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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