Contents

Preface

Contents

1 Getting Started

1.1

1.2

1.3

1.4

Basic Skills . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1.1.1

Using xterms and logging in to the server . . . . . . . . . . . .

1.1.2

About the Python Shell and idle . . . . . . . . . . . . . . . .

1.1.3

Running Python Locally . . . . . . . . . . . . . . . . . . . . .

Fun with Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1.2.1

Basic operations

. . . . . . . . . . . . . . . . . . . . . . . . .

1.2.2

Lists, tuples and strings . . . . . . . . . . . . . . . . . . . . .

1.2.3

Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.2.4

Getting help . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.2.5

Program control: Looping, conditionals and functions . . . . . 12

Progressing in Python . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.3.1

Writing your own modules and executable scripts . . . . . . . 17

1.3.2

List comprehension . . . . . . . . . . . . . . . . . . . . . . . . 18

1.3.3

Using objects in Python . . . . . . . . . . . . . . . . . . . . . 18

1.3.4

The Numeric array package . . . . . . . . . . . . . . . . . . . 20

1.3.5

The Curve object and its uses . . . . . . . . . . . . . . . . . . 25

Advanced Python Topics . . . . . . . . . . . . . . . . . . . . . . . . . 28

1.4.1

Defining your own objects . . . . . . . . . . . . . . . . . . . . 28

v

1.4.2

Dictionaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

1.4.3

Writing text data to files . . . . . . . . . . . . . . . . . . . . . 37

1.4.4

Reading text data from a file . . . . . . . . . . . . . . . . . . 38

2 Thermodynamics and vertical structure

39

2.1

Tutorial: Getting physical properties and constants . . . . . . . . . . 40

2.2

Problem set: Dry thermodynamics . . . . . . . . . . . . . . . . . . . 41

2.3

2.2.1

Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

2.2.2

Ideal gas law . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

2.2.3

Atmospheric composition and mixing ratios . . . . . . . . . . 42

2.2.4

Specific heat: Some basic problems . . . . . . . . . . . . . . . 42

2.2.5

Temperature-dependent specific heat . . . . . . . . . . . . . . 43

2.2.6

Potential Temperature and the Dry Adiabat . . . . . . . . . . 43

2.2.7

Inhomogeneous mixtures; Potential density and virtual temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Data Lab: Analysis of temperature profile data . . . . . . . . . . . . 44

2.3.1

Analysis of tropical Earth soundings . . . . . . . . . . . . . . 44

2.3.2

Analysis of midlatitude Earth soundings . . . . . . . . . . . . 46

2.3.3

Analysis of planetary soundings . . . . . . . . . . . . . . . . . 47

2.4

Tutorial: Numerical solution of differential equations . . . . . . . . . 48

2.5

Problem set: Hydrostatics . . . . . . . . . . . . . . . . . . . . . . . . 52

2.6

2.5.1

Mass of carbon in the Earths atmosphere . . . . . . . . . . . 52

2.5.2

Mass of Titans atmosphere . . . . . . . . . . . . . . . . . . . 52

2.5.3

The dry adiabatic lapse rate . . . . . . . . . . . . . . . . . . . 53

2.5.4

Heat capacity of atmospheric columns . . . . . . . . . . . . . 53

Problem set: Moist thermodynamics . . . . . . . . . . . . . . . . . . 53

2.6.1

Latent heat . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

2.6.2

Using the simplified form of the Clausius-Clapeyron relation . 53

2.6.3

Methane on Titan . . . . . . . . . . . . . . . . . . . . . . . . . 54

2.6.4

Boiling vs. evaporation . . . . . . . . . . . . . . . . . . . . . . 54

vi

1
2.6.5

Comparison of idealized vs. empirical saturation vapor pressure 55

2.6.6

Variable latent heat . . . . . . . . . . . . . . . . . . . . . . . . 55

2.6.7

Latent heat from Clausius-Clapeyron . . . . . . . . . . . . . . 55

2.6.8

Water content of the atmosphere . . . . . . . . . . . . . . . . 57

2.6.9

CO2 condensation in the Martian Winter . . . . . . . . . . . . 57

2.6.10 CO2 condensation on Snowball Earth . . . . . . . . . . . . . . 57

2.6.11 Moist adiabat for atmosphere with two condensible components 58
2.6.12 Springtime for Europa . . . . . . . . . . . . . . . . . . . . . . 58
2.7

Computation Lab: Computing the moist adiabat . . . . . . . . . . . 59

2.8

Problem set: Rayleigh fractionation . . . . . . . . . . . . . . . . . . . 60

3 Elementary radiation balance problems

61

4 Continuous atmosphere radiation problems

63

5 Radiative-convective model problems

65

6 Scattering problems

67

7 Data analysis problems: Earth radiation budget

69

8 Surface energy budget problems

71

9 Seasonal Cycle problems

73

10 Atmospheric evolution modelling problems

75

11 Meridional heat transport modelling problems

77

12 Appendix A: Hints for the user of Unix and its relatives

79

12.1 Simple Unix for the masses . . . . . . . . . . . . . . . . . . . . . . . . 79

12.2 A few useful Unix utilities . . . . . . . . . . . . . . . . . . . . . . . . 80
12.3 Nasty Unix stuff I hope you wont have to deal with . . . . . . . . . . 80
12.4 Public domain software to install on the server . . . . . . . . . . . . . 83

2
12.5 Installing the courseware . . . . . . . . . . . . . . . . . . . . . . . . . 85

Chapter 1
Getting Started

CHAPTER 1. GETTING STARTED

1.1

Basic Skills

To do the labs and the problem sets,you will need some basic computer skills. I will
outline these briefly here. The instructions below assume that the exercises will be
done using what Ill call the default setup. In the default setup, the course software
and the necessary datasets reside on a centralized server; the student logs on to
the server from a workstation that supports the ssh protocol and the X windowing
system. The X window system is needed to allow a remote server to write graphics
(e.g. a plot, or a graphical user interface) to the screen of the local workstation. The
specific instructions below apply most closely to Unix workstations. The necessary
skills for using the default setup are:
Logging in to a Linux server from a workstation on the network.
Setting things up for the Linux machine to display its graphics on the workstation you are sitting at, using the X windowing system.
Working with Linux directories and files (commands cd,ls,mv,rm,mkdir).
Starting up the Python interpreter and using the Python Integrated Development Environment, idle.

