Run Morphometric Analysis #13
Workflow file for this run
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| name: Run Morphometric Analysis | |
| on: | |
| release: | |
| types: [published] | |
| jobs: | |
| download_dataset: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install Python 3 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install git-annex | |
| uses: jstritch/setup-git-annex@v1 | |
| - name: Configure git | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Actions" | |
| - name: Download test data | |
| run: | | |
| # run script | |
| chmod +x scripts/download_spine_generic_test_data.sh | |
| source scripts/download_spine_generic_test_data.sh | |
| - name: Cache dataset | |
| uses: actions/cache@v4 | |
| with: | |
| path: data-multi-subject # NOTE: do not change the name of the folder `data-multi-subject` | |
| key: ${{ runner.os }}-data-multi-subject-${{ hashFiles('scripts/download_spine_generic_test_data.sh') }} | |
| restore-keys: | | |
| ${{ runner.os }}-data-multi-subject- | |
| compute_csa: | |
| runs-on: ubuntu-latest | |
| needs: download_dataset | |
| strategy: | |
| matrix: | |
| batch: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] | |
| include: | |
| - batch: 1 | |
| subjects: "sub-barcelona06 sub-beijingPrisma01 sub-beijingPrisma02" | |
| - batch: 2 | |
| subjects: "sub-brnoCeitec04 sub-brnoUhb01 sub-cardiff03" | |
| - batch: 3 | |
| subjects: "sub-cmrra02 sub-cmrra05 sub-cmrrb01" | |
| - batch: 4 | |
| subjects: "sub-cmrrb03 sub-cmrrb05 sub-fslAchieva04" | |
| - batch: 5 | |
| subjects: "sub-fslPrisma01 sub-fslPrisma02 sub-fslPrisma04" | |
| - batch: 6 | |
| subjects: "sub-fslPrisma05 sub-geneva03 sub-juntendo750w01" | |
| - batch: 7 | |
| subjects: "sub-juntendo750w02 sub-juntendo750w03 sub-juntendo750w06" | |
| - batch: 8 | |
| subjects: "sub-milan03 sub-mniS03 sub-mountSinai01" | |
| - batch: 9 | |
| subjects: "sub-nottwil01 sub-nottwil04 sub-nwu01" | |
| - batch: 10 | |
| subjects: "sub-oxfordFmrib06 sub-oxfordFmrib09 sub-oxfordFmrib10" | |
| - batch: 11 | |
| subjects: "sub-oxfordOhba01 sub-oxfordOhba05 sub-pavia02" | |
| - batch: 12 | |
| subjects: "sub-pavia05 sub-queensland01 sub-sherbrooke02" | |
| - batch: 13 | |
| subjects: "sub-sherbrooke05 sub-sherbrooke06 sub-stanford04" | |
| - batch: 14 | |
| subjects: "sub-strasbourg04 sub-tehranS03 sub-tokyoIngenia05" | |
| - batch: 15 | |
| subjects: "sub-ubc06 sub-ucl02 sub-unf04" | |
| - batch: 16 | |
| subjects: "sub-vuiisAchieva04 sub-vuiisIngenia03 sub-vuiisIngenia04 sub-vuiisIngenia05" | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install Python 3 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install SCT | |
| run: | | |
| cd .. # avoid long path name by not installing in repo subfolder | |
| # for more info about why `cd ..`, refer to | |
| # https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4813#issuecomment-2741165452 | |
| # clone and install SCT | |
| git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox.git | |
| cd spinalcordtoolbox | |
| ./.ci.sh -i | |
| cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV | |
| cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| # re-enter the contrast-agnostic repository | |
| cd $GITHUB_WORKSPACE | |
| - name: Restore cached dataset | |
| uses: actions/cache@v4 | |
| with: | |
| path: data-multi-subject | |
| key: ${{ runner.os }}-data-multi-subject-${{ hashFiles('scripts/download_spine_generic_test_data.sh') }} | |
| restore-keys: | | |
| ${{ runner.os }}-data-multi-subject- | |
| - name: Run morphometric analysis | |
| shell: bash -el {0} # Ensures the Conda environment is properly loaded | |
| run: | | |
| # Get the release details from the GitHub event | |
| RELEASE_ID=${{ github.event.release.id }} | |
| REPOSITORY="${{ github.repository }}" | |
| # List all assets for this release | |
| ASSETS_URL="https://api.github.com/repos/$REPOSITORY/releases/$RELEASE_ID/assets" | |
| ASSETS=$(curl -s -H "Authorization: token ${{ github.token }}" -H "Content-Encoding: gzip" $ASSETS_URL) | |
| echo $ASSETS | |
| # Find the model asset - fix: improve regex pattern matching | |
| MODEL_URL=$(echo "$ASSETS" | jq -r '.[] | select(.name | contains("model") and endswith(".zip")) | .browser_download_url') | |
| echo "Model URL: $MODEL_URL" | |
| # run script | |
| chmod +x scripts/compute_morphometrics_spine_generic.sh | |
