Installation

Python installation

To start with the installation, download the Anaconda installer for your operating system with Python >= 3.8.

Initial steps

These steps need to be performed for all operating systems.

  1. Download the MIA Lab project starter ZIP and extract it to a directory named mialab.
  2. The original GitHub organization is temporarily unavailable. If your group needs a shared remote repository, create a new empty repository under one group member's account and push the extracted starter code there. Do not commit the course data or patient data.

Continue with the operating system specific installation instructions below.

Operating system specific installation steps

macOS

The installation has not been tested.

git installation

Download git and install it. Then, open a terminal in the extracted project directory:

cd /path/to/mialab

Anaconda installation

Follow the instructions on the official website, and then verify the installation:

conda list # which should list all installed Anaconda packages

Create a new Python 3.10 environment with the name mialab (confirm with y when prompted during creation):

conda create -n mialab python=3.10

Activate the environment:

conda activate mialab

Install required packages

cd /path/to/MIALab/repository
pip install -r requirements.txt # will install all required packages

Windows

The installation has been tested on Windows 10.

git installation

Download git and install it. Then, open "Git Bash" in the extracted project directory:

cd path\tomialab

Anaconda installation

Follow the instructions on the official website.

Verify the installation - open "Anaconda Prompt":

conda list # which should list all installed Anaconda packages

Create a new Python 3.10 environment with the name mialab (confirm with y when prompted during creation):

conda create -n mialab python=3.10

Activate the environment by:

conda activate mialab

Install required packages

cd path\toMIALab\repository
pip install -r requirements.txt # will install all required packages

Linux

Run the following commands in the terminal (tested on Ubuntu 16.04 LTS and 18.04 LTS).

git installation

sudo apt-get install git

Open a terminal in the extracted project directory:

cd /path/to/mialab

Anaconda installation

Follow the instructions on the official website, and then verify the installation:

conda list # which should list all installed Anaconda packages

Create a new Python 3.10 environment with the name mialab (confirm with y when prompted during creation):

conda create -n mialab python=3.10

Activate the environment by:

conda activate mialab

Install required packages

cd /path/to/MIALab/repository
pip install -r requirements.txt # will install all required packages

Testing the installation

Finally, if all of the above works without issues, execute the installation test script to verify that all the dependencies are set up correctly:

python ./test/test_install.py

Setting up the IDE

Next, move to the IDE page to set up your favorite development environment, to be maximally productive with the code involved with this course.

MATLAB installation

Follow the instructions on the MathWorks website to install MATLAB on your computer. Operating system specific requirements are here. Once you have MATLAB installed, read through the MATLAB section of the IDE page to learn more about working with this program.