Next: C. Bioimagesuite FAQ Up: 9 Appendices Previous: A. Installing Other Software Contents

Subsections

B. Compiling BioImage Suite

BioImage Suite is an application not a toolkit. Compiling all of BioImage Suite including all its prerequisites is not for the inexperienced or faint-hearted. We suggest using the binary versions whenever possible.

B.1 Overview

Installing BioImage Suite consists of four parts.

Installation of a pre-compiled binary itk241_distribution containing the Insight Toolkit (ITK) v 2.4.1. For more information on ITK see http://www.itk.org">www.itk.org.
Installation of a combo binary vtk44_yale distribution containing the Tcl/Tk scripting language, various extensions and the Visualization Toolkit. This includes binary versions of:
- The Tcl/Tk scripting language v 8.4.11 [34].
- The following Tcl/Tk Extensions:
  1. Incr Tcl 3.2.1 [48] and Iwidgets 4.0.1.
  2. Tcllib 1.8.
  3. Metakit 2.4.93 [6] - this is not really required by BioImage Suite at this point.
  4. BWidget 1.6.1.
- The CLapack numerical library v3.
- A slightly patched version of the Visualization Toolkit v4.4.2 [92] with TCL Wrapping enabled. Two classes have been changed:
  - vtkDataArray.cxx - to eliminate a GetRange() bug - we simply used a later version of the file from the VTK CVS release.
  - vtkImageReslice.cxx - to set Optimization to Off by default as this gave us trouble with some of our nonlinear transformations in certain cases
Optionally the installation of a combo binary bioimagesuite_extra which primarily provides the MINC2 libraries and XERCESC - these are optional. (XERCESC is only really used at this point.)
Installation of the BioImage Suite software package itself.

All of the Open Source software listed in 1,2 and 3 essentially compiled without changes on all platforms.

BioImage Suite itself consists of a mixture of C++ libraries and .tcl code. The development process is described in the online book ``Introduction to Programming for Medical Image Analysis with VTK'' [74].

The BioImage Source code is released under the GNU General Public License (v2) [59].

B.2 Compiling BioImage Suite

Notes

Note that the binary bioimagesuite_extra, itk241 and vtk44 distributions distributed with BioImage Suite are needed for compiling this. While these are open source, it is easier to use the precompiled versions to avoid unnecessary problems. (See Section B.3 for some notes on building these distributions). A certain familiarity with the UNIX operating system and CMAKE is assumed.

The installation assumes you are using CMake 2.4.x. CMake 2.6 might work.

Steps

Place the BioImage Suite source code into a directory we will refer to as $MYSRC.
Edit the setpaths.csh or setpaths.sh file to reflect their new location. i.e. in setpaths.csh change the line
```
setenv BASE /usr/local/bioimagesuite
```
to something like $MYSRC/bioimagesuite ... use absolute paths.
Source the appropriate setpaths file (much like when running the software) to set all environment variables i.e.
```
source \${MYSRC}/bioimagesuite/setpaths.csh
```
(or setpaths.sh if using one of the sh/ksh/bash shells. or modify setpaths.bat on MS-Windows).

Configure the build

cd \${MYSRC}/build;
ccmake ..

Set the following variables as:

LIBRARY_OUTPUT_PATH = \${MYSRC}/bioimagesuite/lib
EXECUTABLE_OUTPUT_PATH = \${MYSRC}/bioimagesuite/bin

Compile - Simply type make
To run from the source tree build version type bis.tcl.
To verify that this is the source build click on the "Which" button on the bottom the main pxmenu application. If it says something like mysrc/bioimagesuite then all is good.

B.3 Compiling the Prerequisites

These are some notes on building the binary distributions vtk44_yale, itk241_yale and bioimagesuite_extra. They are by no means complete. We strongly suggest using the binary versions provided if at all possible.

The exact sources used for these packages are available from the download page.

