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Visualization Environment for Rich Data Interpretation

1. r r 7 4 Configure Plot _ a u 5 Configure Plot E Titles Color Map Labels other Titles Color Map Labels Other Tite Number of Tiles 8 Palette Type Sequential Show Tite F Palette Text Layer 103 1 C iot to dark purple a Font Dialog plain bold 24 CT light to dark blue Color TRIE ight t0 dark orange CTT toh pure to dark bue f Sbiie1 C ight orange to dark red l Ti Ppi l C io to dark red Text 1 CCTM46_P 16 baseO 2a 36k O3MAX lL Lo light yellow to dark green Font Dialog plain 12 C P light yellow to green to dark blue Cir Sic Neuton RGS Avs Interval Automatic Number Format 1 3E Subtitle 2 z Show Tite F Min 6 554426 Max 0 996420 Text Color Font Dialog plain 12 Select m Coor O E Bo Oo Bo E Figure 11 5 Configure Plot Other Tab r 4 Configure Plot x Titles Color map Labels Other Color Vector Arrow Color Institute for the Environment User s Manual for VERDI 1 5 Figure 11 6 Example Plot with Selected Tick Marks for Range Axis and Legend File Configure Controls Plot GIS Layers a Time Step 1 06 01 2002 00 00 00 Layer 1 Stats None a gt lux lamo 5 a Layer 1 O3 1 1J ECCTM46_P16 baseO2a 36k O3MAX 1 008E 1 97 81 7 562E 2 65 49 041E 2 33 2 521E 2 2 790E 7 1 25 49 73 97 121 145 June 01
2. UNC Chapel Hill 24 Institute for the Environment User s Manual for VERDI 1 5 6 4 Adding and Removing a Dataset from a Remote File System VERDI provides users with the ability to select and add variables from datasets on remote file systems To do this press the yellow plus remote plus with a diagonal arrow button at the top of the Datasets pane In the Remote File Access Browser Figure 6 4 that appears enter your user name choose a host from the list and enter your password then click Connect Figure 6 4 Available Hosts in the Remote File Access Browser e L Remote File Access E Remote User Double click a NetCDF file or directory Select one or more variables Cancel 6 4 1 Remote File Browser The top panel displays a listing of the home directory on the remote file system as shown in Figure 6 5 The current path is displayed in the text box and users can edit this information to change to another directory An alternate way to navigate between directories is using the middle panel In the middle panel double click on a directory name to go into that directory or click on the at the top of the middle panel to navigate up a directory As you enter a directory the contents of the directory will be displayed as a list in the middle panel Directory names are followed by a symbol while filenames do not have a symbol after them View the variables w
3. Max 25 06 02 2002 00 00 00 Layers 1 3 F Use Layer Range EiS 3 After the variable names are added to the Formula Editor click on the formula pane and use the cursor and the keyboard to type in the mathematical functions and operators where needed to create a valid formula see Section 7 2 and Chapter 16 After the formula has been created in the Formula Editor click the Add button to place it in the list of formulas available in the Formula pane UNC Chapel Hill 32 Institute for the Environment User s Manual for VERDI 1 5 To remove a formula from the formulas list highlight the name in the list and press the yellow minus button Note that removing a formula from the formula list does not remove plots that were created prior to the deletion of the formula 7 2 Example Formulas To examine the values of ozone in dataset 1 the formula would be O3 1 To examine the difference in ozone between datasets 1 and 2 the formula would be O3 1 O3 2 To calculate the percent difference in ozone between datasets and 2 the formula would be O3 1 03 2 100 03 2 To identify all cells where the ozone concentration exceeds a certain value you can use the Boolean operators to screen out ranges of your data that are of particular interest A Boolean expression will evaluate to either True 1 or False 0 For example to plot the cells in which the ozone values in dataset
4. Time Step 1 3 04 23 2006 00 00 00 Layer 11s Stats None A lt 1 gt gt Slow Layer 1 03 1 1 CCTM4 _aac_spr06 12k CONC 2006113 03 nef 11 5 GIS Layers The GIS Layers menu contains the following options Add Map Layers Configure GIS Layers and Set Current Maps as Plot Default The map layers are currently in the BIN format created by the SHAPE2BIN tool distributed with VERDI but development plans are to replace them with Shapefiles 11 5 1 Add Map Layers Use the Add Maps Layers option in the GIS Layers menu to add maps to a Fast Tile Plot or Areal Interpolation Plot Figure 11 20 A selection of default maps including World North America USA States USA Counties HUCs Rivers and Roads can be selected or deselected by clicking on the respective menu selection A check mark then appears or disappears next to the chosen map name and the selected map appears on the plot UNC Chapel Hill 81 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 20 Add Map Layers File Configure Controls Plot GIS Layers Time Step a E 06 01 Add Map Layers gt World Slow fo E Configure GIS Layers V North America USA States Set Current Maps As Plot Default USA Counties 1 CCTM46_P16 base Tone ppm 1 008E 1 97 Rivers Roads a 8 822E 2 85 Other r3 7 562E 2 73 67 6 302E 2 61 55 5 041E 2 49 43 37 3 781E 2 31 25 2 521E 2 1 260E 2
5. e Load a model output dataset e Load an observational dataset Note that an OBS label appears to the right of the dataset name in the Dataset pane e Double click on a variable in an observational dataset and add it to the Variable pane Note that an OBS label appears to the right of the dataset name in the Variable pane e Create a formula in the Formula pane using a variable from the model output dataset Use this formula to create a fast tile plot NOTE If you attempt to use a formula that contains a variable from an observational dataset the following error will occur Error while evaluating formula Selected dataset is observational e Select Add Overlay gt Observations from the fast tile plot s Plot menu to view observational data as an overlay on a fast tile plot UNC Chapel Hill 76 Institute for the Environment User s Manual for VERDI 1 5 An Observation dialog box e Figure 11 16 appears containing the variables that are available in the observational dataset Select the observational variable to overlay on the Fast Tile Plot from the Observation Details list Multiple observational dataset variables can be overlaid on a Fast Tile Plot e You can control the appearance of the symbols representing the observational data The stroke size controls the thickness of the line used to draw the symbols the shape size controls their diameter You can use up to six different open area shapes circle diamond square st
6. 0 035246 0 033154 0 030519 0 02 28 0 032623 0 036969 0 035841 0 034729 0 036168 0 032747 0 042123 0 037539 0 035504 0 035593 0 035255 0 035239 0 031375 0 02 29 0 037137 0 037331 0 035390 0 034199 0 035865 0 041495 0 044851 0 053485 0 042354 0 039540 0 037651 0 037265 0 033752 0 03 30 0 033536 0 035457 0 033232 0 033810 0 037392 0 043697 0 041630 0 046592 0 040717 0 037479 0 044250 0 043992 0 041343 0 03 31 0 032849 0 033987 0 032938 0 035168 0 041106 0 045695 0 045804 0 044071 0 043165 0 042144 0 044482 0 041803 0 039726 0 04 32 0 036860 0 035103 0 034936 0 036590 0 038033 0 042466 0 042183 0 040958 0 041466 0 044133 0 050567 0 041200 0 059488 0 05 33 0 036164 0 036891 0 036907 0 042552 0 040262 0 040274 0 038489 0 035402 0 037181 0 040692 0 044781 0 043893 0 043640 0 04 34 0 038263 0 041422 0 039721 0 045003 0 042592 0 037677 0 037639 0 037731 0 038619 0 039629 0 040172 0 042938 0 041797 0 03 35 0 036418 0 036926 0 036996 0 036751 0 037591 0 037118 0 037848 0 037609 0 033963 0 048289 0 046564 0 048733 0 037328 0 02 36 0 038168 0 037938 0 036813 0 037516 0 036825 0 040956 0 042698 0 039493 0 042436 0 039759 0 038717
7. BUTADIENE 13 ACROLEIN ACROLEIN_PRIMARY Tolu MXYL a The variables read from the remote dataset will be displayed in the dataset and variable browser in the same way that variables from a local dataset are added and displayed within VERDI The subsetted local dataset names are identical to the file names on the remote host except for an additional extension that enumerates how many times the remote files were read and saved locally by VERDI i e filename1 filename2 filename3 etc as shown in Figure 6 6 To add variables from the same remote dataset click on the plus remote button and repeat the above procedure The Remote File Browser retains the login session and the directory that was last accessed by the user to facilitate ease of accessing remote datasets VERDI increments the numerical extension to the dataset name to indicate that this subset file was created using the same remote dataset but that the subset file with the new numerical extension may contain a different subset of variables Note that VERDI does not check to see if the same variable from the same remote dataset has already been read Also subset files read in by VERDI are saved either to your home directory on your local file system e g C Users username on a Windows 7 computer or to the location that is specified in the config properties file using the verdi temporary dir setting Refer to Section 6 4 2 on how to edit and save the
8. dataset file path name dir dataset file folder pattern dataset file name pattern gtype plot type tile line bar vector vectorTile vector plot variables s variable name ts time step titleString plot title subdomain subdomain xmin ymin xmax ymax subTitlel plot subtitle one subTitle2 plot subtitle two savelmage image file type png jpeg eps etc imageFile image file path name imageDir image file folder drawGridLines draw grid lines on the tile plot if yes imageWidth image width imageHeight image height unitString units RKEKKHRKRHERREHEREHREEREBRERERERE REE HH HH Author IE UNC at Chapel Hill Date 10 27 2014 Version 2 FREE EE EEE EEE EEE EEE HH Figure 17 4 Bottom of Sample Script File VERDI_1 5 data scripts tile_patterns txt HHKHKHHHHRA HEHEHE AHHH AAA AAA AAHAAA AM H AA RT aa Ta T a RERE lt Global gt dir datafmodel pattern CCTM46 s 03 1 savelmage jpeg imageDir data plots subTitle1 Test SubTitle 1 subTitle2 Test SubTitle 2 lt Global gt lt Task gt gtype tile imageFile 03_tile lt Task gt lt Task gt gtype line lt Task gt As shown in Figure 17 3 and Figure 17 4 the Batch Script File format consists of two blocks a Global block and a Task Block The Global block allows you to specify a set of parameters such as the file and directory names on which all other tasks are performed In this block you can
9. 6 4 User s Manual for VERDI 1 5 2 Adding Additional Remote Hosts VERDI contains the RemoteFileUtility and ncvariable programs that enable VERDI to add your T O API netCDF or WRF netCDF formatted dataset from a remote file system A gzipped tar file is available in the VERDI_HOME directory 1 The RemoteFileUtility c shell script and ncvariable binary need to be installed either in usr local bin by the System Administrator or you can place it in a different location and specify that location in the configure properties file located in your USER_HOME verdi directory see section 3 4 for the specific directory location that is used for each platform Linux Windows Mac A template for the configure properties file called configure properties TEMPLATE is provided in the distribution under the VERDI_LHOME directory A README file provided with the software contains instructions on how to compile the source code if the binaries provided do not match your operating system Copy the file configure properties TEMPLATE to configure properties Edit the configure properties file in the USER_HOME verdi directory Add the name or IP address of the Linux server preceded by a comma at the end of the list of machines defined as remote hosts in the configure properties file as shown in Figure 6 7 You then need to restart VERDI in order for it to recognize a newly added remote host name Figure 6 7 Edit configure properties Fil
10. n 1 e STANDARD_DEVIATION VARIANCE e COEFFICIENT_OF_VARIANCE STANDARD_DEVIATION IMEANI e RANGE MAXIMUM MINIMUM e INTERQUARTILE_RANGE THIRD_QUARTILE FIRST_QUARTILE e SUM var i j k tmin var i j k tmin 1 var i j k tmax e TIMESTEP_OF_ MINIMUM 0 based time step when cell contains its minimum value e TIMESTEP_OF MAXIMUM 0 based time step when cell contains its maximum value UNC Chapel Hill 46 Institute for the Environment User s Manual for VERDI 1 5 e HOURS_OF_NON_COMPLIANCE number of time steps that the cell value exceeds a given threshold I Var Lj k t i gt threshold e MAXIMUM_8HOUR_MEAN Max M1 M2 Mn 8 where Mi mean var 1 j k ti var 1 j k ti 1 var i J sk t 42 s Var LJ k ti g for i 1 n 8 10 2 Areal Interpolation Plot The areal interpolation plot displays the interpolated value of the selected formula for each polygon in the selected area file Compare the colors of the polygons to those shown in the legend to see the relative values of the formula for each polygon area The Areal Interpolation Plot includes several capabilities that are not available for other plot types so these are described below rather than in Chapter 11 Plot Menu Bar 10 2 1 Options Menu The Areal Interpolation Plot menu contains an Options menu to allow the user to change the map to display either the Area Averages Figure 10 2 the Area Totals Figure 10 3 or the value of the formu
11. o sqrt 4 Returns 2 0 o sqrt O3 1 Returns a matrix containing the square root of each value in the O3 1 variable s array The following functions return a matrix when passed a dataset variable o abs Returns the absolute value of the argument o sqrt Returns the square root of the argument o sqr Returns the square of the argument o log Returns the base 10 logarithm of the argument o exp Returns Euler s number raised the power of the argument o In Returns the natural logarithm of the argument o sin Returns the sine of the argument The argument is in radians o cos Returns the cosine of the argument The argument is in radians o tan Returns the tangent of the argument The argument is in radians o sind Returns the sine of the argument The argument is in degrees o cosd Returns the cosine of the argument The argument is in degrees o tand Returns the tangent of the argument The argument is in degrees The following functions return a single number in all cases when passed a dataset variable o mean Average cell value for all cells in currently selected domain o sum Sum of all cell values in currently selected domain o min For each cell i j k in the currently selected domain this calculates the minimum value for that cell over the currently selected time steps In other words the minimum value in cells i j k tmin tmax o max For each cell i j k in the currently selected domain this calculates the max
12. remote hosts terrae nesc epa gov vortex pnc epa gov garnet0l rtpnc epa gov tulip rtpnc epa gov RemoteFileRe initial path on remote system ocal bin RemoteFil RemoteFileRead java if exists used as secure shell command on remote system di remote ssh usr bin ssh tility RemoteFileReader java if exists used as location on local machine for downloaded files rdi temporary dir C temp UNC Chapel Hill 28 Institute for the Environment User s Manual for VERDI 1 5 6 5 Variables List The variables list shows all of the variables contained in a loaded dataset see the example in Figure 6 7 To display a variables list select the name of the dataset of interest in the Datasets pane Each of the variables in the list can be used to create a formula in the Formula pane that can then be used to create plots VERDI allows the user to automatically add a formula by double clicking on the name of a variable This automatically creates a formula that contains the variable for the loaded dataset and makes it the default formula for making plots In addition you may right click on the name of the variable to show a popup menu as shown in Figure 6 8 From this menu you can either add the variable as a formula or you can to add it into the formula editor so that it can be used to compose more complex formulas Formulas are described in more detail in Chapter 7 Figure 6 8 Right Click on Variable in Dataset Pane VERDI N File Plots W
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14. 5612 551 4881 995 4151 439 85 Se S ia 3420 883 67 Porma a 2690 327 1959 771 1229 215 Dae r 498 660 1 231 896 UNC Chapel Hill 87 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 3 Mercator Map Projection Example Plot Tile HT 1 File Configure Controls Plot GIS Layers ime Step 1 05 01 2009 00 00 00 Layer 1 iig Stats None salis lt j gt gt Slow Layer 1 HT 1 1 GRIDCRO2D_mercator 1 18 35 52 69 86 103 120 May 01 2009 00 00 00 UTC Min 1 1 0 000 Max 61 88 89 879 UNC Chapel Hill 88 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 4 UTM Map Projection Example Plot Tile POP2000 1 File Configure Controls Plot GIS Layers Time Step 1 01 02 0003 00 00 00 Layer lis Stats None gt lt i gt gt stow Layer 1 POP2000 1 1 grid_pophous_utm nef PO 100000 000 90000 000 80000 000 70000 000 60000 000 z 5 Z Z Z a 50000 000 40000 000 i 30000 000 ae 20000 000 N Vh n ad a 10000 000 1 T T T T T T T T 13 25 37 49 61 73 85 97 12 2 CAMx Gridded Data The netCDF java library used in VERDI includes support for CAMx UAM IV binary files using a preset default projection CAMx or UAM binary files contain information about the x and y offsets from the center of the projection in meters but do not contain inf
15. Areas T 124 10 2 2 Areal Values for Polygon Segment To view the area total value and average value for a selected polygon segment use the mouse cursor to hover over a polygon on the map The values are shown at the bottom left of the information panel Figure 10 6 UNC Chapel Hill 51 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 6 Areal Values for Polygon Segments Eile Plots Window Help r Q Ea Tile Plot Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula DRYOX_N 2 eas Arealinterpolation ox Area Files File Configure Controls Plot GISLayers Options Time Step 01 01 2001 01 00 00 Layer Ce Slow 50 Layer 1 DRYOX_N 2 2 BaseCase dat 1448 2232 Datasets Formulas areas Tile DRYOX_N 2 Arealinterpolation lArea 1363 704919 7 kg 4 56044 kg ha 120 53 10 2 3 View and Export Areal Plot Data in Spreadsheet Format To view the average and total interpolation values for selected formulas in a spreadsheet format right click on the Areal Interpolation Plot and select Area Information Figure 10 7 The Area Information Spreadsheet contains four columns the identification number from the name field for the polygon the total area average interpolated value and total interpolated value Figure 10 8 At the top of the Area I
16. data plots subdomain 20 10 75 50 lt Global gt Data files picked up from patterns specified for names lt Task gt gtype tile lt Task gt If you select Run without highlighting a Text Block then the entire batch script executes and generates the plots To edit the batch script highlight a segment that you would like to copy and use Ctrl C to copy the text then click in an area where you want to paste the text and use Ctrl V to insert the copied text Test your changes to the script by highlighting the text block and click run When your script executes successfully VERDI displays the popup window shown in Figure 17 7 NOTE Click either the Save or the Save As button to save your edits before exiting the Script Editor After saving the script file e g C verdi script myscript txt you can run the batch script directly from command lines without invoking the VERDI GUI On a Windows computer start a UNC Chapel Hill 102 Institute for the Environment User s Manual for VERDI 1 5 command window navigate to the directory containing your run bat file and then run this command run bat batch C verdi script myscript txt On Linux Mac platforms change directory to where the Verdi sh is located and execute this command assuming your script file myscript txt is saved in home user verdi script directory verdi sh batch home user verdi script myscript txt Note the full path to the batch scrip
17. you can use the variables in them to create formulas To use a variable to create a simple formula double click on the name of the variable This will add the formula lt Variable Name gt lt Dataset Number gt to the formula list in the Formulas pane for example O3 1 To add a variable to the formula editor window highlight the variable right click on the variable name in the Datasets pane and select Add Variable s to Formula Editor To add all or a subset of variables from the Dataset pane to the formula editor window click on the first variable to highlight it hold the Shift key down and click at the last variable that you want to include then right click and select Add Variables s The formulas that are highlighted using this method will be added to the formula editor Figure 7 1 UNC Chapel Hill 31 Institute for the Environment User s Manual for VERDI 1 5 Figure 7 1 Adding Multiple Variables to Formula Editor File Plots Window Help Q Eq Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot 1 CCTM46_P16 baseO 2a 36k O3MAX Variables lt Double dick to add the variable as a formula No 1 NO2 1 add NO ppmV 1 NO2 ppmvV 1 Add Variable s to Formula Editor Add Variable s as Formula s a oo 06 02 2002 00 00 00 Time Steps 1 25 F Use Time Range Min 1 06 01 2002 00 00 00
18. 0 043569 0 040421 0 03 37 0 038947 0 037541 0 037227 0 038540 0 039332 0 034024 0 039473 0 049284 0 045034 0 045095 0 040379 0 041451 0 042067 0 03 38 0 033946 0 034763 0 036540 0 038506 0 036142 0 045506 0 046473 0 049007 0 046698 0 043341 0 040272 0 039306 0 044804 0 04 39 0 031566 0 030757 0 032026 0 032534 0 035704 0 037502 0 042843 0 043379 0 043426 0 040352 0 038426 0 039407 0 036961 0 03 40 0 030776 0 029873 0 032459 0 033419 0 037091 0 037394 0 038640 0 038057 0 036953 0 035558 0 034527 0 031756 0 034944 0 03 41 0 038830 0 040798 0 040598 0 036879 0 038008 0 040243 0 039972 0 039219 0 038360 0 035944 0 033914 0 028533 0 032119 0 03 42 0 039192 0 038795 0 039578 0 037584 0 038203 0 040568 0 040725 0 038736 0 037521 0 036049 0 032219 0 028669 0 029256 0 03 43 0 036888 0 037194 0 033159 0 034147 0 039031 0 042578 0 042390 0 041315 0 038375 0 035847 0 029073 0 029201 0 031271 0 03 44 0 034345 0 035557 0 032575 0 035684 0 038127 0 043154 0 042754 0 041860 0 042541 0 038472 0 033779 0 036074 0 037009 0 03 45 0 037364 0 036517 0 034069 0 036697 0 038398 0 042368 0 038337 0 028241 0 039427 0 040902 0 037464 0 040256 0
19. 2 790E 7 f T T Tr 1 19 37 55 73 June 1 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 T T T r 91 109 127 145 The Fast Tile Plot and Areal Interpolation Plot use the BIN format for all maps and GIS layers A shape2bin program that runs on Linux and Windows platforms is provided with the VERDI distribution to allow you to convert new map shapefiles to the BIN format for these plots The shape2bin tool requires an unprojected shapefile as input For example if you try to convert a shapefile in a Lambert projection you will get an error Linux Mac e Extract the shape2bin zip that is located under VERDI_LHOME VERDI_1 5 directory using unzip shape2bin zip e cd shape2bin e Several Linux binary executables are provided with the code under the bin directory A makeit script is provided that documents the compiler flags and options used to build the executables UNC Chapel Hill 82 Institute for the Environment User s Manual for VERDI 1 5 e Edit the runit script to specify DATA_DIR as the directory where your shapefiles are located Run the script using the syntax runit The bin files will be written to the directory containing the shapefiles e After the script has run copy the new bin file from the DATA_DIR directory to the bin map directory VERDI_HOME Verdi_1 5 plugins bootstrap data VERDI looks in this location for bin formatted files Several shapefiles and their converted bin files are
