization Environment for http www cmasc 1 01 README txt Enter Bug YERDI Estimated l i Enter Bug YERDI Hours ue ae Deadline YY YY MM DD URL hte Summary Description Attachment Add an attachment Depends on Blocks Commit Remember values as bookmarkable template We ve made a guess at your platform Please check it and if we got it wrong email zac unc
51. 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 Latest Headlines 8 Adobe Studio Docu VERDI Visualization CMAS Bugzilla Main P CMAQ Community tase J VERDI Visualizati _j Enter Bug YE C3 LJ Bug List LJ Enter Bug VERDI U Bug List LJ Enter Bug VERDI i CMAS Bugzilla Enter Bug VERDI Home New Search Find Reports My Requ
52. 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 e O3 1 2 multiplies each item in the O3 1 array by 2 and returns the result e 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 UNC Chapel Hill 65 Institute for the Environment VERDI User s Manual e 3 2 simply multiplies 3 by 2 The binary operators Le AP atte Returns the sum of the operands Dh EER Returns the difference of the operands Da Tt Res Returns the product of the operands BT aah tae Returns the ratio of the operands DATE enone Returns the left operand raised to the power of the right operand Boolean binary operators return either 1 or O 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 Te E Returns 1 if the l
53. im UNC INSTITUTE FOR THE ENVIRONMENT Visualization Environment for Rich Data Interpretation VERDI User s Manual U S EPA Contract No EP W 05 045 Operation of the Center for Community Air Quality Modeling and Analysis Prepared for William Benjey and Donna Schwede U S EPA ORD NERL AMD APMB E243 04 USEPA Mailroom Research Triangle Park NC 27711 Prepared by Liz Adams and Alison Eyth Institute for the Environment The University of North Carolina at Chapel Hill 137 E Franklin St CB 6116 Chapel Hill NC 27599 6116 Date due May 29 2009 VERDI User s Manual Contents 1 Wnt rr wisssszcscicastaseeics spac pbs cneuans seabencenihense adbcceutpeasedas tne Ravaustesbecastacscacontacnadees tasbecvannieezebine e 1 NG ACK Or OUI 26 2 coats sacs She ae asa sei RASA Ea ae dae ca al ly ach 1 1 2 Whe rteto Obtain VERD recens ool vs Sasa unl a a E eg av ope a es 1 1 3 Where to Obtain VERDI Documentation eee eeeceesseceenseceseeeenaeeeseeeeseeeeneeeenseees 5 1 4 Help Desk Support for VERDI sssrinin esanian tiis ients 7 1 5 Fure VERDI De velopment 52 5655 a E Ne eta gees 9 2 Requirements for Using VERDI e soesssccesessscesssocsessocssesoecessocossssossssoossesoosesosecsssscossseossesso 9 2 1 Java Runtime Environment iisssccissavevscaseascyccdiewsnsccassasveedeesossccvonsace cateabenncdvenbenaaacsupncedenteses 9 2 2 Memory and C PU Re gU OE OS a A AEA E E ses 9 2 3 Requirements to ran VERDI remotely
54. in new_plugin Extract msver71 dll 100 Extract npdeploytk dil 100 Extract npjp2 dll 100 Output folder C Program Files WERDI_1 1 jre1 6 0 ib Extract calendars properties 100 Nullsoft Install System v2 42 lt Back Close Cancel Figure 3 6 Installation Complete Setup was completed successfully Completed Extract plugin xml 100 Output folder C Program Files VERDI_1 1 plugins verdi data loaders ib Output folder C Program Files VERDI_1 1 Extract VERDI exe 100 Create folder C Users Liz AppData Roaming Microsoft Windows Start Menu Progra Create shortcut C Users Liz AppData Roaming Microsoft Windows Start Menu Pro Created uninstaller C Program Files VERDI_1 1 Uninstall exe Create folder C Users Liz AppData Roaming Microsoft Windows Start Menu Progra Create shortcut C Users Liz AppData Roaming Microsoft Windows Start Menu Pro a Completed Nullsoft Install System v2 42 UNC Chapel Hill 15 Institute for the Environment VERDI User s Manual 3 4 Setting VERDI Preferences 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 an
55. ing the Dataset and Formula Panes The Formula pane and Dataset pane 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 5 Navigating VERDI s Main Menu Options Figure 5 1 shows a graphic of the main menu options that are available on the top menu bar in VERDI s main window Figure 4 2 above These options are discussed in detail below Figure 5 1 VERDI Main Menu Options File Plots Window Help Open Project Undock All Plots Datasets Verdi Help Docs Save Project Animate Tile Plots Formulas About Save Project As Tile HO 2 HO2 2 Exit 5 1 File Menu Options 5 1 1 Open Project Open Project retrieves projects that were saved during a previous session using the two Save Project options described next Note that when you use a saved project it is very important to load that project into VERDI before you
56. ion Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula O3 1 Tile O3 1 mod File Configure Controls Plot 06 01 2002 02 00 00 Layer o 4 Layer 0 O3 1 Formulas 1 008E 1 4 8 822E 2 4 7 562E 2 4 6 302E 2 4 Time Steps 0 24 5 0462 4 IV Use Time Range Min 24 06 01 2002 02 00 00 a 06 02 2002 00 00 00 3 78162 4 2 52162 4 Layers 0 21 1 2062 4 I Use Layer Range 1 21 y 61 81 101 121 141 x 2 7967 min o l hd June 01 2002 02 00 00 UTC Datasets Formulas Min 78 17 1 933E 4 Max 16 54 0 074 SSS S UNC Chapel Hill 32 Institute for the Environment VERDI User s Manual 8 2 Specify Layer Range Information on the range of vertical model layers included in a dataset is displayed in the Layers panel Figure 8 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
57. is performed only on previously created plots any newly created plots are docked to the VERDI main window 5 2 2 Animate tile plots This option opens an animate tile dialog box Figure 5 2 that allows you to select 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 tile dialog box you can select plots 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 tile 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 lt filename gt 1 gif lt filename gt 2 gif lt filename gt 3 gif You can view the animated GIF by
