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# Tomato
A library to calculate parametric maps in MRI. It contains ShMOLLI implementation as in [this article](  
**Github** repository can be found [here](  
**Documentation** in doxygen can be found [here](

| 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]                       |
| [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

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.  

# 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](
* **Gitmodules**: after `git clone` run `git submodule update --init --recursive` to get the submodules code.
* It would be nice to follow [CppCoreGuidlines]( as far as C++98 allows.
* Maybe I can write a script for github releases with [github releases REST api]( and [curl REST api](


* provide template yaml config files
* processing without phase data
* output SNR maps
* make sure SNR and nAmoebaCalls is the same as in Shmolli

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