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58 changes: 58 additions & 0 deletions README.md
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<font size="5"><b> TomoPhantom </b> <a href="https://doi.org/10.1016/j.softx.2018.05.003">[1]</a> is a toolbox to generate customisable 2D-4D phantoms (with a temporal capability) and their analytical tomographic projection data (parallel-beam geometry). It can be used for testing various tomographic reconstruction methods, as well as image processing methods, such as, denoising, deblurring, segmentation, and machine/deep learning tasks. </font>
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<img src="docs/source/_static/tomophantom_logo_transp.png" height="350"><br>
<img src="docs/source/_static/models2Dtime/2DtModel14.gif" height="175"><img src="docs/img/models4D/model11_4D.gif "height="175" width="200"><br>
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<h3 class="post-title">About TomoPhantom </h3>
<p> TomoPhantom is recommended for various image processing tasks that require extensive numerical testing: image reconstruction, denoising, deblurring, etc. In particular, TomoPhantom is best-suited for testing various tomographic image reconstruction (TIR) methods. For TIR algorithms testing, the popular <a href="https://en.wikipedia.org/wiki/Shepp%E2%80%93Logan_phantom">Shepp-Logan phantom</a> 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 as well as their analytical <a href="https://en.wikipedia.org/wiki/Radon_transform">Radon transforms</a> .
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### What **TomoPhantom** can do:
* Generate 2D and 3D synthetic phantoms made of Gaussians, parabolas, ellipses, cones and rectangulars.
* Generate simple temporal extensions of 2D and 3D phantoms.
* Calculate analytical Radon transforms of 2D-4D models and also their numerical projections.
* Model a variety of tomographic data artefacts (noise models, zingers, rings, shifts, partial volume effect and others).

### Installation:
Tomophantom is distributed as a Python conda package for Linux/Windows/Mac OS's:
```
conda install -c httomo tomophantom
```
Please see more detailed information on [installation](INSTALLATION.md) and development environments.


#### License:
TomoPhantom is released under [Apache License v.2](http://www.apache.org/licenses/LICENSE-2.0). Note that some demos where ['ASTRA-toolbox'](http://www.astra-toolbox.com/) is used are of GPLv3 license and also BSD-3 license for [TomoPy](http://tomopy.readthedocs.io/en) package.

### Related software projects on GitHub:
- [xdesign](https://github.com/tomography/xdesign) XDesign is an open-source Python package for generating configurable simulation phantoms for benchmarking tomographic image reconstruction.
- [syris](https://github.com/ufo-kit/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.

### References:

[1] [D. Kazantsev et al. 2018, *TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks*, Software X, Volume 7, January–June 2018, Pages 150–155](https://doi.org/10.1016/j.softx.2018.05.003)

[2] [D. Kazantsev, V. Pickalov "New iterative reconstruction methods for fan-beam tomography", IPSE, 2017](https://doi.org/10.1080/17415977.2017.1340946)

### Applications:
* [TOmographic MOdel-BAsed Reconstruction (ToMoBAR)](https://github.com/dkazanc/ToMoBAR)
* [Joint image reconstruction method with correlative multi-channel prior for X-ray spectral computed tomography](https://github.com/dkazanc/multi-channel-X-ray-CT)
* [Deep learning segmentation of synthetic tomographic data using Pytorch U-net](https://github.com/dkazanc/U-Net-tomography)

Software related questions/comments please e-mail to Daniil Kazantsev at dkazanc@hotmail.com
2 changes: 1 addition & 1 deletion README.rst
Expand Up @@ -38,7 +38,7 @@ Tomophantom is distributed as a Python conda package for Linux/Windows/Mac OS's:
$ conda install -c httomo tomophantom
See the detailed page on `Installation <https://dkazanc.github.io/TomoPhantom/howto/installation.html>`_.
See the detailed page on :ref:`ref_installation`.

.. [SX2018] D. Kazantsev et al. 2018, TomoPhantom, a software package to
generate 2D-4D analytical phantoms for CT image reconstruction
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1 change: 1 addition & 0 deletions docs/source/api/tomophantom.rst
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tomophantom.TomoP3D
tomophantom.artefacts
tomophantom.flatsgen
tomophantom.generator
tomophantom.qualitymetrics

Module contents
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7 changes: 5 additions & 2 deletions docs/source/doc-conda-requirements.yml
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- conda-forge
- defaults
dependencies:
- python=3.10
- python=3.9
- sphinx
- sphinx-book-theme
- nbsphinx
- pandoc
- jinja2
- sphinx-panels
- sphinx-copybuttonpyyaml
- sphinx-copybutton
- pyyaml
- ipython
- ghp-import

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