| source scripts/compute_morphometrics_spine_generic.sh "${{ matrix.subjects }}" "$MODEL_URL" | |
| - name: Upload batch processing results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: csa-results-batch-${{ matrix.batch }} | |
| path: logs_results | |
| - name: Setup tmate session | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 | |
| download_results: | |
| runs-on: ubuntu-latest | |
| needs: compute_csa | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install Python 3 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pandas argparse | |
| - name: Download batch processing results | |
| uses: actions/download-artifact@v4 | |
| - name: Merge batch processing results | |
| run: | | |
| ls -la | |
| # create a new folder to download all artifacts uploaded above | |
| mkdir batch_csa_results | |
| # move all the files there | |
| mv csa-results-* batch_csa_results | |
| # # clone the repo | |
| # git clone https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord.git | |
| # # change current working directory | |
| # cd ${PWD}/contrast-agnostic-softseg-spinalcord | |
| # # checkout to the branch | |
| # git checkout nk/add-post-training-script-to-compute-csa | |
| # run script to merge individual csvs | |
| chmod +x scripts/merge_run_batch_results.sh | |
| source scripts/merge_run_batch_results.sh batch_csa_results . | |
| # rename the csv file to contain the model version | |
| mv csa_c2c3_merged.csv csa_c2c3__model_${{ github.event.release.tag_name }}.csv | |
| - name: Upload merged CSV to current release | |
| uses: softprops/action-gh-release@v2 | |
| with: | |
| tag_name: ${{ github.event.release.tag_name }} | |
| files: csa_c2c3__model_${{ github.event.release.tag_name }}.csv | |
| - name: Setup tmate session | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 | |
| generate_plots: | |
| runs-on: ubuntu-latest | |
| needs: download_results | |
| steps: | |
| - name: Install Python 3 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pandas argparse seaborn matplotlib | |
| - name: Generate morphometrics plots | |
| shell: bash -el {0} | |
| run: | | |
| # create new folder to store downloaded CSV files | |
| mkdir -p csvs_model_releases | |
| # list all releases | |
| REPOSITORY="${{ github.repository }}" | |
| RELEASES_URL="https://api.github.com/repos/$REPOSITORY/releases" | |
| RELEASES=$(curl -s -H "Authorization: token ${{ github.token }}" $RELEASES_URL) | |
| # echo "$RELEASES" # Added quotes | |
| # loop through each release and find CSV assets | |
| echo "$RELEASES" | jq -c '.[]' | while read -r release; do | |
| RELEASE_ID=$(echo "$release" | jq -r '.id') | |
| RELEASE_TAG=$(echo "$release" | jq -r '.tag_name') # Get tag from the current release | |
| # list all assets for this release | |
| ASSETS_URL="https://api.github.com/repos/$REPOSITORY/releases/$RELEASE_ID/assets" | |
| ASSETS=$(curl -s -H "Authorization: token ${{ github.token }}" -H "Content-Encoding: gzip" $ASSETS_URL) | |
| # echo "$ASSETS" # Added quotes | |
| # find CSV files | |
| CSV_URLS=$(echo "$ASSETS" | jq -r '.[] | select(.name | endswith(".csv")) | .browser_download_url') | |
| if [ -n "$CSV_URLS" ]; then | |
| echo "Found CSV file(s) for release $RELEASE_TAG:" | |
| # download the CSV files into the folder | |
| echo "$CSV_URLS" | while read -r url; do | |
| if [ -n "$url" ]; then | |
| echo "Downloading $url" | |
| curl -L -H "Authorization: token ${{ github.token }}" -o "csvs_model_releases/$(basename "$url")" "$url" | |
| fi | |
| done | |
| else | |
| echo "No CSV files found for release $RELEASE_TAG" | |
| fi | |
| done | |
| # # clone the repo | |
| # git clone https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord.git | |
| # # change current working directory | |
| # cd ${PWD}/contrast-agnostic-softseg-spinalcord | |
| # # checkout to the branch | |
| # git checkout nk/add-post-training-script-to-compute-csa | |
| # # move the csvs folder inside the repo | |
| # cp -r ../csvs_model_releases . | |
| # run script | |
| chmod +x scripts/generate_morphometrics_plots.sh | |
| source scripts/generate_morphometrics_plots.sh csvs_model_releases | |
| # create a zip file | |
| zip -r morphometric_plots.zip csvs_model_releases | |
| - name: Upload plots to the current release | |
| uses: softprops/action-gh-release@v2 | |
| with: | |
| tag_name: ${{ github.event.release.tag_name }} | |
| files: morphometric_plots.zip | |