Serving and Viewing Vis5D Files Via the Web

Now you can embed links to Vis5D files in your Web pages (just like you can embed links to GIF files) and you can get Mosaic to automatically invoke Vis5D to view them (just as it automatically invokes xv to view GIF files).

Vis5D files are five-dimensional arrays in much the same way that GIF images are two-dimensional arrays. The dimensions of Vis5D files are: row, column, level, time and an index into a set of physical fields (e.g., temperature, pressure, humidity, salinity, wind or current velocity, sulfer dioxide concentration, and so on). Row, column and level may be latitude, longitude and altitude, but don't have to be (the dimensions may be abstract, or may be in a non-Cartesian map projection).

The Vis5D system (here's the Vis5D homepage) provides highly interactive 3-D visualization of the data in Vis5D files. It is generally used to look at the output of models of the Earth's atmosphere and oceans, but can be applied to any 3-D data sampled on a regular grid. To see images generated by Vis5D, click on:

Vis5D files tend to be a bit larger than GIF images (Vis5D files are usually at least several megabytes long), so you probably want a high speed Internet connection (a T1 line is nice) in order to serve or view them via the Web.

This page gives you instructions for serving and viewing Vis5D files via the Web based on the assumption that you are using NCSA's httpd server and mosaic browser. If you can tell us how to amend our instructions for other Web servers and browsers, please let us know at:

Installing Vis5D as an External Web Viewer

You can install Vis5D on your Unix workstation and tell Mosaic to invoke it as an external viewer for Vis5D files (just as it invokes xv to view GIF files). Just follow these four steps:

  1. Click on the appropriate one of: to get the executable file. Your Web browser will ask where to put the file and what to name it. Put it in the directory where you want to install Vis5D, and name it vis5d.tar. NOTE: we assume that your browser will automatically uncompress the file - if it doesn't then you need to do it manually by entering the command "uncompress vis5d.tar.Z".
  2. Enter the command "tar -xvf vis5d.tar" (make sure you're in the dirctory where you want to install Vis5D). Now Vis5D is installed. You can get rid of the tar file by entering the command "rm vis5d.tar".
  3. Add the following line to the .mime.types file in your home directory (if this file doesn't exist, create it):
      application/vis5d    v5d
  4. Add the following line to the .mailcap file in your home directory (if this file doesn't exist, create it):
      application/vis5d; /DIR/WHERE/Vis5D/IS/vis5d %s -path /DIR/WHERE/Vis5D/IS
    NOTE: this line is long and the end may be hidden off the right side of your browser. Substitute the path name of the directory where you installed Vis5D in Step 1 for both occurrences of "/DIR/WHERE/Vis5D/IS" in this line (do not use ~username in this path name).
If you have an SGI system, your Vis5D viewer will use its 3-D graphics hardware. If you have an IBM, HP, DEC or SUN system, your Vis5D viewer will render 3-D graphics in software, which may be a bit slow. However, if you have: then you can compile and install a faster version of Vis5D. Get the file vis5d-5.0.tar.Z and see Section 2 of the Vis5D README file for instructions.

The default viewers are set up to use 32 MB of memory. You can use these viewers even if you do not have 32 MB of memory, as long as you have 32 MB of swap space. If 32 MB is too little or too much for your system, then you can override it by altering the line you add to your .mailcap file as follows:

  application/vis5d; /DIR/WHERE/Vis5D/IS/vis5d %s -mbs N -path /DIR/WHERE/Vis5D/IS
where N is the number of megabytes you want Vis5D to use. NOTE: this line is long and the end may be hidden off the right side of your browser.

See Lawrence Livermore National Laboratory's WWW Viewer Test Page for information about many different Web media and their viewers.

Embedding Links to Vis5D Files in Web Pages

You can embed links to Vis5D files in Web pages in exactly the same way that you would embed links to GIF files. The names of Vis5D files must have the .v5d extension (just as GIF files have the .gif extension). They may have an additional extension if they are compressed.

For example, LAMPS (4 MB) is an embedded link to a Vis5D file on our anonymous ftp server. It was generated with the HTML text:

  <a href="">LAMPS</a>
If you've installed Vis5D as an external viewer then you can click on this link to make sure that your installation was successful (but first you need to exit your Web browser and restart it after setting up the .mime.types and .mailcap files).

Here's another example of an embedded link to a Vis5D file, this one on our Web server: SCHL (3.5 MB). This link was generated with the HTML text:

  <a href="">SCHL</a>
To serve Vis5D files from your Web server you need to add the following line ("vis5d" has been registered as a Media subtype) to the resource configuration file (often named srm.conf) for your server:
  AddType  application/vis5d      v5d
Note that we have added the sizes of the uncompressed files in parentheses after the links to these Vis5D files. This seems like the polite thing to do, since Vis5D files can be very large (e.g., hundreds of megabytes) and some people will have trouble transfering and viewing such large files.

