VERDI Frequently Asked Questions

Welcome to the VERDI FAQ

1. search for VERDI related technical support e-mails on the

   M3USER listserve for VERDI,

2. read the

   VERDI User Manual.

3. search for open VERDI tickets on Bugzilla Open Bugs

FAQ Table of Contents

1. What platforms does VERDI run on?
2. How do I download VERDI and install it on my system?
3. How can I get support for VERDI?
4. What are the known bugs in VERDI?
5. Can I get the source code so I can build my own version of VERDI?
6. What type of plots can I generate using VERDI?
7. How do I get my data into VERDI?
8. How do I view datasets on a remote machine?
9. How do I use my own map background?
10. How do I plot multiple maps (e.g. state + counties, or counties + roads) using different colors and thicknesses as needed?
11. How do I control the size of GIF other image files formats?
12. How do I view data for layers other than layer 1?
13. How do I view a vector plot (e.g. for wind data)?
14. How do I view a vector plot with another (scalar) variable in the background?
15. How do I plot observational data & compare with model data?
16. How do I view a vertical cross-section of data?
17. How do I use the mean, sum, mint, and other similar operators?
18. How can I change the default fonts used by VERDI?
19. How do I create a time series plot for a single grid cell or a group of cells?
20. How can I use VERDI to extract the time-series of data for a specific pollutant at a specific grid cell?
21. How can I view the average of data over multiple time steps (e.g. an at you preprocess the data with a program external to VERDI and then use VERDI to view the results.verage)?
22. Can I use datasets with identical domain sizes but different grid resolutions in a single formula?
23. How do I use scientific notation for numeric labels on tile plots?
24. Can I define the cutoffs between the colors plotted, rather than having each bin of equal size from the min to the max?
25. How do I define the number of color bins?
26. What does the future hold for VERDI?

VERDI Questions and Answers

What platforms does VERDI run on?

The Visualization Environment for Rich Data Interpretation VERDI can run on any platform that supports version 6 of the Java Standard Edition Runtime Environment (JRE). The JRE^TM 6 is provided as part of the VERDI release for Linux 32 bit, Windows, and for the Mac OS.

How do I download VERDI and install it on my system?

For instructions on how to download VERDI for your workstation and install it, please see http://www.cmascenter.org or http://www.ie.unc.edu/cempd.

How can I get support for VERDI?

Determine if your issue has already been reported:
1. Review the VERDI FAQ (this document)
2. Read the VERDI User Manual at VERDI User Manual
3. Search the discussion and technical support M3User Listserve forum for VERDI related M3USER posts
4. Query previously entered bugs or questions and check their status using the Bug tracking system Query Open Tickets in Bugzilla

If issue has not already been reported, request technical assistance from M3User:

1. Submit an e-mail to the M3User Listserve forum M3USER Help e-mail.

If issue is still not resolved, and is a new bug or a request for enhancement, Users are encouraged to submit a ticket on bugzilla:

1. Submit a bug to the bug tracking system at Bugzilla search for VERDI open tickets
2. If you do not already have a login and password, click the "Home" link for instructions on how to obtain them.
3. If you can't enter the bug tracking system for some reason, you may submit a problem or question via email to CMAS Help e-mail.

Please note that although the CMAS VERDI Support staff welcome your suggestions for VERDI enhancements and bug fixes, they can not guarantee implementation of these suggestions. If you require detailed support or would like to fund enhancements to VERDI, a support contract can be put in place. If you are interested in such an arrangement, please contact us via e-mail to cmas@unc.edu

What are the known bugs in VERDI?

The known bugs are described in the VERDI Release Notes.

Can I get the source code so I can build my own version of VERDI?

The VERDI source code is available to the public under a GPL license at SourceForge VERDI Project. Please review the VERDI Developer Instructions

What type of Plots can I create with VERDI?

VERDI can generate the following plots:
1. Tile Plot
2. Fast Tile Plot
3. Tile Plot with Observational Data Overlay
4. Areal Interpolation Plot
5. Vertical Cross Section Plot
6. Time Series Plot
7. Time Series Bar Plot
8. Scatter Plot
9. Vector Plot
10. Contour Plot

How do I get my data into VERDI?