1.1.1

Using xterms and logging in to the server

The software that you will be using, as well as the data you will be looking at,
resides on a server running the Unix operating system. In the examples, we will
suppose that the server is climate.myUniversity.edu; your own server will have
a different name, which will be provided by your instructor. To use the software,
you will need to log into climate, which you can do from any machine anywhere in
the world, as long as the machine has an ssh program. The first step is to get an X
terminal window (xterm for short) on the screen of the workstation at which you
are sitting. If your workstation is a Unix computer the standard window you get
when you request a shell or a terminal window is already an xterm, assuming
the system has been started up into a graphical user environment, as is generally
the case these days. To get a new xterm, you just need to click on the appropriate
icon on the desktop. The specific icon varies somewhat from system to system, but
will generally look like a scallop shell or a computer screen.
Macs running OSX are actually running a form of Unix, but the default graphical interface does not use the X windowing system. This will be less confusing if you
recall that the X in OSX is actually pronounced 10. The standard terminal,
or shell, window you get with the OSX terminal tool is not an xterm. While you can

1.1. BASIC SKILLS

issue Unix commands and log onto remote systems for text-based applications by
issuing the ssh command in this window, the OSX terminal window does not handle
graphics. Further, OSX does not come with the X windowing system installed by
default. Fortunately, Appole provides an excellent implementation for X on OSX,
which can be installed from the system install disk. If you have your own OSX Mac,
or have administrative privileges for some OSX Mac you can use, you can install
X11 yourself very easily. All Macs set up for this course should, in principle, already
have X11 installed. To get an xterm, you just click on the X11 icon in the toolbar
and wait for X to start up. The default windows X puts up on the screen are all
xterms. You can make a window go away by typing ctrl-d in the window (meaning
hold down the ctrl key and type d. If you want a new xterm, just type xterm&
in any existing xterm window, or choose terminal from the Applications menu,
and a new one will pop up. Your instructor can show you how to move and resize
windows or turn them into icons.
Once you have an xterm on your screen, click the mouse in its window to
activate it. You are now ready to log in to the course server. If you happen to be on
a Unix workstation with the course data and software installed locally, you can just
skip the login step. This is one of the beauties of X and Unix the system doesnt
really care which computer is actually doing the calculation. This remark applies
equally to OSX Macs, provided that Unix versions of the course software have been
properly installed.
Now lets assume that you need to log on to the course server. Youll need an
account to go further: a userid and a password. If you already have an account on
climate, you can use that. If not,you can get one of the pre-assigned accounts from
the TA. Once you have this data, you can log in. To log in, just issue the command
ssh -X -l<USERID> climate.myUniversity.edu from an xterm, where <USERID>
is the userid for the course account. Then give your password at the prompt. The
-X option tells the server to forward graphical commands to the local X windowing
system for handling. On many Linux systems, this option is turned on by default,
but it never hurts to include it explicitly.

1.1.2

About the Python Shell and idle

Python is an interpreted language, which means you just type in plain text to an
interpreter, and things happen. There is no compilation step, as in languages such
as c or FORTRAN. To start up the Python interpreter,just type python from the
command line on climate. Youll get a prompt, and can start typing in python
commands. Try typing in 2.5*3+5. and see what happens. To exit the Python
interpreter, type ctrl-d.

CHAPTER 1. GETTING STARTED

Eventually, youll probably want to put your Python programs, or at least your
function definitions, in a file you create and edit with a text editor, and then load it
into Python later. This saves you having to re-type everything every time you run.
The standard Unix implementation of Python provides an integrated development
environment called idle, which bundles a Python interpreter window with a Pythonaware text editor. To start up idle, log in to the server from an xterm and type
IDLE. You will get a Python shell window, which is an ordinary Python interpreter
except that it allows some limited editing capabilities. The real power of idle comes
from the use of the integrated editor. To get an editor window for a new file, just
choose New Window from the File menu on the Python Shell window. If you want
to work with an existing file instead, just choose Open from the File menu, and
pick the file you want from the resulting dialog box. You can type text into the
editor window, and cut and paste in a fashion that will probably be familiar to most
computer users. You can have as many editor windows open as you want, and cut
and paste between them. When you are done with your changes, select Save or
Save as from the File menu of the editor window, and respond to the resulting
dialog box as necessary. Once you have saved a file, you can run it by selecting Run
module from the Run menu.
You can actually use the integrated editor to edit just about any text file,
but it has features that make it especially useful for Python files. For example, it
colorizes Python key words, automatically indents in a sensible way, and provides
popup advice windows that help you remember how various Python functions are
used. As an exercise at this point, you should try creating and saving a short note
(e.g. a letter of gratitude to your TA), and then try opening it up again in a new
editor window. To exit from idle just choose Exit from the File menu of any
window.
An especially useful feature of the idle editor is that it allows you to execute
the Python script you are working on without leaving the window. To do this, just
choose Run Script from the Edit menu of the editor window. Then the script will
run in the Python shell window. When the script is done running, you can type
additional Python commands into the shell window, to check the values of various
quantities and so forth.
IDLE has various other powerful features, including debugging support. You
can manage without these, but you should feel free to learn about and experiment
with them as you go along.
Once you have written a working Python script and saved it,say, as MyScript.py,
you can run it from the command line by typing python MyScript.py. There is no
need to start up IDLE just to run a script.

1.1. BASIC SKILLS

1.1.3

Running Python Locally

Note that many of the Python-based exercises given in the problem sets do not need
the data stored on climate, or the special Python extension modules written for
this course. If you have a computer of your own, you can download your own copy
of Python from the web site python.org. Implementations are available for Macs,
Linux and Windows PCs. The MacPython implementation, available for both OS9
and OSX Macs provides an excellent integrated development environment that in
some ways is superior to IDLE. You can use your own stand-alone machine for any
of the exercises that need only straight Python programming using the standard
modules. You can also use your own machine for any exercises involving reading
and writing of text data files, if you first download any needed data from climate to
your own machine. Also, any Python extension modules that are written as ordinary
human-readable Python scripts (e.g. phys.py ) can be just downloaded and put in
your python directory, regardless of what kind of machine you are using. However,
compiled extension modules, with names like veclib.so need to be compatible with
your specific hardware and Python implementation.
In the rest of this workbook, when we say Start up the Python interpreter,
the choice is up to you whether you use the simple command line interpreter or idle,
or perhaps some other integrated Python development environment you might have
(e.g. MacPython). For results that produce graphics, and for the use of idle, you
must be connected to Python in a way that can display graphics on your screen
(e.g. via an xterm). You wont be reminded of this explicitly in the text. Exercises
that dont produce graphics can be done over any kind of link. Write and run a
script could mean that you enter it using your favorite editor and run it from the
command line, or it could mean using idle.
In general, I have tried to avoid referring to implementation-dependent details
in the rest of this Workbook.

