Cancer Imaging Phenomics Toolkit (CaPTk)
1.4.0_Beta.n
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Source code for the CaPTk graphical interface and applications is distributed for sites that wish to examine the code, collaborate with CBICA in future development, and for compatibility.
Before building CaPTk, the following software libraries are required to be installed. Please note that to build in Windows, CMake needs to be used an appropriate compiler (Win64 version of Visual Studio is recommended). The selected solution platform is needed to match with dependent libraries.
Package | Version | Description |
Archiver | n/a | gzip is recommended Windows Users: 7-zip |
C++ compiler | n/a | MSVC/13.x (Visual Studio 2013) and GCC/4.8.1+ are supported. MSVC/14+ (2015) and GCC/5+ are NOT supported yet |
CMake | 2.8.12 or higher | To configure the CaPTk compilation along with its dependencies |
Qt | 4.8.x | The main GUI interface for CaPTk. Download and install the precompiled library. Windows Users: consider visiting this page to download the precompiled binaries. |
VTK | 5.6.1 - 5.10.1 | Install Qt before setting VTK up. Instructions to compile VTK are given here. During CMake configuration, enable the VTK_USE_QT and VTK_USE_QVTK_QTOPENGL flags. GCC Users: For compilation use the command make CXXFLAGS=-std=c++11. |
ITK | 4.10 and above | Build VTK and GDCM before proceeding to compile ITK. Instructions to compile ITK are given here. During CMake configuration, enable the Module_ITKVtkGlue, ITK_USE_SYSTEM_GDCM and VCL_INCLUDE_CXX_0X flags. GCC Users: For compilation use the command make CXXFLAGS=-std=c++11. |
OpenCV | 3.0 or higher | All machine learning algorithms. This generally comes pre-compiled; if not found for your system, steps similar to those done for VTK and ITK compilation can be followed. GCC Users: For compilation use the command make CXXFLAGS=-std=c++11. |
Doxygen | 1.8+ | [OPTIONAL] For documentation only |
Ensure all dependencies are met before proceeding.
Please follow commands below in a shell/terminal (e.g., Bash). They will configure and build CaPTk using GNU Make. The main CMake configuration file (CMakeLists.txt) is located in the root directory of the package. Windows users need to follow the equivalent graphical interface.
tar xzf CaPTk-${version}-source.tar.gz mkdir CaPTk-${version}-build cd CaPTk-${version}-build
Windows Users: an appropriate compression program (e.g., 7-zip) might be used to extract the files.
cmake ../CaPTk-${version}-source
Use the CMake variable CMAKE_INSTALL_PREFIX to specify the installation directory, as in:
cmake -DCMAKE_INSTALL_PREFIX=/opt/software/captk ../CaPTk-${version}-source
For GCC users, CaPTk needs the C++11 flag, so ensure that "-std=c++11" option gets added for CMAKE_CXX_FLAGS during the CMake configuration step. This should get done automatically by the CMakeLists.txt file provided but in case of custom build environments, it might get overwritten with other options.
Windows Users: open CMake-GUI and select CaPTk-${version}-source
as the "source" directory and select CaPTk-${version}-build
as the "build" directory. Click on "Configure" and select the appropriate C++ compiler. If there weren't any configuration errors, click "Generate".
CMake should be able to find the dependencies if they are specified in the $PATH
variable in your environment. If you have custom installation directories, then ensure that they have been added to the $PATH
variable or point the variable(s) ${Dependency}_DIR to the appropriate build paths where ${Dependency}Config.cmake is/are present (for example, in the case of ITK, point ITK_DIR
to the directory where ITKConfig.cmake
is present) - this should be either the build directory or the installation directory. If you are using a bash shell, it can be done using the following command:
cmake -DITKDIR=${path_to_custom_ITK_build_dir} -DVTK_DIR=${path_to_custom_VTK_build_dir} -DQT_QMAKE_EXECUTABLE=${path_to_custom_qt_installation} CaPTk-${version}-source
Windows Users: set the variables ITK_DIR
, VTK_DIR
and QT_QMAKE_EXECUTABLE
using the CMake-GUI.
This step will generate compiler-specific project files (for example, Make file for GCC and Visual Studio solution file for MSVC). For a full list of generators, please see CMake documentation on generators. CMake can be used to set various other configuration options and some of those options are:
BUILD_DOCUMENTATION | Builds the documentation (HTML and PDF) from scratch |
BUILD_TESTING | Enables unit testing of the software package |
CMAKE_INSTALL_PREFIX | Path where the project will be installed |
PACKAGE_PROJECT | Create installer for project (not available for all platforms) |
make CXXFLAGS=-std=c++11 #this ensures c++11 flag is enabled for this build
Windows Users: you should launch the generated solution file of Visual Studio (by default, only Release
version of the code will be compiled - if this needs to be changed, it can be done so by editing the variable CMAKE_CONFIGURATION_TYPE
during the CMake configuration step), and then build solution.
Open MATLAB runtime and change the directory to CaPTk-${version}-source/src/applications/binaries/libra/Source
within the main directory of the LIBRA package and run the following command in MATLAB environment:
libra_compile('CaPTk-${version}-source/src/applications/binaries/libra/') # In Unix
Windows Users: Use following command:
libra_compile('CaPTk-${version}-source\src\applications\binaries\libra\') # In Unix
make install
Windows Users: you should build the INSTALL project.
Upon the success of the above compilation and build process, CaPTk is installed into the directory specified by the CMAKE_INSTALL_PREFIX
, which was set during step 3.2 above.
To build the documentation from scratch, the BUILD_DOCUMENTATION
option in the CMake configuration needs to be enabled.
make doc
Windows Users: the documentation is built automatically if BUILD_DOCUMENTATION
is enabled.
To perform tests, the BUILD_TESTING
option in the CMake configuration needs to be enabled.
make test
Windows Users: you should build the RUN_TESTS project.
In case of failing tests, re-run the tests, but this time by executing CTest directly with the '-V' option to enable verbose output and redirect the output to a text file, as in the example below (works for both Windows and Linux on the command line or shell):
ctest -V >& CaPTk-test.log
And send the file CaPTk-test.log as attachment of the issue report to softw. are@ cbica .upe nn.ed u
make install/strip
Note - this is not needed if you plan to package the project.
Enable the PACKAGE_PROJECT flag in the CMake configuration step to package the project.
make package sudo dpkg -i CaPTk-Linux.deb
Windows Users: Build the PACKAGE project in Visual Studio; you will need NSIS to package the project as an installer.