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Contents1 What's New?1.1 Version 6.3: May, 20051.2 In the works (``vapourware'')2 Introduction2.1 Acknowledgments3 Installation3.1 System requirements3.2 General Installation3.3 Linux Installation Instructions3.4 Windows Installation Instructions3.5 Mac OS X Installation Instructions3.6 SGI Installation Instructions3.7 Installing from source3.8 Documentation3.9 Bug reporting3.10 How to reach us4 Usage4.1 Typical usage examples4.2 Global Parameters4.3 Geometry specifications4.4 Scalar Data parameters5 Script Files5.1 What are script files?5.2 How to make script files5.3 Examples6 Input files6.1 Geometry input files6.2 Command line control of geometry files6.3 Scalar data files6.4 Channels and leadlinks6.5 Landmark files7 Display features7.1 Multiple surfaces7.2 Surface display 7.3 Mesh Rendering7.4 Surface Data Display7.5 Landmarks7.6 Clipping Planes7.7 Node marking7.8 Time signal display8 Control of map3d8.1 Control by surface8.2 Mouse control, keyboard mapping, dials, and menus8.3 Controlling the time signal window8.4 Color/Size Selection8.5 Interactive GUIs - File Selection, File Saving, and Scaling Options, etc,8.6 Picking mode8.7 Control of landmark display9 Output from map3d9.1 Capturing images for animation, printing, or photos/slides10 BUGSBibliography 1 What's New? In this section, we highlight the latest additions to map3d in the(vain?) hope that people will read at least this much of the manualand be able to quickly make use of the latest and greatest that the programoffers.1.1 Version 6.3: May, 2005This is the fourth version of the ``new'' map3d with a GTK-based GUI. Weare getting very very very close to the complete functionality of the old GLbased version and have gone well beyond it in some features, especially theuser interface. This is a ``dot'' release but is not a minor release forit contains some important new features and the usual set of bug fixes.Some of the specific additions that you should notice over previous versionsinclude:Open Source: map3d is now open source! See Section 3.7 and Section 2.1.1. Jet Color map: map3d3d() has seen the light and added the Matlab Jet color map as the default color map. Fiducial display: Some improvements over the fiducial display and control. (LINK) See fid dialog, display, Section 6.3.4. Geometry in landmark form: Per the recommendation of a user, we have incorporated the landmark file format into an actual geometry See Section 6.1.5. Bug fixes: not that the previous version had any bugs, but we found a few(!) things to fix.1.2 In the works (``vapourware'')A small sampler of things that are in the works:Incorporating fiducials into the matlab format
Better fiducial control
Saving the frames into actual movies.
Dynamic menus that indicate the current parameter selections (a bit more in progress).
New display modes for the display of vectors.
Fixing the bugs listed on the bugs page (see Section 10).
g2 IntroductionThis document describes the function and usage of versionversion of theprogram map3d, a scientific visualization application originally developedat the Nora Eccles Harrison Cardiovascular Research and Training(CVRTI)and now undercontinued development and maintenance at the Scientific Computing andImaging Institute (SCI)at theUniversity of Utah. The original purpose of the program was tointeractively view scalar fields of electric potentials from measurementsand simulations in cardiac electrophysiology. Its present utility is muchbroader but continues to focus on viewing three-dimensional distributionsof scalar values associated with an underlying geometry consisting of nodepoints joined into surface or volume meshes.map3d has been the topic of some papers[1,2,3,4] and a technical report and we'd love it if you would reference at least one ofthem (perhaps  or  are the easiest ones toget 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 keepsgrowing.[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30]One of the big changes in version 6.3 is that we are now completelyopen source. People can download not only the executable but also thecomplete source code for the program. Please note that we do not have agood way yet to incorporate changes people outside our little group maketo the program. If you do wish to change and then contribute back, pleaselet us know as soon as possible and we can try and coordinate as best wecan. Of obvious interest is when someone ports map3d to anotherplatform--please let us know about this and we can add it to the list andrelease it with the rest.2.1 AcknowledgmentsThe history of map3d goes back to 1990 and the first few hundred lines ofcode were the product of a few hours work by Mike Matheson, an inspiredvisualization specialist, now with SGI in Salt Lake City. This was myintroduction to GL and C and this program