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

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

@@ -76,3 +76,73 @@ jobs:
       - name: Cleanup Docker
         run: |
           docker system prune -a --force
+  build-dicom2niix-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 --dicom
+
+      - name: Verify input files
+        run: |
+          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 "ivim_simulation/$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/dicom2nifti/Dockerfile .
+
+      - name: Run Docker container
+        run: |
+          docker run --rm --name TF2.4_IVIM-MRI_CodeCollection \
+            -v ${{ github.workspace }}:/usr/src/app \
+            -v ${{ github.workspace }}:/usr/app/output \
+            tf2.4_ivim-mri_codecollection \
+            /usr/src/app/ivim_simulation
+
+      - name: Verify output files
+        run: |
+          for file in f.nii.gz dp.nii.gz d.nii.gz; do
+            if [ ! -f "$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
+          rm -r -f ${{ github.workspace }}/ivim_simulation || true
+      - name: Cleanup Docker
+        run: |
+          docker system prune -a --force
+

Docker/README.md

@@ -4,11 +4,11 @@ This project is designed to run the `nifti_wrapper` script using a Docker contai
 
 ## Prerequisites
 
-- Docker must be installed on your system. 
+- Docker must be installed on your system.
 
 ## Directory Structure
 
-```
+``` sh
 ~/TF2.4_IVIM-MRI_CodeCollection/
 │
 ├── Docker/
@@ -47,7 +47,9 @@ Before running the Docker container, here are the available options for the `Doc
     ```sh
     sudo docker build -t tf2.4_ivim-mri_codecollection -f Docker/Dockerfile .
     ```
+
     OR (If you need to convert your data from DICOM TO NIfTI images)
+
     ```sh
     sudo docker build -t tf2.4_ivim-mri_codecollection -f Docker/dicom2nifti/Dockerfile .
     ```
@@ -124,9 +126,6 @@ sudo docker run -it --rm --name TF2.4_IVIM-MRI_CodeCollection \
 
 #### It is strongly recommend that users check validate the b-vector directions for their hardware and sequence as [described in a dedicated document](https://www.nitrc.org/docman/?group_id=880)
 
-![DICOM2NiFTI](dicom2nifti/DICOM2NiFTI.png)
-
-#### Output of NIFTI and DICOM objects generated from signal generation test
+- NIfTI follows the Talairach/MNI coordinate system where the X value increases as we move toward the participant's right, the Y increases as we move anteriorly. In contrast, for bipeds DICOM specifies the the X increases as we more toward the participant's left, while the Y increases as we move posteriorly. Both agree that the Z coordinate increases as we move superiorly.
 
-- NIfTI follows the Talairach/MNI coordinate system where the X value increases as we move toward the participant's right, the Y increases as we move anteriorly. In contrast, for bipeds DICOM specifies the the X increases as we more toward the participant's left, while the Y increases as we move posteriorly. Both agree that the Z coordinate increases as we move superiorly. 
 ---

Docker/generate_signal_docker_test.py

@@ -1,9 +1,13 @@
+import datetime
+import os
 from pathlib import Path
+import sys
+import uuid
 import numpy as np
 import nibabel as nib
+import itk
 from utilities.data_simulation.GenerateData import GenerateData
 from WrapImage.nifti_wrapper import save_nifti_file
-from WrapImage.dicom2niix_wrapper import save_dicom_objects
 
 def save_bval_bvec(filename, values):
     if filename.endswith('.bval'):
@@ -18,6 +22,8 @@ def save_bval_bvec(filename, values):
     with open(filename, 'w') as file:
         file.write(values_string)
 
+
+
 # Set random seed for reproducibility
 np.random.seed(42)
