pgljupyter

PlantGL & L-Py jupyter widgets

Quick Examples

• lpy tree model - leuwenberg @nbviewer

• simple PlantGL shapes - spheres @nbviewer

• notebook magics - champignon @nbviewer

• notebook magics with scalar parameters - broccoli @nbviewer

• notebook 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

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

%%lpy

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

# activated by importing pgljupyter
import pgljupyter

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

%lpy_plot

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

# activated by importing pgljupyter
import pgljupyter

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

Installation

Install with pip - inside conda env

JupyterLab < 3.0 requires nodejs. In case it is not available on your system add nodejs to the conda create command.

conda create -y -n pgl -c fredboudon -c conda-forge \
    openalea.lpy jupyterlab ipywidgets ipython=7

For windows specify python 3.7 (there are some issues with jupyter on windows with python 3.8)

conda create -y -n pgl -c fredboudon -c conda-forge python=3.7 \
    openalea.lpy jupyterlab ipywidgets ipython=7

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

For JupyterLab 3:

conda activate pgl
jupyter labextension install @jupyter-widgets/jupyterlab-manager
pip install pgljupyter

For JupyterLab 2:

conda activate pgl
pip install "pgljupyter<1.0.0"
jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager
jupyter lab build && jupyter lab

Build, install and run from source

• install lpy, plantgl, jupyterlab, widgets and widgetsextension

conda create -y -n pgl -c fredboudon -c conda-forge openalea.lpy jupyterlab ipywidgets
conda activate pgl
jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager

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

git clone https://github.com/emscripten-core/emsdk.git
cd emsdk
./emsdk install latest
./emsdk activate latest
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 activation of emsdk i.e. source ./emsdk_env.sh)

npm install
npm run build:all

• install python modules and jupyter extensions

pip install -e .
jupyter nbextension install --sys-prefix --overwrite --py pgljupyter
jupyter nbextension enable --sys-prefix --py pgljupyter
jupyter labextension install .
jupyter lab clean

• run the lab

jupyter lab --notebook-dir=./examples

Docker

Run jupyter as docker container locally. Replace /examples with the path to your notebooks. Tag latest might not always be up-to-date since docker is primarily used for binder

docker pull jvail/plantgl-jupyter:0.2.1
docker run --rm \
    -p 8888:8888 \
    -v $PWD/examples:/home/jovyan/work jvail/plantgl-jupyter:0.2.1 \
    jupyter lab