PythonBasics

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Preface

This guide is intended as a practical introduction to python for astronomers using CASA. Along with the accompanying pages, we hope that this introduction gets you comfortable enough to try taking advantage of CASA's python shell to script your data reduction or integrate your analysis, observation planning, and reduction. Despite the CASA focus, we aim to make this guide useful to any astronomer looking for a first dive into python. Given that similar material exists across the web we will not attempt a comprehensive introduction, just a tour of most of the basic python functionality needed to dive into CASA and python data analysis. If this guide whets your appetite then we recommend digging into the pages linked off PythonOverview.

Environment

We could write a lot on setting up python, a nice shell, installing key packages, etc. Because this is a CASA guide, we can short circuit some of this. CASA installs with it's own nice iPython shell and a core set of third-party packages (numpy, scipy, pylab, matplotlib). We will assume that you have downloaded and installed CASA from here and return to the issue of additional third-party software down the road.

Once you have CASA installed you can start a new session from your shell prompt by just typing

casapy

Depending on your computing environment you likely also have python and perhaps iPython installed, but the versions of these (especially the pre-installed version on the Mac) can vary widely. If you are interested in a non-CASA distribution that folds in a similar (in fact more extensive) suite of packages you might look at the free academic version here (no promises). We focus our discussion on the version of python that comes with CASA (2.6) and the examples will assume that you are working inside of a casapy shell.

Pasting Code

We will fairly rapidly reach the point where we want to cut and paste somewhat complex blocks of code. Python's use of indentation to implement code structure can make for awkward interactions with the shell at times. Even when it goes well after cutting and pasting a 'for' loop you often have to press return twice to execute. In very complex cases, you may end up needing to paste a line at a time.

Fortunately, the iPython shell offers a very nice way around these challenges. You can type

cpaste

to initiate a 'code paste'. You will then be able to paste code directly into the shell and the code will appear exactly as you copied it. When you have pasted all of your code got to a new line and type "--". This ends the code paste and the pasted code should then execute. Use this (really!), it will save you a large amount of pasting-frustration.

Getting Help, Exploring Objects, the Shell

CASA's shell (and iPython shells in general) has a lot of useful functionality. For example, CASA knows some basic operating system commands like "ls", "cat", etc. CASA only knows a few of these but you can issue any commands to your Unix/Linux shell directly by prefacing those commands with an exclamation point. So this works:

ls

and so does this:

!ls -lh

this does not (because CASA does not know "df"):

df -h

but this does:

!df -h

The shell has many other nice features. For example, if you type the name of a variable, it will simply print the variable value.

You can readily get help on most objects via "help thisorthat," for example

help list

Along with "help," the other major exploration capability in the shell is tab-completion. This will let you explore what variables are defined in your shell. Even better, you can take any object, append a ".", hit tab, and the shell will show you list of associated methods.

Try this now by typing "list." and hitting tab. The shell will print all the things that a list can do. In addition to a bunch of system-defined names that begin and end with "__" (e.g., see the equality operator "__eq__") you can see that list has a set of methods "append", "count", "extend", "index", ... "sort".

If you saw that list.append exists and wanted to learn a bit about it you could type

help list.append

We're getting a bit ahead of ourselves but try to bear these exploratory capabilities as you look through the guide. They are a great way to poke around and find new functionality.

One very important thing to bear in mind as you begin more advanced programming is that the shell specific capabilities are not available outside the shell. In practice this means that you cannot, for example, print the name of a variable by just listing the variable inside a program.

Simple Variables

Let's begin by creating an manipulating some basic variables. At the python shell prompt create your first variable by typing

my_first_var = 1

That's it, you've created your first variable. Note that you didn't have to specify the data type, python works this out from context. To see the value of your variable type

print my_first_var

or (if and only if you are at the shell) you can see the value by just typing the variable name

my_first_var

(read: use 'print' when programming).

You can see the type of the the variable by typing

print type(my_first_var)

Now try the same thing with some other data types.

# Make and print a string
a_string = "A String"
print a_string, type(a_string) # a string

Note that this first line does nothing. Python's comment string is "#" and it ignores everything in a line that comes after this character.

Some similar examples for floating point numbers:

type(3.14159) # a float
a_float = 1e-10
print type(a_float) # scientific notation

Notice the in-line comment and the on-the-fly creation of a variable in the first line.

Finally, python has a 'boolean' type that is either 'True' or 'False' (shorthand 'T' or 'F' in CASA, though not iPython in general).

type(True) # a boolean
boo = False
print boo, type(boo)

You can chain variable creation:

x = y = 1
print x, y
x = y = v = u = t = 0
print u, t

Basic Math

We have seen how to create variables. Now we will manipulate them with basic math operations.