 # Create GenerateData instance
@@ -35,28 +41,71 @@ def save_bval_bvec(filename, values):
 # Generate IVIM signal
 signals = gd.ivim_signal(D_in, Dp_in, f_in, S0, bvals_reshaped)
 
-
-# Generate 4D signal by stacking volumes for each bval
-signals_4d = np.stack([
-    gd.ivim_signal(D_in, Dp_in, f_in, S0, np.full(shape, bval))
-    for bval in bvals
-], axis=-1)
-
 # 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]])
 
-bvecs = [[1, 0, 0]] * len(bvals)  # Assuming all x-direction
-
-save_dicom_objects(
-    volume_4d=signals_4d,
-    bvals=bvals.tolist(),
-    bvecs=bvecs,
-    out_dir=Path("ivim_simulation_dicom"),
-    f_vals=f_in,
-    D_vals=D_in,
-    Dp_vals=Dp_in
-)
+
+def save_dicom_files():
+    os.makedirs("ivim_simulation", exist_ok=True)
+    InputImageType = itk.Image[itk.D, 3] 
+    ReaderType = itk.ImageFileReader[InputImageType]
+    NiftiImageIOType = itk.NiftiImageIO.New()
+
+
+    reader = ReaderType.New()
+    reader.SetImageIO(NiftiImageIOType)
+    reader.SetFileName("ivim_simulation.nii.gz")
+
+    try:
+        reader.Update()
+    except Exception as e:
+        print(f"Error occured while reading NIfTI in ivim_simulation: {e}")
+        sys.exit(1)
+
+    OutputPixelType = itk.SS
+    # The casting filter output image type will be 3D with the new pixel type
+    CastedImageType = itk.Image[OutputPixelType, 3]
+    CastFilterType = itk.CastImageFilter[InputImageType, CastedImageType]
+    caster = CastFilterType.New()
+    caster.SetInput(reader.GetOutput())
+    caster.Update()
+
+
+    OutputImageType = itk.Image[OutputPixelType, 2]
+    FileWriterType = itk.ImageSeriesWriter[CastedImageType, OutputImageType]
+    GDCMImageIOType = itk.GDCMImageIO.New()
+    writer = FileWriterType.New()
+    size = reader.GetOutput().GetLargestPossibleRegion().GetSize()
+    fnames = itk.NumericSeriesFileNames.New()
+    num_slices = size[2]
+
+    fnames.SetStartIndex(0)
+    fnames.SetEndIndex(num_slices - 1)  # Iterate over the Z dimension (slices)
+    fnames.SetIncrementIndex(1)
+    fnames.SetSeriesFormat(os.path.join("ivim_simulation", f"ivim_simulation_%04d.dcm"))
+
+    # meta_dict = itk.MetaDataDictionary()
+    # include correct headers here to be tuned for Vendor
+    # GDCMImageIOType.SetMetaDataDictionary(meta_dict)
+    # GDCMImageIOType.KeepOriginalUIDOn()
+    writer.SetInput(caster.GetOutput())
+    writer.SetImageIO(GDCMImageIOType)
+    writer.SetFileNames(fnames.GetFileNames())
+    try:
+        writer.Write()
+    except Exception as e:
+        print(f"Error occurred while writing DICOMs in ivim simulation: {e}")
+        sys.exit(1)
+
+args = sys.argv[1:]
+if "--dicom" in args:
+    # read the generated nii file to dicom files
+    save_dicom_files()
+    # Save the bval in a file
+    save_bval_bvec(os.path.join("ivim_simulation","ivim_simulation.bval"), [0, 50, 100, 500, 1000])
+    # Save the bvec value 
+    save_bval_bvec(os.path.join("ivim_simulation","ivim_simulation.bvec"), [[1, 0, 0], [0, 1, 0], [0, 0, 1]])

WrapImage/dicom2niix_wrapper.py

@@ -6,101 +6,7 @@
 import subprocess
 import sys
 import inquirer
-import itk
 import numpy as np
-import datetime
-import uuid
-
-def save_dicom_objects(
-    volume_4d: np.ndarray,
-    bvals: list,
-    bvecs: list,
-    out_dir: Path,
-    f_vals: np.ndarray = None,
-    D_vals: np.ndarray = None,
-    Dp_vals: np.ndarray = None,
-    patient_id: str = "SIM123",
-    modality: str = "MR",
-    pixel_spacing=(1.0, 1.0),
-    slice_thickness=1.0,
-    series_description="Simulated IVIM",
-    protocol_name="SimulatedProtocol",
-    patient_position="HFS",
-    manufacturer="Simulated Manufacturer",
-):
-    out_dir.mkdir(parents=True, exist_ok=True)
-    x, y, z, t = volume_4d.shape
