populse_mia: Multiparametric Image Analysis

Documentation

The documentation is available on populse_mia's website here: https://populse.github.io/populse_mia

Installation

• From PyPI

  Available soon

• From source, for Linux distributions

  • A compatible version of Python must be installed

  • Install a Version Control System, for example git, and clone the source codes

    • Depending of your distribution, package management system can be different

      sudo apt-get install git # Debian like
      sudo dnf install git # Fedora 22 and later
      # etc.
      

    • Get source code from Github. Replace [mia_install_dir] with a directory of your choice

      git clone https://github.com/populse/populse_mia.git [mia_install_dir]
      

  • Or download the zip file of the project (green button "Clone or download")

    • Extract the data in the directory of your choice [mia_install_dir]

  • Then, install the Python module distribution

    cd [mia_install_dir]  
    sudo python3 setup.py install # Ensure that you use python >= 3.5 (use python3.x to be sure)  
    

  • To run populse_mia from the source code, don't remove it. Otherwise:

    cd ..  
    rm -r [mia_install_dir]  
    

Usage

• For Linux: launching from the source code directory via command line

  • Add the module directory to the python path

    • Depending of your command-line interpreter, the environment variables management can be different

      export PYTHONPATH=$PYTHONPATH:[mia_install_dir]/python/populse_mia/src/modules # bash  
      setenv PYTHONPATH ${PYTHONPATH}:[mia_install_dir]/python/populse_mia/src/modules # tcsh / csh  
      # etc.  
      

  • Then interprets the main.py file

    cd [mia_install_dir]/python/populse_mia/src/scripts  
    python3 main.py  
    

Usage instructions for other platforms available soon

Tests

• Unit tests written thanks to the python module unittest

• Continuous integration made with Travis (Linux, OSX), and AppVeyor (Windows)

• Code coverage calculated by the python module codecov

• The module is ensured to work with Python >= 3.5

• The module is ensured to work on the platforms Linux, OSX and Windows

• The script of tests is python/populse_mia/src/scripts/test.py, so the following command launches the tests:

  python3 python/populse_mia/src/scripts/test.py (from populse_mia root folder, for example [mia_install_dir])
  

Requirements

• SIP
• pyqt5
• pyyaml
• python-dateutil
• sqlalchemy
• lark-parser
• scipy
• nibabel
• snakeviz
• pillow
• matplotlib
• traits
• capsul
• soma_workflow
• nipype
• scikit-image
• populse-db

Other packages used

• copy
• os
• six
• tempfile
• unittest

License

• The whole populse project is open source
• Populse_mia is precisely released under the CeCILL software license
• You can find all the details on the license here, or refer to the license file here