RSML

Authors : C. Pradal and J. Diener

Institutes : INRIA / CIRAD

Status : Python package

License : Cecill-C

URL : http://rootsystemml.github.io/

About

The rsml python package provides:

• import/export between .rsml files and MTG
• plot
• standard root system measurements
• export to table file

Installation

Conda

The rsml package is an openalea package that can be installed using conda. After installing conda, enter the following command on your conda environment::

conda install rsml -c openalea/label/unstable -c openalea

From the source

The rsml package is an openalea package and thus requires openalea.deploy to be installed. To install it, go to the rsml folder and enter the following command::

python setup.py install

Use

    import rsml
    
    # load rsml
    g = rsml.rsml2mtg( filename )
    
    # plot
    plot2d(g)  # requires matplotlib
    plot3d(g)  # requires openalea.plantgl

    # save mtg into rsml
    rsml.mtg2rsml(g, filename)
    
    # export mesurements to tabular file
    from rsml import measurements
    measurements.export(g, filename[:-5]+'.csv')

Tutorial

RSML tutorial in Python

Limit order 1(primary) order 2 (secondary)

4/5 different array with key : plant

• Total Length,
• nb racine (t absolute) (P1),
• primary length
• nude tip length
• frequency vs IBD (P2)

Axis : time in raw

time is known

Plant Lateral lenght

• Length by root (t) (question unit?)
  • time as col
  • name : Ln nth root along primary from base

Tab Position

• col : L1 ... Ln

• position on primary

• root , position lateral (from base , distance)

script : rsmlanalysis rsmls.txt| *.rsml TODO: define options to group all the analysis in a same file (csv) or in several files.