Install ROMI software for plants reconstructionLink
To follows this guide you should have an existing
conda or a Python
venv, see here.
We prefer to use conda and will use examples command lines with it.
Simply replace the
conda activate plant_imager commands with
For the sake of clarity the environment will be called
To save you the hassle of installing Colmap & its dependencies, we wrote a mechanism allowing you to run the Colmap command straight into a docker container where it is already done!
Choose between option A (recommended) OR B!
A - Use of docker imageLink
You can use a pre-built docker image with Colmap & its dependencies installed (named
This requires to install the docker-engine.
To do so, follows the official instructions here: https://docs.docker.com/get-docker/
If you upgrade from an older install, you may have to install the Python docker SDK:
conda activate plant_imager python -m pip install docker
Make sure you can access the docker engine as a non-root user! On Linux:
1. Create the docker group: `$ sudo groupadd docker` 2. Add your user to the docker group: `$ sudo usermod -aG docker $USER` 3. Log out and log back in so that your group membership is re-evaluated. Official instructions [here](https://docs.docker.com/engine/install/linux-postinstall/)
B - System installLink
If you are a warrior or a computer expert, you can follow the procedure from the official documentation here. Make sure to use version 3.6.
If you are using a conda environment, you can install
ceres-solver dependency for Colmap from the conda-forge channel:
conda activate plant_imager conda install ceres-solver -c conda-forge
By default we use the docker mechanism, to enable the system install you need to export the environment variable
Install ROMI packages with
Since this is still under development, the packages are installed in "editable mode" with the
You need an active ROMI database to import the images fileset to reconstruct. If it's not done yet, follow the installation instructions of a ROMI database (here).
To start "reconstruction jobs", you have to install the
Here we use the submodules but if you wish to edit other packages than
plantdb, install them from source!
conda activate plant_imager git clone --branch dev https://github.com/romi/plant3dvision.git cd plant3dvision git submodule init git submodule update python3 -m pip install -e ./plantdb/ --no-cache-dir python3 -m pip install -e ./romitask/ --no-cache-dir python3 -m pip install -e ./romiseg/ --no-cache-dir python3 -m pip install -e ./romicgal/ --no-cache-dir python3 -m pip install -e ./dtw/ --no-cache-dir python3 -m pip install -r requirements.txt --no-cache-dir python3 -m pip install -e . --no-cache-dir
We use some algorithms from CGAL and propose a minimal python wrapper called
romicgal. To install it:
conda activate plant_imager python3 -m pip install -e git+https://github.com/romi/romicgal.git@master
This takes some time since it has to download dependencies (
boost-1.72.0) and compile them.
To install the additional Machine Learning based segmentation module:
conda activate plant_imager python3 -m pip install -e git+https://github.com/romi/romiseg@dev
If not using CUDA 10.*, you have to install the matching
pytorch distribution. For example, for CUDA 9.2, use:
conda activate plant_imager pip install torch==1.4.0+cu92 -f https://download.pytorch.org/whl/torch_stable.html
conda install pytorch==1.8.0 torchvision==0.9.0 torchaudio==0.8.0 cudatoolkit=11.1 -c pytorch -c conda-forge