style: markdown files cleanup

Author: MRKonrad

.travis.yml

@@ -120,6 +120,7 @@ after_success:
   # Generate and deploy documentation only in linux g++
   - if [ "$EXTENDED_BUILD" == "ON" ]; then
       cd ${TRAVIS_BUILD_DIR} ;
+      cp ${TRAVIS_BUILD_DIR}/scriptsBuild/generateDocumentationAndDeploy.sh generateDocumentationAndDeploy.sh;
       chmod +x generateDocumentationAndDeploy.sh;
       ./generateDocumentationAndDeploy.sh;
     fi

CONTRIBUTING.md

@@ -17,34 +17,34 @@ We use GitHub issues to track public bugs. Report a bug by [opening a new issue]
 ## Pull Requests
 We actively welcome your pull requests.
 
-1. Fork the repo and create your branch from `master`.
-2. If you've added code that should be tested, add tests.
-3. If you've changed APIs, update the documentation.
-4. Ensure the test suite passes.
-5. Make sure your code lints.
-6. Issue that pull request!
+1.  Fork the repo and create your branch from `master`.
+2.  If you've added code that should be tested, add tests.
+3.  If you've changed APIs, update the documentation.
+4.  Ensure the test suite passes.
+5.  Make sure your code lints.
+6.  Issue that pull request!
 
 ## Any contributions you make will be under the MIT Software License
-In short, when you submit code changes, your submissions are understood to be under the same 
-[MIT License](http://choosealicense.com/licenses/mit/) that covers the project. 
+In short, when you submit code changes, your submissions are understood to be under the same
+[MIT License](http://choosealicense.com/licenses/mit/) that covers the project.
 Feel free to contact the maintainers if that's a concern.
 
 ## Coding style
-* Write code compatible with C++98
-* Use underscore (`_variable`) in the name of a class member variable.
-* C++98 does not allow me to use constructor delegation. 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.
+*   Write code compatible with C++98
+*   Use underscore (`_variable`) in the name of a class member variable.
+*   C++98 does not allow me to use constructor delegation. 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.
 
 ## License
 By contributing to Draft.js, you agree that your contributions will be licensed
 under its BSD license.
 
 ## References
-This document was adapted from the open-source contribution guidelines for 
-[Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md) 
-and [qMRLab](https://github.com/qMRLab/qMRLab/blob/master/CONTRIBUTING.md).
+This document was adapted from the open-source contribution guidelines for
+[Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md)
+and [qMRLab](https://github.com/qMRLab/qMRLab/blob/master/CONTRIBUTING.md).

README.md

@@ -1,4 +1,5 @@
 # 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).
@@ -14,50 +15,56 @@ A library to calculate parametric maps in MRI. It contains ShMOLLI implementatio
 
 
 # Usage
-* App - download the latest version of `TomatoExe` from the [Releases][downloads_link] page and follow the youtube tutorial below 
+
+*   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` 
+*   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 https://www.microsoft.com/en-us/download/details.aspx?id=48145 as suggested in https://stackoverflow.com/questions/32998902/msvcp140-dll-missing
+
+*   missing msvcp140.dll  
+Download <https://www.microsoft.com/en-us/download/details.aspx?id=48145> as suggested in <https://stackoverflow.com/questions/32998902/msvcp140-dll-missing>
 
 # 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.  
+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
+*   **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:
 
-* output SNR maps
-* make sure SNR and nAmoebaCalls is the same as in Shmolli
-* fix downloadITK_linux_osx
-* seperate 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)
+*   output SNR maps
+*   make sure SNR and nAmoebaCalls is the same as in Shmolli
+*   fix downloadITK_linux_osx
+*   seperate 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

CODE_OF_CONDUCT.md codeofconduct.mdCODE_OF_CONDUCT.md renamed to codeofconduct.md

@@ -14,21 +14,21 @@ appearance, race, religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+*   Using welcoming and inclusive language
+*   Being respectful of differing viewpoints and experiences
+*   Gracefully accepting constructive criticism
+*   Focusing on what is best for the community
+*   Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or
+*   The use of sexualized language or imagery and unwelcome sexual attention or
   advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
+*   Trolling, insulting/derogatory comments, and personal or political attacks
+*   Public or private harassment
+*   Publishing others' private information, such as a physical or electronic
   address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+*   Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Our Responsibilities
@@ -68,9 +68,9 @@ members of the project's leadership.
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>
 
-[homepage]: https://www.contributor-covenant.org
+[homepage]: <https://www.contributor-covenant.org>
 
 For answers to common questions about this code of conduct, see
-https://www.contributor-covenant.org/faq
+<https://www.contributor-covenant.org/faq>

notepad.md

@@ -1,4 +1,4 @@
-# Different results from the configurations:
+# Different results from the configurations
 
 parameter_to_map: T1_SHMOLLI  
 functions_type: **FunctionsBasic/FunctionsShmolli**  
@@ -23,4 +23,5 @@ Default: 2.2s and wrong results
 StartPointSHMOLLI: 10s and seemingly correct results
 
 # 5 vs 7 samples
-5 samples are calculated way slower. Maybe playing with fmax and maxIter would reduce the time?
+
+5 samples are calculated way slower. Maybe playing with fmax and maxIter would reduce the time?

generateDocumentationAndDeploy.sh …sBuild/generateDocumentationAndDeploy.shgenerateDocumentationAndDeploy.sh renamed to scriptsBuild/generateDocumentationAndDeploy.sh generateDocumentationAndDeploy.sh renamed to scriptsBuild/generateDocumentationAndDeploy.sh

@@ -3,7 +3,7 @@
 # Title         : generateDocumentationAndDeploy.sh
 # Date created  : 2016/02/22
 # Notes         :
-__AUTHOR__="Jeroen de Bruijn"
+# __AUTHOR__="Konrad Werys"
 # Preconditions:
 # - Packages doxygen doxygen-doc doxygen-latex doxygen-gui graphviz
 #   must be installed.
@@ -109,4 +109,4 @@ else
     echo 'Warning: No documentation (html) files have been found!' >&2
     echo 'Warning: Not going to push the documentation to GitHub!' >&2
     exit 1
-fi
+fi

scriptsPython/tomatoPython.py

@@ -31,9 +31,9 @@
         yaml_data = myfile.read()
     yaml = YAML()
     yaml_dict = yaml.load(yaml_data)
-    
-    # ### 2.c. define/modify params in the structure. Input params are obligatory for calculation, the rest are optional
 
+    # ### 2.c. define/modify params in the structure. Input params are obligatory for calculation, the rest are optional
+    
     # ## input params ##
     yaml_dict['files_magnitude'] = ''
     yaml_dict['files_phase'] = ''