Docker for plant-3d-visionLink

PrerequisitesLink

Follow the getting started with docker instructions to install the required software.

Important

We advise to assign an existing local database directory to $ROMI_DB, it will be mounted at container startup. To see how to create a local database directory, look here.

Start a containerLink

Assuming you have a valid ROMI database directory under /data/ROMI/DB, you can easily download and start the pre-built roboticsmicrofarms/plant-3d-vision docker image with one of the following command:

run.sh & ROMI_DBrun.sh & -dbdocker run

From the root directory of the repository, use the convenience run.sh script:

export ROMI_DB=/data/ROMI/DB
./docker/run.sh

From the root directory of the repository, use the convenience run.sh script:

./docker/run.sh -db /data/ROMI/DB

From any directory, use the docker run command as follows:

export ROMI_DB=/data/ROMI/DB
docker run --runtime=nvidia --gpus all \
--env PYOPENCL_CTX='0' \
-v $ROMI_DB:/myapp/db \
-it roboticsmicrofarms/plant-3d-vision:latest

This should start the latest pre-built roboticsmicrofarms/plant-3d-vision docker image in interactive mode. The database location inside the docker container is /myapp/db.

Note

-v $ROMI_DB:/myapp/db performs a bind mount to enable access to the local database by the docker image. See the official documentation.
Use ./docker/run.sh -h to get all details about how to use it.

Build a docker imageLink

If you do not wish to use one of the roboticsmicrofarms/plant-3d-vision pre-built image, you may build an image using the docker/Dockerfile recipe accessible in the repository of plant-3d-vision.

We provide a convenience bash script to ease the build of roboticsmicrofarms/plant-3d-vision docker image. You can choose to use this script OR to "manually" call the docker build command.

build.shdocker build

From the root directory of the repository, use the convenience build.sh script:

./docker/build.sh

From the root directory of the repository, use the docker build command as follows:

export VTAG="latest"
docker build -t roboticsmicrofarms/plant-3d-vision:$VTAG .

Tips

By default, the image tag is 'latest', you can change it, e.g. to 'dev' with -t dev.
Use ./docker/build.sh -h to get all details about how to use it.

You may want to clean the build cache, at least from time to time, with:

docker builder prune -a

Publish docker imageLink

To push a newly built image on docker hub:

export VTAG="latest"
docker push roboticsmicrofarms/plantdb:$VTAG

This requires a valid account & token on dockerhub!

Example usageLink

NVIDIA GPU testLink

To make sure the host GPU will be accessible from the container, use:

./docker/run.sh  --gpu_test

Pipelines testsLink

To performs test reconstructions, you have several possibilities:

test the geometric pipeline, with:
```
./docker/run.sh  --geom_pipeline_test
```
test the machine learning pipeline, with:
```
./docker/run.sh  --ml_pipeline_test
```
test both pipelines, with:
```
./docker/run.sh  --pipeline_test
```

Note

This use test data & test models (for ML) provided with plant3dvision in plant3dvision/tests/testdata.

Executing a ROMI taskLink

To call a ROMI task, as defined in the romitask library, you should use the romi_run_task CLI.

For example to reconstruct a plant, named <my_scan>, using the geometric pipeline and to estimate the angles and internodes, you may use the following command:

romi_run_task AnglesAndInternodes \
  /myapp/db/<my_scan>/ \
  --config plant-3d-vision/configs/geom_pipe_real.toml

You can use it two ways: 1. start a container using the roboticsmicrofarms/plant-3d-vision image, then call the ROMI tasks. 2. use it with the -c option of the run.sh script or with docker run.

Note

You may have to source the .profile file before calling romi_run_task.

Important

source .profile is important to add .local/bin/ to the $PATH environment variable. If you don't do this, you might not be able to access the romi_run_task binary from bash in the docker container.