Plant Dashboard

Requirements

System requirements

The Plant Dashboard require graphviz to generates a tasks dependency graph figure.

Debian & Ubuntu

On Debian and Ubuntu, you may install the system library with:

sudo apt-get install graphviz graphviz-dev

MacOS

On macOS, you may install the system library using the Homebrew package manager as follows:

brew install graphviz

Conda environment & Python packages

To install the source, let's first create a conda environment:

conda create -n plant_dashboard python=3.9
conda activate plant_dashboard

The Plant Dashboard require some additional Python packages, you may install them with pip as follows:

python -m pip install -e .

ROMI libraries sources

As the Plant Dashboard project is still under development, it requires to install the following ROMI libraries from the sources:

• romitask
• plantdb
• romicgal
• romiseg
• plant3dvision

You can install them all at once with the plant-3d-vision sources that list the other ones as submodules:

# - Clone the sources from the GitHub repository:
git clone https://github.com/romi/plant-3d-vision.git
# - Move to the source directory and initialize the submodules:
cd plant-3d-vision/
git submodule init
git submodule update
# - Install the `plant-3d-vision` & submodule dependencies and sources:
# -- `plantdb` dependencies and sources:
python3 -m pip install --user plantdb/
# -- `romitask` dependencies and sources:
python3 -m pip install --user romitask/
# -- `romiseg` dependencies and sources:
python3 -m pip install --user torch==1.12.1+cu102 torchvision==0.13.1+cu102 --extra-index-url https://download.pytorch.org/whl/cu102 && \
python3 -m pip install --user romiseg/
# -- `romicgal` dependencies and sources:
python3 -m pip install --user pybind11
python3 -m pip install --user romicgal/
# -- `plant-3d-vision` dependencies and sources:
python3 -m pip install --user -r requirements.txt
python3 -m pip install --user .
# -- Clean pip cache:
python3 -m pip cache purge

Getting started

PlantDB

First we have to start a (test) REST API serving an FSDB database. It can be done as follows:

fsdb_rest_api --test

Note that the --test option will create a test database by cloning dataset from Zenodo in /tmp/ROMI_DB. To use an existing database, export the path to the $ROMI_DB environment variable or use the -db option with a path.

localhost:5000.

Luigi central scheduler

You may create a Luigi central scheduler (luigid server deamon) as follows:

mkdir /tmp/luigi_log
luigid  --logdir /tmp/luigi_log

Then you can access luigi WebUI under localhost:8082.

If you do not do this, you need to call the luigi CLI with the --local-scheduler argument.

See Using the Central Scheduler for more details.

Redis

We use a docker container to provide a Redis broker and backend to Celery.

Start a redis container named plant-dashboard-redis, in background mode and binding port 6379 from host to 6379 in container:

docker run --name plant-dashboard-redis --rm -p 6379:6379 redis

You may want to use the -d option to detach the process and let it run in the background.

To get the IP address of the running container "plant-dashboard-redis", use:

docker inspect -f '{{range.NetworkSettings.Networks}}{{.IPAddress}}{{end}}' plant-dashboard-redis

Use this in the Celery app configuration or in celeryconfig.py, e.g. with 172.17.0.2 as IP:

celery_app = Celery(__name__,
                    broker="redis://172.17.0.2:6379/0",
                    backend="redis://172.17.0.2:6379/1",
                    # ...
                    )

Celery

We now have to create a celery worker to receive the long callbacks (like reconstruction pipelines) from the WebUI. From the plant-dashboard root directory, it can be started as follows:

cd plant_dashboard/webui
celery -A app:celery_app worker --loglevel=INFO

Flower

To access Celery tasks & worker statuses we use flower to get an API that serve such information. From the plant-dashboard root directory, it can be started as follows:

cd plant_dashboard/webui
celery -A app:celery_app flower --port=5555 --basic-auth=${FLOWER_USER}:${FLOWER_PWD}

The flower web-interface should be accessible under 0.0.0.0:5555. Do not forget to define ${FLOWER_USER} & ${FLOWER_PWD} as environment variables.

WebUI

Finally, you can start the Dash WebUI. From the plant-dashboard root directory, it can be started as follows:

cd plant_dashboard/webui/
python app.py

Our web-interface should be accessible under localhost:3000.

We have to start our Dash App in this folder, so it knows where the pages directory is.

Sources and documentation

• Dash
• Dash-Bootstrap-Components
• Bootstrap-Icons
• Luigi
• Celery