58. lly create a formula that contains 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 From this menu you can either add the variable as a formula or you can to add it UNC Chapel Hill 26 Institute for the Environment VERDI User s Manual into the formula editor so that it can be used to compose more complex formulas Formulas are described in more detail in Section 7 6 5 Time Steps Layers Panels The range that is available for the dataset is listed in the Time Steps or Layers Panel in parenthesis next to the label for the panel e g for a dataset that has 5 time steps the range would be displayed as Time Steps 1 5 The user can select to use a subset of the full time step range by clicking on the Use Time Range checkbox and then using the Min and Max spinner controls to set a new minimum or maximum values for example choosing time step 2 as the minimum time step and time step 4 as the maximum When a tile plot is created it will only display time steps 2 4 Detailed instructions for using the Time Steps Layers and Domain panels that you see in Figure 6 4 are discussed in Section 8 Spatial and Temporal Data Subsetting 6 6 Domain Panel The domain panel contains an Edit button and a Metadata button Detailed instructions for using the Edit button are provided in Section 8 Spatial and Temporal Data Subset
59. lot option you select a formula for the Tile option in the vector plot dialog box Figure 9 11 in addition to specifying the formulas UNC Chapel Hill 43 Institute for the Environment VERDI User s Manual to be used for the horizontal and vertical vector components See Section 10 4 4 for more information on vector overlays Figure 9 10 Vector Plot UWIND 3 x WIND 3 Vector File Configure Controls Plot Time Step 0 07 24 2001 00 00 00 Layer bps een x MANDER gt Layer 0 b T Too aN a 7 7 70 REAT Af 7 aa eee eater e 68 x y assist l iy it Hier Beas zii Zi Spy Siesta 4 Bes gt eo eres See s ee SNe sl Ren 3 F rie ey ae Je j 52 51 KA 50 A WK 4 ns Bg A 78 80 82 84 86 88 90 92 94 100 102 X July 24 2001 00 00 00 UTC UWIND 3 x VWIND 3 Vector Horizontal Component UWIND 3 vertical Component WIND 3 Tile Optional UNC Chapel Hill 44 Institute for the Environment VERDI User s Manual 9 8 Contour Plot The contour plot shows a 3 D representation of values over a geographic area Figure 9 12 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 9 13 In addition the contour plots can be rotated in three dimensions to achieve different viewing angles by using the left mouse bu
60. mponent 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 lt row column gt 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 17 Licenses for JAVA Libraries used by VERDI VERDI has been developed using a number of open source Java libraries Table 17 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 UNC Chapel Hill 71 Institute for the Environment VERDI User s Manual Table 17 1 JAVA Libraries used by VERDI List of Java Where to acquire Reference to Link to license or the Libraries software Software License for specific license number Software JTS java http sourceforge net pr http www vividsolutions http www gnu org copyleft less topology suite ojects jts topo suite er html
61. n 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 6 8 Configuring Default Directories 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 Vverdi 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 SUSER_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 UNC Chapel Hill 28 Institute for the Environment VERDI User s Manual 7 Working with Formulas All plots in VERDI are generated from formulas A formula is used to compare or manipulate variables in one or more datasets 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 Formulas are used to create visualizations that can assist with model performance evaluation
62. n example of an ozone concentration tile plot with wind vector overlays is shown in Figure 10 15 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 10 18 Wind Vector Overlay on an Ozone Tile Plot File Configure Controls Plot Time Step w 06 01 2002 00 00 00 Layer w4 o3 4 Layer 0 4 CCTM46_P16 base02a 36k 20020060 UWIND and VWIND Vector Overlay 85 90 95 100 105 110 115 120 125 130 x June 01 2002 00 00 00 UTC Min 123 44 0 005 Max 53 47 0 08 Tile 03 4 11 Supported Grid and Coordinate Systems Map Projections VERDI obtains the grid and coordinate system information about the data directly from the I O API files For more information see http www baronams com products ioapi GRIDS html UNC Chapel Hill 61 Institute for the Environment VERDI User s Manual 12 I O API Utilities Data Conversion Programs and Libraries As discussed in Section 4 3 if the data you want to use in VERDI are not already in I O API or WRF input format we recommend that you convert them to one of those formats You can do this either by using the available routines
63. n in Lower Right Min o o9 07 5 Max 464 09 09 o p Layers 0 5 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Use Layer Range x Be i September 07 1983 00 00 00 UTC Datasets Formulas Min 1 1 0 03 Max 22 1 0 074 _ 0 0 7 23 0 04967739060521126 Clas D 10 3 3 Probing a domain region of data To probe the values of a selected region of grid points select the Probe option under the Controls pull down menu then draw a rectangle by clicking on a point on the map holding down the left mouse button and then releasing the mouse button once the rectangle encloses the region of interest VERDI will create a spreadsheet displaying the grid values and will place it in the plot area of the VERDI main window as a tabbed window Figure 10 10 The File gt Export menu option at the top of the spreadsheet allows you to save probed data as a comma delimited text file csv UNC Chapel Hill 54 Institute for the Environment VERDI User s Manual Figure 10 10 Spreadsheet Showing Probed Values for Region of Interest j File Plots Window Help i0 x m E Tile Plot Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot vector Plot Contour Plot belec Tile Probe O3b_ 1 0 0 7 21 12 31 ox File Tile Probe O3b_ 1 0 0 7 21 12 31 0 05208801 o 05313238 0 05393084 0 057743
