Commit 4917a4c7 authored by Jeremy Cohen's avatar Jeremy Cohen
Browse files

Updates to README formatting.

parent 9da59273
......@@ -29,15 +29,19 @@ The steps for preparing your environment are as follows:
- Clone the repository from GitLab
- Set up a virtual environment and install dependencies
- Prepare the data
- Start Jupyter Notebook server
- Start the Jupyter Notebook server
##### 1. Clone the repository
Open a terminal window and create a directory in which to place the tutorial materials. This directory will be referred to as `$TUTORIAL_DIR`. Change into `$TUTORIAL_DIR` and clone the repository from GitLab as follows:
* Open a terminal window and create a directory in which to place the tutorial materials.
```shell
$ git clone https://gitlab.doc.ic.ac.uk/bglocker/rcs-summer-school.git
```
* This directory will be referred to as `$TUTORIAL_DIR`.
* Change into `$TUTORIAL_DIR` and clone the repository from GitLab as follows:
```shell
$ git clone https://gitlab.doc.ic.ac.uk/bglocker/rcs-summer-school.git
```
##### 2. Set up a virtual environment and install dependencies
......@@ -69,39 +73,39 @@ You should have the `pip` package manager and `virtualenv` tool installed.
[rcs-tutorial] $ pip install -r requirements.txt
```
Continue with **Section 3 - Prepare the data**
* Continue with **Section 3 - Prepare the data**
##### 2B. Set up a virtual environment and install dependencies (Anaconda distribution)
*Creating a conda virtual environment is optional but is recommended as a way to keep any packages installed for this tutorial separate from your main conda environment.*
* Using `conda`, create and activate the virtual environment - here we use the name (specified with the -n switch) *img-tutorial*, if you wish, you can use a different name for your virtual environment:
```shell
$ conda create -n img-tutorial python=3 anaconda
# You will be prompted to confirm the installation of a number of packages.
$ conda activate img-tutorial
```
Using `conda`, create and activate the virtual environment - here we use the name (specified with the -n switch) *img-tutorial*, if you wish, you can use a different name for your virtual environment:
```shell
$ conda create -n img-tutorial python=3 anaconda
# You will be prompted to confirm the installation of a number of packages.
$ conda activate img-tutorial
```
Now install the required additional package:
* Now install the required additional package:
```shell
$ conda install -c simpleitk simpleitk
```
```shell
$ conda install -c simpleitk simpleitk
```
Continue with **Section 3 - Prepare the data**
* Continue with **Section 3 - Prepare the data**
##### 3. Prepare the data
**NOTE:** *If you are a DoC user running this tutorial on a DoC system using the pre-configured virtual environment, the data is already in place and you do not need to undertake this step.*
**NOTE:** *If you are a DoC user running this tutorial on a DoC system using the pre-configured virtual environment, the data can be copied directly from `/vol/lab/course/416/data` rather than downloading and extracting the zip file.*
A [ZIP file](https://www.doc.ic.ac.uk/~bglocker/teaching/rcs/data.zip) is available containing the data required for this tutorial.
Download the ZIP file to `${TUTORIAL_DIR}` and extract it in this location. This will give you a directory named `data` containing the sample imaging data used in the tutorial.
* Download the ZIP file from [here](https://www.doc.ic.ac.uk/~bglocker/teaching/rcs/data.zip) and save it to `${TUTORIAL_DIR}`.
* Extract the ZIP file in `$TUTORIAL_DIR`. This will give you a directory named `data` containing the sample imaging data used in the tutorial.
##### 4. Start Jupyter Notebook server
......@@ -114,9 +118,9 @@ This should open your default web browser with the Jupyter notebook homepage dis
**_NOTE:_** *If you are running your jupyter server on a remote system then you may need to specify the --ip= switch on the jupyter command line to get the jupyter server to listen on the public network interface on your server. Likewise, if you want to run the jupyter server on a different port to the default port 8888, you can specify the --port switch.*
##### DoC environment configuration
#### DoC environment configuration
If you are an Imperial Department of Computing user and have access to DoC systems, you can activate a pre-configured virtual environment an undertake the tutorial on a DoC system:
If you are an Imperial Department of Computing user and have access to DoC systems, you can activate a pre-configured virtual environment and undertake the tutorial on a DoC system:
If you are using `tcsh`, activate the environment by running:
......
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