Vis5D Version 4.3
                                        

1. OVERVIEW OF Vis5D

     Vis5D is a software system for visualizing data made by numerical weather
models and similar sources.  Vis5D works on data in the form of a five-
dimensional rectangle.  That is, the data are real numbers at each point of a
"grid" which spans three space dimensions, one time dimension and a dimension
for enumerating multiple physical variables.  Of course, Vis5D works perfectly
well on data sets with only one variable or one time step (i.e. no time
dynamics).  However, your data should have some depth in all three spatial
dimensions.

     The Vis5D system includes the vis5d visualization program, several programs
for managing and analyzing five-dimensional data grids, and instructions and
sample source code for converting your data into its file format.  We have
included the Vis5D source code so you can modify it or write new programs.  We
have also included sample data sets from the LAMPS model and from Bob
Schlesinger's thunderstorm model, so you can work through our examples.

     Vis5D version 1.0 was written by Bill Hibbard and Dave Santek of the
University of Wisconsin Space Science and Engineering Center, supported by the
NASA Marshall Space Flight Center, and by Marie-Francoise Voidrot-Martinez of
the French Meteorology Office.  Later version enhancements were written by Bill
Hibbard, Brian Paul, and Andre Battaiola.  Dave Kamins and Jeff Vroom of Stellar
Computer, Inc. provided substantial help and advice in using the Stellar
software libraries.  Simon Baas and Hans de Jong of the Netherlands ported Vis5D
to HP workstations.  Pratish Shah of Kubota Inc. ported Vis5D to the Kubota
Alpha/Denali workstation.  Mike Stroyan of Hewlett Packard added PEX support.

     Vis5D is offered under the terms of the GNU General Public License, which
you can find in the file "NOTICE".  As the notice states, there is no warranty
for the Vis5D system, but we would be interested in hearing about your questions
and problems.  Also, if you would like to be added to the Vis5D mailing list,
send email to:

     Bill Hibbard  (email: whibbard@macc.wisc.edu) at:
     
     Space Science and Engineering Center
     University of Wisconsin - Madison
     1225 West Dayton Street
     Madison, WI  53706


This document is the complete guide for using Vis5D.  It is available in
PostScript or ASCII.

Contents:
     Section 1 Overview
     Section 2 System requirements and installation
     Section 3 Putting your data into Vis5D
     Section 4 McIDAS files
     Section 5 Vis5D utilities
     Section 6 Using vis5d to visualize your data
     Section 7 The v5dimport utility
     Section 8 Sample data sets
     Section 9 Version history


1.1 Vis5D Documentation on the World Wide Web

The Vis5D Home Page is available on the World Wide Web page at URL:

     http://www.ssec.wisc.edu/~billh/vis5d.html

This is linked to another Web document that describes how to use Vis5D files as
a World Wide Web medium for exchanging model output, at URL:

     http://www.ssec.wisc.edu/~billh/view5d.html

There is a Web document describing the Vis5D API (Application Programmer
Interface), intented to help system developers use Vis5D as a visualization
subsystem of other systems, at URL:

     http://www.ssec.wisc.edu/~billh/api.html

There is a Web document describing the Vis5D Tcl scripting interface at URL:

     http://www.ssec.wisc.edu/~billh/script.html

Copies of the api.html and script.html files are included with the Vis5D ftp
distribution.


2. SYSTEM REQUIREMENTS AND INSTALLATION

     In the following sections we describe the hardware and software required to
run Vis5D and detail how to install Vis5D on your system.


2.1 System Requirements

Vis5D currently works with the following systems.  In all cases, at least 32MB
of RAM is recommended and at least an 8-bit color display are required:

     1. Silicon Graphics workstations:
          IRIX version 4.0.1 or higher.
          Multiple processors are used when present.

     2. IBM RS/6000 workstations:
          Model 320H or higher
          AIX version 3 or later
          3-D graphics hardware is supported through OpenGL
          
     3. HP series 7000 or 9000 workstations:
          HP-UX A.09.01 or later
          PEX optional
          
     4. Sun Sparc workstations:
          SunOS 5.x or later
          
          ** IMPORTANT NOTE FOR SunOS 5 USERS **
          SunOS 5.x users:  The X shared memory extension may not work
          correctly.  If Vis5D prints an error message to the effect of "Shared
          memory error" then you'll have to append the following three lines to
          the end of your /etc/system file then reboot:
               set shmsys:shminfo_shmmax = 0x2000000
               set shmsys:shminfo_shmmni = 0x1000
               set shmsys:shminfo_shmseg = 0x100
          
     5. DEC Alpha workstations:
          OSF/1 V1.3 or later
          Kubota Denali Graphics hardware supported with KWS V1.3.3 or later and
               NPGL Run-time license.
          
          ** IMPORTANT NOTE FOR OSF USERS **
          you need to run 'limit stacksize 32m' before you run Vis5D
          
     6. IBM PC compatibles with Linux:
          75MHz Pentium CPU or faster recommended
          Linux 1.0 or later
          XFree86 (X window system) must be installed


Note that on systems which don't have 3-D graphics hardware or OpenGL, all 3-D
rendering is done in software using Mesa (an OpenGL work-alike).  Be aware that
software rendering is rather slow.  3-D graphics hardware is recommended.

     If you would like to port Vis5D to a new graphics system or workstation
read the "PORTING" file which gives more information.  If you succeed, please
inform us so that we may add your work to the distribution.


2.2 Installing Vis5D

     Vis5D is obtained via anonymous ftp.  If you don't have Internet access,
you can obtain Vis5D on tape by sending us a blank QIC or DAT and a note
explaining what you need.

Here are the installation instructions:

     1. Go to the directory in which you want Vis5D installed:
          % cd /usr/mydir
          
          NOTE:  The installation of Vis5D will result in a new subdirectory
          named "vis5d-4.3/" being created in the current directory.
          
          NOTE:  Be sure that you have write permission in this directory.  If
          you do not, you should become superuser before proceeding.  When
          finished installing Vis5D be sure to set the file ownership and
          permissions accordingly.

     2. Start ftp:
          % ftp iris.ssec.wisc.edu
          or
          % ftp 144.92.108.63

     3. Login as anonymous and send your email address as the password:
          Name: anonymous
          Password: email-address

     4. Go to the pub/vis5d directory:
          ftp> cd pub/vis5d
     
     5. Transfer files in binary mode:
          ftp> binary

     6. Get the Vis5D archive file:
          ftp> get vis5d-4.3.tar.Z

     7. Get the optional sample data archive file:
          The vis5d-data.tar.Z file contains topography, map outlines and sample
          data sets.  If you've used Vis5D in the past you can should already
          have these files and can move them into your new "vis5d-4.3"
          directory.
          
          ftp> get vis5d-data.tar.Z
          
     8. Exit ftp:
          ftp> bye

     9. Uncompress and un-tar the archive file:
          % uncompress vis5d-4.3.tar.Z
          % tar -xvf vis5d-4.3.tar

     10. Change to the newly created vis5d directory:
          % cd vis5d-4.3

     11. Optionally uncompress and untar the data file:
          % mv ../vis5d-data.tar.Z .
          % uncompress vis5d-data.tar.Z
          % tar -xvf vis5d-data.tar

     12. Run make:
          % make
     
          Make will print a list of systems supported for Vis5D.  Look for yours
          on the list and type the appropriate make command.  For example,
          suppose you have an IBM RS/6000 without OpenGL and 3-D graphics
          hardware.  You should type:
          
          % make ibm-x
          
          Vis5D and its utility programs will now be compiled.  If you do not
          have C and/or FORTRAN compilers on your system, this step will fail
          with an error message such as "cc: Command not found." or "f77:
          Command not found."  In this case you will have to get the appropriate
          archive of executable programs:
          
          a. List the "viewer" files.  These files are archives which contain
           vis5d exectuables for common Unix systems:
               ftp> dir *viewer*
          b. Make sure you're still in the vis5d-4.3 directory and download the
             viewer file for your operating system (xxx):
               ftp> get vis5d.xxx.viewer.tar.Z
          c. Exit ftp:
               ftp> bye
          d. Uncompress and un-tar the archive:
               % uncompress vis5d.xxx.viewer.tar.Z
               % tar -xvf vis5d.xxx.viewer.tar
          
     13. Test Vis5D:
          % ./vis5d LAMPS.v5d
          
          NOTE:  To quit, click on the "EXIT" widget button.

     14. You may delete the .tar files if desired.



2.3 Manifest

     When you are finished installing Vis5D you should have a directory named
"vis5d-4.3" which contains the following files and subdirectories:

     README         this documentation file in ASCII
     README.ps      this documentation file in PostScript
     NOTICE         the GNU general public license (copyright)
     PORTING        an ASCII document with notes on porting Vis5D
     LAMPS.v5d      Sample LAMPS data set
     SCHL.v5d       Sample data set:  Bob Schlesinger's thunderstorm model
     OUTLSUPW       World continental map lines file
     OUTLUSAL       Low resolution map of US with state boundaries
     OUTLUSAM       Medium resolution map of US with state boundaries
     EARTH.TOPO     Earth topography file
     api.html       documentation file for the API between Vis5D and its user
     interface
     script.html    documentation file for Vis5D scripting language
     *.tcl          example scripts
     vis5d          this is the vis5d visualization program
     v5dappend      utility to join v5d files together
     v5dinfo        utility to see summary of a v5d file
     v5dstats       utility to see statistics of a v5d file
     v5dedit        utility to edit the header of a v5d file
     v5dimport      utility to convert, resample, and reduce v5d files
     gr3d_to_v5d    utility to convert a McIDAS GR3D file to v5d format
     comp_to_v5d    utility to convert (a) comp5d file(s) to v5d format
     listfonts      utility to list fonts available on SGI systems for IRIS GL
     src/           source code for vis5d
     util/          source code for the Vis5D utilities
     lui5/          source code for LUI user interface library
     Mesa/          source code for the Mesa 3-D graphics library
     import/        source code for the v5dimport program
     userfuncs/     directory of user-written analysis functions
     contrib/       software contributed by Vis5D users
     convert/       source code for sample data conversion programs



2.4 Customizing

     After installation and testing you may want to customize the vis5d program
by editing the src/vis5d.h file:

     1.    The visualization program vis5d assumes your system has 32 megabytes
      of memory.  Although you can override this when you invoke vis5d, it may
      be convenient to change the default if your system has more than 32MB.
      The default number of megabytes is defined by the value of MBS in the
      src/vis5d.h include file.
     
     2.    If you want to specify a different default topography or map file,
      you can edit src/vis5d.h and change the values for TOPOFILE and/or
      MAPFILE.  For example, if you move the map and topography files to
      /usr/local/bin, you would specify "/usr/local/data/EARTH.TOPO" and
      "/usr/local/data/OUTLUSAM" respectively.
  
     When finished changing the src/vis5d.h file you must recompile the programs
by repeating installation step 12 above.

     If Vis5D is going to be used by multiple users on your system you may
want to move the vis5d executables and data files to a common directory
tree such as /usr/local:
     % mv vis5d /usr/local/bin
     % mv v5d* /usr/local/bin
     % mv OUTL* /usr/local/data
     % mv EARTH.TOPO /usr/local/data
then change change the vis5d.h file as described above to indicate where
the map and topography files are stored.
     


3. PUTTING YOUR DATA INTO Vis5D

     Vis5D works with data organized as a 5-D rectangle.  The first 3 dimensions
are spatial:  rows, columns, and levels (or latitutude, longitude, and height).
The 4th dimension is time.  The 5th dimension is the enumeration of multiple
physical variables such as temperature, pressure, water content, etc.

     In addition to the data itself, there are a number of parameters needed to
describe a Vis5D dataset:  the sizes of the five dimensions (number of rows,
columns, levels, timesteps, and variables), geographic position and orientation
of the data (map projection), the names of the variables, the actual times and
dates associated with each timestep, etc.

     The vis5d visualization program accepts two file formats:  v5d files and
comp5d files.  Both store 3-D data in a compressed format which vis5d can use
quickly and efficiently.  Comp5d files are those which were produced by the
comp5d program in previous versions of Vis5D.  The v5d file format is the new,
and prefered, file format used in version 4.0 and later of  Vis5D.  It is
intended to be a replacement for the comp5d format because it more flexible and
may be extended in the future.

     To view your data with vis5d you will typically write a conversion program
to convert your data files to v5d format.  To help you do this we've included
four sample conversion programs to guide you.  Basically, you just add the
instructions to read your file format, we provide the instructions to write the
v5d file.  See section 3.1 below.

     If you have used Vis5D in the past, you may continue to convert your data
to McIDAS format and use comp5d to make a compressed file.  However, to take
full advantage of the new map projections and vertical coordinate system in
version 4.0 and higher, you should write a new conversion program to make v5d
files.

     Another option for getting your data into Vis5D is the v5dimport utility.
v5dimport is a new program for file conversion, combining, and resampling.  It
reads a number of different file formats and can be extended to read new
formats.  See section 7 for more details.


3.1 Converting Your Data to v5d Format

     Files in the v5d format are created with functions from the v5d library.
We've included four sample conversion programs which outline how to make a v5d
file.  They are located in the convert/ subdirectory.  You can choose which one
to use as a template for your data converter:

     foo_to_v5d.f   A Fortran program which assumes a rectangular lat/lon
                    map projection and equally spaced linear vertical
                    coordinate system.
     
     foo2_to_v5d.f  A Fortran program which allows any map projection and
                    vertical coordinate system as well as a different
                    number of vertical levels for each variable.
     
     foo_to_v5d.c   A C program which assumes a rectangular lat/lon map
                    projection and equally spaced linear vertical
                    coordinate system.
     
     foo2_to_v5d.c  A C program which allows any map projection and
                    vertical coordinate system as well as a different
                    number of vertical levels for each variable.


     In any case, each conversion program uses three functions to write the v5d
file: v5dCreate (or v5dCreateSimple), v5dWrite, and v5dClose.  v5dCreateSimple
is used to create v5d files which only specify the most basic parameters.
v5dCreate allows more complicated parameters.  There are versions of these
functions for C and Fortran programs.

     Here are the descriptions of the v5dCreate and v5dCreateSimple functions in
a format similar to man page documentation.  C programmers should note that in
the argument descriptions we describe arrays by FORTRAN convention, i.e. A(1) is
the first element of A whereas in C this would be A[0].