1.2

CHAPTER 1. GETTING STARTED

Fun with Python

This is a very simple lab designed to help you get used to programming with Python.
Throughout this and the rest of the Python labs, it is expected that you will try out
all the examples in the Python interpreter window, and make up additional examples
on your own until you feel you understand the concept being introduced. For the
most part, you wont be bothered with any further reminders of this expectation.
First, start up the Python interpreter. For this lab, you can type your input
directly into the interpreter, if you wish. As you begin to do more complex programs,
however, you will want to write your programs using a text editor, and then save
them before running. This way, you wont have to retype everything when you need
to correct a mistake in just one or two lines, and you can re-run the program or a
modification of it very easily. Although none of the exercises in this lab are complex
enough to really require the text editor, you can use this lab as an opportunity to
become familiar with the use of the idle editor.

1.2.1

Basic operations

Once youre at the Python interpreter prompt, try some simple statements using
Python like a calculator, e.g.:
52.5*51.2+37.
a = 7.
b=10.
a/b
a*b
a = 7
b = 10
a*b
a/b
2**1000
1717%3
and so forth. This is so nice,youll probably want to load Python onto your laptop
and use it in place of a pocket calculator, especiallly once you learn how to import the
standard math functions into your Python world. These examples illustrate the use
of floating point numbers, multiplication and addition (*, + and /) assignment
to variables, integers, and exponentiation **. The final example illustrates the
use of the mod operator, % which is a binary operator applied to integers. The
expression n%m yields an integer whose absolute value is less than m, which is the

1.2. FUN WITH PYTHON

result of subtracting off the maximum possible multiples of m (if you are familiar
with clock arithmetic, this is the operation that turns regular arithmetic into clock
arithmetic modulo m). The assignments to the variables a and b illustrate that
Python is not a typed language. You do not have to declare the variables as being
of a certain type before you use them. They are just names, which are used as long
as necessary to refer to some value. This extends not just to numbers, but to all the
object which Python can deal with, including arrays, lists, functions, strings and
many other entities which will be introduced shortly. In the example above, first
a and b are floats, and behave like floats on division. Then they are integers, and
behave like integers. The last line illustrates the exponentiation operator, denoted by
**. The large number you get as a result has an L tacked on the end, signifying
that the result is a long integer, which can have arbitrarily many digits (until you
run out of memory). Python automatically creates this type of integer whenever
necessary. The standard Python floating point number has double precision, though
Python extensions are available which allow you to specify arbitrary precision for
floats as well.
Python also has floating point complex numbers as a native data type. A
complex number with real and imaginary parts a and b respectively is written as
a + bj. All the usual operations apply. After setting z = 7.5 + 4.j try z + 1, z z,
1/z, z 1.5 and z z. If you need to make a complex number out of two real
variables, say x and y, the easiest way is to use the complex function, e.g. z =
complex(x,y). Python does not have complex integers (known as gaussian integers
to mathematicians) as a native data type, but you will learn how to define these,
and virtually any other specialized type you need, in Section 1.4.1

1.2.2

Lists, tuples and strings

Tuples and lists are among the most basic and versatile data structures in Python.
Lists contain any kind of data at all, and the elements can be of different types
(floats, int, strings, even other tuples or lists). Many functions return tuples or lists.
Try out the following examples in the interpreter
Heres an example showing two ways defining a list and getting at an element:
a = [1,two]
a[0]
a[1]
b = [ ]
b.append(1)
b.append(two)
b[0]

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CHAPTER 1. GETTING STARTED

b[1]
In the second part of the example, note that a list, like everything else in Python,
is in fact an object with actions (called methods) which you can perform by
appending the method name to the object name. The mod operator is useful for
making circular lists, which begin over from the first element when one reaches the
end. For exammple, if a is any list, a[i%len(a)] will access the list as if it were
bent around in a circle. The same trick works for any integer-indexed object.
Python distinguishes between lists and tuples. These are similar, except that
lists can be modified but tuples cannot. Lists are denoted by square brackets,
whereas tuples are denoted by parentheses. The above example is a list rather than
a tuple. You can define a tuple, but once defined you cannot modify it in any way,
either by appending to it or changing one of its elements. There are a very few cases
where Python commands specifically require a tuple rather than a list, in which case
you can turn a list (say, mylist) to a tuple by using the function tuple(mylist).
Strings are also objects, with their own set of useful methods. For example:
a = Five gallons of worms in a 3 gallon barrel!
a.split()
b = a.split()
print b[0],b[3],b[4]
Note that the split() method returns a list,whose elements are strings. By the way,
in Python, you can use either single quotes or double quotes to enclose a string, as
long as you use them consistently within any one string. There is no difference in
the behavior of single quoted and double quoted strings. For strings, the + operator
is concatenation, i.e. a+b is the concatenation of the two strings a and b.
It is very often useful to be able to build strings from numerical values in your
script. This need often arises in formatting printout of results to look nice, or in
generating filenames. Suppose a = 2 and b = 3. Then, the following example show
how you can insert the values into a string:
s = %d + %d = %d%(a,b,a+b)
print s
note that the input to the format string must be a tuple, not a list; recall,
however, that if L is a list, the function call tuple(L) will return a tuple whose
elements are those of the list input as the argument. If the tuple has only one
element, you can leave off the parentheses. The format code %d (or equivalently %i)
converts an integer into a string. You use %f for floating point numbers, and %e for

1.2. FUN WITH PYTHON

11

floats in scientific notation. There are other options to these format codes which
give you more control over the appearance of the output, and also several additional
format codes.
Now make up a few examples of your own and try them out.

1.2.3

Modules

To do almost any useful science with Python, you will need to load various libraries,
known as modules. Actually, a module can be just an ordinary Python script,
which defines various functions and other things that are not provided by the core
language. A module can also provide access to high-performance extensions written
using compiled languages.
To make use of a module with name myModule, you just type: import myModule.
Members of the module are accessed by prepending the module name to the member
name, separated by a .. For example, if myModule contains the constant r earth,
and the function sza, these constant is accessed using myModule.r earth and the
function is evaluated at t using myModule.sza(t). If you dont need to keep the
modules members separate, you can avoid the need of prepending the module name
by using from myModule import *.
The standard math functions are in the module math, and you make them available by typing import math. To see whats there, type dir(math); this works for
any module. Now, to compute sin(/7.) for example, you type math.sin(math.pi/7.).
To find out more about the function math.sin, just type help(math.sin). If you
dont like typing math.sin, you can import the module using from math import *
instead, and then you can just use sin,cos, etc. without the prefix.

