TubeTK/Build Instructions

Recommended Build Procedure

TubeTK is known to compile on Windows, Macs, and Linux.

Overview

• Process
  • Install system-level pre-requisites
  • Download source
  • Configure using CMake (http://cmake.org)
  • Build

• Requirements
  • The following must be installed prior to trying to build TubeTK
  • CMake
  • git
  • svn
  • Qt (optional)

• Packaged with TubeTK
  • The following are automatically downloaded and built when TubeTK is built
  • ITK
  • VTK
  • Slicer's command-line registration tools

Windows

• CMake
• git
• svn
• Qt

run CMake (cmake-gui)
Where is the source code: your TubeTK source directory
Where to build the binaries: your new TubeTK build directory
Press the 'Configure' button

Build the Code

• Open Microsoft Visual Studio
• File -> Open -> Project/Solution -> open tubetk-Release/TubeTK.sln

• Perform the initial build using your compiler at the top-level of tubetk-Release. This will update and build the libraries that TubeTK depends on (ex. VTK, ITK), and then build TubeTK.
  • Right click on the "ALL_BUILD" project and select "Build".
• Subsequent builds should be initiated in the subdir tubetk-Release/TubeTK-Build to save time. This will build TubeTK only. You may have to periodically build from the top-level of tubetk-Release to get updates to the libraries that TubeTK depends on.
  • Right click on the "TubeTK" project and select "Build".

Macs

• CMake
  • Install CMake Mac OS X Universal binary from CMake download website.
• X11
  • Install X11 ( Note: Mac OS X 10.7 Lion already ships with X11 )
• git
• svn
• Qt

Launch the X11 terminal to install git, svn and and Qt. Then, follow the steps described in the Linux build section to download, configure and build tubetk in Mac OS X. During CMake configuration, select "Unix Makefiles" generator. Tubetk has been successively built on Mac OS X 10.7 using gcc 4.2 ( dash5.kitware ).

Linux

Install system-level dependencies

TubeTK makes heavy use of ITK, VTK, Git, Qt (optional), and Subversion. Each of these packages depends on a variety of system-level packages, many of which are not installed by default on Linux systems. These dependencies are similar to the dependencies needed to install ParaView. So, the following will install all of the dependencies needed to build VTK and ITK (as needed by ParaView and TubeTK).

 sudo apt-get build-dep paraview
 sudo apt-get install qt-sdk
 sudo apt-get install git gitk
 sudo apt-get install cmake-curses-gui
 sudo apt-get install subversion

Establish directory structure

mkdir ~/src
cd ~/src

Download the source

You have two options:

1. Download manually via Git

git clone git://tubetk.org/TubeTK.git
mkdir ~/src/TubeTK-Release

Run CMake to configure

cd ~/src/tubetk-Release
ccmake ../tubetk
press 'c' to configure
Set CMAKE_BUILD_TYPE to Release
press 'c' to configure again
press 'g' to generate

Build the code

Perform the initial build using your compiler at the top-level of tubetk-Release. This will update and build the libraries that TubeTK depends on (ex. VTK, ITK), and then build TubeTK.

cd ~/src/TubeTK-Release
make -j4

Subsequent builds should be initiated in the subdir tubetk-Release/TubeTK-Build to save time. This will build TubeTK only. You may have to periodically build from the top-level of tubetk-Release to get updates to the libraries that TubeTK depends on.

cd ~/src/tubetk-Release/TubeTK-Build
make -j4

Advanced

Using KWStyle

For introductory information, see: http://public.kitware.com/KWStyle/

 cvs -d :pserver:anoncvs@public.kitware.com:/cvsroot/KWStyle co KWStyle
 mkdir KWStyle-Release
 cd KWStyle-Release
 ccmake ../KWStyle
 # Set BUILD_TYPE to Release
 # Configure
 # Generate
 make
 sudo make install

 cd tubetk-Release
 ccmake .
 # Turn on advanced options
 # Turn on TubeTK_USE_KWSTYLE
 # Configure
 # Set KWSTYLE_EXECUTABLE to /usr/local/bin/KWStyle
 # Configure
 # Generate
 make
 make StyleCheck

Using a pre-existing ITK or VTK installation

You can configure CMake variables to use an existing ITK or VTK installation instead of its embedded versions. This is NOT recommended, because of inter-dependencies that require specific version of these libraries, and built using specific options, to be used.

