From 8d5bc53612230e1d3873acfa2e08223800c15c34 Mon Sep 17 00:00:00 2001
From: Usman Akinyemi <usmanakinyemi202@gmail.com>
Date: Sat, 1 Jun 2024 09:04:32 -0400
Subject: [PATCH 1/2] created the dockerise version of the
 TF2.4_IVIM-MRI_CodeCollection

---
 .dockerignore    | 16 ++++++++++++++++
 Dockerfile       | 17 +++++++++++++++++
 requirements.txt |  3 +--
 3 files changed, 34 insertions(+), 2 deletions(-)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..31bf074
--- /dev/null
+++ b/.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
+
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..70edb3c
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,17 @@
+FROM python:3.9-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"]
diff --git a/requirements.txt b/requirements.txt
index 18d4f2e..0d0e85b 100644
--- a/requirements.txt
+++ b/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
\ No newline at end of file
+sphinx_rtd_theme

From d44c6e7b2a43ab8a6fb8369b6e5088ce8ad14df1 Mon Sep 17 00:00:00 2001
From: Usman Akinyemi <usmanakinyemi202@gmail.com>
Date: Wed, 5 Jun 2024 10:41:21 -0400
Subject: [PATCH 2/2] Make the python to use version 3.11 docker version,
 created a dedicated directory for the Dockerfile and also added a README file
 to explain the build and run process

---
 .dockerignore => Docker/.dockerignore |  0
 Dockerfile => Docker/Dockerfile       |  6 +--
 Docker/README.md                      | 61 +++++++++++++++++++++++++++
 3 files changed, 64 insertions(+), 3 deletions(-)
 rename .dockerignore => Docker/.dockerignore (100%)
 rename Dockerfile => Docker/Dockerfile (83%)
 create mode 100644 Docker/README.md

diff --git a/.dockerignore b/Docker/.dockerignore
similarity index 100%
rename from .dockerignore
rename to Docker/.dockerignore
diff --git a/Dockerfile b/Docker/Dockerfile
similarity index 83%
rename from Dockerfile
rename to Docker/Dockerfile
index 70edb3c..a5537f9 100644
--- a/Dockerfile
+++ b/Docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.9-slim
+FROM python:3.11-slim
 
 WORKDIR /usr/src/app
 
@@ -8,10 +8,10 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-COPY requirements.txt ./
+COPY ../requirements.txt ./
 
 RUN pip install --no-cache-dir -r requirements.txt
 
-COPY . .
+COPY .. .
 
 ENTRYPOINT ["python3", "-m", "WrapImage.nifti_wrapper"]
diff --git a/Docker/README.md b/Docker/README.md
new file mode 100644
index 0000000..5d77553
--- /dev/null
+++ b/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 brain.nii.gz brain.bvec brain.bval
+    ```
+
+    Replace `brain.nii.gz`, `brain.bvec`, and `brain.bval` with the actual file names you want to use.
+
+---