RTK wiki help: Difference between revisions
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== Tutorial 0 - Building a HelloWorld application with RTK == | == 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 | RTK is a library, therefore it's meant to be integrated into application. This tutorial shows how to create a simple FirstReconstruction project that links with RTK. The source code for this tutorial is located in [https://github.com/SimonRit/RTK/tree/master/examples/FirstReconstruction RTK/examples/FirstReconstruction]. | ||
* First you need to create a [https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt CMakeLists.txt], | * First you need to create a [https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt CMakeLists.txt], | ||
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* Run CMake on the FirstReconstruction directory and create a HelloWorld-bin, | * Run CMake on the FirstReconstruction directory and create a HelloWorld-bin, | ||
* Configure and build the project using your favorite compiler, | * Configure and build the project using your favorite compiler, | ||
* Run <code>FirstReconstruction image.mha geometry.xml</code>. If everything runs correctly, you should see a few messages ending with <code>Done!</code> and two new files in the current directory, image.mha and geometry.xml | * Run <code>FirstReconstruction image.mha geometry.xml</code>. If everything runs correctly, you should see a few messages ending with <code>Done!</code> and two new files in the current directory, image.mha and geometry.xml. image.mha is the reconstruction of a sphere from 360 projections and geometry.xml is the geometry file in the [http://www.openrtk.org/Doxygen/DocGeo3D.html RTK format]. | ||
== Tutorial 1 - Modifying a basic RTK application == | == 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. | In [https://github.com/SimonRit/RTK/tree/master/applications/rtktutorialapplication applications/rtktutorialapplication/], you will find a very basic RTK application that can be used as a starting point for building more complex applications. There are many existing applications in [https://github.com/SimonRit/RTK/tree/master/applications applications] which can directly be used. See examples below. | ||
= Wrapping = | = Wrapping = | ||
Latest revision as of 16:05, 8 December 2019
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:
GettingStarted.md
See the Getting started and installation pages.
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 FirstReconstruction project that links with RTK. The source code for this tutorial is located in RTK/examples/FirstReconstruction.
- First you need to create a CMakeLists.txt,
- Create a FirstReconstruction.cxx file,
- Run CMake on the FirstReconstruction directory and create a HelloWorld-bin,
- Configure and build the project using your favorite compiler,
- Run
FirstReconstruction image.mha geometry.xml. If everything runs correctly, you should see a few messages ending withDone!and two new files in the current directory, image.mha and geometry.xml. image.mha is the reconstruction of a sphere from 360 projections and geometry.xml is the geometry file in the RTK format.
Tutorial 1 - Modifying a basic RTK application
In applications/rtktutorialapplication/, you will find a very basic RTK application that can be used as a starting point for building more complex applications. There are many existing applications in applications which can directly be used. See examples below.
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)