became my personal sand box toplay in. Along the way, Phil Ershler made valuable contributions infiguring out the magic of Formslib for some user interface controls anddeveloping with me graphicsio, the geometry and data file librarythat supports map3d. Ted Dustman has recently taken up maintenance andextensions of graphicsio and remains my main man when I needprogramming lessons.This is one in a series of ``new'' versions of map3d, the series (labeled5.x or above) that marks the move from GL to OpenGL library and thus tobecoming truly portable. In fact, we call the old one map3dGL now toindicate its links to SGI's original GL library. We seem permanently stuckin the middle of this big conversion project, moving support to OpenGL andadding lots of power as we convert functionality. The reason for theversion 6.x, was the move to gtk as the GUI library with which we createall the dialog and display elements of the program. This move has allowedus to extend dramatically the set of dialog boxes map3d offers and thisnewest version 6.3 contains many examples.There are some people who have been instrumental in the process and deservespecial mention. Chris Moulding is a graphics programmer and generalsoftware whiz who surveyed my sand box architecture, pulled together theessential walls, created new ways to make rooms, and still left lots of thesand 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 codingand fixing. He strayed off to some other project for a while, but neverlost his love for map3d; we are really pleased that he has returned topick up the torch again. Most recently, J.R. Blackham has joined the teamwhile still an undergraduate in Computer Science at Utah. Jeroen Stinstrais my super-postdoc, helpful in more ways than I knew I even needed andfull of inventive ideas. He has created the support for MATLAB that we usein 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 realinspiration 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 hisstudents from Northeastern University are also regular users who haveprovided many suggestions and great enthusiasm. Also invaluable in theconstant improvement of the program are my post docs, Jeroen Stinstra, andgraduate student Quan Ni, Rich Kuenzler, Bulent Yilmaz, Bruce Hopenfeld,Shibaji Shome, Lucas Lorenzo, Andrew Shafer, and Zoar Englemann. They giveme new energy every day and remind me why I am a professor. Notable newadditions to the family are Randy Thomas from Universite d'Evry Vald'Essonne in Evry, France. The great thing about Randy is that he usedmap3d to visualize concentrations of ions in his simulation of thenephron! Also, Ed Ciaccio from Columbia University has become a big userand even takes it to his classes.The first user and long-time collaborator and friend was Chris Johnson andthis new version of map3d is possible because of the success he and I havehad in creating the SCI Institute and specifically the NIH/NCRR Center forGeometric Modeling, Simulation, and Visualization in Bioelectric FieldProblems (www.sci.utah.edu/ncrr).We gratefully acknowledge the financial support that has come from the NIH,National Center for Research Resources(NCRR)the Nora EcclesTreadwell Foundation, and the University of Utah, which provides us withspace and materials to create this sand box. The Nora Eccles TreadwellFoundation has also provided support for the development of map3d and thehuge pile of data we have used it to analyze.Rob MacLeod, May 19, 2005.2.1.1 Open Source LicenseThe terms of the license agreement under which we release map3d are simpleand as follows:Permission is hereby granted, free of charge, to any person obtaining acopy of this software and associated documentation files (the``Software''), to deal in the Software without restriction, includingwithout limitation the rights to use, copy, modify, merge, publish,distribute, sublicense, and/or sell copies of the Software, and to permitpersons to whom the Software is furnished to do so, subject to thefollowing conditions:The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
Use of this software in preparing any publication material must be cited as follows: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, EXPRESSOR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THEAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHERLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISINGFROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHERDEALINGS IN THE SOFTWARE.2.1.2 Libraries used by map3dmap3d incorporates the functionality of several external libraries. Theyare:GTK- The GIMP Toolkit - Copyright (C) 1995-1997 Peter Mattis, Spencer Kimball and Josh MacDonald
GtkGLExt- GtkGLExt - OpenGL Extension to GTK+ Copyright (C) 2002-2004 Naofumi Yasufuku
PNG- Copyright (c) 1998-2002 Glenn Randers-Pehrson
Jpeglib- Copyright (C) 1991-1998, Thomas G. Lane.
