🔨Building and 🧪testing the container


Building

Once your scripts are ready, you can build the container by calling ./build.sh. The recommendation is for your containers to be tested locally before they are uploaded to grand-challenge.org. Uploading a container always takes time and it's best to keep grand-challenge.org out of your development loop.

Testing

The templated repository made by evalutils provides a testing script (test.sh). You can extend this template to build your own test suite.

In our example, we restructured the test folder by placing the first retinal fundus image from the test set of the DRIVE challenge. The ./test/input/ folder contains the raw image and the ./test/expected_output/ folder contains the outputs our algorithm would have to write for the test to pass.

test
├── expected_output
│   ├── images
│   │   └── 01_test.tif
│   └── results.json
└── input
    └── 01_test.tif


We further modified the automatically created test script test.sh to customize it for our use case. The customized snippet now has two major steps:

  1. Mount a temporary Docker volume to /output/ and write the algorithm's outputs there
  2. Mount the temporary Docker volume and check if the outputs there match the outputs in ./test/expected_output/. Here, we have used biocontainers/simpleitk:v1.0.1-3-deb-py3_cv1 to access SimpleITK within a Docker.
#!/usr/bin/env bash

SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"

./build.sh

VOLUME_SUFFIX=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 8 | head -n 1)

docker volume create vesselsegmentation-output-$VOLUME_SUFFIX

# run the forward pass and store the outputs in a temporary Docker volume
docker run --rm \
        --gpus=all \
        -v $SCRIPTPATH/test/input/:/input/ \
        -v vesselsegmentation-output-$VOLUME_SUFFIX:/output/ \
        vesselsegmentation

# compare the outputs in the Docker volume with the outputs in ./test/expected_output/
docker run --rm \
        -v vesselsegmentation-output-$VOLUME_SUFFIX:/output/ \
        -v $SCRIPTPATH/test/expected_output/:/expected_output/ \
        biocontainers/simpleitk:v1.0.1-3-deb-py3_cv1 python3 -c """
import SimpleITK as sitk

output = sitk.ReadImage('/output/images/01_test.tif')
expected_output = sitk.ReadImage('/expected_output/images/01_test.tif')

label_filter = sitk.LabelOverlapMeasuresImageFilter()
label_filter.Execute(output, expected_output)
dice_score = label_filter.GetDiceCoefficient()

if dice_score == 1.0:
    print('Test passed!')
else:
    print('Test failed!')
"""

docker volume rm vesselsegmentation-output-$VOLUME_SUFFIX


You can invoke the testing script by calling ./test.sh

💡 If you already have exported containers in your working directory, you can add *.tar.gz files into a .dockerignore file to make your builds much faster. This speeds up your development and testing processes.

⚠️Docker Desktop for Windows 10 does not have GPU support. You either need Windows 11 or an Insider version of Windows 10. Note that this does not compromise your building and exporting processes. It only hampers your testing process. You can avoid this by testing with CPU-only mode if possible. Make sure to remove the --gpus=all flag. Otherwise, you will have to test your container by running it on an Ubuntu environment if you need GPU access.

💡 Our modifications from the templated repository generated by evalutils can be found here: https://github.com/DIAGNijmegen/drive-vessels-unet/tree/master/VesselSegmentation