Fortran-callable functions:
     integer function v5dcreatesimple( name, numtimes, numvars,nr, nc, nl,
                              varname, timestamp, datestamp, northlat, latinc,
                              westlon, loninc, bottomhgt, hgtinc )
     character* (*) name
     integer numtimes
     integer numvars
     integer nr
     integer nc
     integer nl
     character*10 varname(MAXVARS)
     integer timestamp(*)
     integer datestamp(*)
     real northlat
     real latinc
     real westlon
     real loninc
     real bottomhgt
     real hgtinc

     integer function v5dcreate( name, numtimes, numvars, nr, nc, nl, varname,
                              timestamp, datestamp, compress, projection,
                              proj_args, vertical, vert_args )
     character* (*) name
     integer numtimes, numvars
     integer nr
     integer nc
     integer nl(*)
     character*10 varname(MAXVARS)
     integer timestamp(*)
     integer datestamp(*)
     integer compress
     integer projection
     real proj_args(*)
     integer vertical
     real vert_args(*)



C-callable functions:
     int v5dCreateSimple( name, numtimes, numvars, nr, nc, nl, varname,
                              timestamp, datestamp, northlat, latinc, westlon,
                              loninc, bottomhgt, hgtinc )
     char *name;
     int numtimes;
     int numvars;
     int nr, nc, nl;
     char varname[MAXVARS][10];
     int timestamp[], datestamp[];
     float northlat, latinc;
     float westlon, loninc;
     float bottomhgt, hgtinc;
     
     int v5dCreate( name, numtimes, numvars, nr, nc, nl, varname, timestamp,
                              datestamp, compress, projection, proj_args,
                              vertical, vert_args )
     char *name;
     int numtimes, numvars;
     int nr, nc, nl[];
     char varname[MAXVARS][10];
     int timestamp[], datestamp[];
     int compress;
     int projection;
     float proj_args[];
     int vertical;
     float vert_args[];

Arguments used by v5dCreate and v5dCreateSimple:
     name        The name of the v5d file to create
     numtimes    Number of timesteps (at least 1)
     numvars     Number of variables (at least 1)
     nr          Number of rows in all 3-D grids (at least 2)
     nc          Number of columns in all 3-D grids (at least 2)
     varname     Array of variable names:
                      varname(1) = name of first variable
                      varname(2) = name of second variable
                      ...
                      varname(numvars) = name of last variable
     timestamp   Array of time labels for the timesteps in HHMMSS format:
                      timestamp(1) = time of first timestep
                      timestamp(2) = time of second timestep
                      ...
                      timestamp(numtimes) = time of last timestep
     datestamp   Array of date labels for the timesteps in YYDDD format
                      datestamp(1) = date of first timestep
                      datestamp(2) = date of second timestep
                      ...
                      datestamp(numtimes) = date of last timestep
     
     
Arguments used only by v5dCreateSimple:
     nl          Number of levels in all 3-D grids (at least 1)
     northlat    Latitude of northern edge of box in degrees
     latinc      Increment between rows in degrees  (positive)
     westlon     Longitude of western edge of box in degrees (positive West
     longitude)
     loninc      Increment between columns in degrees  (positive)
     bottomhgt   Bottom boundary of box in km
     hgtinc      Increment between levels in km (positive)

Arguments used only by v5dCreate:
     nl          Number of levels in the 3-D grids per variable:
                      nl(1) = number of levels for first variable
                      nl(2) = number of levels for second variable
                      ...  = ...
                      nl(numvars) = number of levels for last variable
     compress    Compression mode (1, 2 or 4 bytes per grid point)
     projection  Indicates type of map projection:
                      0 = linear, rectangular, generic units
                      1 = linear, rectangular, cylindrical-equidistant
                      2 = Lambert Conformal
                      3 = Stereographic
                      4 = Rotated
     proj_args   Projection arguments:
                      if projection=0 then
                           proj_args(1) = North boundary of 3-D box
                           proj_args(2) = West boundary of 3-D box
                           proj_args(3) = Increment between rows
                            proj_args(4) = Increment between columns
                      else if projection=1 then
                           proj_args(1) = North Latitude bound of 3-D box
                           proj_args(2) = West Longitude bound of 3-D box
                           proj_args(3) = Increment between rows in degrees
                           proj_args(4) = Increment between cols in degrees
                       else if projection=2 then
                           proj_args(1) = Standard Latitude 1
                           proj_args(2) = Standard Latitude 2
                           proj_args(3) = Row of North/South pole
                           proj_args(4) = Column of North/South pole
                           proj_args(5) = Longitude parallel to columns
                           proj_args(6) = Increment between columns in km
                      else if projection=3 then
                           proj_args(1) = Latitude of center (degrees)
                           proj_args(2) = Longitude of center (degrees)
                           proj_args(3) = Row of center of projection
                           proj_args(4) = Column of center of projection
                           proj_args(5) = Spacing between columns at center
                      else if projection=4 then
                           proj_args(1) = North boundary on rotated sphere
                           proj_args(2) = West boundary on rotated sphere
                           proj_args(3) = Increment between rows
                            proj_args(4) = Increment between columns
                           proj_args(5) = Earth Latitude corresponding to (0,0)
                           proj_args(6) = Earth Longitude corresponding to
                      (0,0)
                           proj_args(7) = Rotation angle
                      endif
     vertical    Indicates type of vertical coordinate system:
                      0 = equally spaced levels in generic units
                      1 = equally spaced levels in km
                      2 = unequally spaced levels in km
                      3 = unequally spaced levels in mb
     vert_args   Vertical coordinate system arguments:
                      if vertical=0 then
                           vert_args(1) = height of bottom level
                           vert_args(2) = spacing between levels
                      else if vertical=1 then
                           vert_args(1) = height of bottom level in km
                           vert_args(2) = spacing between levels in km
                      else if vertical=2 then
                           vert_args(1) = height (km) of grid level 1 (bottom)
                           vert_args(2) = height (km) of grid level 2
                           ...
                         vert_args(N) = height (km) of grid level N (top) where
                                N is the maximum value in the nl array.
                      else if vertical=3 then
                           vert_args(1) = pressure (mb) of grid level 1
                      (bottom)
                           vert_args(2) = pressure (mb) of grid level 2
                           ...
                         vert_args(N) = pressure (mb) of grid level N (top)
                                where N is the maximum value in the nl array.
                      endif


The v5dWrite function is used to write a single 3-D grid of data to a v5d file.
The grid is identified by a timestep and physical variable number.  Here is the
synopsis of v5dWrite:

Fortran-callable function:
     integer function v5dwrite( time, var, data )
     integer time
     integer var
     real data(*)

C-callable function:
     int v5dWrite( time, var, data )
     int time;
     int var;
     float data[];

Arguments descriptions:
     time      A timestep number in the range [1..numtimes]
     var       A variable number in the range [1..numvars]
     data      3-D array of grid values; number of values = nr*nc*nl(var)
               ordered as data[row+nr*(col+nc*lev)] where row increases from
               North to South, col increases from West to East, and lev
               increases from bottom to top


The v5dClose function closes the v5d file after the last grid has been written.
No arguments are needed.  Here is the synpsis of v5dClose:

Fortran-callable function:
     integer function v5dclose

C-callable function:
     int v5dClose()


Each of the create functions returns 1 when successful and 0 when an error
occurs.

     Looking at any of the example data conversion programs, you'll see that
there are variables which directly correspond to the arguments to
v5dCreate/v5dCreateSimple.  It is up to you to initialize these variables.  For
example, you'll have to assign to numtimes the number of timesteps in your
dataset, assign to numvars the number of variables in your dataset, etc.  After
you've initialized all these variables, the v5dCreate (or v5dCreateSimple) call
will create the v5d file.  If you've failed to initialize any of the variables
you will see an appropriate error message.

     Next, the conversion program will enter a nested loop inside of which you
must insert the code to read your data for the appropriate time step and
physical variable number.  Read your data into the array specified.  The
v5dWrite call will then compress and write the data to the v5d file.  Finally,
the v5dClose function will be called after all the data has been written.

     After you've written and compiled your file converter, you should test it
with one of your data files then check that it worked by running the v5dinfo and
v5dstats utility programs on the v5d file.  If everything looks OK, try running
vis5d.

     Here is an example of typical values that might be assigned to each
variable if one were using the foo_to_v5d.f program:

     Assignment          Comments
     numtimes = 5        5 time steps
     numvars = 4         4 physical variables
     nr = 30             30 rows in each 3-D grid
     nc = 40             40 columns in each 3-D grid
     nl = 20             20 levels in each 3-D grid
     varname(1) = "U"    U (east/west) wind component
     varname(2) = "V"    V (north/south) wind component
     varname(3) = "T"    Temperature
     varname(4) = "P"    Pressure
     timestamp(1) = 140000    2:00:00 pm
     timestamp(2) = 141500    2:15:00 pm
     timestamp(3) = 143000    2:30:00 pm
     timestamp(4) = 144500    2:45:00 pm
     timestamp(5) = 150000    3:00:00 pm
     datestamp(1) = 94036     36th day of 1994 (February 5)
     datestamp(2) = 94036     "
     datestamp(3) = 94036     "
     datestamp(4) = 94036     "
     datestamp(5) = 94036     "
     northlat = 60.0     Northern boundary of box is at 30 degrees latitude
     latinc = 1.0        There is 1 degree of latitude between each of the 30
     rows
     westlon = 100.0     Western boundary of 3-D box is at 100 degrees longitude
     loninc = 0.5        0.5 degree of longitude between each of the 40 columns
     bottomhgt = 0.0     Bottom of box is at 0km (sea level)
     hgtinc = 1.0        1 km between each of the 20 grid levels (top at 19.0km)
     

     The product of the number of rows, columns, levels, timesteps, and
variables is the total number of data points.  In this example:  30*40*20*5*4 =
480,000.  A real dataset may be 100 rows by 100 columns by 20 levels, have 50
timesteps, and 10 variables for a total of 100,000,000 data points.

     The difference between the foo_to_v5d program (which uses v5dCreateSimple),
and the foo2_to_v5d program (which uses v5dCreate), is the later allows you to
specify any map projection, vertical coordinate system, a different number of
grid levels for each physical variable, and to control data compression.  To
specify a map projection, you must set the value of projection to 0,1,2 or 3 to
indicate which projection, then specify the projection-dependent parameters in
the proj_args arrray.  Specifying the vertical coordinate system is done
similarly.

     It is sometimes useful to specify a different number of grid levels for
each variable.  For example, suppose most of your variables have 30 grid levels
but a some variables have fewer grid levels, perhaps only one.  Prior to version
4.0 of Vis5D, you would have had to fill in the extra levels with redundant,
missing or dummy data values.  With the v5dCreate function you can specify how
many grid levels are present for each individual physical variable with the nl
array parameter.  Be aware that the amount of data passed to the v5dWrite call
will depend on which variable you're writing.  For example, if your grid has C
columns and R rows then the number of values in the data array passed to
v5dWrite for variable V must equal C*R*nl(V).

     By default, the bottom-most grid level of each variable is displayed at the
bottom of the 3-D box; each grid extends upward for how ever many levels are
present.  Sometimes, however, the bottom-most grid level of a particular
variable should be positioned higher up.  An example of this is a combined
ocean/atmosphere dataset.  There may be a total of 18 grid levels:  the bottom 8
grid levels being ocean data and the top 10 grid levels being atmospheric data.
In this case, the bottom of the atmospheric data should be offset or shifted
upward by 8 grid levels.

     Elaborating on the ocean/atmosphere example, suppose we have 2 ocean
variables named S (salinity) and T (temperature) and 2 atmosphere variables
named P (pressure) and T1 (temperature).  There are 8 layers of ocean data and
10 layers of atmospheric data.  Here is a summary showing how the lowlev array
is the solution to this situation:





     varnum varname(varnum)        nl(varnum)     lowlev(varnum)
       1       S          8          0
       2       T          8          0
       3       P          10         8
       4       T1         10         8
       

The lowlev array is not specified in the v5dCreate function because it was
developed after the v5dCreate function was well established.  Instead, the new
v5dSetLowLev function is called with the lowlev array.  This separate function
was added to extend the functionality of v5dCreate without changing its calling
sequence.  Here is the synopsis of v5dSetLowLev:

Fortran-callable function:
     integer function v5dsetlowlev( lowlev )
     integer lowlev(*)

C-callable function:
     int v5dSetLowLev( lowlev )
     int lowlev[];

Argument description:
     lowlev      Specifies the vertical offset, in grid levels, for each
     variable.
                      lowlev(1) = offset for first variable
                      lowlev(2) = offset for second variable
                      ...  = ...
                      lowlev(numvars) = offset for last variable

v5dSetLowLev may be called at any point between v5dCreate and v5dClose.


     The v5dCreate and v5dcreate functions allow you to control how the grid
data are compressed.  The default is for grid values to be linearly scaled to
one byte integers.  This works very well for most data sets, since the scaling
factors are chosen independently for each combination of time step, variable and
vertical level.  Furthermore, the compression to one byte per grid point enables
Vis5D's high degree of interactivity, since compression allows entire data sets
to be resident in memory.  However, the compress argument of the v5dCreate and
v5dcreate functions lets you pick whether grid point values are scaled to 1-byte
integers, scaled to 2-byte integers, or left as 4-byte floating point values (no
compression).  We recommend that you try compression to 1-byte integers first,
and only use 2 or 4 bytes if you have precision problems at 1-byte.

     Vis5D version 4.2 and later allow you to specify the physical units for
each variable in your dataset.  The v5dSetUnits() function takes two arguments:
a variable number and a units character string.  If the first variable in your
file is P and the units are millibars then you can specify that with:

     C:  v5dSetUnits( 1, "millibars" )
     Fortran: call v5dsetunits( 1, "millibars" )

The units will be displayed by the v5dinfo program and in Vis5D when using the
probe.

     To compile your program which uses v5dCreate, v5dWrite, and v5dClose you
must link with the src/v5d.o and src/binio.o files.  See the makefiles in the
convert/ directory for examples.

     Finally, if your data is generated by an atmospheric or oceanic model, you
may want to consider modifying your model to generate v5d files directly using
the v5dCreate, v5dWrite, and v5dClose functions.  Look at the sample data
conversion programs for ideas.


3.2 Map Projections and Vertical Coordinate Systems

     Version 4.0 of Vis5D added support for new map projections and vertical
coordinate systems.  When we use the term map projection, we're referring to the
relationship between the rows and columns of data in the 3-D grid to the
latitude/longitude of the earth.  The term vertical coordinate system refers to
the relationship between the vertical levels of data in the 3-D grid to altitude
in the atmosphere (or depth in the ocean).

Vis5D 4.3 supports the following map projections:

(0) Generic rectilinear:  this is a linear, regularly-spaced coordinate system
     with no implied units.  This system is useful when your data is not related
     to earth science (computational fluid dynamics for example.)  North/south
     coordinates increase upward and east/west coordinates increase to the left.
     The projection is defined by four parameters:

     NorthBound  Northern boundary of 3-D box
     WestBound   Western boundary of 3-D box
     RowInc      Increment (spacing) between grid columns
     ColInc      Increment (spacing) between grid rows

     Example:  Suppose your 3-D grid has 80 rows and 60 columns and NorthBound =
          100.0 meters, WestBound = 50.0 meters, RowInc = 0.5 meters, and ColInc
          = 0.5 meters, then:
     
          the south boundary will be at 60.5 meters.  i.e. southbound =
               NorthBound - (RowInc * (rows-1))
          and the east boundary will be at 20.5 meters.  i.e. eastbound =
               WestBound - (ColInc * (columns-1))
     


(1) Rectilinear lat/lon (cylindrical equidistant):  this is the rectangular
     latitude/longitude coordinate system used in previous versions of Vis5D.
     Latitude increases to the North (upward in the graphical display) and
     longitude increases to the West (leftward in the graphical display;
     positive west latitude).  The projection is defined by four parameters:

     NorthBound  Northern boundary of 3-D box in degrees of latitude in the
                 range [-90S,90N].
     WestBound   Western boundary of 3-D box in degrees of longitude in the
                 range [-180E,180W].
     RowInc      Increment (spacing) between grid rows in degrees of latitude
                 greater than zero.
     ColInc      Increment (spacing) between grid columns in degrees of
                 longitude greater than zero.

     Example:  If your 3-D grid has 30 rows and 60 columns and if NorthBound =
          70.0, WestBound = 140.0, RowInc = 1.0, and ColInc = 0.5, then:
     
          the south boundary will be at 41 degrees latitude.  i.e. (NorthBound -
               RowInc * (rows-1))
          and the east boundary will be at 110.5 degrees longitude. i.e.
               (WestBound - ColInc * (columns-1))
          
          
(2) Lambert conformal:  a conic projection defined by the following six
parameters:

     Lat1, Lat2     First and second standard latitudes in the range [-90S,90N].
                    Lat1 and Lat2 define where the imaginary cone intersects the
                    sphere of the Earth.  Lat1 and Lat2 must have the same sign,
                    that is, they must both be positive or both negative.  Also,
                    Lat1 must be greater than or equal to Lat2.
     PoleRow, PoleCol    These parameters indicate the position of the north or
                    south pole with respect to the 3-D grid coordinate system.
                    These values may be outside the 3-D grid.  If Lat1 and Lat2
                    are positive, the north pole is assumed, else, the south
                    pole is assumed.
     CentLon        Central longitude:  this parameter indicates which Earth
                    longitude is to be parallel to the 3-D grid columns.
     ColInc         Increment (spacing) between grid columns at the central
                    longitude and standard latitudes, in km.  This parameter
                    controls the scale of the projection.

     Example 1:  Suppose your 3-D grid has 35 rows and 40 columns and you want a
     Lambert conformal projection of the United States centered over Wisconsin:
          Lat1 = 70.0
          Lat2 = 20.0
          PoleRow = -35.0
          PoleCol = 20.0
          Central Longitude = 90.0
          ColInc = 100.0
     
     Example 2:  Suppose your 3-D grid has 35 rows and 40 columns and you want a
     Lambert conformal projection over Australia:
          Lat1 = -20.0
          Lat2 = -70.0
          PoleRow = 60.0
          PoleCol = 20.0
          Central Longitude = -130.0
          ColInc = 200.0
     
     Note:  Beware that when the pole is visible in a Lambert conformal
     projection, there is usually a wedge-shaped region (with its apex at the
     pole) which is undefined (i.e. Longitude is >180 AND <-180).  In this
     region, there will be no map lines and the topography will be incorrect.
     

(3) Azimuthal Stereographic: an aximuthal stereographic projection defined by
five parameters:

     CentLat, CentLon    Latitude and longitude of the center of projection.
                    The apex of the imaginary cone will be over this coordinate.
     CentRow, CentCol    Row and column of the center of projection.  The grid
                    row and column indicated will be at the center of the
                    projection.  These values may be outside the 3-D box.
     ColInc         Increment (spacing) between grid columns in km at the center
                    of the projection.  This parameter controls the scale of the
                    projection.

     Example:  Suppose your 3-D grid has 40 rows and 40 columns and want an
     azimuthal stereographic projection centered over of the north pole:
          CentLat = 90.0
          CentLon = 0.0
          CentRow = 20.0
          CentCol = 20.0
          ColInc = 200.0


(4) Rotated rectilinear lat/lon:  this is the rectangular latitude/longitude
     coordinate system on a sphere rotated with respect to the Earth's natural
     latitude/longitude.  North/south coordinates increase upward on the rotated
     sphere and east/west coordinates increase leftward on the rotated sphere.
     The projection is defined by seven parameters:

     NorthBound     Northern boundary of 3-D box in degrees of latitude in the
                    range [-90S,90N].
     WestBound      Western boundary of 3-D box in degrees of longitude in the
                    range [-180E,180W].
     RowInc         Increment (spacing) between grid rows in degrees of latitude
                    greater than zero.
     ColInc         Increment (spacing) between grid columns in degrees of
                    longitude greater than zero.
     CentLat, CentLon    Latitude and longitude on Earth corresponding to
                    Latitude/Longitude = (0,0) on the rotated sphere.
     Rotation       Clockwise angle of rotation of rotated sphere about its
                    (0,0) point.

     Example:  Over small regions the Earth is nearly flat and we can exploit
     this to create nearly square grids for small scale models.  We can generate
     a nearly square grid of 41 rows by 41 columns over a small region over
     Wisconsin with:
          NorthBound = 2.0
          WestBound = 2.0
          RowInc = 0.1
          ColInc = 0.1
          CentLat = 43.0
          CentLon = 90.0
          Rotation = 0.0
     

Vis5D 4.3 supports the following vertical coordinate systems:

(0) Equally spaced, generic units:  this is a linear vertical coordinate system
     in which levels in the 3-D grid are equally spaced.  No specific units are
     implied.  The coordinate system is defined by two parameters:

     BottomBound Bottom boundary boundary of 3-D box.
     LevInc      Increment(spacing) between grid levels.
     
     Example:  Suppose your 3-D grid has 20 levels and you want the bottom
     boundary to be 0.0 meters and you want .1 meters between levels.  Then:
          BottomBound = 0.0
          LevInc = 0.1


(1) Equally spaced, kilometers:  this is a linear vertical coordinate system
     used in previous versions of Vis5D.  Grid levels are equally spaced.  The
     coordinate system is defined by two parameters:

     BottomBound Bottom boundary of 3-D box in km.
     LevInc      Increment (spacing) between grid levels in km greater than
     zero.
     
     Example:  Suppose your 3-D grid has 20 levels and you want .5 kilometers
     between grid levels.  Then:
          BottomBound = 0.0
          LevInc = 0.5


(2) Unequally spaced, kilometers:  this is a linear vertical coordinate system
     in which grid levels can be unequally spaced.  The coordinate system is
     defined by an array of N height parameters where N is the number of levels
     in the 3-D grids.  If the number of grid levels is different for each
     variable, N is the maximum number of grid levels.

     Height(1)   Height of first (bottom) grid level in km
     Height(2)   Height of second grid level in km
     ...         ...
     Height(N)   Height of Nth (top) grid level in km
     
     Note that the Height values must increase with N.
     
     Example:  Suppose your 3-D grids have 10 levels and you want the grid
     levels to be more closely spaced near the bottom than near the top.  Then:
          Height(1) = 0.0
          Height(2) = 0.1
          Height(3) = 0.2
          Height(4) = 0.3
          Height(5) = 0.4
          Height(6) = 0.6
          Height(7) = 0.8
          Height(8) = 1.0
          Height(9) = 1.3
          Height(10) = 1.6


It is also possible to display the vertical axis on a logarithmic scale.  This
is done with the -log  command line option when you start vis5d.  In this case,
the vertical axis is logarithmic with respect to height but linear with respect
to pressure.  The relationship between height (H) and pressure (P) is:
     
          P = 1012.5 * e^( H / -7.2 )        (^ denotes exponentiation)
          
          H = -7.2 * Ln( P / 1012.5 )        (Ln denotes natural log)
          
The constants 1012.5 and -7.2 are just defaults which can be overriden when you
specify the -log option.  See section 6.1 for details.

(3) Unequally spaced, millibars:  this is a linear vertical coordinate system in
     which grid levels can be unequally spaced.  The coordinate system is
     defined by an array of N pressure parameters where N is the number of
     levels in the 3-D grids.  If the number of grid levels is different for
     each variable, N is the maximum number of grid levels.

     Pressure(1) Pressure of first (bottom) grid level in km
     Pressure(2) Pressure of second grid level in km
     ...         ...
     Pressure(N) Pressure of Nth (top) grid level in km
     
     Note that the Pressure values must decrease with N.
     
For the purposes of calculating wind trajectories, Vis5D assumes the
relationship between height (H) and pressure (P) is:
     
          P = 1012.5 * e^( H / -7.2 )        (^ denotes exponentiation)
          
          H = -7.2 * Ln( P / 1012.5 )        (Ln denotes natural log)
          


     Only the v5d file format is capable of storing the new map projection and
vertical coordinate system information.  When a v5d file is read into vis5d this
information is used to setup the topography, map lines, and compute wind
trajectories.

     The vis5d program also supports two other display projections:  spherical
and cylindrical.  Instead of drawing a rectangular 3-D box, these projections
will actually warp the 3-D box into a spherical or cylincrical shape.  These
projections are used by specifying the -projection option with the value
spherical or cylindrical; they are not specified in the v5d file.  The spherical
option can be used to display your data on a 3-D globe.  The cylindrical option
can be used to display your data on a flat, round topography.  It's probably
best to just experiment with these options using the LAMPS dataset for example.
See the section on vis5d's command line options for more information.


3.3 Special Variables and Data Values

     Analysis and visualization of wind information is an important part of
Vis5D.  Specifically, the vis5d program looks to see if your data set contains
variables named U, V and W.  If present, they are assumed to be the three
components of wind vectors and are used to display trajectory tracings and wind
slices.

     The U wind component is parallel to rows, with positive U values pointing
toward increasing column numbers (i.e., positive eastward in a cylindrical
equidistant map projection).  The V wind component is parallel to columns, with
positive V values pointing toward decreasing row numbers (i.e., positive
northwardward in a cylindrical equidistant map projection).  Positive W values
are upward, negative W is downward.  The units for U, V and W are assumed to be
meters per second except when a generic map projection or vertical coordinate
system is used.  In that case, the units are in X per second where X is the
units used to specify the northbound, westbound, rowinc, and colinc parameters.

     If you do not like to use U, V, and W for wind vector components you can
either specify other wind variable names on the vis5d command line or enter them
while running vis5d.

     Strictly speaking, U, V and W do not have to represent wind motion.  They
can be used to represent any flow field such as ocean currents.  However, you
may want to scale U, V, and W by some constant for visualization purposes.

     Vis5D allows any grid data value to be undefined or 'missing'.  For
example, datasets based on observations are often incomplete or contain
erroneous values.  In your data conversion program you can indicate a grid value
is missing by assigning it a value greater than 1.0e30.  Missing data in vis5d
will show up as holes in isosurfaces and contour slices and as black regions in
colored slices.  The data probe will report missing values as 'Missing'.



4. McIDAS 3D GRID DATA FILES

     In previous versions of Vis5D, it was standard practice to put one's data
into a McIDAS GR3D file, then compress it with comp5d prior to using vis5d.
While directly converting to the v5d format is prefered, we still include this
information on the McIDAS format.  If you don't want to put your data into
McIDAS files, you may skip to section 5 now.

     WE RECOMMEND AGAINST THIS WAY OF GETTING YOUR DATA INTO VIS5D - INSTEAD USE
THE TECHNIQUES DESCRIBED IN SECTION 3 OF THIS DOCUMENT.

     A McIDAS GR3D file contains a sequence of 3-D grids of data.  The three-
dimensional grids are organized into short sequences to enumerate the values of
multiple physical variables at a single time.  The short sequences of physical
variables are repeated into a longer sequence which steps through many time
steps.  These files have a names of the form GR3Dnnnn where nnnn is a 4-digit
number between  0001 and 9999.  The McIDAS utility programs then refer to files
only by a number (1 through 9999).

     A 3D grid file contains a directory entry for each 3D grid, which describes
the size and geographic location of the grid, and the date, time and name of
physical variable of the data in the grid array.  A five-dimensional data set
consists of a sequence of 3D grids in a 3D grid file, all with the same size and
geographic locations.  The grid sequence repeats the same short sequence of
physical variables stepping forward through time.  For example, the grid
sequence from a weather model could be:

                      PHYSICAL
   GRID               VARIABLE
  NUMBER  DATE  TIME    NAME
     1   88035 000000    U
     2   88035 000000    V
     3   88035 000000    W
     4   88035 000000    T
     5   88035 000000    P
     6   88035 010000    U
     7   88035 010000    V
     8   88035 010000    W
     9   88035 010000    T
    10   88035 010000    P
    11   88035 020000    U
    12   88035 020000    V
    13   88035 020000    W
    14   88035 020000    T
    15   88035 020000    P

     This data set consists of 3 time steps of 5 physical variables.  The
physical variables are the U, V and W components of the wind vector, the
temperature T and the pressure P.  The date is February 4, 1988 and the time
steps are midnight, 1 AM and 2 AM.  Dates are in YYDDD format and times are in
HHMMSS format as described earlier.


4.1 Putting Your Data Into a McIDAS 3D Grid File

     The following sample program creates a 3D grid file and fills its 3D grids
with data for a five-dimensional data set.  This program can be found in the
file sample.F, it's makefile is sample.m.  The easiest way to read your data
into a 3D grid file is to alter the sample.F program.  The subroutines it calls
are all in the libmain.a library, and their source is in the src subdirectory.
Here is a listing of sample.F:

  1 C THE MAIN PROGRAM OF YOUR CONVERSION PROGRAM MUST
  2 C BE NAMED SUBROUTINE MAIN0
  3 C
  4       SUBROUTINE MAIN0
  5 C
  6 C THE NEXT TWO COMMENTS ARE PRINTED BY THE 'help sample' COMMAND
  7 C ? SAMPLE program to convert data to 3D grid files
  8 C ? sample gridf#
  9 C
 10 C DIMENSIONS OF 3D GRID
 11 C NOTE NLATS AND NLONS MUST BOTH BE LESS THAN OR EQUAL TO 150
 12 C NLATS, NLONS AND NHGTS MUST ALL BE AT LEAST 2
 13       PARAMETER (NLATS=31,NLONS=51,NHGTS=16)
 14 C
 15 C NUMBER OF PHYSICAL VARIABLES AND NUMBER OF TIME STEPS
 16 C NOTE EITHER OR BOTH MAY BE EQUAL TO 1.  THAT IS, Vis5D DOES
 17 C NOT FORCE YOU TO HAVE MULTIPLE VARIABLES OR TIME DYNAMICS.
 18       PARAMETER (NVARS=5,NTIMES=100)
 19 C
 20 C ARRAY FOR 3D GRID DATA
 21       REAL*4 G(NLATS, NLONS, NHGTS)
 22 C ARRAYS FOR GRID FILE ID AND GRID DIRECTORY
 23       INTEGER ID(8), IDIR(64)
 24 C ARRAY FOR VARIABLE NAMES
 25       CHARACTER*4 CNAME(5)
 26 C
 27 C LATITUDE, LONGITUDE AND HEIGHT BOUNDS FOR SPATIAL GRID
 28       DATA XLATS/20.0/,XLATN/50.0/
 29       DATA XLONE/70.0/,XLONW/120.0/
 30       DATA XHGTB/0.0/,XHGTT/15.0/
 31 C
 32 C STARTING DATE IN YYDDD AND TIME IN HHMMSS
 33       DATA JDAY/88035/,JTIME/020000/
 34 C TIME STEP IN HHMMSS
 35       DATA JSTEP/000100/
 36 C
 37 C NAMES OF THE FIVE PHYSICAL VARIABLES
 38       DATA CNAME/'U   ', 'V   ', 'W   ', 'T   ', 'P   '/
 39 C INITIALIZE GRID DIRECTORY TO ZEROS
 40       DATA IDIR/64*0/
 41 C
 42 C READ GRID FILE NUMBER FROM COMMAND LINE.  IPP WILL
 43 C CONVERT THE PARAMETER # 1 TO AN INTEGER, WITH A DEFAULT
 44 C VALUE OF 0.
 45       IGRIDF=IPP(1,0)
 46 C IF ILLEGAL GRID FILE NUMBER, PRINT ERROR MESSAGE AND RETURN
 47       IF(IGRIDF .LT. 1 .OR. IGRIDF .GT. 9999) THEN
 48         CALL EDEST('BAD GRID FILE NUMBER ',IGRIDF)
 49         CALL EDEST('MUST BE BETWEEN 1 AND 9999 ',0)
 50         RETURN
 51       ENDIF
 52 C
 53 C CALCULATE GRID INTERVALS
 54       XLATIN=(XLATN-XLATS)/(NLATS-1)
 55       XLONIN=(XLONW-XLONE)/(NLONS-1)
 56       XHGTIN=(XHGTT-XHGTB)/(NHGTS-1)
 57 C
 58 C DATE AND TIME FOR FIRST TIME STEP
 59 C IDAYS CONVERTS YYDDD FORMAT TO DAYS SINCE JAN. 1, 1900
 60       IDAY=IDAYS(JDAY)
 61 C ISECS CONVERTS HHMMSS FORMAT TO SECONDS SINCE MIDNIGHT
 62       ISEC=ISECS(JTIME)
 63 C
 64 C INITIALIZE GRID IDENTIFIER TEXT TO BLANKS
 65 C NOTE LIT CONVERTS A CHARACTER*4 TO AN INTEGER*4
 66       DO 10 I=1,8
 67 10    ID(I)=LIT('    ')
 68 C
 69 C SET UP DIRECTORY ENTRY
 70 C
 71 C DIMENSIONS OF GRID
 72       IDIR(1)=NLATS*NLONS*NHGTS
 73       IDIR(2)=NLATS
 74       IDIR(3)=NLONS
 75       IDIR(4)=NHGTS
 76 C
 77 C LATITUDES AND LONGITUDES IN DEGREES * 10000
 78       IDIR(22)=4
 79       IDIR(23)=NINT(XLATN*10000.)
 80       IDIR(24)=NINT(XLONW*10000.)
 81       IDIR(25)=NINT(XLATIN*10000.0)
 82       IDIR(26)=NINT(XLONIN*10000.0)
 83 C
 84 C HEIGHTS IN METERS
 85       IDIR(31)=1
 86       IDIR(32)=NINT(XHGTT*1000.)
 87       IDIR(33)=NINT(XHGTIN*1000.)
 88 C
 89 C CREATE THE GRID FILE
 90       CALL IGMK3D(IGRIDF, ID, NLATS*NLONS*NHGTS)
 91 C
 92 C LOOP FOR TIME STEPS
 93       DO 200 IT=1,NTIMES
 94 C
 95 C SET DATE AND TIME IN DIRECTORY ENTRY
 96 C IYYDDD CONVERTS DAYS SINCE JAN. 1, 1900 TO OUR YYDDD FORMAT
 97       IDIR(6)=IYYDDD(IDAY)
 98 C IHMS CONVERTS SECONDS SINCE MIDNIGHT TO OUR HHMMSS FORMAT
 99       IDIR(7)=IHMS(ISEC)
100 C
101 C LOOP FOR PHYSICAL VARIABLES
102       DO 190 IV=1,NVARS
103 C
104 C SET VARIABLE NAME IN DIRECTORY ENTRY
105       IDIR(9)=LIT(CNAME(IV))
106 C
107 C *************************************************************
108 C READ YOUR DATA FOR TIME STEP NUMBER IT AND VARIABLE NUMBER IV
109 C INTO THE ARRAY G HERE.
110 C NOTE THAT G(1,1,1) IS THE NORTH WEST BOTTOM CORNER AND
111 C G(NLATS,NLONS,NHGTS) IS THE SOUTH EAST TOP CORNER.
112 C MARK A GRID POINT AS 'MISSING DATA' BY SETTING IT = 1.0E35
113 C *************************************************************
114 C
115 C CALCULATE 3D GRID NUMBER
116       IGRID=IV+NVARS*(IT-1)
117 C WRITE DATA IN G AND DIRECTORY IN IDIR TO 3D GRID
118 C NOTE WE PASS THE NEGATIVE OF THE GRID NUMBER (I.E. -IGRID)
119       CALL IGPT3D(IGRIDF,-IGRID,G,NLATS,NLONS,NHGTS,IDIR,IGNO)
120 C
121 C END OF PHYSICAL VARIABLE LOOP
122 190   CONTINUE
123 C
124 C INCREMENT DATE AND TIME, CONVERT JSTEP FROM HHMMSS TO SECONDS
125       ISEC=ISEC+ISECS(JSTEP)
126 C IF SECONDS CARRY PAST ONE DAY, ADJUST SECONDS AND DAYS
127       IDAY=IDAY+ISEC/(24*3600)
128       ISEC=MOD(ISEC,24*3600)
129 C
130 C END OF TIME STEP LOOP
131 200   CONTINUE
132 C
133       RETURN
134       END