1.2.4

Getting help

Python has extensive built-in help functions, which make it possible to learn new
things and avoid programming errors without frequent recourse to manuals. Given
that so much of Python is found in various language extensions the Python community has written, the availability of embedded documentation is beholden to the good
behavior of the programmer. Python fosters a culture of good behavior, and tries
to make it easy for developers to provide ample help and documentation integrated
with the tools they have developed.
The main ways of getting help in Python are the help() and dir() functions.
For example, you have learned about the split() method that is one of the methods
available to strings. Suppose you didnt know what methods or data attributes went

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CHAPTER 1. GETTING STARTED

along with a string, though? Rather than going to a handbook, you can use the
dir() function to find out this sort of thing. For example, if a is a string, you can
type dir(a) to get a list of all its methods, and also all its data attributes (e.g.
its length). Then, if you want to know more about the split() method you can
type help(a.split) (Warning: dont type help(a.split()), which would look
for help items on the words in the content of the string!). Both strings and lists
have many useful and powerful methods attached to them. Many of these will be
illustrated in the course of the examples given in the rest of this Workbook, but
you are encouraged to explore them on your own, by finding out about them using
dir() and help(), and then trying them out.
So when in doubt, try help and dir. One or the other will give you some useful
information about just about anything in Python. If the system you are working
on has the Python HTML documentation files installed, you can even get help on
Python syntax and Python key words online. For example, to find out what the
Python keyword for means, you just type help("for").
Further, since Python is interpreted rather than compiled into machine language, if you have some Python programs written by somebody else, you can almost
always look under the hood to see how they work. That is not generally possible
with compiled languages where you often dont have access to the original source
code.

1.2.5

Program control: Looping, conditionals and functions

Now were ready for some more involved programming constructions. The basic
technique for writing a loop is illustrated by the following example, which prints out
the integers from 0 through 9:
for i in range(10):
x = i*i
print i,x
Note that in Python, indentation is part of the syntax. In the above example,
the indentation is the only way Python has to identify the block of instructions
that is being looped over. Indentation in a block of code must line up, and you
need to be cautions not to confuse spaces and tabs. The use of indentation as
a syntactic element in Python enforces code readability and reduces the need for
special identifiers to terminate blocks.
The construct range(10) is actually shorthand for the 10-element list
[0,1,2,3,4,5,6,7,8,9]

1.2. FUN WITH PYTHON

13

In fact, one of Pythons many charms is that a for loop can loop over the elements
of any list at all, regardless of what the elements of the list may be. Thus, the
following example sums up the length of four strings:
myList = [bob,carol,ted,alice]
n = 0
for name in myList:
n = n + len(name)
This can be very useful for looping over file names with data needing to be processed,
or data arrays which need something done to them, and all sorts of other things that
will occur to you once you get accustomed to the concept.
An alternate to looping over a list is to use the while construction, as in:
x = 1.
while x < 100.:
print x
x = 1.1*x
Now, for practice, write a loop to compute 52 factorial (i.e. 52*51*...*1). Note
that Python automatically starts using long integers when it needs to.
In doing computations, it is typical that one needs to test for the satisfaction
of a condition at some point before proceeding. For example, one might need to test
whether a temperature is below or above freezing to decide whether to form ice or
liquid water. Programming languages generally provide some conditional control to
handle this situation, and Python is no exception. The following illustrates the use
of an if block in Python:
if T < 273.15:
print "Too cold!"
and an extended if block:
if T < 273.15:
print "Too cold!"
elif T > 373.15:
print "Too hot!"
else:
print "Just right!"

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CHAPTER 1. GETTING STARTED

An if block can have as many elif blocks as you need, and the conditional being
tested can be anything that reasonably evaluates to a truth value. To distinguish
from assignment, the equality relation is expressed by the symbol ==. The symbols
<= and >= have the obvious meanings. The exclamation point negates a relation,
and Python also provides the operator not to negate the truth value of an arbitrary
logical expression. For example 1 != 0 and not (1 == 0) mean the same thing.
Compound expressions can be built up from the Boolean operators for and (&) and
or (|, the vertical bar). Python also provides the keywords True and False for
logical values, but regular integers 1 and 0 generally do just as well in conditionals.
The organization of almost any program can benefit from the subdivision of
the labor of the program into a number of functions. This makes the program easier
to debug, since functions can be tested individually. It also allows the re-use of code
that is needed in many different places in the program. The basic means of defining
a function is illustrated in the following example, which returns the square of the
argument:
def f(x):
return x*x
From the command line, you would invoke this function, once it is defined, by typing,
e.g. f(3).
Python can even handle recursion in functions. That is, functions can be
defined in terms of themselves. As an example, a function to compute the factorial
of n could be written:
def factorial(n):
if n == 0:
return 1
else:
return n*factorial(n-1)
Functions can return multiple arguments, as in:
def powers(x):
return x,x*x,x*x*x
This returns a tuple containing the three values. It can be very nicely used with
Pythons ability to set multiple items to corresponding items of a tuple, using constructions of the form:
x1,x2,x3 = powers(2)

1.2. FUN WITH PYTHON

15

Python functions work only on a copy of the arguments. It is important to

keep this in mind, since it means that any changes made to these arguments (sideeffects) do not affect the variables value in the calling program. Try this:
def f(myValue):
myValue = 0
x = 1
print x
f(x)
print x
In this example, x is unchanged because functions work only on a local copy of their
arguments. However, if the argument is a name which points to the location of
some data, the data pointed to can be modified in the function. This may seem
somewhat arcane, but the following simple example modifying an element in a list
should illustrate the general principle:
def f(myList):
myList[0] = myList[1]
L = [1,2,3,4,5]
f(L)
print L
If you want to replace the list with a completely new list, based on the old one, the
right way to do this is to return the new list, rather than doing anything to the
argument:
def bump(myList):
newList = [ ]
for item in myList:
newList.append(item+1)
return newList
Then, if the user really intended to replace the old list, he or she would use L =
bump(L)
Often, the evaluation of a function will require a number of constants or parameters which you might not need to change very often, or which are common to
a great many different functions. These could always be added to the parameter
list. If there are many of them, that could become tedious. Soon you will learn how

16

CHAPTER 1. GETTING STARTED

to create objects which provide a way to package data in a way that allows you to
keep the argument list of functions under control. There is yet another technique,
though, that can be useful if used with discretion, namely the global variable.
Global variables are set outside functions, and can be accessed by any function
that needs them. In many languages, global variables need to be declared explicitly,
but Python simply makes an intelligent guess about what you intend to be global.
Basically, if a variable is used within a function, but is neither set in the function nor
is in the argument list, Python assumes it to be global. Note that the same variable
name can be local in one function (if it is set internally), but global in another.
As an example of the use of global variables, consider the function computing the
acceleration of gravity towards the center of a planet at the origin:
def grav(r):
return -G*M/(r*r)
This has a problem, because the gravitational constant G and the mass of the planet
M have not been defined anywhere. Its bad practice to hard-wire their values in the
function, because then its inconvenient to change them later. If you try evaluating
the function after youve defined it, youll get an error message (try it). However, if
you type:
G = 6.6742e-11 # In mks units
M = 6.4185e23 #Mass of Mars inkg
grav(1.e12)
everything will work fine. You do not need to define the globals until you want to
evaluate the function, and you can change their values at any time.
This is convenient, but if you have too many globals being set in too many
places, it can be hard to keep track of what is going on. It is also bad practice
to use globals for things you will change a lot, which would more appropriately be
arguments. The behavior of globals can become even more confusing if you have
functions spread across several different files. Nonetheless, you will encounter many
cases where using a few globals does the job nicely.