• USE_SYSTEM_ITK: OFF
  • If "ON", then you can tell TubeTK to use an ITK build that is already present on your system (using the CMake variable ITK_DIR). See the warning below.
• USE_SYSTEM_VTK: OFF
  • If "ON", then you can tell TubeTK to use a VTK build that is already present on your system (using the CMake variable VTK_DIR). See the warning below.

• Dependencies on ITK and VTK versions and build options
  • Note that TubeTK relies on ITK and VTK from 3D Slicer (https://github.com/Slicer/ITK and https://github.com/Slicer/VTK, respectively)
  • Slicer's repositories for ITK/VTK contain enhancements that have not yet made it into the ITK/VTK repositories themselves.

Inside TubeTK

• As noted above, TubeTK uses CMake's Superbuild include other libraries, as needed for the options selected.
• Libraries that may be automatically downloaded and included by TubeTK include:
  • ITK
  • VTK
  • CTK
  • Select tools from the NA-MIC Kit:
    • TCLAP, GenerateCLP, ModuleDescriptionParser, RegisterImages
• Libraries that must be externally installed if you want to use them with TubeTK
  • CMake (2.8.2 or greater - REQUIRED)
  • Qt (4.6.2 or greater - OPTIONAL)
• You can manually install the above toolkits and then configure TubeTK to use those installations instead of building its own copies of those toolkits, BUT we don't recommend heading down that road.
  • Requires CMake expertise
  • Requires making sure each of the toolkits is correctly configured (via their own cmake configuration processes) for use with TubeTK.
  • If you still want to try this complex, manual, unsupported approach, then the following steps will help somewhat:
    1. Read tubetk/SuperBuild.cmake to find out the current set of cmake options required for each library.
    2. For example, at one point in tubetk history, you were required to build ITK v3.20.0, as mirrored and customized on the Slicer github account, using the following cmake vars
       • BUILD_SHARED_LIBS = OFF (or ON, but libs are VERY small in ITK because of templates)
       • ITK_USE_LIBXML2 = ON
       • ITK_USE_REVIEW = ON
       • ITK_USE_OPTIMIZED_REGISTRATION_METHODS = ON
       • ITK_USE_TRANSFORM_IO_FACTORIES = ON
       • CMAKE_CXX_FLAGS = -fPIC
       • CMAKE_C_FLAGS = -fPIC
         • adding -fPIC to both c and cxx flags can be ignored if you build with shared libs ON.
    3. You must also build non-cmake libraries, such as Qt 4.6.2 or greater
       • Tips for installing Open Source Qt to run with Visual Studio
         1. Open a visual studio command shell.
         2. Go to the Qt source directory and run "configure -platform win32-msvc2005". This will tell Qt to prepare itself for being compiled by the Visual Studio compiler. If you use another version of VS than 2005, replace win32-msvc-2005 with the appropriate one.
         3. Type "nmake" and take a break when it compiles.
         4. Add QMAKESPEC=win32-msvc2005 as a system environment variable and add QTDIR=your_dir into the system path. It is done.
       • Tips for installing Qt on Linux
         1. apt-get qt4
    4. After Qt, you must also build the Slicer customized version of VTK v5.6, from the Slicer github account, using the appropriate cmake vars, such as
       • BUILD_SHARED_LIBS = ON
       • VTK_USE_GUISupport = ON
       • VTK_USE_QVTK
    5. Again, many details are missing in the above list. We really recommend using Superbuild instead.

References

• Superbuild and EXTERNAL_PROJECTS
  • Dave Cole's article in the October Kitware Source [1]