20. 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 01 0E 2 11 2 2 Save Configuration If you have made changes to the configuration of a plot and want to reuse that configuration for other plots use the Save Configuration selection from the Configure menu It is very important 1 to name the file in a manner that you will remember what it contains and 2 to save the file in a logical place so you will be able to find it when you need it The file name should indicate the formula name the dataset and the type of plot from which it was saved Also use the cfg extension to indicate that it is a configuration file An example file name is lt FormulaName gt _ lt DatasetFilename gt _ lt PlotType gt cfg or O3_CCTM_ base tile cfg You may decide to keep your configuration files with projects to which they relate or in a common directory If you put them into a directory a convenient place may be under the USER_HOME verdi directory For example in Windows you already have a Users username verdi directory Add a config_files subdirectory and save your configuration files there In a Linux based system create the verdi config_files directory UNC Chapel Hill 66 Institute for the Environment User s Manual for VERDI 1 5 When you choose to save your configuration VERDI displays a popup box asking if you want to save the title subtitles When VERDI displays a file chooser navigate to your directory and enter the
21. 36E 02 6 79E 03 3 39E 03 3 52E 03 7 05E 03 1 06E 02 1 41E 02 1 76E 02 2 11E 02 2 47E 02 2 82E 02 3 17E 02 3 52E 02 3 88E4 NO2 1 ppmV August 01 2006 00 00 00 UTC Layer 1 NO2 1 03 1 Figure 10 18 Scatter Plot Dialog Box Select Formulas for Axes NO 1 X Axis NO2 1 NO 1 iatt Y Axis 03 1 UNC Chapel Hill 58 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 19 Scatter Plot Export Data into a CSV file File Configure Controls Time Step C 10 08 01 2006 00 00 00 Layer 1 8 Scatter Plot 1 CCTM_D502addm_Linux2_x86_64intel ACONC CMAQ BENCHMARK_20060801 3 73E 02 G wacaeaas E A czeaceceasene Liss 3 39E 02 3 05E 02 Layers 271602 C a Current layer 1 C AIl layers Time steps 2 37E 02 Cas Pees ae Current time step 1 Q AIl time E 2 047 02 LSA x fa OK Cancel 03 1 ppmV 1 70E 02 e po 1 36E 02 1 02E 02 3 39E 03 presses eee ee eee sobs ee ee eee eee 3 52E 03 7 05E 03 1 06E 02 1 41E 02 1 76E 02 2 11E 02 2 47E 02 2 82E 02 3 17E 02 3 52E 02 3 88E1 NO2 1 ppmV August 01 2006 00 00 00 UTC Layer 1 NO2 1 03 1 10 7 Contour Plot The contour plot shows a three dimensional 3 D representation of values over a geographic area Figure 10 20 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
22. 5 06 01 2002 04 00 00 4 235E 2 Max 25 06 02 2002 00 00 00 1 r 1 r r 1 7 540E 6 Layers 1 3 1 25 49 73 97 121 145 s Layer Range June 4 2002 00 00 00 UTC wine 21 gt Min 95 55 9 082E 3 Max 54 48 8 147E 2 Max 3 Domain Datasets Formulas I Areas 9 3 Specify Domain Range Datasets contain data for cells over a particular geographic area The VERDI program refers to this area as a domain By default the entire domain contained in a dataset is used in creating plots Use the Edit Domain dialog box to select a subset of this domain for plotting To access the Edit Domain dialog box first use the vertical slide bar to bring the Domain panel located below the Layers panel into view if it is not already visible Figure 9 3 To select a subset of the domain press the Edit button The Edit Domain dialog box then appears Figure 9 4 If the area of interest is large background data such as state and county outlines will be shown on the map The magnifying glass buttons above the map can be used to zoom in and out UNC Chapel Hill 40 Institute for the Environment User s Manual for VERDI 1 5 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 the selected
23. 5 data model gtype tile imageDir LOCAL_ DIR verdi_1 5 data images saveImage jpeg lt Global gt lt Task gt f CCTM46_ P16 base02a 36k O3MAX imageFile CCTM46_ P16 base02a 36k O3MAX tstepmax layerl s max 03 1 lt Task gt Figure 17 11 Fast Tile Plot of Maximum Air Temperature aggregated over 25 time steps Layer 1 max O3 1 1 21 41 61 81 101 121 141 June 1 2002 00 00 00 UTC Min 99 51 0 022 Max 123 50 0 101 17 2 2 Batch Script Example Minimum Ozone layer 1 Figure 17 12 lt Global gt dir LOCAL_DIR verdi_1 5 data model UNC Chapel Hill 107 Institute for the Environment User s Manual for VERDI 1 5 gtype tile imageDir LOCAL_ DIR verdi_1 5 data images saveImage jpeg lt Global gt lt Task gt f CCTM46_ P16 base02a 36k O3MAX imageFile CCTM46_P16 base02a 36k O3MAX tstepmin layerl s min 03 1 lt Task gt Figure 17 12 Fast Tile Plot of Minimum Ozone aggregated over 25 time steps Layer 1 min O3 1 5 888E 2 5 152E 2 4 416E 2 3 680E 2 ppm 2 944E 2 2 208E 2 1 472E 2 7 361E 3 2 790E 7 T T T T T T T 1 21 41 61 81 101 121 141 June 1 2002 00 00 00 UTC Min 89 19 2 790E 7 Max 19 46 5 452E 2 17 2 3 Batch Script Example Mean of Ozone layer 1 Figure 17 13 lt Global gt dir LOCAL DIR verdi_1 5 data model gtype tile imageDir LOCAL_ DIR verdi_1 5 data images saveImage jpeg UNC Cha
24. Data in Spreadsheet Format cee eeeeeeeereeeee 52 10 2 4 Export Areal Plot Data to Shapefiles ssnssenssesssnsessseessesssessseeessseesseessresseesseee 53 10 3 Vertical Cross Section Plot cisistscscievseveass iassaccvasavasgisdsea deg spoeades e a 54 VO AS Time Series POE sisccsccaszsivs vaceaavestesecaventesashaeadaeayenastasygtedeatancswaeed suck yon aee En eti ko TESES 56 10 5 Time Series Bar Plots sisi wn jaicsconsncisdessgaaasureaiavesgscets seasadsalassaectounead euuscpaatasiatac D a 56 LO O35 CaMlet FOE s cares asc enn a a Mott niles gion a E A oa tineatangeetetoons 57 LOTA OE PLD AEEA A EP EET AEE E E EE E E E E EE 59 Pl t Menu Bar essers rsersessseasecseecoseeesien reesei ee sao taoen SEACE Eso ree SEET oia 62 DING AVEC dieen a E E e a 62 T1 2 Configure Ment shr e SE ATE AT AE E a IE a ATE 62 2i CONF BUTS Ploterinesorinen a e a E kt cts E 63 112 2 Sav COMM Sur aun a sne n i a a a E a A R iaa 66 11 2 3 Load COMM SULA ON sse i eea aaie E e E E 67 Mo COO NAG HU a a E A O EE ESA 67 113 ZooM n e a E a aa E a aeS 67 TI 3 2 Proben ious a A R a a a aE es 68 1133 21 Probe at a Single POM sisissdiccsessieacicrgeaeas arunesas nna nu aa aadsiaes 68 11 3 2 2 Probing a Domain Region of Data cee ceesceceencecesececeeececeeeeeceteeeenteeeesaes 69 INS S23 el Row and Colimn Rafes eesin in tiem a gates coauete tac 70 Ke3 4A Sbow Gnd IMSS oe saci st ie ctasn stidas a get teneectusies atone tetetiat SASS 12 11 3 5 Show
25. Example Are a File 2 45 ts stot es cata argent conrad a day titu ns weds adnan dash ws ecoad N Ea deai 34 8 3 Adding and Removing an Area File cia sede esse case tueeadies anges tenes ad ase anieadaennasieteoes 34 GFE JATCAS Li Steer e a a a E OES ESES 35 Sid Areal Interpolation s sinnn ies E AR E R A a R as 35 9 Subsetting Spatial and Temporal Data cccsccssssscssssccsssccssssccssssssssssssssssssssssscssssscees 39 Mh Eeo ea DUCESE FR Ne sce E E T RE 39 9 2 Specily Layer Ram ge ionuteniann chs a a aE E N A a aaa 40 9 3 Specify Domain Rahic resunenieeni ie nn a e e a a a RS 40 UNC Chapel Hill iii Institute for the Environment 10 11 User s Manual for VERDI 1 5 9 4 Rules of Precedence for Subsetting Data j iccc scesasecssassavsdactasssscaessadecatecesactoanedeataneceanie 42 Creating PUG GG ic saacas ces sacescs et cea stawe seose a aa dca ences ee tease td ee 44 POA PASC PATS PIO aA SEEE E E E E dean E E E E 44 10 1 1 Time Selection and Animation Controls sssesesseeesseessesssessseressseesseesseesseesseee 45 As TD bayer Sel CC UOR senetan a aa E SA 45 10 1 3 Grid Cell Time Aggregate Statistics sssessseseseseesseessetssessseresseeessressresseesseee 46 10 2 Areal Interpolation Plot gases sces acs innn e e T E 47 102 1 Options Menu menu a n A A RG R 47 10 2 2 Areal Values for Polygon Segment ssesesesssessssseesseessersseesseresseeessressresseesseee 51 10 2 3 View and Export Areal Plot
26. For example if three plots were selected the animated plots would be saved as UNC Chapel Hill 18 Institute for the Environment User s Manual for VERDI 1 5 lt filename gt 1 gif lt filename gt 2 gif lt filename gt 3 gif You can view the animated GIF by opening the file in a web browser Creating a QuickTime movie is also an option but this is not done through the Plots 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 Figure 5 2 Animate Plots Dialog and Fast Tile Plots eC SX WieW File Configure Controls Plot GIS Layers 4 Animate Plots _ Time Step 14 gt 06 01 2002 13 00 00 Layer 15 Stats None Select Plots ee aeara Layer 1 03 1 7 O3 1 06 01 2002 00 00 00 06 02 2002 00 00 00 24 Steps 1 ECCTM46_P16 baseO2a 36k O3MAX 1 008E 1 8 822E 2 7 562E 2 Starting Time Step 0 06 01 2002 00 00 00 6 302E 2 Ending Time Step 24 06 02 2002 00 00 00 5 041E 2 Make Animated GIF s 3 781E 2 2 521E 2 1 260E 2 z 2 790E 7 File Configure Controls Plot GIS Layers 1 37 73 409 145 Time Step 14 06 01 2002 13 00 00 Layer 1 4 Stats None June 1 2002 14 00 00 UTC Min 40 86 4 975E 3 Max 20 46 6 426E 2 Layer 1 NO2 1 Layer 1 NO 1 1 ECCTM46_P16 baseO2a 36k O3MAX 0 020 CCTM46_P16 base02a 36k 03MAX 97
27. Latitude and Longitude aig aly oon te wine ada dn ledge Se Sade Mas ease cndaiae three 73 Te AS Plot Memi Options iienaa T O E A S 74 AE Time Seres FNS scat rs Sacco ep vad Sane ga loch eae Was oan coeds 75 DD Permian Au e OIEA E EE nse cesses ace easy ous nea deeuds tecacsanenaeea ease aah A 75 WB PG OV CTI AVS 52 lenn ta adlad sah eeaet a cath git iS hase ei sh Saleen Sek a cat de 76 11 4 3 1 Observational Data Overlays ocssccesiccsissatsaacasecsesesd yiausesabeevscessesaseenccegcedoeasees 76 UNC Chapel Hill iv Institute for the Environment User s Manual for VERDI 1 5 17 4 3 27 Vector OVerlay sissies nnne niian eiei E A aa EE 79 IIS GIS TSA CS tea nane o a a a e n a aaa 81 115 t Add Map LACES A e A T a S O EO A E 81 iih5 2 Conli gure GIS Laye Sinia a E let aha A E N E 83 12 Supported Grid and Coordinate Systems Map Projections sesseesesssesoosseesossoossossseeo 85 IVO API formatted Data csie a a E A E ERES 85 122 CAMX Gndded Data tired saarcattet tiated cits eects n l a etnias aris a an 89 13 T O API Utilities Data Conversion Programs and Libraries seeessocssocsssecssocesocesooseose 92 14 Contributing to VERDI Development essesessocsssesssecesecesooesoocssseessccesocesoosssocsssecssocesocessosssse 93 15 MO WAT BOS visidseacisindesicanecavcieincandescsunethtiuiesacacisausesincascoauacentsduntacoeasesvecieixeacceauspetiaanenstiausenathes 94 16 Mathematical Pun Choi ic iessessedsscsvssiessssecessessevsoseussoceven
28. Manual for VERDI 1 5 9 2 Specify Layer Range Information on the range of vertical model layers included in a dataset is displayed in the Layers panel Figure 9 2 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 matches the subset of layers specified when the Use Layer Range box is checked Subsetting a dataset s or formula s layer range affects plots produced with those data Section 9 4 describes the precedence rules Figure 9 2 Edit Layer Range in Formula Pane j VERDI Te elaka File Plots Window Help r g Ea Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula O3 1 MES o oes Datasets File Configure Controls Plot GIS Layers HEE z 1 CCTM46_P16 baseO2a 36k O3MAX eae a ars Stats fone m gt Erik Layer 2 O3 1 1FCCTM46_P16 base02a 36k 03MAX 100 4 9 871E 2 Variables 8 637E 2 Double diick to add the variable as a formula 7 403E 2 6 170E 2 03 ppmv 1 ppm 4 936E 2 Time Steps 1 25 3 702E 2 F Use Time Range 28 2 468E 2 Min
29. N a e SIS pisser SurrogateToolUserGuide v3 6_files 1389 3206 723523436829 1596897 2 4 9798403 Se a UAE 2222 2ies 7eo7soio77s05 902749 25 132026 ve P ia _eess ssesisozeoos 53895 fs oso06t My Documents JAGR Updaters 2225 3373 2908771270318 1293966 2 3 835917 E dryox shp 1404 2276 128379094424 963203 0 4 2317605 g 3 DRYOX_N1 DRYOX_N3 shp 1417 3355 0225950614754 15148614 4 5152044 gt E dryox_tot shp 1424 6172 757287822339 2985992 2 4 837372 My Computer 1440 4378 35502573675 2168069 5 44 9517903 1473 2334 434805271438 1042260 25 4 464722 e L D ile name Save My Network iepa Places Files of type Shape Files shp Pe Cancel 10 3 Vertical Cross Section Plot The vertical cross section plot allows you to show a slice of data Figure 10 13 A popup dialog box Figure 10 14 prompts you for information needed to create the plot 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 which also changes the date and time shown in the bottom of 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 and changes as you change the spinner control UNC Chapel Hill 54 Institute for the Environment
30. User s Manual for VERDI 1 5 Figure 10 13 Vertical Cross Section Plot O3 1 vertical Cross Section File Configure Controls Plot Time Step 28 18 5 16 4 145 12 4 10 4 Layer 1 UNC Chapel Hill 11 21 O3 1 vertical Cross Section 06 30 2006 20 00 00 Row he 03 1 Row 1 1 CCTM47_36k CONC ncf 8 0000E 2 7 0000E 2 6 0000E 2 5 0000E 2 4 0001E 2 3 0001E 2 2 0001E 2 1 0001E 2 31 41 51 61 71 81 91 101 111 121 131 141 Domain Column 1 2890E 6 June 30 2006 20 00 00 UTC Min 0 019 Max 0 07 Figure 10 14 Vertical Cross Section Dialog Box Select Cross Section X Axis Cross Sect Column Y Axis Cross Sect Row 1k _oK_ cones _ 55 Institute for the Environment User s Manual for VERDI 1 5 10 4 Time Series Plot The time series plot shows a line graph with the average values over time Figure 10 15 The plot is made for the formula s selected domain layer range and time step range Each time step s data are averaged linearly to produce that time step s data point The current layer can be changed using the Layer spinner control above the plot The layer value listed in the title is updated when you change the layer Figure 10 15 Time Series Plot File Configure Controls Layer i Layer 1 O3 1 1 CCTM46_P16 base02a 36k 03MAX 0 045 0 044 0 043 0 042 4
31. 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 affects plots produced with those data Section 9 4 describes the precedence rules Figure 9 3 Move the Domain Panel into View oe a File Plots Window Help mE jE Selected Formula 03 1 Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Tie osig el tells Eile Configure Controls Plot GIS Layers Stats None TimeStep 11 06 01 2002 00 00 00 Layer Layer 2 O3 1 1 ECCTM46_P16 baseO2a 36k 03MAX Variables Double click to add the variable as a formula 100 4 9 871E 2 8 637E 2 7 403E 2 Min V Use Layer Range 24 UNC Chapel Hill Time Steps 1 25 E Use Time Range 64 _ 6170E 2 Min 514 06 01 2002 04 00 00 E 4936E 2 Max 25 06 02 2002 00 00 00 37 3 702E 2 Layers 1 3 T T T T T T T 1 25 49 73 97 121 145 June 1 2002 00 00 00 UTC Min 95 55 9 082E 3 Max 54 48 8 147E 2 41 2 468E 2 1 235E 2 7 540E 6 Institute for the Environment User s Manual for VERDI 1 5 Figure 9 4 Edit Domain Dialog Box LI x A e amp Sele
32. 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 UNC Chapel Hill 29 Institute for the Environment User s Manual for VERDI 1 5 panels that you see in Figure 6 8 are discussed in Chapter 9 Spatial and Temporal Data Subsetting 6 7 Domain Panel The domain panel contains an Edit button and a Metadata button Detailed instructions for using the Edit button are provided in Chapter 9 Spatial and Temporal Data Subsetting To display the metadata information about a dataset click on the Metadata button in the Domain panel A window containing the metadata will appear Figure 6 9 Each dataset includes metadata information that is part of the file header The metadata provided include the map projection information the number of time steps in the file the number of columns and rows and other information Figure 6 9 Dataset Metadata Information a E Sa File Plots Window Help r g E Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula 03 1 Datasets a S Dataset Metadata Name LambertConformal Parameters origin 40 0N 97 0W parallels 33 0 45 0 L Dataset Dimensions Variables TSTEP UNLIMITED 25 currently Double click to add the variable as a formula DA
33. be undocked or externalized so that you can move them into separate floating windows This allows side by side comparisons of plots Note that undocking is performed only on previously created plots each plot is placed within the VERDI main window when it is generated 5 2 2 Animate Tile Plots This option opens an Animate Plots dialog box Figure 5 2 that allows you to select one or more plots select a subset of the time range and create an animated GIF file There is also a separate way to create a QuickTime movie instead of a GIF if desired Within the Animate Plots dialog box you can select plot s to animate by clicking the check box beside each plot name You can choose to animate a single plot or animate multiple plots synchronously To view multiple animated plots synchronously undock the plots see Section 5 2 1 and arrange them so that they are located side by side for visual comparison during the animation Once a plot has been selected you can select the time range by specifying both the starting time step and ending time step of the animation To create an animated GIF check the Make Animated GIF s option in the Animate Plots dialog box In the Save dialog box that appears select the directory in which to store the file and the name to use for the animated GIF then click the save button When saving as an animated GIF when multiple plots are selected each animated plot will be saved to a separate animated GIF file
34. data are not loaded until later when plots are created To view the variables for a particular dataset that has been loaded click on the dataset name in the list to highlight it and the variables will be listed in the panel below Datasets can be removed by highlighting the name of the dataset in the dataset list and pressing the yellow minus button Note that although the dataset will be removed the number that was assigned to that dataset will not be reused by VERDI during the current session unless there had been only one dataset loaded and it was removed in that case the next dataset that is loaded will be labeled number 1 Figure 6 2 Open Dataset File Browser Open Lookin jy model PEE _ BaseCase dat _ CCTM46_P16 baseO2a 36k 03MAX _ grid_pophous_utm ncf __ GRIDCRO2D_2006075_polar_stereographic ncf _ GRIDCRO2D_mercator _ world_NOX_latlon ncf UNC Chapel Hill 23 Institute for the Environment User s Manual for VERDI 1 5 Figure 6 3 Datasets Pane Displaying Information about a Dataset Datasets 1 CCTM46_P 16 baseO 2a 36k O3MAX 2 agg cctm33fx nh3 200 ibase lambert ncf 4 GRIDCRO2D_2006075_polar_stereographic ncf Variables Double click to add the variable as a formula ppmv 2 ppmv 3 ppmv Time Steps 1 25 F Use Time Range Min 1 06 01 2002 00 00 00 Max 25 06 02 2002 00 00 00 Layers 1 3 F Use Layer Range
35. listserv for VERDI related technical support questions and report errors and or requests for enhancement to the m3user UNC Chapel Hill 6 Institute for the Environment User s Manual for VERDI 1 5 forum The m3user forum is supported by the community and also by CMAS to help users resolve issues and identify and fix bugs found in supported software products 1 5 Future VERDI Development As stated in Schwede et al 2007 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 believe may be useful to the modeling community Examples could include user developed readers for additional file formats and modules for additional plot types Users may wish to contribute data analysis routines such as adding the ability to do bilinear interpolation smoothing or to contribute other enhancements to the existing plot types The direction of future development will depend on the resources and the needs of the modeling community If you are interested in contributing code to VERDI please review the information in Chapter 14 Contributing to VERDI Development Schwede D N Collier J Dolph M A Bitz Widing T Howe 2007 A New Tool for Analyzing CMAQ
36. location of your VERDI distribution type run and press the Enter key Figure 18 2 Figure 18 2 Submit run bat from Command Window E Command Prom C Users myUserName WERDI A 5 gt run_ Script commands that can be used for command line scripting listed in alphabetical order are described below Adding support for these script commands in the Script Editor is planned for a future VERDI release alias 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 the verdi subdirectory under your home directory VERDI uses this type of optional file in your home UNC Chapel Hill 113 Institute for the Environment User s Manual for VERDI 1 5 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 U
37. org help faq cfm UNC Chapel Hill 1 Institute for the Environment User s Manual for VERDI 1 5 Use pulldown menu to select VERDI product to view its FAQs 4 To query M3USER listserv for VERDI related technical support questions and answers http lists unc edu read forum m3user To query bugs and submit bug reports questions and or requests http bugz unc edu enter_bug cgi product VERDI If you do not already have a login and password click the Home link for instructions on how to obtain them 1 2 Where to Obtain VERDI You can download the latest version of VERDI from https www cmascenter org verdi see Figure 1 1 When you click on DOWNLOAD to download VERDI you will be sent to the CMAS Model Download Center To download and install VERDI follow the instructions below beginning at step 4 Alternatively you may also begin at the CMAS web site http www cmascenter org and follow the instructions below 1 2 Log in using an existing CMAS account or create a new CMAS account Hover the cursor over the Download Center link on the left hand side of the web site and choose SOFTWARE from the menu that appears Select a model family to download as shown in Figure 1 2 Use the pull down list to select VERDI and then click Submit 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 o
38. s 03 1 17 lt Task gt UNC Chapel Hill 105 Institute for the Environment User s Manual for VERDI 1 5 Figure 17 10 Fast Tile Plot of Ozone at Time step 17 Layer 1 Layer 1 O3 1 17 1 Paik 41 61 81 101 121 141 June 1 2002 16 00 00 UTC Min amp 0 86 0 006 Max 110 29 0 073 17 2 Mathematical function capability in batch script mode This update provides the user the ability to perform mathematical functions in VERDI using the scripting mode For example Find maximum over all time steps at each grid cells The batch script can be used to generate plots for each mathematical function by using the task block to define each function The notation used within the task block is s Formula Variable dataset For example s max 03 1 to plot the Maximum value over all timesteps for each grid cell in the domain s min 03 1 to plot the Minimum value over all timesteps for each grid cell s mean 03 1 to plot the Mean value over all timesteps for each grid cell s sum 03 1 to plot the Sum of the variable over all timesteps for each grid cell The mathematical functions operate over all time steps at each grid cell Examples for the batch script notation and the images produced are provided in the following sections 17 2 1 Batch Script Example Maximum Ozone layer 1 Figure 17 11 lt Global gt UNC Chapel Hill 106 Institute for the Environment User s Manual for VERDI 1 5 dir LOCAL DIR verdi_1