1.3

Progressing in Python

Having covered the basics, we now introduce some Python techniques that will be
of use in writing programs to do more complex tasks.

1.3. PROGRESSING IN PYTHON

1.3.1

17

Writing your own modules and executable scripts

A module should be thought of as a library of useful definitions, including values of

constants,lists, definitions of functions, objects,definition of object types, and what
have you. A module can also contain executable commands of any type, which
are executed by the interpreter when the module is imported. In fact, Python
doesnt make any real distinction between a module and any other executable script.
Generally, you should think of modules as a place to store things that you will use
repeatedly. Although you can execute a module any way that a Python script can
usually be executed, a module is intended to be used by importing it into some other
script that needs the entities defined by the module.
Generally, when developing code in Python, you always have an interpreter
window open and an idle editor window. You try things out in the interpreter
window, and if things work, you move things into the editor window, which you
save for use as an executable script or as a module.
Lets say that youve written a Python script and saved it as myModule.py.
This script might execute a bunch of calculations, or it might just define functions
that you want to use interactively from the Python command line, or it might
do both. You can run this Python script from within the Python interpreter by
typing import myModule. This will run all the executable statements, and also load
any functions and so forth that youve defined in your file. This way of running
is especially useful if youve defined a lot of nifty functions in your file, and then
want to load them in so that you can try them out interactively in the interpreter.
Note that all variables and functions imported in this way must be referred to with
myModule. stuck on the beginning of its name. Thus, if your file had the statement
radius = 6.0e6 in it, once you imported the file, you would use myModule.radius
to get at the value of radius. Suppose now that you want to change the Python
program youve just tried out. For example, you might want to change the definition
of the radius to radius = 6.0e07. You can edit myModule.py in the editor window
and save it, but to get the interpreter to recognize the changes, it doesnt work
to simply import it again. Instead, you need to type reload(myModule) into the
interpreter.
You can import many different scripts into your Python interpreter session,
and also use the import command in scripts you write yourself. Indeed, this is the
way that extensions to Python are handled.
If youve written a script that performs some one task (e.g. making a plot
of a temperature profile), it is not good practice to execute it by importing it as a
module. Rather, you should save the file (say, myprog.py, then execute it from the
command line by typing python myprog.py, or by loading it into an editor window

18

CHAPTER 1. GETTING STARTED

in idle and executing it from there.

1.3.2

List comprehension

List comprehension refers to the ability to create new lists by processing elements
of old lists. It is one of the powerful features of Python that allows one to write
compact, readable code, often doing without multiline loops. As a simple example,
say we want to generate a list of 10 real numbers equally spaced by increments of
1. Instead of writing a for loop and appending the values to a list, one can simply
write [.1*i for i in range(10)]. Combined with the ability of Python to loop
over any list at all, this is very versatile. For example, one can write [ f(.1) for
f in [math.sin,math.cos,math.exp]]. Suppose we have an averaging function
avg which returns the average of the elements of a list. Then, if L is a list of lists
we want to average, we can create a list of average values by writing [avg(list)
for list in L] The power of list comprehension is further enhanced by Pythons
ability to do multiple assignments on a single line. For example, suppose we want
to open three files, with names data0, data1, and data2. This can be done on a
single line using
file0,file1,file2 = [open(name) for name in [data%d%i for i in range(3)] ]
The open statement which appears in this example is a built-in Python function
that opens a file and returns a file object that can be used to read the contents of
the file, or write new contents to the file.

1.3.3

Using objects in Python

An object is a collection of data and functions that act on the data. The functions in
an object are known as methods Almost everything in Python is an object, and you
have in fact working with many objects all along. For example, if mystring = "Use
the force!", then when you split it using mystring.split() you are invoking
the split method of a string object. The elements of an object are referenced by
separating the name of the object from the element by a period, as in the string
example. A function is called with parentheses, like any other function, and a value
is simply referred to without parentheses. Objects can, if the designer so provides,
do many other things. Objects can be called like functions. They can be indexed like
lists or arrays (as in myobject[frodo], and they can even be used in arithmetic
expressions.
The designer of an object does not actually define the object itself. The designer defines a class of objects. When you use an object, you create an instance

1.3. PROGRESSING IN PYTHON

19

of the object, just like an individual guinea pig is an instance of the general type
of object known as GuineaPig. Suppose somebody has defined a class GuineaPig,
which when instantiated has to be given a name and a weight in kilograms. You
create an instance by typing myPiggy = GuineaPig("Fluffy",1.2). Thereafter,
you can get the weight by typing myPiggy.weight and the name by myPiggy.name.
The object might also have various methods, such as myPiggy.squeak("loud"),
or myPiggy.purr() or myPiggy.eat(). The eat method might do something like
increment the weight when it is called. You can create as many GuineaPig objects
as you like, and each will keep track of the data belonging to itself.
In Python, objects can be dynamically modified. That means that new methods can be added to an existing instance of an object at any time. This can be very
handy for packaging up functions and parameters for handing off as an argument
to another function. The ClimateUtilities module written for this Workbook
provides a Dummy class for this purpose. It creates an object with nothing in it,
which you can modify as you like. The following example shows how you can create
an object with the gravitational constant, the mass of the Mars, and a function as
members.
from ClimateUtilities import *
info = Dummy()
info.G = 6.6742e-11
info.M = 6.4185e23
#
def f(x):
return x/(1.+ x)
#
info.function = f
The following shows how you might define a function using this information:
def g(r,input):
return input.G * input.M * input.function(r)/r**2
You would call this function with a statement like g(1.e7,info). Try it.
This brief discussion is intended to provide enough background to allow you
to work with classes others have defined. The usage of objects will become clearer
as you gain more experience working with them. In the Advanced Topics section to
follow, we will take up the matter of designing your own objects.