We use GTK and GtkGLExt to interface with the window manager to give uswindows with OpenGL capability, as well as giving us widgets we need forinteractive 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 GNULGPL, which is included in thedistribution of map3d.As of version 6.3, we also release internal libraries under thesame license as above for the rest of map3d. 3 Installation3.1 System requirementsmap3d is written in standard C/C++ and uses the OpenGL and GTK+ libraries, both choices made to ensure broad portability of the program.All platforms: OpenGL now comes standard on most systems. Instructions on how to install GTK+ are described in detail below based on which platform you are installing. described below Requirements for all systems.OpenGL libraries (GL and GLU)version 1.1 + 1OpenGL/window interface library (GLX) GTK+libraries and dependenciesversion 2.0+Linux (i386): map3d requires the OpenGL library, which is available as the mesa library at www.mesa3d.orgfor any Linux platform. For better performance, graphics cards from companies such as nVidia (www.nvidia.com)usually provide OpenGL libraries. RequirementsOperating Systemkernel 2.2.xArchitecturei386 (+ maybe PPC)Applications Binary Interfacelibc2.1RecommendationsWindow systemXFree86 version 4.0 +Hardware3D graphics card (nVidia, 3dfx, ati) 128 MB main memoryWindows: RequirementsOperating SystemW2K/NT4.0/9xArchitecturei386Applications Binary Interfacewin32RecommendationsHardware3D graphics card (nVidia, 3dfx, ati) 128 MB main memoryMac OS X: RequirementsOperating SystemMac OS 10.3(Panther)ArchitecturePPCRecommendationsHardware3D graphics card (nVidia, 3dfx, ati) 256 MB main memorySGI: map3d runs on virtually any SGI that will support Irix version 6.5+. We have tested it on Indigo2, O2, Octane, and Origin workstations running various flavors of Irix 6.5. If you need a version for a different SGI configuration, please let us know (firstname.lastname@example.org)RequirementsOperating SystemIrix 6.5+Architecturemips3 or mips4 (maybe mips2)Applications Binary Interfacen32 or 64RecommendationsHardwareTexture mapping hardware 128 MB main memory3.2 General InstallationUnfortunately, with our move to GTK+ for window support, it is not as easyas past versions, which required just the download of an executable. Wehope (in vain, perhaps) to be able to do that again in the future, but fornow we will attempt to make installation as easy as we can. Simplifiedinstructions will be in a README file which comes with each package, andare also listed below:To download the software, use this URLwww.sci.utah.edu/software/map3d.html, and click on the``Download'' button. You'll need to sign into the SCI archive. Foreach of the installation instructions below, you can grab those filefrom this page.To test the installation, use the test files that accompany thisdistribution. Each has some script files included that show how to calland execute map3d.3.3 Linux Installation InstructionsThe Linux installation is relatively straightforward. You'll need to download map3d's dependencies, then download map3d itself.3.3.1 Linux DependenciesThere are two phases to this part. First we need to get GTK+ and itsdependencies. The easiest way to do this is from your distribution's installation CDs, or you can download the RPMs at www.rpmfind.net. To get the dependencies from your distribution, run the Package Manager(Add/Remove Applications, configure-packages or something of that sort).Search for gtk, and install gtk2 (if you can't find that directly, then installing the gnome environment will take care of it).To get the dependencies from the internet, navigate your favorite browserto , andsearch for gtk-2.0. Try to find one that matches yourdistribution (redhat, mandrake, etc.). We directly support development forgtk2-2.2.1 and gtk2-2.0.6, so if you can find one ofthese that would be encouraged.The next part is to download gtkglext, the library that supports OpenGL forGTK widgets. As of this release, this is not standard in mostdistributions. If