39. specify any parameters that are used to run any other tasks If the same parameters are specified with different values in a subsequent Task block those values will overwrite the values UNC Chapel Hill 100 Institute for the Environment User s Manual for VERDI 1 5 specified in the Global block One Global Block specifies the common parameters shared by all Task blocks and multiple task blocks can be defined to specify the type of batch operations that will be performed e g defining formulas and creating plots Unload all datasets before running a batch script within the Script Editor If any dataset is not unloaded a warning message will pop up Figure 17 5 requesting that you close all datasets before running your batch script Figure 17 5 Close Datasets Warning Message 860 0 Close Datasets G Please close all datasets before running any batch script Eon The multifiles txt sample script that is provided as part of the VERDI 1 5 release demonstrates how to create a tile plot using a mathematical combination of variables An excerpt of that script is shown below lt Task gt dir D verdi dist2 data model f copy 36k O3MAX f CCTM46_P16 baseO2a 36k O3MAX f another 36k O3MAX s O03 1 03 2 03 3 2 gtype tile saveImage jpeg imageDir D werdi dist2 imageFile three_components_36k 03MAX lt Task gt The above task specifies the name of three input files The input files are assigned a number based on the order in
40. the Areal Interpolation Plot Figure 11 2 through Figure 11 5 show the dialog boxes that appear when you select Configure Plot The Configure Plot dialog box contains four tabs Titles Color Map Labels and Other Titles tab Figure 11 2 Use the selections on this tab to edit title text and select the font type size and color for the title and two subtitles of the plot Subtitles may be turned on or off by selecting or deselecting the check box for each subtitle If a check box is not selected the associated text font type and size and color boxes are grayed out However you must provide a title or VERDI will provide its default title for you To blank out the title you must select it and then enter spaces for the name of the title If you deselect the title VERDI will provide its default title for you O Text Enter the desired text directly in the textbox You can enter text for the plot s title and up to two optional subtitles Font Press the Select button to the right of the Font line for the title or subtitle you wish to change Your system s standard Select Font dialog box is then displayed for you Select a font family font style and size press the OK button to return to the Configure Plot tab Color Press the Select button to the right of the Color line for the title or subtitle to edit There are five types of color palettes that you can use to select a color Swatches HSV HSL RGB and CMYK each on its own ta
41. the addition of the Fast Tile Plot Beginning with version VERDI 1 4 memory was more effectively managed As a user opens new Fast Tile plots or other plot types the memory requirements increase As the user then closes the plots the memory is correctly released by VERDI 2 3 Requirements to Run VERDI Remotely VERDI may be used to run on a remote compute server and have the graphics display locally on your desktop machine Unix workstation Mac or PC using the Fast Tile Plot Your computer needs to be configured to run X Windows Typically you will connect to the remote compute server using secure shell SSH If you are using an X Server and wish to generate 3 D plots using Open GL you need to turn on Open GL support within the X Server 2 4 Graphics Requirements Three dimensional contour plots require a graphics card with OpenGL or DirectX capability By default VERDI uses OpenGL for 3D rendering If you would like to use DirectX instead add the line j3d Dj3d rend d3d to the verdi ini file UNC Chapel Hill 8 Institute for the Environment User s Manual for VERDI 1 5 2 5 Display Properties VERDI works best on screen displays that have been set to a high or perhaps the highest screen resolution 1280 x 1024 pixels for Windows XP 1440 x 900 for Mac or 1680 x 1050 for Windows 7 Follow these general instructions to adjust your screen resolution on the following types of computers e Windows XP Right click on your desktop cli
42. verdi_1 5 data e Linux VERDI_HOME verdi_1 5 data These datasets may be used to recreate example plots that are provided in this user guide including a tile plot with observational data overlay in Section 11 4 3 1 and the example datasets for the various dataset projections that VERDI supports including LCC polar stereographic UTM and Mercator The data directory currently contains four subdirectories 1 CAMx contains sample CAMx dataset and camxproj txt file 2 hucRegion contains Hydrologic Unit Code HUC shapefiles for region 3 southeast US 3 Model contains sample WRF and CMAQ I O API datasets 4 Obs contains an ASCII formatted observational dataset Chapter 6 1 and an observational dataset created by airs2m3 converter Chapter 13 6 3 Adding and Removing a Dataset from a Local File System To load a data set from a local file system press the yellow plus button at the top of the Datasets pane A file browser Figure 6 2 allows you to select a dataset for use in VERDI Support for UNC Chapel Hill 22 Institute for the Environment User s Manual for VERDI 1 5 loading data from a remote file system has been added beginning in version 1 4 The use of the yellow plus remote button will be discussed in Section 6 4 After you select a dataset VERDI will load header information and display the available variables time steps layers and domain used by the file in the Datasets pane Figure 6 3 The actual model
43. which they are specified 1 Copy 36k O3MAX 2 CCTM46_P16 baseO2a 36k 0O3MAX 3 another 36k O3MAX s O3 1 03 2 03 3 2 defines a formula that uses variables from the three filenames This formula takes ozone in file 1 and subtracts the ozone in file 2 and adds two times the ozone in file 3 UNC Chapel Hill 101 Institute for the Environment User s Manual for VERDI 1 5 The type of plot is specified as a tile plot by setting the parameter gtype to tile i e gtype tile The image file format is specified by setting the parameter savelmage to jpeg i e saveIlmage jpeg The output directory where the images will be stored is specified by setting the parameter imageDir i e imageDir D verdi dis2 The image file name is specified by setting the parameter imageFile imageFile three_components_36k 03MAX Use the left mouse button to highlight the task that you would like to run and then click Run in the Script Editor window A popup window then appears to indicate the task ran successfully Figure 17 6 In this example the title and subtitle were obtained from the definition in the global block Aspects of the plot defined in the global block are used for multiple tasks and are applied even if only a highlighted task is run Figure 17 6 Highlight Text to Select Task and Click Run lt Global gt configFile data configs o3_10bin cfg dir data model pattern CCTM46 s 03 1 savelmage png imageDir
44. 0 05 2 0 016 73 0 04 61 gt Ol 0 012 age 49 Z a 37 0 008 0 02 25 0 004 0 01 13 iat 0 000 0 00 1 37 73 109 G1 June 1 2002 14 00 00 UTC June 1 2002 14 00 00 UTC A aad aAa a aAA 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 Areas and Formulas Select from the Window pull down menu to bring to the front either the Datasets pane Areas pane or Formulas pane when those panes are docked UNC Chapel Hill 19 Institute for the Environment User s Manual for VERDI 1 5 5 3 2 Script Editor This option appears in the Window menu if you have a script editor window open You can select this menu item instead of pressing the Script Editor tab at the bottom of its pane 5 3 3 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 e g Tile O3 1 Click on a plot entry to bring that plot to the front for viewing Alternatively you can bring a plot to the front by selecting the desired plot tab underneath the plots area of the main window As in the menu entries each plot tab is labeled with the plot type and the formula used 5 4 Help Menu Options The Help pull down menu contains two items that you can use to l
45. 010203 2184 7607501077305 902749 25 4 132028 3040101 6298 539515028009 2538349 5 4 030061 m 40408 3010107 3373 2908771270318 1293966 2 3 835917 39 i 3020102 2276 128379094424 963203 0 4 2317605 37 3020101 3355 0225950614754 1514861 4 4 5152044 3 sits 3020201 6172 757287822339 2985992 2 4 837372 dH 3030002 4378 35502573675 2168069 5 4 9517903 3 3040102 2334 434805271438 1042260 25 4 464722 a 3050101 6084 9079734726265 2718787 2 4 4680824 29 6 082 3040103 3086 777843056976 1519024 9 4 9210696 a 3030003 3734 570705962271 1607924 5 4 3055134 3020103 2532 450120517577 901513 06 3 5598452 25 Iw 3020203 2618 741050173038 976491 75 3 7288597 23 3020104 2928 108448659794 943170 75 3 210922 a n ArealInterpolation Area Information DRYOX_N 1 0 0 19 2 059 17 15 13 0 047 99 104 109 T 114 119 T T 124 129 ArealInterpolation Figure 10 9 Export Spreadsheet mem Area Information DRYOX_N 2 0 0 gt a k Export Shape Fles wane Area km2 DRYOX_N 2 kg DRYOX_N 2 _A kg ha 1315 Se55 875740826468 2433536 5 4 302669 1327 4515 625631 195322 2046187 5 45313487 1309 1903 3636596603767 966721 5 5 0790167 1323 4392 830729537164 2160675 8 4 918641 1339 4105 370007776452 1804585 9 4 395672 1363 1545 727366164398 704919 7 4 56044 1384 5278 531687088094 2507917 2 4 7511644 137
46. 041071 0 03 Tie o1 Tile Probe O3 1 1 1 94 128 22 45 11 3 3 Set Row and Column Ranges The Controls gt Set Row and Column Ranges menu item will bring up a popup window that allows the user to configure the minimum and maximum values used in the columns x axis domain and rows y axis range Figure 11 10 and Figure 11 11 Specify the values and then click the OK button to redraw the plot UNC Chapel Hill 70 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 10 Select Set Row and Column Ranges Tile O3 1 File Configure KE Plot GIS Layers v m 5 Time Step se 1 8 Stats None s JES Slow pune Set Row and Column Ranges 03 1 Show Grid Lines baseO2a 36k 03MAX Show Lat Lon 1 008E 1 97 91 8 822E 2 85 79 7 562E 2 73 67 6 302E 2 61 55 49 5 041E 2 43 37 3 781E 2 31 25 2 521E 2 19 13 1 260E 2 2 790E 7 ee ge ae na eee 1 19 37 55 73 91 103 127 145 June 01 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 UNC Chapel Hill 71 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 11 Enter Row and Column Values File Configure Controls Plot GIS Layers Time Step 1 B 06 01 2002 00 00 00 Layer v Slow 50 6 Stats None gt fo12 elie Layer 2 03 1 1 CCTM46_P16 baseO2a 36k O3MAX 1 008E 1 59 4 58 4 8 822E 2 57 4 56
47. 1 5 Figure 10 4 Areal Interpolation Plot Show Gridded Data File Configure Controls Plot GISLayers Options Time Step 01 01 2001 01 00 00 Layer 1 Slow 50 Layer 1 DRYOX_N 4 4 J BaseCase dat kgfha 6 082 4 070 2 059 0 047 89 94 99 104 109 114 119 124 129 134 January 1 2001 01 00 00 UTC Min 135 15 0 202 Max 94 28 13 249 4realInterpolation UNC Chapel Hill 50 Institute for the Environment File Plots Window Help User s Manual for VERDI 1 5 ir Ea Tile Plot Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot CE eteo Area Files Areas 1389 2222 1413 2225 1404 1417 1424 1440 1473 1486 1469 1468 1443 1461 1448 2232 1526 1491 1505 1545 1537 1485 1508 1569 1553 1502 1531 1601 1AIA R Figure 10 5 Areal Interpolation Plot Show Selected Areas Eel Selected Formula DRYOX_N 4 ie File Configure Controls Plot GISLayers Options Time Step 1 01 01 2001 01 00 00 Layer 12 Layer 1 DRYOX_N 4 4 BaseCase dat L lt Cie C2 _ sow bo 16 139 14 128 12 116 10 105 kg ha 6 082 4 070 2 059 0 047 T T T T T T 89 94 99 104 109 114 119 January 1 2001 01 00 00 UTC Min 135 15 0 202 Max 94 28 13 249 Datasets Formulas
48. 1 Probe at a Single Point To probe a single data point use the mouse to hover the cursor over that grid cell on the plot the coordinates of the grid cell are shown in the lower right hand side of the plot in the format column row Once you click on the grid point of interest the value of the datum at that grid point is displayed in the lower left hand area of VERDI main window Figure 11 8 UNC Chapel Hill 68 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 8 Click on Plot to Probe Data Value Shown in Lower Left of VERDI Latitude Longitude Values Shown in Lower Right File Configure Plot GIS Layers m Zoom lt Time Step ils Stats None gt 0 12 Set Row and Column Ranges 1 03 1 Show Grid Lines baseO2a 36k 03MAX 1 008E 1 97 at 8 822E 2 85 E 7 562E 2 73 67 6 302E 2 61 55 49 5 041E 2 43 37 3 781E 2 31 25 2 521E 2 19 13 1 260E 2 2 790E 7 S re A A S 1 19 37 55 73 91 109 127 145 June 01 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 1 1 85 44 3 387E 2 lt 35 39301N 87 53247W 11 3 2 2 Probing a Domain Region of Data When you have Probe selected you can examine the values of a region of grid cells Use your mouse to draw a rectangle on the plot by clicking on a point on the map dragging the mouse to the opposite corner of your desired rectangle and then release the mouse button VERDI will create a spreadsheet d
49. 1 exceed 0 080 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 03 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 Chapter 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 were discussed in Section 5 1 7 5 Time Step Range Layer Range and Edit Domain Instructions for using the Time Steps Layers and Domain panels that you see in Figure 7 1 Adding Multiple Variables to Formula Editor are discussed in the next section Spatial and Temporal Data Subsetting UNC Chapel
50. 2 1534 467680366486 667539 25 4 3502984 2220 9742 857916457127 3446319 2 3 5372775 1389 3206 723523436829 1596897 2 4 9798403 2222 2184 7607501077305 902749 25 4 132028 1413 6298 539515028009 2538349 5 4 030061 2225 3373 2908771270318 1293966 2 3 835917 1404 2276 128379094424 963203 0 4 2317605 1417 3355 0225950614754 1514861 4 4 5152044 1424 6172 757287822339 2985992 2 4 837372 1440 4378 35502573675 2168069 5 4 9517903 1473 2334 434805271438 1042260 25 4 464722 Area Information DRYOX_N 2 0 0 Figure 10 10 Save in My Recent Documents My Documents My Computer i My Network Places 10 2 4 Export Areal Plot Data to Shapefiles UNC Chapel Hill 53 Name and Save Spreadsheet File name Files of type dryox_N csv Text Files txt csv Institute for the Environment User s Manual for VERDI 1 5 NOTE The capability described in this section has been disabled in VERDI 1 5 due to errors in geolocating data in the shapefile during the export An improved version of this feature should be available in a future VERDI release At the top of the Area Information tab Figure 10 11 the user may select File gt Export Shape Files to export the data to a shapefile In the Save popup window Figure 10 12 input the name in the File Name field and select file type Shapefile shp The data provided in the spreadsheet name field total area average valu
51. 20 00 00 UTC Min 1 1 0 0000 Max 116 24 0 0065 UNC Chapel Hill 91 Institute for the Environment User s Manual for VERDI 1 5 13 I O API Utilities Data Conversion Programs and Libraries As discussed in Section 6 1 routines are available to convert gridded input data to I O API format or new code can be written and contributed to VERDI for use by the community The I O API routines that have been written to convert data into this format are discussed in this section If you are unable to use the available routines to convert your data and have a gridded dataset that VERDI is unable to read please contact VERDI support via m3user listserv unc edu with a description of the dataset The I O API Interface contains an extensive set of utility routines There are example conversion programs to convert data from different data formats into the I O API format The I O API Utilities are command line programs that are easy to script for automating analysis and post processing An example of an I O API Utility that may be useful to VERDI users is m3merge This utility merges selected variables from a set of input files for a specified time period and writes them to a single output file with optional variable renaming in the process Another utility that you may find useful is m3xtract This program allows you to extract a few species from a large file and save them to a smaller file on your local computer so you can explore them using VERDI
52. 22E 2 7 562E 2 6 302E 2 5 041E 2 3 781E 2 2 521E 2 1 260E 2 2 790E 7 1 21 41 61 81 101 121 141 June 01 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 10 1 1 Time Selection and Animation Controls At the top left of the fast tile plot the spin control can be used to change the time step by clicking the up or down arrow Alternatively highlight the value shown for the current time step and type in the desired value press the Enter key Buttons in the top right corner of the plot allow you to use play stop reverse forward and speed options to control the animation of the plot Control the speed of the animation through the text box labeled Slow the default delay is 50 milliseconds between frames If that text box is not visible expand the plot window s width by clicking with the left mouse button on the right edge of the window and dragging to the right Enter a number in the box for the length of the delay and then press the Enter key A larger plot with multiple map layers may require a shorter delay between frames than a small zoomed in plot with few map layers 10 1 2 Layer Selection The Layer displayed for the plot can be controlled by clicking on the up or down arrow for the Layer spin control in the top center of the plot UNC Chapel Hill 45 Institute for the Environment User s Manual for VERDI 1 5 10 1 3 Grid Cell Time Aggregate Statistics The pull down menu
53. 4 55 4 7 562E 2 54 53 6 302E 2 52 4 514 50 4 5 041E 2 49 4 48 X 47 4 3 781E 2 46 4 45 4 2 521E 2 44 4 43 4 42 1 260E 2 414 40 2 790E 7 T T T T T T T T 31 35 99 103 107 111 115 119 123 127 131 June 01 2002 00 00 00 UTC Min 95 55 9 082E 3 Max 97 59 6 356E 2 2 90 O Set Rowand Colump Ranges Rows Columns Cancel 11 3 4 Show Grid Lines Use the Show Grid Lines selection on the Controls menu if you want to have grid lines overlaid on your plot Figure 11 12 shows one reason for wanting grid lines There is a set of grid cells with relatively high ozone values for the selected time step and layer By zooming in on the plot and then showing the grid lines the individual cells can be identified for further analysis NOTE You cannot change your zoom level while the grid lines are showing If you need to zoom in or out uncheck the Show Grid Lines set your zoom level and then check the Show Grid Lines UNC Chapel Hill 72 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 12 Show Grid Lines on a Fast Tile Plot File Configure Controls Plot GIS Layers Time Step 1 06 01 2002 00 00 00 Layer 1 Stats None Layer 1 O3 1 1J CCTM46_P16 baseO2a 36k O3MAX 041E 2 2 521E 2 2 790E 7 35 38 41 44 June 01 2002 00 00 00 UTC Min 43 20 2 454E 2 Max 38 31 7 91 0E 2 11 3 5 Show La
54. 5 Figure 10 16 Time Series Bar Plot File Configure Controls Layer 16 Layer 1 O3 1 1 CCTM46_P16 base02a 36k 03MAX 0 045 0 044 0 043 5 0 042 4 0 041 z 0 040 4 amp 0 0394 0 038 0 037 0 036 0 035 0 034 4 O O O O O O O O O O O O O O O O O O O O O O O O O i i D ov Ov i Ov o ov ov OV OV OV Ov OV ov ov av ov ov ov ov Qa Baa D o o o o a a a e a e G a o a a o a a amp O O O O O O O O O O O O H ang ani H H H Cang e Cang H H H H Cang H Lang ani ia Nd Se fF Ff S amp S fF amp SF f amp amp amp amp BS EEEE G E A amp ff BR E D N ES W W N ES N N ES N N ES N W N N W N N WN N ES N iN ES ES Q Q Q Q Q Q o Q O Q Q Q oO Q Q Q O O O O O O O O O O O O O O O Q QO O O QO O O O O O S N N N Nm N N N N S N N N N N N N N N N N Nm Nm N Nm Q O O O O O O O O O n e m led la e l m mond W N S N O O rN WY A QA Ny 0 0 O rR N U A Wey oO fo fF NUOD Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q o O O O O O O O O O O O O O O O O O O O O O O O Q Q QO Q QO Q Q Q QO O QO Q QO QO QO o O O O O O O O O O O O O O O O O O O O O O Time Step E Avg Value ppmv 10 6 Scatter Plot The scatter plot shows the relationship between two formulas using dots Figure 10 17 Specify the formulas using the d
55. 5 time stepS eee 108 Figure 17 13 Fast Tile Plot of Mean Ozone aggregated over 25 time StepS eeceeeeeeeetees 109 Figure 17 14 Fast Tile Plot of the Sum of Ozone aggregated over 25 time steps eee 110 Figure 18 1 Location of run bat script in WiNdOWS c cccessceceeececeseeeceeeeeceneeeeneeeeneeeenaeeeeaaees 112 Figure 18 2 Submit run bat from Command Window ceseescesseeereeeseeceseeeeeeeeneecnaeeneensees 113 UNC Chapel Hill Vili Institute for the Environment User s Manual for VERDI 1 5 1 Introduction 1 1 Background This manual describes how to use the Visualization Environment for Rich Data Interpretation VERDI VERDI is a flexible and modular Java based visualization software tool that allows users to visualize multivariate gridded environmental datasets created by environmental modeling systems such as the Community Multiscale Air Quality CMAQ modeling system and the Weather Research and Forecasting WRF modeling system These systems produce files of gridded concentration and deposition fields that users need to visualize and compare with observational data both spatially and temporally VERDI can facilitate these types of analyses Initial development of VERDI was done by the Argonne National Laboratory for the U S Environmental Protection Agency EPA and its user community Argonne National Laboratory s work was supported by the EPA through U S Department of Energy contract DE A
56. C02 06CH11357 Further development has been performed by the University of North Carolina Institute for the Environment under U S EPA Contract No EP W 05 045 and EP W 09 023 by Lockheed Corporation under U S EPA contract No 68 W 04 005 and Argonne National Laboratory VERDI is licensed under the GNU General Public License GPL version 3 and the source code is available through verdi sourceforge net Instructions for developers within the community are included in the VERDI Developer Instructions see Section 1 3 VERDI is supported by the Community Modeling and Analysis System CMAS Center under U S EPA Contract No EP W 09 023 The batch script and VERDI Script Editor were developed and documented under U S EPA Contract No EP D 07 102 through an Office of Air Quality Planning and Standards project managed by Kirk Baker The CMAS Center is located within the Institute for the Environment at the University of North Carolina at Chapel Hill This guide describes VERDI version 1 5 released in October 2014 The following are useful web links for obtaining VERDI downloads and support 1 VERDI Visualization Tool web site http www cmascenter org verdi CMAS download page for users of VERDI requires a CMAS account http www cmascenter org download forms step_1 cfm 2 CMAS SourceForge net website for developers of VERDI http sourceforge net projects verdi 3 VERDI Frequently Asked Questions FAQs https www cmascenter
57. Controls pull down menu contains the following options Zoom Probe Set Row and Column Ranges Show Grid Lines and Show Lat Lon 11 3 1 Zoom To zoom in and enlarge a subdomain of the plot select the Zoom option Then use your left mouse button to draw a rectangle around your region of interest on the plot To zoom out click on the map using your right mouse button to bring up the context menu Figure 11 7 Move your cursor over either Zoom Out or Max Zoom Out and press the left mouse button The Zoom Out selection performs a step zoom and the Max Zoom Out selection zooms out to the full extent of the plot UNC Chapel Hill 67 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 7 Right Click on Fast Tile Plot to Zoom Out File Configure Controls Plot GIS Layers Time Step y8 06 01 2002 00 00 00 Layer 1l Stats None a gt lt e gt stow Layer 1 03 1 1 CCTM46_P16 baseO2a 36k O3MAX om 1 008E 1 42 4 404 8 822E 2 38 4 36 4 a 7 562E 2 32 7 30 4 6 302E 2 28 1 26 7 E a4 2 5 041E 2 22 Properties 20 7 Save Image As 3 781E 2 18 Print 16 4 144 Zoom_In 2 521E 2 Zoom_Out 12 Max_Zoom_Out 10 4 1 260E 2 6 4 4 e EIDES 46 51 56 61 66 71 76 81 86 91 June 01 2002 00 00 00 UTC Min 87 22 8 525E 3 Max 47 40 7 914E 2 11 3 2 Probe To determine the data value at a specific point or within a subregion select the Probe option 11 3 2
