Python your new best friend

Disclaimer

Though I’ve extensively programmed in Python, I have ~0 formal programming training.

So some terminology I use may be total gibberish to those better taught than I.

My mantra is: “If it works it works, who cares about the fancy

terminology”.

Python version

• Here I will talk about functions within Python 2.6.x / 2.7.x (the JBCA system default)

• The separate development stream of Python 3.x ... Most of what I say won’t work, or will work very differently.

Why Python?

• The current astronomers favourite...• CASA (interferometric data reduction package

is written in it).• Its free! (unlike IDL...*)

• *I’m yet to find something IDL can do that Python can’t...

Why Python?

• First we need to set up which version of python your linux box will default to.

• In your home area type:>emacs –nw .cshrc• This will open an in terminal text editor.• Press the down key until you see the line:

#USER MODIFICATIONS• After this type alias python2.7 ‘/usr/local/lib/python2.7/bin/python2.7’• The type ctrl-x ctrl-s. Close your terminal and open another

and we’re good to go.

BEFORE GETTING STARTED

Getting started

• From the command line ‘python’ will get you into the python environment. Within which you can start some basic work. e.g.

>>> a=3.141*0.005>>> b=7.0**2.0>>> c=a+b>>> print c49.015705

Scripting

• Adding those lines into a file named e.g. ‘test.py’ will then be executable by the command

>python test.py

Will result in ...49.015705

Dynamic whitespace

• In python whitespace is important, unlike e.g. Perl. Your left hand indentation matters.

So this will work:

for x in range(len(array)):print xy=x**2.7print y

print y # will print the last #value of y

This won’t:

for x in range(len(array)): print x

y=x**2.7 print y

print y # we’ll have crashed #before we reach here

• Remember for later your ‘if’s, ‘elif’s and ‘else’s need to line up!

Importing modules• A lot of functionality can be imported into your scripts with import commands e.g.

import numpy

• As python is object orientated you call a ‘numpy’ task as follows:

numpy.sqrt(2.0) #will give us square-root of 2

• But because we’re lazy we don’t want to type numpy over and over so we can instead use:

import numpy as np

• So the above becomesnp.sqrt(2.0) #will still give us square-root of 2

Importing modules 2.• Some times we only want a couple of functions from a

module for this we can use a ‘from’:

from numpy import sqrt , other_function• Now:

sqrt(2.0) #will give us what we’re after

Why isn’t there a function for this?• If the function you’re after doesn’t exist... Write your own!• In your code you can create your own functions, here is an

example:def my_function(arg1, arg2):

z=np.sqrt(arg1)*np.exp(arg2)return z

• Which can then be called later in your code simply as:something=my_function(arg1, arg2)#something will then == z

• With the same number of arguments.

Example functions• Example functions I’ve created:

1. Calculating colour-colour plots from incomplete data lists.2. Find the peak flux in a spectrum.3. Finding Zeeman split line pairs and calculating the local magnetic

field strength in ex-OH masers.4. Calculating the rms noise in an ALMA map... Etc etc

• Functions are good because they mean you don’t have to re-type code umpteen times throughout a script.

Useful python modules for Astronomy

• numpy – array and matrix mathematics, nice load from txt options...

• scipy – Scientific functions, e.g. correlation, signal processing, ffts...

• matplotlib – plotting... Makes beautiful plots.• pyfits – FITS file manipulation.• astropy - many useful astronomy modules and

packages all in one... • APLpy for making nice FITS images.

Examples

resFOV.py

Basic syntax stuff and quick plot Page 1 of 2

import numpy as npimport matplotlib.pyplot as plt

x=np.arange(1.0,10.0,1.0) #creates an array from 1 to 9

for value in x:if value ==4.0:

print “wow a 4!”elif value == 5.0:

print “and now a 5!”else:

print value

y=np.sqrt(np.exp(x)) #just for something to plot against x!

fig1 = plt.figure(1)ax1 = fig1.add_subplot(111) #sets up a plot environment to

# plot onax1.plot(x,y,’bo-’) #plots x v. y , ‘bo-’ sets it to

#plot blue circles with a solid #line joining them

ax1.set_xlabel(‘x’)ax1.set_ylabel(‘y’) #take a guess!

plt.show() #shows our plot

Basic syntax stuff and quick plot Page 2 of 2

Challenge

• Using the basics demonstrated in this tutorial write a script which calculates the Schwarzschild radius for black holes of mass = to each of the solar system planets.

• Extra credit, plot mass vs. radii and label each planet.