B.3.1 The vtk44_yale distribution

Tcl/Tk and Extensions

* Tcl and Tk - use tcl 8.4.11/tk 8.4.11

cd unix;
./configure  --enable-shared --prefix=/usr/local/vtk44_yale

* Mac OX X X11

Tcl:  ./configure  --prefix=/usr/local/vtk44_x11_yale \
  --disable-framework --enable-shared --enable-thread
Tk:   ./configure  --prefix=/usr/local/vtk44_x11_yale \
  --disable-framework --enable-shared --enable-threads --with-x \
  --disable-aqua
Itcl: ./configure  --prefix=/usr/local/vtk44_x11_yale \
  --disable-framework --enable-shared --enable-threads --with-x \
  --disable-aqua

Incr Tcl (3.2.1)

./configure  --enable-shared --prefix=/usr/local/vtk44_yale --with-gcc

Iwidgets 4.0.1

./configure  --enable-shared --prefix=/usr/local/vtk44_yale --with-itcl=../itcl3.2.1

Tcllib - 1.8

./configure  --enable-shared --prefix=/usr/local/vtk44_yale

VTK 4.4

Use the patched source provided - to change

vtkDataArray.cxx - to eliminate a GetRange() bug - we simply used a later version of the file from the VTK CVS release.
vtkImageReslice.cxx - to set Optimization to Off by default as this gave us trouble with some of our nonlinear transformations in certain cases
Enable all libraries - set Java/Python OFF, Tcl ON. Build Shared.

Before running CMAKE set

TCL_LIBRARY_PATH=/usr/local/vtk44_yale/lib:/usr/local/vtk44_yale/lib/vtk/tcl
TK_LIBRARY_PATH=/usr/local/vtk44_yale/lib:/usr/local/vtk44_yale/lib/vtk/tcl

When configuring cmake

CMAKE_INSTALL_PREFIX=/usr/local/vtk44_yale
BUILD_SHARED_LIBS=ON
VTK_WRAP_TCL=ON

Mac OS X X11

BUILD_EXAMPLES                   OFF
 BUILD_SHARED_LIBS                ON
 CMAKE_BACKWARDS_COMPATIBILITY    2.2
 CMAKE_BUILD_TYPE
 CMAKE_INSTALL_PREFIX             /usr/local/vtk44_x11_yale
 TCL_INCLUDE_PATH                 /usr/local/vtk44_x11_yale/include
 TCL_LIBRARY                      /usr/local/vtk44_x11_yale/lib/libtcl8.4.dylib
 TK_INCLUDE_PATH                  /usr/local/vtk44_x11_yale/include/;
                                  /Users/xenios/x11vtk/tk8.4.11/xlib/;
                                  /Users/xenios/x11vtk/tk8.4.11/generic
 TK_INTERNAL_PATH                 /Users/xenios/x11vtk/VTK/Rendering/tkInternals/tk84OSX
 TK_LIBRARY                       /usr/local/vtk44_x11_yale/lib/libtk8.4.dylib
 VTK_DATA_ROOT                    VTK_DATA_ROOT-NOTFOUND
 VTK_USE_CARBON                   OFF
 VTK_USE_COCOA                    OFF
 VTK_USE_HYBRID                   ON
 VTK_USE_PARALLEL                 ON
 VTK_USE_PATENTED                 ON
 VTK_USE_RENDERING                ON
 VTK_USE_X                        ON
 VTK_WRAP_JAVA                    OFF
 VTK_WRAP_PYTHON                  OFF
 VTK_WRAP_TCL                     ON
 CMAKE_X_CFLAGS                   -I/usr/X11R6/include
 CMAKE_X_LIBS                     -lSM;-lICE;/usr/X11R6/lib/libX11.a;/usr/X11R6/lib/libXext.a
 OPENGL_INCLUDE_DIR               /usr/X11R6/include
 OPENGL_gl_LIBRARY                /usr/X11R6/lib/libGL.dylib
 OPENGL_glu_LIBRARY               /usr/X11R6/lib/libGLU.dylib

CLAPACK

Compiling CLAPACK This can be a pain, as Makefiles need to be edited by hand. Using the " -fPIC" flag us helpful. This needs to be added to both "make.inc" but also to all other Makefiles!

Since CLAPACK is in C, there is no good reason to not use the binary version provided. It will link just fine with libraries compiled with other compilers.

On linux, you can also use the lapack library that comes with the operating system.

