Use palom to read prob map #23
Workflow file for this run
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name: CI | |
on: [push, pull_request, workflow_dispatch] | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
env: | |
IMG: exemplar-001-cycle6.ome.tif | |
PMAP: exemplar-001-cycle6_Probabilities_1.tif | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build the Docker container | |
run: | | |
docker build -t s3seg:test . | |
docker build -t s3seg:test-large large/ | |
# Cache test data to avoid repeated download | |
- uses: actions/cache@v3 | |
id: cache-data | |
with: | |
path: ~/data/*.tif | |
key: testdata-2022-05-12 | |
# Download test data only if no cache is present | |
- name: Test data download | |
if: steps.cache-data.outputs.cache-hit != 'true' | |
run: | | |
mkdir ~/data | |
cd ~/data | |
curl -f -o $IMG "https://mcmicro.s3.amazonaws.com/ci/$IMG" | |
curl -f -o $PMAP "https://mcmicro.s3.amazonaws.com/ci/$PMAP" | |
- name: Test the default container | |
run: | | |
cd ~/data | |
rm -rf exemplar-001-cycle6 | |
docker run -v "$PWD":/data s3seg:test /bin/bash -c "cd /data; \ | |
python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath ." | |
- name: Test the large container | |
run: | | |
cd ~/data | |
rm -rf large | |
mkdir large | |
docker run -v "$PWD":/data s3seg:test-large /bin/bash -c "cd /data; \ | |
python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath large" | |
# If the action is successful, the output will be available as a downloadable artifact | |
- name: Upload processed result | |
uses: actions/upload-artifact@v2 | |
with: | |
name: ex001-s3seg | |
path: | | |
~/data/exemplar-001-cycle6/** | |
~/data/large/** | |