58. DI s main menu as discussed in Section 5 2 1 The Fast Tile Plot was added in VERDI version 1 1 As of VERDI 1 4 the Tile Plot was removed because its functionality had been replaced by the Fast Tile Plot The Fast Tile Plot has an option Plot gt Add Overlay gt Vectors to create a Fast Tile Plot of a variable with a vector overlay of wind vectors or other vector types The Vector Plot has now been removed because the Fast Tile Plot with vector overlay is superior The functions that are currently enabled for Fast Tile Plots are described in Section 10 1 4 3 Floating the Dataset Formula and Area Panes The Datasets Formulas and Areas panes can each be configured to float to allow you to position them alongside one another To allow a pane to float click the icon at the top of the pane that looks like a rectangle with an angle bracket above the upper right corner You can then click on the pane and move it independently of the VERDI main window This is useful when you are entering a formula in the Formula pane if you have difficulty remembering the variables that are in a loaded dataset Once a pane is disconnected from the frame the icon changes to be a box with an arrow pointing inward with the hover over text tip Connects this panel to the frame Click on the box with the inward arrow to reconnect the panel with the frame This will return the floating pane back to where it was last connected within the main VERDI window UNC C
59. Figure 8 5 Projection Information S Open Area File Coordinates ercator Projection ransverse Mercator Projection UNC Chapel Hill 37 Institute for the Environment User s Manual for VERDI 1 5 Figure 8 6 Additional Data Fields for Selected Projection S Open Area File Coordinates Latitude of Origin False Easting False Northing lt Back Next gt Finish Figure 8 7 Area Name Fields in Current Shapefile huc03 shp UNC Chapel Hill 38 Institute for the Environment User s Manual for VERDI 1 5 9 Subsetting Spatial and Temporal Data Both the Dataset pane and the Formula pane include the three panels discussed in Sections 9 1 through 9 3 Time Steps Layers and Domain respectively Section 9 4 then discusses the precedence rules for subsetting data that determine whether Datasets or Formulas take priority 9 1 Specify Time Step Range The Time Steps panel Figure 9 1 displays the range of time steps included in a dataset 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 initially displays data for
60. Hill 33 Institute for the Environment User s Manual for VERDI 1 5 8 Working with Area Files 8 1 Area File Formats Area files are defined in VERDI as shapefiles that contain area features such as watersheds and counties or any other shapefile that consists of a set of closed polygons The shapefile format ESRI 1998 consists of four files 1 The shp file contains the actual shape vertices 2 The shx file contains the index data pointing to the structures in the shp file 3 The dbf file contains the attributes e g gridded concentrations 4 The prj file contains the map projection information used for the gridded concentrations 8 2 Example Area File Shapefiles that contain closed polygons are used by VERDI to interpolate gridded data to geographic boundary regions to create Areal Interpolation Plots Shapefiles containing state county or census block for example or any other shapefile containing polygon areas may be used in VERDI to calculate and map formulas to the user selected geographic regions An example shapefile containing the 8 digit HUC watershed boundary map for the Southeast HUC 3 is provided in the VERDI release under the VERDI_HOME data HucRegion directory Example on line data archives for these shapefiles include http datagateway nrcs usda gov https www census gov geo maps data index html 8 3 Adding and Removing an Area File To load a shapefile press the yellow plus button at the
61. I 1 4 1 10 16 14 CMAQ 5 0 2 10 07 14 CMAQ 5 0 2 10 03 14 Training Registration Not registered for any upcoming classes Register Now Conference Registration 13th Annual CMAS Conference Oct 27 Oct 29 2014 Your registration is free UNC Chapel Hill COMMUNITY MODELING amp ANALYSIS SYSTEM Coogi custom semen Search HOME ABOUT CMAS NEWSLETTER CONTACT SITEMAP HOME gt DOWNLOAD gt STEP 2 Software Download Step 2 Please select a particular software from the list and provide information about your platform and compiler Select the product you wish to download VERDI 1 5 Please Make a Selection On which types of computers do you run or anticipate running this product Linux PC Other Please Make a Selection Which compilers do you anticipate using GNU Compilers IRIX Fortran 90 Submit Community Modeling and Analysis System CMAS General inquiries about the CMAS Center and questions about the web site should be directed to cmas unc edu For technical questions about software and data please refer to our Help Desk Page Last Modified 06 12 2014 05 04 08 PM 4 Institute for the Environment User s Manual for VERDI 1 5 Figure 1 4 Downloading VERDI from the CMAS Web Site Step 3 Welcome Elizabeth Adams Navigation ee VERDI 1 5 DOWNLOAD CENTER one NC MEETINGS Installation instructions documentation and software for VERDI 1 5 G COMMUNITY e MODELI
62. Modeling Results Visualization Environment for Rich Data Interpretation VERDI Proceedings CMAS 2007 Conference UNC Chapel Hill 7 Institute for the Environment User s Manual for VERDI 1 5 2 Requirements for Using VERDI 2 1 Java Runtime Environment VERDI requires version 7 of the Java Standard Edition Runtime Environment JRE The JRE 7 is provided as part of the VERDI release for 32 and 64 bit Linux and Windows Instructions for how to download JRE 7 are provided in section 3 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 1024 megabytes of RAM while larger datasets may need considerably more If you are using datasets that require either more or less than 1024 MB of memory you can change the default maximum memory setting used by VERDI e On Windows edit the Verdi ini file to specify a different heap size from the default 1024M e On Linux or another Unix platform you can edit verdi sh and replace the 1024 in Xmx1024M with a different value for example Xmx2048M will allow VERDI to access up to 2048MB or 2GB of RAM Note that even slower CPUs can quickly view and animate smaller datasets whereas larger datasets can take longer Initially VERDI s performance was slow when it was used across the network via ssh This problem was addressed in version 1 1 with
63. NG ee amp ANALYSIS SYSTEM October 16 2014 HOME ABOUT CMAS NEWSLETTER CONTACT SITEMAP RESEARCH amp DEVELOPMENT NOTE Save the files that you download into a common directory Download link Right click on link and choose Save Target As COMMUNITY RESOURCES BENMAP File type Documentation View Windows 32 bit Zip File Download Windows 64 bit Zip File Download Gzipped tar archive for Linux 32 bit Download Gzipped tar archive for Linux 64 bit Download User Details Zipped archive of shape2bin Download DMG File for Mac OSX Download You are logged in as Example Data Files lizadams email unc edu p Example Data is provided in the release archive Edit Contact Info Recent Downloads VERDI 1 5 10 16 14 VERDI 1 4 1 10 16 14 CMAQ 5 0 2 10 07 14 Training Registration Not registered for any upcoming classes Register Now Conference Registration 13th Annual CMAS Conference Oct 27 Oct 29 2014 Your registration is free Log Out Community Modeling and Analysis System CMAS General inquiries about the CMAS Center and questions about the web site should be directed to cmas unc edu For technical questions about software and data please refer to our Help Desk Page Last Modified 10 16 201 4 01 56 41 PM 1 3 Where to Obtain VERDI Documentation Documentation is available in several locations described below Each lo
64. P Community Multiscale Air Quality CMAQ Fertilizer Emission Scenario Tool for CMAQ FEST C Input Output Programmers Application Interface I O API e Package for Analysis and Visualization for Environmental PAVE data MM5 Meteorology Coupler MCPL Multimedia Integrated Modeling System MIMS Research Line source dispersion model for near surface releases R LINE Sparse Matrix Operator Kernel Emissions SMOKE System SPATIAL ALLOCATOR VERDI User Details Documentation is also available for the following unsupported Products You are logged in as a Select the unsup ich you desire documentation lizadams email unc edu MM5 Modeling System M Edit Contact Info Recent Downloads VERDI 1 5 10 16 14 VERDI 1 4 1 10 16 14 CMAQ 5 0 2 10 07 14 We have also created a Porting Guide for building different CMAS software components on unsupported environments Training Registration Due to the nature of mode 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 Not registered for any upcoming ness notices when the documentation differs from the available models Register Now If you wish to download any of the CMAS supported models please visit the Software Download page Conference Registration 13th Annual CMAS Conference Oct 27 Oct 29 2014 Your registration is free Log Out Community Mode
65. PM gt multifiles explicitpath txt Wednesday October 22 2014 12 17 PM 5 multifiles txt Wednesday October 22 2014 12 17 PM 03_tileplot_png txt Wednesday October 22 2014 12 17 PM 03_tileplot_png_nosubdomain txt Wednesday October 22 2014 12 17 PM gt vectorplot txt Wednesday October 22 2014 12 17 PM File Format All Files al Cancel Open After you select a script file and click Open in the Open popup window the Script Editor window Figure 17 3 and Figure 17 4 appears in the right hand side of VERDI Use the Script Editor to edit save and run batch scripts within VERDI The Batch Scripting Language used for the VERDI Script Editor is described in the header of the sample text format script files Figure 17 3 UNC Chapel Hill 99 Institute for the Environment User s Manual for VERDI 1 5 Figure 17 3 Top of Sample Script File VERDI_1 5 data scripts file_patterns txt Script Editor olo x FERRET EEE HEE HEHEHE HEE HEH NOTE Batch Scripting Language All parameter value pairs should be inside one of the two blocks lt Global gt or lt Task gt Number of blocks is not limited Only one lt Global gt block is recommended lt Global gt blocks should contains different items if use multiple lt Global gt blocks Parameter values in lt Task gt blocks will override those in lt Global gt Currently supported parameters keys case insensitive configFile configuration file full path f
66. Panel and then click on the User Account icon 3 3 Installation Instructions for computer that that requires a JRE 7 other than what was provided in the distribution 1 Download Java 7 for your platform from http www java com en download manual jsp 2 Follow the installation instructions 3 4 Setting VERDI Preferences The VERDI installation package contains a file called config properties TEMPLATE On Windows this file is copied into the VERDI subdirectory of your USERPROFILE directory e g C Users yourusername verdi and renamed to config properties On Linux this file is copied into the username verdi subdirectory and renamed to config properties Users are encouraged to edit this file to specify default directories for saving files for placing the location of configuration files and for saving project files Contents of config properties TEMPLATE This file should be put in USER_HOME verdi subdirectory Please use double backslash for Windows platform or slash for UNIX like platforms Please uncomment the following lines and modify them to suit your local settings Windows example settings format verdi project home C Users yourusername VERDI_1 5 project verdi config home C Users yourusername VERDI_1 5 config Linux example settings format verdi project home data project verdi config home data configs verdi user home data model verdi dataset home data model v
67. T UNC INSTITUTE FOR THE ENVIRONMENT Visualization Environment for Rich Data Interpretation VERDI 1 5 User s Manual U S EPA Contract No EP W 09 023 Operation of the Center for Community Air Quality Modeling and Analysis CMAS Prepared for Prepared by Date William Benjey and Donna Schwede U S EPA ORD NERL AMD APMB E243 04 USEPA Mailroom Research Triangle Park NC 27711 Liz Adams and Jo Ellen Brandmeyer Institute for the Environment The University of North Carolina at Chapel Hill 100 Europa Drive Suite 490 CB 1105 Chapel Hill NC 27599 1105 October 26 2014 User s Manual for VERDI 1 5 Contents L Tar OCU sates cacieasteassnceeecs dateetecusccis iciweatucenecentad dacesnacbsceneacancetucstebans ccuudssesaiGeunecaesteecetweesbanendens 1 LL Back srounnd iore enean eaea anae A E E easavad OE ceeded La S 1 1 27 Whe reto Obt ain VERDI eer mmer enn enter Me mere ene etme NING one Maes erie Penn ee Senn ere 2 1 3 Where to Obtain VERDI Documentation 0 0 eeececeseeceeeeeceeeeeceeeeeceeeeenaeeeeseeeenaees 5 1 4 Help Desk Support for VERDI saccades teen el E Sina oodles 6 1 5 Future VERDI Development aaa e e e coed a GG alee acca ase eee 7 2 Requirements for Using VERDE oc ssssssissssvavsscassassoasonsdosssecsdesssenevcseaesdeessesvesoesseasdansenavonnvonssen 8 2A Java Runtime Environment e soree n ian re Sate pad T S EOR 8 2 2 Memory and CPU Requirements esseeeeeseeseeseessee
68. TE TIME et LAY 3 NO ppmv 1 Ta NO2 ppmv 1 ee ROW 102 COL 145 Dataset global attributes Time Steps 1 25 5 F Use Time Range IOAPI_VERSION Id ioapi library version 3 0 Min 1 06 01 2002 00 00 00 _ WTVDF 1 Max 25 06 02 2002 00 00 00 o Layers 1 3 T Use Layer Range Min if Max 3 Domain Edit Metadata Datasets Formulas Areas 6 8 Saving Projects As noted in Section 5 1 2 lists of datasets and formulas can be saved as projects using the Save Project option in the File pull down menu on the VERDI main window Refer back to that section for discussion on saving new projects and loading existing projects Note again that the plots created in VERDI are not saved with the project UNC Chapel Hill 30 Institute for the Environment User s Manual for VERDI 1 5 7 Working with Formulas All plots in VERDI are generated from formulas A formula is used to compare or manipulate variables in one or more gridded datasets A formula can be as simple as a single variable from one gridded dataset or it can be an equation that uses variable s from one or more gridded datasets Formulas are used to create visualizations that can assist with model performance evaluations for example or that help in comparing model results with observations 7 1 Adding and Removing a Formula After loading the desired gridded datasets
69. The I O API Related Programs and Examples can be found at the following web site https www cmascenter org ioapi documentation 3 1 html 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 represents the hour 00 01 You may wish to represent that data segment by the ending hour In that case a 1 should be entered here 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 O3_OBS UNC Chapel Hill 92 Institute for the Environment User s Manual for VERDI 1 5 14 Contributing to VERDI Development If you have made an improvement to VERDI s source code or documentation please consider contributing it back to the community You can start by requesting update notifications from VERDI s SourceForge site http sourceforge net projects verdi Instructions on how to set up the Eclipse Development Environment and for running and building VERDI within Eclipse are available on the official VERDI web site https www cmascenter org verdi If you anticipate doin
70. and gridded data file format conventions are currently supported by VERDI NetCDF and I O API files are portable across computing platforms This means that these files can be read regardless of what computer type or operating system you are using There are routines available to convert data to these formats or new code can be written and contributed to VERDI for use by the community Discussion of the I O API conversion programs and how to use them can be found in Chapter 13 I O API Utilities Data Conversion Programs and Libraries If you write a routine for VERDI to read gridded data from other formats please consider contributing your code to the user community using sourceforge net as described in Chapter 14 6 1 2 Observational Data Formats Observational data in ASCII format can be obtained from EPA s Remote Sensing Information Gateway RSIG http badger epa gov rsig To use a consistent set of units for the model data and the observational data you may need to import the ASCII data into an Excel spreadsheet and perform a unit conversion VERDI doesn t allow the user to use an observational variable to create a formula so conversions to different units should be done within an Excel spreadsheet Import the ASCII file that is generated by RSIG into Excel change the units to match the units found in the gridded model data file and then save using a tab delimited ASCII file format The observational data ASCII format re
71. ar sun and triangle to distinguish among multiple observational datasets A circle is the default symbol shape e Select Add Variable and then OK to overlay the observational data on the fast tile plot Figure 11 17 Repeat the above process to add multiple variables To remove the symbols for a variable on an observational data overlay or to reset their size shape or stroke thickness reopen the Observation dialog by using Add Overlay gt Observations select the observational variable you want to adjust and then change its stroke size shape size or symbol You can also remove a variable or move it up or down in the list When you are finished click the OK button The center of the observational data point corresponds to the lat lon value that is provided in the T O API observational data file If observations are collocated they are placed on top of one another If that happens you may want to select different symbols or sizes for each dataset and place them from largest on the bottom to smallest on the top UNC Chapel Hill 77 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 16 Fast Tile Plot Observation Dialog eoo Observation Dialog Observation Details ID none 2 Stroke Size a0 038 PPM 2 a _ lly Shape Size 8 Symbol O CIRCLE A Selected Observation Variable s 03 2 CIRCLE stroke 1 size 8 Add Variable Move Up Move Down Remove V
72. ariable v Show symbols legend OK Cancel UNC Chapel Hill 78 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 17 Fast Tile Plot with Observational Data Overlay File Configure Controls Plot GIS Layers Time Step 1 06 01 2002 00 00 00 Layer 1 Stats None A gt Layer 1 03 1 1 CCTM46_P16 base02a 36k O3MAX 2 AQS_overlay_2002 2hr 2002152 ncf OB 3 1 008E 1 is 8 822E 2 85 78 7 562E 2 71 64 6 302E 2 57 50 5 041E 2 43 3g 3 781E 2 29 2 521E 2 22 15 1 260E 2 8 2 790E 7 1 21 41 61 81 101 121 141 June 01 2002 00 00 00 UTC Min 124 45 5 111E 3 Max 54 48 8 010E 2 Symbol O 03 2 11 4 3 2 Vector Overlays Follow these instructions to add a vector overlay to a fast tile plot Typically these are created to show wind speed and direction on a plot of gridded air quality data The length of the calculated vectors is proportional to their magnitude e Create your Fast Tile Plot e If the data for your vectors are not in the same dataset load the correct one and select the formulas that you will need for the vectors e Select the Add Overlay gt Vectors option from the fast tile plot s Plot pull down menu Figure 11 14 UNC Chapel Hill 719 Institute for the Environment User s Manual for VERDI 1 5 e Select the two components of your vector in the Vector Overlay dialog box Figure 11 18 Typically these are the E
73. aries between colors in the legend If you uncheck the Show Tick Labels checkbox the tick labels disappear from the legend You cannot remove the legend entirely at this time in VERDI o Footer This tab is divided into three parts Line One Line Two and Observations Data Legend Lines One and Two are for the first and second lines of footers respectively VERDI automatically creates these lines for you but you can either edit or remove them here You cannot enter text for the Observational Data Legend if you do not have observational data on your plot e Other tab Figure 11 5 You can use the widgets on this tab to enable or disable showing the grid lines and to edit the vector arrow color and the series color UNC Chapel Hill 64 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 2 Configure Plot Titles Tab Figure 11 3 Configure Plot Color Map Tab Figure 11 4 Configure Plot Labels Tab 4 Configure Plot xs Titles Color Map Labels Other Label Ticks v Domain Axis Range Axis Legend Footer Text ppmv Font Dialog plain 12 Select Color i Selec Renter p gt Font Dialog plain 12 Select Show Tick Labels Cow ok cae Tg UNC Chapel Hill 65
74. ast West u and North South v components of the wind Assign the u component to Horizontal and the v component to Vertical e Click the OK button and the vector overlays are displayed on the plot NOTE At this time you cannot control how the vectors are displayed and there is no option to remove the vectors from the plot If you need to make a change you must start again with your Fast Tile Plot Currently vectors are plotted in the center of the grid cell UWIND and VWIND are typically obtained from METCRO3D which are defined at dot points or cell corners Plotting the wind vector at their calculated locations will be added to the Fast Tile Plot in a future release Figure 11 18 Vector Overlay Dialog Box r Vector Overlay Select Components osig Horizontal Component UWIND 9 VWIND 9 B Vertical Component cm An example of an ozone concentration Fast Tile Plot with a wind vector overlay is shown in Figure 11 19 The length of each vector is proportional to its length The direction of the vector is calculated from the direction and magnitudes of its two components This figure illustrates how the wind changes speed and direction in this portion of the modeling domain for layer 1 time step 1 UNC Chapel Hill 80 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 19 Wind Vector Overlay on an Ozone Fast Tile Plot File Configure Controls Plot GIS Layers
75. b When you select a color examples of its use are shown in the Preview portion of the Select Color window Select the OK button to accept the color and return to the Titles tab of the Configure Plot dialog box Color Map tab Figure 11 3 This tab provides many widgets for you to configure your legend colors break points range etc You can select the number of tiles the palette type to be used the color interval the number format and the scale O Number of Tiles Start by selecting the number of tiles Options in some other selections such as the available palettes and break points change as you vary the number of tiles Palette Type Three palette types are available Diverging Qualitative and Sequential Diverging has dark colors at the maximum and minimum of the range and light colors in the middle Qualitative has a mixture of colors Sequential has a dark color on one end typically the maximum with lighter shades of the same color proceeding to the lightest shade at the minimum The color palette that is frequently associated with air quality modeling results is one of the Newton RGB palettes of the Sequential type Reverse The reverse button reverses the order of the colors in the selected palette For example if a sequential palette is used the reverse button changes the color intensities such that the darkest color is at the minimum instead of the maximum of the scale Interval The interval can be set to either Automat