If you embed links to Vis5D files in your Web pages, you may want to add text telling people that they need to install Vis5D to view these files, and you may want to include a link to this page to tell them how to do it. The link would look like this:

  <a href="">how to install Vis5D</a>
To learn how to put your data into Vis5D files, see Section 3 of the Vis5D README file.

Daily Weather Forecasts Available

Sites regularly serving model output as Vis5D files via the Web include: Of course, you must have Vis5D installed as an external viewer to visualize these data sets.

If you are in Europe

Recently users in Europe have had problems with low bandwidth to North American ftp servers. The Deutsches Klimarechenzentrum has offered to serve as a mirror site for our software. See the Vis5D homepage for links to their ftp server for getting the executable or source code versions of Vis5D.

The Vis5D User Interface

After you click on a link to a Vis5D file, your Web browser will transfer the file, possibly uncompress it, and then invoke Vis5D to view it. When Vis5D comes up, you should see a black window with a box in it (this is a 3-D box where you will visualize the data in the file) and a window on the left side of your screen containing a bunch of widgets for controlling the visualization. Click here to see a screen shot of Vis5D applied to the LAMPS data set. In this shot the 3-D box is in perspective and has been rotated, and some graphics have been turned on - when Vis5D first comes up you will see a non-perspective top view of the box and no graphics will be turned on.

If Vis5D is correctly installed as a viewer, you will see widgets marked MAP and TOPO - clicking on these will cause map outlines and topography to appear in the 3-D box (if you are using a version of Vis5D that you got from our ftp site before 19 April 1995 then the MAP and TOPO may not appear correctly). Put the mouse cursor over the 3-D box, then hold the left mouse button down and slide the mouse. The box should rotate. If it is too slow, resize the 3-D window to a smaller size (the way to do this varies between different window managers). You can also speed the graphics up by clicking again on the TOPO widget to disable the shaded topography.

You should see a rectangular array of widgets labelled with the names of model output fields. For the LAMPS data file these names are:

Each field name is repeated under five or six columns. Each column is labelled with a different way of rendering the fields. You can click the left mouse button on any widget in this array to select a particular field and a particular way of seeing it. Click the left mouse button on it again to de-select it. You can select any combination of different buttons to compare different fields and different ways of looking at them. Each way of rendering fields has its own special types of control widgets. These are:
You set the iso-level of the surface on a slider widget, and then click on the NEWSURF widget to actually calculate surfaces.
Horizontal contour slice
You set the spacing between contour lines on a type-in widget. Put the mouse cursor over the number, backspace, type a new number, and hit the Enter key.
Vertical contour slice
The controls are just like the horizontal contour slice.
Horizontal colored slice
You set the colors on the color table widget. You can move the mouse cursor into the black area of the color widget and then click the arrow keys on the keyboard to change the shape of the color graphs. You can also draw the color graphs by hand (the left mouse button controls the red graph, center controls green, and right controls blue).
Vertical colored slice
The controls are just like the horizontal colored slice.
Volume (this column will not appear on some systems)
The controls are just like the horizontal colored slice, except that there is also a white graph in the color table widget that controls the transparency of voxels. Hold the Alt key down to control the white graph (i.e., to change its shape with the arrow keys or to draw it with the left mouse button).
You can move the contour or colored slices through the volume. First, click on the SLICE widget. Then move the mouse cursor onto a corner of a slice, click and hold the right mouse button, and move the mouse to drag the slice.

You can animate the graphics you have selected by clicking the left mouse button on the ANIMATE widget. You can stop the animation by clicking again on ANIMATE. Clicking the left mouse button on the STEP widget moves ahead one time step, and clicking the right mouse button on STEP moves back one time step.

To rotate the 3-D display, move the mouse cursor over the 3-D box, click and hold the left mouse button, then slide the mouse. Every time you release and re-click the left mouse button you change your "grip" for rotations (as long as the mouse cursor is over the 3-D box). To make complex rotations, you may need to change your grip a couple of times. Practice makes 3-D rotations easier.

Vis5D has lots of other useful controls. You can zoom into or away from the 3-D box, you can make a cut-away view of the 3-D graphics, you can change the colors of graphics and make them semi-transparent, you can place text labels over the graphics, you can retrieve numerical values and locations, and so on. You can compute new fields as functions of old fields, either by typing a mathematical expression or by writing a Fortran function that dynamically links to Vis5D. If your data file includes U, V and W wind components, then you can generate slices full of wind arrows and you can generate wind trajectories. To learn about these and other controls for Vis5D, see Section 6 of the Vis5D README file.

The SSEC Visualization Project

The Vis5D system was created by the SSEC Visualization Project.

For more information please contact Bill Hibbard.