Merge Dev to main

.github/workflows/DCE.yml

@@ -1,34 +1,40 @@
-name: Bash script
+name: Run DCE then build docker
 
 on:
   push:
-    branches: [ "freesurfer", "main" ]
+    branches: [ "dev", "main" ]
   pull_request:
-    branches: [ "freesurfer", "main" ]
+    branches: [ "dev", "main" ]
 
 permissions:
   contents: read
 
 jobs:
-  build:
+  run:
 
     runs-on: self-hosted
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/checkout@v3
+    - name: Checkout
+      uses: actions/checkout@v5
+
+    - name: Checkout ROCKETSHIP repo
+      uses: actions/checkout@v5
       with:
         repository: petmri/ROCKETSHIP
         ref: dev
         path: ROCKETSHIP
+
     #- name: Set up Python 3.10
     #  uses: actions/setup-python@v3
     #  with:
     #    python-version: "3.10"
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install --upgrade hd-bet
     #    pip install flake8 pytest
 
 
@@ -38,29 +44,71 @@ jobs:
    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     #- name: Test with pytest
     #  run: |
     #    pytest
+
     #- name: Set up MATLAB
     #  uses: matlab-actions/setup-matlab@v1
-    - name: Clean the runner subject data
-      run: |
-        cd /media/network_mriphysics/USC-PPG/RUNNER_DATA/1101743_runner/1st_timepoint
-        shopt -s extglob
-        rm -f !(2.nii|5.nii|10.nii|12.nii|15.nii|DCE.nii|aif.nii)
-        cd /home/mrispec/actions-runner/_work/in-house_toolbox/in-house_toolbox
 
     - name: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA -b -Z
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -b -Z -m -c
 
     - name: Run DCE
-      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA -b -Z
+      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -f
 
+    - name: Output logs
+      run:  |
+        date=$(date +"%Y-%m-%d")
+        cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/preprocessing_log_${date}.txt
+        cat /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/logs/dce_log_${date}.txt
+
+    - name: Convert HTML to PDF
+      run:  wkhtmltopdf --enable-local-file-access /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html /media/network_mriphysics/USC-PPG/RUNNER_DATA/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+      continue-on-error: true
+
     - name: Upload analysis results
-      uses: actions/upload-artifact@v3.1.0
+      uses: actions/upload-artifact@v4
       with:
-        name: T1_Ktrans_graphs
-        path: /media/network_mriphysics/USC-PPG/RUNNER_DATA/1101743_runner/1st_timepoint/report.png
-        retention-days: 5
+        name: HTML_report
+        path: |
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.pdf
+          /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/
+        retention-days: 7
         if-no-files-found: error
 
+  docker:
+    needs: run
+    strategy:
+      fail-fast: false
+      matrix:
+        release: [R2020a, R2020b, R2021a, R2021b, R2022a, R2022b, R2023a]
+
+    runs-on: self-hosted
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Extract branch name
+      id: extract_branch
+      shell: bash
+      run: echo "branch=$(echo ${GITHUB_REF#refs/heads/})" >> "$GITHUB_ENV"
+
+    - name: Build Dockerfile
+      id: docker_build
+      run: |
+        docker image prune -f
+        docker build --build-arg MATLAB_RELEASE=${{ matrix.release }} . -t lsaca05/dce:${{ matrix.release }}-$branch
+
+    # - name: Run Docker
+    #   if: ${{ matrix.release }} == "R2020a"
+    #   run: |
+    #     ./run_docker.sh
+    #     exit
+
+    # - name: Push to Docker Hub
+    #   if: steps.docker_build.outcome == 'success'
+    #   run: |
+    #     docker push lsaca05/dce:${{ matrix.release }}-$branch

.gitignore

@@ -1,2 +1,4 @@
 .project
 .pydevproject
+docker/files/license.txt
+__pycache__