Merge branch 'main' into wrapper_dev

Docker/.dockerignore

@@ -0,0 +1,16 @@
+# Ignore editor and system files
+.vscode/
+.git/
+.gitignore
+*.md
+
+# Exclude development and test artifacts
+__pycache__
+conftest
+
+# Docs
+docs
+doc
+
+# Others
+

Docker/Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.11-slim
+
+WORKDIR /usr/src/app
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    libssl-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY ../requirements.txt ./
+
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY .. .
+
+ENTRYPOINT ["python3", "-m", "WrapImage.nifti_wrapper"]

Docker/README.md

@@ -0,0 +1,61 @@
+# TF2.4_IVIM-MRI_CodeCollection
+
+This project is designed to run the `nifti_wrapper` script using a Docker container. Below are the steps to build and run the Docker image.
+
+## Prerequisites
+
+- Docker must be installed on your system. 
+
+## Directory Structure
+
+```
+~/TF2.4_IVIM-MRI_CodeCollection/
+│
+├── Docker/
+│   └── Dockerfile
+│
+├── WrapImage/
+│   └── nifti_wrapper.py
+│
+└── requirements.txt
+```
+
+## Options
+
+Before running the Docker container, here are the available options for the `Docker image` script:
+
+- `input_file`: Path to the input 4D NIfTI file.
+- `bvec_file`: Path to the b-vector file.
+- `bval_file`: Path to the b-value file.
+- `--affine`: Affine matrix for NIfTI image (optional).
+- `--algorithm`: Select the algorithm to use (default is "OJ_GU_seg").
+- `algorithm_args`: Additional arguments for the algorithm (optional).
+
+## Building the Docker Image
+
+1. Open a terminal and navigate to the project directory:
+
+    ```sh
+    cd ~/TF2.4_IVIM-MRI_CodeCollection
+    ```
+
+2. Build the Docker image using the `docker build` command:
+
+    ```sh
+    sudo docker build -t tf2.4_ivim-mri_codecollection -f Docker/Dockerfile .
+    ```
+
+## Running the Docker Container
+
+1. Once the image is built, you can run the Docker container using the `docker run` command. This command runs the Docker image with the specified input files:
+
+    ```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 Downloads/brain.nii.gz Downloads/brain.bvec Downloads/brain.bval \
+    ```
+
+    Replace `brain.nii.gz`, `brain.bvec`, and `brain.bval` with the actual file names you want to use.
+
+---

WrapImage/nifti_wrapper.py

@@ -84,7 +84,7 @@ def loop_over_first_n_minus_1_dimensions(arr):
     parser.add_argument("bval_file", type=str, help="Path to the b-value file.")
     parser.add_argument("--affine", type=float, nargs="+", help="Affine matrix for NIfTI image.")
     parser.add_argument("--algorithm", type=str, default="OJ_GU_seg", help="Select the algorithm to use.")
-    parser.add_argument("algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
+    parser.add_argument("--algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
 
     args = parser.parse_args()
 

requirements.txt

@@ -2,7 +2,6 @@ numpy
 scipy
 torchio
 torch
-logging
 joblib
 dipy
 matplotlib
@@ -13,4 +12,4 @@ pytest
 tqdm
 pandas
 sphinx
-sphinx_rtd_theme
+sphinx_rtd_theme