RTToolbox

RTToolbox is a software library to support quantitative analysis of treatment outcome for radiotherapy.

The RTToolbox was designed following object-oriented design (OOD) principles and was implemented in the language C++.

Features include:

• import of radiotherapy data (e.g. dose distributions and structure sets) from DICOM-RT format and other standard image processing formats
• DVH calculation
• Dose statistic calculation
• arithmetic operations on dose distributions
• structure relationship analyses (e.g. fully-contained, partially-contained)
• Calculation of dose comparison indices such as Conformity Index (CI), Homogeneity Index (HI) and Conformation Number (CN)
• Calculation of biological models including TCP, NTCP, EUD and BED

Also, the RTToolbox provides apps e.g. for DVH/Dose Statistic calculation or Dose accumulation that provides a convenient access of RT scenarios without computer-science knowledge.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

Build system

• CMake, version 3.1 or higher

Compiler

• Visual Studio 2013
• Visual Studio 2015
• Visual Studio 2017
• GCC 5.4
• GCC 7.3

Other compilers may work as well, but are not tested.

Linking Static/Dynamic library support

Can be changed with advanced option BUILD_SHARED_LIBS

:warning: building RTToolbox as dynamic library under Windows and as static library under Linux is an experimental feature.

Third party libraries

• boost, version 1.64.0 or higher
• DCMTK 3.6.5 or higher
• ITK, version 5.2 or higher (optional)
  • for DoseInterpolation support with ITK transformation or ITK File IO support
• MatchPoint, version 0.12 or higher (optional)
  • for DoseInterpolation support with MatchPoint registration objects

:information_source: To make sure everything runs smoothly, please make sure that all libraries and the RTToolbox are either compiled with /MD or /MT flags.

Boost

In case you work with Windows, we recommend using the pre-build versions of boost.

If you want to build the library yourself, consider the following:

Build (using the same compiler options as RTToolbox, usually STATIC LINKING and x64 architecture). The following components are needed:

• filesystem,
• system and
• program_options
  • if you plan to build the apps (optional)

:information_source: eventually, it might be needed to add the CMake variable BOOST_LIBRARYDIR and set it to the respective library path of boost.

For Windows:

To build Boost open a command prompt, change to your boost source directory and copy following command(s): Debug: b2 -j12 --with-filesystem --with-system --with-thread --with-program_options --with-date_time --with-atomic --with-chrono toolset=<your toolset identifier> address-model=64 variant=debug threading=multi link=shared define=_BIND_TO_CURRENT_VCLIBS_VERSION Release: b2 -j12 --with-filesystem --with-system --with-thread --with-program_options --with-date_time --with-atomic --with-chrono toolset=<your toolset identifier> address-model=64 variant=release threading=multi link=shared

Set the in the commands above accordingly. If you don´t require program_options delete --with-program_options from the command before executing it.

DCMTK

For Windows: To compile DCMTK with /MD flags (standard for all other libs), you need to set DCMTK_COMPILE_WIN32_MULTITHREADED_DLL to "ON".

BUILD_APPS can be switched off. Then build DCMTK.

For Linux: install required dependencies (Ubuntu 18.04 and newer): sudo apt-get install libpng-dev libtiff5-dev libxml2-dev libjpeg8-dev zlib1g-dev libwrap0-dev libssl-dev install required dependencies (Ubuntu 17.10 and older): sudo apt-get install libpng12-dev libtiff5-dev libxml2-dev libjpeg8-dev zlib1g-dev libwrap0-dev libssl-dev Enable BUILD_SHARED_LIBS. BUILD_APPS can be switched off.

ITK

Build ITK with default options. :warning: ensure that compiler enables C++11 features by setting CMAKE_CXX_STANDARD=11 (default for supported compilers)

:warning: Only use one ITK version consistently throughout all libraries and RTToolbox! Otherwise, linker errors will occur.

MatchPoint

Configure MatchPoint. Please disable BUILD_TESTING before building it. :warning: ensure that compiler enables C++11 features by setting CMAKE_CXX_STANDARD=11 (default for supported compilers)

:warning: Only use one ITK version consistently throughout all libraries and RTToolbox! Otherwise, linker errors will occur.

