OpenAlea.Strawberry

Authors : Marc Labadie, Christophe Pradal, Gaëtan Heidsieck

Institutes : INRA / CIRAD / Inria

Status : Python package

License : Cecill-C

URL : https://github.com/openalea/strawberry

Funding : The European Union’s Horizon 2020 BreedingValue project

Description

Strawberry is a package for architecture analysis and 2D/3D reconstruction of strawberry plants.

Content

The Strawberry package contains :

• import_mtgfile : Load mtg file
• geometry : Definition of geometric shapes for mtg visualisation
• visualisation : 2D and 3D representation of mtg. Plot analysis results
• analysis : extraction of data from mtg

NOTE: An user friendly way to access the package content through an application based on Voila & jupyter Notebook.

Installation

Requirements

---

• Python > 3.0
• Jupyter Notebook
• Matplotlib
• Pandas
• oawidgets
• pvis
• k3d
• voila
• voila-vuetify
• nodejs
• cufflinks
• ipyvuetify
• plotly
• openpyxl
• openalea.deploy
• openalea.mtg
• openalea.plantgl

---

User installation

conda create --name strawberry -c openalea3 -c conda-forge openalea.strawberry

Docker install

It is possible to use the package through a docker image. You can access a functioning environment with:

docker run -it openalea/strawberry 

To start the notebook, you need to open the ports when starting the docker:

docker run -it -p 8888:8888 openalea/strawberry 

and start the notebook in the docker terminal with:

jupyter notebook --ip='*' --port=8888 --no-browser

then copy the link (e.g. http://127.0.0.1:8888/?token=xxx) into your browser.

Developpers installation

conda create --name strawberry -c openalea3 -c conda-forge openalea.strawberry

git clone https://github.com/openalea/strawberry.git
cd strawberry
python setup.py develop

Quick start

You can construct a 3d architecture and some analyses by doing:

import openalea.mtg as mtg
from oawidgets.plantgl import PlantGL
import openalea.strawberry as strawberry
g = strawberry.import_mtgfile.import_mtgfile(filename= ["Gariguette"])
g.properties()['order'] = mtg.algo.orders(g)
scene=straberry.visu3d.plot3d(g,by=["Sample_date"],hide_leaves=False,display=False)
PlantGL(scene, group_by_color=True)

meta_g = strawberry.import_mtgfile.import_mtgfile(filename=["Gariguette","Capriss","Darselect","Cir107","Ciflorette", "Clery"])
extracted_data = analysis.extract_at_module_scale(meta_g)
fig = strawberry.application.app_module_scale.plot_module_pointwisemean(meta_g, "nb_total_leaves")
display(fig)

You have more examples at: https://strawberry.readthedocs.io/en/latest/user/gallery.html.

Application usage

Once you installed the package, you can start the interactive application using:

cd strawberry/src/openalea/strawberry/application
voila "Strawberry Application.ipynb" --template vuetify-default --VoilaConfiguration.enable_nbextensions=True --VoilaConfiguration.file_whitelist="['.*\.(png|jpg|gif|svg|mp4|avi|ogg|html|py|js)']" 

Documentation

You can see the complete documentation with tutorials at: https://strawberry.readthedocs.io.

Contributing

All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome.

A detailed overview on how to contribute can be found in the .

contributors