     The routines IGMK3D and IGPT3D are the interface to the 3D grid structures.
The call to IGMK3D at line 90 creates a 3D grid file. Its parameters are:

   1  INTEGER*4 - number of 3D grid file to create
   2  array of 8 INTEGER*4 - a 32 byte text ID for the file
   3  INTEGER*4 - maximum number of grid points in any 3D grid.

After the 3D grid file is created, IGPT3D is called in line 119 once for each
combination of time step and physical variable to put 3D grids into the file.
Its parameters are:

     1  INTEGER*4 - number of 3D grid file to write to
     2  INTEGER*4 - minus the number of the 3D grid to write.  This is 0 or
          positive to indicate write to next empty grid.
     3  array of REAL*4 - array of grid points to write
     4  INTEGER*4 - first dimension of grid array, # of latitudes
     5  INTEGER*4 - second dimension of grid array, # of longitudes
     6  INTEGER*4 - third dimension of grid array, # of heights
     7  array of 64 INTEGER*4 - directory for 3D grid
     8  INTEGER*4 - number of 3D grid actually written, returned by IGPT3D.

     Vis5D allows data sets which span more than one 3D grid file.  In this case
the grid sequence of repeating variables and repeating time steps continues
across grid file boundaries.  A single 3D grid file is limited to 100,000,000
grid points (400 megabytes).  If your data set contains more than this number of
grid points, then you should alter sample.F to create a new 3D grid file (by
incrementing IGRIDF and calling IGMK3D) on every Nth time step, where N time
steps will fit in one 3D grid file.  Note that the comp5d command described in
section 4 references data sets as sequences of 3D grid files.

     The Vis5D system processes the gridded data based on the information in the
grid directories, which is contained in the IDIR array in the sample.F program.
It is a good idea to initialize IDIR to all zeros, as in line 40.  The size of
the 3D grid is set in entries 1 to 4 of IDIR (lines 72 to 75).  Note the
restrictions on data set size described in section 4 of this document.

     The date and time of the 3D grid are set in entries 6 and 7 of IDIR, as in
lines 97 and 99.  Note that they are represented in our YYDDD and HHMMSS formats
described above.  Four functions are available in libmain.a for converting
between these formats and a format which makes date and time calculations easy.
The IDAYS function converts YYDDD format to days since January 1, 1900, as in
line 60.  The ISECS function converts HHMMSS format to seconds since midnight,
as in lines 62 and 125.  This makes it easy to do calculations with dates and
times, as in lines 125, 127 and 128.  Then the IYYDDD function converts days
back to YYDDD and the IHMS function converts back to HHMMSS, as in lines 97 amd
99.

     The physical variable name is 4 ASCII characters packed into entry 9 of
IDIR, as in line 105.  The LIT function in libmain.a converts a CHARACTER*4 to
an INTEGER*4.

     The spatial location of the grid is described in terms of latitude and
longitude in ten-thousandths of a degree, and in terms of height (altitude) in
meters.  The grid element G(1,1,1) is in the north west bottom corner of the
grid, and the grid element G(NLATS,NLONS,NHGTS) is in the south east top corner.
The grid latitude and longitude are described in entries 21 to 25 of IDIR, as in
lines 78 to 82.  The grid heights are described in entries 31 to 33, as in lines
85 to 87.  The NINT function is a FORTRAN intrinsic for converting a REAL to the
nearest INTEGER.  The latitude, longitude and height spacings are simply the
distances between between successive grid points.  Latitudes are positive in the
northern hemisphere, longitudes are positive in the western hemispere, and of
course heights are positive above sea level.

     The real work in modifying the sample.F program is writing code for getting
your data into the G array, in lines 107 to 113.  For some data you may want to
fake the latitude, longitude and height coordinates.  However, if your data is
geographical and large scale, then you may want to describe its location
accurately, and it may be necessary to resample your data to a regularly spaced
grid in latitude, longitude and height from some other map projection.  It may
also be necessary to transpose your data array to get the index order to be LAT,
LON and HGT, and to invert your data array in some index to make sure G(1,1,1)
is the north west bottom corner.  Even in faked coordinates, you may need to
transpose or invert your data array to get the right 'handedness' in the
display.  The Vis5D system allows grid points marked as missing, indicated by
array values greater than 1.0E30.  If you do fake the latitude, longitude and
height coordinates, then the topography and map display of the vis5d program
will be meaningless.  If you calculate trajectories for your data set, either
use accurate coordinates, or take great care to get relative time, distance and
velocity scales consistent in the faked coordinates.  Otherwaise trajectory
paths will not be realistic.

     The IPP function in libmain.a returns the value of a command parameter as
INTEGER*4, as in line 45.  There are similar functions CPP and DPP in libmain.a
which return CHARACTER*12 (converted to upper case) and REAL*8 values for
command parameters.  They get command parameters based on their sequential
position in the command line.  They all have similar function parameters:

     1  INTEGER*4 - sequence number of command parameter
     2 (IPP) INTEGER*4 - default value of command parameter
          or
     2 (CPP) CHARACTER*12 - default value of command parameter
          or
     2 (DPP) REAL*8 - default value of command parameter.

There is also a mechanism for picking up command parameters based on keywords.
This is done with the functions IKWP, CKWP and DKWP in libmain.a.  They get
command parameters based on position after a keyword of the form '-keyword'.
IKWP returns an INTEGER*4, CKWP returns a CHARACTER*12 (converted to upper case)
and DKWP returns a REAL*8.  They all have similar function parameters:

     1  CHARACTER*12 - keyword string in command line
     2  INTEGER*4 - sequence number of command parameter after keyword
     3 (IKWP) INTEGER*4 - default value of command parameter
          or
     3 (CKWP) CHARACTER*12 - default value of command parameter
          or
     3 (DKWP) REAL*8 - default value of command parameter.

The NKWP function in libmain.a returns the number of sequential parameters after
a keyword.  Its function parameter is:

     1  CHARACTER*12 - keyword string in command line.

     On the most machines the REAL*4 format is not a subset of the REAL*8
format, so make sure to declare DPP and DKWP as REAL*8, as well as their third
function parameters (for default values of command parameters).

     If you would rather write your grid conversion program in C instead of
FORTRAN, look at the file 'sample.c'.  It contains examples of how to easily
read and write grid files using C structures and routines in stdio.


4.2 Using the McIDAS Utilities

     Once your data set is in a 3D grid file, you can list directory information
about the grids using the command:

     igg3d list I J -gr3df N

where N is the 3D grid file number, and I and J give the range of grid numbers
to list.  You can get a quick idea of the data values using the command:

     igg3d info I J -gr3df N

which will list the minimum and maximum values, the mean, the standard deviation
and the number of grid points marked for missing data, for grid numbers I to J
in 3D grid file number N.

     There are restrictions on the dimensions of data sets which can be
visualized using the vis5d program.  Currently, you are limited to a maximum of
30 physical variables and 400 times steps.  The vis5d program will also fail if
there is a trivial spatial dimension:

     NLATS < 2
     NLONS < 2
     NHGTS < 2

The vis5d program will perform badly, possibly making errors, if the total 5-D
size:

     NLATS * NLONS * NHGTS * NTIMES * NVARS

is too large.  The limit depends on the amount of memory in your system.  For a
64MB system, the limit is around 25,000,000, with performance degrading as the
data set size exceedes the limit.

     Vis5D provides the gg3d and igg3d programs which can be used to reduce the
resolution and scale of a data set to meet these limits.  The gg3d program
resamples a 3D grid to new array dimensions and new extents in latitude,
longitude and height, using the command:

     gg3d samp N I M J
     gg3d ave  N I M J
     
where N and I are the numbers of the source 3D grid file and grid, and M and J
are the numbers of the destination 3D grid file and grid.  The 'samp' version
calculates destination grid point values by linearly interpolating between
source grid point values, and is appropriate for increasing resolution.  The
'ave' version calculates destination grid points by averaging multiple source
grid point values, and is appropriate for decreasing resolution.  Without any
keywords gg3d will do a straight copy operation.  Invoke the gg3d command with
the keyword:

     -size NLATS NLONS NHGTS

to set the grid dimensions for the destination grid as different from the
dimensions for the source grid.  Invoke gg3d with the keywords:

     -lat XLATS XLATN
     -lon XLONE XLONW
     -hgt XHGTB XHGTT

to set extents (range bounds) for the latitude, longitude and height for the
destination grid as different from the extents for the source grid.  The -lat, -
lon and -hgt keywords take real arguments.

     The igg3d program provides options for copying and deleting 3D grids and
for interpolating between 3D grids in time.  Sequences of 3D grids are copied
using the command:

     igg3d get N I J M K

where N is the source 3D grid file number, I and J are the range of source grid
numbers, M is the destination grid file number, and K is the starting
destination grid number.  A single grid may be copied within a 3D grid file
using the command:

     igg3d copy I J -gr3df N

where N is the 3D grid file number, I is the number of the source grid and J is
the number of the destination grid.  A range of grids may be deleted with the
command:

     igg3d del I J -gr3df N

where N is the 3D grid file number and grid numbers between I and J are to be
deleted.

The igg3d command provides two different options for time interpolation.  The
first is:

     igg3d ave K I J D T -gr3df N

where grid number K is produced by interpolating between grid numbers I and J,
all in 3D grid file number N.  Grid number K will be assigned day D (in YYDDD
format) and time T (in HHMMSS format).  The relative weighting of grids I and J
is calculated from this date and time, assuming linear time interpolation.  If
grid K is not between grids I and J in date and time, igg3d prints an error
message.  The igg3d command also provides a more complex time interpolation
option:

     igg3d int I D T -setdel S M -lag U V -gr3df N

     This will put a grid in the next empty slot of 3D grid file number N,
assigned to day D (in YYDDD format) and time T (in HHMMSS format).  This grid
will be interpolated from a sequence of grids, all in file number N, at grid
numbers I, I+S, I+2S, ... , I+(M-1)S.  This sequence of grids should be
ascending in date and time.  igg3d will search the sequence and linearly
interpolate between the two consectutive grids from the sequence which bracket
day D and time T.  Furthermore, the interpolation will be done in a coordinate
system moving at constant velocity (U, V), where U and V are in meters per
second, with V positive for motion from south to north and U positive for motion
from west to east.  The two bracketing grids from the sequence will be shifted
in latitude and longitude to their positions at day D and time T, and the result
interpolated between these two spatially shifted grids.  Furthermore, if the
grids in the sequence are identified in their directory entries with variable
name 'U   ' or 'V   ', then the corresponding component of the velocity (U, V)
will be subtracted from the grid values.

     The 'int' option of igg3d may seem complex, but it is just what you need if
you want to write a script to re-interpolate a five-dimensional data set to a
new sequence of time steps.  It is particularly useful if the source sequence
does not have uniform time steps, or if the physics are moving through the
spatial grid and you want to avoid blurring in the time re-interpolation.  You
would set M equal to the number of time steps and S equal to the number of
physical variables in the source five-dimensional data set.  The I parameter
would be set equal to the grid number in the first time step of the variable
being interpolated.  Note that this igg3d option will put the new grid at the
end of the grid file containing the source data set, but you can use 'igg3d get'
to move it to another grid.

You can use the command:

     igu3d make N M

to create 3D grid file number N, which allows 3D grids of up to M points each.
The names of 3D grid files have the form:

     GR3Dnnnn

where nnnn is the four digit decimal grid file number, padded with leading zeros
if needed to make four digits.




5. Vis5D UTILITIES

Vis5D includes a number of utility programs.  This section describes each one.
The new v5dimport program is described seperately in section 7.


v5dinfo
     Usage:  v5dinfo file
     
     Description:  v5dinfo prints information about the given v5d file such
     as the size of the 3-D grid, the number of time steps, the names of
     the variables, etc.
     
