L-grass User Guide¶
Contents
Introduction¶
A Functional Structural Plant Model of ryegrass morphogenesis of leaf and roots, based on self regulations.
These researches lead to the following publications:
Migault V. 2015. Insertion de la morphogenèse racinaire dans L grass, un modèle structure-fonction de graminées fourragères. Verdenal A. 2009. De la simulation de la morphogénèse de l’appareil aérien du ray-grass anglais (Lolium perenne L.). Exploration d’un schéma cybernétique inspiré du concept d’auto-organisation et applications. Verdenal A, Combes D, Escobar-Gutiérrez AJ. 2008. A study of ryegrass architecture as a self-regulated system, using functional-structural plant modelling. Functional Plant Biology 35: 911–924.
For installation, testing and deployment: please see file README.md
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Implementation and architecture¶
Software design¶
Programming language¶
L-grass is a software implemented as a Python package, using the L-Py platform (http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=packages:vplants:lpy:doc:install), a programming framework for Lsystems in Python (http://www.python.org/).
Project tree¶
The project of L-grass consists of several files and directories:
- lgrass/ is the Python package, i.e. the sources of L-grass (see Package dependencies),
- :mod:`lgrass.lpy`: the script used to run the model,
- inputs/: the inputs of L-grass,
- outputs/: the outputs generated by L-grass,
- test/ is for the unit test,
- test_lgrass.py: the script to run the unit test,
- input/: the inputs used for the unit test,
- outputs/: the expected and actual outputs of the unit test,
- doc/ contains the user and reference (i.e. API) documentations,
- index.rst: the main page of the documentation,
- user.rst: the user guide (this is what you are currently reading…),
- ref.rst: the reference guide (a.k.a. API documentation),
- conf.py: the configuration file used to build the documentation,
- _static/: custom static files (such as style sheets or script files) generated by library Sphinx,
- AUTHORS: the authors of L-grass,
- LICENCE: the license of L-grass,
- README.md: the Read Me file,
- setup.cfg: the configuration file used by Setuptools for the deployment of L-grass,
- setup.py: the setup script used for the installation of L-grass,
Package dependencies¶
L-grass relies on several Python libraries:
Python (http://www.python.org/), Openalea Vplants (http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=download:windows), NumPy (http://www.numpy.org/) for model installation, deployement and run
Pandas (http://pandas.pydata.org/): for tests
L-grass dependencies
Running an example¶
In one word¶
To run a simulation example, two options:
- open Lpy platform,
- load lgrass.lpy file from lgrass folder, Use Run or animate button to launch a simulation
- Run lgrass from a python script (see main.py in test folder for an example)