64. ndows To start VERDI open the Start menu then highlight the Programs directory followed by the VERDI directory then select the VERDI icon as shown in Figure 4 1 UNC Chapel Hill 16 Institute for the Environment VERDI User s Manual Figure 4 1 Starting VERDI in Windows fa Programs 1GH VERDI J Uninstall A Documents b Fe ite Settings gt 2 j2 Search gt QJ Help and Support Windows XP Professional 4 1 2 Linux and Other non Windows JRE 6 Supported System Configurations To start VERDI from Linux and other non Windows JRE 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 VERDT 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
65. nt 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 makxt 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
66. nts 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 e Starting year month day hour GMT e g 1997 07 10 12 e Ending year month day hour GMT e g 1997 07 16 12 e Name of output variable 8 characters max e g 03_OBS The Network Common Data Form netCDF is an interface to a library of data access functions for storing and retrieving data in the form of arrays This is an abstraction that supports a view of data as a collection of self describing network transparent objects that can be accessed through a simple interface By using direct file access netCDF achieves the goal of supporting efficient access to small subsets of large datasets See http www unidata ucar edu packages netcdf UNC Chapel Hill 62 Institute for the Environment VERDI User s Manual 13 Contributing to VERDI Development 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 setup 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
67. nual 8 Spatial and Temporal Data Subsetting Both the Dataset pane and the Formula pane include the three panels discussed in Sections 8 1 through 8 3 Time Steps Layers and Domain Section 8 4 then discusses the precedence rules for subsetting data that determine which pane s subsettings Dataset or Formula take priority 8 1 Specify Time Step Range Information about the range of time step values included in a dataset is displayed in the Time Steps panel Figure 8 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 8 4 to learn the precedence rules Figure 8 1 Specify Time Step Range l0 x File Plots Window Help m Q ae Tile Plot Vertical Cross Sect
68. okii a 48 Figure 10 3 Configure Plot Color Map Tab ssesessseesseseseseesresseserssressessrsrssressesseserssresseseeeeresre 48 Figure 10 4 Configure Plot Labels Tab zis 0214 2 ica See eee le ates Bee eats 48 Figure 10 5 Configure Plot Other Pab cis c teed pectinases 48 Figure 10 6 Configure Maps for a Tile Plot sssesseseeeeesesesessessesseserssressessesrssresesseseresressesereeresre 50 Figure 10 7 Fast Tile Plot Map Options sssssssssessesseessseessseessresesssseesssesseesseessseeesresseesseeesseesseest 51 Figure 10 7 Manage Layers Add Layer Edit Stylesiid cc niauenuninaiaeiieealis 52 Figure 10 8 Right Click on Plot to Zoom Out sssseesessesesessessesseseresressesseserssresesserereseesseseeeeresre 53 Figure 10 9 Click on Plot to Probe Data Value Shown in Lower Left of VERDI Grid Valu s Shown in Lower Rights cissscssisseceateccsessescansesnedcauancaedaccoansecaste sud E E 54 Figure 10 10 Spreadsheet Showing Probed Values for Region of Interest 55 Figure 10 12 Configure Min and Max Range Values 00 eee eeseeecesseceneeeseeeesceneesseeesaeesaeesees 55 Figure 10 11 Lat Lon Values Shown in Lower Right of VERDI s essssssseseereesessireresressesereeresre 56 Figure 10 14 Plot Meni Opu Gis s ernunon cote ces outta aes n E E E 57 Figure 10 15 Animate Plot Dialog Box 2 tiscci ete nies edhe ened ae 58 Figure 10 16 Observational Dialog BOX seksi Scat ctas Secured tebe eo eees ai ewune esl dh Seed apa caeaneln
69. 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 UNC Chapel Hill 5 Institute for the Environment VERDI User s Manual the right hand side of the www verdi tool org home page take you to the documentation available for VERDI Figure 1 5 Getting Documentation on VERDI from the CMAS Web Site lysis CMAS M lodel Documenta tion Mozil File Edit View History Bookmarks Yahoo Tools Help Z o X 3 http www cmascenter org help documentation cfm temp_id 74384373456 LY Cl Google A Community Modeling and Analysi E3 COMMUNITY PA MODELING amp ANALYSIS SYSTEM my Welcome Elizabeth Adams SearchCMAS Search HOME A T RTERLY C me HOME gt HELP gt DOCUMENTATION Model Documentation Documentation is available for the following CMAS Supported Products n ppa Select the Product for which you desire documentation e Environmental Benefits Mapping and Analysis Program BenMAP e Community Multiscale Air Quality CMAQ e Sparse Matrix Operator Kernel Emissions SMOKE System e Package for Analysis and Visualization for Environmental PAVE data e Input Output Programmers Application Interface I O API e MM5 Mete
70. opening the file in a web browser Creating a Quicktime movie is also an option but this is not done through the Plots gt 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 UNC Chapel Hill 20 Institute for the Environment VERDI User s Manual Figure 5 2 Animate Plots Dialog and Tile Plots F4 vervi r File Plots Window Help Tile o3 2 x Fie Configure Controls Plot m I ea l Tile Plat Vertical Croce Sertinn Time Series Time Series Rar Datasets xj Time Step 1 06 01 2002 01 00 00 Layer Layer 0 03 2 Select Plots 1 00861 5 IV 03 2 06 01 2002 00 00 00 06 02 2002 00 00 00 24 Steps V 03 2 06 01 2002 00 00 00 06 02 2002 00 00 00 24 Steps 8 823E 2 4 7 50362 4 6 30262 4 a9 S 042E 2 3 78162 4 Starting Time Step 0 06 01 2002 00 00 00 a TER Ending Time Step 244 06 02 2002 00 00 00 e ae ae T a 1 2662 4 J Make Animated GIF s x dala i June 01 2002 01 00 00 UTC Min 124 45 0 002 Max 16 54 0 08 Tile 03 2 Tile O3 2 xl Tie O3 1 z x Fie Configure Controls Plot File Configure Controls Plot Time Step 14 06 01 2002 01 00 00 Layer w4 Time Step 1 06 01 2002 00 00 00 Layer oj Layer 0 03 2 Layer 0 03 1 2 CCTM46_P16 sens_airc 36k 200200601 1 CCMT4