     This program will also work on comp5d files.  Therefore, the old
     compinfo program has been removed.


v5dstats
     Usage:  v5dstats file
     
     Description:  v5dstats prints simple statistical information about the
     grid data in the named v5d file.  Again, comp5d files are also
     accepted.


v5dedit
     Usage:  v5dedit file.v5d
     
     Description:  v5dedit allows you to change header information such as
     the map projection, vertical coordinate system and variables names in
     the named file.  It is an interacive, menu-driven program and is
     intended to be self explanatory.  This program does NOT work with
     comp5d files.
     
     
v5dappend
     Usage:  v5dappend [-var] [...] file.v5d [...] target.v5d
     
     Description:  v5dappend allows you to append a number of v5d files
     together to make one larger file.  This might be useful if your
     weather model generates a separate .v5d file for each timestep because
     youll want to join those files together to view the data in vis5d.
     
     The arguments are, in order:
          An optional list of variables to omit from the output file. For
          example, if you want to omit the variables U and THETA you would
          use the arguments -U and -THETA.
          The list of v5d files to append onto the target file.
          The name of the target v5d file to create (if it doesnt exit)
          or append onto (if the target file already exists).
     
     Note that the dimensions of the grids (rows, columns and levels) must
     be the same in each file to append them together.  The map projection
     and vertical coordinate system information will be taken from the
     first input file and ignored the the remaining files.
     
     
gr3d_to_v5d
     Usage:  gr3d_to_v5d N M file.v5d C
     
     Description:  gr3d_to_v5d converts (a) McIDAS GR3D file(s) to a v5d
     file.  N is a number which indicates the name of the first grid file,
     M is the number of grid files to convert, file.v5d is the name of the
     file to produce, and C is 1, 2 or 4 to indicate how many bytes per
     grid point to use for compression (the default is 1).  Example:  if
     N=20 and M=4 then the files GR3D0020, GR3D0021, GR3D0022, and GR3D0023
     will be read an converted to the named file.v5d.


igg3d
     Usage:  igg3d ...
     
     Description:  igg3d is used to perform a variety of manipulations on
     McIDAS GR3D files.  See section 4.2 for more details.
     
     
igu3d
     Usage:  igu3d  ...
     
     Description:  igu3d is a utility to perform a variety of manipulations
     on McIDAS GR3D files.  See section 4.2 for more details.
     

gg3d
     Usage:  gg3d ...
     
     Description:  gg3d is a utility for resampling McIDAS GR3D files.  See
     section 4.2 for more details.


listfonts
     Usage:  listfonts
     
     Description:  listfonts, used on SGI systems only, lists the IRIS GL
     fonts available for use in vis5d's 3-D window.  After listing the
     fonts you may use one in vis5d by specifying it with the -font option.
     For non-SGI systems or systems using OpenGL, use the xlsfonts or
     xfontsel program to select a font.
     
     
comp5d
     Usage:  comp5d N M filename
     
     Description:  comp5d converts one or more McIDAS GR3D files to the
     comp5d format used in previous (and the current) versions of vis5d.
     
     N is the first 3D grid file number and M is the number of grid files
     in the data set.  The M parameter allows data sets which span multiple
     grid files and should not be confused with the total number of 3D
     grids in the data set.
     
     filename is the name of the compressed grid file.  You can choose
     whatever name you want, but note that comp5d will convert the name to
     all upper case characters.
     
     If your data set contains wind vector components you can use the -wind
     keyword to select a subset of wind components or calculate horizontal
     wind speed, named 'SPD ', for the compressed file.  The longitude,
     latitude, and vertical components of the wind vector must be named 'U
     ', 'V   ' and 'W   ' respectively.  If you use the -wind keyword, then
     only those wind-relevant variables (i.e. U, V, W & SPD) whose names
     are listed after -wind will be included in the compressed file.  For
     example, to include SPD and W in the compressed file, from a 3D grid
     file containing U, V and W components, use the command:

     comp5d N M F -wind SPD W
     
     
help
     Usage:  help utilityname
     
     Description:  The help command will list a quick reference to the parameter
     formats for the named utility such as igg3d, igu3d, gg3d, and comp5d
     utilities.  Example:  help igg3d


maketopo.c
     This program, found in the util directory, is a template program for
     generating your own new topography (*.TOPO) files.  Read the information at
     the top of the file for instructions.  To compile maketopo see the makefile
     named maketopo.m.
     

makemap.c
     This program, found in the util directory, is a template program for
     generating your own new McIDAS map outline (OUTL*) files.  Read the
     information at the top of the file for instructions.  To compile makemap
     see the makefile named makemap.m.  If you create a map with lots too many
     line segments, it will be displayed with some line segments missing and
     some extra crazy line segments.  You can fix this by increasing MAXMAPVERT
     and MAXMAPSEG in src/globals.h, then re-making vis5d.
     
     
newmap.c
     This program and mapfunc.f, found in the util directory, is used to
     transform the vertices of an existing map outline file to make a new map
     outline file.  This might be useful if you need to transform a map to a new
     coordinate system.  Read the newmap.c and newmap.m files for more
     information.



6.  USING Vis5D TO VISUALIZE YOUR DATA

     This section describes how to use the Vis5D visualization program, vis5d.
It is almost completely controlled using the mouse with a graphical user
interface.  The best way to learn to use it is to experiment.  There is no way
to harm your data from within the program.


6.1 Starting vis5d

          ** IMPORTANT NOTE FOR OSF USERS **
          you need to run 'limit stacksize 32m' before you run vis5d

          ** IMPORTANT NOTE FOR SunOS 5 USERS **
          SunOS 5.x users:  The X shared memory extension may not work
          correctly.  If Vis5D prints an error message to the effect of "Shared
          memory error" then you'll have to append the following three lines to
          the end of your /etc/system file then reboot:
               set shmsys:shminfo_shmmax = 0x2000000
               set shmsys:shminfo_shmmni = 0x1000
               set shmsys:shminfo_shmseg = 0x100

After you have made a v5d file, you can interactively visualize it with the
command:

     vis5d file.v5d [options]

[options] may be any combination of the following (though none are usually
needed):

     -alpha
          Use alpha blending instead of "screen door" transparency.
     -area N
          [SGI only]  Specifies the first of a sequence of McIDAS area files to
          read and then display inside the 3-D box.  See section 6.15 for more
          information.
     -box x y z
          This lets you specify the aspect ratio or proportions of the 3-D box.
          Default values are 2 2 1.
     -barbs
          Use wind barbs in place of wind vectors.
     -date
          Use 'dd month yy' in place of 'yyddd' on the clock.
     -font xfontname
     -font glfontname height
          Set the font used for the clock and text labels in the 3-D window.
          You can determine which form of the font option is used on your system
          by typing vis5d alone and examining the options.
          The first form expects the name of an X window system font.  Use the
          xlsfonts command to see a list of X fonts on your system.
          The second form expects the name and size (72=1 inch) of an IRIS GL
          font.  Use the listfonts command included with Vis5D to see a list of
          GL fonts on your system.
          Example 1:  vis5d LAMPS.v5d -font fg-30
          Example 2:  vis5d LAMPS.v5d -font Helvetica 30
     -full
          Open the 3-D window as a borderless, full-screen size window.
     -funcpath pathname
          Specify the directory to search for user Fortran functions.
          Example  vis5d LAMPS.v5d -funcpath /usr/local/vis5d/userfuncs
     -geometry WxH+X+Y  (or WxH or +X+Y)
          Specify the geometry of the 3-D window.
          Example  vis5d LAMPS.v5d -geometry 640x480-10+10
     -hirestopo
          Display a high-resolution topography.  This is only recommended on
          systems with fast graphics hardware.
     -legend position size
          Set color legend position and size.  Position values are 1 (bottom,
          the default), 2 (top), 3 (left) and 4 (right).  Size is the height of
          the legend bar and is between 10 and 1000 (default=128).
     -log [a] [b]
          Display height on a logarithmic axis instead of linear.  This is
          discussed in section 3.2.  The optional arguments a and b are the
          scale and exponent factors in the height/pressure equation.  The
          defaults are 1012.5 and -7.2, respectively.
     -map file
          Use a map file other than the default of OUTLSUPW.  See section 2.3 to
          setup a different default.
          Example:  vis5d LAMPS.v5d -map OUTLUSAL
     -mbs n
          Override the assumed system memory size of 32 megabytes.  See section
          2.3 to setup a different default value.
     -path pathname
          Use a different path for map and topo files instead of the current.
          Example:  vis5d LAMPS.v5d -path /usr3/data
     -projection p
          Set the display map projection, default is to display data in its
          natural projection (obtained from the data file).
          p may be one of:
               cylindrical    - display data on a cylindrical Earth
               spherical - display data on a spherical Earth
          Only the first 3 characters are significant/needed.  You will be
          promted for
          additional parameters.
          Example:  vis5d LAMPS.v5d -projection spherical
     -quickstart
          Dont load any grids when starting vis5d, even if the whole file will
          fit into memory.  The grids will be read as needed.  This option is
          useful when reading a file via NFS.
     -rate ms
          Change the default animation rate.  ms is the minimum delay in
          milliseconds between frames.  Default is 100 ms.
     -script script.tcl
          Specifies a Vis5D/Tcl script to execute automatically.
     -sequence filename
          [not available on all systems]  Specifies a file containing a sequence
          of images to texture map over the topography.  See section 6.15 for
          more information.
     -texture rgbfile
          [not available on all systems]  Specify an SGI .rgb file to texture
          map over the topography.  See section 6.15 for more information.
     -topo file
          Use a topography file other than the default of EARTH.TOPO.  See
          section 2.3 to setup a different default.
     -trajvars uvar vvar [wvar]
          Specify which variables are to be used for trajectory tracing.
          Defaults are U, V, and W.
          Example:  vis5d LAMPS.v5d -trajvars U2 V2 W2
     -vertical v
          Set the vertical coordinate system, default is obtained from datafile.
          v may be one of:
               generic   - linear, equally spaced levels in generic units
               equal     - linear, equally spaced levels in km
               nonequal  - linear, unequally spaced levels in km
          Only the first 3 characters of v are significant/needed.  You will be
          prompted for additional parameters.
          Example:  vis5d LAMPS.v5d -vertical nonequal
     -wdpy xdisplay
          Put the widgets on a different X display.  Useful in combination with
          -full for making slides and videos.
          Example:  vis5d LAMPS.v5d -full -wdpy pluto:0
     -wide w
          Set width of line segments in pixels (default is 1.0).  Again, useful
          for making videos.
          Example:  vis5d LAMPS.v5d -wide 3.0
     -wind2 uvar vvar [wvar]
          Specify the names of a secondary set of U, V, and (optionally) W wind
          component variables to use when drawing the Hwind2, Vwind2 and Strm2
          vector slices.  Useful when you have two sets of wind vector
          components that you want to visualize simultaneously.
          Example:  vis5d MYDATA -wind2 U2 V2 W2
          

     If you start vis5d without arguments you will get a list of all the command
line options and keyboard functions.  Otherwise, vis5d will begin by reading the
data file.

     Previous versions of vis5d required that the entire file be read into main
memory; if you didn't have sufficient memory you couldn't visualize the file.
In version 4.0 and higher, this restriction is lifted; you may visualize files
which are larger than main memory.  This is implemented with a grid cache: vis5d
reads data only when needed and discards it on a least-recently-used basis.
Small files will be read in their entirety as in previous versions.

     For the user, this means vis5d will allow you to visualize large files even
with only 32MB of main memory.  However, performance will degrade as the ratio
of file size to main memory size increases.  If you observe sluggish performance
and a lot of disk activity while running vis5d you should get more memory.


6.2  The Control Panel

     After vis5d has opened/read your file, two windows will appear:  a 3-D
window on the right and a control panel on the left of the screen.  The 3-D
window is used to view and interact with the data.  In its upper-left corner is
a combination analog/digital clock which indicates the current time step.  The
control panel contains several groups of buttons.

     Starting at the top, the first button group contains the following buttons:

          [ANIMATE]  [STEP]     NEW VAR    EXIT
          [TEXTURE]  TOP        SOUTH      WEST
          [TOPO]     [MAP]      BOX        CLOCK
          SAVE       RESTORE    GRID #'s   CONT #'s
          [ANIM-REC] REVERSE    [SAVE PIC] [PERSPEC]
          SCRIPT     INTERP     UVW VARS

     These buttons are used to control the primary functions of vis5d.  Some of
the above buttons are enclosed in brackets [] to indicates that they may be
blank upon starting vis5d.  This will happen when the button does not apply to
the current data set, because the button would conflict with a command line
option, or because the feature is not available on your hardware.

     The next group of radio buttons control the viewing mode which determines
how the mouse is used in the 3-D window:

     Normal    Normal mouse mode is used to rotate, zoom, and pan the
               graphics in the 3-D window.  See section 6.3.
     
     Trajectory     This mode is used for creating and displaying wind
               trajectories.  See section 6.7.
     
     Slice     This mode is used to reposition horizontal and vertical
               slices.  See section 6.5.
     
     Label     This mode is used to create and edit text labels in the 3-D
               window.  See section 6.8.
     
     Probe     This mode is used to inspect individual grid values by
               moving a 3-D cursor through the 3-D grid.  See section 6.9.
     
     Sounding  This mode is used to display a vertical sounding and SkewT
               at the location of a moveable vertical cursor.  See section
               6.12.

     These modes are mutually exclusive; only one may be selected at a time.  To
the immediate right of these buttons is the mouse button legend.  It is there to
remind you of the use of each mouse button in the 3-D window for the currently
selected mode.

Next are buttons labeled:

      Hwind1   Vwind1   HStrm   Hwind2   Vwind2   VStrm

     A wind vector slice (Hwind or Vwind) depicts wind values by drawing small
arrows which point in the direction of the wind.  The length of each line
segment indicates its magnitude.  The tails of the line segments are all
anchored within a horizontal or vertical plane through the 3-D box.  The
horizontal wind streamline slice (HStrm) depicts wind values by drawing
streamlines on a horizontal plane.  The vertical wind streamline slice (VStrm)
depicts wind values by drawing streamlines on a vertical plane.  The location of
slice planes can be changed with the mouse while in "Slice" mode.  See section
6.5 for more details.

     The bottom part of the control panel window contains a 2-D matrix of
buttons. Each row corresponds to a physical variable in your dataset.  Each
column corresponds to one type of graphical representation.  By selecting the
correct row and column you can view any variable as a 3-D isosurface, horizontal
contour slice, vertical contour slice, horizontal colored slice, vertical
colored slice, or volume rendering.  This matrix of button is scrollable if
there are more rows of buttons than will fit in the window.  You can use the
mouse to drag the scrollbar or press the up/down arrow keys on your keyboard to
scroll the button matrix.

     The display of any graphic is controlled by clicking on its widget button
with the left mouse button.  Each type of graphic also has a small pop-up
control window which appears when turned on.  The control windows are different
for each type of graphic and are explained below.  To bring up a graphic's
control window without toggling its display, use the middle mouse button.  When
the graphic is displayed it will be the same color as the widget button, making
it easy to distinguish and identify different variables in the display.  To
change the color of the graphic, click on its widget button with the right mouse
button and a small window with four slider widgets will appear.  By changing the
levels of red, green, and blue you can make any color.

     If the control panel window becomes obscured by other windows, you can
bring it to the top by pressing the "F1" key while the mouse pointer is in the 3-
D window.  This is especially useful when using the '-full' option.


6.3 Controlling vis5d

     The topmost group of buttons in the control panel operate the main
functions of vis5d.  Some will be discussed in more detail later.

     ANIMATE   This toggle button turns animation on or off. Use the left or
               middle mouse buttons for forward animation and the right mouse
               button for reverse animation.  Does not appear when viewing data
               sets with one time step.  To make the animation slower or faster,
               hit the S and F key on the keyboard while the mouse cursor is
               inside the 3-D viewing window.
     
