Installing the ROMI softwareLink
In the following subsections we will detail how to install ROMI software for a few usage cases:
- Create a database server here.
- Plant scans acquisition using the ROMI plant scanner to a database here.
- Plant reconstruction pipelines from existing plant scans in a database here.
- Virtual plant creation (3D modelling of plant architecture with LPY), virtual scan (mimic plant scanner with blender) & reconstruction (same as 2.) here.
- Create a web server hosting the plant 3d explorer GUI here.
You can find docker images for use cases #1, #3 & #5 in the dockerhub repository of the ROMI project here.
To clone the git repository, you will need:
Start with these system dependencies:
sudo apt-get install git ca-certificates
Downloading from URLsLink
Sometimes the documentation will provide commands with
wget to download archives or other types of files, here is the command line to install it if you do not have it:
sudo apt install wget
Creating isolated Python environmentsLink
We recommend using
conda to create isolated environments as some packages, like
openalea.lpy, are available as
conda packages but not from
pip and can be tricky to install from sources!
Follow this link to learn how to install
miniconda3 & create isolated Python environments with
If you have no idea why you should use isolated Python environments, here is a quote from the official Python documentation:
venv (for Python 3) and
virtualenv (for Python 2) allow you to manage separate package installations for different projects.
They essentially allow you to create a "virtual" isolated Python installation and install packages into that virtual installation.
When you switch projects, you can simply create a new virtual environment and not have to worry about breaking the packages installed in the other environments.
It is always recommended using a virtual environment while developing Python applications.
List of sourcesLink
For the ROMI projects, several libraries have been developed in various languages and made available on GitHub. Here is a list of the important repositories for the plant scanner project:
plantdb: the database module is accessible here;
plantimager: the scanner interface, and the virtual scanner is accessible here;
plant3dvision: the computer vision algorithms to reconstruct the plants is accessible here;
romiseg: the ML-based plant segmentation models is accessible here;
plant-3d-explorer: the Node JS web viewer for plant scan, reconstruction and quantification is accessible here
Additionally, we also have: