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3D Sorghum phenotyping

Pipeline: Traits computation from 3D Sorghum root models

Optional Text

Example of 3D Sorghum root models (genotype 3A10)

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Example of 3D Sorghum root models (genotype 5A22)

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One sample trait computed from 3D Sorghum point cloud model

Angle of simplified root structure curve line

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Computed traits illustration

Input

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)

Output

trait.xlsx Excel format file contains computed root traits

Requirements

Docker is required to run this project in a Linux environment.

Install Docker Engine (https://docs.docker.com/engine/install/)

Usage

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.

  1. 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 .
  1. Download prebuild docker image directly from Docker hub, without building docker image on your local PC
docker pull computationalplantscience/3d_sorghum_phenotyping
  1. 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
  1. Run the pipeline inside the docker container
python3 /opt/code/pipeline.py -i /srv/test/test.ply -o /srv/test/result/

Author

Suxing Liu ([email protected]), Wesley Paul Bonelli([email protected]), Alexander Bucksch

Other contributions

Docker container was maintained and deployed to PlantIT by Wes Bonelli ([email protected]).

License

GNU Public License