71. orology Coupler MCPL e Multimedia Integrated Modeling System MIMS SMOKE SPATIAL ALLOCATOR it Contact Info Documentation is also available for the following unsupported Products e MM5 Modeling System MMs MM5 Recent Downloads Figure 1 6 VERDI Documentation on the CMAS Web Site HOME gt HELP gt DOCUMENTATION Model Documentation The following documents are available for VERDI 1 1 INSTALL LINUX TXT RELEASE NOTES TXT HTM Search for other Model Documentation We have also created a Porting Guide for building different CMAS software components on unsupported environments Due to the nature of model research and development the model documentation may not always be up to date with the code We will make every effort to provide current documentation or notices when the documentation differs from the available models If you wish to download any of the CMAS supported models please visit the Model Download page UNC Chapel Hill 6 Institute for the Environment VERDI User s Manual 1 4 Help Desk Support for VERDI You are encouraged to submit questions 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
72. osecesssecsssossses 29 7 1 Adding and Removing a Formula ss ssssseeesseeesseessessseesseeesseesseeseessseesseesesseeesssessseeseessee 29 172 Example F rm las p eae a e e A V A E OKEE EET ESF 30 7 3 Selecting a Formula for Plotting eeeeeeesesseseesesesesessessessresressessererssressessreereseessesereeessee 31 TA Savine Formulas ea a E a a a caiaas eaten ensenaate 31 7 5 Time Step Range Layer Range and Edit Domain ssseessssesessrssrseresressesstseresressesersessee 31 8 Spatial and Temporal Data Subsetting essseossseessccssecsooesoocsssessscesocesoocesoeesocesocesoosessessoses 32 Sl Specify Time Step RAMEE 15 26 5 3 ccs e T E R E E 32 8 2 Specify ayer Range meiras ne Ses nae ee eet ed ca A a edad 33 8 3 Specify IG WAITER AMOS E E E os eee Saas ant cg naa 33 8 4 Rules of Precedence for Subsetting Data wien seviseees jars daccaalvas despasdy anys BR ateiegse a teyeeed aeeecs 35 DAG sd CIA A AT E E EITT 36 g HR Ei alo a E E ENE A A A A a O Coe 36 9 27 Fast Ele Plotrane focin E E E eae asd eee ene Beda ese eae eases 37 OS Vertical Cross Section Plotis eersten eranen E A E EES 39 9 4 Tame S ries Plotis nienie n N N E KaSS 40 9 5 Time Series Bar Plots secs eitecantneshucwsurdouetiae iea a that ae alae E S 4 9 6 Scatter Plots isnene anen a e n duos facaaguss deca O E a 41 97 Nestor PLO aa eases pete i Guts E E E Sue GT es Ea A S 43 OS Contour Plotare eie errea rE E EE A sash ohana V caeeeband dean sovadeatannactant
73. ove Up or Move Down 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 UNC Chapel Hill 51 Institute for the Environment VERDI User s Manual Figure 10 7 Manage Layers Add Layer Edit Style Edit Style Please edit this layers style Manage Layers _ imap_workd hae Catia Move Up Layer The Canadian Provinces Move Down Simple Style Rule Based Style Remove Layer Fil OK Cancel ae E Fil Transparency I Outine Outine Color z Outline Transparency 1 Outline Thickness 1 Preview Previous Ned Finish Cancel 10 3 Controls Menu Options The Controls pull down menu contains the following options Zoom Probe and Show Lat Lon 10 3 1 Zooming in and out To zoom in and enlarge a subdomain of the data select the Zoom option Then use the left mouse button to click on a region of the map and hold down the button to draw a rectangle around the region of interest To zoom out use your mouse to right click on the map A pop up window will appear allowing you to select Zoom Out gt Both Axes or Zoom In gt Both Axes or to select Auto Range g
74. phics Requirements Three dimensional contour plots require a graphics card with OpenGL or DirectX capability By default VERDI uses OpenGL for 3D rendering If you would like to use DirectX instead add the line j3d Dj3d rend d3d to the verd1 ini file 3 VERDI Installation Instructions 3 1 VERDI Installation Installing VERDI on a Windows operating system is accomplished by running a standard installer program For Linux and other non Windows platforms VERDI is distributed as a gzipped tar file that contains the executable application and the third party libraries needed for VERDI Currently the VERDI distributions provide a platform specific Java Runtime Environment 6 0 see Section 2 1 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 JRE 6 for other system configurations that run it are also provided 3 2 Installation Instructions for Linux and Other non Windows JRE 6 Supported System Configurations The VERDI tar file contains all of the third party software needed to run VERDI to run ona Linux platform using 32 bit versions VERDI requires the following third party software JRE 6 Java3D and Java Advanced Imaging JAI 1 tar xvf
75. ple file name is lt FormulaName gt _ lt DatasetFilename gt _ lt PlotType gt 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 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 10 2 3 Configure Maps The Maps option in the Configure pull down menu is used to add maps to a tile plot Figure 10 6 The tile plot and fast tile plots are the only plots that have maps For the Tile Plot a world map a North America map and the counties of the United States may be selected or de selected by clicking with the left mouse button on one of th
