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WIP foreground model for sensor noise bypass #139

WIP foreground model for sensor noise bypass

WIP foreground model for sensor noise bypass #139

Workflow file for this run

name: CI
on:
# Don't trigger when only the docs are modified
push:
paths-ignore:
- 'docs/**'
pull_request:
paths-ignore:
- 'docs/**'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Build the Docker container
run: docker build -t ashlar:test .
# Cache test data to avoid repeated download
- uses: actions/cache@v3
id: cache-data
with:
path: |
~/data/
!~/data/exemplar-001.ome.tif
key: testdata-2022-04-25
# Download exemplar-001 only if no cache is present
- name: Exemplar-001 download
if: steps.cache-data.outputs.cache-hit != 'true'
run: |
mkdir ~/data
cd ~/data
curl -f -o exemplar-001.zip https://mcmicro.s3.amazonaws.com/exemplars/exemplar-001.zip
unzip exemplar-001.zip
mv exemplar-001/raw/*.ome.tiff .
mv exemplar-001/illumination/*.tif .
rm -r exemplar-001
rm exemplar-001.zip
- name: Test the container
run: |
cd ~/data/
rm -f exemplar-001.ome.tif
docker run -v "$PWD":/data ashlar:test /bin/bash -c "cd /data; \
ashlar $imgs -m 30 --dfp $dfp --ffp $ffp -o exemplar-001.ome.tif"
env:
imgs: 'exemplar-001-cycle-06.ome.tiff exemplar-001-cycle-07.ome.tiff exemplar-001-cycle-08.ome.tiff'
dfp: 'exemplar-001-cycle-06-dfp.tif exemplar-001-cycle-07-dfp.tif exemplar-001-cycle-08-dfp.tif'
ffp: 'exemplar-001-cycle-06-ffp.tif exemplar-001-cycle-07-ffp.tif exemplar-001-cycle-08-ffp.tif'
# 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: exemplar-001
path: |
~/data/exemplar-001.ome.tif