# 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 | Status | |-------------------------------------------|:------------------------------------------------------------------:| | [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] | | [Code quality - Codacy][codacy_link] | [![Codacy Badge][codacy_badge]][codacy_link] | | [Test coverage - Codecov][codecov_link] | [![codecov][codecov_badge]][codecov_link] | | [Downloads][downloads_link] | [![GitHub Releases (by Release)][downloads_badge]][downloads_link] | ## Usage * App - download the latest version of `TomatoExe` from the [Releases][downloads_link] page and follow the youtube tutorial below [![Tomato tutorial](https://img.youtube.com/vi/0tzNZNiZh18/0.jpg)](https://www.youtube.com/watch?v=0tzNZNiZh18) * Lib - download the latest version of `TomatoLib` from the [Releases][downloads_link] page * Code - if you want to build the code please take a look at the scripts in the `scriptsBuild` and the continuous integrations scripts `.appveyor.yml` and `travis.yml` ## 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. ## Troubleshooting * missing msvcp140.dll Download as suggested in ## 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. ## Contributing and code of conduct Please see [contributing.md](contributing.md) and [codeofconduct.md](codeofconduct.md). ## 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)? * LMFIT - somehow windows does not like the static library, so the dynamic is used ## TODO * add acceptance test for 2param * maybe rename calculatormolli to calculator3param? * maybe add calculator2param to produce different results? * Deployment: exe and lib in one zip * Deployment: cmake to download ITK and lmfit * update comments in configuration yaml files * output SNR maps * make sure SNR and nAmoebaCalls is the same as in Shmolli * fix downloadITK_linux_osx * separate projects for building tomato dependencies (done for lmfit) * possibly I could make all FunctionsT1 object static * write user-friendly build scripts (and use them in CI) [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 [travis_link]: https://travis-ci.org/MRKonrad/tomato [travis_badge]: https://img.shields.io/travis/MRKonrad/tomato/master.svg?style=flat-square [appveyor_link]: https://ci.appveyor.com/project/MRKonrad/tomato [appveyor_badge]: https://img.shields.io/appveyor/ci/MRKonrad/tomato/master.svg?style=flat-square [codacy_link]: https://www.codacy.com/app/MRKonrad/tomato?utm_source=github.com&utm_medium=referral&utm_content=MRKonrad/tomato&utm_campaign=Badge_Grade [codacy_badge]: https://img.shields.io/codacy/grade/1ca5a2f31ee040cc9258fc5018e51c1e?style=flat-square [codecov_link]: https://codecov.io/gh/MRKonrad/tomato [codecov_badge]: https://img.shields.io/codecov/c/github/MRKonrad/tomato.svg?style=flat-square [downloads_link]: https://github.com/MRKonrad/tomato/releases [downloads_badge]: https://img.shields.io/github/downloads/MRKonrad/tomato/total.svg?style=flat-square