Compiling Paul's Software

1. Unpacking

The source code is distributed in a tar archive named cpsm.tar.

1.1. Linux, MacOSX, Cygwin, Solaris, IRIX, HPUX

This tar file contains its own extraction script. By default it will extract all 22 of the subdirectories into your HOME directory. To define another destination subdirectory for the files, first define the environment variable PSM_HOME to be the new destination. For example, setenv PSM_HOME /usr/local/src/psm or PSM_HOME=/usr/local/src/psm ; export PSM_HOME

Copy cpsm.tar into whatever directory you have chosen for PSM_HOME. Then

cd $PSM_HOME
tar xvf cpsm.tar bin/ctarx.sh
bin/ctarx.sh

2.2. Microsoft Windows

Additional software is required for Windows to extract files from cpsm.tar such as 7-Zip, WinRAR, WinZIP, or PowerArchiver.

Extract the contents of cpsm.tar to a folder, e.g., C:\c\psm

2. Configuring

The first time the source code is unpacked, a configuration file must be generated to specify compilation flags for the particular system.

2.1. Linux, MacOSX, Cygwin, Solaris, IRIX, HPUX

In the psmlib subdirectory, copy and rename the file psmlocalflags_default.mk to psmlocalflags

Edit psmlocalflags and read through the file. The main points are -

• Specify the compiler command. This is usually cc but there may be other options on Cygwin or MacOS.
• zlib. To created compressed NIFTI images, the zlib library is required. This is often installed by default on GNU-based systems, in which case the default settings in psmlocalflags should work. However, even if zlib is part of the default installation, it may be spilt into two packages, the libraries (often named zlib1g) and the development header files (often named zlib1g-dev or similar). Both packages are required.
  On non-GNU based systems, zlib may be installed under /opt or you may need to install it manually. If so, ZLIB_INC may have to be uncommented and set to the subdirectory containing the zlib.h file, and ZLIB_PATH set to the subdirectory containing the libraries.
  To disable zlib support comment out all four lines starting ZLIB_...
• Specific Operating System & compiler options. Major systems are listed in this section. Find your system and uncomment the pair of lines PSMLOCAL_INC and PSMLOCAL_LIB. Ensure these are commented out for other systems.
• 32/64 bit. The software has been developed and tested using 32 bit compilers. The graphical programs will only compile under 32 bit environments. The command line programs should compile under 64 bit, but unless you have to use a 64 bit compiler, I would suggest compiling using 32 bit compatibility mode on 64 bit systems. To enable this, uncomments the PSMLOCAL_INC32 and PSMLOCAL_LIB32 lines, which specify the 32 bit compiler options.
• USEGNU should be uncommented if using the GNU compiler version 4 or later (type gcc --version to display the version).
• Location of Openwindows/xview development files and libraries for programs with a graphical under interface.

2.2. Microsoft Windows

In the psmlib subdirectory, select either psmlocalflags_mc_default.mak if using Microsoft Visual Studio C++, or psmlocalflags_bc_default.mak if using Borland C++. Copy and rename this file to psmlocalflags_mc or psmlocalflags_bc respectively.

To created compressed NIFTI images, the zlib static library is required. By default, zlib support is switched off in psmlocalflags_mc. However, the file contains brief instructions regarding how to compile zlib. Once the zlib library has been created, the four lines in psmlocalflags_mc starting ZLIB_... can be uncommented which will allow zlib support to be included during future compilations. The unzipped zlib folder should be renamed just zlib and placed in the ext subdirectory. After compiling, the required library file should be ext\zlib\zlib.lib

Older versions of Microsoft Visual C++ can give an internal compiler error when trying to compile and optimise certain files. To avoid this compiler error, edit the psmlocalflags_mc file and change the optimisation flag from /O2 to /Ot in the bottom two lines of this file.

3. Compiling

If the configuration file has been editted appropriately, above, then compilation should be straightforward.

3.1. Linux, MacOSX, Cygwin, Solaris, IRIX, HPUX

Either change into each subdirectory in turn and type make or change into the bin subdirectory and type ./makeall

If the Openwindows/xview headers and libraries are not installed, the graphical programs will fail to compile. However, the command line programs should still compile fine.

To allow compilation with different architectures in the same directory structure, the object and executable files are suffixed with the name of the operating system. For example, compiling ptoa under Linux will produce an executable named ptoa_Linux and under MacOS 10.5 an executable named ptoa_Darwin. The shell script ptoa in the bin subdirectory should call the correct binary for the current architecture, and so the recommendation is that both the general shell script and architecture-specific binary be included in the PATH.

The file dicom3.tpl in ext should also be available in the PATH.

3.2. Microsoft Windows

Open a Command Window. Ensure that the compiler has been set in the PATH. For example, in recent versions of Microsoft Visual Studio, open a Visual Studio Command Prompt from the Visual Studio Tools submenu.

Change into each subdirectory in turn (e.g., cd \c\psm\utils) and type

• Microsoft Visual Studio C++: nmake /f makefile_mc.mak
• Borland C++: make -f makefile_bc.mak

The executables are created in the same subdirectory as the source code, and should be copied into the appropriate Windows PATH manually.

The file dicom3.tpl in ext should also be copied to the same location as the executables in the PATH.