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https://github.com/MIC-DKFZ/RTTB

Swiss army knife for radiotherapy analysis
https://github.com/MIC-DKFZ/RTTB

anaylsis dicom-rt dose dose-statistics medical-physics radiotherapy

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Swiss army knife for radiotherapy analysis

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README 

        

# 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](https://cmake.org), 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](http://www.boost.org ), version 1.64.0 or higher

* [DCMTK](http://dicom.offis.de/dcmtk.php.en ) 3.6.5 or higher

* [ITK](https://itk.org ), version 5.2 or higher (*optional*)

  * for DoseInterpolation support with ITK transformation or ITK File IO support

* [MatchPoint](http://mitk.org/download/thirdparty/MatchPoint_rev1610.tar.gz ), 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](https://sourceforge.net/projects/boost/files/boost-binaries/).



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= 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= 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. `/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](https://cmake.org/Wiki/CMake/Testing_With_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](https://phabricator.mitk.org/) 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](https://github.com/MIC-DKFZ/RTTB/tags). 



## Authors



See the list of [contributors](https://github.com/MIC-DKFZ/RTTB/contributors) who participated in this project.



## License



This project is licensed under the BSD License - see the [LICENSE](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](https://github.com/PurpleBooth)