76. bat script using the Windows run command Unfortunately this command does not accept directory names that have a space them such as the Program Files If you would like to enter the script command line options after run bat please move the data directory to C VERDI data or some other similar location Enter the following in the Run command cmd UNC Chapel Hill 112 Institute for the Environment User s Manual for VERDI 1 5 When a command line window opens do the following cd C Program Files WERDI_1 5 run bat f C WWERDI data CCTM46_P16 baseO2a 36k O3MAX s O3 1 gtype tile The other option is to place the script commands within the run bat itself Remove the 1 statement at the end of the run bat that is provided in the distribution and add the script options that you would like to use The following run bat contains script options that will read in the file C VERDI_1 5 data CCTM46_P16 baseO2a 36k O3MAX select O3 1 as the formula and create a fast tile plot The changes that you need to make to the run bat are highlighted in red cd plugins bootstrap SET JAVA jre1 6 0 bin java IJAV 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 VERDL_1 5 data CCTM46_P16 baseO2a 36k O3MAX s O3 1 gtype fasttile Run the run bat script by clicking on Start then entering cmd Navigate to the
77. cation provides links to the available documentation for VERDI which can downloaded and saved to your computer be viewed in your web browser or e The VERDI download page on the CMAS website see 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 documentation for VERDI 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 To go directly to the VERDI 1 5 documentation click on Documentation from the VERDI software http www cmascenter org verdi Figure 1 6 shows the list of documentation that is available for download for VERDI 1 5 UNC Chapel Hill 5 Institute for the Environment User s Manual for VERDI 1 5 Figure 1 5 Getting Documentation on VERDI from the CMAS Web Site COMMUNITY MODELING amp ANALYSIS Welcome Elizabeth Adams October 16 2014 HOME gt HELP gt DOCUMENTATION Model Documentation Documentation Is available for the following CMAS Supported Products Select the Product for which you desire documentation Atmospheric Model Evaluation Tool AMET Environmental Benefits Mapping and Analysis Program BenMA
78. ck on the Settings tab in the popup window and move the slider under the screen resolution section to set the resolution to 1280 x 1024 pixels e Windows 7 Click on the Start button and select Control Panel Select Display then Adjust resolution Use the drop down boxes to select your type of display screen resolution etc e Mac Go to Applications and double click on System Preferences Under Hardware select Displays and then Select 1440 x 900 UNC Chapel Hill 9 Institute for the Environment User s Manual for VERDI 1 5 3 VERDI Installation Instructions This chapter provides instructions for installing VERDI 1 5 on a variety of computer platforms The supporting libraries required by VERDI are included in the installation along with a version of the JRE 7 for your convenience If you already have JRE 7 installed on your computer you will not need to uninstall it and you can choose to use that one VERDI 1 5 is distributed as a zip or gzip file as appropriate for each of the following supported platforms e 32 bit Windows 7 e 64 bit Windows 7 e 32 bit Linux e 64 bit Linux e Mac If you have a different computer system select the distribution for a computer system as close to yours as possible and proceed with the installation Although Java is considered a write once run anywhere computer language that is not necessarily true for graphical software Therefore an appropriate version of some graphics libraries is inclu
79. cognized by VERDI is an ASCII file with tab separated columns where the first four columns are provided in the order shown in and one or more additional columns are arbitrary but must have the header format name units as shown in Figure 6 1 Spreadsheet programs can be used to edit and write the files by choosing ASCII output and tab as the delimiting character instead of comma Data within a column must be complete as empty fields within a column will prevent VERDI from reading the observational UNC Chapel Hill 21 Institute for the Environment User s Manual for VERDI 1 5 data VERDI allows the user to specify an alphanumeric value either numbers and or letters for the fourth column Station ID Figure 6 1 Observational File ASCII Format Timestamp UTC I GITUDE LATITUDE deg STATIO pm25 ug m3 2005 08 26T 1 6875 0 2005 08 26T 7660 0 2005 08 26T 4829 1 z0 2005 08 26T 3485 lt 0 2005 08 26T 6875 0 2005 08 26T 0 2005 08 26T 0 2005 08 26T 0 2005 08 26T 0 7660 4829 3485 6875 0 0 0 0 0 0 0 0 OOO OOOO T CEO SS A a Alternatively users may use a converter such as AIRS2M3 see Chapter 13 to convert ASCII observational data into I O API observational data files 6 2 Example Datasets Several example datasets are provided under the VERDI_HOME data directory For example e Windows VERDI_HOME VERDI 1 5 data e Mac VERDI_HOME
80. config properties file UNC Chapel Hill 26 Institute for the Environment User s Manual for VERDI 1 5 The files are saved on your local machine to facilitate project management To be able to save and then load a project for future use the files need to be saved on the local machine To avoid filling up your local file system regularly inspect the file list in the home or verdi temporary dir directory and manually delete unneeded subset files Remote datasets can be removed from the dataset list in VERDI using the same procedure as for removing local datasets highlight the name of the dataset in the dataset list and press the yellow minus button Note that although the dataset will be removed from the dataset list the number that was assigned to that dataset will not be reused by VERDI during the current session Figure 6 6 Remote Dataset Labeled with Number at End of the Filename Datasets Datasets 1 CCTM46_P16 baseO2a 36k 03MAX 2 CCTM47_cbOShatx_64paf52 aba07 12k CONC 2007131 ncf1 Variables Double click to add the variable as a formula NO ppm 2 NOZ ppmv 2 NOS ppmv 2 03 ppm 2 Time Steps 1 10 C Use Time Range Min 1 05 11 2007 00 00 00 A v Max 10 05 11 2007 09 00 00 Layers 1 34 C Use Layer Range Min 1 Max 341 Domain Datasets UNC Chapel Hill 27 Institute for the Environment
81. ct Region Clear Region y y B ok cancel 9 4 Rules of Precedence for Subsetting Data Use the subsetting feature to combine variables from two or more datasets that originally contained different but overlapping layer time step and domain ranges Select identical subsets of the data available in each dataset such that their time steps layers and domain ranges match Then you can select variables from those datasets to create a formula and plot the data Because both the Dataset pane and the Formula pane have the Time Steps Layers and Domain panels described above precedence rules determine which pane s settings take priority It is important to understand these rules NOTE You must check the appropriate boxes to have your selected ranges take effect e Dataset precedence A subset of data specified in the Dataset pane takes precedence over any subset specified in the Formula pane However VERDI does not change the ranges displayed in the Formula pane when you select a subset on the Datasets pane For example if a dataset has a full time step range of 0 48 and you select a time step range of 2 40 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 you subsequently create a plot the time step range subset you chose in the Dataset pane 2 40 is displayed e Formula ranges If you do not specify a subset for a particular data type time steps layers o
82. ction plot time series plot time series bar plot scatter plot and contour plot All of these are described in this chapter Note that not all datasets are appropriate for all plot types To generate a plot first highlight a formula in the list of formulas you have created in the Formula pane You can also see the selected formula in the top right corner of the main VERDI screen i e to the right of the plot buttons Next generate a plot by clicking on that plot type s button If VERDI needs additional information to generate your chosen plot a dialog box appears to prompt you for that information Each plot contains its own menu bar at the top of its window with options for configuring and exploring that type of plot The menus may include File Configure Controls Plot and GIS Layers The options for each of these menus are described in more detail in Chapter 11 Plot Menu Bar 10 1 Fast Tile Plot The Fast Tile Plot allows the user to display the time steps and vertical layers contained in a gridded dataset and to display grid cell time aggregate statistics An example of the Fast Tile Plot window is shown in Figure 10 1 UNC Chapel Hill 44 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 1 Fast Tile Plot iS File Configure Controls Plot GIS Layers Time Step 1 06 01 2002 00 00 00 Layer 16 Stats None x gt 0 12 Slow 50 Layer 1 O3 1 1 ECCTM46_P16 baseO2a 36k O3MAX 1 008E 1 8 8
83. d else 0 o gt Returns 1 if the left operand is greater than the right operand else 0 o gt Returns if the left operand is greater than or equal to the right operand else 0 o Returns 1 if the left operand is not equal to the right operand else 0 o Returns if the left operand is equal to the right operand else 0 o amp amp Returns 1 if both operands are nonzero else 0 o Il Returns 1 if either operand is nonzero else 0 16 4 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 UNC Chapel Hill 97 Institute for the Environment User s Manual for VERDI 1 5 17 VERDI Batch Script Editor To open the Script Editor use File gt View Script Editor Figure 17 1 Prior running a batch script remove all datasets from the dataset list To remove a dataset click on each dataset in the dataset panel and press the yellow minus button Figure 17 1 File View Script Editor Plots Window Help Open Project Save Project Save Project As View Script Editor An Open popup window will be displayed click on a sample script file in the VERDIL_1 5 data scripts directory Figure 17 2 UNC Chapel Hill 98 Institute for the Environment User s Manual for VERDI 1 5 Figure 17 2 Open Popup Window eoo Open scripts Sl Name Date Modified gt file_patterns txt Wednesday October 22 2014 12 17
84. ded in each of the above VERDI distributions 3 1 Installation Instructions for Linux and Mac Follow these instructions to install VERDI 1 tar xvf verdi_1 5 tar into a location where you would like to install VERDI 2 Edit verdi_1 5 verdi sh Change the path for the VERDI_HOME variable to reflect the location where VERDI was installed e g VERDI_HOME usr local verdi 3 VERDI should now run if you execute the verdi sh executable script e g verdi sh 3 2 Installation Instructions for Windows To install VERDI for Windows unzip the file to a local directory on your Windows 7 computer NOTE You do not need to install VERDI under a Program Files directory or in the root directory on one of your hard disk drives Therefore you should not need Administrator rights to install VERDI 1 5 If your system is under strict control from your Administrator you may be able to unzip the VERDI distribution under your documents directory however you may have problems with a space in your PATH If you are unable to install VERDI on your computer please check to see whether your user account is authorized to install software You may need to request that a user with a computer administrator account install VERDI or provide you with an account that has permission to UNC Chapel Hill 10 Institute for the Environment User s Manual for VERDI 1 5 install software For more information about user account types click Start and select Control
85. e total value are exported to the shapefile A GIS program such as User friendly Desktop Internet GIS uDig http udig refractions net an open source Java program may be used to view the shapefiles generated by VERDI The shapefiles are saved as five separate files that must be kept together as part of the ESRI format shp dbf prj shx and fix There are no units assigned to the data that are saved in the shapefile so it is important for the user to keep a copy of the comma delimited text file or to keep some alternative text file that specifies the units for each data field e e Figure 10 11 Export Shapefile Figure 10 12 Name and Save Shapefile Area Information DRYOX_N 2 0 0 g Export Area Information DRYOX_N 2 0 0 Save in My Documents prana Area km2 DRYOX_N 2 kg DRYOX_N 2 _A kgiha lE N Downloads 1315 5655 875740826468 2433536 5 4 302669 a 4 E My archives 1327 4515 625631195322 2046187 5 4 5313487 pas ib i A My Recent a My Music 1309 1903 3636596603767 966721 5 5 0790167 Documents ila 1323 4392 830729537 164 2160675 8 4 918641 E My Pictures 1339 4105 370007776452 1804585 9 4 395672 lt E My videos 1363 1545 727366164398 704919 7 4 56044 L OneNote Notebooks 1384 5278 531687088094 2507917 2 4 751644 Desktop Raster_Users_Guide 3 6_files 1372 1534 467680366486 667539 25 4 3502984 s E Reports zza
86. e E E a 22 6 3 Adding and Removing a Dataset from a Local File System sesesseeeeseessessseresseressee 22 6 4 Adding and Removing a Dataset from a Remote File System eee eeeeceeeseeeeeteeeeeee 25 6 4 1 Remote File Browser sisiscsccasiacsetaseccsassavenscdesndccedstuasaitesoesvesnanaicevessdetateausdaceesnszeets 25 6 4 2 Adding Additional Remote Hosts eeeececssccecseececsseceeesecessseceeseeeeseeeeneeeees 28 o VAT A SOD 1S E a EE E E E EAE 29 6 0 Time Steps Layers Panels atone a i sade ng dane a A va eee ass 29 6 1 Domain Panelu ts 22ctestes ctaavedccttatspetatesaraiaates ccanceduaubtes E O ES 30 6 8 Savi NAR PrOjeCIS mya E A a E R E aQoeenieas 30 7 Working with Formulas esessseoesssooesssooecssooecesooccesssoosessoocessooecesosocsessooesssooesssosecessseossssoosse 31 7 1 Adding and Removing a Formula sesssessseeseseeesseessesssesesseesssttssrsseesseresseeesseesseesseessees 31 72 Example Portnulas cis an a r oak a AE S 33 7 3 Selecting a Formula for Plotting 260 6G 5a eee Ne ese Se 33 Taks SAV ATA Formula Sanoa sich est cig vad ee vas acdc peg Se ne wasnt ee vente ays 33 7 5 Time Step Range Layer Range and Edit Domain ssessssssssessssssesseresseeessresseesseesseee 33 Working with Area Piles occiicacsccceicsscdigivcescieascsstucasecccosacenesagavesvecevoesoeieavoas conaecpececisencearenvenes 34 Old AreaFil Formats enana vcd deco deli tale nda at da echo oases oda E E A ae ae ers 34 8 2
87. e Environment
88. e 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 18 1 Example Command Line Script for Linux Users Set an environment variable VERDI_HOME by using setenv VERDI_HOME home a_username VERDI_1 5 Where a_username is your username The following script options will read in the file as the first dataset select O3 1 as the formula from dataset 1 and create a tile plot of the O3 1 verdi sh f VERDILHOME data model CCTM46_P16 baseO2a 36k 03MAX s O3 1 gtype tile Example script file Note that quotes as shown highlighted in red may be needed around the entire list of parameters bin csh f 8hO3 Daily Max Plot setenv DIR home training verdi_1 5 data OBS verdi sh f SDIR ACONC 03 8hr dmax f SDIR AQS overlay 2002 07 ncf configFile home training config txt UNC Chapel Hill 111 Institute for the Environment User s Manual for VERDI 1 5 03 1 s 038 2 1000 Note Curren
89. e to Add a Remote Host eoo lizadams killdevil login1 nas01 depts ie cempd public_html cmas verdi vim 146x49 This file should be put in USER_HOME verdi subdirectory B Please use double backslash for windows plat er slash for UNIX like platforms as file Please uncomment the following lines and modify them te suit your local settings Win a verd ver a ver Lin verdi verdi a ver verdi WDT verdi For verdi remote file util ver a ve dows example settings format VerdiApplication java used i install home C Program File di project home cols java di config home initial current file location y I_1 5 0 DI_1 5 0 project n on if null uses user home Program Files VERDI_1 5 0 config ux example settings format see above install home Users lizadams 1 5 0 workspace data project config home ta configs VerdiApplication java used as initial location of datasets di dataset home data model VerdiApplication java used as initial location of VERDI batch scripts script home data scripts Tools java used as VERDI_HOME if environment variable is not set default area file folder TargetFileCard java used as default location of HUC area datasets shucData data hucRegion VERDI to access remote big NetCDF data files DataSetPanel java if exists used as location returned from readRemoteHosts
90. earn more about VERDI When you select VERDI Help Docs the VERDI user s manual is displayed in a VERDI Help window This window is not searchable but it does allow you to navigate via hyperlinks in the Table of Contents and to scroll down and read the user s manual When you select About a popup window that contains the name of the product the version number and the date the software was built is displayed UNC Chapel Hill 20 Institute for the Environment User s Manual for VERDI 1 5 6 Working with Gridded Datasets 6 1 Gridded Input File Formats 6 1 1 Model Formats VERDI currently supports visualizing files in the following file format conventions CMAQ Input Output Applications Programming Interface I O API netCDF WRF netCDF and CAMx UAM IV and ASCII format for observational data VERDI uses version 4 3 22 of the thredds NetCDF java I O library http www unidata ucar edu software netcdf java The CMAQ I O API was designed as a high level interface on top of the netCDF Java library see https www cmascenter org ioapi and http www unidata ucar edu software netcdf for further information The I O API library provides a comprehensive programming interface to files for the air quality model developer and model related tool developer in both FORTRAN and C C I O API files are self describing and include projection information within the gridded dataset See Chapter 12 for additional information on what projections
91. ee COMMUNITY MODELING amp ANALYSIS SYSTEM ENUEN Search HOME ABOUT CMAS NEWSLETTER CONTACT SITEMAP HOME gt DOWNLOAD gt STEP 1 Software Download Step 1 Please select a software family to download VERDI Periodically check the release notes for each software to find out about patches or bugs associated with each AMET version of the software in the Software Documentation section of the site Join the software listserv services to BENMAP Stay informed about updates releases and news about all CMAS supported software CMAQ COST More information on the software available for download EMF COST FEST C e AMET 1 0 API MCIP MCPL NETCDF PAVE R LINE SMOKE SPATIAL ALLOCATOR SPECIATION TOOL VERDI Use the select menu on the left to select a software family to download Community Modeling and Analysis System CMAS General inquiries about the CMAS Center and questions about the web site should be directed to cmas unc For technical questions about software and data please refer to our Help Desk Page Last Modified 07 07 2014 11 29 22 AM Figure 1 3 Downloading VERDI from the CMAS Web Site Step 2 Welcome Elizabeth Adams October 16 2014 Navigation DOWNLOAD CENTER RESEARCH amp DEVELOPMENT COMMUNITY RESOURCES BENMAP FEST C R LINE SMOKE SPATIAL ALLOCATOR VERDI User Details You are logged in as lizadams email unc edu Edit Contact info Recent Downloads VERD
92. eeesececneceseesseeesneecsaeceaeesseeesaeees 22 Figure 6 2 Open Dataset File Browser essseseesseeeeesesssesressrsnresresseseresrersessessreeseeseeseesseeseeseresreses 23 Figure 6 3 Datasets Pane Displaying Information about a Dataset seeeeeseeeseeeeeseesesresseseresreses 24 Figure 6 4 Available Hosts in the Remote File Access BrOWSsSer esseesesseeseeersrreeresresseseresresss 25 Figure 6 5 Select One or More Variables from Remote Dataset eeeceeceeeseeeeeceseeeeeeeeneees 26 Figure 6 6 Remote Dataset Labeled with Number at End of the Filename 27 Figure 6 7 Edit configure properties File to Add a Remote Host eee eeecesseeeseceseeeeeeeeneees 28 Figure 6 8 Right Click on Variable in Dataset Pane 0 0 ieee eeeeeeeseecseeceseceseeeeneecsaecsseesseeeenee es 29 Figure 6 9 Dataset Metadata Tiina ats On gots 84 2 5s a aces Tate sacees as os Sack canes lah oeantuaen ected aes 30 Figure 7 1 Adding Multiple Variables to Formula Editor cece esseceeeceeeeeeeecesecnseeeseeeeneees 32 Ute eis PAT ASP ANG sores oe alt it ed a ans Shes ME pacar eee has ak oe a lea eh aeai hat Bent 35 Figure 8 2 Open Area Pile Browsetccssc scc dectectacsteteoicuseneedetstees daesacs et Whereas eee 36 Figure 8 3 Open Area Pile Select Name Field 2 4 ofosssscedec ctaeet cst Snes taretaeseeneeuaenty 36 Figure 8 4 Coordinate System sisisi iesiri iiini i s EKE asc ali ASTES AEE EESE 37 Figure 8 5 Projection nformat oesi ea eG eee lee E E 37 Figure 8 6 Add
93. eiesresseserssresesrrestesseserssressesstssresseseresees 8 2 3 Requirements to Run VERDI Remotely esseeeseseeesessessesesssressrsrresresseseresressessresreesersresees 8 24 Graphics Re iremetntSi sig elasin nlr aaa E S a a as aaisan 8 25 Display Properties aeaee a eaa a A A E E AREN 9 3 VERDI Installation Instructions seseesossesossossessossesossossesossossessossesossossesossossessossesossossesessse 10 3 1 Installation Instructions for Linux and Mac cee eeescecssccecseececeeeeecseeeeesseeeenteeeeneeeeaas 10 3 2 Installation Instructions for WInGOWS jicscetivesdestpcerseecss ch hnags aitcaad sa a heis asd head eee 10 3 3 Installation Instructions for computer that that requires a JRE 7 other than what Was provided in the CSM DUO ay44103sacszs boacaysacsaess ghesuanenoandepscuadeaiabtecaaenbooeancabdadavageadtens 11 3 4 Detling VERDI Preferences aenean a da toceadcoayasennt EEE a A R E S 11 4 Starting VERDI and Getting Your Data into VERDI ssesessessesessossesessossoscosoesossossesessos 13 AL Startins VERD Ennet e eh Ae tes tae ea i ae Rae ERE 13 ALI WAndOWS cociescezea2teveedesctiaces neskeri es a eG este teeta 13 4 1 2 Linux and Other Non Windows JRE 7 Supported System Configurations 4 5 ssieccsdssdeceavecvoskivs k p nar E Ea ENEE E o EEE A AAEE SENES 14 AD Main WHdoW sesepan ngenes E E E E oiai et 14 4 3 Floating the Dataset Formula and Area Panes ceecceeseceeeseceeeteeeeeeeeeeeeeeneeeenaeeees 16 5 Nav
94. eoo Manage Layers Manage Layers Users lizadams VERDI_1 5 0 VERDI_1 5 0 plugins bootstrap data map_counties bin Users lizadams VERDI_1 5 0 VERDI_1 5 0 plugins bootstrap data map_states bin Move Up Move Down Remove Layer OK Cancel e To rearrange the order in which the GIS layers are displayed on the plot select a layer in the Manage Layers dialog box and then select Move Up or Move Down Click the OK button 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 e To remove a GIS layer from the plot select that layer in the list and select Remove Layer Then click the OK button to remove it UNC Chapel Hill 84 Institute for the Environment User s Manual for VERDI 1 5 12 Supported Grid and Coordinate Systems Map Projections VERDI makes calls to the netCDF Java library to obtain the grid and coordinate system information about the data directly from the model data input files when the input data files are self describing CMAQ SMOKE WRF netCDF format files 12 1 I O APl formatted Data For I O API files support for Lambert conformal conic LCC map projection Universal Transverse Mercator UTM map projection and polar stereographic map projection was added in VERDI 1 1 and Mercator projection i
