XNAT-Interact

This repository contains scripts for getting your source and derived fluoroscopic image data to and from our XNAT RPACS server.

First Things First:

• You will need to register with XNAT and then be added as a member to the RPACS XNAT server by the Data Librarian.

  • Make sure that you register a new account with your HawkID.
  • You must be using your VPN when you access the link included in the invitation email!

• NOTE: the SSL certificate for our accounts seems to require an annual renewal. It was most recently requested for renewal as of 2025-03-04.

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Installation

Option 1: Cloning the Repository (For General Use)

If you only need to use the software and do not plan to contribute changes, follow these steps:

0. Open a command prompt/terminal.

1. Ensure that git is installed on your machine:

   git --version

   • If you get an error, install git (for Windows, go here).

2. Ensure that Python 3.8 (64-bit) is installed:

   python --version

   • If Python 3 is not installed, download Python 3.8.
   • If you have both Python 2 and Python 3 installed, use python3 instead.

3. Navigate to your preferred directory:

   cd path_to_my_fav_local_folder_for_storing_repositories_of_code

4. Clone the repository:

   git clone https://github.com/domattioli/XNAT-Interact.git

5. Navigate into the cloned directory:

   cd XNAT-Interact

6. Create and activate a virtual environment:

   python -m venv .my_venv_for_xnat_interact

   Activate the virtual environment:

   • Windows:

     .my_venv_for_xnat_interact\Scripts\activate

   • Unix (Mac/Linux):

     source .my_venv_for_xnat_interact/bin/activate

7. Install the required dependencies:

   pip install -r requirements.txt

8. Run a test to verify correct installation:

   python update_and_test.py

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Option 2: Forking the Repository (For Contributing Changes)

If you want to make changes to the code and push them to GitHub, follow these steps instead:

1. Fork this repository:

   • Go to XNAT-Interact on GitHub.
   • Click the Fork button (top right) to create your own copy of the repository.

2. Clone your forked repository (replace YOUR-USERNAME with your GitHub username):

   git clone https://github.com/YOUR-USERNAME/XNAT-Interact.git

3. Navigate into the directory:

   cd XNAT-Interact

4. Set the upstream remote (so you can sync with the original repo later):

   git remote add upstream https://github.com/domattioli/XNAT-Interact.git

5. Create and activate a virtual environment (same as in Option 1).

6. Create a new branch for your changes:

   git checkout -b my-feature-branch

7. Make your changes and commit them:

   git add .
   git commit -m "Describe the changes you made"

8. Push your changes to your fork:

   git push origin my-feature-branch

9. Create a pull request:

   • Go to your fork on GitHub (https://github.com/YOUR-USERNAME/XNAT-Interact).
   • Click "Compare & pull request".
   • Select:
     • Base repository: domattioli/XNAT-Interact
     • Base branch: main
     • Head repository: YOUR-USERNAME/XNAT-Interact
     • Head branch: my-feature-branch
   • Add a description and click "Create pull request".

Option 2: Installing via pip (To-Do)

🚧 Note: This installation method is not yet implemented. Future versions of this repository may support installation via pip. 🚧 - This will require setting up the environment.yaml github workflow, I think. Once available, you will be able to install XNAT-Interact directly using:

pip install XNAT-Interact

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Example Usage

UIowa VPN -- Required

• If you are not running the following code from a university machine, you must be logged into the UIowa Cisco VPN before running any commands.
• Note: You cannot go back once you begin one of the tasks (e.g., uploading a case). If you make a mistake, press Ctrl + C to exit and restart the task.

Best Practice: Run the following script at the start of each session:

python update_and_test.py