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This document describes the function and usage of versionversion of the program map3d, a scientific visualization application originally developed at the Nora Eccles Harrison Cardiovascular Research and Training (CVRTI) and now under continued development and maintenance at the Center for Integrative Biomedical Computing (CIBC), which is an NIH/NCRR funded center hosted by the Scientific Computing and Imaging Institute (SCI) at the University of Utah. The original purpose of the program was to interactively view scalar fields of electric potentials from measurements and simulations in cardiac electrophysiology. Its present utility is much broader but continues to focus on viewing three-dimensional distributions of scalar values associated with an underlying geometry consisting of node points joined into surface or volume meshes.
map3d has been the topic of some papers [12,11,13,10] and a technical report [9] and we'd love it if you would reference at least one of them (perhaps [13] or [10] are the easiest ones to get copies of) as well as this manual when you publish results using it. There have been many many more papers that use map3d and the list keeps growing.[13,10,9,8,17,18,14,7,15,16,22,23,27,26,31,30,29,28,20,19,21,6,5,4,1,2,3,24,25]
As with our past versions, this edition of map3d is completely open source. Anyone can download not only the executable for the major platforms (OSX, Windoze, and Linux) but also the complete source code for the program. Please note that we do not have a good way yet to incorporate changes people outside our little group make to the program. If you do wish to change and then contribute back, please let us know as soon as possible and we can try and coordinate as best we can. Of special interest are any ports of map3d to another platform--please let us know about this and we can add it to the list and release it with the rest.
The history of map3d goes back to 1990 and the first few hundred lines of code were the product of a few hours work by Mike Matheson, an inspired visualization specialist, now with SGI in Salt Lake City. This was my (Rob) introduction to GL and C and this program became my personal sand box to play in. Along the way, Phil Ershler made valuable contributions in figuring out the magic of Formslib for some user interface controls and developing with me graphicsio, the geometry and data file library that supports map3d. Ted Dustman has recently taken up maintenance and extensions of graphicsio and remains my main man when I need programming lessons.
This is one in a series of ``new'' versions of map3d, the series (labeled 5.x or above) that marks the move from GL to OpenGL library and thus to becoming truly portable. In fact, we call the old one map3dGL now to indicate its links to SGI's original GL library. We seem permanently stuck in the middle of this big conversion project, moving support to OpenGL and adding lots of power as we convert functionality. The reason for the version 6.x, was the move to gtk as the GUI library with which we create all the dialog and display elements of the program. This move has allowed us to extend dramatically the set of dialog boxes map3d offers and this newest version 6.5 contains many examples.
There are some people who have been instrumental in the process and deserve special mention. Chris Moulding is a graphics programmer and general software whiz who surveyed my sand box architecture, pulled together the essential walls, created new ways to make rooms, and still left lots of the sand box around so we could continue to play. From version 5.2 onward, Bryan Worthen replaced Chris and really has found the spirit of map3d. Bryan has become the main driving force behind the actual work of coding and fixing. He strayed off to some other project for a while, but never lost his love for map3d; we are really pleased that he has returned to pick up the torch again. J.R. Blackham joined the team in about 2003 while still an undergraduate in Computer Science at Utah. He is now a graduate student in the department and destined for great things. Jeroen Stinstra is my super-postdoc, helpful in more ways than I knew I even needed and full of inventive ideas. He has created the support for MATLAB that we use in map3d (and the SCIRun project) and is best bug-catcher I know.
The largest thanks must go to the users of map3d, who provided the real inspiration and identified the needs and opportunities of such a program. Among the most supportive and helpful are Bruno Taccardi, Bonnie Punske, and Bob Lux, all colleagues of mine at the CVRTI. Dana Brooks and his students from Northeastern University are also regular users who have provided many suggestions and great enthusiasm. Also invaluable in the constant improvement of the program are my post docs, Jeroen Stinstra, and graduate student Quan Ni, Rich Kuenzler, Bulent Yilmaz, Bruce Hopenfeld, Shibaji Shome, Lucas Lorenzo, Andrew Shafer, and Zoar Englemann. They give me new energy every day and remind me why I am a professor. Notable new additions to the family are Randy Thomas from Universite d'Evry Val d'Essonne in Evry, France. The great thing about Randy is that he used map3d to visualize concentrations of ions in his simulation of the nephron! Also, Ed Ciaccio from Columbia University has become a big user and even takes it to his classes.
The first user and long-time collaborator and friend was Chris Johnson and this new version of map3d is possible because of the success he and I have had in creating the SCI Institute and specifically the NIH/NCRR Center for Integrative Biomedical Computing (www.sci.utah.edu/cibc).
We gratefully acknowledge the financial support that has come from the NIH, National Center for Research Resources (NCRR), the Nora Eccles Treadwell Foundation, and the University of Utah, which provides us with space and materials to create this sand box. The Nora Eccles Treadwell Foundation has provided support not only for the development of map3d but also the experiments that provide the huge pile of data we have used map3d to analyze.
Rob MacLeod, Feb 16, 2007.
The terms of the license agreement under which we release map3d are simple and as follows:
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ``Software''), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
R.S. MacLeod and C.R. Johnson. Map3d: Interactive scientific visualization for bioengineering data. In IEEE Engineering in Medicine and Biology Society 15th Annual International Conference, pages 30-31, IEEE Press, 1993.
THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
map3d incorporates the functionality of several external libraries. They are:
We use GTK and GtkGLExt to interface with the window manager to give us windows with OpenGL capability, as well as giving us widgets we need for interactive control. We use PNG and JpegLib to be able to save .png and .jpg images of map3d. All four of these libraries are covered by the GNU LGPL, which is included in the distribution of map3d.
As of version 6.5, we also release internal libraries under the same license as above for the rest of map3d.
Rob Macleod 2007-03-01