RSML Tutorial in Python

First, we activate matplotlib and qt in the Notebook

%matplotlib inline
%gui qt

import sys; print('Python %s on %s' % (sys.version, sys.platform))
sys.path.extend(['../src'])

Python 3.13.11 | packaged by conda-forge | (main, Jan 26 2026, 23:57:06) [GCC 14.3.0] on linux

Then, we import main modules and function to work with RSML format in Python

import os
from pprint import pprint
from matplotlib import pyplot as plt
import openalea.rsml as rsml
from openalea.rsml.plot import multiple_plot
from openalea.rsml.data import data_dir
from openalea.rsml import measurements

Let first get the path to rsml files to work with.

arabido = data_dir/'AR570'
_generator = arabido.glob('*.rsml')
files = []
for f in _generator:
    files.append(os.path.normpath(f))
pprint(files)

['/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_25_09h00_chl110_1_1.rsml',
 '/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_19_18h00_chl110_1_1.rsml',
 '/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_23_09h00_chl110_1_1.rsml',
 '/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_24_09h00_chl110_1_1.rsml',
 '/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_21_09h00_chl110_1_1.rsml',
 '/home/bauget/Documents/Dev/rsml/src/openalea/rsml/data/AR570/2012_11_20_08h30_chl110_1_1.rsml']

Plot the rsml architectures from these files

multiple_plot(files, image=False)

Plot the above rsml architectures over the corresponding images

multiple_plot(files, image=True)

Plotting the lateral lengths versus their porisiton the primary root

1. read and convert the 1st rsml file of the above list and convert it to MTG

2. get the id of the lateral roots with the root order, 1 for primary and 2 for 1st order lateral root

g = rsml.rsml2mtg(files[0]) # read and convert the 1st rsml file of the above list and convert it to MTG
root = measurements.root_order(g) # dictionary with order of the root 1 for the primary, 2 for the laterals in this case
lr = [r for r,o in root.items() if o==2] # list of ids of the lateral root

3. get the length of these laterals

4. get their position on the primary from the tip

length = measurements.root_length(g,lr)       # length of the lateral
ppos = measurements.parent_position(g,roots=lr,distance2tip=True)  # branching position on parent

5. plot length vs position, unit are pixels here for demo

x = list(ppos.values()) # just convert dict to list
y = list(length.values())
plt.scatter(x,y)

<matplotlib.collections.PathCollection at 0x72cd7edb4190>

Let do it over all the rsml files, just with a loop

• we use a python script demo_plot_rsml.py that can be found in doc/example directory

%run demo_plot_rsml.py

<Figure size 640x480 with 0 Axes>