Build in Mac OSX

Revision as of 10:02, 9 July 2012

These instructions give details how we build all necessary libraries and setup BioImageXD in Mac OSX. In some cases there might be some libraries not installed that are needed to build VTK/ITK libraries. Those errors are reported by CMake. If you cannot find correct library to install, contact info@bioimagexd.net. In most cases, only packages mentioned in prerequisites are needed. Whole process takes full day (about 8h), but gladly computer will do most of the job.

Prerequisites:

• Python 2.7, http://www.python.org
• wxPython 2.9.3 or newer, http://www.wxpython.org/
• CMake 2.6 or newer, http://www.cmake.org
• SWIG 1.3.38 or newer (2.x.x series haven't been tested), http://www.swig.org/
• Subversion client

Important note:

• The source, build and install directories should be kept separate. Mixing source, build and install files in one or two directories can result in build and/or install errors.
• If you need to rebuild a library, clean out (remove) the build directory files and start again.

Building VTK

1. Download VTK 5.6.1 (or newer, might work, but no guarantees), http://www.vtk.org/files/release/5.6/vtk-5.6.1.tar.gz
2. Extract package
3. Create new build directory for building VTK
4. Go to build directory and issue command 'ccmake ${VTK_SOURCE}'
5. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure):

   BUILD_SHARED_LIBS: ON

   BUILD_TESTING: OFF

   CMAKE_BUILD_TYPE: Release

   CMAKE_INSTALL_PREFIX: Change to some location where you have write access if you don't have admin rights

   VTK_USE_PARALLEL: ON

   VTK_WRAP_PYTHON: ON

6. Click 'c' to configure and set

   VTK_USE_TK: OFF

7. If you're running a version of OS X that doesn't include Python 2.7 by default (and you have to install it separately) set the following parameters:

   PYTHON_EXECUTABLE: /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7

   PYTHON_INCLUDE_DIR: /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/

   PYTHON_LIBRARY: /Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib

8. Click 'c' to configure and 'g' to generate and exit
9. Issue command 'make', get a cup of coffee and wait about 30-60 minutes for VTK to get build
10. Set ${VTK_INSTALL_DIR}/lib/python2.7/site-packages/ to PYTHONPATH so you can install VTK correctly, if you are installing VTK outside path
11. Issue command 'make install' to install built VTK to directory defined in CMAKE_INSTALL_PREFIX
12. If you experience a PYTHONPATH issue when installing VTK, you can try using the command sudo python setup.py install in your build directory's Wrapping/Python sub-directory.

Building ITK

1. Download ITK 3.20.1 (ITK 4.x.x will not work, we'll update this guide when we move to ITK 4), http://sourceforge.net/projects/itk/files/itk/3.20/InsightToolkit-3.20.1.tar.gz/download
2. Extract package
3. Create new build directory for building ITK
4. Go to build directory and issue command 'ccmake ${ITK_SOURCE}'
5. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure):

   BUILD_EXAMPLES: OFF

   BUILD_SHARED_LIBS: ON

   BUILD_TESTING: OFF

   CMAKE_BUILD_TYPE: Release

   CMAKE_INSTALL_PREFIX: Change to some location where you have write access if you don't have admin rights

   ITK_USE_OPTIMIZED_REGISTRATION: ON

   ITK_USE_REVIEW: ON

   ITK_USE_REVIEW_STATISTICS: ON

6. Click 'c' to configure (don't care about attentions) and 'g' to generate and exit
7. Issue command 'make', get another cup of coffee and wait about 10 minutes for ITK to get build
8. Issue command 'make install' to install built ITK to directory defined in CMAKE_INSTALL_PREFIX

Building CableSwig (needed for WrapITK)

1. Download CableSwig-ITK 3.20.0, http://voxel.dl.sourceforge.net/sourceforge/itk/CableSwig-ITK-3.20.0.tar.gz
2. Extract package
3. Create new build directory for building CableSwig
4. Go to build directory and issue command 'ccmake ${CABLESWIG_SOURCE}'
5. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure):

   CMAKE_BUILD_TYPE: Release

   CMAKE_INSTALL_PREFIX: Change to some location where you have write access if you don't have admin rights

6. Click 'c' to configure and 'g' to generate and exit
7. Issue command 'make', get another cup of coffee and wait about 5 minutes for CableSwig to get build
8. Issue command 'make install' to install built CableSwig to directory defined in CMAKE_INSTALL_PREFIX

Building WrapITK (the long-lasting part)

1. Create directory for WrapITK source
2. Go to directory and fetch sources using command 'svn checkout http://wrapitk.googlecode.com/svn/branches/maint .'
3. Create new build directory for building WrapITK
4. Go to build directory and issue command 'ccmake ${WRAPITK_SOURCE}'
5. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure, don't care about missing ITK_DIR error):

   BUILD_TESTING: OFF

   CMAKE_BUILD_TYPE: Release

   CMAKE_INSTALL_PREFIX: Change to some location where you have write access if you don't have admin rights

