Added the feature to read DICOM images into a 4D Nifti image

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

@@ -98,9 +98,10 @@ jobs:
 
       - name: Verify input files
         run: |
+          IVIM_SIM_DIR = "${{ github.workspace }}/ivim_simulation"
           for file in ivim_simulation_0000.dcm, ivim_simulation_0001.dcm, ivim_simulation_0002.dcm ivim_simulation_0003.dcm ivim_simulation_0004.dcm; do
-            if [ ! -f "${{ github.workspace }}/ivim_simulation/$file" ]; then
-              echo "Error: $file not found"
+            if [ ! -f "$IVIM_SIM_DIR/$file" ]; then
+              echo "Error: $IVIM_SIM_DIR/$file not found"
               exit 1
             fi
           done

Docker/README.md

@@ -74,7 +74,6 @@ Before running the Docker container, here are the available options for the `Doc
     ```sh
     sudo docker run -it --rm --name TF2.4_IVIM-MRI_CodeCollection \
         -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/src/app \
-        -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/app/output \
         tf2.4_ivim-mri_codecollection \
         /usr/src/app/dicom_folder
     ```

Docker/dicom2nifti/Dockerfile

@@ -33,10 +33,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 
 COPY --from=build /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
 
-COPY ../../requirements.txt ./
-
-RUN pip install --no-cache-dir -r requirements.txt
-
 COPY ../.. .
 
+RUN pip install --no-cache-dir .
+
 ENTRYPOINT ["python3", "-m", "WrapImage.dicom2niix_wrapper"]

pyproject.toml

@@ -4,7 +4,6 @@ version = "0.1.0"
 description = "IVIM MRI signal processing and NIfTI/DICOM processing tools"
 requires-python = ">=3.9"
 readme = "README.md"
-license = {text = "Apache 2"}
 dependencies = [
     "numpy<2",
     "nibabel",