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# 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 * output SNR maps * make sure SNR and nAmoebaCalls is the same as in Shmolli [travis_badge]: https://img.shields.io/travis/MRKonrad/tomato/master.svg?style=flat-square [travis_link]: https://travis-ci.org/MRKonrad/tomato [appveyor_badge]: https://img.shields.io/appveyor/ci/MRKonrad/tomato/master.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/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