20

1.3.4

CHAPTER 1. GETTING STARTED

The Numeric array package

Lists look like arrays, and are versatile objects, but they are not very efficient at
fulfilling the functions one expects of the kind of arrays that appear in moderate to
large scale scientific computation. It would be possible to write a 2D matrix as a list
of lists, and even implement matrix multiplication and vector addition for such an
object. However, it would be very inefficient, because lists provide for a very general
and mutable data structure. Python does have a native array data type, which is
somewhat more efficient, but is still not very good for scientific computing.
This is where the real power of the extensibility feature of Python comes in.
When the language is missing some feature some community really needs, the community gets together and writes an extension module which fills the bill. Sometimes
this is a cooperative process. Sometimes it is an evolutionary process, with many
competing extensions co-existing until one comes to dominate. For scientific arrays,
the solution that has come to the fore is the Numeric module, which provides highly
efficient Matlab-style array objects.
Numeric is not written in Python. It is written in very highly optimized c++,
which is why it is so efficient. This does not mean the developers of Numeric had
to learn a lot about the internal structure of Python or spend much time at all
turning their compiled library of objects into commands that could be accessed
within Python. In fact, once such a library is developed, it can be turned into a
Python module more or less automatically using a preprocessor known as swig (see
swig.org for more details). Compiled FORTRAN libraries can be similarly spliced
into Python using pyfort or f2py. For this reason, a great variety of numerical
analysis libraries are already available as Python modules. Moreover, if you know
how to program in c, c++ or FORTRAN, you can very easily learn to build your own
customized Python modules. The general strategy is to do as little as possible at the
compiled level, building tools there that are very general and of broad applicability.
One seeks to isolate the computationally intensive work in a few compiled toolkits,
and build more complex models out of these building blocks at the Python level.
Numeric provides one of the most fundamental building blocks for scientific
programming in Python, and most other Python modules doing numerical analysis
or data analysis deal with Numeric arrays. The Numeric module is imported like
any other module, using import Numeric. Numeric arrays can have however many
dimensions you need.
The first step in using a Numeric array is to create it. Numeric provides
various ways to do this. To create an array, you need to specify its dimensions
and its datatype. Commonly used data types are default float (Numeric.Float,
usualy double precision), default complex (Numeric.Complex), and default integer

1.3. PROGRESSING IN PYTHON

21

(Numeric.Int, typically a 32-bit int). Numeric does not currently support 64-bit
integers unless they are the default integer type on the machine you are using. It
also does not support the unlimited precision Python integers, though other modules
are available which do. Dimensions are specified as a tuple or a list of integers. For
example, the dimensions of a 3 by 5 array are specified as (3,5) or [3,5]. If the
array is one-dimensional, you can just use an integer in place of a list or tuple, if
you wish.
One way to create an array in Python is to call a creation routine which makes
an array of the desired dimension and fills it in with default data of some particular
type. For example, the following lines create a 5 by 10 floating point array of zeroes,
a one-dimensional integer array of ones of length 100, and a 10 by 10 complex
identity matrix. You can see the values of an array, if it is not too big, by just
typing its name.
A = Numeric.zeros((5,10),Numeric.Float)
B = Numeric.ones(100,Numeric.Int)
C = Numeric.identity(10, Numeric.Complex)
A typical thing to do would be to create an array of zeroes, then fill in the values
you want in a loop, as in:
A = Numeric.zeros((5,10),Numeric.Float)
for i in range(5):
for j in range(10):
A[i,j] = .1*i*i + i*j/10.
This example also illustrates the way one refers to elements of an array in Python.
Python arrays are zero-based, i.e. A[0,0] is the first element in the case above.
The designers of Numeric provided a very versatile indexing handler, so in fact you
could equally well refer to the i,j element as A[i][j]. In essence, multidimensional
Numeric arrays act like a list of lists. Well return to this shortly, in our discussion of
array cross section notation. Another important thing to know about Numeric array
indexing is that it conforms to Python list usage with regard to negative numbers.
For example, if B is a one-dimensional array, B[-1] is the last element of the array,
B[-2] is the next to last, and so forth. Try this with a 2D array, to make sure you
understand the indexing convention.
An array can also be created from a list. You can let Numeric infer the data
type from the contents of the list, or you can specify it explicitly, in which case a
conversion is performed. Try the following statements, and see what kind of array
is produced:

22

CHAPTER 1. GETTING STARTED

A = Numeric.array([.1,.2,.3])
B = Numeric.array(range(20),Numeric.Complex)
C = Numeric.array( [ [1.,2.],[-2.,1.] ])
Another useful way to create an array is to define it in terms of a function
on the indices, so A[i,j] = f(i,j), f being some function you have defined. This
is probably the most common way of creating the kind of array used in scientific
computation without employing a loop. It will generally operate much faster than
a Python loop, especially for large arrays. The following illustrates how to create a
10 by 10 array from a function:
dx = .1
dy = .2
def f(i,j):
x = dx*i
y = dx*j
return x*x + y*y
A = Numeric.fromfunction(f,(10,10))
The two parameters dx and dy are provided to the function f as globals, because that
is the only way Numeric has provided to pass auxiliary information to the function
defining the array. There is an important subtlety in the use of fromfunction. The
parameters i and j look like integers, but in fact they are arrays of the same dimension as the array being created. The above example works because the arithmetic
being done on the arguments is actually array arithmetic. This allows fromfunction
to call the function only a single time, rather than in a loop, and results in a much
faster computation. If you are using other functions or list indexing inside your
creation function, you must take this into account. For example, the following code
will work:
dx = .1
dy = .2
def f(i,j):
x = dx*i
y = dx*j
return Numeric.sin(x)*Numeric.sin(y)
A = Numeric.fromfunction(f,(10,10))
but if we used math.sin and math.cos instead, it would not work, since these
functions do not operate on and return Numeric arrays. Similarly, an expression like
myList[i] will not work inside the function f since i is not an integer, and so cant

1.3. PROGRESSING IN PYTHON

23

be used as an index. There are workarounds, but generally speaking, fromfunction

does not work very gracefully with table look-up operations. If you are still confused
about just what i and j are, try putting a print statement in the function to print
out the arguments.
There are other ways to create arrays, but the above methods should take care
of any cases you are likely to encounter. We have already illustrated how to refer
to individual array elements, but it is worth knowing about some of the powerful
array cross section indexing features allowed by Numeric, which allow you to refer
to subarrays easily. Python uses the colon (:) as an identifier to build cross sections.
The colon by itself stands for the full range of values of the corresponding index. For
example, if A is a 5 by 5 array, the subarray A[:,0] is the one dimensional array with
elements A[0,0],A[1,0],...,A[4,0]. An index of the form m:n would denote the
range of values m,m+1,...,n-1, so that A[1:3,0] would be the array with elements
A[1,0],A[2,0]. If you leave off one of the endpoints, Python substitutes the first
array element for the starting point, or the final array element for the ending point.
If B were a 100 element array, for example, B[:25] would be the same as B[0:25]
and B[50:] would be the same as B[50:100]. Finally, you can specify a stride,
allowing you to pick off every k t h element. Thus, 0:10:3 represents the set of
indices 0,3,6,9. You can combine subarray indices for the various dimensions of
an array in any way you want, as in A[0:8:2,5:].
Now we come to the most powerful aspect of Numeric arrays, namely that one
can do arithmetic with them just as if they were scalars, avoiding the writing of
inefficient and cumbersome loops. The following statements illustrate the kind of
arithmentic operations that can be performed with arrays. Note that you will get
an error if you try to perform arithmetic on incompatibly sized arrays (e.g. adding
a 10 by 10 array to a 5 by 5 array).
A = Numeric.ones((10,10),Numeric.Float)
B = Numeric.identity(10,Numeric.Float)
C = (A-B)*10. #You can multiply by a scalar
C1 = (A-B)*B #You can multiply by an array
D = A/(A+2) #You can divide arrays.
E = C**5.2 #Exponentiation
The expressions can be as complicated as you want. Note that Numeric array
multiplication is element-by-element multiplication, rather than matrix multiplication (and similarly for division). If you want matrix multiplication you use the
Numeric.dot(...) function, as in C = Numeric.dot(A,A). When the two arrays
are 1D, this reduces to the conventional vector dot product. There is also a function
Numeric.outerproduct which computes the outer product of two arrays. Numeric