Manually create /usr/local/vtk44_yale/lib/lapack and

cp F2CLIB/libf77.a /usr/local/vtk44_yale/lib/lapack
cp F2CLIB/libI77.a /usr/local/vtk44_yale/lib/lapack
cp blas.a /usr/local/vtk44_yale/lib/lapack/libblas.a
cp lapack.a /usr/local/vtk44_yale/lib/lapack/liblapack.a

Config Files

The following two files need to be created in /usr/local/vtk44_yale/lib/lapack.

* CLAPACKConfig.cmake

#-----------------------------------------------------------------------------
#
# CLAPACKConfig.cmake - CLAPACK CMake configuration file for external projects.
#
# This file is  used by the UseCLAPACK.cmake module to load CLAPACK's settings f
or an external project.


# The CLAPACK include file directories.
SET(CLAPACK_INCLUDE_DIRS "/usr/local/vtk44_yale/lib/lapack/")

# The CLAPACK library directories.
SET(CLAPACK_LIBRARY_DIRS "/usr/local/vtk44_yale/lib/lapack/")

# The location of the UseCLAPACK.cmake file.
SET(CLAPACK_USE_FILE "/usr/local/vtk44_yale/lib/lapack/UseCLAPACK.cmake")

# The name of the CLAPACK project
SET(CMAKE_BUILD_SETTING_PROJECT_NAME "CLAPACK")

* UseCLAPACK.cmake

#
# This module is provided as CLAPACK_USE_FILE by CLAPACKConfig.cmake.  It can
# be included in a project to load the needed compiler and linker
# settings to use CLAPACK.
#

# Add include directories needed to use CLAPACK.
INCLUDE_DIRECTORIES(\${CLAPACK_INCLUDE_DIRS})

# Add link directories needed to use CLAPACK.
LINK_DIRECTORIES(\${CLAPACK_LIBRARY_DIRS})

SET(CLAPACK_LIBRARIES lapack blas I77 F77 )

B.3.2 The itk241_yale distribution

ITK 2.4.1

BUILD_SHARED_LIBS: ON
CMAKE_INSTALL_PREFIX: /usr/local/itk241_yale

B.3.3 The bioimagesuite_extra distribution

Xercesc

After you untar the source tree

cd xerces-c-src_2_7_0/
setenv XERCESCROOT `pwd`
cd src
cd xercesc
./runConfigure -P /usr/local/bioimagesuite_extra -x g++ -c gcc

For 64-bit linux install add -b 64 to the line above (and perhaps -p linux)

Minc2, Netcdf 3.6.1, HDF5 1.6.5

setenv FC ""
setenv CXX ""

On Solaris setenv CFLAGS "-fPIC" !

Netcdf

cd src
./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale

hdf5

./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale \
  --disable-shared

minc2

./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale \
   CFLAGS=-I/usr/local/bioimagesuite_extra/minc20_yale/include/ \
   LDFLAGS=-L/usr/local/bioimagesuite_extra/minc20_yale/lib/ \
   --enable-minc2

On Solaris add -fPIC to CFLAFS.

B.4 Miscellaneous

BioImage Suite is developed primarily on Linux workstations running CentOS 4.4/5.0 and the gcc 3.2 compiler. In addition the development team has access to a Sparc Ultra 10, an SGI Octane (2xR12K), a pair of Mac Minis (powerpc and intel) and a number of Windows XP/2000/VISTA computers.

Some of the versions are compiled and/or tested inside virtual machines hosted using VMware Server. Such virtual machines include Linux versions: Red Hat 7.3, Red Hat 8.0, Fedora Core 3-5, Debian Sarge 3.1, Ubuntu 5.10,6.06 and OpenSUSE 10.0. In addition we have virtual machines for Solaris x86 v10, Darwin x86 v8.01 and Free BSD 6.0, as well as Windows 98.

BioImage Suite has been successfully compiled using gcc versions 2.95, 2.96, 3.2, 3.3, 3.4 and 4.01 on Linux and other operating systems, as well as Microsoft Visual Studio .NET 2003/2005 (and also using gcc3.3 under cygwin).

Next: C. Bioimagesuite FAQ Up: 9 Appendices Previous: A. Installing Other Software Contents