     STEP      This button has three possible uses depending on which mouse
               button is pressed:
                 Left Button - Step ahead one time step
                 Middle Button - Go to first time step.
                 Right Button - Backward one time step.
               This button does not appear when viewing data sets with one time
               step.
     
     NEW VAR   Used to duplicate physical variables or invoke external analysis
               functions. This is explained further in section 6.11
     
     EXIT      Exit the program.  A window will appear to ask you to verify your
               decision.
     
     TEXTURE   Toggles display of texture maps on/off if they are loaded.  See
               section 6.15 for more information.
     
     TOP       Depending on which mouse button is pressed:
                 Left or Middle:  Reset the 3-D window to the default top-view.
                 Right:  Set the 3-D window to a bottom-view.
     
     SOUTH     Depending on which mouse button is pressed:
                 Left or Middle: Set 3-D window to a south-view.
                 Right:  Set 3-D window to a north-view.
     
     WEST      Depending on which mouse button is pressed:
                 Left or Middle:  Set 3-D window to a west-view.
                 Right:  Set 3-D window to an east-view.
     
     TOPO      Toggle the display of topography.  This button will not appear if
               the topography file was not found.  Click on TOPO with the right
               mouse button to edit the topography color.
     
     MAP       Toggle the display of map lines.  This button will not appear if
               the map file was not found.  Click on MAP with the right mouse
               button to edit the color of the map lines.
     
     BOX       Toggle the display of the 3-D box.
     
     CLOCK     Toggle the display of the clock.
     
     SAVE      Save current graphics and colors.  After you've setup a variety
               of isosurfaces, slice, wind trajectories and colors it is useful
               to be able to save them and restore them the next time the data
               set is visualized.  You'll be prompted for a filename.  The file
               format, as of Vis5D 4.2 is a Tcl script.  See section 6.16 for
               more information.
     
     RESTORE   Restore the information save with the SAVE button.  See section
               6.16 for more information.
     
     GRID #s   Normally the bounds of the data set in latitude, longitude and
               kilometers are displayed along the edges of the box.  Use this
               button to display the numbers in grid coordinates instead.
     
     CONT #s   The numbers which are drawn on contour line slices can be toggled
               on or off with this button.
     
     [ANIM-REC]     This button works just like ANIMATE but allows fast
               animations on system with slow 3-D rendering.  After each time
               step is rendered the image is saved in memory.  When the
               animation loop repeats the images are quickly copied from memory
               to the 3-D window resulting in a faster animation.
     
     REVERSE   Normally, the 3-D box and clock are drawn in white on a black
               background.  This option reverses that and draws a black box and
               clock on a white background.  This is useful for making paper
               print outs.
     
     SAVE PIC  Used to save the image in the 3-D window to a file.  Depending on
               what system you're using a number of different picture file
               formats are supported.  On SGI systems be sure you have the
               'tops', 'frombin', and 'togif' program installed from your IRIX
               CD-ROM.  When using OpenGL on SGIs the 'fromxwd' program is also
               needed.  Unfortunately there is a bug in this program which often
               causes it to fail.  Included with vis5d however is a patched
               version of fromxwd.
     
     PERSPEC   Toggle between perspective and orthogonal viewing projections.
     
     SCRIPT    Used to run Vis5D Tcl scripts.  When you click on this button a
               file request will appear in which you can select the Tcl script
               to run.  For more information see section 6.16.
     
     INTERP    Starts the Vis5D interactive interpreter.  In your shell window
               you may then enter Tcl commands.  Vis5D will be suspended while
               the interpreter is active.  Type 'exit' to exit the interpreter.
               For more information see section 6.16.
     
     UVW VARS  Opens a window in which you can specify the names of the
               variables to use for computing trajectories and wind slices.
     
     LEGENDS   Toggles the display of colorbar legends in the 3-D window.
     
     

6.4 Viewing Modes

     In 'Normal' mouse mode the mouse is used to view the data in the 3-D
window.  By pressing the left mouse button and moving the mouse while the cursor
is in the 3-D window, the 3-D image can be rotated.  At any instant you can only
control two of the three degrees of freedom of box rotations.  However, by
releasing and re-pressing the left mouse button you can change your "grip" on
the box.  With practice you will learn to control the box through a series of
mouse moves, releasing and re-pressing the left button between moves.

     The center button controls two very different things depending on how the
mouse is moved.  Holding the center button down and sliding the mouse away from
yourself zooms in, making the box get bigger.  Sliding the mouse towards
yourself zooms out and makes the box get smaller.  Holding the center button
down and sliding the mouse right moves a plane of invisibility (i.e. a clipping
plane) into the box, creating a cut away view of the box contents.  Sliding the
mouse left brings the clipping plane toward yourself, eventually out of the box
altogether.

     The right mouse button is pressed to translate the box in the window.  This
is useful if you want to zoom in to something that is not in the center of the
box.  Note that the center of rotation for box rotations stays at the center of
the screen rather than in the center of the box.

     The other five viewing modes will be discussed in detail in following
sections.


6.5 Isosurfaces

     An isosurface (3-D contour surface) shows the 3-D volume bounded by a
particular isovalue.  The isosurface has the specified iso-level, the volume
inside contains values greater (or less) than the isovalue.  The volume outside
contains values less (or greater) than the isovalue.

     The first column of buttons in the control panel's button matrix controls
isosurfaces.  Clicking on one of these buttons with the left mouse button causes
a pop-up window with a slider and OK button to appear below.  Select an isovalue
on the slider and click on the OK button to generate an isosurface for all time
steps.

     Toggling ANIMATE on will let you watch the time dynamics of the iso-level
contour surfaces.  Note that the surfaces are generated asynchronously with the
animation, so you may not see the surfaces for all the time steps as the clock
hand makes it revolution.  The new surfaces will appear on successive clock
revolutions.

     Clicking on an isosurface button with the middle mouse button will summon
the pop-up window without toggling the surface on or off.


6.5.1 Isosurface Color

     An isosurface may either be drawn entirely in one color or colored
according to the values of another physical variable.

     To change the color of an isosurface, click on the appropriate isosurface
button with the right mouse button.  A window will appear with a column of
variable names (first button labeled "monocolor") and four sliders labeled red,
green, blue, and transparency.

     By default, monocoloring is used.  To change the isosurfaces's color just
move the red, green, and blue sliders.

     If you click on a button other than "monocolor" you will tell vis5d to draw
the isosurface according to another physical variable.  The red,green,blue
sliders will be replaced with a color table editor.  You can change the color
table (which maps data values to colors) by drawing new curves with the mouse or
by pressing the up, down, left, and right cursor keys on your keyboard.

     As an example, suppose you're viewing the LAMPS.v5d data set.  Make an
isosurface of wind speed at 40 m/s.  The isosurface should be blue.  Click on
the SPD isosurface button with
your right mouse button.  The color window appears.  Click on the T button in
that window and
the isosurface will now be colored according to temperature.  You can modify the
mapping from
temperature values to colors by "drawing" the red, green, and blue curves in the
color table window with the mouse buttons or by pressing the cursor keys.
Changing the color table is explained more below in the section about colored
slices.



6.6 Slices

     Slices allow you to look at planar cross sections of data in the 3-D box.
These slices can be oriented either horizontally or vertically and may depict
either contour lines, colored slices, wind vectors, or wind stream lines.

     As described in section 6.1, the last group of buttons on the control panel
is a matrix of buttons, the second through fifth columns of which control
slices.  There is a column of buttons for horizontal contour slices, vertical
contour slices, horizontal colored slices and vertical colored slices,
respectively.  If your data set contains U, V, and W variables, there will also
be a row of wind vector slice buttons as described in 6.2.  There are two
buttons for horizontal wind slices and two buttons for vertical wind slices.

     To activate/turn on a slice, click on the appropriate widget button with
the left mouse button.  The initial position for slices is the middle of the
box.  The exact slice location in terms of latitude, longitude or elevation is
given by a small numeric labels near the one corner of each slice.  To print the
numbers as grid coordinates instead of geographic coordinates, toggle the "GRID
#s" widget button on the control panel.

     The position of slices can be changed interactively using the mouse.  To do
so you must first be in SLICE mode by selecting the SLICE radio button.  To move
any slice, simply point at the slice's corner with the mouse, press the right
mouse button and drag it to a new position.  Vertical slices may also be moved
in a perpendicular motion by "grabbing" the middle of the top or bottom edge and
dragging it.  A slice may be moved while in animation mode, however, some
jumpiness may occur because new slices are computed asynchronously.


6.6.1 Contour Line Slices

     When viewing a horizontal or vertical contour line slice (button columns
two and three) a small control window will appear as well.  In this pop-up
window you can enter the interval to
use between contour lines.  Just type in a new number to change the interval.
Decreasing the interval will cause denser contour lines to be generated,
increasing the interval will result in sparser lines.

     If you enter a negative interval then all contour lines with a negative
value will be drawn with dashed lines while positive values will be drawn with
solid lines.

     Optionally, after the interval value you may specify a range of values
(a,b) which will cause only contour values between a and b to be drawn.  For
example, suppose you enter

     -10 (-30,20)

This will result in contour lines for values between -30 and 20 at intervals of
10 with negative lines drawn as dashed lines.

     The "CONT #s" button on the control panel toggles the display of the
contour numbers within the slice.


6.6.2 Colored Slices

     When a viewing a horizontal or vertical colored slice (button columns four
and five) a color table window will appear.  In this pop-up window you can
change the mapping from data values to colors.  If the LEGENDS control panel
button is selected the color table will also be displayed in the 3-D viewing
window.

     The window shows graphs of red, green, and blue over the range of data
values.  To change the red, green, or blue function press the left, middle, or
right mouse button, respectively, and drag the mouse to draw a new function.  By
default, low data values are mapped to blue and high data values are mapped to
red.

     Instead of using the mouse you can use the keyboard cursor (arrow) keys to
modify the shape and position of the default function curves.  Press the
left/right keys to move the curves left or right.  Press the up/down keys to
change the shape of the curves.

     You may also change the transparency of the slice as a function of the data
values.  Press and hold the SHIFT key while using the mouse or up/down keys to
change the transparency.

There are a number of other keyboard controls for the color table window:
     r    reset red, green and blue values
     R    reset transparency values
     c    copy color to an off-screen clipboard
     p    paste colors from the off-screen clipboard
     s    save color values to a file, enter filename in your shell window
     l    load color values from a file, enter filename in your shell window


6.6.3 Wind Vector Slices

     Wind vector slices are displayed with the buttons near the center of the
control panel labeled HWIND-1, VWIND-1, HWIND-2 and VWIND-2.  The pop-up window
for these
graphics contains two type-in fields to control the density and scaling of the
wind vectors.  The scale parameter is used to multiply the length of vectors
drawn.  If you want to double the length of all vectors, enter 2.0.  If you want
to halve the lengths, enter 0.5.  The density parameter controls how many wind
vectors are displayed.  This value can only be between zero and one.  To make
one-half the number of vectors, enter 0.5, for one-fourth enter 0.25, etc.  The
default values for both parameters is 1.0.
     
6.6.4 Wind Stream Slices

     Wind stream slices show the path of wind as connected line segments.  The
pop-up control window contains a type-in widget to control the density of
streamlines (note that the scale parameter is not used).  The density parameter
controls how many streamlines are displayed.  This value can only be between 0.5
and 2.0.  To make one-half the number of streamlines, enter 0.5, to make twice
the number of streamlines, enter 2.0, etc.  The default density is 1.0.

6.6.5 Slice colors

     The color of a slice's control button matches that of the slice itself
(except for colored slices for which the slice's tick mark matches the slice's
button.)  To change the color of a slice
click on the slice's button with the right mouse button.  A window with red,
green, and blue sliders will appear.  Move the sliders to change the color.
     

6.7 Volume Rendering

     Volume rendering is a technique for displaying a 3-dimensional field as a
semi-transparent colored fog.  Though volume renderings of some physical
variables don't look, others can be displayed very effectively with the right
color mapping.

     The volume rendering feature is available in Vis5D on almost all systems.
One exception is older SGI computers using IRIS GL which don't support alpha
blending.  Be warned that systems without 3-D graphics hardware (i.e. those
using Mesa) will render volumes very slowly.

     The sixth column of buttons on the control panel are the volume buttons.
Only one may be displayed at a time.  When a volume rendering is activated a pop-
up window with a color table appears.  This color table is used in exactly the
same way as described for colored slices above.  That is, using the mouse or
keyboard you can change the function which maps data values to color and
transparency.  Again, the transparency can be changed while holding down the
SHIFT key and drawing a curve with the mouse or pressing the up/down keys.

For those who are curious about the implementation of this feature, the volume
rendering is made as follows:
     1.Examine the current viewing transformation to determine which axis of
       the 3-D box is most nearly parallel to the view direction.
     2.Create a number of colored slices perpindicular to that axis which map
       data values to colors and opacity.
     3.Render the colored slices in back to front order.  The alpha values at
       vertices are interpolated and blended to make smooth transitions between
       and within slices.

     Despite the simplicity of the algorithm, most fields are rendered
acceptably.  Those that aren't can be improved by adjusting the color and
opacity mappings.  While more attractive volume rendering techniques are known,
this technique can be implemented quickly on many systems.


6.8 Wind Trajectories

     Wind trajectories trace the motion of air through the 3-D volume much line
smoke trails in a wind tunnel.  To enter trajectory mode select the TRAJECTORY
radio button on the control panel.  A pop-up window will appear near the bottom
of the screen and a 3-D cursor will appear inside the 3-D view box.  This 3-D
cursor is used to specify where a new wind trajectory should be made.  The STEP
button on the main control panel is also important because it is used to select
the time step at which to create the trajectory.

     Wind trajectories are dealt with in sets.  Currently, eight sets are
available.  Each set is represented in the trajectory window with a button
labeled Set1, Set2, ..., Set8.  Each set can be individually displayed, colored,
or deleted.  As you create new trajectories you may want to group them in sets
corresponding to location, time, etc.

     The first step in creating a trajectory is to select a position with the 3-
D cursor.  Use the right mouse button to drag the 3-D cursor around inside the 3-
D box.  The 3-D cursor will move in 2-D in a plane parallel to the plane of
projection.  That is, the cursor will stay at a constant distance of depth.  By
alternately rotating the view box with the left mouse button and placing the
cursor with the right mouse button, the 3-D cursor can be placed anywhere inside
the view box.  The TOP, SOUTH, and WEST buttons as explained in section 6.2 can
also be useful when making trajectories.

     Second you should select a time step with the STEP button on the control
panel.  When the trajectory is made, it will be traced forward from the current
time step to the last time step and will be traced backward through time to the
first time step.

     Finally, to make a trajectory at the current cursor location and current
time step, press the middle mouse button when pointing inside the 3-D window.
The trajectory will appear as a line segment.  By turning on the ANIMATE button,
you can observe how the trajectory travels through time and space.  Typically,
you will repeat the process of positioning the 3-D cursor and clicking the
middle mouse button to create a set of trajectories.

     Interesting results can be seen by making a trajectory when the ANIMATE
button is turned on:  a trajectory will be created for every time step instead
of just one.  This will show you the path of every air parcel which passes
through a single point in space.

Here is a summary of the various trajectory functions:

      1.To position the 3-D cursor, use a combination of rotating the view box
        with the left mouse button and dragging the 3-D cursor with the right
        mouse button.
     
      2.Use the STEP button or ANIMATE option to select a time step.
     
      3.Press the middle mouse button to create a trajectory at the current
        cursor location and time step.
     
      4.To toggle the display of a trajectory set on or off, click on the set
        button with the left mouse button.
     
      5.Select the current trajectory set by clicking on the set button with
        the middle mouse button.
     
