An ipython notebook-based book on the Fundamentals of Radio Interferometry. This is a community effort with the aim to be constantly improving and adding to the content in an effort to make interferometry as accessible as possible. Please contribute, whether it is content, editing, or even suggestions.
This book is currently being used to teach the NASSP 2016 Fundamentals of Radio Interferometry Masters' Course.
There are additional large files (> 1MB), mainly FITS images, which are needed for some of the sections, these can be downloaded here (alt), the original simulated KAT-7 measurement sets can be downloaded here (alt). These are tarballs which should be extracted in the data directory.
cd fundamentals_of_interferometry/data/
tar xvzf fundamentals_fits.tar.gz
cd simulated_kat_7_vis
tar xvzf simulated_KAT-7_ms.tar.gz
In order to keep the content consistent across sections we have written a style guide in the introduction. Additionally, we have an editing guide for those who wish to suggest changes and edits to the current content.
If you would like to contribute to notebooks it is useful to setup a python virtual environment to ensure your environment is consistent with other contributors. This section provides a guide for how to do this in an Ubuntu system (tested on 14.04), other systems should work with slight modifications.
Currently we are using pip to install packages, the most important package versions are:
- pip 7.1.2
- python 2.7.6
- numpy 1.10.1
- matplotlib 1.5.0
- scipy 0.16.1
- ipython 4.2.0
- astropy 1.1.1
- aplpy 1.0
- ipywidgets 4.1.1
- healpy 1.10.3
This guide was developed from these references:
- http://jeffskinnerbox.me/posts/2013/Oct/06/ipython-notebook-in-virtualenv/
- http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
- http://jonathanchu.is/posts/virtualenv-and-pip-basics/
- https://warpedtimes.wordpress.com/2012/09/23/a-tutorial-on-virtualenv-to-isolate-python-installations/
Before setting up a virtual environment there are a few system level libraries which need to be installed
sudo apt-get install libpng-dev libncurses5-dev
To setup a clean environment to run our ipython-notebook standard system, start by making sure virtualenv is installed on your system. Run:
$ which pip
If there is no output, then you need to install pip:
$ sudo easy_install pip
Next, run:
$ which virtualenv
If there is no output, then you need to install virtualenv:
$ sudo apt-get install python-virtualenv
$ sudo pip install virtualenvwrapper
Once you have all the basic packages installed you can create a vitrualenv, I tend to keep all my virtualenvs in one place, e.g. a .virtualenv directory in my home directory
$ cd .virtualenv
$ virtualenv --no-site-packages fundamentals
This creates a virtualenv called fundamentals in the .virtualenv directory which is completely independent of any system site-packages, to active the virtualenv run the activation script
$ cd fundamentals
$ source bin/activate
First, lets clone the repository from github, you should use your own forked version if you want to make changes
$ git clone https://github.com/[username]/fundamentals_of_interferometry.git
If you just want to run the notebooks interactively you can just use this repository.
$ git clone https://github.com/griffinfoster/fundamentals_of_interferometry.git
Now this is a completely clean environment, there are no python packages installed, we need to set those up. There are two ways to do this, first is by running the following pip install commands, the other is by installing from the requirements file included in the this repository. I recommend the requirements file as it contains current version information (but, this may fail due to the package ordering, then you will need to try the to install packages manually, described below). The file is in the main directory of the repository or can be downloaded here. This will take a bit of time to setup, I recommend a tea break.
$ pip install --upgrade pip
$ pip install -r [path to file]/requirements.txt
or
$ pip install --upgrade pip
$ pip install yolk
$ pip install numpy
$ pip install matplotlib
$ pip install scipy
$ pip install ipython[all]
$ pip install --no-deps astropy
$ pip install aplpy
$ pip install healpy
$ pip install ipywidgets
We are now ready to start the ipython notebook server:
$ cd fundamentals_of_interferometry
$ jupyter notebook
To kill the server, type ctrl-c at the terminal and input y. To deactivate the virtualenv and return to your normal environment run:
$ deactivate
In the future, when you wish to return to the virtualenv, change to the fundamentals directory and run:
$ source bin/activate
We have tried to not include too many large files (e.g. FITS, measurement sets) into the repository to keep the size small. In order to fully utilize the notebooks please download the data sets here, and the simulated KAT-7 measurement sets here.
In the root directory of the repository there is a data/ directory, this is where we want to decompress the data into. To do so:
$ cd [fundamentals root]/data/
$ mv [location of download]/fundamentals_fits.tar.gz .
$ tar xvzf fundamentals_fits.tar.gz
$ cd simulated_kat_7_vis/
$ mv [location of download]/simulated_KAT-7_ms.tar.gz .
$ tar xvzf simulated_KAT-7_ms.tar.gz
The system setuptools/distribute (0.6.24) is not new enough and needs to be updated with easy_install
easy_install -U distribute
Matplotlib and numpy have many system-level dependencies, you may be required to install package before the virtualenv setup will work.
If there is a freetype related error, try:
sudo apt-get install libfreetype6-dev
If there is a fortran related error, try:
sudo apt-get install gfortran
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