VERDI uses the netCDF-java v4.1 library to read data from the following models: CAMx (UAM-IV), CMAQ (netCDF) and WRF (netCDF). These formats are decribed further:
1. Models-3 IO/API
2. WRF netCDF
3. CAMx UAM IV

If you have another data format which you would like to look at using VERDI, please submit an inquiry as to whether that data format is supported using the M3USER Listserve, and if needed, submit a request to bugzilla with a sample dataset attached.

How do I view datasets on a remote machine?

VERDI 1.3 added the ability to retrieve data from a remote host using a remote access file browser. A remote file reader and other software are provided with VERDI and will need to be installed by a system administrator on the linux server that you would like to access datasets remotely.

How do I use my own map background?

There is a utility called shape2bin that allows you to convert shapefiles files from a GIS into bin map files that are read it into VERDI. A zip file containing shape2bin is distributed with VERDI under $VERDI_HOME directory.

How do I plot multiple maps (e.g. state + counties, or counties + roads) using different colors and thicknesses as needed?

Use the GIS Layers>Configure GIS Layers>Edit Layer to specify the color, thickness, and transparency of the each map layer.

How do I control the size of GIF and postscript files output from VERDI?

You can adjust the size of the GIF and postscript images produced by VERDI by resizing the plot window before saving the image.

How do I view data for layers other than layer 1?

Use the spinner control on the Plot window to change the layer. The layer number listed in the plot title will automatically change.

How do I view a vector plot (e.g. for wind data)?

To view a vector plot, first load and select the data set that contains the vector data. Let's assume that this is wind data for this example. Next, click on each of the vector variable in the variable list for the file (e.g. UWIND and VWIND) to add them to the formula list. Click on Vector Plot, and select the UWIND variable as the Horizontal Component and the VWIND variable as the Vertical Component A vector plot will be created.

How do I view a vector plot with another (scalar) variable in the background?

To create a vector plot of wind direction overlayed on the wind speed: Add the UWIND and VWIND variables Create a formula for wind speed in the formula menu: sqrt(UWIND[1]*UWIND[1]+VWIND[1]*VWIND[1]) Click on Tile Plot to create a tile plot of the wind speed formula. Select Plot> Add Overlay > Vectors then select the UWIND variable as the Horizonal Component, and the VWIND variable as the Vertical Component Click OK.

How do I view a vertical cross-section of data?

To view a vertical cross section of data, first select the dataset in the Dataset List for which you would like to view the cross section, and then double click on the variable to add it as a formula. Click on Vertical Cross Section
• For a vertical cross section along the X axis: Select X-Axis Cross Section, and the Column number and click OK.
• For a vertical cross section along the Y axis: Select Y-Axis Cross Section and the Row number and click OK.
You will see the plot of that cross section.

How do I use the mean, sum, mint, and other similar operators?

The operators you mention produce a single number calculated over the currently selected levels, rows, columns, and time steps for the given formula.

mean    average cell value for all cells in currently selected domain
sum     sum of all cell values in currently selected domain
min     min of all cell values in currently selected domain
max     max of all cell values in currently selected domain
mint    time step index with minimum value in currently selected domain
maxt    time step index with maximum value in currently selected domain
minx    x index with minimum value in currently selected domain
maxx    x index with maximum value in currently selected domain
miny    y index with minimum value in currently selected domain
maxy    y index with maximum value in currently selected domain
minz    z index with minimum value in currently selected domain
maxz    z index with maximum value in currently selected domain

        where "currently selected domain" includes the currently
        selected rows, columns, layers, and time steps.  So the
        currently selected domain is bounded by

                (minx,miny,minz,mint)<->(maxx,maxy,maxz,maxt)

In future would like to support finding the minimum value for each cell over the time steps selected

minc     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).

maxc     For each cell (i,j,k) in the currently selected domain,
        this calculates the maximum value for that cell
        over the currently selected time steps.  In other words,
        the maximum value in cells (i,j,k,tmin..tmax).

How can I change the default fonts used by VERDI?

If you don't like the default fonts used by VERDI, you can use the Configure Plot to select the Title, and edit the font name, size, style.

How do I create a time series plot for a single grid cell or a group of cells?

