HydroShoot

Purpose

HydrShoot is a functional-structural plant model that simulates the interactions between shoot’s hydraulic structure, gas-exchange and energy-budget, at the organ level.

HydroShoot may be useful for example if you would like to explore:

• how leaf net carbon assimilation rate (𝐴𝑛), transpiration rate (𝐸), temperature (𝑇) and bulk water potential (Ψ𝑙𝑒𝑎𝑓) interact across the canopy
• how soil water status impacts 𝐴𝑛, 𝐸, 𝑇, and Ψ𝑙𝑒𝑎𝑓
• how the structure of the shoot impacts 𝐴𝑛, 𝐸, 𝑇, and Ψ𝑙𝑒𝑎𝑓
• how soil water potential (Ψ𝑠𝑜𝑖𝑙) propagates across plant’s shoot

Try it !

HydroShoot can be installed automagically using the openalea3 channel from anaconda:

conda create -n hydroshoot -c openalea3 -c conda-forge openalea.hydroshoot 
conda activate hydroshoot

Hydroshoot also provides pre-built workflow that can be imported into Visualea for visual programming.

Example

Let’s take the simple example provided in ‘~/example/potted_grapevine/’. We will use for this example architecture and display modules provided with HydroShoot package. This example runs HydroShoot on a small potted grapevine canopy having two primary shoots.

Let’s build the mock-up using the digitalization data provided in “grapevine_pot.csv” file:

from os import getcwd

from openalea.mtg import traversal
from openalea.plantgl.all import Scene
from hydroshoot import architecture, display, model

# Path for plant digitalization data.
g = architecture.vine_mtg('grapevine_pot.csv')

# Local Coordinates Correction
for v in traversal.iter_mtg2(g, g.root):
    n = g.node(g.Trunk(v, Scale=1)[0])
    theta = 180 if int(n.index()) < 200 else -90 if int(n.index()) < 300 else 0
    architecture.vine_orientation(g, v, theta, local_rotation=True)

# Scene rotation
for v in traversal.iter_mtg2(g, g.root):
    architecture.vine_orientation(g, v, 90., local_rotation=False)

for v in traversal.iter_mtg2(g, g.root):
    architecture.vine_phyto_modular(g, v)
    architecture.vine_mtg_properties(g, v)
    architecture.vine_mtg_geometry(g, v)
    architecture.vine_transform(g, v)

# Display the scene
scene = display.visu(g, def_elmnt_color_dict=True, scene=Scene(),
                     view_result=True)

# Run the model
model.run(g, str(getcwd()) + '/', scene, psi_soil=-0.5,
          gdd_since_budbreak=1000.)                     

LICENSE

This package is distributed under the CeCILL-C license. A full description of the license can be found here .

Links

• Link to github
• Link to the official documentation

Reference

• R Albasha, C Fournier, C Pradal, M Chelle, J A Prieto, G Louarn, T Simonneau, E Lebon, HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange dynamics of complex plant canopies under water deficit—application to grapevine (Vitis vinifera), in silico Plants, Volume 1, Issue 1, 2019, diz007, https://doi.org/10.1093/insilicoplants/diz007