Revision 7d9b638ffbc5d864584da0132a29debd315a9fd7 authored by Konrad Werys on 03 December 2018, 14:07:11 UTC, committed by Konrad Werys on 03 December 2018, 14:07:11 UTC
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README.md
# Tomato
A library to calculate parametric maps in MRI. It contains ShMOLLI implementation as in [this article](https://jcmr-online.biomedcentral.com/articles/10.1186/1532-429X-12-69).
**Github** repository can be found [here](https://github.com/MRKonrad/tomato).
**Documentation** in doxygen can be found [here](https://mrkonrad.github.io/tomato/html).
| System | Badge |
|----------|:-------------:|
| [DOI][zenodo_link] | [![DOI][zenodo_badge]][zenodo_link] |
| [OSX/Linux build - Travis][travis_link] | [![Travis (.org)][travis_badge]][travis_link] |
| [Windows build - AppVeyor][appveyor_link] | [![AppVeyor][appveyor_badge]][appveyor_link] |
| [Test coverage - Codecov][codecov_link] | [![codecov][codecov_badge]][codecov_link] |
| [Downloads][downloads_link] | [![GitHub Releases (by Release)][downloads_badge]][downloads_link] |
## Tomato and Numerical Recipes
**Important**
Original ShMOLLI (and based on it Tomato) uses code based on Numerical Recipes book. Due to Numerical Recipes licence I cannot share this part of the code online. Please contact me if you would like to use this part of the code. To make up for this limitation we provide a number of alternative fitting procedures.
# Software Requirements Specification
1. Calculate ShMOLLI with exactly the same results as these from the previous implementation.
2. API for easily choosing
* a map calculation algorithm,
* a fitting algorithm,
* a model function and corresponding energy function.
3. Compatibility with:
* main operating systems (Windows, MacOS, Linux),
* C++98 (to include the library in older code).
4. Handling DICOM files.
5. Fast calculation.
6. Easily interfaced to calculation environments MATLAB, IDL and Python.
# Coding style
* Underscore (`_variable`) means a class member variable.
* C++98 does not allow me to use constructor delegation. I am using methods like `setAllPointersToNull()` to make up for it.
* Order of methods in a class definition:
* functional (calculation, helpers etc)
* getters/setters
* disp()
* constructors/destructors
* In **copy constructors** copy primitive types, set all pointers to zero.
# Notes
* **Continuous integration** was tested [in this repo](https://github.com/MRKonrad/ContinousIntegrationPlayground).
* **Gitmodules**: after `git clone` run `git submodule update --init --recursive` to get the submodules code.
* It would be nice to follow [CppCoreGuidlines](https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md) as far as C++98 allows.
* Maybe I can write a script for github releases with [github releases REST api](https://developer.github.com/v3/repos/releases/#create-a-release) and [curl REST api](http://www.codingpedia.org/ama/how-to-test-a-rest-api-from-command-line-with-curl/#12_HEAD_requests)?
# TODO:
* provide template yaml config files
* processing without phase data
[travis_badge]: https://img.shields.io/travis/MRKonrad/tomato.svg?style=flat-square
[travis_link]: https://travis-ci.org/MRKonrad/tomato
[appveyor_badge]: https://img.shields.io/appveyor/ci/MRKonrad/tomato.svg?style=flat-square
[appveyor_link]: https://ci.appveyor.com/project/MRKonrad/tomato
[codecov_badge]: https://img.shields.io/codecov/c/github/MRKonrad/tomato.svg?style=flat-square
[codecov_link]: https://codecov.io/gh/MRKonrad/tomato
[downloads_link]: https://github.com/MRKonrad/tomato/releases
[downloads_badge]: https://img.shields.io/github/downloads/MRKonrad/tomato/v0.1/total.svg?style=flat-square
[zenodo_link]: https://zenodo.org/badge/latestdoi/142749215
[zenodo_badge]: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.1489791-blue.svg?style=flat-square
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