pgljupyter

PlantGL & L-Py jupyter widgets

Currently supports openalea.lpy>=3.9.0 and openalea.plantgl>=3.14.0 from conda channel 'fredboudon'.

Quick Examples

PlantGL

• simple PlantGL shapes - spheres @nbviewer

L-Py

• a tree model - leuwenberg @nbviewer

• plot magic - leuwenberg @nbviewer

• champignon @nbviewer

• magics with scalar parameters - broccoli @nbviewer

• magics with curve parameters - sweep surface @nbviewer

Usage

from pgljupyter import SceneWidget, LsystemWidget

SceneWidget

Renderer for PlantGL Scenes, Shapes, Geometries

Arguments:

• arg0 list | plantgl.Shape | plantgl.Scene: a list of shapes or scenes or a single object
• position tuple (float, float, float): x, y, z position of arg0 (default (0, 0, 0))
• scale float: scale factor for arg0 (default 1)
• size_display tuple (int, int): width and height of the canvas (minimum 400)
• size_world float: extend on the 3D scene in all directions

Example:

from openalea.plantgl.all import Scene, Sphere
from pgljupyter import SceneWidget

s = Scene([Sphere()])
sw = SceneWidget(s)
sw

Tutorial:

• Display of spheres @nbviewer

LsystemWidget

Renderer for lpy.Lstrings derived from lpy.Lsystem code

Arguments:

• arg0 string: file name / path of lpy code file
• unit string enum: the unit used in the Lsystem model ('m', 'dm', 'cm', 'mm', default 'm')
• scale float: scale factor for arg0 (default 1)
• animate bool: if True runs animation automatically
• size_display tuple (int, int): width and height of the canvas (minimum 400)
• size_world float: extend on the 3D scene in all directions

Important property/methods:

• editor : display an editor of the graphical parameters
• get_lstring(self) : return the lstring corresponding to the current step of the simulation display in the widget.
• get_namespace(self) : return the namespace of variables of the simulation

Example:

from pgljupyter import LsystemWidget

lw = LsystemWidget('myfile.lpy')
lw

lw.editor

Tutorial:

• Display of the simulation of a lpy file : @nbviewer

%%lpy

A cell magic to inline L-Py code in a notebook

Arguments:

• --size, -s int,int: same as size_display
• --world, -w float: same as size_world
• --unit, -u enum: same as unit
• --params, -p LsystemParameters: name of LsystemParameters instance
• --animate, -a True: runs animation automatically
• --extended-editor, -e False: show/hide all parameter controls

Example:

# activated by importing pgljupyter
import pgljupyter

%%lpy -u cm
from openalea.plantgl.all import *
Axiom: ;(1)+(10)_(2)F(10);(0)@g(Paraboloid(10,10,2,False))
derivation length: 100
production:
F(x) --> F(x+0.2)
@g(p) --> @g(Paraboloid(p.radius + 0.15, p.height + 0.2, 2, False))
_(x) --> _(x+0.02)

Example with graphical parameters:

# activated by importing pgljupyter
import pgljupyter
from openalea.lpy.lsysparameters import LsystemParameters

lp = LsystemParameters()
lp.add_scalar(name='a', value=1, minvalue=0, maxvalue=100)
lp.add_function(name='b') # default graphical function created

%%lpy -p lp

Axiom: SetGuide(b,a)F(a)

Tutorials:

• simple L-systems @nbviewer
• graphical scalar parameters - broccoli @nbviewer
• graphical curve parameters - sweep surface @nbviewer

%lpy_plot

A line magic to plot all derivation steps of an Lsystem on a square plane

Arguments:

• arg0, string: L-Py file
• --size, -s int,int: width and hight of the canvas
• --cell, -c float: size of cell for a single derivation step
• --derive, -d int[,int[,int]]: start, stop, step derivation

Example:

# activated by importing pgljupyter
import pgljupyter

%lpy_plot myfile.lpy

Tutorial:

• Display of the simulation from a lpy file :@nbviewer

Installation

Install with pip - inside conda environment

Some examples also require matplotlib, xarray-simlab and rpy2.

conda create -y -n pgl -c fredboudon -c conda-forge \
    openalea.lpy jupyterlab ipywidgets pip

conda activate pgl
pip install pgljupyter

Development install

• install lpy, plantgl, jupyterlab, widgets and widgetsextension

mamba env create -f environment-dev.yml
conda activate pgljupyter-dev

• install emsdk: https://emscripten.org/docs/getting_started/downloads.html

git clone https://github.com/emscripten-core/emsdk.git
cd emsdk
./emsdk install 2.0.29
./emsdk activate 2.0.29
source ./emsdk_env.sh
cd ..

• get pgljupyter source

git clone https://github.com/jvail/plantgl-jupyter.git
cd plantgl-jupyter

• fetch plantgl and install pgljs deps

git submodule update --init --recursive
cd src/pgljs
npm install
cd ../..

• install pgljupyter deps and build (requires activated emsdk i.e. source ./emsdk_env.sh)

npm install
npm run build:all
pip install -e .
jupyter labextension develop . --overwrite

• run lab

jupyter lab --notebook-dir=./examples

Development uninstall

pip uninstall pgljupyter

In development mode, you will also need to remove the symlink created by jupyter labextension develop command. To find its location, you can run jupyter labextension list to figure out where the labextensions folder is located. Then you can remove the symlink named pgljupyter within that folder.