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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| name: Build and Run Docker | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| types: [opened, synchronize, edited] | ||
| 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 -r requirements.txt | ||
| - 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 | ||
|
|
||
| - name: Build Docker image | ||
| run: | | ||
| docker build -t tf2.4_ivim-mri_codecollection -f Docker/Dockerfile . | ||
| - name: Run Docker container | ||
| run: | | ||
| docker run --rm --name TF2.4_IVIM-MRI_CodeCollection \ | ||
| -v ${{ github.workspace }}:/usr/src/app \ | ||
| -v ${{ github.workspace }}:/usr/app/output \ | ||
| tf2.4_ivim-mri_codecollection ivim_simulation.nii.gz ivim_simulation.bvec ivim_simulation.bval | ||
| - name: Verify output files | ||
| run: | | ||
| for file in f.nii.gz dp.nii.gz d.nii.gz; do | ||
| if [ ! -f "$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: | | ||
| docker rmi tf2.4_ivim-mri_codecollection || true | ||
| rm -f tf2.4_ivim-mri_codecollection.tar.gz | ||
| 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 | ||
| - name: Cleanup Docker | ||
| run: | | ||
| docker system prune -a --force |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| 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_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() | ||
|
|
||
| # Generate random input data | ||
| shape = (10, 10, 5) | ||
| f_in = np.random.uniform(low=0, high=1, size=shape) | ||
| D_in = np.random.uniform(low=0, high=1e-3, size=shape) | ||
| Dp_in = np.random.uniform(low=0, high=1e-1, size=shape) | ||
| S0 = 1000 # Setting a constant S0 for simplicity | ||
| bvals = np.array([0, 50, 100, 500, 1000]) | ||
| bvals_reshaped = np.broadcast_to(bvals, shape) | ||
|
|
||
| # Generate IVIM signal | ||
| signals = gd.ivim_signal(D_in, Dp_in, f_in, S0, bvals_reshaped) | ||
|
|
||
| # Save the generated image as a NIfTI file | ||
| save_nifti_file(signals, "ivim_simulation.nii.gz") | ||
| # Save the bval in a file | ||
| save_bval_bvec("ivim_simulation.bval", [0, 50, 100, 500, 1000]) | ||
| # Save the bvec value | ||
| save_bval_bvec("ivim_simulation.bvec", [[1, 0, 0], [0, 1, 0], [0, 0, 1]]) |
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doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb
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