Introduction to data analysis in Python

This repository contains short introductions to Python data analysis and machine learning for the 2019 FMRIB Graduate Programme.

Content

- intro_talk.ipynb
- pandas.ipynb
- scikit_learn.ipynb
- keras1.ipynb
- keras2.ipynb

Preparation

The talks are in the form of an interactive Jupyter notebook. If you would like to follow along on your own laptops, please follow the below instructions.

Updating from a previous tutorial

   git stash  # this removes any changes you made to the existing notebooks
   git pull

New installations

These instructions are for macOS or Linux (or Windows, if you are using a VM or the Windows Subsystem for Linux), and assume that you have FSL 5.0.11 or newer installed:

1. Choose a location on your file system. E.g.:

   mkdir -p ~/grad_course/python_intro
   cd ~/grad_course/python_intro

2. Download the conda environment file - this contains a list of Python libraries to install.

   On Mac:

   curl https://git.fmrib.ox.ac.uk/paulmc/grad_course_2019_python_intro/raw/master/env.yml > env.yml

   On Linux:

   wget https://git.fmrib.ox.ac.uk/paulmc/grad_course_2019_python_intro/raw/master/env.yml

3. Create the Python environment. This will download about 1GB of data, and will ~5 min with a good internet connection:

   $FSLDIR/fslpython/bin/conda env create -f env.yml -p ./python_env

4. Download a small data set for use in the first talk (you can skip this step for the other pracs).

   On Mac:

   curl -L https://users.fmrib.ox.ac.uk/~paulmc/data.tar.gz > data.tar.gz

   On Linux:

   wget http://users.fmrib.ox.ac.uk/~paulmc/data.tar.gz

5. Clone a copy of this repository

   git clone https://git.fmrib.ox.ac.uk/paulmc/grad_course_2019_python_intro.git
   cd grad_course_2019_python_intro

   If you don't have git, find the Download button on the gitlab page to download a copy of the repository.

6. Install the data you downloaded in step 4 (you can skip this step for the other pracs):

   tar xf ../data.tar.gz

Running the notebook

Open a terminal, navigate to the git repository you cloned earlier, and run these commands:

source $FSLDIR/fslpython/bin/activate ../python_env
jupyter notebook