Rob's Documentation Page

Here are some documentation pieces I have done or installed for programs and procedures.

CVRTI and SCI Institute Software

General Info

• SCI Internal web site
• CVRTI general computing page
• All about mom and the other SGIs at CVRTI. Also see the CVRTI page on mom.
• CVRTI OSX page
• Bug tracking for map3d

SCIRun

• Main SCI software page (with links to documentation)
• Current SCIRun Documentation library
• Future SCIRun Documentation library
• Documentation inventory
• SCIRun documentation master plan (for internal use).
• SCIRun developers site not for general use.
• Latest SCIRun build list

map3d Visualization Program

• map3d version 6.5 also in PDF format
• map3d version 6.3 also in PDF format
• map3d version 6.1
• map3d version 6.0 also in PDF format
• map3d version 5.2 also in PDF format
• map3d version 3.0 (map3dgl)
• map3d to-do list

Lab Procedures

• Aligning geometries with the align program.
• Needle geometry processing, also in PDF formats.
• Manual for cleanleads
• Filename conventions for time series files. Please comment!
• MUX mapping files, how to understand and make them (PDF). Also, the zipped file that contains the scripts to make them automatically.
• obituary checking software

Other Software

• All about LaTeX
• Matlab links
• CVS, the code control system.
• Official CVS Manual by Per Cederqvist
• My favorite CVS commands.
• Subversion intro
• Subversion manual
• My favorite Subversion commands.
• Summary of version control tools (from Ted)
• Managing literature search, references, and citations
• Getting equations into Powerpoint and Keynote (from LaTeX).
• rsync web page
• txt2html, a program for converting plain text to HTML.
  • There is no real documentation but these files show a
    • sample text file and
    • the corresponding HTML.
    • And a script I use called makehtml.sh that handles the details.
• MacPorts repository a place to find all your favorite Unix type software for the Mac (see below for more information).
• GNU Manuals online
• More Gnu Manuals online I like the way this one is organized better and it seems more complete, although perhaps not as up to date.
• TOM document conversion server for converting all sorts of files to all sorts of other files....
• Media Wiki Help pages

Other CVRTI Software

• Graphicsio library manual, also available as postscript version.
• Everett tutorial.
• Interp3d interpolation program.
• tsdir program for listing time series data. files.
• pscont program for plotting of maps in postscript. There is also a postscript version.
• makelmarks program for making landmarks from sock geometry (postscript version).
• mapop a program for map analysis, also available in postscript format.
• CVRTI mail server
• No more entering passwords , not really CVRTI software but written by Ted Dustman from CVRTI. This is a guide to creating trusted relationships between computers. A huge time saver in the distributed computer world we live it.

Emacs

• The emacs info site!, more than you ever wanted to know.
• To indent a region of text: C-x
• Using ispell in emacs

Unix utilities for OSX

1. Install XCode tools from your system DVD under the Optional Installed or from the Apple developers' website
2. Go to the MacPorts website and download and installed the binary version of the programs needed on your Mac. (shortcut )
3. Read the rest of the instructions on the MacPorts help page . They are a little tedious but also one-time affair.
4. Perform a self update of the MacPort software itself

        sudo port selfupdate
         

5. Install away!

        sudo port install  progr_name
        

   Where the progr_name is whatever you need to install, e.g., emacs, texlive, latex2html, etc.

Mac OSX

• Sloppy Focus (getting focus to change with the cursor position instead of having to click on each window first) Tricks:
  For just Terminal windows:
  

   %  defaults write com.apple.Terminal FocusFollowsMouse -string YES 

  For X11 windows:
  

    % defaults write com.apple.x11 wm_ffm true 

  For most other Mac apps use Codetek Virtual Desktop
• Zooming the display:
  To toggle the ability to zoom (think *).
  

   Command-Option-8

  And to zoom in or out (think "+" but without the need for the shift key.)
  

   Command-option-= (or -) 

Other Topics

• Scanner and printing tips a nice essay and also a book) about scanning and printing images.
• Our text editing markup scheme