   ITK_DIR: Set to your ITK build directory

   WRAP_double: ON

   WRAP_unsigned_char: ON

   WRAP_unsigned_long: ON

6. Click 'c' to configure (don't care about possible errors) and set

   CableSwig_DIR: Set to your CableSwig build directory

   WRAP_ITK_PYTHON: ON

   INSTALL_WRAP_ITK_COMPATIBILITY: OFF

7. If you needed to install SWIG to comply with the prerequisites, set the following parameters to correspond to your installed version (here 1.3.38):

   SWIG_DIR: /usr/local/share/swig/1.3.38

   SWIG_EXECUTABLE: /usr/local/bin/swig

   SWIG_VERSION: 1.3.38

8. If you're running a version of OS X that doesn't include Python 2.7 by default (and you have to install it separately) set the following parameters:

   PYTHON_EXECUTABLE: /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7

   PYTHON_INCLUDE_DIR: /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/

   PY_SITE_PACKAGES_PATH: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages

9. Click 'c' to configure, nothing to set so click 'c' to configure again, and 'g' to generate and exit
10. Issue command 'make'. Since you have now drinked 3 cups of coffee you might not feel like having a lunch right now. Go for nice 30-60 minutes walk outside. After that you can have lunch or dinner. Then wait a while for building of WrapITK to finish. It will take about 3-5 hours.
11. Issue command 'make install' to install built WrapITK to directory defined in CMAKE_INSTALL_PREFIX
12. Go into directory ${WrapITK_source}/ExternalProjects/ItkVtkGlue
13. Create build directory for ItkVtkGlue
14. Go to build directory and issue command 'ccmake ${ITKVTKGLUE_SOURCE}'
15. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure, don't care about missing ITK_DIR error):

    BUILD_WRAPPERS: ON

    CMAKE_BUILD_TYPE: Release

    CMAKE_INSTALL_PREFIX: Same as selected for WrapITK

    ITK_DIR: Set to your ITK build directory

    LIBRARY_OUTPUT_PATH: Same as selected for WrapITK

16. Click 'c' to configure (don't care about possible errors) and set

    VTK_DIR: Set to your VTK build directory

    CableSwig_DIR: Set to your CableSwig build directory

17. Set the SWIG and PYTHON parameters as you set them for WrapITK. (In other words SWIG_DIR, SWIG_EXECUTABLE, SWIG_VERSION, PYTHON_EXECUTABLE, PYTHON_INCLUDE_DIR, PY_SITE_PACKAGES_PATH.)
18. Click 'c' to configure and set

    WrapITK_DIR: Set to WrapITK build directory

19. Click 'c' to configure, and 'g' to generate and exit
20. Issue command 'make'
21. Issue command 'make install'

Get BioImageXD sources and build vtkBXD and itkBXD

1. Create directory for BioImageXD sources and fetch sources using command 'svn co https://bioimagexd.svn.sourceforge.net/svnroot/bioimagexd/bioimagexd/trunk .'
2. Go into directory ${BXD_SOURCE}/vtkBXD
3. Create new build directory for vtkBXD
4. Go into build directory and issue command 'ccmake ${VTKBXD_SOURCE}'
5. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure, don't care about possible errors):

   CMAKE_BUILD_TYPE: Release

   CMAKE_INSTALL_PREFIX: Same as selected for VTK

   VTK_DIR: Set to your VTK build directory

6. Click 'c' to configure, 'c' to configure, and 'g' to generate and exit
7. Issue command 'make'
8. Issue command 'make install'
9. Go into directory ${BXD_SOURCE}/itkBXD
10. Create new build directory for itkBXD
11. Go into build directory and issue command 'ccmake ${ITKBXD_SOURCE}'
12. Set following settings (click 't' to toggle advanced mode on, and 'c' to configure, don't care about possible errors):

    CMAKE_BUILD_TYPE: Release

    CMAKE_INSTALL_PREFIX: Same as selected for WrapITK

    ITK_DIR: Set to your ITK build directory

    WrapITK_DIR: Set to your WrapITK build directory

    LIBRARY_OUTPUT_PATH: Same as selected for WrapITK

13. Click 'c' to configure, 'c' to configure and 'g' to generate and exit
14. Issue command 'make'
15. Issue command 'make install'

Final setup

Now you can go to root of BioImageXD source and launch BioImageXD by 'python BioImageXD.py'. Depending where you installed libraries, you might need to set PYTHONPATH and/or LD_LIBRARY_PATH. You might even want to set path to your shared libraries to /etc/ld.so.conf.d if your built libs aren't in path already, and you have permission to write to /etc/ld.so.conf.d. If you don't have any additional rights and you have built BioImageXD outside any previously defined paths, you can set PYTHONPATH and LD_LIBRARY_PATH as (notice building of VTK, part 8):
PYTHONPATH=${VTK_INSTALL_PATH}/lib/python2.6/site-packages/VTK-5.6.1-py2.6.egg/:${VTK_INSTALL_PATH}/lib/python2.6/site-packages/:${WRAPITK_SOURCE}/Languages/Python/:${WRAPITK_INSTALL_PATH}/lib/InsightToolkit/WrapITK/Python
LD_LIBRARY_PATH=${VTK_INSTALL_PATH}/lib/vtk-5.6/:${VTK_INSTALL_PATH}/lib/:${ITK_INSTALL_PATH}/lib/InsightToolkit