• Select a formula, then create a Fast File Plot
• On the Fast Tile Plot use the pull down menu; Controls> Probe.
• Use your left mouse button to draw a box around the group of cells that you would like to create a time series plot.
• This will create a spreadsheet with the probed values.
• Click on the Fast Tile plot, and then use the Pull Down Menu; Plot> and select Time Series of Probed Cell(s)
• A Time Series plot for the group of cells that were selected in the earlier probe will be created.

How can I use VERDI to extract the time-series of data for a specific pollutant at a specific grid cell?

• Select a formula, and specify the layer
• Select the single x/y cell of the variable you want using Controls> Probe
• click on the single cell
• This will create a spreadsheet of the probed value
• Click on the Fast Tile Plot, then Plot> Select Time Series of Probed Cell
• A timeseries plot will be created

How can I view the average of data over multiple time steps (e.g. an 8 hour average)?

Calculation of N-hour averages:
• The formula notation to subset the data with time:

  O3[1]:1 is defined as the formula Ozone from dataset 1 and timestep 1
  

• To calculate an 8 hour average the notation would be:

  (O3[1]:1+O3[1]:2+O3[1]:3+O3[1]:4+O3[1]:5+O3[1]:6+O3[1]:7+O3[1]:8)/8

Alternatively, you preprocess the data with a program external to VERDI and then use VERDI to view the results. M3TPROC can be used to compute time period aggregates (e.g., 08:00-16:00 gridded daily maxima) and write them to an output file see: IOAPI Tools

Can I use datasets with identical domain sizes but different grid resolutions in a single formula?

You cannot combine two datasets with different grid resolutions in a formula in VERDI (e.g. to calculate a difference). Think of the datasets as matrices - you can't add or subtract two matrices of different dimensions and get a meaningful result. If you need to do something like this, use a program external to VERDI to aggregate the finer grid to the same dimensions as the coarser one or to interpolate the coarser grid to the same dimensions as the finer one, then load the resulting dataset into VERDI.

How do I use scientific notation for numeric labels on tile plots?

The Number Format field on a tile plot's Control> Configure Plot> Color Map dialog box can be set to adjust the tile plot legend's number format. For example, if you set it to (in the C language's printf() routine's format syntax) %1.2E (then hit return), the numbers on the legend will then look like:

9.49E-02

These configurations can be saved to a file, and used in future verdi sessions. Using the tile plot's Configure> Save Configuration Then after you create a tile plot, you can use Configure> Load Configuration to use your saved number format and font settings.

What does the future hold for VERDI?

Some of the features we would like to add are listed below.
• Improve scripting capabilities

  The Script Editor allows users to create plots within VERDI using a batch script. Expanding this capability to create tile plots for each hour, or layer, and other subsetting will be targeted for a future release.

• Improved statistical capabilities

  People often want to use simple statistics to assist with there data analysis (e.g. mean, std. dev.). It would be good if VERDI could produce these. In addition, people may want to slice the data in different ways to obtain these statistics (e.g. mean for each time step or for each vertical layer). There are also a number of commonly used statistics that deal with comparing model data with observations. We may want to examine the "tables" generated for OTAG for ideas for other typically used statistics.

• Add new types of plots and options for existing ones

  Additional kinds of plots have been requested by users. Some examples include: vertical cross section plots where the size of the layers is proportional to actual layer size, vertical profiles, flux plots, PIG plots, nested grid plots, adaptive grid plots, box & whisker plots.

• Improve usability of long formulas

  Currently, long formulas are often difficult to use. This might be improved by providing some defaults for commonly used long formulas (e.g. VOC, TOC, wind speed). Allowing user-defined aliases for long formulas and hierarchical formulas (e.g. NOy - NOx) would be very useful. Allowing the user to specify that multiple parts of a formula refer to the same data set would reduce the complexity involved with long formulas (e.g. [NO + NO2]a where the a is applied to both NO and NO2).

• Increase configurability of plots

  Allow the user to choose to assigning bins according to percentiles.

• Improve Data Import / Export capabilities

  It may be possible to include additional readers for VERDI. Also, enhancements of the data export facility would be very useful. For example, one might want to create a new data set out of components several other data sets, or from the result of several complex formulas. For this, VERDI would need to allow multiple formulas to be selected for export, and allow the renaming of variables in the output dataset (e.g. call a variable NOy instead of the long formula used to calculate NOy).

• and many more...

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