Generated the testing images during docker building and added confirmation to ensure files are being generated

Author: Unique-Usman

.github/workflows/docker-build-and-run.yml

@@ -1,5 +1,4 @@
 name: Build and Run Docker
-
 on:
   push:
     branches:
@@ -9,15 +8,37 @@ on:
     branches:
       - main
       - "docker/**"
-
 jobs:
   build-and-run-docker:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy nibabel
+
+      - name: Generate input files
+        run: |
+          python -m Docker.generate_signal_docker_test
+
+      - name: Verify input files
+        run: |
+          for file in ivim_simulation.nii.gz ivim_simulation.bval ivim_simulation.bvec; do
+            if [ ! -f "$file" ]; then
+              echo "Error: $file not found"
+              exit 1
+            fi
+          done
+          echo "All input files generated successfully"
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
@@ -40,7 +61,17 @@ jobs:
           docker run --rm --name TF2.4_IVIM-MRI_CodeCollection \
             -v ${{ github.workspace }}:/usr/src/app \
             -v ${{ github.workspace }}:/usr/app/output \
-            tf2.4_ivim-mri_codecollection Docker/ivim_simulation.nii.gz Docker/ivim_simulation.bvec Docker/ivim_simulation.bval
+            tf2.4_ivim-mri_codecollection ivim_simulation.nii.gz ivim_simulation.bvec ivim_simulation.bval
+
+      - name: Verify output files
+        run: |
+          for file in f.nii.gz dp.nii.gz d.nii.gz; do
+            if [ ! -f "$file" ]; then
+              echo "Error: $file not found"
+              exit 1
+            fi
+          done
+          echo "All output files generated successfully"
 
       - name: Clean up artifacts and Docker image
         run: |
@@ -49,3 +80,6 @@ jobs:
           rm -f ${{ github.workspace }}/f.nii.gz
           rm -f ${{ github.workspace }}/dp.nii.gz
           rm -f ${{ github.workspace }}/d.nii.gz
+          rm -f ${{ github.workspace }}/ivim_simulation.nii.gz
+          rm -f ${{ github.workspace }}/ivim_simulation.bval
+          rm -f ${{ github.workspace }}/ivim_simulation.bvec

.gitignore

@@ -21,4 +21,4 @@ md5sums.txt
 .cache
 nosetests.xml
 coverage.xml
-*.pyc
+*.pyc

Docker/generate_signal_docker_test.py

@@ -1,17 +1,24 @@
 import numpy as np
 import nibabel as nib
 from utilities.data_simulation.GenerateData import GenerateData
+from WrapImage.nifti_wrapper import save_nifti_file
 
-def save_nii(data, filename='ivim_image.nii.gz'):
-    """
-    Save the data as a NIfTI file (.nii.gz)
-    """
-    nii_img = nib.Nifti1Image(data, affine=np.eye(4))
-    nib.save(nii_img, filename)
+
+def save_bval_bvec(filename, values):
+    if filename.endswith('.bval'):
+        # Convert list to a space-separated string for bval
+        values_string = ' '.join(map(str, values))
+    elif filename.endswith('.bvec'):
+        # Convert 2D list to a line-separated, space-separated string for bvec
+        values_string = '\n'.join(' '.join(map(str, row)) for row in values)
+    else:
+        raise ValueError("Unsupported file extension. Use '.bval' or '.bvec'.")
+
+    with open(filename, 'w') as file:
+        file.write(values_string)
 
 # Set random seed for reproducibility
 np.random.seed(42)
-
 # Create GenerateData instance
 gd = GenerateData()
 
@@ -25,7 +32,11 @@ def save_nii(data, filename='ivim_image.nii.gz'):
 bvals_reshaped = np.broadcast_to(bvals, shape)
 
 # Generate IVIM signal
-images = gd.ivim_signal(D_in, Dp_in, f_in, S0, bvals_reshaped)
+signals = gd.ivim_signal(D_in, Dp_in, f_in, S0, bvals_reshaped)
 
 # Save the generated image as a NIfTI file
-save_nii(images)
+save_nifti_file(signals, "ivim_image.nii.gz")
+# Save the bval in a file
+save_bval_bvec("ivim_image.bval", [0, 50, 100, 500, 1000])
+# Save the bvec value 
+save_bval_bvec("ivim_signal.bvec", [[1, 0, 0], [0, 1, 0], [0, 0, 1]])