76. rent time step or for all time steps Specify the time and layer ranges 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 UNC Chapel Hill 41 Institute for the Environment UNC Chapel Hill HO 2 File Time Step 0 09 07 1983 00 00 00 Layer o gt Scatter Plot HO2 2 PPM VERDI User s Manual Figure 9 7 Scatter Plot x HO2 2 Scatter Configure Controls 7 27E 06 6 61E 06 5 95E 06 5 29E 06 4 4 63E 06 4 3 96E 06 4 3 30E 06 4 2 64E 06 4 1 98E 06 gt 1 32E 06 6 61E 07 8 71E 09 1 74E 08 2 61E 08 3 48E 08 4 35E 08 5 22E 08 6 10 08 6 97E 08 7 84 08 8 7 1E 08 9 58E HO 2 PPM September 07 1983 00 00 00 UTC Layer 0 H0 2 H02 2 HO 2 x HO2 2 Scatter Figure 9 8 Scatter Plot Dialog Box Scatter Plot Select Formulas for Axes X Axis HO 2 Axis HO2 2 Y Axis 42 Institute for the Environment VERDI User s Manual Figure 9 9 Scatter Plot Export Data into a CSV file NO 1 x NO2 1 Scatter cle File Configure Controls Time Step 4 02 16 2004 23 00 00 Layer j Scatter Plot 7 45E 02 6 77E 02 o a 6 09E 02 oo ir C0
77. ructions below 1 Log in using an existing CMAS account or create anew 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 VERDI Visualization Enviro a aa File Edit View History Bookmarks Yahoo Tools Help lt ie G aY O http www verdi tool org VERDI Visualization Environmen J VERDI Tool ORG Visualization Environment for Rich Data Interpretation VERDI home Overview Documentation Download VERDI Help with VERDI VERDI Training Links Welcome to VERDI tool org Sites Redulraauate This is the official VERDI website hosted by the Community Modeling and An
78. s for example or that help in comparing model results with observations 7 1 Adding and Removing a Formula After loading the desired datasets you can use the variables in them to create formulas To add a variable name as a new formula on the Formula pane or to put it in the formula editor so that it can be used to compose a more complex formula To bring up the formula editor window right click on the variable name in the Dataset pane Figure 7 1 Double click on the name of the variable if you want to use the variable to create a simple formula this will add the formula lt Variable Name gt lt Dataset Number gt to the formula list e g O3 1 Figure 7 1 Right Click on Variable in Dataset Pane 3 zioz Fie Pets Window Hep IEE z THe Plot vertical Cross Secton Time series Te Series Bar Pct Scatter Piot vector Plt Contour Hat Selected Formda WNDI L Datasets Tine Stops 0 43 7 Use Tine Range Nine o 09 07 1993 0000 00 wax 40 09 09 1983 0000 00 Layers 0 5 7 Lie Layer Range rine o2 mxf s Donan aiil i Datasets Foemndss j E E E An alternate method for adding a formula is to type the string representing that formula into the text box on the Formula pane and then click the Add button Figure 7 2 To bring up the UNC Chapel Hill 29 Institute for the Environment VERDI User s Manual Formula pane click on the tab at the bottom labeled Formulas The variables found in the d
79. s Manual Figure 3 2 License Agreement GNU General Public License version 3 GPLv3 Submitted by nelson on Tue 2007 10 23 03 13 GNU GENERAL PUBLIC LICENSE Version 3 29 June 2007 Copyright C 2007 Free Software Foundation Inc lt http fsf org gt Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed VERDI License Nullsoft Install System v2 42 Figure 3 3 Selecting an Installation Directory UNC Chapel Hill 13 Institute for the Environment VERDI User s Manual Choose Install Location Choose the folder in which to install VERDI 1 1 Please select the directory to install VERDI C Program Files VERDI_1 1 Space required 168 4MB Space available 36 7GB Nullsoft Install System v2 42 Choose Start Menu Folder Choose a Start Menu folder for the VERDI 1 1 shortcuts Select the Start Menu folder in which you would like to create the program s shortcuts You can also enter a name to create a new folder Nullsoft Install System v2 42 UNC Chapel Hill 14 Institute for the Environment VERDI User s Manual Figure 3 5 File Extraction Installing Please wait while VERDI 1 1 is being installed Eorsi snini iii Output folder C Program Files VERDI_1 1 jre1 6 0 bin dient Extract Xusage txt 100 Extract dasses jsa 100 Extract jvm dll 100 Output folder C Program Files WERDI_1 1 jre1 6 0 b
80. s shown in Figure 9 2 The motivation for developing the fast tile plot was due to the slow 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 UNC Chapel Hill 37 Institute for the Environment VERDI User s Manual Figure 9 2 Fast Tile Plot be OS FE File Configure Controls Plot Timestep W lt gt gt Slow 50 Layer Q Layer 1 O3 1 ppm 1 008E 1 8 822E 2 562E 2 6 302E 2 041E 2 3 781E 2 2 521E 2 1 260E 2 2 7 90E 1 25 49 3 97 121 145 June 1 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 Tile O3 1 Tile 03 1 At the top left of the fast tile plot there is a slider that can be used to change the time step by clicking and dragging the slider with the mouse The top center 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 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 f
81. see Section 8 4 to learn the precedence rules Figure 8 2 Edit Layer Range in Formula Pane ini xi Fie Plots Window Help E Q ae Tile Piot Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula O3 1 Formulas Tile o3 t role x rTime Steps 0 24 af File Configure Controls Plot Time Step m 06 01 2002 00 00 00 Layer 3 O3 1 J Use Time Range Min os 06 01 2002 00 00 00 Max 24 06 02 2002 00 00 00 9 19262 4 8 048E 2 4 v Use Layer Range 6 905E2 4 Min 34 61 5 762E 2 4 gt 51 z p Domain a 5 4 81962 4 31 3 47662 4 21 2 33362 4 11 1 1 1962 5 1 21 4 61 81 101 121 141 xX 467364 izl June 01 2002 00 00 00 UTC Datasets Formulas J Min 95 55 0 023 Max 107 32 0 086 ee as 8 3 Specify Domain Range Datasets contain data for cells over a particular geographic area In the VERDI program this area is referred to as a domain By default the entire domain contained in a dataset is used in creating plots The Edit Domain dialog box can be used to select a subset of this domain for plotting To access the Edit Domain dialog box first use the vertical slide bar to bring the Domain panel located below the Layers panel into view if it is not already visible Figure 8 3 To select a subset of the domain press the Edit button The Edi
