Peter's notes on building cmgui

This is the process I followed for getting cmgui to compile on a windows machine. Note that cmgui is usually developed on a linux machine.

Compiling cmgui on a windows machine

• Step 1: Install Cygwin to provide a linux like environment

  To install Cygwin you will need to have administrator privileges on your machine. See Installing Cygwin for more info on how to do this.

• Step 2: Create a short cut on the desktop to the Cygwin bash shell

  This shortcut will be used a lot as you are going to be using the bash shell a fair bit.

• Step 3: Create a directory for cmiss root where the code and libraries will be placed

  I opened up a shell and created my cmiss root in the default home directory (ie in /cygdrive/n on my machine):

     mkdir cmiss
  

• Step 4: Set up a .bash_profile file to set all your environmental variables up every time you start up a shell

  An easy way to setup your .bash_profile is to start up a cygwin bash shell and then type:: xemacs .bash_profile

  Now add the following lines to this file and then save:

     export CMISS_ROOT=/cygdrive/n/cmiss
     export SYSNAME=win32
  

  Note you will set CMISS_ROOT to be the appropriate directory on your system. Exit xemacs, close your shell script and restart your shell. Check the environmental variables have been set up by typing env | grep CMISS_ROOT

  You should see a line telling you that CMISS_ROOT=/cygdrive/n/cmiss (or whatever you have set CMISS_ROOT to).

• Step 5: change into the cmiss root directory and use Subversion to checkout the cmgui module

  Assuming you have Subversion and your CMISS enironment variables set up correctly just type:

     cd $CMISS_ROOT
     svn checkout https://svn.physiomeproject.org/svn/cmiss/cmgui/trunk cmgui
  

• Step 6: copy over the required image_libraries

  I used scp to copy over the required lib and include files for i386-win32 machines from bioeng22. If you want to have a look around the file structure on bioeng22, ssh there using:

     ssh yourusername@bioeng22.bioeng.auckland.ac.nz
  

  To secure copy the required image_libraries directories do the following:

     cd $CMISS_ROOT
     mkdir image_libraries
     mkdir image_libraries/lib
     mkdir image_libraries/include
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/image_libraries/lib/i386-win32/ image_libraries/lib
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/image_libraries/include/i386-win32/ image_libraries/include
  

• Step 7: check out or copy over the required perl_interpreter code

  I used scp to copy over the required lib and source files for i386-win32 machines:

     cd $CMISS_ROOT
     mkdir perl_interpreter
     mkdir perl_interpreter/lib
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/perl_interpreter/lib/i386-win32/ perl_intrpreter/lib
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/perl_interpreter/source/  perl_interpreter 
  

• Step 8: copy over the ITK source

  The ITK source is huge and takes a while to copy over:

     cd $CMISS_ROOT
     mkdir itk
     mkdir itk/lib
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/itk/lib/i386-win32 i386-win32/ itk/lib
     scp -r yourusername@bioeng22.bioeng.auckland.ac.nz:/hpc/cmiss/itk/src/ itk
  

  Alternatively to build ITK from source you need to compile it using the MinGW windows environment or you have to patch the cygwin build so that it builds a MinGW version in cgywin.

  For MinGW (The disadvantage of this method is that it is likely to confuse a debugger if you need to debug cmgui and ITK and that was compiled with MinGW in cygwin, plus you need a different set of tools):

     download and install MinGW.  I used the windows installer, used the default installation path and selected the C++ compiler and the MinGW make.
     Download and install the Windows GUI version of cmake.
     Run cmake and point it to your itk source.
     Specify your build directory, a new directory you select.
     Push the configure.
     Select MinGW and if you used the default path for that, it should detect it and configure.
     Some of the tests seem to crash and show a windows prompt on my Vista box, just tell them to close.
     Specify your install path, probably $CMISS_ROOT/itk/i386-win32 as this is what cmgui will expect by default.
     Note you will save most of the disk space required if you don't build the examples and tests (my builds are 3.3GB with and 0.12GB without)
     Push the generate button.
     Open a windows command prompt, navigate to your build directory
     Ensure the c:\MinGW\bin directory is in your path
     Run 'mingw32-make'
     Run 'mingw32-make install'
  

  For cygwin mingw ITK-3.14.0-cygwin-mingw.patch:

     I applied some patches to Imagemagick to make the kwsys project realise it is win32 not unix,
     to fix a return code, and to fix some cast errors.  If I understood cmake I'm sure I could do better.
     The patch file is below, use the "patch -P0 < ITK-3.14.0-cygwin-mingw.patch" command to apply it to your source 
     Make a new empty build directory in a cygwin shell.
     In that directory run cygwin's cmake, replacing the path at the end of this command..
     ccmake -DCMAKE_CXX_FLAGS=-mno-cygwin -DCMAKE_C_FLAGS=-mno-cygwin PATH_TO_YOUR_ITK_SOURCE
     Push c to configure.
     Change the install path to somewhere you want, say $CMISS_ROOT/itk/i386-win32
     Maybe you want to save the disk required to build the examples and tests.
     Push c to configure again.
     Push g to generate.
     make
     When it fails (itktif and itksysEncodeExecutable) then restart the process with
     make VERBOSE=1
     so it shows you the failing command, and then repeat with the cygwin path replaced with a windows like path.
     Then keep going with
     make
     Finally
     make install
  

• Step 9: change into the cmgui directory and run make

  Compiling should now be fairly simple:: cd $CMISS_ROOT/cmgui make

  All going well, this should compile an executable and copy it to the appropriate directory. Check it has been built by looking in the following directory:

     ls $CMISS_ROOT/cmgui/bin/i386-win32
  

  Note this executable will not be able to open up graphics consoles but it can still be used to run comfiles. You may like to create an alias to it so that you can run it from anywhere without typing the full path name. I put the following in my .bash_profile file:

     alias cmgui=$CMISS_ROOT/cmgui/bin/i386-win32/cmgui-debug.exe