      6.A trajectory set may be deleted with the 'Delete Set' button in the
        trajectories window.  You will asked to verify your decision.
     
      7.You can delete the last trajectory made by clicking on the 'Delete
        Last' button in the trajectories window.

     Wind trajectories can be depicted in two ways:  as line segments or as
ribbons.  You can select ribbons by clicking on the RIBBON button in the
trajectory window.  Toggling the RIBBON button will not effect trajectories you
have already made; it only controls how new trajectories will be displayed.

     The trajectory window also contains two type-in widgets labeled STEP and
LENGTH.  The STEP value is used to control the step size used in the trajectory
tracing algorithm.  The LENGTH value is used to control the length of
trajectories.  1.0 is the default value for each.  Each acts as a multiplier.
If you want the trajectory tracer to integrate in steps 1/2 the default size,
enter a step value of 0.5.  If you want trajectories to be twice as long as the
default length, enter a length value of 2.0

     The color of trajectories is controlled in the same way as for isosurfaces.
That is, a trajectory set may either be mono-colored or colored according to
another physical variable.  Click on the trajectory set button with the right
mouse button to bring up its color window.  See section 6.5.1 for details on
using the color window.

     When viewing color-mapped trajectores be aware that the color of a
trajectory is time dependent.  Only the head of the trajectory is colored
according to the value of another variable for the current time step.  The tail
of the trajectory is colored according to the color of the other variable when
the head was at that location.


6.9 Wind Variables

     By default, wind trajectories and the first set of wind slices are computed
from the variables named U, V, and W while the second set of wind slices are
computed from the variables named U2, V2, and W2.  Other variables can be
specified through the "UVW VARS" button on the control panel.  When you click on
this button a pop-up window appears in which you can
specify the names of the variables to use for computing trajectories, the first
set of wind slices, and the second set of wind slices.  Just type in the new
variables names.  Be aware that uppercase and lowercase are significant.  Be
sure you enter valid names otherwise vis5d may not compute the graphic you
select.

     After you've entered new wind component variable names click on APPLY to
use the new values but keep the window visible.  Click on OK to use the new
values and close the window.  Click on CANCEL to discard your changes and close
the window.

     You can also specify the wind component variables on the command line when
you start vis5d.  See section 6.1.


6.10 Text Labels

     Text labels are used to annotate the image in the 3-D viewing window.
Typically this is used for making presentation graphics.  You could add a title,
your name, the date, highlight a particular feature of the data, or document the
meaning of the data seen in the window.

     To enter text labeling mode select the LABEL radio button on the control
panel.

     To create a text label position the mouse pointer somewhere in the 3-D
window and press the left mouse button.  A vertical bar cursor will appear at
that location and you can now type in the text.  The <Backspace> key can be used
to correct errors.  When you are finished, press <Return>.

     To move a text label to a new position, point at it with the mouse, hold
down the middle mouse button and drag the mouse.  As you move the mouse an
outline of the text will be dragged with the pointer until you release the mouse
button.

     To delete a text label, pointing at it with the mouse and pressing the
right mouse button.  Be careful, you will not be asked for verification before
deleting a label.  Once it's deleted you can only restore it by retyping it.

     The SAVE button on the control panel will save any text labels you have
made.

     Use the '-font' command option to select a different font.


6.11 Data Probe

     Sometimes it's useful to be able to inspect individual data values at
various locations in the 3-D volume.  You can do this with the data probe.
Click on the PROBE radio button on the control panel.  A 3-D cursor appears in
the 3-D box which you can move around using the right mouse button.  For each
physical variable the value for the current time step is printed along the left
edge of the 3-D window.  If physical units are specified for the variable they
will be printed next to the value.  Units can be assigned with the v5dSetUnits()
function in your data conversion program as described in section 3.1.

     If you turn on the GRID #'s button, the probe will be constrained to
integral grid coordinates.  That is, the cursor will 'snap' to the nearest
discrete grid coordinate.


6.12  Vertical Sounding and SkewT

     When you select Sounding mode, Vis5D displays a vertical line cursor that
runs from the bottom to the top of the 3-D box, and displays a vertical sounding
window.  The sounding window includes a SkewT diagram generated for grid data at
the location of the vertical cursor (unless your data set uses generic vertical
coordinates), and vertical plots of up to three variables.  The user can
interactively select and change which variables are used for temperature, dew
point and wind fields in the SkewT diagram.  Variables named T, TD, U and V are
used as defaults if they exist.  The user can also interactively select and
change which variables are used for the vertical plots.  Users can interactively
control the background of the SkewT diagram and vertical plots, including dry
adiabats, moist adiabats, constant mixing ratio lines and height tick marks.
They can also interactively resize and reposition the sounding window.


6.13  Making New Variables

     The NEW VAR button on the control panel is used to add new physical
variables to the button matrix.  There are three kinds of new variables you can
add:

     1. Cloned variables:  these are copies of existing variables.  You can use
a cloned variable to make two different isosurfaces of the same variable
simultaneously, for example.

     2. External function variables:  you can invoke an external function (which
you write) to compute a new variable as a function of existing variables.

     3. Computed variables:  you can compute a new variable by typing in a
formula involving values of existing variables.

     When you click on the NEW VAR button a window appears which lists the
variables that you can clone, lists the external functions that you can invoke,
and lets you type in a formula for computing a new variable.  After a new
variable has been created anew row of buttons will be added to the control panel
for the new variable.  You can use then make isosurfaces, contour slices, etc.
of the that variable like any other.


6.13.1  Cloned Variables

     Suppose you want to clone the U wind component variable so that you can
make both +20 and -20 isosurfaces of it.  First, click on NEW VAR and then
select U from the pop-up window.  The cloned variable will be named U'.  You can
then treat U' as any other variable and make an isosurface of it.


6.13.2  Type-in Formulas

     Type-in formulas let you type in mathematical expressions to compute new
variables as a function of existing variables.  For example, to compute wind
speed from U, V, and W you would enter the formula:

     SPD3D = SQRT( U*U + V*V + W*W )

To compute the ration of the dew point (TD) to the temperature you would enter
the formula:

     RATIO = TD / T

     Formulas may use the names of existing variables, numbers, the arithmetic
operations +, -, *, / and ** (exponentiation), and the functions SQRT, EXP, LOG,
SIN, COS, TAN, ATAN (arc tangent), ABS (absolute value), MIN and MAX.  MIN and
MAX take two arguments, while the other functions all take one argument.

     Click on the OK button to compute the new variable or CANCEL to discard the
formula.  You can edit the formula later by selecting it again from the NEW VAR
pop-up window.


6.13.3  External Analysis Functions

     External analysis functions are an advanced feature, so new Vis5D users may
want to skip this section for now.

     An external analysis function is a function written by you in FORTRAN which
is called by Vis5D to produce a new variable as a function of the existing
variables.  As an example, there is included a function SPD3D which computes
wind velocity as:  SPD3D = SQRT( U*U + V*V + W*W ).  Be aware that the external
function feature is intended for experienced Vis5D users who are also proficient
FORTRAN programmers.

     All external functions must be placed in a directory named "userfuncs"
(this may be changed in the vis5d.h file).  This is relative to the current
directory when you run vis5d.  For example, suppose you always run vis5d while
in "/usr/jones/data", then your analysis functions must be in
"/usr/jones/data/userfuncs".  Also, this directory contains a script "externf"
which is used to compile your function.

     To write an external function it's best to copy one of the supplied
examples and then modify it.  The included "userfuncs/example.f" is fully
commented for this purpose.  Later, when you call your function from within
vis5d, the function will be invoked once for each time step.  The arguments
passed to the function include:

     1. the number of physical variables in the data set
     2. the name of each variable
     3. the size of the 3-D grid
     4. the date and time of the time step
     5. map projection and vertical coordinate system information
     6. the actual 3-D grids of data for each physical variable

     Your function will have to scan the list of variable names to find the ones
it needs for the computation.  Then it must do the actual computation,
generating a new grid of data to return to vis5d.  The examples we've included
demonstrate how to do this.  Specifically, you should look at example.f which
has detailed documentation of the function arguments.  The map projection and
vertical coordinate system arguments work in exactly the same way as the
v5dCreate library call discussed insection 3.1

     Suppose you want your function to be named "delta".  Then the name of the
FORTRAN program must be "delta.f".  You would compile the function by typing
"externf delta".  If there are no errors, an executable file "delta" will be
written.  Then in vis5d when you select NEW VAR, "delta" should appear in the
list of functions in the pop-up window.

     There are two places for vis5d to get the grid data which it passes to your
external function:  from the original, uncompressed McIDAS file or the
compressed v5d/comp5d file.  The uncompressed McIDAS data is better because it
has more precision.  If the McIDAS file can't be found, then the compressed data
which vis5d has in memory will be passed to your external function.  Note that
this has no bearing whatsoever on the construction of your external function.

     You can retrieve the position and values of the data probe from within your
function.  To get the position of the probe use:

     CALL PROBEPOS( ROW, COL, LEV, LAT, LON, HGT )

The position in grid coordinates will be returned in ROW, COLumn, and LEVel.
The position in geographic coordinates will be returned in LATitude, LONgitude,
and HeiGhT.

To get the value of any physical variable at the current probe position and
current time step use:

     VALUE = PROBEVAL( VAR )

where VAR specifies which physical variable you want.


6.14 Saving Image Files and Printing

     The SAVE PIC button on the control panel can be used to save the image in
the 3-D window to a file.  When you click on SAVE PIC a pop-up window appears in
which you can select the file format and filename.  The choices of file formats
depends on the computer you're using.  The formats supported by Vis5D are:

     XWD - X Window Dump, displayable with xwud or xv.
     RGB - SGI image file format, displayable with ipaste or xv.
     GIF - Standard GIF format, displayable with xv and many other programs.
     PostScript - may be printed or viewed on-screen with a program like
     ghostview.
     Color PostScript - may be printed or viewed with a ghostview-like program.

     The irix4 and irix5 configurations of Vis5D (using GL) directly write RGB
files.  To make a GIF file the togif program must be available.  To make a
PostScript file requires the tops program.  togif and tops and many other RGB
file converters are shipped standard with IRIX.  If they're not found in
/usr/sbin install them from your IRIX CD-ROM.

     All other configurations of Vis5D (using OpenGL) directly write XWD files.
To make an RGB file the fromxwd program is used.  Unfortunately, the fromxwd
program shipped by SGI has a bug which causes it to fail.  Since source code for
fromxwd is shipped with IRIX we include a patched version which works correctly.
To make a gif file requires both fromxwd and togif (only available on SGI
systems).  To make a grayscale PostScript file requires the xpr utility
(standard with X11).  To make a color PostScript file the tops program is needed
(only available on SGI systems).

     If you don't have any of the utilities mentioned above you should try using
xv to convert your image files.  xv is available by ftp from export.lcs.mit.edu
in contrib/ and from ftp.cis.upenn.edu in the pub/ directory.

     To print a Vis5D image, position the mouse pointer over the 3-D window and
press the P key.  You'll be asked to verify your action.  Vis5D uses lpr to send
a PostScript image file to the default printer or the printer specified by the
PRINTER environment variable.  To generate the PostScript file Vis5D uses the
utilities described above.  If you have problems printing you should try to
first save your image as a PostScript file then try to print it manually using
lpr or lp.  Another option is to save your image as an XWD file then use xpr (a
standard X11 utility) to convert it to PostScript and print it.

     To learn more about the xwud, xpr, fromxwd, tops and togif program read the
man pages.  Many of these programs have options which you may find useful.


6.15 Texture mapping

     Texture mapping is a term from computer graphics which means to display a 2-
D image over a surface in 3-D.  In Vis5D you can display images over the
topography (or bottom of the 3-D box when topography is turned off) such as
satellite or map images.  Texture mapping is only available on SGI systems and
those using the Mesa library.  Hardware support for texture mapping is highly
recommended.

There are three types of texture/image mapping in Vis5D which can specified on
the command line:

     -area N   N is the number of the first of a sequence of McIDAS area files.
               The number of files read equals the number of timesteps in your
               datafile.  Images should all be of the same size.  You must use
               McIDAS to do remapping if necessary.
     
               Example:  Suppose your datafile has 4 time steps and you specify
               -area 100, then AREA0100, AREA0101, AREA0102 and AREA0103 will be
               loaded and displayed.
               
               This option needs the McIDAS library which is only available on
               SGI systems.
               
     -sequence file This works like the -area option, except that the data come
               from a very simple file format rather than from McIDAS area
               files.  The file starts with 3 int's that contain the number of
               images in the sequence, the number of lines per image, and the
               number of pixels per line.  The rest of the file contains the
               images, one byte per pixel.  The function read_texture_sequence
               in the image.c file of the src directory reads this file and
               serves as a file format reference for those wishing to create
               such image sequence files.

     -texture file  This options specifies a single image to display over the
               topography for all time steps.  The file format is the SGI RGB
               format.  The free XV program can be used to convert your image to
               RGB format.
     
When a texture map is available the TEXTURE button on the control panel is used
to toggle the display of the imagery on or off.



6.16 Tcl scripting

     Vis5D 4.3 features a scripting facility.  That is, you can control Vis5D
with a text file of commands using the Tcl language.  Scripting is an advanced
subject and documented separately in the Vis5D scripting document at
http://www.ssec.wisc.edu/~billh/script.html.

     Note that the SAVE and RESTORE buttons on the control panel write and read
Tcl files.  You may want to use bits of these files as a basis a new Tcl
scripts.


6.17 Keyboard Functions

     The following keyboard functions can be invoked while the mouse pointer is
inside the 3-D viewing window:

     Key  Function
     F1   Raise or lower the control panel window.  This is useful with the -
          full option.
     F2   Toggle display of system information including memory used and number
          of graphics to be computed.
     P    Print the current window image.  A PostScript printer must be
          available.  Set the PRINTER environment variable from your shell to
          specify which printer to use.
     S    Slower animation - increases the minimum time between frames by 10
          msec.
     F    Faster animation - decreases the minimum time between frames by 10
          msec.
     
     If you want to program your own keyboard functions look the in the file
src/gui.c for the
func1(), func2(), func3(), etc functions.  They are called when the
corresponding function key is pressed.


6.18  Final Notes

     The SGI version of vis5d use multiple CPUs if available to compute graphics
in the background thereby increasing vis5d's speed.  On other systems, vis5d
tries to interleave the computation of graphics with user interaction.  This
results in the user interface being a bit sluggish until all pending graphics
computations are completed.

     The vis5d user interface may be complex to describe in words, but we have
tried hard to make it simple in reality.  After a little practice using the
sample data sets we hope it feels natural.

     Since version 3.2 of Vis5D there is a user-contributed software directory:
contrib/.  See the README file in that directory for a description of current
contributions.



7.  THE v5dimport UTILITY

     The v5dimport utility is a new program for converting grid files to v5d
format, combining multiple source files, resampling to new coordinate systems
and culling variables and timesteps.  It has both a graphical and command line
user interface.

     For example, you may use v5dimport to read 2 McIDAS GR3D files and a 2-D
McIDAS GRID file, resample all the data to a Lambert Conformal projection, omit
the CWAT and VORT variables and then write the data to a Vis5D file called
lambert1.v5d.

The basic order of events when using v5dimport is:
     1. Read the input file(s).
     2. Select grids for output according to timestep, physical variable, map
       projection or vertical coordinate system.
     3. Setup a map projection and vertical coordinate system for the output
       file.
     4. Write the output file.  Resampling is done at this time.
     5. Optionally, start Vis5D on the output file.

