Modelling with OpenAlea#

MTG#

https://readthedocs.org/projects/mtg/badge/?version=latest

Multiscale Tree Graph datastructure and interfaces

../_images/mtg_plantframe.png
MTG package aims to define :

  • A share data structure for plant architecture representation.

  • Read and write MTG files.

  • Export to various graph format.

  • Several algorithms for MTG.

Authors : Christophe Pradal, Christophe Godin

Institutes : Cirad, Inria

Source Code : Github

L-Py#

https://readthedocs.org/projects/lpy/badge/?version=latest

Plant simulation using Lindenmayer Systems with Python

../_images/lpy_lpymagic.png

L-systems were conceived as a mathematical framework for modeling growth of plants. L-Py is a simulation software that mixes L-systems construction with the Python high-level modeling language.

Authors : Frédéric Boudon, Christophe Pradal, Thomas Cokelaer, Przemyslaw Prusinkiewicz, Christophe Godin

Institutes : Cirad, Inria, U. Calgary

Citation : Boudon et al., 2012, https://doi.org/10.3389/fpls.2012.00076

Source Code : Github

PlantGL#

https://readthedocs.org/projects/plantgl/badge/?version=latest

An open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants

../_images/plantgl.png

Authors: Frédéric Boudon, Christophe Pradal, Christophe Nouguier, Jérôme Chopard, Christophe Godin

Institutes : Cirad, Inria

Citation : Pradal, Boudon et al., 2009, https://doi.org/10.1016/j.gmod.2008.10.001

Source Code : Github

OpenAlea Framework#

Documentation status

OpenAlea Framework is able to discover and manage packages and logical components, build and evaluate dataflows and Generate final applications

../_images/openalea_web.png

Authors : Christophe Pradal, Samuel Dufour-Kowalski, Frédéric Boudon, Christian Fournier, Christophe Godin

Institutes : Cirad, Inria, INRA

Citation : Pradal et al., 2008, https://doi.org/10.1071/FP08084

Source Code : Github

VisuAlea#

Documentation status

An application that allows to use OpenAlea packages and to build dataflow graphically

../_images/visualea_workflow.png

Authors : Christophe Pradal, Samuel

Institutes : Cirad, Inria

Citation : Pradal et al., 2008, https://doi.org/10.1071/FP08084, Chopard et al., 2011, https://inria.hal.science/hal-00790635v1

Source Code : Github



Scipack#

Documentation status

OpenAlea Scientific Python Packages (aka OpenAlea.SciPack) is a set of wrappers of standard Python packages for Visualea (OpenAlea Visual Programming application)

../_images/scipack.png

These packages are not plant related, they do not convey specific scientific knowledge on plant modeling but are usefull to build efficient visual programs.

  1. Stdlib: standard logical components based on python libraries.

  2. Numpy: some functionalities like trigonometric and hyperbolic functions, array manipulation, etc (numpy.org).

  3. Pylab: plotting functionalities from matplotlib/pylab.

  4. Images: the possibilities range from image loading/saving to morphology operations or registration.

Authors : Christophe Pradal

Institutes : Cirad

Source Code : Github

Openalea Widgets#

Documentation status

widgets is a set of OpenAlea widgets for jupyter notebooks

../_images/oawidgets.png

This package allows to:

  • use a magic to use LPy language

  • display interactive 3D plant architectures, using openalea.plantgl

  • display MTG

Authors : Baptiste Brument, Christophe Pradal

Institutes : Cirad, Inria

Source Code : Github

RSML#

Documentation status

OpenAlea package managing the RootSystemML file format that represents root architectural data

../_images/rsml_logo.png

The rsml python package provides:

  • import/export between .rsml files and MTG

  • plot

  • standard root system measurements

  • export to table file

Authors : Christophe Pradal, Julien Diener

Institutes : Cirad, Inria

Source Code : Github