82. seseeseresre 17 Fig t 4 2 VERDI iain WINdOW 29 ss sca tesa nces irinta a a tata edentenueee ins 18 Figure 5 1 VERDI Main Menu Options 2 22cceie died ee ee eee 19 Figure 5 2 Animate Plots Dialog and Tile Plots sseeseseseseeeesseesesesesressesseseresresseserereseesseseeseresre 21 Figure 6 1 Lambert Conformal Conic Map Projection Example Plot ceeceeeseceeeseeeeeteeeeees 23 Figure 6 2 Polar Stereographic Map Projection Example Plot 00 0 0 ee eeeeeeeeeeseeeeeeeeeeeeeeneeeees 24 Fig re 6 3 Open Dataset File Browser wc Ge eG Se A ONE OS nai 25 Figure 6 4 Datasets Pane Displaying Information about a Dataset eeeseseeeeeseeseeereereeseserereeee 26 Figure 6 5 Dataset Metadata Information o ci2cssccccccce2jess0 otsecs stot scade Hee cetsieeeduisiediedasatlcdesgelacntes 28 Figure 7 1 Right Click on Variable in Dataset Panes tucts cctseteen due addr owed cei ell 29 Fig re 7 21 Formala Pane sirni a ate Ananda a a e e e O Manat ERER E 30 Figure 8 1 Specify Time Step Rangi nencnecnoreiiieiein ae i aa iai 32 Figure 8 2 Edit Layer Range in Formula Pane essesesseseseeseesessessresresseseserssresesseseresressesereeresee 33 Figure 8 3 Using the Slider to View the Domain Panel 0 0 0 0 cee ceecsesseceseceseeeeseeeeeeseeeeneesaeenees 34 Figure 8 4 Edit Domain Dialog BOX esig 8 se uac dea helatccta dest beatles ade BO ak Gad i eden lwassme tle teesiaee 34 Figure 8 5 Error obtained when incompatible subset domains are cr
83. t Time Step m 06 01 2002 00 00 00 Column pb 03 1 Column 30 Layer 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 Domain Row June 01 2002 00 00 00 UTC Min 0 037 Max 0 07 O3 1 vertical Cross Section UNC Chapel Hill 39 Institute for the Environment VERDI User s Manual Figure 9 4 Vertical Cross Section Dialog Box 9 4 Time Series Plot Yertical Cross Section X Select Cross Section X Axis Cross Section Column 30 Axis Cross Section Row os OK Cancel The time series plot shows a line graph with the average values over time Figure 9 5 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 UNC Chapel Hill Time Series HO 2 HO2 2 Eile Configure Controls Layer J 0 0000275 10 0000250 0 0000225 10 0000200 0 0000175 10 0000150 amp 0 0000125 10 0000100 00 0000075 10 0000050 10 0000025 0 0000000 0 0000025 Time Series HO 2 HO2 2 Figure 9 5 Time Series Plot HO 2 HO2 2 Layer 0 Weeeeeeee 09 07 1983 00 00 00 09 07 1983 04 00 00 09 07 1983 08 00 00 09 07 1983 12 00 00 09 07 1983 16 00 00 09 07 1983 20 00 00 09 08 1983 00 00 00
84. t Both Axes to recover the plot of the full domain Figure 10 8 The pop up window also allows you to select the option to zoom only along the domain axis or only along the range axis UNC Chapel Hill 52 Institute for the Environment VERDI User s Manual Figure 10 8 Right Click on Plot to Zoom Out File Configure Controls Plot Time Step J oj 09 07 1983 00 00 00 Layer m O3b_ 1 Layer 0 20 19 18 17 iS Properties 15 Save as 14 13 Print 12 Zoom In b gt a Both Axes 11 10 4 Auto Range gt Domain Axis R Axi 4 ange Axis 8 7 6 54 4 3 x September 07 1983 00 00 00 UTC Min 1 1 0 03 Max 22 1 0 074 Tile og 2 Tile O3 2 Tile O3b_ 1 Tile Probe O3b_ 1 0 0 9 16 13 23 UNC Chapel Hill 53 Institute for the Environment VERDI User s Manual 10 3 2 Probing values at specific points To determine the data value at a specific point select the Probe option under the Controls pull down menu To probe a single data point use the mouse to hover the cursor over that grid point on the map the coordinates of the grid points are shown in the lower right hand side of the plot in the format column row Once you click on the grid point of interest the value of the datum at that grid point is displayed in the lower left hand area of VERDI main window Figure 10 9 Figure 10 9 Click on Plot to Probe Data Value Shown in Lower Left of VERDI Grid Values Show
85. t Domain dialog box will appear Figure 8 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 UNC Chapel Hill 33 Institute for the Environment VERDI User s Manual 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 8 3 Using the Slider to View the Domain Panel 5 x File Plots Window Help m a Tie Faa Vertical Cross Section Tine Series Time Series Ber Piot Scatter Plat vector Plot Contour Plat Formulas ep J 4 Selected Formule O3 1 o FEE EE T a Fie Configure Cortrols Piot 7 Use Time Range Time Step OJ 06 01 2002 00 00 00 Layer 0 mn 0 06 01 2002 00 00 00 Layer 0 O3 1 Max 242 06 02 2002 00 00 00 Lovers 0 21 I Use Layer Range min 054 Max fas June 01 2002 00 00 00 UTC Datasets Formulss Min 124 45 0 005 Max 54 48 0 08 E Fig
86. tcdf java er html java v2 2 16 javadoc uc ar ma2 package summary html Repast symphony http repast sourceforge http repast sourceforge net repa GIS net st license html UNC Chapel Hill 12 Institute for the Environment
87. te 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 13 Contributing to VERDI Development 2 Requirements for Using VERDI 2 1 Java Runtime Environment VERDI requires version 6 of the Java Standard Edition Runtime Environment JRE At this time JRE 6 is available from Sun at http java sun com for Windows XP Vista and 2000 as well as Linux and Solaris and for the Mac OS X running Leopard VERDI will not run under Java 1 5 JRE 6 is currently not available for download for Mac operating systems versions that precede Leopard In addition to JRE 6 VERDI requires several third party libraries Instructions for how to download JRE 6 and the third party libraries are provided in section 3 2 2 Memory and CPU Requirements VERDI s memory and CPU requirements largely depend on the size of the datasets to be visualized Small datasets can be visualized and manipulated using less than 512 megabytes of RAM while larger datasets may need considerably more If you are using datasets that require either more or less than 512 MB of memory you can change the default maximum memory setting used by VERDI e On Windows edit the Verdi ini file
