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Sallys notes

These notes are from my past experience and I hope that this is useful in explaining to beginners how to use cmgui. I know this is the Wiki for cmgui, but I got some notes here on using the Terminal too.

  • To start using cmgui

    • To open cmgui, first go to "Applications", "Accessories", and open "Terminal".
    • Type "cmgui" in the Terminal
    • Once the CMISS Command Window is opened, we can now try the examples of cmgui under <a target="_self" href="http://cmiss.bioeng.auckland.ac.nz/development/examples/a/index.html">examples</a> to become familiar with using CMISS front end graphics.
    • To open an example, for instance the 1st example under "a/a1". Just type "open example a/a1" in the CMISS Command Window and it will open up a new window where you can read it though and click on the commands individually to see what the code does. <p>
    • Examples can also be opened in the Terminal with "cmgui -example a/a1", but this runs all the command till the end and so is not very useful if you want to learn what each command does.

  • Some Useful Commands to use in the Terminal (or must know commands)

    • " ls " (list out all the files that is contained within the directory you are in)

    • " pwd " ( tells you what directory path you are in)

    • Always type "&" at the end of commands so that you can go back to the terminal to type further commands, otherwise the terminal can't be used until you close what you had opened.

    • If you forgot to type "&" at the end of your last command, you can:

      • hit ctrl - " z " ( which suspends what you're doing)
      • and type "bg" for background, so you can keep using what you have suspended, e.g.: cmgui. If you don't, the program you suspended will close or give no respond.
    • " mv traces.exdata traces.020206.exdata "

      ( this creates a new " traces.020206.exdata " file from the old " traces.exdata " file. The orignal file will be deleted.)

    • " cp traces.exdata traces.020206.exdata "

      ( this copies the old traces.exdata and creates a new one called traces.020206.exdata. The original file is kept.)

    • " less cornea.exdata"

      ( prints out the .exdata file in the Terminal, hit " Enter " to continue to next row, " Page Down " to next page, and " q " to exit)

  • What Program to Use to Open different File Types

    • For Photos (jpg, tif etc), use "gqview" or "gimp"
    • To edit perl script, use the program emacs (but type "xemacs" in terminal) or use "gedit" (also a text editor)
    • To run perl script, type "perl" before the file name, eg: perl crop.pl, in the Terminal

To Digitise Visible Human Data

  • What does crop.pl script do?
    • As mentioned above, crop.pl is opened and edited with emics or gedit, but to run it you use perl crop.pl
    • This perl script is used to create a subset version of dataset, for example: the visiable human dataset, according to the parameters inputted at the top of the script. These must be changed according to the individual's needs.
    • Change the directory at which the cropped images are stored. It is recommended to store the cropped images on our local disk drive because that doesn't take up the universal disk drive, and faster to access, only you will need to use it anyway.
    • First: save the file crop.pl onto your disk drive.
    • Then open visible human data pictures with gimp. Pick out the coordinates of the part of the images that you want to be cut.
    • Change the perl script accordingly to get the part of the images that you want.
    • When all parameters are changed, run it in the Terminal with "perl crop.pl"
    • Note that there is an updated crop.pl file on the web modified by Shane on the 1/2/06.
  • ** Digitising **
    • There is a detail example on the web on digitising. Change the variables at the start of the code according to your needs. "Example a/digitise":http://cmiss.bioeng.auckland.ac.nz/development/examples/a/digitise/index.html
    • You can also try out the new digitiser with the latest realease of "mozCmugi":http://www.cmiss.org/cmgui/mozcmgui
    • Once you have downloaded and installed mozCmgui, you can follow the instructions at the top of the digitise example page. It gives you the xml file you need to run the digitiser and the link of it.
    • You can now save the traces file, or save as a new file, or split the groups into seperate exdata files.

Physiome Eye Model

mozCmgui

  • The eye model can be view directly in Firefox (both Linux and Windows) as long as you have installed the latest "mozCmgui":http://www.cmiss.org/cmgui/mozcmgui.
  • Follow the download and installation instructions to install mozCmgui and configure.
  • There are other applications that mozCmgui can be used for.
  • I plan to write a few notes here on mozCmgui to hopefully help Beginners of mozCmgui.

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