Currently, v5dimport can read the following file formats:
     McIDAS GR3D and GRID files
     Vis5D v5d and comp5d files
     GRADS files
     "UW vis" files (used at the University of Wisconsin)
     EPA MM4 and RADM files (on Crays only)
     

7.1 Using v5dimport's graphical interface

Start v5dimport from your shell with

     v5dimport [-path pathname] [files]

where [files] is an optional list of input files and [-path pathname] specifies
that the directory named "pathname" is to be used as the default, in place of
the current directory, for the input file browser and for making output files.

When v5dimport has started you'll see its main window appear.  It consists of:
     1. a scrollable list of all grids scanned from the input files
     2. buttons used for selecting/culling grids according to variable name,
       timestep, projection or vertical coordinate system
     3. buttons and type-in fields for describing and creating the output file.


7.1.1 Reading input grids

     You may read additional grid files into v5dimport at any time by clicking
on the "Read file..." button.  Use the file selector to locate your file and
click on OK or CANCEL.  It's best to read all input files right at the beginning
because whenever a new file is read all grids are selected for output,
overriding any selections you may have previously made.

     The button labeled "Discard all grids" does exactly what it says.  It's
equivalent to exiting v5dimport and restarting it.

     After reading each input file, the list of grids shown in the top half of
the window, will be resorted by time then variable name.

The columns in this list are:
     Grid - grid number (no significant meaning)
     YYDDD - the year and date of the grid
     HHMMSS - the time of the grid in hours, minutes, and seconds
     Variable - the variable name
     Nr - number of grid rows
     Nc - number of grid columns
     Nl - number of grid levels
     Proj# - the projection number (see "Select by projection..." window)
     VCS# - the vertical coordinate system number (see "Select by VCS...")
     Filename - name of file the grid was found in


7.1.2 Selecting grids for output

     It's often the case that one wants to discard some physical variables or
timesteps from the input file so they aren't written to the output file.  By
default, all variables are selected for output.

     To select/cull variables, click on the "Select by variable..." button.  A
pop-up window will appear which lists all the variables.  The ones that are high
lighted are selected for ouput.  Click on variables names to select or deselect
them.

     Similarly, you can select timesteps via the "Select by time..." button.  A
pop-up window listing all time steps will appear.  Use the mouse to select the
time steps you want and unselect the timesteps you wish to omit.  Note that you
can select/deselect a number of timsteps by just dragging the mouse while
holding down the button.

     Finally, grids may be selected or discarded according to their map
projection or vertical coordinate system (VCS) via the "Select by
projectiion..." and "Select by VCS... buttons.

     Note that as you select/deselect timesteps, variables, projections, or VCSs
the effected grids will be high-lighted/unhigh-lighted in the main grid list.

     The "Select All" and "Select None" buttons do just what they imply.


7.1.3 Defining the output file

     The default parameters for the output file (grid size, projection, etc) are
taken from the first file read in.  You should always review these parameters
before making your output file.  It will often be necessary to change these
values.

     The number of rows, columns, and levels for the output file is specified by
the type-in fields on the main window labeld "Rows", "Columns" and "Max Levels".
Type in new values if the defaults are incorrect.

     The map projection for the output file can be viewed and changed by
clicking on the "Map projection..." button.  In this pop-up window you'll be
able to choose a map projection type then enter the specific projection
parameters.  There is also a "Guess" button which will attempt to find a
reasonable output projection given the currently selected grid list.  It's often
helpful to have the "Select by Projection" pop-up window on-screen to compare
the output projection to the input projections.

     The vertical coordinate system for the output file can be viewed and
changed by clicking on the "Vertical Coord System..." button.  In this pop-up
window you'll be able to choose a vertical coordinate system type and enter the
specific parameters.  This window also has a "Guess" button to try to find a
reasonable default.  Similarly, it's often helpful to have the "Select by VCS"
pop-up window on-screen to compare the output VCS to the input VCSs.


7.1.4 Making the output file

     Enter a filename for the output file in the type-in field at the bottom of
the main window then click on "Make".  Messages will be printed as the file
conversion takes place.  If there are any errors the process will halt.  Note
that generating the output file can be time-consuming if data must be resampled
from the input grid's coordinate system to a new coordinate system for the
output file.

     If you click on "Visualize" this will make the file and then automatically
start up Vis5D on that file (i.e., you don't need to click on "Make" first).  If
you type a filename in the type-in field, it wil use that name.  Otherwise, it
will use your login name followed by ".v5d".  If you want command line options
on the Vis5D command, put them in a file named "vis5d_options".  For example, "-
mbs 64".


7.1.5 Miscellaneous

An options window is available by clicking on the "Options..." button.

     The first item controls the "combining of co-located data".  It may be the
case that several 3-D grids, selected for output, are co-located in space and
time.  When computing the value to put in the output file you can either choose
the data value from the higher resolution grid at that location, or take the
average of all grid values at that grid location.

     The second item controls how grid data is compressed in the output file.
By default, grid values are scaled down to 1-byte integers.  Alternately, you
can scale down to 2-byte integers for better resolution, or perform no
compression/scaling by selecting 4-byte floating point values.  This option
respresents a tradeoff in file size and precision.


7.2 Using v5dimport's text interface

     The text/type-in interface to v5dimport is useful when X is not availableor
when you want to run v5dimport with a script.  To start v5dimport in text mode
enter:

     v5dimport -t [-path pathname] [files]

where [files] is an optional list of input files and [-path pathname] specifies
that the directory named "pathname" is to be used as the default, in place of
the current directory, for the input file browser and for making output files.
Through the text interface it's possible to run v5dimport with a script by using
your shell's import redirection feature:

     v5dimport -t <script

After you've invoked v5dimport with the -t option you'll see a >> prompt at
which you can issue any of these commands:

     exit   exit v5dimport
     help   online help
     list   show lists of grids, timesteps, variables, map projections, or
            vertical coordinate systems.
     read   read an input file
     keep/omit   used to select which grids, according to timestep, variable,
            map projection or vcs, are to be included in or omitted from the
            output file.
     info   display parameters of output file
     rows   specify number of grid rows for output file
     columnsspecify number of grid columns for output file
     levels specify max number of grid levels for output file
     projection  specify the output file's map projection
     vertical    specify the output file's vertical coordinate system
     make   make the output file
     visualize   make the output file and start Vis5D

Using the text interface to v5dimport is similar in strategy to the graphical
interface:
     1. Read input files
     2. Select grids by timestep, variable, projection, and/or VCS.  This is
       typically done by a series of list, omit, and keep commands.
     3. Set/adjust output file parameters. Typically a series of info, rows,
       columns, levels, projection, and vertical commands.
     4. Make the output file, or make the output file and start Vis5D.

Use the help command to learn the exact syntax for each command.

A v5dimport script is simply an ASCII file of v5dimport commands and their
arguments.  In the simplest case it may contain only a few commands such as:

     # read my file, omit two vars, write v5d file
     read mydata.dat
     omit var CW
     omit var RW
     make outdata.v5d
     exit
     
As v5dimport executes a script it prints each command and its result.  Lines
which start with a # are considered comments and ignored.


7.3 Adding support for new file format

     v5dimport was written so that adding code to read new file formats should
be easy.  The source code for v5dimport is in the import/ subdirectory.  Look
for the comment /*** ADD NEW FORMATS HERE ***/ to see where code has to be added
to support a new file format.

     Basically, you need to write two new functions.  One which scans your file
format to build a list of grid_info structs.  The other reads the actual grid
data from your file given a grid_info struct.  These functions should be put in
a new file named read_foo.c where foo is the name of your file format.  Then,
update the file.c file to use your functions.  Use the existing read_*.c files
as a guide.


7.4 Notes on specific file formats

     The symbol EPA is defined on the cc command line with -DEPA only on systems
which can read EPA files.  Currently, only Cray systems can read EPA files
because the EPA-provided file reading functions only work on Cray computers.

     The symbol MCIDAS is defined on the cc command line with -DMCIDAS only on
systems which can use the libmcidas.a file.  Only SGI's in 32-bit mode are
supported now.



8. SAMPLE DATA SETS

To demonstrate or experiment with Vis5D we provide two sample datasets.


8.1  Bob Schlesinger's thunderstorm simulation

To visualize the Schlensinger thunderstorm file enter the command

     vis5d SCHL.v5d

To view an isosurface of QL (moisture content):

     1. Click on the QL button in the left column of the button matrix.
     2. On the slider, select a value near 1.0, then click on the OK button.
     3. Turn on animation with the ANIMATE button.

To view a vertical contour line slice of QL:

     1. Turn off animation by clicking on ANIMATE again.
     2. Click on the QL button in the third column.
     3. Move the slice by first selecting the SLICE radio button.  Then use the
        right mouse button to drag any corner of the slice along the edges of
        the 3-D box.


8.2  LAMPS model

To visualize a LAMPS (Limited Area Meso-Scale Prediction System) model
simulation of an extratropical cyclone, enter the command:

     vis5d LAMPS.v5d

To view an isosurface of wind speed over a topography with map lines:

     1. Click on the TOPO and MAP buttons.
     2. Click on the SPD button in the first column.  Then select a value near
        45.0 on the slider and click on OK.
     3. Turn on ANIMATE and you will see an animation of the 45 m/s wind
        isosurface.

To make some interactive wind trajectories:

     1. Turn off the wind speed isosurface by clicking on the SPD button again
     2. Select the TRAJECTORY button.
     3. Move the mouse pointer into the 3-D window and press the middle mouse
        button.  You will get a series of white wind trajectory lines passing
        through the 3-D cursor location.
     4. Move the 3-D cursor by dragging it with the right mouse button then
        click the middle button to make more trajectories.
     5. Select RIBBON and then the SET 2 button and try making some yellow
        ribbon trajectories.


8.3  Example McIDAS files and utilities

     The Schlesinger and LAMPS data sets are also available as the 3D McIDAS
grid files named GR3D0001 and GR3D0002.  They are available on the Vis5D ftp
site.  See section 2 for more information.

To list the grids in GR3D0001 and to see statistics about them, enter the
commands:

     igg3d list 1 190 -gr3df 1
     igg3d info 1 190 -gr3df 1

The SCHL.v5d file was made from the GR3D0001 file with the command:

     gr3d_to_v5d 1 1 SCHL.v5d


To list the grids in GR3D0002 and to see statistics about them, enter the
commands:

     igg3d list 1 189 -gr3df 2
     igg3d info 1 189 -gr3df 2

The LAMPS.v5d file was made from the GR3D0002 file with the command:

     gr3d_to_v5d 2 1 LAMPS.v5d

A variety of other sample datasets are available on the ftp site or upon
request.



9. VERSION HISTORY

This is a summary of the versions of Vis5D.

1.0  (December 1988)
     This was the original version of Vis5D for the Stellar GS-1000.  It was
     used to give demonstrations at the ECMWF in December 1988 and at the AMS
     conference in Anahiem in January 1989.  It had the following features:
          Depict time series of multivariate 3-D grids by animated isosurfaces
               and horizontal contour line slices.
          World topography map with map boundaries.
          Wind trajectory tracing with the traj5d program.
     
2.0  (Fall 1991)
     This version was only available for the Stellar GS-1000/2000 and introduced
     the following features:
     
          Faster isosurface generation.
          Horizontal and vertical slices moved interactively with the mouse.
          Colored slices.
          Interactive wind trajectory creation.
          Ribbon trajectories.
          Label / text annotations.
          "Pretty" rendering option.
               
     The format of the compressed grid file was changed slightly with version
     2.0.  Specifically, the trajectory files of version 1.0 were eliminated,
     trajectories are now stored in the compressed grid file itself.  Also, the
     internal storage representation for surfaces and slices has been changed.
               
2.1  (February 1992)
     This is the first version of Vis5D available for the SGI and IBM
     workstations.  It was also modified to use less memory during isosurface
     generation.
     
2.2  (April 1992)
     This version of Vis5D runs on the base SGI Indigo with 8-bit color though
     some features not available.  It also has the following improvements:
     
          The -box option for changing the proportions of the 3-D box (SGI and
               Stardent only).
          User topography files.  Vis5D now uses the EARTH.TOPO file instead of
               TOPOHRES to make the map.  The maketopo.c program shows how to
               make new .TOPO files.  (SGI and Stardent only)

3.0  (August 1992)
     This version features the following improvements:
          Horizontal and vertical wind vector slices.
          Improved SAVE and RESTORE functionality.
          New trajectory widget options.
          Separate map and topography controls.
          CLONE option added.
          Simultaneous colored and contour line slices.
          Improved transparency, PRETTY option on SGI.
          Same source code for SGI, Stardent, and IBM.
          Improved portability and porting guide added.
          New video and hardcopy convenience features.

3.1  (July 1993)
     New features:
          User-written analysis functions.
          SAVE PIC button to save window image to a file.
          Perspective viewing mode.
          New contour line options to draw dashed negative lines and restrict
               contouring to a specific range of values.
          Data Probe mode.
          Topography color editing.
          Grid compression done layer-by-layer.

3.2  (August 1993)
     New features and changes:
          Volumetric rendering on SGI systems with VGX, VGXT, VTX, RE, or RE2
               graphics hardware.
          User-contributed software directory.
          2-D contour function rewritten in C.

3.3  (January 1994)
     New features:
          Vis5D ported to HP, DEC, Sun, and Kubota (DEC Alpha) workstations.
               The most important part of this work was the enhancement and
               integration of the VOGL library.  This work was done by Simon
               Baas and Hans de Jong for the Dutch Meteorological Institute,
               KNMI.  Porting to the Kubota Denali graphics system was done by
               Pratish Shah of Kubota Inc.  Thanks guys!
          -wdpy option now creates a window on the widget display which can be
               used to move and interact with the 3-D view using the widget
               display's mouse.
          SAVEPIC button let's you save the window image in PostScript or color
               PostScript formats (SGI only).
          -wind2 option added to specify a second set of U,V,W variables for the
               second set of wind vector slices.
          -texture option added for a texture mapping an image onto the
               topography (SGI only).
          user functions are computed faster on SGI multi-processor systems by
               computing time steps in parallel.
          
4.0  (December 1994)
     New features:
          Map projections and new vertical coordinate systems.
          Type-in formulas for computing new variables.
          Time sequences of satellite images can be texture mapped onto the
               topography for visual comparison with model data.
          Data may be displayed over a spherical Earth.
          File caching:  compressed grid files which are too large to read into
               memory in their entirety are read in piece-by-piece as needed, a
               least-recently-used replacement policy is used to purge data when
               memory is full.
          New compressed grid format.  New format allows new header information
               to be added in the future, currently stores additional projection
               information.  Also allows control of data compression.
          New command line options:  -geometry, -trajvars, -projection,
               -vertical, -area, -sequence
          External functions can query the probe position and values with
               PROBEPOS and PROBEVAL functions.
          Interactive control over animation rate (using F and S keys)
          When the "GRID #'s" button is turned on, the probe/trajectory cursor
               snaps to discrete grid points.
          New utilities for .v5d files:  v5dinfo, v5dstats, v5dedit,
               comp_to_v5d, and gr3d_to_v5d.

4.1  (May 1995)
     New features:
          Rotated map projection.
          Improved widgets.
          Stored-frame animation.
          Better 3-D rendering in software using Mesa instead of VOGL.
          Vis5D files defined as a World Wide Web medium for exchanging model
               output.

4.2  (April 1996)
     New features:
          Wind streamlines.
          Colored isosurfaces and trajectories.
          Scripting with Tcl.
          UVW variable widget.
          Pressure vertical coordinate system.
          programmer's API between Vis5D and its user interface.
          v5dSetLowLev function allows fields to occupy any sub-interval of
               vertical levels.
          physical units can be specified for each variable in a v5d file.
          v5dimport program.

4.3  (April 1997)
     New features:
          Vertical sounding window.