Docker for Virtualvirtualplantimager

Prerequisites

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 container

Assuming you have a valid ROMI database directory under /data/ROMI/DB, you can easily download and start the pre-built roboticsmicrofarms/virtualplantimager 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, assuming you created a romi group, use the docker run command as follows:

export ROMI_DB=/data/ROMI/DB
# Get the GID associtated to the 'romi' group:
gid=$(getent group romi | cut --delimiter ':' --fields 3) # get the 'gid' of this group
# Start the container:
docker run --runtime=nvidia --gpus all \
--env PYOPENCL_CTX='0' \
--user romi:${gid} \
-v $ROMI_DB:/myapp/db \
-it roboticsmicrofarms/virtualplantimager:latest

This should start the latest pre-built roboticsmicrofarms/virtualplantimager 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 image

If you do not wish to use one of the roboticsmicrofarms/virtualplantimager pre-built image, you may build an image using the docker/virtualplantimager/Dockerfile recipe.

We provide a convenience bash script to ease the build of roboticsmicrofarms/virtualplantimager 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/virtualplantimager:$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 image

To push a newly built image on docker hub:

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

This requires a valid account & token on dockerhub!

Example usage

Test

You can test the creation of a virtual plant and its acquisition by the virtual scanner as follows:

./docker/virtualplantimager/run.sh --test

Executing a ROMI task

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

For example to create a virtual plant and acquire it with the VirtualScanner, as <my_vscan>, using the Blender server , you may use the following command:

romi_run_task VirtualScan \
  /myapp/db/<my_scan>/ \
  --config plant-imager/configs/vscan_lpy_blender.toml

Important

The previous command rely on the presence of a vscan_data directory, as it contains the LPY model, background and textures to use (as defined by the TOML configuration file). It is accessible in the repository under plant-imager/database_example/vscan_data.

TOML config

Todo

The following subsections need to be reviewed!

VirtualPlant

To generate a virtual plant using LPY, the default configuration is as follows:

[VirtualPlant]
lpy_file_id = "arabidopsis_notex"

[VirtualPlant.lpy_globals]
BRANCHON = false
MEAN_NB_DAYS = 40
STDEV_NB_DAYS = 5
BETA = 51
INTERNODE_LENGTH = 1.3
STEM_DIAMETER = 0.25

VirtualScan

To perform a scan of a virtual plant, the default configuration is as follows:

[PaletteFileset]
scan_id = "vscan_data"

[HdriFileset]
scan_id = "vscan_data"

[LpyFileset]
scan_id = "vscan_data"

[ScanPath.kwargs]
center_x = 0
center_y = 0
z = 32
tilt = 3
radius = 40
n_points = 36

[ScanPath]
class_name = "Circle"

[VirtualScan]
load_scene = false
scene_file_id = ""
use_palette = true
use_hdri = true
obj_fileset = "VirtualPlant"
hdri_fileset = "HdriFileset"
scene_fileset = "SceneFileset"
palette_fileset = "PaletteFileset"
render_ground_truth = true
colorize = true

[VirtualScan.scanner]
width = 1440
height = 1080
focal = 16
flash = false
port = 9001
add_leaf_displacement = true