your GTK version is 2.0.6 or 2.2.1 (you can find out bylooking at gtkversion.h which will be where you installed gtk(normally /usr/include/gtk-2.0/gtk/gtkversion.h), and look forGTK_MAJOR_VERSION, GTK_MINOR_VERSION, andGTK_MICRO_VERSION. There will be numbers on the same lines as eachof these, and if you put them together it will be something like 2.2.1).If you are using one of these versions downloadgtkglext-linux-2.2.1.tar.gz or gtkglext-linux-2.0.6.tar.gz fromthe map3d download pageand follow theseinstructions: cd gunzip gtkglext-linux-.tar.gz tar xf gtkglext-linux-.tar cp libgtkglext-x11-1.0.so.0 /usr/local/lib cp libgdkglext-x11-1.0.so.0 /usr/local/libYou can copy them to some directory other than /usr/local/lib ifyou wish.If this doesn't work, you will need to download the gtkglext source andcompile it yourself (don't worry--if your gtk is properly set up, thiswill be very easy). Download the sources from Source Forge follow these instructions: cd gunzip gtkglext-1.0.6.tar.gz tar xf gtkglext-1.0.6.tar cd gtkglext-1.0.6 configure make make installIf you don't want these to end up in /usr/local/lib, you need to configure --prefix=where dir is where to put the libraries. 3.3.2 Linux ExecutableDownload the map3d-6.2-linux.tar.gz file from the map3d() download pageand unzip it to a directory of your choice. We will call thatRUN-DIR. This is the directory from which you will run map3d.To run map3d, you will need to make sure that all the libraries are inyour LD_LIBRARY_PATH environment variable. For this we will assumethat your gtk libraries are in /usr/lib and your gtkglextlibraries are in /usr/local/lib. Do the following:tcsh users: setenv LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATHorbash users: export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATHyou might want to put this line in your .cshrc or.profile file to avoid having to run this multiple times.3.4 Windows Installation InstructionsThe Windows installation is relatively straightforward. You'll need to download map3d's dependencies, then download map3d itself.3.4.1 Windows DependenciesDownload the map3d-win-environment.zip file from the map3ddownload pageand unzip (using winzip,native windows xp zip file browser, or another windows zip program) it into a locationof your choice - we will call that INSTALL-DIR. It will create adirectory called INSTALL-DIR\map3d.Add INSTALL-DIR\map3d\lib to your path. To do this, open theControl Panel, select System, and click on the `Advanced' tab on the top ofthe screen. Click on the Environment Variables button. You should see avariable called Path or PATH in the System Variables section. Click on it,and select Edit. Go to the end of the line, add a semi-colon (;) and typeINSTALL-DIR\map3d\lib.3.4.2 Windows ExecutableThere is an executable of map3d in the environment directory. We have alsoplaced an executable here to facilitate future downloads, so you only haveto download the environment once. If you wish, download themap3d-6.2-windows.zip file from the map3d download page and unzipit to a directory of your choice. We will call that RUN-DIR. Thisis the directory from which you will run map3d.3.5 Mac OS X Installation InstructionsThe Mac OS X installation is relatively straightforward. You'll need to download map3d's dependencies, then download map3d itself.3.5.1 Mac OS X DependenciesMap3d requires the gtk+2 and gtkglext libraries. You can easilyinstall these libraries using fink.If you do not currently have fink installed on your system you willneed to go to the instructions on how to install it and the gtk+2 andgtkglext libraries.3.5.2 Mac OS X ExecutableDownload the map3d-6.2-mac.tar.gz file from the map3ddownload pageand unzip it to a directory of your choice. We will call thatRUN-DIR. This is the directory from which you will run map3d.3.6 SGI Installation InstructionsThe SGI installation is relatively straightforward. You'll need to download map3d's dependencies, then download map3d itself.3.6.1 SGI DependenciesThere are two phases to this part. First we