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‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to make participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies within all project spaces, and it also applies when
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an individual is representing the project or its community in public spaces.
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Examples of representing a project or community include using an official
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project e-mail address, posting via an official social media account, or acting
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as an appointed representative at an online or offline event. Representation of
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a project may be further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at [Konrad's email](konradwerys2@gmail.com). All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq

‎CONTRIBUTING.md‎

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# Contributing to TOMATO
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We want to make contributing to this project as easy and transparent as
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possible.
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## Our Development Process
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We use GitHub to sync code to and from our internal repository. We'll use GitHub
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to track issues and feature requests, as well as accept pull requests.
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## Issues
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We use GitHub issues to track public bugs. Please ensure your description is
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clear and has sufficient instructions to be able to reproduce the issue.
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## Report bugs using Github's [issues](https://github.com/MRKonrad/tomato/issues)
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We use GitHub issues to track public bugs. Report a bug by [opening a new issue](); it's that easy!
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## Pull Requests
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We actively welcome your pull requests.
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1. Fork the repo and create your branch from `master`.
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2. If you've added code that should be tested, add tests.
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3. If you've changed APIs, update the documentation.
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4. Ensure the test suite passes.
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5. Make sure your code lints.
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6. Issue that pull request!
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## Any contributions you make will be under the MIT Software License
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In short, when you submit code changes, your submissions are understood to be under the same
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[MIT License](http://choosealicense.com/licenses/mit/) that covers the project.
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Feel free to contact the maintainers if that's a concern.
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## Coding style
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* Write code compatible with C++98
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* Use underscore (`_variable`) in the name of a class member variable.
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* C++98 does not allow me to use constructor delegation. Using methods like `setAllPointersToNull()` to make up for it.
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* Order of methods in a class definition:
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* functional (calculation, helpers etc)
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* getters/setters
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* disp()
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* constructors/destructors
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* In **copy constructors** copy primitive types, set all pointers to zero.
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## License
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By contributing to Draft.js, you agree that your contributions will be licensed
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under its BSD license.
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## References
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This document was adapted from the open-source contribution guidelines for
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[Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md)
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and [qMRLab](https://github.com/qMRLab/qMRLab/blob/master/CONTRIBUTING.md).

‎README.md‎

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5. Fast calculation.
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6. Easily interfaced to calculation environments MATLAB, IDL and Python.
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# Coding style
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* Underscore (`_variable`) means a class member variable.
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* C++98 does not allow me to use constructor delegation. I am using methods like `setAllPointersToNull()` to make up for it.
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* Order of methods in a class definition:
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* functional (calculation, helpers etc)
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* getters/setters
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* disp()
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* constructors/destructors
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* In **copy constructors** copy primitive types, set all pointers to zero.
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# Notes
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* **Continuous integration** was tested [in this repo](https://github.com/MRKonrad/ContinousIntegrationPlayground).

‎scriptsRun/codeocean.sh‎

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#!/usr/bin/env bash
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# In this script a sample use of TOMATO software is presented
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# The TOMATO code can be found here: https://github.com/MRKonrad/tomato
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# Binaries used here have been build in continous integration systems, their scripts can be found here:
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# Travis (Linux and Osx): https://github.com/MRKonrad/tomato/blob/master/.travis.yml
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# Appveyor (Windows): https://github.com/MRKonrad/tomato/blob/master/.appveyor.yml
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# The code has not been built using Codeocean to avoid redundancy with the builds listed above
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echo ""
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echo "### Get TOMATO executable"
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curl -L -O https://github.com/MRKonrad/tomato/releases/download/v0.4/TomatoExe_v0.4_linux.zip
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unzip -a -q TomatoExe_v0.4_linux.zip
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echo ""
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echo "### Get some sample data"
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mkdir testData
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cd testData
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curl -L -O https://github.com/MRKonrad/tomato/releases/download/v0.4/testData.zip
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unzip -a -q testData.zip
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cd ..
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echo ""
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echo "### Check the contents of the main folder"
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ls -la
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echo ""
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echo "### Check the contents of the data folder"
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ls -la testData
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echo ""
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echo "### Run an example"
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echo "### the configuration file (tomatoConfig_Shmolli_inputFilePaths.yaml) contains all the adjustable calculation parameters"
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./TomatoExe testData/tomatoConfig_Shmolli_inputFilePaths.yaml
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echo ""
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echo "### Check the contents of the output folder with T1 maps"
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ls -la testData/tomatoOutput_Shmolli/map
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echo ""
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echo "### Check the contents of the output folder with other maps"
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ls -la testData/tomatoOutput_Shmolli/fitparams

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