24

CHAPTER 1. GETTING STARTED

does not provide a function for matrix inversion; that can be found in various other
linear algebra packages made to work on Numeric arrays.
Numeric also provides versions of the standard math functions, that work
on entire arrays. For example B = Numeric.sin(A) returns an array of the same
dimension as A, whose elements are the sin of the corresponding elements of A
Array arithmetic can be done between arrays of different types, if the operation
makes sense. The result is promoted to the higher of the two operands. For example,
adding an integer and a complex results in a complex, or adding a single precision
float to a double precision float yields a double precision float. The default float
type for Numeric arrays is double precision. All floating point scalars in Python are
also treated as double precision, so an operation involving a Python float constant
and a Numeric float array will yield a double precision array.
Cross sections can be used with array arithmetic to compute many useful
derived quantities without the need of writing loops. For example, an approximation
to the derivative of a function whose values at an array of points x are tabulated in
the array F (i.e. F[j] = f(x[j]) ) can be computed using:
#We assume the function f and the array x have been defined already
F = Numeric.array([f(x1) for x1 in x])
n = len(x)
dx = x[1:n]-x[0:(n-1)]
df = F[1:n]-F[0:(n-1)]
dfdx = df/dx
xmid = (x[1:n]+x[0:(n-1)])/2.
The final line defines the array of midpoints, where the derivative has been estimated.
Note the use of list comprehension to generate the array F. Array cross sections can
also be used to do matrix row and column operations efficiently. For example,
suppose A is an n by n matrix. Then a set of row and column reductions can be
done with the following 1D loop:
for i in range(n):
A[i] = A[i] - 2.*A[0]
A[:,i] = A[:,i] - 3.*A[:,0]
You can even do a fairly broad class of conditional operations on arrays, using
the Numeric.where function. This function takes three arguments. The first is a
conditional involving an array. The second is an array expression, to be evaluated
and returned if the conditional is satisfied. The third argument is the expression
to be returned if the conditional is not satisfied. For example, the following use of

1.3. PROGRESSING IN PYTHON

25

where returns the array A where B is negative, and returns the value 1. where B is
non-negative:
C = Numeric.where(B<0,A,1)
Note that the array A must have the same dimensions as B, since the conditional
is evaluated element-by-element. The expressions can be quite complicated. For
example:
C = Numeric.where(Numeric.sin(B)>0, Numeric.exp(1.+ B*B),Numeric.exp(1.-B*B))
The combination of array cross sections, conditionals and array arithmetic is
so powerful that one should only rarely need to resort to writing a loop. This is
a good thing, since large loops run very slowly in Python, as in other interpreted
languages. Try computing the matrix product of two 200 by 200 arrays using an
explicit loop, and compare to the time taken to do the same multiplication using
Numeric.dot. Avoiding loops is also good practice because it makes the meaning
of your code more transparent.
Numeric offers a rich variety of other useful array operations, such as convolution. For additional information on Numeric, just type help(Numeric) after youve
imported it. Full documentation can be found at www.pfdubois.com/numpy/.

1.3.5

The Curve object and its uses

The ClimateUtilities module written for use with this Workbook provides a
Curve object, which is intended to simplify the process of reading, and writing
plain-text tabular data, and of plotting data which has either been read in from a
file or generated by some calculation in your script. In essence, a Curve object is a
set of data columns, each of which must be the same length, together with optional
auxiliary information describing the data. The auxiliary information also allows you
to specify certain things about how the data will look when it is plotted.
To use a Curve object, you create one, and then install data columns using
the addCurve(...) method. Since Curve objects are intended to represent data sets
in which any element of a column can be regarded as a function of the corresponding
element of another column, all data columns installed must have the same length.
You can install any one-dimensional indexable object, including lists and Numeric
arrays. If you install a list, it will be converted automatically to a Numeric array,
so you can do arithmetic with it.
The following example creates a curve object containing values of x, sin(x)
and cos(x).

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CHAPTER 1. GETTING STARTED

import math
from ClimateUtilities import *
x = [(i/10.)*2.*math.pi. for i in range(101)]
y1 = [math.sin(xx) for xx in x]
y2 = [math.cos(xx) for xx in x]
c = Curve()
c.addCurve(x,x,x axis label)
c.addCurve(y1,y1,sin(x))
c.addCurve(y2,y2,cos(x))
The first argument is mandatory, since it defines the data you want to install in the
Curve. The second argument of addCurve defines a variable name, which you will
use to refer to that data column. It is optional. If you omit it, the Curve object will
create a variable name of the form v0,v1,v2,.... If you specify a variable name
yourself, you can also optionally specify a long name, or label, which is used to
label the corresponding data when plotting, and also to provide more long-winded
information about what the variable represents. The label can be a good place to
record the units of a variable.
Curve objects are indexed. You refer to a data column by its variable name.
In the above example, c[x] returns a Numeric array of the x column, and
c[x][30] would return item 30 of that array. You can get a list of variable names
in a Curve object by using the listVariables method, as in c.listVariables()
A good general technique for putting data from a calculation into a Curve
object for saving, plotting or further analysis is to accumulate the data into a set of
lists, and then install the lists in a Curve object. This way, there is no need to know
in advance how long the data objects will be. When data from a list is installed in a
Curve object it is automatically converted to a Numeric array. The following code
snippet provides an example:
xlist = [ ]
ylist = [ ]
x = 1.
xfact = 1.1
while x < 100.:
xlist.append(x)
ylist.append(x*x)
x = x*1.1 # or, equivalently x *= 1.1
c = Curve()
c.addCurve(xlist,x)
c.addCurve(ylist,y)