Begin by creating a new variable with value 1.

x=1

and print the value after we add 2.

print x+2

We can assign the output of the operation to a new variable, which now exists in addition to x

y = x + 2
print y

z = x - 3
print z

Implicit operations work, e.g., "x += 3" will add three to the value of x

x = 1
print x
x += 3
print x
x *= 10
print x
x /= 20
print x

Exponents are done with "**", so for example

x = 2
y = x**2
print x, y

or to take the square root

x = 4
print x**0.5

Ints and Floats

We saw that python assigns a new variable the appropriate type based on context. Overall this is a nice feature, it lets us quickly develop scripts and programs without a lot of traditional programming overhead. However, there are a few rules that we need to keep in mind.

The first point to see is that dividing two integers returns an integer that is the "floor" (value rounded to the nearest integer closer to zero) of the result. For example, declare a new integer x and divide it by 20:

x = 1
print x / 20

or try these

print 19 / 20
print -1 / 20
print -19 / 20

That's the division of two integers. If we divide a float and an integer, on the other hand, we get a float:

x = 1
print type(x)
print x / 1.5
print type(x/1.5)

the operation implicitly casts the result as a float.

Explicit casts are okay and a reasonable way around this. Again, int() floors. For example:

x = 0.6
int_version = int(x)
int_version # remember this prints in the shell

Similarly, float() casts as a float:

float_version = float(int_version)
float_version

The order does matter. Notice the difference between these two cases:

print float(19)/20
print float(19/20)

The takeaway for the average CASA user here is: be careful tossing integers around in math because things may unexpectedly round on you. When in doubt, you should probably make things floats.

Booleans

Python includes booleans as a basic data type. These are variables that have two possible values: True or False (for CASA the shorthands "T" and "F" work as well). You can declare booleans efficiently:

b = True
print b
b = False
print b

Booleans are particularly interesting as the output of many operators. For example:

b = 1 == 1
print b

or

c = 1 != 1
print c

Deleting Variables

Python variables at the shell level will hang around forever until you declare a variable with the same name or actively get rid of them (by contrast variables declared inside of a procedure will go away when the procedure ends). You can get rid of a variable (module, object, whatever) like so:

x = 1
del x
print x

and just like that x is gone. Be careful with this.

Checking Whether a Variable Exists

We just gave a practical example of using "print" to check variable existence. But this sort of catastrophic approach isn't ideal. A more robust way to check if a variable exists is:

try:
    the_answer
except NameError:
    print "Does not exist!"

The try statement accepts an "else":

the_answer = 42.
try:
    the_answer
except NameError:
    print "Does not exist!"
else:
    print "We're cool."

Now try the same thing after deleting your variable:

del the_answer
try:
    the_answer
except NameError:
    print "Does not exist!"
else:
    print "We're cool."

This kind of approach gives you the ability to write non-explosive scripts. There are other ways to approach this. If you are interested you may want to read up further on the locals and globals python dictionaries.

Data Collections: Lists

Python has several built in types of data collections. Here we'll look at "lists", which are loose collections of potentially mixed types of data. You can declare a list by placing a comma-delimited list of variables inside a set of square brackets. For example, let's create a list called "bands":

bands = ['L', 'S', 'C', 'X', 12]

One potentially surprising feature of python lists is that they freely mix and match data types. Notice that "bands" mixes strings and integers. You can print the type and number of elements of the list via

print type(bands)
print len(bands)

Simple Slicing

You "slice" a list, accessing parts of the data using square brackets:

bands = ['L', 'S', 'C', 'X', 12]
print bands[0]
print bands[4]

Notice that python is "zero-indexed" which means that for a 5-element list like "bands" the indices run from 0 (first) to 4 (last). As a result this will not work

print bands[5])

because there is no element 5.

Also notice that python allows you to use negative indices to index "backwards" from the last element of the array

print bands[-1]
print bands[-2]

You can pick out a range of indices using a ":" and the following syntax

print bands[1:3]

Notice that it prints elements 1 and 2 but not element 3 of the list. So "n:m" retrieves elements n through m-1.

Similarly "0:3" will retrieve elements 0, 1, and 2. For example

print bands[1:3]

A free ":" retrieves everything along the axis:

print bands[:]

while ":n" implicitly takes "0" as the initial index and "n:" runs n through the last index. For example:

print bands[2:]

Assignment

These same tricks can be used for assignment. We'll recreate bands and then replace the last element:

bands = ['L', 'S', 'C', 'X', 12]
bands
bands[4] = "Ku"
print bands

or use the more complex slicing to replace the first three elements:

bands[0:3] = [1.4,3.0,6.0]

Notice that the sizes of the left and right side of the assignment need to match. So this will not work

bands[0:3] = 3.0

In addition to replacing elements you can add to the list like so:

bands.append("Ka")

Exploring List Functionality (Back to the Shell)

Lists have several neat abilities in addition to "append." If you don't remember them offhand you can easily find them using the shell functionality discussed earlier. This is great opportunity to apply these techniques in practice. Do so now, making sure that "bands" is defined as above.