Building RT-Toolbox

• Configure with CMake
• Set BOOST_INCLUDE_DIR to the main boost directory. Eventually set BOOST_LIBRARYDIR to the respective path (e.g. <boost_directory>/lib64-msvc-14.1\ for Visual Studio 2017 and 64-bit)
• Select all packages you like to build (Parameters BUILD_* ; e.g. BUILD_IO_Dicom).
  • BUILD_IO_Dicom: Reading and writing of DICOM-RT files
  • BUILD_IO_HELAX: Reading of Helax DICOM files
  • BUILD_IO_ITK: Generic reading/writing with ITK
  • BUILD_Interpolation: Dose Interpolation
  • BUILD_InterpolationMatchPointTransformation: Dose Interpolation with Match Point registration support.
  • BUILD_Masks: Voxelization support
  • BUILD_Models: Calculation of dosimetrical models like TCP, NTCP etc.
  • BUILD_Apps: To build the RTTB command line apps (five available)
    • BioModelCalc: calculate the radiobiological effect based on dose
    • DoseAcc: Do dose accumulation
    • DoseMap: Do dose mapping
    • DoseTool: Compute Dose statistics and DVH
    • VoxelizerTool: Voxelize an RTSTRUCT file

Some modules of RT-Toolbox are mandatory (e.g. RTTBCore) and build automatically.

:information_source: enabling BUILD_All_Modules builds all modules (except Apps and Testing modules).

:information_source: if you build RTTB with VS dynamic, you must ensure that code that uses RTTB DLLs uses the same STL

Set DCMTK_DIR to your dcmtk binary file directory and DCMTK_SOURCE_DIR to your dcmtk source directory.

If you want to build RT-Toolbox with ITK and/or MatchPoint set your ITK_DIR to your itk binary file directory and/or MatchPoint_DIR to your binary matchpoint directory.

All directory entries left empty do not require a manual input.

Finally, Generate the compilation files for your environment and built it.

Examples

Some examples can be found in ´testing/examples´:

• RTBioModelExampleTest: Computation of Biological model indices (TCP/NTCP) from a given DVH
• RTDoseStatisticsDicomTest: Computation of dose statistics (max dose/mean dose/min dose/Dx/Vx) based on dose data for a specified structure
• RTDVHTest: Computation of statistics (max value/mean value/min value/Dx/Vx) based on a DVH

Other examples include:

• DVHCalculatorTest (testing/core): Computation of a DVH from dose and structure
• VoxelizationValidationTest (testing/validation): Computation of a voxelization
• ITKDoseAccessorConverterTest: (testing/io/itk): Saving image RTToolbox image data as an ITK file
• DoseIndex tests: (testing/indices): Computation of different dose indices (e.g. Conformation Number, Conformal Index, Conformity index)

Running the tests

CTest is used as testing framework. See their documentation for general testing questions.

:information_source: The used testing library Litmus is build automatically.

:warning: currently, you have access to testing data only with ssh. That means that a phabricator account and access to RTTB-data repository is mandatory. Please contact rttb(at)dkfz.de for further information.

Enabling testing is done as follows:

• Enable BUILD_TESTING
• Configure with CMake
• Enable tests of interest
• Generate CMake configuration
• Build RT-Toolbox
• Run tests (build RUN_TESTS project or call ctest in commandline) to ensure that everything is correct.

:information_source: BUILD_Tester_All builds all test modules.

Contributing

Please add a github issue and send a pull request if you want to contribute.

Versioning

We use the Ubuntu Release versioning scheme. v2017.02 was released in February 2017. We aim at releasing stable versions once a year. For the versions available, see the tags on this repository.

Authors

See the list of contributors who participated in this project.

License

This project is licensed under the BSD License - see the LICENSE file for details

Contact

Software Development for Integrated Diagnostics and Therapy (SIDT), German Cancer Research Center (DKFZ), Heidelberg, Germany.

Web: https://www.dkfz-heidelberg.de/en/mic/research/SIDT/sidt_projects.html E-mail: rttb(at)dkfz.de

Acknowledgments

• Billie Thompson - Template of the readme - PurpleBooth