Pipeline: Traits computation from 3D Sorghum root models
Example of 3D Sorghum root models (genotype 3A10)
Example of 3D Sorghum root models (genotype 5A22)
One sample trait computed from 3D Sorghum point cloud model
Angle of simplified root structure curve line
Computed traits illustration
3D root models (*.ply) in Polygon File Format or the Stanford Triangle Format.
computed from Computational-Plant-Science / 3D_model_reconstruction_demo (https://github.com/Computational-Plant-Science/3D_model_reconstruction_demo)
trait.xlsx Excel format file contains computed root traits
Docker is required to run this project in a Linux environment.
Install Docker Engine (https://docs.docker.com/engine/install/)
We suggest to run the pipeline inside a docker container,
The Docker container allows you to package up your application(s) and deliver them to the cloud without any dependencies. It is a portable computing environment. It contains everything an application needs to run, from binaries to dependencies to configuration files.
There are two ways to run the pipeline inside a docker container,
One was is to build a docker based on the docker recipe file inside the GitHub repository. In our case, please follow step 1 and step 3.
Antoher way is to download prebuild docker image directly from Docker hub. In our case, please follow step 2 and step 3.
- Build docker image on your PC under linux environment
git clone https://github.com/Computational-Plant-Science/3D_Sorghum_phenotyping_pipeline.git
docker build -t 3d-model-traits -f Dockerfile .- Download prebuild docker image directly from Docker hub, without building docker image on your local PC
docker pull computationalplantscience/3d_sorghum_phenotyping- Run the pipeline inside the docker container
link your test 3D model path (e.g. '/home/test/test.ply', $path_to_your_3D_model = /home/test, $your_3D_model_name.ply = test.ply)to the /srv/test/ path inside the docker container
docker run -v /$path_to_your_3D_model:/srv/test -it 3d-model-traits
or
docker run -v /$path_to_your_3D_model:/srv/test -it computationalplantscience/3d_sorghum_phenotyping
- Run the pipeline inside the docker container
python3 /opt/code/pipeline.py -i /srv/test/test.ply -o /srv/test/result/
Suxing Liu (suxingliu@gmail.com), Wesley Paul Bonelli(wbonelli@uga.edu), Alexander Bucksch
Docker container was maintained and deployed to PlantIT by Wes Bonelli (wbonelli@uga.edu).
GNU Public License