Type in "bands." and hit <tab>. the shell will offer you the the available auto-completions. Leave aside all those system defined __ items and look at the rest. We see a list from "append," "count," through "sort." These are methods of list and so will be called as "append" above.

Let's say that you want to find out more about the "count" function. Use the "help" function like so:

help(bands.count)

so bands.count() checks the number of occurrences of a value. Try it out:

bands = ['L', 'S', 'C', 'X', 'Ka']
bands.count("Ka")

Let's play a bit with the other functions. "Pop" returns the most recent addition (last element) in the list and simultaneously removes it:

bands = ['L', 'S', 'C', 'X', 'Ka']
print bands
print bands.pop()
print bands

Another function, "index" returns the index at which the specified element occurs for the first time in the list:

bands = ['L', 'S', 'C', 'X', 'Ka']
bands.index("Ka")

though it gets unhappy when asked to find an item not in the list

bands.index("Q")

"insert" places an item before the specified location. So we can for example combine "insert" and "index" to place "K" in the list before "Ka":

bands = ['L', 'S', 'C', 'X', 'Ka']
bands.insert(bands.index("Ka"),"K")
bands

Now is a good time to explore the other functionality found here: removal, sorting, reversing, and so on.

A First Look at Iteration

We'll see much more on iteration in a moment, but one of the most important aspects of a list is that you can easily iterate over it. This simple syntax will get each element in bands, in order of their syntax, print its value, and tell you what type it is.

for element in bands:
    print element, type(element)

one of python's quirks is that looping occurs via iteration across collections like lists.

Unpacking

Lists and other collections like tuples or sets have the ability to "unpack." This means that they can be compactly assigned to a series of variables like so:

bands = ["X","Y","Z"]
a, b, c = bands
print a
print b
print c

Data Collections: Dictionaries

Dictionaries are another basic python data collection. Dictionaries store data in pairs, with a set of unique keys each mapped to some value (the values do not have to be unique). Dictionaries are extremely useful in scripting. For example, imagine that we are reducing a complex set of observations and want to be able to look up a the calibrator associated with a given source.

You can define a dictionary using the curly braces {} and "key"-"value" pairs separated by ":". For example

my_dict = {"a key":10,
           "b key":20}

You can then extract the value for a given key in a way similar to how we accessed lists. Index the dictionary with the key in square braces [].

print my_dict["a key"]

Dictionary keys can be numbers, strings, or tuples of either (this is a place where tuples are useful compared to lists or sets - you cannot have a list as a key for a dictionary). So you could, for example, define a dictionary holding source coordinates and fluxes using tuples (defined in parentheses, e.g., as "(1,2)").

catalog = {(1,2):10,
           (4,5):50,
           (10,10):10}
print catalog[(1,2)]

You can mix and match key types and use any data type for the value. For example:

my_dict = {1:5,
           "b":[1,2,3],
           (1,2):"string"}
my_dict[1]
my_dict["b"]
my_dict[(1,2)]

For scripting inteferometry reductions one useful application might be to pair sources and calibrators like so:

phasecal = {"source_1":"phasecal_1",
            "source_2":"phasecal_2",
            "source_3":"phasecal_1"}

Then during the reduction, one can simply call:

source_name = "source_1"
phasecal[source_name]

Manipulating Dictionaries

You can append new elements to a dictionary like so:

my_dict = {"a":1,
           "b":2,
           "c":3}
my_dict["d"] = 4

Check if it has a given key like so (very useful for making sure you don't index with an invalid key).

print my_dict.has_key("a"), my_dict.has_key("e")

1. List the keys like so:

print my_dict.keys()

1. And iterate over dictionaries like so

for key in my_dict.keys():
    print key

1. And iterate over dictionaries like so

for key, value in my_dict.iteritems():
    print key, value

There are more aspects to explore, but this gives a good introduction to the large functionality of dictionaries.

Other Types of Data Collections

You may also want to read up on sets (collections of unique elements) and tuples (immutable collections).

More Complex Programs

Executing Scripts

The most basic way to execute a set of python commands (aside from just copying and pasting to the shell) is to use the execfile command. Calling execfile('myscript.py') from inside a python shell will execute 'myscript.py' one line at a time. You can use this to run a series of reduction commands or other simple scripts. In fact, calling execfile on one or more scripts will almost certainly be sufficient to script most basic CASA data reductions.

A simple example

You can combine the control flow that we learned above with execfile to refine your scripts. For example, you might have a sophisticated reduction path that requires a few user inputs, which could be collected at the top of the script as variables. The reduction might have several discrete parts, which you could turn on or off using booleans and if statements. As an example, try creating a file that holds the following:

An example with a bit of control flow.

As you edit the variables and booleans, various parts of the script will run tuned by the variables you set. This simple but powerful approach can (if you desire) form the infrastructure for a lot of your CASA reduction scripting.

Functions

Python allows you to define functions either from the command line (or an execfile call) or as part of modules.