liuze-nwafu/digital-plant-phenotyping-platform

In silico plant phenotyping environment

Contributors

Shouyang Liu (刘守阳) ([email protected]), Bruno Andrieu ([email protected]), Pierre Martre ([email protected]), Fred Baret ([email protected])

Basic Overview

D3P provides the tools to conduct in silico phenotyping experiment over typical sensors, including RGB/Multispectral camera and LiDAR.

Install

a. Install OpenAlea environment

OpenAlea is a 3D plant modeling platform that includes modules to analyse, visualize and model the functioning and growth of plant architecture. To install OpenAlea, please ensure Conda has been installed. Conda is an open source package management system and environment management system that can run in Windows, Linux, Mac. Please use the Python 2.7 based installation (Conda Download).

Create an environment named openalea: Launch a console

conda create -n openalea -c openalea openalea.plantgl openalea.lpy boost=1.66

Activate the openalea environment:

[source] activate openalea

source should be written only on linux and macos. Install the different packages

conda install notebook=5.4 matplotlib pandas nbformat git

conda install -c openalea openalea.mtg alinea.caribu openalea.plantscan3d openalea.visualea 

conda install -c openalea -c conda-forge pvlib-python alinea.astk

conda install pyprosail

b. Install Phenotyping package

c. Install POV-Ray

POV-Ray is a free and open-source ray tracing program which generates images from a text-based scene description (POV-Ray Download). For 3D model meshes in other formats (*.obj, *DXF etc.), PoseRay can convert to POV-Ray scenes (PoseRay download). However, as OpenAlea supports to export POV-Ray scenes directly, installing PoseRay is necessary only if using 3D mmeshes generated by external softwares.

Demo

a. Manipulate view configuration to mimic sensor movement

b. Change Light condition

Citation

If you use material here, please consider to cite the following paper:

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgement

Thanks a lot for help from: Chistophe pardal ([email protected]), Fredieric Boudon ([email protected]), Christian Fournier ([email protected])