95. erdi script home data scripts WDT default area file folder verdi hucData data hucRegion For VERDI to access remote big netCDF data files verdi remote hosts terrae nesc epa gov vortex rtpnc epa gov garnetO0 1 rtpnc epa gov tulip rtpnc epa gov remote file util usr local bin RemoteFileUtility verdi remote ssh usr bin ssh on local machine where VERDI is running Used to hold temporary data file downloaded from a remote machine verdi temporary dir C temp UNC Chapel Hill 11 Institute for the Environment User s Manual for VERDI 1 5 The items in the config properties TEMPLATE file that is installed with VERDI are commented out Uncommented them 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 Here are how the settings are used by VERDI 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 e verdi project home Default location from which to load and save projects e verdi config home Default location from which to load and save plot configuration files e verdi dataset home Default location from which to load datasets e verdi script home Default location from which to load and
96. ertical 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 UNC Chapel Hill 116 Institute for the Environment User s Manual for VERDI 1 5 19 Areal Interpolation Calculations Before calculating the average value for a polygon segment the area for each polygon is calculated using the projection of the grid system loaded The system then calculates the area of overlay between each grid cell and the polygon segment The total contribution of a value concentration deposition rainfall etc from each cell for a given polygon segment is calculated using the following equation TV sum Orci Vic where Orci Area of overlay of cell at row r and column c with segment i Vic value of cell at row r and column c and r and c iterate across the rows and columns of the grid The Average Value is calculated by dividing the total value by the area of the polygon segment AverageVj TV Ai where A Area of the polygon segment i UNC Chapel Hill 117 Institute for the Environment User s Manual for VERDI 1 5 20 Licenses for JAVA Libraries used by VERDI VERDI has been developed using a number of open source Java libraries Table 21 1 contains a list of the jar files or Java libraries that are used by VERDI a link to where each library may be acquired a link to the location where the license
97. file name Press the Save button Although the configuration files generated by VERDI look similar to HTML or XML files they are just text files containing tags compatible with the parser in VERDI You can look at the contents of these files in a plain text editor e g Notepad but be very careful if you decide to change their contents you could make the file unusable 11 2 3 Load Configuration To load a plot configuration file first create a new plot that is of the same type and uses the same formula as that within the configuration file Then select the Load Configuration option from the Configure menu on that plot An Open File Dialog window enables you to navigate to the directory in which you saved the configuration file Select the file you need and press the Open button The plot title if saved color map and other plot configuration features are then applied to the plot Note that it is possible to load a saved configuration file that does not apply to the selected plot VERDI may try to load what it can which may result in something other than what you had expected Therefore before loading a saved plot configuration check carefully to be sure the plot type and formula of the configuration file match those of the new plot You can also load configuration files in batch or command line scripts by setting the parameter configFile e g configFile C User username VERDI_1 5 data configs o3_10bin cfg 11 3 Controls Menu The
98. g software development on VERDI you should contact the members of the VERDI project via m3user listserv unc edu VERDI developers will test contributions to the source code and review the applicable documentation changes for inclusion in future VERDI releases Note that anything you contribute must have the same license as the rest of VERDI i e GPL The m3user listserv can be used to query known errors bugs suggested enhancements or submitted code contributions using the following website http lists unc edu read search forum m3user First check to see if your issue is already listed as a bug or request for enhancement If you do not see a matching entry please submit an email to the listserv m3user listserv unc edu If you are not yet a member use the following web site to join http www cmascenter org help listserves cfm m3user UNC Chapel Hill 93 Institute for the Environment User s Manual for VERDI 1 5 15 Known Bugs As discussed in Section 1 4 you are encouraged to use the VERDI FAQ http www cmascenter org help faq cfm and m3user listserv http lists unc edu read forum m3user for searching questions and answers bug reports and suggestions UNC Chapel Hill 94 Institute for the Environment User s Manual for VERDI 1 5 16 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 c
99. goel decesos seoda a anssi ssoi toirse 95 16 1 Mary PCE OMS ania E E A Gags E E teens 96 1G 2 EENE 01 eI EEEE E A EN EA 96 16 3 Boolean Operator S enii EE E sue a te ae a 97 16 4 Time Step dek saai te coated eden cau i I a R E E N E 97 17 VERDI Batch Script Editor sisissccsscesesasavescscovousvasnavececonsnepuaugavenscorusepecusuasavccsseupecisuncascoesnenweues 98 17 1 Specify hour time step formula in batch script mode ssseeeeseeeesseeesssressereresrerserereses 104 17 2 Mathematical function capability in batch script mode eseseseeeseeeessereeseseresrerserereses 106 17 2 1 Batch Script Example Maximum Ozone layer 1 Figure 17 11 106 17 2 2 Batch Script Example Minimum Ozone layer 1 Figure 17 12 107 17 2 3 Batch Script Example Mean of Ozone layer 1 Figure 17 13 ee 108 17 2 4 Batch Script Example Sum of Ozone layer 1 Figure 17 14 109 18 Command Line Scripting sissies sicies ecescssccosvivwcdscaaceivvensvonssstivoceseucessesacsudessieseessnacevanosaaeunsoeneee 111 18 1 Example Command Line Script for Linux Users 00 e cc eeesceeeceeeesececeeeeeeeeeeeeeteeeeneeees 111 18 2 Example Command Line Script for Windows Users ssessseesseeeesseesseessersserssseesssees 112 19 Areal Interpolation Calculations scissscssssecsecssssadssoxsoscssesscseasoveesssecssendsenusvnasdoissbensesosncenanses 117 20 Licenses for JAVA Libraries used by VERDI ccsssccssssccssscscssccssscccsss
100. gure 12 6 shows the definition for the grid projection parameters for a Lambert conformal conic projection Figure 12 6 Models 3 I O API Map Projection Parameters for Lambert Conformal Conic Projection Lambert Conformal Conk GDTYP 2 P_ALP lt P BET are the two latitudes which determine the projection cone P GAM is the central meridian X_CENT Y_CENT are the lat lon coordinates for the center 0 0 of the Cartesian coordinate system Coordinate units are meters Figure 12 7 shows the values of the camxproj txt after editing it to match the values of the camx diag file Figure 12 5 using the definitions of the Models 3 grid parameters Figure 12 6 Figure 12 8 shows the resulting Fast Tile Plot of the CAMx sample dataset UNC Chapel Hill 90 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 7 Edited Example Projection File camxproj txt f Projection parameters are based on IOAPI For details see www baronams com products ioapi GRIDS html GDTYP 2 P ALP 33 0 P BET 45 0 P GAM 97 0 XCENT 37 0 YCENT 40 0 Figure 12 8 CAMx Example Plot Tile HNO3 1 File Configure Controls Plot GIS Layers Time Step 21 8 04 28 2006 20 00 00 Layer 1 Layer 1 HNO3 1 1 camx example grdO1 lt Stats None A lt 1 gt gt Slow 109 103 97 91 85 79 73 67 61 55 49 43 37 31 25 19 13 1 19 37 55 73 31 109 127 145 April 28 2006
101. hapel Hill 16 Institute for the Environment User s Manual for VERDI 1 5 5 Navigating VERDI s Main Menu Options Figure 5 1 illustrates 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 Areas VERDI Help Docs Save Project Animate Tile Datasets Plots About Save Project As Formulas View Script Editor 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 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 use Note that plots are not saved with a project only datasets and formulas are saved If you wish to save a plot configuration for later use see Section 11 2 2 Loading and Savi
102. ialog box that comes up before the plot is displayed Figure 10 18 The current time step and layer can be adjusted using the spinner controls above the plot The data from a scatter plot may be exported by selecting the File menu option and then selecting Export data If your dataset has more than one layer or time step a popup window see Figure 10 19 allows you to specify whether you want to export the data for the current layer or for all layers and for the current time step or for all time steps Specify the time and layer ranges and then click the OK button A Save popup dialog box appears Navigate to the directory in which you want to save this file and enter a file name with a csv extension The CSV file will be comma delimited and will contain the following columns of data layer time step x axis formula y axis formula You can open this file in Microsoft Excel or another spreadsheet program if your data does not contain too many rows 65 536 or 1 048 576 depending upon Excel version UNC Chapel Hill 57 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 17 Scatter Plot NO2 1 x O3 1 Scatte File Configure Controls Time Step _ 1 5 08 01 2006 00 00 00 Layer 1 Scatter Plot 1 CCTM_DS02addm_Linux2_x86_64intel ACONC CMAQ BENCHMARK_20060801 3 73E 02 3 39E 02 3 0SE 02 2 71E 02 2 37E 02 2 04E 02 a seal baer Sb Be Deere eter Bree pete oper ere E eee 03 1 ppmv 1 70E 02 1
103. ic or Custom The typical setting is Automatic meaning that VERDI calculates the interval break points based on the minimum and maximum values in the dataset Change the interval to Custom if you need to edit the values for Interval Start for each color tile UNC Chapel Hill 63 Institute for the Environment User s Manual for VERDI 1 5 o Number Format 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 for 1 2E a zero in the legend would be printed with the format 0 00E0 for 1 2F the format would be 0 00 Then click the Rebuild button o Scale Select either Linear or Logarithmic The interval start values are automatically adjusted when you change the scale o Min and Max The minimum and the maximum values are computed for the data to be plotted If you set the Interval to Automatic you can change the values for the minimum and maximum Then press the Rebuild button and the Apply button to see your changes both in the legend and on the map You cannot edit the minimum or the maximum value if the Interval is set to Custom Instead directly edit the Interval Start values the Interval Start value for the lowest interval is the same as the minimum value o Rebuild The Rebuild button is either active or inactive i e grayed out depending upon what other widgets are active If you make changes and the Rebuild button is active pre
104. ields associated with each shapefile are appended to the bottom of the Areas list Use the scrollbar on the right side of the Areas pane to view the additional name fields that are available To remove a shapefile click on the name of the shapefile and press the yellow minus button at the top left corner of the Areas pane 8 5 Areal Interpolation When you select the Areal Interpolation Plot your selected formula is remapped over the polygon areas that are listed in the Areas pane To select a subset of the polygon areas and view the average and total values for selected formulas see Section 10 2 Areal Interpolation Plot Figure 8 1 Areas Pane UNC Chapel Hill 35 Institute for the Environment User s Manual for VERDI 1 5 Figure 8 2 Open Area File Browser ff Open Area lefile X Select one or more shapefiles containing areas An example file would be a shapefile containing HUC regions in J hucRegion huc03 shp a File name huco3 shp Network Files of type Shapefiles shp lt Back Next gt Finish lt Back Next gt Finish UNC Chapel Hill 36 Institute for the Environment User s Manual for VERDI 1 5 Figure 8 4 Coordinate System S Open Area File Coordinates Please select the name field and the coordinate projection to use Coordinate System Geographic lat lon
105. igating VERDI s Main Menu Options ssesssesssesssoossoosssossssessoesssoessoosssossssssssesssosssooses 17 SL FleMetOptIonS retine e Eae a re ty ork gee O ASR ESSET G 17 DLL Open Projection aa a a E E E A A n ATA TES 17 Dye Saye PLOje Ch cvsgtpaske Rechte acaaec Saeed a e A acai a e a T i 17 5 1 3 View Script Bator sro sncnunnmnn tina a R acai NDER Aaa 18 52 Plots Menu Optiohisees nerina a E a a e RESEN 18 5 2 1 Undok All Plots nnns cnusisionssantenuanst inni eee 18 UNC Chapel Hill ii Institute for the Environment User s Manual for VERDI 1 5 5 2 2 Animat Tile Plots iias sugssdessuedcnds odctaaends na has haved E aaa aac 18 5 3 Widow Ment OptionSai eei ee Ges aandwueeecy ae aa a aSa 19 5 3 1 Datasets Areas and Formulas enesseesseeseressessseeceresessssessecrsessssessecrsessssessees 19 5 3 2 SCPL EdItO e Fata aaa e shies aae eed ated a a at aie aE EESE EnS 20 5 3 3 Listof PIOUS io earnan T A E sods EA RSE 20 5S4 Help Ment Options rtint e eet e ta ee a Eie e t 20 6 Working with Gridded Datasets ssccccscsssssssssssssssssssssscssscsssssssssossssssssssssssessssesssasersnes 21 6 1 Gridded Input Pile Formats cis jsacinsscveisisssszecassacecessoseaseavagacessoccecenssavantesobenesannecegensdeneds 21 GT Model Formatsion a 21 6 1 2 Observational Data Formats scicisscccedecissscedsssnied ot desedate hussadevansdeetendadad st dayededassncaase 21 6 2 Example DL Alase ts xcejescsumiatevgacriaeatigtocsatde
106. ile 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 75 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 15 Animate Plot Dialog Box e090 Animate Plot Animate Plot Starting Time Step 1 06 01 2002 00 00 00 Ending Time Step 25 gt 06 02 2002 00 00 00 Make Animated GIF Make Movie Start 11 4 3 Add Overlays VERDI supports two types of overlays observations and vectors For both types of overlays you may need to add data from another data file onto that in the underlying plot 11 4 3 1 Observational Data Overlays It is useful to visually compare the results contained in model output datasets with the data points in observational datasets You can do this by creating a Fast Tile Plot of the model output and then overlaying it with observational data points The observational dataset needs to be in a csv or tab delimited format or an I O API observational data format See Chapter 13 for more information about how to convert AIRS observational data into this latter format Sample observational data are provided in the directory VERDI_LHOME data obs so you can create a sample Observational Data Overlay Plot Follow these instructions to create your plot
107. imum value for that cell over the currently selected time steps In other words the maximum value in cells i j k tmin tmax 16 2 Binary Operators Binary operators are not passed a value but operate on the operands to their left and right Typically they 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 return a single number For example UNC Chapel Hill 96 Institute for the Environment User s Manual for VERDI 1 5 o O3 1 2 multiplies each item in the O3 1 array by 2 and returns the result o 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 o 3 2 multiplies 3 by 2 The binary operators o Returns the sum of the operands o Returns the difference of the operands o Returns the product of the operands o Returns the ratio of the operands o Returns the left operand raised to the power of the right operand 16 3 Boolean Operators 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 o lt Returns 1 if the left operand is less than the right operand else 0 o lt Returns if the left operand is less than or equal to the right operan
108. in 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 UNC Chapel Hill 115 Institute for the Environment User s Manual for VERDI 1 5 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 time 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
109. indow Help rm r2 E Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Contour Plot Selected Formula 03 1 Tie 031 eax File Configure Controls Plot GIS Layers Time Step 1 06 01 2002 00 00 00 Layer 1 Stats None gt 0 12 lt I gt Slow 50 Layer 1 O3 1 1 ECCTM46_P16 baseO2a 36k O3MAX 1 008E 1 Variables 8 822E 2 Double click to add the variable as a formula s5 No Pomin a 7 562E 2 l 102 ppmV 1 71 6 302E 2 ppmv 041E 2 Time Steps 1 25 43 E Use Time Range 36 3 781E 2 Min 11 06 01 2002 00 00 00 29 2 521E 2 Max 25 4 06 02 2002 00 00 00 22 1 260E 2 e ayers 1 3 _ Use Layer Range 2 790E 7 T T T T T T 1 21 41 61 81 101 121 141 June 01 2002 00 00 00 UTC Domain Min 124 45 5 111E 3 Max 54 48 8 010E 2 Edit Metadata Datasets Areas Formulas 6 6 Time Steps Layers Panels The range that is available for the dataset is listed in the Time Steps or Layers Panel in parenthesis next to the label for the panel Figure 6 8 shows that the dataset has 25 time steps with the range displayed as Time Steps 1 25 You 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
110. is referenced by the documentation for each library as well as a link to each license The distribution for VERDI contains a sub directory called licenses This directory contains a copy of the licenses for the open source Java libraries used by VERDI Table 20 1 JAVA Libraries used by VERDI List of Java Where to acquire Recreate n Link to license or the Software License for e Libraries software specific license number Software JTS java topology suite http sourceforge net proje http www vividsolutions http www gnu org copyleft less cts jts topo suite com JTS jts_frame htm er html log4j 1 2 13 jar http www unidata ucar ed u software netcdf java http ogging apache org log4j 1 2 license html saf core runtime jar http safr sourceforge net http www eclipse org stp http www eclipse org legal epl cf saf S AFcore html v10 html vecmath jar http java3d dev java net https vecmath dev java n http www gnu org licenses old et licenses gpl 2 0 html geoapi http geoapi sourceforge n http www codeplex com LGPL V2 1 Feb 1999 et GeoAPI license Gt2 http sourceforge net proje http docs codehaus org d http www gnu org licenses gpl cts geotools isplay GEOTDOC 00 So_ 2 1 txt urce License hsqldb http hsqldb org http hsqldb o
111. isplaying the grid values and will place it in the plot area of the VERDI main window as a tabbed window Figure 11 9 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 69 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 9 Spreadsheet Showing Probed Values for Region of Interest File Tile Probe O3 1 1 1 94 128 22 45 A B G D E F G H 1 J K L M N o 94 95 96 97 98 99 100 101 102 103 104 105 106 107 22 0 027580 0 027515 0 029328 0 031373 0 028157 0 027243 0 029888 0 028442 0 030164 0 029929 0 030790 0 030685 0 031342 0 03 23 0 029812 0 027260 0 029667 0 029054 0 025718 0 026896 0 028648 0 028493 0 030602 0 033948 0 031202 0 026896 0 032911 0 03 24 0 029541 0 029570 0 027049 0 027593 0 032845 0 032058 0 031502 0 033304 0 035540 0 033176 0 030438 0 025593 0 033069 0 03 25 0 030236 0 033048 0 031125 0 032960 0 029462 0 037871 0 030889 0 034706 0 032497 0 031717 0 028245 0 026134 0 029724 0 03 26 0 032446 0 036269 0 036327 0 036362 0 029529 0 031679 0 034204 0 035593 0 038735 0 036122 0 031066 0 030512 0 024665 0 03 27 0 030815 0 036870 0 038399 0 038480 0 032431 0 032510 0 037138 0 038358 0 037837 0 036624
112. ithin each file of interest by double clicking on the netCDF filename listed in the middle panel NOTE if the selected file has a format that is not supported by VERDI then the following message will be displayed in the bottom panel Not a valid NetCDF file For supported netCDF files VERDI will provide a list of variables that are available within the file in the bottom panel labeled Select one or more variables To select variables from the list use your mouse to click on a single variable or use either the Shift key with the mouse to select a contiguous list of variables or the Control key with the mouse to select a set of individual variables Once the variables that you would like VERDI to read are highlighted click on the Read button UNC Chapel Hill 25 Institute for the Environment User s Manual for VERDI 1 5 Figure 6 5 Select One or More Variables from Remote Dataset Remote File Access z Remote User lizadams Host emerald Password eeececeee netscr fizadams VERDI verdi_1 31 data model Double click a NetCDF file or directory sf BaseCase dat CCTM46_P 16 base02a 36k ACONC 2002060 1 dave CCTM46_P 16 baseO2a 36k O3MAX GRIDCRO2D_2006075_polar_stereographic ncf GRIDCRO2D_mercator lagg cctmJ3fx nh3 200 ibase lambert ncf cmaq_max803_PHASEsum02 ioapi grid_pophous_utm ncf world_NOX_latlon ncf Select one or more variables mo ALD2 W TOL FORM_PRIMARY ALD2_PRIMARY
113. itional Data Fields for Selected Projection eseeeesseseeseeeseersesrrssrsrrssressrseresreses 38 Figure 8 7 Area Name Fields in Current Shape tiles cu tsee asi eee eeiecs ce eevteeeau eae ans 38 Pieure Specify Time Step Rte niia ansias font a a R T aN a 39 Figure 9 2 Edit Layer Range in Formula Pane eesesessseeseeseessesressereresresstssresreeseesersereseesreseresreses 40 Figure 9 3 Move the Domain Panel into View i245 5n cece keane Se 41 Figure 9 4 Edit Domain Dialog BOX ssssssssessesseseesseseresresseseresresseseresrenstsstssteesetseeserssreseseeesreses 42 Figure 9 5 Error Generated When a Formula Uses Unequal Domains sseeeseeeceseeeeeereesesereeeess 43 Figur 10 1 Fast Tile Plot eteste2csetecedsiets tect iecs soc heileaeet cies ses tee au eee Se En nuE ts E iEn a iS 45 Figs re 10 2 Areal Plot Area Average ssis sisino sensie a istea t 48 UNC Chapel Hill vi Institute for the Environment User s Manual for VERDI 1 5 Figure 10 3 Areal Plot Area Totals ii 2 cninctwknsendideen ni wide duh sade 49 Figure 10 4 Areal Interpolation Plot Show Gridded Data eee esseceseeeeeeeneeesaeeeseeeeeeeeneees 50 Figure 10 5 Areal Interpolation Plot Show Selected Areas e ce eeeeeseceseceeeeeeeecsaecsseeeeeeeeneees 51 Figure 10 6 Areal Values for Polygon Segment scccsseeseccessceconeeecenseecenseeeenteccenteneenseees 52 Figure 10 7 Right Click on Area Plot ic0 1 cco oo cat tied coes ceca cenit ened
114. l Plot Pull down Menu Options ee eesceeceeeseeeseeeeseeeeeeeeaeees 62 Pisure 1 2 Contigure Piot Titles Tab e cee GG RE RES AAA OS 65 Figure 11 3 Configure Plot Color Map Tab viissccndiceien ci ainnandieincelindadenieek 65 Figure 11 4 Configure Plot Labels WaDiis csacccccics swssecesaeagetsstiasaancutagnactquedecaguhedeacseedacteneseaes aeaeave 65 Figure 11 5 Configure Plot Other Tab eeseseesesesesesesesresseseresresstserssresseesrssreeseeseeseesseeseeseresreses 65 Figure 11 6 Example Plot with Selected Tick Marks for Range Axis and Legend 66 Figure 11 7 Right Click on Fast Tile Plot to ZOOM Out sesssseseeseseseesesserssesreesersrserssresseserssreses 68 Figure 11 8 Click on Plot to Probe Data Value Shown in Lower Left of VERDI Latitude Longitude Values Shown in Lower Right cee ceeceeseesseceseceseeeeseeceaeceseenseeeeaeees 69 Figure 11 9 Spreadsheet Showing Probed Values for Region of Interest 0 0 eee eeeeeeeeeeeeees 70 Figure 11 10 Select Set Row and Column Ranges 2 0 0 0 cee cesesseeeneecseeceseeeseeeeneecaecnseenseeeeneees 71 Figure 11 11 Enter Row and Column V ales 3 2 0 g ecient tig ees cea ot iadeatead tel este aia 12 Figure 11 12 Show Grid Lines on a Fast Tile Plot 2 4 234 2 5 ee ee 173 Figure 11 13 Lat Lon Values Shown in Lower Right of VERDL seeseeesesseesesrrssreerssrersesererresss 14 Proure ld Plot Men Opt nS ininig a is dente NE E a e S ETENE 75 Figure 11 15 Animate Plot Dial
