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Introduction to OpenAlea.PlantConvert

OpenAlea.PlantConvert is a package for converting plants in mtg format into different other file formats.

Installation

You need to install the conda environment. Make sur you have one of conda / miniconda / mamba / micromamba installed, and then:

conda env create -f environment.yaml
conda activate plantconvert

Quick Start

>>> import openalea.plantconvert

MTG and its input/output into multiple formats

This project allows you to read and write mtg into mulitiple formats :

  1. homemade .mtg and .opf file formats
  2. gltf/glb
  3. vtk/vtp

If you would like to have example dataset of mtg with geometries, please install the conda envrionment strawberry.yml and please also install pygltflib and vtk by pip in the new environment.

For instance, there is not yet available setup tool for current package, please source the bash script add.sh one time before you launch Python scripts that require the package. This bash script

.mtg and .opf

They are encoded in ascii and directly parsed to construct a mtg object. .mtg is the default file format used by openalea and it only allows to save geometric parameters and not meshes. The .opf is a historical file formats used by archimed plateform and allows to save both the topologic and geometric information.

.gltf and .glb

They are .json styled file format designed to transmit computer graphics object by web. It allows to save topologic information by creating a scene graph (tree graph that explains the hierarchy of visible objects), we exploit this functionality to save the plants’ topology in those file format. The attributes of an mtg are saved as extras field of each node of the scene graph.

We can insert references to meshes inside the .gltf file. .glb is the same as .gltf but with mesh data embedded inside the same file.

We parse the .gltf file by using the Python package pygltflib. It constructs a gltf Python object that is converted to a mtg object.

vtk/vtp

They are classic file formats with a large spectrum of geometric tools associated. We use this file formats to save the topology of a plants using polylines. A mtg node is viewed as a point with coordinates of the polylines, the branching system is viewed as segments of polylines, the edge type can be seen as an edge variable of polyline.

The attributes can be saved as points variables.

These formats are very efficient in terms of memory usage, they allow to save data in binary format.

Workflow for developers/contributors

For best experience create a new conda environment (e.g. DEVELOP) with Python 3.9:

conda create -n DEVELOP -c conda-forge python=3.9
conda activate DEVELOP

Before pushing to GitHub, run the following commands:

  1. Update conda environment: make conda-env-update
  2. Install this package: pip install -e .
  3. Sync with the latest template (optional): make template-update
  4. Run quality assurance checks: make qa
  5. Run tests: make unit-tests
  6. Run the static type checker: make type-check
  7. Build the documentation (see Sphinx tutorial): make docs-build

License

Copyright 2023, European Union.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.