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Digits Data ingestion plugin to support tiled tiffs coming from WIPP

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WIPP Digits Data plugin

Login to Docker registry nvcr.io

Please refer to the Nvidia documentation: https://docs.nvidia.com/ngc/ngc-user-guide/pullcontainer.html#accessing_registry

Build the container

docker build . -t wipp-digits

Run the container

nvidia-docker run --name wipp-digits -d -p 8888:5000 -v $WIPP_DATA_FOLDER:/data/WIPP-plugins -e WIPP_API_URL=$WIPP_API_URL wipp-digits

  • $WIPP_API_URL is the WIPP REST API URL (for example: http://wipp-backend:8080/api)
  • $WIPP_DATA_FOLDER is the WIPP Data folder path on the host (for example /data/WIPP-plugins), images collections are expected to be in a sub folder called collections

Note: nvidia-docker run can be replaced by docker run --gpus all or docker run --runtime=nvidia depending on the nvidia-docker/nvidia-docker-runtime version installed.

For testing - mock WIPP API

docker run -p 9999:80 -v $PATH_TO_CURRENT_FOLDER/json-server:/data clue/json-server --routes /data/routes.json /data/db.json this will create a mock WIPP REST API containing mock information for two collections: digits-train-images and digits-train-masks

Run the WIPP Digits container using this mock API: nvidia-docker run --name wipp-digits -d -p 8888:5000 -v $WIPP_DATA_FOLDER:/data/WIPP-plugins -e WIPP_API_URL=http://localhost:9999 wipp-digits

$WIPP_DATA_FOLDER is the WIPP Data folder path on the host (for example /data/WIPP-plugins), the sub-folder collections is expected to have the following structure:

├── data
│   └── WIPP-plugins
│       └── collections
│           ├── digits-train-images
│           │   └── images
│           │       ├── img_001302.ome.tif
│           │       ├── img_001823.ome.tif
│           │       ├── img_002782.ome.tif
│           │       ├── ...
│           └── digits-train-masks
│               └── images
│                   ├── img_001302.ome.tif
│                   ├── img_001823.ome.tif
│                   ├── img_002782.ome.tif
│                   ├── ...

Kubernetes deployment

Prerequesites:

  • WIPP is deployed on the Kubernetes cluster and the WIPP Data Permanent Volume Claim is named wippdata-pvc (otherwise the name has to be changed in wipp-digits.yaml)
  • Replace WIPP_API_URL_VALUE by the URL of the WIPP API (for example "http://IP_ADDRESS:30101/api") in the file wipp-digits.yaml.

Deployment

Run kubectl apply -f wipp-digits.yaml

WIPP Digits will be available at http://HOST:30701 (where HOST is the IP address/host name of the host server).

Notes

Code tested succesfully with the versions 19.10 and 20.01 of Nvidia DIGITS containers. Both classification (MNIST dataset) and segmentation (VOC2012 dataset) worked with the Caffe version. Only the classification (MNIST dataset) worked with the Tensorflow version.

Links to WIPP

Disclaimer

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