diff --git a/LICENSE.txt b/LICENSE.txt index 5afa424..b9926c4 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,49 +1,13 @@ -/** RTToolbox - DKFZ radiotherapy quantitative evaluation library -Copyright (C) 2015 German Cancer Research Center (DKFZ), -Software development for Integrated Diagnostics and Therapy (SIDT) -All rights reserved. +Copyright (C) 2015 German Cancer Research Center (DKFZ), Software development for Integrated Diagnostics and Therapy (SIDT). All rights reserved. -Redistribution and use in source and binary forms, with or -without modification, are permitted provided that the -following conditions are met: +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - * Redistributions of source code must retain the above - copyright notice, this list of conditions and the - following disclaimer. + * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the - following disclaimer in the documentation and/or other - materials provided with the distribution. + * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - * Neither the name of the German Cancer Research Center, - nor the names of its contributors may be used to endorse - or promote products derived from this software without - specific prior written permission. + * Neither the name of the German Cancer Research Center, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND -CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, -INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR -CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, -INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE -GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR -BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT -OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -POSSIBILITY OF SUCH DAMAGE. -========================================================================= - -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@dkfz.de -**/ \ No newline at end of file +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md index 0bf4798..d0b73ed 100644 --- a/README.md +++ b/README.md @@ -1,237 +1,241 @@ # 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 Other compiler 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), with RT support - 3.6.1_20121102 or newer * [ITK](https://itk.org), version 4.4 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 Build (using the same compiler options as RTToolbox, usually `STATIC LINKING` and `x64` architecture). The following components are needed: * `filesystem`, * `system`, * `thread` and * `program_options` * if you plan to build the apps (*optional*) :information_source: eventually, it might be needed to add the CMake variable `BOOST_LIBRARY_dir` and set it to the respective library. ##### DCMTK For Windows: To compile DCMTK with `/MD` flags (standard for all other libs), you need to patch the CMAKE options of DCMTK (`PathToDCMTK\CMake\dcmtkPrepare.cmake`), either by replacing `"/MT"` with `"/MD"` or by explicitly replacing lines 135 to 171 with the following lines: ``` IF(DCMTK_OVERWRITE_WIN32_COMPILER_FLAGS AND NOT BUILD_SHARED_LIBS) # settings for Microsoft Visual Studio IF(CMAKE_GENERATOR MATCHES "Visual Studio .*") # get Visual Studio Version STRING(REGEX REPLACE "Visual Studio ([0-9]+).*" "\\1" VS_VERSION "${CMAKE_GENERATOR}") # these settings never change even for C or C++ SET(CMAKE_C_FLAGS_DEBUG "/MDd /Z7 /Od") SET(CMAKE_C_FLAGS_RELEASE "/DNDEBUG /MD /O2") SET(CMAKE_C_FLAGS_MINSIZEREL "/DNDEBUG /MD /O2") SET(CMAKE_C_FLAGS_RELWITHDEBINFO "/DNDEBUG /MDd /Z7 /Od") SET(CMAKE_CXX_FLAGS_DEBUG "/MDd /Z7 /Od") SET(CMAKE_CXX_FLAGS_RELEASE "/DNDEBUG /MD /O2") SET(CMAKE_CXX_FLAGS_MINSIZEREL "/DNDEBUG /MD /O2") SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/DNDEBUG /MDd /Z7 /Od") # specific settings for the various Visual Studio versions IF(VS_VERSION EQUAL 6) SET(CMAKE_C_FLAGS "/nologo /W3 /GX /Gy /YX") SET(CMAKE_CXX_FLAGS "/nologo /W3 /GX /Gy /YX /Zm500") # /Zm500 increments heap size which is needed on some system to compile templates in dcmimgle ENDIF(VS_VERSION EQUAL 6) IF(VS_VERSION EQUAL 7) SET(CMAKE_C_FLAGS "/nologo /W3 /Gy") SET(CMAKE_CXX_FLAGS "/nologo /W3 /Gy") ENDIF(VS_VERSION EQUAL 7) IF(VS_VERSION GREATER 7) SET(CMAKE_C_FLAGS "/nologo /W3 /Gy /EHsc") SET(CMAKE_CXX_FLAGS "/nologo /W3 /Gy /EHsc") ENDIF(VS_VERSION GREATER 7) ENDIF(CMAKE_GENERATOR MATCHES "Visual Studio .*") ENDIF(DCMTK_OVERWRITE_WIN32_COMPILER_FLAGS AND NOT BUILD_SHARED_LIBS) ``` Then build DCMTK. `BUILD_APPS` can be switched off. -#####ITK +##### 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 +##### MatchPoint Build MatchPoint 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. -###Building RT-Toolbox +### Building RT-Toolbox * Configure with CMake * Set `BOOST_INCLUDE_DIR` and `BOOST_DIR` to the main boost directory (where `boost_build.jam` is located). Eventually, you have to set `BOOST_LIBRARYDIR` * 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_Masks_Legacy`: Legacy 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, Testing modules and Masks_Legacy). Set the third party library paths. 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 * `RTDoseIndexTest`: Computation of dose indices (Conformation Number, Conformal Index, Conformity index) 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 ## 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 * 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.txt](LICENSE.txt) file for details ## Contact -Please contact rttb(at)dkfz.de +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)