med_to_csv

A simple way to parse MedAssociate output file in tidy data

https://github.com/hedjour/med_to_csv

Repository

A simple way to parse MedAssociate output file in tidy data

README.rst

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|Contributors| |Forks| |Stargazers| |Issues| |GPLv3.0 License| |Doc| |DOI|

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MedAssociates to CSV file
==========================

A simple way to parse MedAssociate output file in tidy data :
   * 1 row = 1 observation
   * 1 col = 1 var
   

`Explore the docs » `_

`View Demo `_ ·
`Report Bug `_ ·
`Request Feature `_

.. TABLE OF CONTENTS
.. .. contents:: Table of Contents
..    :depth: 2

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Table of Contents
     

       

         About The Project
         

           
Built With
         
       
       

         Getting Started
         

           
Prerequisites
           
Installation
           
Make Executable 
         
       
       

         Usage
         

           
Graphical User Interface
           
Command Line Interface
           
Config file
         
       
Roadmap
       
Contributing
       
License
       
Contact
       
Acknowledgements
     
   


About The Project
-----------------

This program parses MedAssociates data files and transforms them into tidy csv files, containing the information selected by the user

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Built With
^^^^^^^^^^


* `Python 3 `_
* `Gooey `_

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Getting Started
---------------

To get a local copy up and running follow these simple steps.

Prerequisites
^^^^^^^^^^^^^

This is an example of how to list things you need to use the software and how to install them.

* pip

   .. code-block:: bash

      pip install numpy argparse pyaml pandas
      pip install Gooey #For graphical interface

Installation
^^^^^^^^^^^^


#. Clone the repository

   .. code-block:: bash
      
      git clone https://sourcesup.renater.fr/anonscm/git/medanalysis/medanalysis.git

#. Install the required packages

   .. code-block:: bash

      pip install numpy argparse yaml pandas
      pip install Gooey #For graphical interface
      cd path/to/directory_of_git_clone
and one of the two lines below :
   .. code-block:: bash
      
      python setup.py install 
      python setup.py install --user #For windows users
or
   .. code-block:: bash
      
      pip install .


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Make Executable (Portable)
^^^^^^^^^^^^^^^^^^^^^^^^^^

To make a gui onefile executable run these commands in terminal.

   .. code-block:: bash

      cd path/to/directory_of_git_clone
      pyinstaller build_gui.spec 

To make a cli onefile executable run these commands in terminal.

   .. code-block:: bash

      cd path/to/directory_of_git_clone
      pyinstaller build_cli.spec

Data organisation
-------------------

The file is just an output of MedAssociate software.
The path directorie can contains the sub_directories of sessions that containing
the raw data files, or just Medassociate files.

   .. warning:: 
      Your raw data directories must only contain med output files.

Example of data organisation for batch run
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. note:: 

   Experiment directorie/
   └── dir 01
      ├── file_med_associates_to_compil
      ├── file_med_associates_to_compil
      └── file_med_associates_to_compil
   └── dir 02
      ├── file_med_associates_to_compil
      ├── file_med_associates_to_compil
      └── file_med_associates_to_compil
   
   or

   Experiment directorie/
   ├── file_med_associates_to_compil
   ├── file_med_associates_to_compil
   └── file_med_associates_to_compil



Example
-----------------

Graphical User Interface
^^^^^^^^^^^^^^^^^^^^^^^^

Run the application and follow the steps on the interface

   .. code-block:: bash

      ./main_gui

Command Line Interface
^^^^^^^^^^^^^^^^^^^^^^

The software runs on the experiment directory that contains the directories containing the raw data files or on the file itself and returns a csv file 

   .. code-block:: bash

      ./main_cli.py path_to_medassociate_file config_file.yml output_csv_file

   .. warning:: Your path must contain only ASCII characters  (No : éèàï)

Config file
^^^^^^^^^^^

The config file is a necessary file that specifies the setup of your data to the software.
You can find as an example the config.yml which contains all possibilities of setup.
You can mix 1 col file dir and annotated directory file in experiment dir.


#. There are three types of parameters:

   * info_col : One column file
   * info_lab : annotated file
   * options : further options

#. For the first two types of parameters.
   You need to indicate the information in this format: "Key : Value"

   * Keys are the column names that you want in the output file
   * Values are:

     * for infos_col: row number - 1 (Start index :0)
     * for infos_lab: letters used in medAssociate exercise
     * for infos_opt: (see next point)

#. Options:

   * remove_zero_ending : True or False to keep or remove Zeros at the end of arrays
   * Cut : for cutting an output on a special character usually a dot into 2 columns. The value must be a list of list of 4 elements :

     * key to cut
     * separator usually the dot character
     * Col names of first sub-element
     * Col names of second sub-element

   * Eval : for some columns the values must be the result of a Python command line (e.g to get information in a path). It must be a python dictionary with Key as column name and value a short command line as a string.

#. The following Keys are med associate keywords only usable with annotated file :

   * Start Date (automatically added)
   * End Date
   * Subject
   * Experiment
   * Group
   * Box
   * Start Time (automatically added)
   * End Time
   * MSN: Medassociate exercice names

.. note:: Templates are available in the config.yml file


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Roadmap
-------


* Add possibility for annotated file to not specify the YAML file and use YAML in parameter path with the same
  names as MPC name obtained from MSN []

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FAQ
-----
If you get the  
   .. code-block:: python

         A problem has occured while processing the data :  local variable 'lab_folder' referenced before assignment

Have you filled your sub_directories with med associates output files ?

Contributing
------------

Contributions are what make the open-source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.

If you have any suggestion that would improve this software, please fork the repository and create a pull request. You can also simply open an issue with the tag "enhancement".
Don't forget to give the project a star! Thanks again!


#. Fork the Project
#. Create your Feature Branch (\ ``git checkout -b feature/AmazingFeature``\ )
#. Commit your Changes (\ ``git commit -m 'Add some AmazingFeature'``\ )
#. Push to the Branch (\ ``git push origin feature/AmazingFeature``\ )
#. Open a Pull Request

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License
-------

Distributed under the GPL v3.0 License. See ``LICENSE.txt`` for more information.


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Contact
-------


* Jean-Emmanuel Longueville - jean.emmanuel.longueville@univ-poitiers.fr
* Myriam Hanna - myriam.hanna@univ-poitiers.fr
* Marcello Solinas

Project Link: `https://github.com/hedjour/med_to_csv `_


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Acknowledgments
---------------


* `IRESP `_: This work was supported by a grant from the IRESP « IRESP-19-ADDICTIONS-20 » to MS
* `LNEC `_
* `Université de Poitiers `_
* `INSERM `_
* `Logo FreeVector.com `_
*  Thanks to our old contributors as Ekter, Myriam Hanna.

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Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Longueville"
  given-names: "Jean-Emmanuel"
  orcid: " https://orcid.org/0000-0002-9057-1602 "
- family-names: "Hanna"
  given-names: "Myriam"
  # orcid: ""
- family-names: "Mulac"
  given-names: "Nino"
  # orcid: ""
- family-names: "Solinas"
  given-names: "Marcello"
  orcid: " https://orcid.org/0000-0002-0664-5964"
title: "med_to_csv Software"
version: 1.1
doi: 10.5281/zenodo.6241131
date-released: 2025-01-15
url: "https://github.com/hedjour/med_to_csv"

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