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 <a href="ITK-3.14.0-cygwin-mingw.patch">ITK-3.14.0-cygwin-mingw.patch</a>:

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
```

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Peter's notes on building cmgui