115. la contained in the Gridded Dataset uninterpolated Figure 10 4 The Options pull down menu may also be used to display All area segments that are loaded in the area list or to display only the area segments that are selected by highlighting the name field from the area list Figure 10 5 UNC Chapel Hill 47 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 2 Areal Plot Area Average BQ re lnter Sti File Configure Controls Plot GIS Layers Show Area Averages Time Step 01 01 2001 01 00 5 Area Totals Slow Show Grid Selected Areas PRYOX_N 4 All Areas jaseCase dat on 0 89 94 99 104 109 114 119 124 129 134 January 1 2001 01 00 00 UTC Min 135 15 0 202 Max 94 28 13 249 ArealInterpolation UNC Chapel Hill 48 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 3 Areal Plot Area Totals File Configure Controls Plot GISLayers Options Time Step 01 01 2001 01 00 00 Layer Slow Layer 1 DRYOX_N 4 4 BaseCase dat on i 6294901 000 508038 412 4721175 824 3934313 236 a 3147450648 2360588 060 1573725 472 786862884 0 296 89 94 99 104 109 114 119 124 129 134 January 1 2001 01 00 00 UTC Min 135 15 0 202 Max 94 28 13 249 4realInterpolation UNC Chapel Hill 49 Institute for the Environment User s Manual for VERDI
116. ling and Analysis System CMAS General inquiries about the CMAS Center and questions about the web site shouid be directed to cmas unc edu For technical questions about software and data please refer to our Help Desk Page Last Modified 09 16 2014 10 57 41 AM Figure 1 6 VERDI Documentation on the CMAS Web Site COMMUNITY MODELING amp ANA SIS Welcome Elizabeth Adams October 26 2014 HOME ABOUT CMAS NEWSLETTER CONTACT SITEMAP Navigation HELP DESK DOWNLOAD CENTER Model Documentation The following documents are available for VERDI 1 5 HONE gt HELP gt DOCUMENTATION e INSTALL LINUX TXT e INSTALL MAC TXT e INSTALL WIN TXT e RELEASE NOTES TXT e VERDI DEVELOPER INSTRUCTIONS PDF e VERDIUSERMANUAL1 5 HTM e VERDIUSERMANUAL1 5 PDF 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 You are logged in as effort to provide current documentation or notices when the documentation differs from the available models lizadams email unc edu Edit Contact Info If you wish to download any of the CMAS supported models please visit the Software Download page User Details 1 4 Help Desk Support for VERDI You are encouraged to check the VERDI FAQs search the M3USER
117. lled in the directory C myPrograms VERDI_1 5 0 JAVA_DIR needs to point to the directory where your JRE7 is installed In this figure JRE7 is installed in the jre1 7 0 directory under the VERDI_HOME directory If you are using a JRE ina different location on your computer change the path in your run bat file All other locations are specified relative to the VERDI_HOME or the JAVA_DIR so you should not need to change any of those 4 1 2 Linux and Other Non Windows JRE 7 Supported System Configurations To start VERDI from Linux and other non Windows JRE 7 Supported System Configurations find the directory where VERDI was installed then run the verdi sh script On a Mac go to the Applications verdi_1 5 directory and run the verdi command script 4 2 Main Window When VERDI starts it displays its title screen as it loads The main window is then displayed Figure 4 2 The top of the main window contains a menu bar with the main window options File Plots Window and Help Below the menu bar 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 Chapter 5 Navigating VERDI s Main Menu Options To the right of these three shortcut icons are buttons that list all of
118. ly selected The currently selected dataset is usually the most recently added dataset g lt tile fasttile line bar contour gt instructs VERDI to create a plot using the specified type and the currently selected formula s data gtype lt tile fasttile line bar contour gt instructs VERDI to create a plot using the specified type and the currently selected formula s data note tile and fasttile will both generate a fasttile plot starting with VERDI version 1 4 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 be created with three colors that correspond to values of 1 10 10 100 and 100 1000 UNC Chapel Hill 114 Institute for the Environment User s Manual for VERDI 1 5 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 mapName lt pathna
119. me gt lt mapFileName gt causes VERDI to use the supplied map name instead of the default map for tile plots printAlias prints existing alias definitions project lt VERDIProjectName gt save dataset lists and associated formulas as a project for later re use 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 e brings it to the front 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 case 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 doma
120. menu Figure 10 21 In addition the contour plots can be rotated in three dimensions to achieve different viewing angles by using the left mouse button to grab and rotate the plot Figure 10 22 UNC Chapel Hill 59 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 20 Contour Plot Contou0321 10 rrr 2 File Configure Controls Plot Time Step 23 06 01 2002 22 00 00 Layer 0 100 0 095 0 090 0 085 0 080 0 075 0 070 0 065 0 060 0 055 0 050 0 045 0 040 0 035 0 030 0 025 0 020 0 015 0 010 0 005 Figure 10 21 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 UNC Chapel Hill 60 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 22 Rotated Contour Plot File Configure Controls Plot Time Step 23 06 01 2002 22 00 00 Layer 0 1000 0 0975 0 0950 0 0925 0 0900 0 0725 0 0700 0 0675 0 0650 0 0625 0 0600 0 0575 0 0550 0 0450 0 0425 0 0 0175 0 0150 0 0125 0 0100 0 0075 0 0050 UNC Chapel Hill 61 Institute for the Environment User s Manual for VERDI 1 5 11 Plot Menu Bar Each VERDI plot contains its own menu bar that has options specific to that type of plot As an example the menu options at the top of a Fast Tile Plot include those shown in Figure 11 1 Most op
121. n VERDI 1 2 The grid projections listed on the following website are supported although not all have been tested https www cmascenter org ioapi documentation 3 1 html GRIDS html Users that need VERDI to support other projections are encouraged to provide small input datasets as attachments to emails to the m3user listserv or via ftp for testing and to facilitate future development efforts Figure 12 1 through Figure 12 4 illustrate sample plots generated for datasets with LCC polar stereographic Mercator and UTM map projections respectively UNC Chapel Hill 85 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 1 Lambert Conformal Conic Map Projection Example Plot Tile DRY_N 1 File Configure Controls Plot GIS Layers Time Step 1 5 01 01 2001 01 00 00 Layer 1 Stats None a Layer 1 DRY_N 1 1 agg cctmJ3fx nh3 200 1base lambert ncf kg hectare 37 55 January 01 2001 01 00 00 UTC Min 147 1 0 050 Max 93 29 36 122 UNC Chapel Hill 86 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 2 Polar Stereographic Map Projection Example Plot Tile HT 1 File Configure Controls Plot GIS Layers a Time Step 1 03 16 2006 00 00 00 Layer 1 Layer 1 HT 1 127 Stats None A lt 1 gt gt Slow GRIDCRO2D_2006075_polar_stereographic ncf s Ne y z D Fos N
122. n the imageDir directory to load and view the image file in your default visualization software Figure 17 9 illustrates the tile plot image that was generated by running the highlighted text block Figure 17 9 Plot Image Generated by Task Block Layer 1 03 1 03 2 03 3 2 Test SubTitle 1 Test SubTitle 2 ay 2 017E 1 92 1 764E 1 85 ng 1 512E 1 71 64 1 260E 1 57 50 1 008E 1 43 36 7 562E 2 29 5 041E 2 22 15 2 521 2 5 580E 7 1 21 41 61 81 101 121 141 June 1 2002 00 00 00 UTC Min 124 45 1 022E 2 Max 64 48 1 602E 1 17 1 Specify hour time step formula in batch script mode Specify the timestep using the format VARIABLE dataset number timestep UNC Chapel Hill 104 Institute for the Environment User s Manual for VERDI 1 5 The batch script notation used to specify an hour time step involves specifying the formula then the hour O3 1 17 will result in Ozone for hour 17 from a given file in scripting mode see Figure 17 10 The batch script can be used to generate plots of a specific hour or time step using the formula s Variable dataset hour for example s 03 1 17 to plot the Temperature in first dataset for hour 17 Batch Script Example lt Global gt dir LOCAL_ DIR verdi_1 5 data model imageDir LOCAL DIR verdi_1 5 data images saveImage jpeg lt Global gt lt Task gt gtype tile f CCTM46 P16 base02a 36k O3MAX imageFile CCTM46 P16 base02a 36k O3MAX tstep 17
123. nformation tab the user may select File gt Export to export the data to a spreadsheet file Figure 10 9 The save popup window allows the user to specify with either a text txt or comma separated values csv format also known as a comma delimited text file Figure 10 10 UNC Chapel Hill 52 Institute for the Environment User s Manual for VERDI 1 5 Figure 10 7 Right Click on Area Plot Figure 10 8 Area Information Spreadsheet Area Information DRYO gt _NE1 0 0 File Configure Controls Plot GIS Layers Options File Time Step 1 _ 01 01 2001 01 00 00 Layer L lt Lie gt stow 50 a Area Information DRYOX_N 1 0 0 eee Name Area km2 DRYOX_N 1 ka DRYOX_N 1 _A koha E Layer 1 DRYOX_N 2 o1o101 I5655 875740826468 2433536 5 4 302669 a 3010102 4515 625631195322 2046187 5 4 5313487 2 BaseCase dat Properties 16 139 3010202 1903 3636596603767 966721 5 5 0790167 Save Image Asi 3010201 4392 830729537 164 2160675 8 4 918641 3010204 4105 370007776452 1804585 9 4 395672 Printi 3010105 1545 727366164398 704919 7 4 56044 Zoom tn 14 128 3010103 5278 531687088094 2507917 2 4 7511644 Zoom_Out 3010106 1534 467680366486 667539 25 4 3502984 Max_Zoom_Out 3010205 9742 857916457127 3446319 2 3 5372775 45 12 116 3010104 3206 723523436829 1596897 2 4 9798403 ie 3
124. ng Configuration UNC Chapel Hill 17 Institute for the Environment User s Manual for VERDI 1 5 5 1 3 View Script Editor Use the View Script Editor to modify and run batch scripts within VERDI Several sample script files are provided with the VERDI distribution under the VERDI_LHOME data scripts directory Use the Open popup window to specify eps txt which is one of the sample script files The contents of the eps txt will be displayed in the Script Editor in the right side of the VERDI window Modify it to specify the local directory path name for the sample data files the formulas the type of plots and the image format The plots are not rendered within VERDI but may be viewed using an image viewer The batch scripting language is described in the sample script files and will be described in more detail in Chapter 17 VERDI Batch Script Editor 5 2 Plots Menu Options VERDI opens a single pane for plots to the right of the Dataset Formula and Area tabbed pane Each plot is created in its own subwindow and is placed in the plot pane The most recent plot is display on the top 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 subwindow underneath the current plot the selected plot is then displayed on top 5 2 1 Undock All Plots As with the Dataset Formula and Area panes Section 4 3 plot subwindows can
125. og BOX s1i8 toned alicia el A A EE a 76 UNC Chapel Hill vii Institute for the Environment User s Manual for VERDI 1 5 Figure 11 16 Fast Tile Plot Observation Dialog eee eeseeeeceseeeeneecnseceeeeeeeeeneecaecnaeesseeeeneees 78 Figure 11 17 Fast Tile Plot with Observational Data Overlay 000 eee eeeeeeeeeeneeceneceneeeeeeeeneees 79 Figure 11 18 Vector Overlay Dialog BOX ss ssssssesssesssssessseesseesseesseesseresseeesseesseesseesseeesseeessresseesse 80 Figure 11 19 Wind Vector Overlay on an Ozone Fast Tile Plot eseeneeseseeeeeeeeesreerssressrsererresss 81 Fig r 11 20 Add Map ayers lt cse svasites ioacasate aude ccveadangaeaste eiren raro sieno ta ce cemaa ni Tasnia 82 Figure 11 21 shape bin command Usage 260i pode leet del ged teenie ene eel agatieions 83 Figure 11 22 Manage Layers Dialog BOX ics 42 34 aoe cee ek eee ee aha 84 Figure 12 1 Lambert Conformal Conic Map Projection Example Plot eee eeseeeeeeeeeeeeneees 86 Figure 12 2 Polar Stereographic Map Projection Example Plot ee eeeeeeceeeseeceseceseeeeeeeeneees 87 Figure 12 3 Mercator Map Projection Example Plot eccceesccecsseceeeeeeeceeeeeeseeceeseeeeneeeenaeeees 88 Figure 12 4 UTM Map Projection Example Plot 255k aici 8 Socata ol Wes tae Cgensdeta le Seinescadeeaeed aes 89 Figure 12 5 Example CAMx diagnostic text file ecscesseeceseeseccesncesenteccetececesscecoseescetseaeessetes 90 Figure 12 6 Models 3 I O API Map Projection Paramete
126. onsists of a single variable for example O3 1 is the parameter O3 from current dataset 1 Using infix notation you can construct more complicated formulas using the mathematical operators and functions listed below 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 Note that the Batch Script method does not support all of the mathematical functions that are supported within the VERDI GUI and or the command line script options Listed in order of precedence the functions and operators are 1 abs sqr sqrt exp log In sin cos tan sind cosd tand mean sum min max 2 power 3a le 8 Il VERDI also supports the following constants 1 E 2 7182818284590452354 2 PI 3 14159265358979323846 3 NROWS Number ofrows in the formula s currently selected domain 4 NCOLS Number of columns in the formula s currently selected domain 5 NLEVELS Number of levels in the formula s currently selected domain UNC Chapel Hill 95 Institute for the Environment User s Manual for VERDI 1 5 16 1 Unary Functions Unary functions are passed a single argument Depending on the argument and the function type the function returns a single value or a matrix of data by performing the function on each cell of the arguments array For example
127. option labeled Stats provides the option to display grid cell time aggregate Statistics e g per cell minimum maximum mean geometric mean median first quartile third quartile variance standard deviation coefficient of variance range interquartile range sum time step of minimum time step of maximum maximum 8 hour average and hours of noncompliance VERDI calculates the grid cell time aggregate statistics as follows For each cell i j k in the currently selected domain independent of neighboring cells the aggregated statistical value is calculated over the currently selected time steps In other words the aggregated statistical value is calculated for the plotted formula for cells i j k tmin tmax with the number of time steps n where n tmax tmin 1 e MINIMUM min varG j k tmin var i j k tmin 1 var ij k tmax e MAXIMUM max var i j k tmin var i j k tmin 1 var i j k tmax e MEAN SUM n e GEOMETRIC_MEAN var i j k tmin var i j k tmin 1 var i j k tmax 0 e MEDIAN value at 50 percentile of sorted var i j k tmin var i j k tmin 1 var i j k tmax e FIRST_QUARTILE value at 25 percentile of sorted var i j k tmin var i j k tmin 1 var i j k tmax e THIRD QUARTILE value at 715 percentile of sorted var i j k tmin var i j k tmin 1 var i j k tmax e VARIANCE var i j k tmin MEAN var i j k tmin 1 MEAN var i j k tmax MEAN
128. ormation about the projection The projection information is available in separate diagnostic files which are part of the CAMx output along with the UAM binaries Figure 12 5 UNC Chapel Hill 89 Institute for the Environment User s Manual for VERDI 1 5 Figure 12 5 Example CAMx diagnostic text file We We We we we We We We le ae he We ele ae ee ee he CAMx We We ee We ee ee he ee ee ee ee CAM x Simulation start time date 0 060428 06118 Simulation end time date 0 060429 06119 Time zone 0 Max timestep min 15 Met Input interyal min A 60 Emiss Input interval min 60 Output interval min 60 Grid Projection Type LAMBERT LAMBERT center lon lat 37 000 40 000 LAMBERT true latitudes 45 000 33 000 Master Grid X Y Origin 2736 000 2088 000 Master Grid cell size z 36 000 36 000 Master Grid NCOL NROW NLAY 148 112 15 The netCDF java library writes the default projection information to a text file in the directory where the CAMx binary UAM IV file is located You can then review and edit the projection information to make it consistent with the projection specified in the CAMx diagnostic text files The definitions of the projection parameters used in the camxproj txt file are defined using Models 3 I O API format https www cmascenter org ioapi documentation 3 1 html GRIDS html You must edit the camxproj txt file to match the grid description information provided in the corresponding camx diag file Fi
129. pel Hill 108 Institute for the Environment User s Manual for VERDI 1 5 lt Global gt lt Task gt f CCTM46_ P16 base02a 36k O3MAX imageFile CCTM46_ P16 base02a 36k O3MAX tstepmean layerl s mean 03 1 lt Task gt Figure 17 13 Fast Tile Plot of Mean Ozone aggregated over 25 time steps Layer 1 mean O3 1 0 065 0 059 0 052 0 045 ppmy 0 038 0 032 0 025 0 018 0 012 T T T T T T T T 1 21 41 61 81 101 121 141 June 1 2002 00 00 00 UTC Min 96 55 0 012 Max 20 45 0 062 17 2 4 Batch Script Example Sum of Ozone layer 1 Figure 17 14 lt Global gt dir LOCAL_DIR verdi_1 5 data model gtype tile imageDir LOCAL_ DIR verdi_1 5 data images saveImage jpeg lt Global gt lt Task gt f CCTM46 P16 base02a 36k 03MAX UNC Chapel Hill 109 Institute for the Environment User s Manual for VERDI 1 5 imageFile CCTM46 P16 base02a 36k O03MAX tstepsum layerl s sum 03 1 lt Task gt Figure 17 14 Fast Tile Plot of the Sum of Ozone aggregated over 25 time steps Layer 1 sum O3 1 1 632 97 4 iat 1 465 85 4 a 1 297 734 67 ei _ 1130 554 a ve 0 962 43 374 0 794 314 25 4 0 627 19 4 134 0 459 74 1 T T T T T T T T 0 292 1 21 41 61 81 101 121 141 June 1 2002 00 00 00 UTC Min 96 55 0 292 Max 20 45 1 557 UNC Chapel Hill 110 Institute for the Environment User s Manual for VERDI 1 5 18 Command Line Scripting Th
130. provided under the bin map directory Windows e Extract the win_shape2bin zip file provided under the VERDI_LHOME verdi_1 5 directory by double clicking on the file e Copy the two files cygwin1 dll and shape2bin exe to the bin map directory VERDI_HOME plugins bootstrap data e Place the shapefile s that you would like to convert into the bin map directory e Start a command window by pressing the Start button and entering cmd e cd VERDI_HOME plugins bootstrap data e Type the command shape2bin and it will provide the format that you should use to convert a shapefile to a bin file see Figure 11 21 Figure 11 21 shape2bin command usage shape2bin Convert Shapefile shp to map bin file usage shape2bin file shp gt map file bin example shape2bin NCA shp gt map estuaries bin head 4 map estuaries bin Email questions and comments to plessel todd epa gov 11 5 2 Configure GIS Layers To show an additional map on the plot select the Configure GIS Layers option in the GIS Layers menu When you click on this item a dialog box titled Manage Layers gives you the following options Move Up Move Down and Remove Layer Figure 11 22 The Edit Layer option has been removed in VERDI 1 5 A new edit option will be provided in a future release as part of changing from BIN to Shapefile GIS layers UNC Chapel Hill 83 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 22 Manage Layers Dialog Box
131. r s Manual for VERDI 1 5 Figure 11 14 Plot Menu Options Tile O3 1 File Configure Controls M40 GIS Layers Time Series of Probed Cell s Time Step 1 06 03 Time Series Bar of Probed Cell s Time Series of Min Cell s Time Series of Max Cell s Animate Plot 60 Add Overlay b 58 11 4 1 Time Series Plots The Time Series of Probed Cell s and Time Series Bar of Probed Cell s allows the user to select a set of cells and then produce a time series or time series bar plot of the chosen subset of probed cells The Time Series of Min or Max Cell s option creates a time series plot using data for the currently selected formula at that formula s domain layer range and time step range The minimum or maximum value of that formula over the domain and layer range at that time step is calculated by VERDI and used for each of the time step s data points For examples of the Time Series Plot and the Time Series Bar Plot see Figure 10 15 and Figure 10 16 respectively 11 4 2 Animate Plots You can create an animated plot by selecting the Animate Plot option The Time Series and Time Series Bar Plots do not have an Animate Plot option The plots that may be animated include Fast Tile Areal Interpolation Vertical Cross Section and Contour Plot An Animate Plot dialog box Figure 11 15 will appear allowing you to save animations either as an animated GIF with a file extension of gif or as a QuickTime movie with a f
132. r domain in the Dataset pane then any subsetting for that data type in the Formula pane takes effect e New formulas If you create a formula using variables from multiple datasets it is important to use the Formula pane to subset the domain range if needed Do not try to create matching subset domain ranges for multiple datasets using the Dataset pane for each dataset if all of the subsets do not match exactly VERDI will generate an error when you attempt to map a UNC Chapel Hill 42 Institute for the Environment User s Manual for VERDI 1 5 formula using variables from those datasets Figure 9 5 Instead using the Formula pane to specify the subset of the domain to be applied for all dataset variables used in the formula Figure 9 5 Error Generated When a Formula Uses Unequal Domains B zox Gp E ret vert cros sesten time seres rme series tar ot scatter piot vector pi cortou mit E 225 meste 0 Note 03 2 Layer 0 ot 7 ostz ostt LD n Po EEE x 100 05 mo ni5 120 X June 01 2002 00 00 00 UTC Min 123 44 0 005 Max 105 31 0 06 UNC Chapel Hill 43 Institute for the Environment User s Manual for VERDI 1 5 10 Creating Plots After creating a formula you are ready to create and view some plots The available plot types are shown on the buttons at the top of the VERDI main window fast tile plot areal interpolation plot vertical cross se
133. r 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 As shown in Figure 1 4 follow the links to the appropriate version of the Linux Mac or Windows installation files Links are also available for the current version of the documentation and the shape2bin utility UNC Chapel Hill 2 Institute for the Environment Welcome Elizabeth Adams October 16 2014 User Details You are logged in as lizadams emall unc edu Edit Contact Info Recent Downloads VERDI 1 5 10 16 14 VERDI 1 4 1 10 16 14 CMAQ 5 0 2 10 07 14 Training Registration Not registered for any upcoming classes Register Now Conference Registration 13th Annual CMAS Conference Oct 27 Oct 29 2014 Your registration is free og Out UNC Chapel Hill CEEE search HOME ABOUT CMAS NEWSLETTER CONTACT SITEMAP User s Manual for VERDI 1 5 Figure 1 1 Top of VERDI Page COMMUNITY MODELING amp ANALYSIS SYSTEM Visualize gridded netCDF data with this easy to use Java program PAVE or VERDI How do you know if you should use PAVE or VERDI replacement for the PAVE program Because PAVE is no longer in active development and support is limited VERDI offers the best option as a state of the art visualization program VERDI is a Java program for visualizing meteorology emissions and air quality modeling data Wi
