fixes for ROCKETSHIP 2.0

.github/workflows/DCE.yml

@@ -2,85 +2,135 @@ name: Run DCE then build docker
 
 on:
   push:
-    branches: [ "dev", "main" ]
   pull_request:
-    branches: [ "dev", "main" ]
 
 permissions:
   contents: read
 
 jobs:
-  run:
+  run_case_matlab:
 
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
     runs-on: self-hosted
+    env:
+      ROCKETSHIP_PATH: ${{ github.workspace }}/ROCKETSHIP
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Checkout ROCKETSHIP repo
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
       with:
         repository: petmri/ROCKETSHIP
         ref: dev
         path: ROCKETSHIP
+        clean: true
+        fetch-depth: 0
 
-    #- name: Set up Python 3.10
-    #  uses: actions/setup-python@v3
-    #  with:
-    #    python-version: "3.10"
+    - name: Set up ROCKETSHIP venv
+      working-directory: ROCKETSHIP
+      run: python3 install.py -G -M
 
     - 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
-
-
-   # - name: Lint with flake8
-   #   run: |
-   #     # stop the build if there are Python syntax errors or undefined names
-   #     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: Preprocess the data
-      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -b -Z -m -c
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -A A -w /home/mrispec/Code/DCEPrep/docker/files/model_weight_huber1.h5
 
     - name: Run DCE
-      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/rawdata -f
+      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -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: 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: Validate analysis results
+      run: |
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+        test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
+
+    - name: Upload analysis results
+      uses: actions/upload-artifact@v7
+      with:
+        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/figures/
+        retention-days: 7
+        if-no-files-found: error
+
+  run_case_python:
+
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
+    runs-on: self-hosted
+    env:
+      ROCKETSHIP_PATH: ${{ github.workspace }}/ROCKETSHIP
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v7
+
+    - name: Checkout ROCKETSHIP repo
+      uses: actions/checkout@v7
+      with:
+        repository: petmri/ROCKETSHIP
+        ref: dev
+        path: ROCKETSHIP
+
+    - name: Set up ROCKETSHIP venv
+      working-directory: ROCKETSHIP
+      run: python3 install.py -G -M
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install --upgrade hd-bet
+
+    - name: Preprocess the data
+      run:  ./preprocess_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -b -Z -m -c -p -A A -w /home/mrispec/Code/DCEPrep/docker/files/model_weight_huber1.h5
+
+    - name: Run DCE
+      run:  ./DCE_all.sh -d /media/network_mriphysics/USC-PPG/RUNNER_DATA/sourcedata/raw -f -p
+
+    - name: Output logs
+      run:  |
+        date=$(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: Validate analysis results
+      run: |
+        test -f /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/reports/sub-1101743_ses-01_desc-casereport.html
+        test -n "$(find /media/network_mriphysics/USC-PPG/RUNNER_DATA/derivatives/dceprep/sub-1101743/ses-01/figures/ -type f -print -quit)"
 
     - name: Upload analysis results
       uses: actions/upload-artifact@v7
       with:
         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
+    needs: run_case_matlab
+    if: github.ref == 'refs/heads/dev' || github.ref == 'refs/heads/main'
     strategy:
       fail-fast: false
       matrix:
@@ -89,7 +139,7 @@ jobs:
     runs-on: self-hosted
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
 
     - name: Extract branch name
       id: extract_branch