-    assert t == len(bvals) == len(bvecs), "Mismatch in timepoints and bvals/bvecs"
-
-    # Define 2D image type (DICOM expects 2D slices)
-    ImageType = itk.Image[itk.SS, 2]  # 2D image with short (int16) pixel type
-    WriterType = itk.ImageFileWriter[ImageType]
-
-    for t_idx in range(t):
-        volume_3d = volume_4d[:, :, :, t_idx].astype(np.int16)
-
-        # Generate common metadata for this timepoint
-        study_uid = f"1.2.826.0.1.3680043.2.1125.{uuid.uuid4().int >> 64}"
-        series_uid = f"1.2.826.0.1.3680043.2.1125.{uuid.uuid4().int >> 64}"
-        now = datetime.datetime.now().strftime("%Y%m%d")
-        series_number = str(t_idx + 1)
-
-        for slice_idx in range(z):
-            # Create 2D slice
-            slice_2d = volume_3d[:, :, slice_idx]
-            image_2d = itk.image_view_from_array(slice_2d.T)  # Transpose for proper orientation
-            image_2d = itk.cast_image_filter(image_2d, ttype=(type(image_2d), ImageType))
-
-            # Set image properties
-            image_2d.SetSpacing(pixel_spacing)
-            image_2d.SetOrigin([0.0, 0.0])
-
-            # Create metadata dictionary
-            meta_dict = itk.MetaDataDictionary()
-            meta_dict["0010|0010"] = "Simulated^Patient"
-            meta_dict["0010|0020"] = patient_id
-            meta_dict["0008|0060"] = modality
-            meta_dict["0008|0020"] = now
-            meta_dict["0008|0030"] = "120000"
-            meta_dict["0020|000d"] = study_uid
-            meta_dict["0020|000e"] = series_uid
-            meta_dict["0020|0011"] = series_number
-            meta_dict["0008|103e"] = f"{series_description} Volume {series_number}"
-            meta_dict["0018|1030"] = protocol_name
-            meta_dict["0018|5100"] = patient_position 
-            meta_dict["0008|0070"] = manufacturer
-
-            meta_dict["0018|9087"] = str(float(bvals[t_idx]))
-            gx, gy, gz = bvecs[t_idx]
-            meta_dict["0018|9089"] = f"{gx}\\{gy}\\{gz}"
-
-            if f_vals is not None:
-                meta_dict["0011|1001"] = f"f_in_mean={np.mean(f_vals):.6f}"
-            if D_vals is not None:
-                meta_dict["0011|1002"] = f"D_in_mean={np.mean(D_vals):.6e}"
-            if Dp_vals is not None:
-                meta_dict["0011|1003"] = f"Dp_in_mean={np.mean(Dp_vals):.6e}"
-
-            sop_uid = f"1.2.826.0.1.3680043.8.498.{uuid.uuid4().int >> 64}"
-            meta_dict["0008|0018"] = sop_uid
-            meta_dict["0020|0013"] = str(slice_idx + 1)
-            meta_dict["0020|0032"] = f"0\\0\\{slice_idx * slice_thickness}"
-            meta_dict["0020|0037"] = "1\\0\\0\\0\\1\\0"
-
-            # Create and configure writer
-            writer = WriterType.New()
-            writer.SetInput(image_2d)
-            writer.SetFileName(str(out_dir / f"vol_{t_idx:03d}_slice_{slice_idx:03d}.dcm"))
-
-            # Use GDCMImageIO for DICOM writing
-            gdcm_io = itk.GDCMImageIO.New()
-            gdcm_io.SetMetaDataDictionary(meta_dict)
-            gdcm_io.KeepOriginalUIDOn()
-
-            writer.SetImageIO(gdcm_io)
-            writer.Update()
-
-    print(f" DICOMs written to {out_dir.resolve()}")
 
 def prompt_input_directory():
     return inquirer.prompt([

pyproject.toml

@@ -1,11 +1,10 @@
 [project]
 name = "TF2.4_IVIM-MRI-CodeCollection"
 version = "0.1.0"
-description = "IVIM MRI signal simulation and DICOM/NIfTI processing tools"
-authors = [{ name="Jackson Hardee", email="jphardee@gmail.com" }]
-requires-python = ">=3.11"
+description = "IVIM MRI signal processing and NIfTI/DICOM processing tools"
+requires-python = ">=3.9"
 readme = "README.md"
-license = {text = "MIT"}
+license = {text = "Apache 2"}
 dependencies = [
     "numpy<2",
     "nibabel",