Master | Development | Anaconda binaries |
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TomoPhantom [1] is a toolbox written in C language to generate customisable 2D-4D phantoms (with a temporal capability) and their analytical projection data (parallel beam geometry) for various image processing (e.g. reconstruction, denoising, deblurring, segmentation, etc.) and machine learning tasks (e.g. deep learning, classification, clustering, etc.).
TomoPhantom is recommended for various image processing tasks that require extensive numerical testing: image reconstruction, denoising, deblurring, etc. Specifically, TomoPhantom is best-suited for testing various tomographic image reconstruction (TIR) methods. For TIR algorithms testing, the popular Shepp-Logan phantom is not always a good choice due to its piecewise-constant nature. This toolbox provides a simple modular approach to efficiently build customisable 2D-4D phantoms consisting of piecewise-constant, piecewise-smooth, and smooth analytical objects.
Generate 2D models made of Gaussians, parabolas, ellipses, cones, rectangulars
Generate 3D models and 4D (temporal) extensions of them
Calculate analytical Radon transform of 2D-4D models and also their numerical projections
Model Gaussian or Poisson noise and some typical acquisition artifacts (zingers, rings, shifts)
Demos provided to perform 2D-4D reconstructions avoiding 'Inverse Crime'. Using ToMoBAR, ASTRA-toolbox or TomoPy packages.
- Python (tested ver. 2.7/3.5/3.6); Cython OR
- MATLAB
- C compilers: GCC/MinGW/TDM-GCC/Visual Studio
- CMake (if this installation route is chosen)
Tomophantom is distributed as conda package for linux-64 from the ccpi channel. To install
conda install tomophantom -c ccpi
The package comes as a CMake project so you will need CMake (v.>=3) to configure it. Additionally you will need a C compiler, and a build tool as make
(on linux). The toolkit may be used with Python and/or Matlab for which we provide wrappers. TomoPhantom's core is built as shared library and it should be possible to call it directly from C/C++, but currently no C/C++ API is available.
Prerequisites:
- CMake >= 3.0
- a C compiler with OpenMP
- libm on linux
- Cython to build the Python wrappers (optional)
- MATLAB installation to build MATLAB wrappers (optional)
- Clone this repository to a directory, i.e.
TomoPhantom
, - create a build directory.
- Issue
cmake
to configure (orcmake-gui
, orcmake
, orcmake3
). Use additional flags to fine tune the configuration.
Flags used during configuration
CMake flag | type | meaning |
---|---|---|
BUILD_PYTHON_WRAPPER |
bool | ON|OFF whether to build the Python wrapper |
BUILD_MATLAB_WRAPPER |
bool | ON|OFF whether to build the Matlab wrapper |
CMAKE_INSTALL_PREFIX |
path | your favourite install directory |
PYTHON_DEST_DIR |
path | python modules install directory (default ${CMAKE_INSTALL_PREFIX}/python ) |
MATLAB_DEST_DIR |
path | Matlab modules install directory (default ${CMAKE_INSTALL_PREFIX}/matlab ) |
CONDA_BUILD |
bool | ON|OFF whether it is installed with setup.py install |
Matlab_ROOT_DIR |
path | Matlab directory |
PYTHON_EXECUTABLE |
path | /path/to/python/executable |
Here an example of build on Linux:
git clone https://github.com/dkazanc/TomoPhantom.git
mkdir build
cd build
cmake ../ -DCONDA_BUILD=OFF -DMatlab_ROOT_DIR=/home/algol/matlab2016/ -DBUILD_MATLAB_WRAPPER=ON \
-DBUILD_PYTHON_WRAPPER=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
make install
# let Python find the shared library
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:./install
# let MATLAB find the shared library and mex files
PATH="./install/matlab:$PATH" LD_LIBRARY_PATH="./install/lib:$LD_LIBRARY_PATH" matlab
See run.sh
script for additional examples on build.
git clone https://github.com/dkazanc/TomoPhantom.git
cd TomoPhantom
export CIL_VERSION=1.4.3
conda build Wrappers/Python/conda-recipe --numpy 1.12 --python 3.5
conda install -c file://${CONDA_PREFIX}/conda-bld/ tomophantom --force-reinstall
- Phantom2DLibrary.dat and Phantom3DLibrary.dat are editable text files with parametrised models (2D/3D versions of Shepp-Logan, Defrise, and QRM phantoms are included). The generation of new phantoms is highly encouraged, please submit them through pull requests or via e-mail bellow.
- See MATLAB and Python demos
TomoPhantom is released under Apache License v.2. Note that some demos where 'ASTRA-toolbox' is used are of GPLv3 license and also BSD-3 license for TomoPy package.
- xdesign XDesign is an open-source Python package for generating configurable simulation phantoms for benchmarking tomographic image reconstruction.
- syris Syris (synchrotron radiation imaging simulation) is a framework for simulations of X-ray absorption and phase contrast dynamic imaging experiments, like time-resolved radiography, tomography or laminography.
[2] D. Kazantsev, V. Pickalov "New iterative reconstruction methods for fan-beam tomography", IPSE, 2017
- TOmographic MOdel-BAsed Reconstruction (ToMoBAR)
- Joint image reconstruction method with correlative multi-channel prior for X-ray spectral computed tomography
Software related questions/comments please e-mail to Daniil Kazantsev at dkazanc@hotmail.com