88. ted in alphabetical order alias lt aliasname definition gt 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 lt aliasname gt 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 lt filename gt 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 UNC Chapel Hill 68 Institute for the Environment VERDI User s Manual closeWindow lt windowid gt closes the window with the specified
89. ting 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 5 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 UNC Chapel Hill 27 Institute for the Environment VERDI User s Manual Figure 6 5 Dataset Metadata Information rE a File Plots Window Help i Ela Datasets Ea Tile Plot Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula O3 1 Tile O3 1 Hex a File Configure Controls Plot Time Step os 06 01 2002 00 00 00 Layer os Layer 0 O3 1 I Use Time Range Min J 0 06 01 2002 00 00 00 Max J 24 06 02 2002 00 00 00 Layers 0 21 1 008E 1 I Use Layer Range 8 82262 min o 7 56262 Max J 21 lt r taset Metadata Projection information Edit Metadata Name LambertConformal Parameters origin 40 0N 97 0W parallels 33 0 45 0 Dataset Dimensions TSTEP UNLIMITED f f 25 currently DATE TIME 2 LAY 22 3 102 Datasets J Formulas J COL 145 Dataset global attributes 6 7 Saving Projects As noted in Section 5 5 1 lists of datasets and formulas ca
90. tions for each of these menus are described in more detail in Section 10 Configuring Plots Using the Plot Menu Bar 9 1 Tile Plot Tile plots show a color contour of the selected formula Figure 9 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 UNC Chapel Hill 36 Institute for the Environment VERDI User s Manual the plot You can use the Layer spinner control to change the current layer To access the ability to zoom in and out use the mouse to right click on the plot Zooming and other plot configuration options are discussed further in Section 10 Figure 9 1 Tile Plot File Configure Controls Plot Time Step o 4 06 01 2002 00 00 00 Layer o Layer 0 03 2 101 4 1 008E 1 5 917 8 822E 2 4 814 x 7 56262 4 61 Properties 6 30262 4 ae Save as Print 414 Zoom In gt KA 3 78162 4 zoom Out gt a1 Both Axes 2 52162 4 11 Domain Axis Range Axis 81 x June 01 2002 00 00 00 UTC Min 124 45 0 005 Max 54 48 0 08 9 2 Fast Tile Plot The fast tile plot is currently under development and once it is fully functional it will replace the previous tile plot option An example of the Fast Tile Plot window i
91. to specify a different heap size from the default 512M e On Linux or another Unix platform you can edit verdi sh and replace the 512 in Xmx512M with a different value for example Xmx1024M will allow VERDI to access up to 1024MB or 1GB of RAM Schwede D N Collier J Dolph M A Bitz Widing T Howe 2007 A New Tool for Analyzing CMAQ Modeling Results Visualization Environment for Rich Data Interpretation VERDI Proceedings CMAS 2007 Conference UNC Chapel Hill 9 Institute for the Environment VERDI User s Manual Note that even slower CPUs can quickly view and animate smaller datasets whereas larger datasets can take longer Initially VERDI s performance is slow when it is used across the network via ssh This problem has been addressed in version 1 1 with the addition of the Fast Tile Plot Once the Fast Tile Plot supports configuration options of the original tile plot it will replace the original tile plot 2 3 Requirements to run VERDI remotely It is possible to run VERDI on a remote compute server and have the graphics display locally on your desktop machine Unix workstation Mac or PC although the performance may be slow 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 Hummingbird Exceed X Server and wish to generate 3 D plots using Open GL you need to turn on Open GL support in Hummingbird 2 4 Gra
92. troke Size 4 Shape Size ha 5 OC micrograms m3 OMC micrograms m3 OMC_BEXT micrograms m3 PM25 micrograms m3 RCFM fmicrnorams ma OK Cancel If the time step ranges are compatible select the observational variable 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 filled in circles that represent the observational data The stroke size controls the thickness of the line used to draw the circles while the shape size controls their diameter After you select the variable and optionally set the stroke size and shape size select OK to overlay the observational data on the tile plot Figure 10 14 At this time VERDI does not have an option to remove or to reset the size of the symbols on an observational data overlay on a tile plot If the user wishes to resize or change the symbol of the observational data overlay they will need to draw a new tile plot and re add the observational data overlay using the new stroke size or shape size UNC Chapel Hill 59 Institute for the Environment VERDI User s Manual Figure 10 17 Tile Plot with Observational Data Overlay Pl OS lF File Configure Controls Plot Time Step 06 01 2002 00 00 00 Layer oo O3 1 Layer 0 AQS_overlay_2002 24hr 2002152 ncf 1 CCTM46_P16 base02a 36k 03MAX 92 94 96 98 100 102 104 106 108 1