134. re system Argonne National Laboratory developed VERDI to duplicate the functionality of PAVE in a Java program VERDI Training Support e CMAS Help Desk e M3User Listserv Online Resources A New Tool for Analyzing CMAQ Modeling Results Visualization Environment for Rich Data interpretation VERDI presented by Donna Schwede at the 2007 CMAS Conference Previous Documentation 1 4 1 submit System Requirements ols Windows Linux Memory 1024 Mb RAM Soft All needed VERDI components are contained in the installation package Partners e Institute for the Environment e CMAS Center e U S EPA ASMD e EPA Environmental Modeling and Visualization Laboratory e Argonne National Lab s Decision and Analysis Group Institute for the Environment User s Manual for VERDI 1 5 Figure 1 2 Downloading VERDI from the CMAS Web Site Step 1 Welcome Elizabeth Adams Navigation HELP DESK DOWNLOAD CENTER CONFERENCES amp MEETINGS TRAINING RESEARCH amp DEVELOPMENT COMMUNITY RESOURCES FESTC R LINE SPATIAL ALLOCATOR User Details You are logged in as lizadams email unc edu Edit Contact Info Recent Downloads CMAQ 5 0 2 10 07 14 CMAQ 5 0 2 10 03 14 VERDI 1 4 1 9 18 14 Training Registration Not registered for any upcoming classes Register Now Conference Registration 13th Annual CMAS Conference Oct 27 Oct 29 2014 Your registration is fr
135. rg web hsqlLicens e html jfreechart http sourceforge net proje http developer vrjuggler LGPL V2 1 Feb 1999 cts 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 hci http www cs umd edu he http opensource org licenses bs Mjazz il jazz download open d license php source shtml Ucar_ma2 http www unidata ucar ed http www unidata ucar e http www gnu org copyleft less u software netcdf java du software netcdf java er html Repast symphony http repast sourceforge ne http repast sourceforge net repa GIS t st license html UNC Chapel Hill 118 Institute for the Environment User s Manual for VERDI 1 5 Acknowledgments Contributions to VERDI from the community are greatly appreciated Data Contributions Sample CAM x Dataset Marco Rodriguez CIRA at Colorado State University http www cira colostate edu Sample Mercator Projection Dataset Tanya Otte Atmospheric Modeling and Analysis Division http www epa gov amad index html Data Reader Contributions I O Service Provider IOSP Interface for CAMx Barron Henderson ORISE Fellow EPA Ph D student UNC Chapel Hill Incorporating the IOSP into netcdf java Library John Carron Unidata http www unidata ucar edu software netcdf index html UNC Chapel Hill 119 Institute for th
136. rs for Lambert Conformal Conic PO GCUON Sofie Andes teh eed andes haere Mel psa ede eR IG see tet Ete tet Eoas 90 Figure 12 7 Edited Example Projection File camxproJ txt 0 00 cee eesecsseceseceseeeeneecsaeceseeeseeeeneees 91 Figure 12 8 CAMx Example Plots 2 cccainieiek ated deme alieeiel red edad ete 91 Figure 17 1 File View Script Editof oe aes sas cost tet os ciel h aie aeh ons tet maa ie at cece Mat aot nt Rt 98 Figure 17 2 Open Popup WindoW s 2ic ucieiecen caida iid aie eee 99 Figure 17 3 Top of Sample Script File VERDI_1 5 data scripts file_patterns txt 100 Figure 17 4 Bottom of Sample Script File VERDI_1 5 data scripts tile_patterns txt 100 Figure 17 5 Close Datasets Warning Message ai secs nda ctstais cas chngcetaeidsacaeteas se Qeatenees 101 Figure 17 6 Highlight Text to Select Task and Click Run oe eeceeseesseceeeeeeeeesseesnaeeneensees 102 Figure 17 7 Successful Batch Script Message sete act ars docs watyancis oe Gyan de dace eee domecle enews 103 Figure 17 8 Unsuccessful Batch Script Message File not found eee eeeceeeseeeesteeeenneeeenaees 103 Figure 17 9 Plot Image Generated by Task Blockiis cts etitean ane ieieniigan Gehan ees 104 Figure 17 10 Fast Tile Plot of Ozone at Time step 17 Layer 1 oe eee eeeeeeeeseeeesteeeenteeeeaees 106 Figure 17 11 Fast Tile Plot of Maximum Air Temperature aggregated over 25 time steps 107 Figure 17 12 Fast Tile Plot of Minimum Ozone aggregated over 2
137. save batch scripts e verdi hucData Default location where area shapefiles are located VERDI navigates to this directory when the user selects to add a dataset in the Area pane e verdi remote hosts Contains a list of machines that the user can select to browse when adding a remote dataset using VERDI s Remote File Access capability e verdi remote util Location of the RemoteFileUtility script for Linux and Mac installations of VERDI Starting in VERDI version 1 4 the ui properties file was removed and the user configurable settings such as the default directory locations were moved to the config properties file UNC Chapel Hill 12 Institute for the Environment User s Manual for VERDI 1 5 4 Starting VERDI and Getting Your Data into VERDI 4 1 Starting VERDI 4 1 1 Windows To start VERDI open a command window If you do not have a shortcut to launch a command window press the Start button and type cmd in the Search programs and files textbox If your window is too small go to the window s title bar and right click select Properties and then Layout and change your Screen Buffer Size and your Window Size appropriately Next navigate to where you installed VERDI on your computer You see the run bat file Its contents are shown in Figure 4 1 If you have previously executed this VERDI installation just type run and press the Enter key Otherwise you may need to customize some of the settings in this file for your configura
138. scsssscsssescees 118 Acknowledgments iisi siseses sonirosa osai osakesi rataa seska saas aosan Sosine Eeo doka sieaa oain 119 Data C ntrib tlonS scsi stisne ae n o EEE OE EEEREN 119 Data Reader Contributi nS scssi antisin nes ai RE nie E E AE SEE E iE sieas 119 T O Service Provider IOSP Interface for CAMX cccccccccccccessessssececececeesessnseceeeeees 119 Incorporating the IOSP into netcdf java Library esseeeeeseessessseesseessseesseessersseesseee 119 UNC Chapel Hill Vv Institute for the Environment User s Manual for VERDI 1 5 Figures Prouresl T p of VERDI Palenica ts coos ooeneuedt x a E Wacas atte E recta ees mate ace 3 Figure 1 2 Downloading VERDI from the CMAS Web Site Step Looe eeeeeneeesneceneeteees 4 Figure 1 3 Downloading VERDI from the CMAS Web Site Step 2 0 ee eeeeeeneeenecnteeteees 4 Figure 1 4 Downloading VERDI from the CMAS Web Site Step 3 0 eee ceeeeeeneeeneeneeeteees 5 Figure 1 5 Getting Documentation on VERDI from the CMAS Web Site eseese 6 Figure 4 1 Starting VERDI in Windows seic2i ccc2 e2e hee ddee teeta eee le detain 13 Proure 4 2 VERDI Main Widow es 55 22 t recite Get 2 e aro eei lates tae Daas iaee t eosa 15 Figure 5 1 VERDI Main Menu Options iiscsdeinin diesen tiiehasundnikaenaiadaiad 17 Figure 5 2 Animate Plots Dialog and Fast Tile Plots 0 eescscceessceeoesesceeseccenseeseteescenteccenseees 19 Figure 6 1 Observational File ASCII Format 0 eesceessecssecss
139. se the printAlias command to view what aliases are already defined Note you define an alias VERDI will use that alias if you make a request to plot that variable again If you are having issues with variable names being redefined remember to check your verdi alias file and remove it if needed 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 avi lt filename gt saves an animated plot of each of the time steps in the tile plot to the AVI video format closeWindow lt windowid gt closes the window with the specified 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 host 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 complete
140. 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 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 component Note that the formulas for the three components should already have been loaded into VERDI and they are case sensitive version prints out information about the VERDI version being used on the standard output stream verticalCrossPlot X Y lt row column gt NEW creates a v
141. ss it before continuing e Labels tab Figure 11 4 This tab provides widgets for you to edit more labels on your plot There are four tabs through which you can edit the labels of the Domain Axis x axis the Range Axis y axis Legend and Footer o Domain Axis This tab has two parts Label and Ticks Use the Label panel the same way as the Titles tab above by editing the Text Font and Color The Ticks panel allows you to change the labels associated with the ticks on the Domain Axis The Show Tick Labels checkbox is typically checked but you can uncheck it to not show any ticks or labels on this axis Number allows you to decrease the number of tick labels Note that you cannot increase the number of ticks via this screen and the values of the ticks do not change you are effectively turning tick labels on off via this checkbox The Font and Color widgets work the same as for the Titles tab o Range Axis All the widgets on this tab are the same as on the Domain Axis tab You are just making the changes for the Range Axis Figure 11 6 shows an example plot where the number of Tick Labels has been reduced in both the Range Axis and the Legend but the number of tick labels has not been reduced in the Domain Axis o Legend All the widgets on this tab are the same as on the tabs for the axes Use the Label part to designate and format the label that appears vertical in the left side of the legend box The tick labels are for the bound
142. t must be specified Neglecting to provide the full path along with the batch script name generates the following error No such file or directory The batch script usage see Figure 17 3 will also be displayed from the command line after typing the following command Windows run bat batch Linux Mac verdi sh batch Figure 17 7 Successful Batch Script Message eoo Run Batch Script G n Finished running batch script file Users lizadams VERDI_1 5 0 plugins bootstrap data scripts O3_tileplot_png txt If the user has specified an incorrect path or incorrect filename for the input dataset then a series of error messages will appear starting with the message shown in Figure 17 8 Figure 17 8 Unsuccessful Batch Script Message File not found r Dataset Loading Error paa o i No dataset handler registered for C Program Files VERDI_1 4 data model O3 test UNC Chapel Hill 103 Institute for the Environment User s Manual for VERDI 1 5 The VERDI Batch Editor checks to see if the path specified by the user as the imageDir exists If the path does not exist VERDI displays the error message Java io FileNotFoundException with the path and filename listed followed by the message No such file or directory Verify that you supplied the correct path and filename The directory specified as the image directory must exist prior to running the batch command Double click on the file i
143. ta The parameters area contains three tabbed panes e The Datasets pane is used to load in the dataset files that you want to work with in this session see Chapter 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 Double click on the name of a variable listed on the variables panel to add it as a formula on the Formula pane it will be the default formula for new plots that are created UNC Chapel Hill 15 Institute for the Environment User s Manual for VERDI 1 5 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 Chapter 7 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 variables from one or more datasets e Use the Areas pane to load area files for creating areal interpolation plots see Chapter 8 An area file is defined as a shapefile that contains polygon features such as watersheds counties or any other set of closed polygons Any plots that are created are shown in the plots area on the right hand side of the main window These plots can be placed into their own movable windows using Plots gt Undock all Plots on VER
144. th options for overlaying GIS Shapefiles and observational data onto model output VERDI offers VERDI was developed as a 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 Latest Version VERDI version 1 5 DOWNLOAD DOCUMENTATION Features Java VERDI has been updated to use Java 7 0 It is easy to install and portable across different operating systems GUI The VERDI user environment is an intuitive GUI that makes importing datasets creating formulas and generating plots easy Supported Plot Types VERDI currently can be used to create 2 d tile plots vertical cross sections scatter plots line and bar timeseries contour plots vector plots and vector tile plots Scriptable VERDI can be driven with a scripting language to allow batch generation of images Updates e This is a maintenance upgrade to use Java 7 and the latest underlying libraries such as thredds netcdf java History of VERDI Driven by the air quality modeling community s need for a replacement to PAVE the U S EPA sponsored the development of VERDI PAVE is a Unix based software system written in C and Motif While the EPA is satisfied with the functionality of PAVE and desired to keep those capabilities they recognize that the PAVE technology is outdated and wanted an updated more efficient flexible and modular visualization softwa
145. the available plot types The Selected Formula is displayed on the far right The Selected Formula refers to the formula that has been selected in the Formula pane discussed briefly below and in detail in Chapter 7 and that will be used to create plots Below the icons and plot buttons the VERDI window is divided into two main areas a parameters area consisting of tabbed panes on the left side and a plots area on the right side You can resize the entire window with your mouse You can also resize the tabbed pane separately from the plot area by placing your mouse over the dividing line between them and then moving it to the left or the right If you want you can separate the tabbed pane into 3 panes by using your mouse to hold onto the pane s title bar and then move it slightly out of alignment To reassemble the 3 panes into a tabbed pane use your mouse to hold onto the title bar of one pane drag it until its outline fills the outline of another pane and then release the mouse UNC Chapel Hill 14 Institute for the Environment User s Manual for VERDI 1 5 Figure 4 2 VERDI Main Window File Plots Window Help r amp Ea Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Contour Plot Variables Double click to add the variable as a formula Time Steps N A Use Time Range Min 0 N A Max 0H N A Layers N A Use Layer Range Min os Max OK Metada
146. the minimum time step specified in the Time Steps panel The range of time steps shown in the Time Step spinner control at the top of the plot reflects the subset of time steps specified when the Use Time Range box is checked The date and time of the time step displayed in the plot are shown below the x axis labels Subsetting a dataset s or formula s time step range affect plots produced with those data Section 9 4 describes the precedence rules Figure 9 1 Specify Time Step Range D T ee camm File Plots Window Help r E Fast Tile Plot Areal Interp Vertical Cross Section Time Series Time Series Bar Plot Scatter Plot Vector Plot Contour Plot Selected Formula 03 1 Datasets le elles Datasets Eile Configure Controls Plot GIS Layers Parreren mesen sJ ojonjaoazosooon Laves i si nee gt BA Layer 1 O3 1 1 CCTM46_P16 baseO2a 36k O3MAX 1 008E 1 Variables 8 822E 2 Double click to add the variable as a formula 81 m 7 562E 2 6 302E 2 ppmv 5 041E 2 Time Steps 1 25 V Use Time Range 251 ma 596 012002 04 00 00 gt Max 25 06 02 2002 00 00 00 3 781E 2 2 521E 2 1 260E 2 Layers 1 3 14 gt E Use Layer Range 2 790E 7 Min 18 June 1 2002 04 00 00 UTC Min 78 17 1 865E 6 Max 20 45 6 776E 2 Datasets UNC Chapel Hill 39 Institute for the Environment User s
147. tion If so edit your run bat in a text editor such as Notepad Figure 4 1 Starting VERDI in Windows File Edit Format View Help ECHO OFF SET BATCHFILE f2 SET VERDI_HOME C myPrograms VERDI_1 5 0 CD plugins bootstrap set JAVADIR VERDI_HOME jre1 7 0 ee JAVA IAVADIR bin java set CLASSPATH JAVADIR bin JAVADIR lib VERDI_HOME p1 ugi ns bootstrap bootstrap jar VERDI_HOME plugins bootstrap lib VERDI_HOME p lugins bootstrap lib saf core runtime jar VERDI_HOME plugins bootstrap lib VERDI_HOME plugins core 1lib REM set PATH based on 32 64 windows set bit64 n if I Processor_Architecture AMD64 set bit64 y if I PROCESSOR_ARCHITEW64 32 AMD64 set bit64 y if I bit64 y GOTO proc64 set PATH PATH VERDI_HOME plugins core 1ib win32 REM echo set to Win32 path GOTO proc32 proc64 set PATH PATH SVERDI_HOME plugins core 1ib win64 REM echo set to win64 path iproc32 REM path has been reset for DLLs continue i set JAVACMD JAVA Xmx1024M classpath CLASSPATH saf core runtime Boot b GOTO scripting batch GOTO scripting IAVACMD GOTO end scripting IAVACMD 1 BATCHFILE end er ce TS UNC Chapel Hill 13 Institute for the Environment User s Manual for VERDI 1 5 VERDI_HOME needs to point to the directory where VERDI is installed which is also the directory containing the run bat file In this figure VERDI is insta
148. tions are common to all plots and function in the same way unless the option is grayed out for all plot types Therefore this chapter is organized by menu instead of by plot type Figure 11 1 Fast Tile and Areal Plot Pull down Menu Options File Configure Controls Plot GIS Layers Print Configure Plot Zoom Time Series of Add Map Layers Probed Cell s Export as Load Probe Image Configuration Time Series Bar of Probed Cell s Save Configuration Time Series of Min Cell s Set Row and Configure GIS Layers Column Ranges Time Series of Max Cell s Show Grid Lines Animate Plot Set Current Maps as Plot Default Show Lat Lon Add Overlay 11 1 File Menu Options in the File menu include printing a plot and exporting a plot to an image file Plots can be saved as BMP EPS JPEG PNG or TIFF image file formats The ASC format is an ASCII dump of the cell values NOTE The export to Shapefile is not available in VERDI 1 5 11 2 Configure Menu The Configure pull down menu contains the following options Configure Plot Load Configuration and Save Configuration When you want to see your changes on the plot press the Apply button When you have finalized the settings for your plot click the OK button to close the Configure Plot dialog box UNC Chapel Hill 62 Institute for the Environment User s Manual for VERDI 1 5 11 2 1 Configure Plot This feature is available for only the Fast Tile Plot and
149. titude and Longitude To view the latitude and longitude values for a point on the plot select the Show Lat Lon option on the Controls menu then hover your cursor over the location for which you would like to know those values The lat lon coordinates will be displayed in the lower right hand side of the window Figure 11 13 The option to display the lat lon coordinates may be selected and works with either the Zoom or the Probe option UNC Chapel Hill 73 Institute for the Environment User s Manual for VERDI 1 5 Figure 11 13 Lat Lon Values Shown in Lower Right of VERDI Tile O3 1 File Configure einige Plot GIS Layers Zoom g Time Step v probe 1 6 Stats maximum gt 0 12 lt gt gt Slow 50 Set Row and Column Ranges 4 O3 1 Show Grid Lines baseO2a 36k 03MAX 31 109 June 01 2002 00 00 00 UTC Min 99 51 0 02 Max 123 50 0 10 3 29432N 83 64759 11 4 Plot Menu Options The Plot pull down menu Figure 11 14 contains the following options Time Series of Probed Cell s Time Series Bar of Probed Cell s Time Series of Min Cell s Time Series of Max Cell s Animate Plot and Add Overlay NOTE The Time Series of Probed Cells and the Time Series Bar of Probed Cells selections are grayed out until you select a grid cell or multiple grid cells using Controls gt Probe menu selection UNC Chapel Hill 74 Institute for the Environment Use
150. tly the syntax for the command line script is slightly different than the syntax for the batch script For example the batch script method supports requesting a plot of hour 12 using the notation O3 1 12 but the command line script option requires the variable name and time step be specified independently s 03 1 ts 12 18 2 Example Command Line Script for Windows Users Edit the run bat script in the VERDI_1 5 directory by right clicking on the file and selecting edit Figure 18 1 Location of run bat script in Windows Organize E Open Share with Print Burn New folder pack Name Date modified Type a data 10 26 2014 5 11 PM File folder A Libraries J jret 7 0 10 26 2014 5 11 PM File folder Ji licenses 10 26 2014 5 11PM File folder jm Computer Ji plugins 10 26 2014 5 12PM File folder I config properties 10 26 2014 1 36 PM TEMPLATE File 2 KB Ge Network T Functions 10 26 2014 1 36 PM NSH File 7 KB _ RELEASE NOTES 10 26 2014 3 15PM Text Document 22 KB RemoteFileReader tgz 10 26 2014 1 36 PM TGZ File 1 793 KB E run 10 26 2014 4 16 PM Windows Batch File 2 KB verdi 10 26 2014 1 36 PM Configuration sett 1 KB i win_shape2bin 10 26 2014 1 36 PM Compressed zipp 730 KB Windows Batch File Size 1 06 KB Z gt run Date modified 10 26 2014 4 16 PM Date created 10 26 2014 4 16 PM The current run bat in notepad contains a 1 at the end that allows it to accept input following the run
151. top left corner of the Areas pane Figure 8 1 A file browser Figure 8 2 allows you to change directories and select a shapefile file for use in VERDI Click on the shapefile name and click Next The Open Area popup window is displayed next allowing you to select the name of the field to read from the file and supply projection information if needed Use the pull down menu and click on the Name Field Figure 8 3 to be used If a prj file is not provided with the dataset you must specify the projection information A pull down menu prompts you to select the coordinate system used in the file either the Geographic lat lon coordinate system or a Projected x y coordinate system Figure 8 4 If you select Projected an additional pull down menu asks what type of projection enter the required information to perform the project in the text box Figure 8 5 Figure 8 6 After UNC Chapel Hill 34 Institute for the Environment User s Manual for VERDI 1 5 specifying the Name Field and the Coordinate System select Finish The resulting plot will be in the same projection as the gridded information used in the plot 8 4 Areas List The shapefile name s are listed in the top panel of the Areas pane and the name fields for the polygons provided in the shapefile s are listed in the panel underneath Figure 8 7 The actual model data are not loaded until the Areal Interpolation plots are created As additional shapefiles are added the name f
152. ute deed sede cena ein 53 Figure 10 8 Area Information Spreadsheet c2c poised niliceien Geek del ged neandgenieenel agate 53 Figure 10 9 Export SS re AS CE she a esas cs sae iagctns on aoe yas amas cod oes na tdeieces A E ay waa oes aa egos eases 53 Figure 10 10 Name and Save Spreadsheet iiio23 tessa dhe Avs Nees eevee eae 53 Fig re 10 11 Export oa pe les scx cnscbeet ae ccateasytecand vsccaueatncetiatedccautaaeuctecaneeneeeniaaes Gea 54 Figure 10 12 Name and Save Shapetilescccs cs 2c sessed eel een nee 54 Fig re 10 13 Vertical Cross Section Plot fnic 4 64 ieee accede tah eiiie tisiko 55 Figure 10 14 Vertical Cross Section Dialog BOX s sessssseessesesesessesseseresressessresreeseesersessresseseresreses 55 Fig r 10 15 Time Series Plotare Sieh sas cae Mech teal a weal a eai Ta 56 Figure 10 16 Time Series Bar Plot sssisisisissusisisiissisioriisunaisiiessinrisiisiisisiisi ii 57 Fig re 10 17 Scatter Plot coseson a ai na e a iosas aitas 58 Proure 0 18 Scatter Plot Dialog BOX asisip inercei na ia pis aTa e aiaa ainis 58 Figure 10 19 Scatter Plot Export Data into a CSV file eeseseeeeseeeseeressersresreeseesrrsrersresseseresreses 59 Figure 10 20 Contour Plot 2222s aao aa oe oa a AEA ia ea RA a ace ee 60 Figure 10 21 Contour Plot Menu Options eseesseeeeesssesesresseseresresstseresressessrssrenseesetsersseeseseresreses 60 Fig f 10 22 Rotated Contour Plot Secesia nanses a a a EESE 61 Figure 11 1 Fast Tile and Area

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