RTK wiki help
Welcome to RTK
The Reconstruction Toolkit (RTK) is an open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK). RTK is developed by the RTK consortium. This is the wiki documentation, other information is available here:
RTK is an open source C++ library, not an executable. This means that you must write code that uses RTK and compile it before you will obtain something that you can run and get a result from. It also means that you can adapt or extend RTK to address your problem at hand. To facilitate this over multiple operating systems, compilers, and system configurations, RTK itself must be built from its source code. RTK is based on The Insight Toolkit, therefore you would need to get, configure and compile The Insight Toolkit first.
The three steps to starting to work with RTK are therefore:
- Download and Build the ITK source
- Download/Obtain/Get the RTK source
- Build the RTK library
- Write your own code that uses RTK and build it, linking to the RTK library.
In the next sections we describe each of these steps. Danny Lessio has developped and shared a script that automatically downloads and compiles ITK and RTK, see the auto-build-RTK GitHub repository.
Requirements
In order to compile RTK you will need the following:
- GIT (in order to get the software)
- CMake (in order to configure RTK)
- C/C++ compiler
Step 0 - Getting ITK
RTK currently uses ITK > 4.12.0.
We recommend to look into the ITK wiki in order to compile ITK for your system. The documentation for ITK should be fairly straight forward. Moreover, the concepts for building ITK are very similar to those for RTK. In order to get ITK 4.13.0:
git clone git://itk.org/ITK.git cd ITK git checkout v4.13.0
Once ITK source code is downloaded you need to configure and generate the CMake files:
mkdir ITK-bin cd ITK-bin ccmake ../ITK
It is also recommended to use the FFTW library via the options
ITK_USE_FFTWD ON ITK_USE_FFTWF ON
Note that you do not need to build the examples, the documentation or any of the tests to use ITK with RTK. You can set them off in order to speed up the process with the following flags:
BUILD_DOCUMENTATION OFF BUILD_EXAMPLES OFF BUILD_TESTING OFF
After generating your CMake files you are ready to start the compilation process, run:
make
Step 1 - Getting RTK
This page documents how to download RTK through Git. Follow the ITK Git download instructions to install Git.
To get the latest source code for RTK:
git clone git://github.com/SimonRit/RTK.git
Step 2 - Building RTK
Like ITK, in order to build RTK you would need to install [CMake www.cmake.org]. CMake supports out of source build so we recommend to create a binary directory 'RTK-bin'
mkdir RTK-bin cd RTK-bin ccmake ../RTK
When CMake asks for the ITK_DIR, specify the binary directory where ITK is built and choose CMAKE_BUILD_TYPE (default: Release),
ITK_DIR /path_to_directory/ITK-bin CMAKE_BUILD_TYPE Release
Finally, after configuring and generating your CMake files, you can start the compilation running the following command:
make
Step 3 - Running the HelloWorld application
In order to verify the installation of your RTK library, you can run the HelloWorld application. This application is part of the RTK examples and should be built by default. Otherwise make sure that
BUILD_EXAMPLES ON
when configuring RTK with CMake.
Docker
Another installation solution is to use the Docker solution provided by Thomas Baudier:
docker pull tbaudier/rtk:v1.3.0 docker run -ti --rm -e DISPLAY=$DISPLAY -v [Documents]:/home tbaudier/rtk:v1.3.0 bash
Information on what is installed can be reached using the commands:
docker images docker ps -a
To clean it after use, you can do:
docker rm -f [container id] docker rmi -f [image id]
Tutorials
Tutorial 0 - Building a HelloWorld application with RTK
RTK is a library, therefore it's meant to be integrated into application. This tutorial shows how to create a simple HelloWorld project that links with RTK. The source code for this tutorial is located in RTK/examples/HelloWorld.
- First you need to create a CMakeLists.txt with the following lines:
# This project is designed to be built outside the RTK source tree. PROJECT(HelloWorld)
# Find the RTK libraries and includes
FIND_PACKAGE(RTK REQUIRED)
INCLUDE(${RTK_USE_FILE})
# Executable
ADD_EXECUTABLE(HelloWorld HelloWorld.cxx )
TARGET_LINK_LIBRARIES(HelloWorld ${RTK_LIBRARIES})
TARGET_LINK_LIBRARIES(HelloWorld ${ITK_LIBRARIES})
- Create a HelloWorld.cxx file
#include <rtkFDKBackProjectionImageFilter.h>
int main(int argc, char **argv)
{
// Define the type of pixel and the image dimension
typedef float OutputPixelType;
const unsigned int Dimension = 3;
// Define the type of image typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
// Define and allocate the FDK Back Projection Filter typedef rtk::FDKBackProjectionImageFilter<OutputImageType, OutputImageType> BPType; BPType::Pointer p = BPType::New();
std::cout << "RTK Hello World!" << std::endl;
return 0; }
- Run CMake on the HelloWorld directory and create a HelloWorld-bin
- Configure and build the project using your favorite compiler
- Run the HelloWorld application. If everything runs correctly you should see "RTK Hello World!" written on the console.
Tutorial 1 - Modifying a basic RTK application
In RTK/applications/rtktutorialapplication/, you will find a very basic RTK application that can be used as a starting point for building more complex applications. The code suggests ways to modify the application, which should help beginners get the hang of ITK and RTK.
Tutorial 2 - My first reconstruction
Wrapping
SimpleRTK provides a wrapping mechanism to several languages such as Python and C#.
WaterPreCorrection is an example of SimpleRTK processing to correct for cupping.
FanBeam is an example of SimpleRTK processing to do 2D fan-beam reconstructions.
You can also compile them yourself.
Applications
RTK also provide a set of command line applications that are compiled if the cmake option BUILD_APPLICATIONS is turned on. Each application uses [gengetopt] to allow parsing of the command line options. The manual of each application can be obtained with the --help or -h option. They can be executed sequentially in bash scripts. We provide below links to examples of use for RTK applications.
- FDK Shepp Logan
- 3D Conjugate Gradient
- Forward projection
- Ray/box projections and reconstruction
- 3D geometric phantom
- 3D gammex phantom
- Amsterdam Shroud image
- Reconstruct from Elekta Data
- Reconstruct from Varian Data
- Motion-compensated reconstruction
- Total variation-regularized reconstruction
- Daubechies wavelets-regularized reconstruction
- 4DROOSTER: Total variation-regularized 3D + time reconstruction
Image quality
Summary of existing and future developments for image quality in RTK
Geometry
The description of the 3D circular geometry is based on the international standard IEC 61217 which has been designed for cone-beam imagers on isocentric radiotherapy systems, but it can be used for any 3D circular trajectory. The fixed coordinate system of RTK and the fixed coordinate system of IEC 61217 are the same. A clear understanding of the geometry is essential for the use of a tomography package. The geometry description has been written in this Doxygen page.
ImagX geometry
We provide as an example of geometry conversion the File:GeometryImagX.pdf specifications of the geometry used by the ImagX project (IBA/UCL) with the File:GeometryImagX.txt script file developed in Maxima to do the conversion.
Developer's corner
Developer's documentation
We only provide the doxygen documentation at the moment.
Coding style
RTK is based on ITK and aims at following its coding conventions. Any developer should follow these conventions when submitting new code or contributions to the existing one. We strongly recommend you to read thoroughly ITK's style guide.
Testing
- The RTK dashboard is available at RTK Dashboard
- Documentation on how to add datasets for testing (Girder+CDash)