93. ts 45 UNC Chapel Hill iii Institute for the Environment VERDI User s Manual 10 Configuring Plots Using the Plot Menu Barr ssccsssssscssssssccsssscccssssscssssssessscssscseees 45 tO File Ment Options inei xs seal ae easy carseat cused tuned th a a ARa ans ae eo nae 46 10 2 Configure Men Options nss 2d atin led an eta ed eee 46 10 2 1 C nfisurina NOUS eae fe ees oe cian diated cate ee eel ants tose h cate EES 46 10 2 2 Loading and saving configuration eee eeeeeeseecseeceseeeseeceaeceeeesaeecaeceeeeeaees 49 1023 OMT BUTS MAIS oot asses eres deed aleedcaanazvewgseaseecgetadtvbaeetbeteneasuemeetecettenseneszenes 49 10 3 Controls Menu Options cjcississceccassceescccasaveccasarcestcctasaaedaceasesunchte secdsaseaescdedeesncedasaseducdeas sac 52 10 31 ZOOMING mand OU sd shesdicnrssionnees tesnagenesedeubvasendecs bceat e e ei E aE 52 10 3 2 Probing values at specific points esseeessesssseseeeesseseresresseesessresressessesnrsrressessesees 54 10 3 3 Probing a domain region of data eeseeseseeeseesseseresresseesessresresserstsererressessesee 54 10 3 4 Set Rows and Columns wisiscicsaccussccdccaticeasiedssececdica staaccnssetaecdaccundacdassendiataseancaatases 55 10 3 5 Showing latitude and longitude sseeeeeeesesseeeeeessesesesresresseseresresresstsnrerressessesees 56 10 4 Plot Menu Options ii cissccescstss noseci ae EE E E TEE a 57 104 1 Time seri s Plots i ira oo E E EEE RAE EER ERE E 57 1042r Ammate O
94. tton to grab and rotate the plot Figure 9 12 Contour Plot Contour UWIND 1 0 File Configure Controls Plot Time Step 3 07 24 2001 03 00 00 Layer Uy oy liime B 4 By X DAN w amp l eee paasi odos oN i z 8 P 5 w w Figure 9 13 Contour Plot Menu Options File Configure Controls Plot Print Configure Plot Show Lat Lon Animate Plot Export As Image Load Configuration Show IsoContours Save Configuration 10 Configuring Plots Using the Plot Menu Bar Each VERDI plot contains its own menu bar that has options specific to that type of plot As an example the menu options at the top of a tile plot include those shown in Figure 10 1 These options are common to all plots and function in the same way unless the option is grayed out UNC Chapel Hill 45 Institute for the Environment VERDI User s Manual 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 Plot configuration options that are available in VERDI are discussed in this section Figure 10 1 Tile Plot Pull down Menu Options File Configure Controls Plot Print Configure Plot Zoom Time Series of Probed Cell s Export As Image Load Configuration Probe Time Series Bar of
95. ure 8 4 Edit Domain Dialog Box Pje sees he Clear Region D Cancel UNC Chapel Hill 34 Institute for the Environment VERDI User s Manual 8 4 Rules of Precedence for Subsetting Data 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 Dataset 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
96. urther slow the animation The fast tile plot uses a new format for the maps called the bin format A shape2bin program that runs on linux platforms has been provided with the Verdi_1 1 distribution to allow users to convert new map shapefiles to the bin format for the fast tile plot The user can extract the shape2bin zip and then follow the instructions in the README file to build and run the code UNC Chapel Hill 38 Institute for the Environment VERDI User s Manual Once the bin files have been created the user needs to copy them to the VERDI_LHOME Vverdi_1 1 plugins bootstrap data directory Follow the instructions to add a new map layer that are found in Section 10 2 3 Configure Maps to add the new map to the Fast Tile Plot 9 3 Vertical Cross Section Plot The vertical cross section plot allows you to show a slice of data Figure 9 3 A popup dialog box Figure 9 4 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 9 3 Vertical Cross Section Plot O3 1 Vertical Cross Section File Configure Controls Plo
97. using If your data are not already in I O API format we recommend that you use the available routines that have been written to convert data into this format or at least start from one of these routines to write your own Discussion of these conversion programs and how to use them can be found in Section 12 I O API Utilities Data Conversion Programs and Libraries If you write a routine to create input data for VERDI please consider contributing your code to the user community using sourceforge net as described in Section 13 Figure 6 1 shows an example of a plot generated for a dataset with an LCC map projection Figure 6 2 shows a plot based on data with a polar stereographic map projection Support for the polar stereographic map projection was added in VERDI 1 05 UNC Chapel Hill 22 Institute for the Environment VERDI User s Manual Figure 6 1 Lambert Conformal Conic Map Projection Example Plot Tile DRY_N 3 fo x File Configure Controls Plot Time Step oj 01 01 2001 01 00 00 Layer i Layer 0 DRY_N 3 agg cctmJ3fx dep_wa annual lambert Lambert Projection 111 4 101 4 31 613 5 914 81 714 22 595 4 614 51 18 086 4 41 314 January 01 2001 01 00 00 UTC Min 147 1 0 05 Max 93 29 36 122 FastTilePlot Tile O3 2 Tile DRY_N 3 UNC Chapel Hill 23 Institute for the Environment VERDI User s Manual Figure 6 2 Polar Stereographic Map Projection Example Plot Til
98. valuating Formula Dataset domain ranges are incompatible Time Steps 0 2 0 06 J Use Time Range Min o 06 01 2002 00 00 00 Max 24 06 02 2002 00 00 00 Layers 0 21 I Use Layer Range 95 100 105 om0 115 120 1235 Min oj 85 20 x uo Max 24 June 01 2002 00 00 00 UTC 3 Min 123 44 0 005 Max 105 31 0 06 Domain xl Min Tile 03 2 Datasets Formulas Tile oxfi Tile O3 17 Tile j EE SSS SSS 9 Creating Plots ppmv 0 05 4 0 04 After creating a formula you are ready to 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 op
99. window ID configFile lt configFileName gt 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 lt filename gt 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 lt tile line bar contour gt instructs VERDI to create a plot using the specified type and the currently selected formula s data gtype lt tile line bar contour gt 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 lt bin0 binl bin_n gt 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

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