1.3. PROGRESSING IN PYTHON

27

The readTable(...) function in ClimateUtilities will read columnar tab

or space-delimited data from a text file and return a Curve object with the data. It is
called with the filename as the argument; for example to read the file "profile.txt",
you would type c = readTable("profile.txt"). The filename can also contain
the path to the directory where the data is located, if necessary. Note that you do
not have to create the Curve object yourself; that is done for you by the readTable
function. If the data set contains column headers containing variable names (without spaces or tabs in them), readTable will recognize that and use them as variable
names. readTable will also do a pretty smart job of recognizing what is data and
what is text description of the data set, such as often is found at the beginning or
end of a file. Descriptive text will be separated out from the data, and returned as
the description element of the Curve object.
ClimateUtilities also provides an easy-to-use plot function which produces
line graphs from Curve objects. One of the data columns must be designated as the
independent, or x axis; other data will be plotted as a function of this. By default,
the first column installed is designated the x axis, but any other curve can be so
designated using the Xid element (e.g. c.Xid = y1 in the above example.
If you want to plot the data in a Curve object c, you can simply type plot(c).
The Curve object has the following plot options, which can be set to control the
appearance of the plot. If c is the Curve object, then:
c.XlogAxis = True plots the x axis with a log scale, and similarly for c.YlogAxis.
c.reverseX = True plots the x axis data with the largest values at the left,
and c.reverseY plots the y axis data with the largest values at the bottom.
c.switchXY = True switches the x and y axes. For example if you are plotting
temperature T as a function of pressure p (which is designated as the x axis)
and you want to make the pressure appear on the vertical axis, you would
invoke this option. If you are just plotting one column, the same effect could
be achieved by just changing the specification c.Xid, but if you are plotting
multiple curves on the same graph, you would need to use the c.switchXY
option.
If you want any data column to be plotted as a scatter plot, i.e. with symbols
at the data points but no line drawn, you can set c.scatter(varname) =
True, where varname is the name of the variable you wish to affect for
example, y1 in the sin and cos curve we defined earlier.
When you call plot it puts up the plot in a window which you can move around,
but which you wont be able to get rid of until you terminate the Python shell. plot

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CHAPTER 1. GETTING STARTED

actually returns a plot object which you can use to do further things with the plot.
In particular, if you were to write w = plot(c), then you can make use of the plot
object w. For example w.delete() gets rid of the plot window. You can also use the
plot object to save the plot as a postscript file, for later printing or incorporating
into a lab report. You do this by typing w.save(myplot), which save the plot into
the file myplot.eps. You can of course replace the filename myplot with whatever
name you want.
If you dont want to use the python-based graphics, you can always use
c.dump(myfile.txt) which makes a tab-delimited text file, and then plot it
using the program of your choice.

1.4
1.4.1

Advanced Python Topics

Defining your own objects

You define a new type of object by using the class statement. This will define the
data and functions (known as methods) that will be part of the object. The class
statement should specify a special method called init (...) which is known as
a constructor. This method is invoked when a new instance of the object is created,
and says what needs to be done to create the object. Sometimes the creation process
is very simple, but the creation process can also be very complex. Certain methods,
like init have special meaning. All such methods have names with begin and
end with a double underscore.
As a simple example, the following class defines an object which can be used
to evaluate the gravitational acceleration as a function of distance to a planet with
mass M:
class gravity:
def __init__(self,M,G):
self.M = M
self.G = G
def accel(self,r):
return -self.G*self.M/(r*r)
The argument self must be the first argument to every method defined in the
object. It provides a way to refer to the members of the particular instance of the
object being worked on. When you actually call the methods, or create the object,
you leave off the self argument and Python puts it in automatically. To make an

1.4. ADVANCED PYTHON TOPICS

29

object of the type we have just defined, and use it to compute the acceleration at a
certain distance, you would use
g = gravity(6.4185e23,6.6742e-11) #Invokes the __init__ method to create an
#instance of a gravity object
g.accel(1.e12) #Computes the acceleration
You can improve the object by making it callable, so it acts just like a function.
You do this by adding a call method:
class gravity:
def __init__(self,M,G):
self.M = M
self.G = G
def __call__(self,r):
return self.accel(r)
def accel(self,r):
return -self.G*self.M/(r*r)
If you create an instance g of this object, the acceleration can be computed by just
typing g(r). This is a convenient technique for creating functions that remember
the parameters needed to compute themselves.
Now, since the gravitational constant is a universal constant which should never
change from one planet to another, it is rather silly to have to specify it separately for
each planet. Python objects allow you to specify data that is common to all objects
of a given type. If this class data is changed somewhere, the change applies to all
objects. This behavior is useful not just for shared constants, but it also provides
a way for one instance of an object to communicate with all other instances of an
the same kind of object. Class data is specified within the class definition without
any identifier. It is referred to using the name of the class, rather than the name
of an instance. The following example re-implements the class, making G into class
data, and also implementing a class-level counter that keeps track of the number of
planets created:
class gravity:
G = 6.6742e-11
nPlanets = 0
def __init__(self,M):
self.M = M
gravity.nPlanets = gravity.nPlanets + 1
def __call__(self,r):

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CHAPTER 1. GETTING STARTED

return self.accel(r)
def accel(self,r):
return -gravity.G*self.M/(r*r)

Now, you can create two planets using planet1 = gravity(6.4e23) and planet2
= gravity12.e23. The two masses are still planet1.M and planet2.M, and you
compute the gravity for the two planets using planet1(1.e6) and planet2(1.e6)
as before. Now, however, if you need to change the value of the gravitational constant, you can update it for all the planets by writing, for example, gravity.G =
6.672e-11. At any time, the number of gravity objects instantiated so far will be
gravity.nPlanets.
In many applications, an object will store data in the form of arrays. In such
cases, the init method typically will create the arrays and set their initial value.
For example, the following class creates and initializes pressure and temperature
arrays of a specified length:
class profile:
def __init__(self,n,p0,T0):
self.p = Numeric.array(range(n),Numeric.Float)*p0/(n-1)
self.T = Numeric.ones(n)*T0
def warm(self,dT):
self.T = self.T + dT
The class provides a method which increments the temperature by an amount
dT. Once you have imported Numeric, you can create an instance using pT1 =
profile(100,1000.,300.). If you want to find the pressure at index 4, you would
type pT1.p[4], and similarly for temperature. You can also change the values of the
arrays as you would for any other Numeric array, using, e.g. pT1.T[10] = 301..
The special methods getitem and setitem allow you to make an object
indexable, so that individual elements of an object can be retrieved by specifying
an index of some type. Array elements are indexed by specifying sequences of
integers, but the object used for doing the indexing can be quite general. The
following example shows how to make and use a tridiagonal array object, which can
be addressed as if it were a full matrix.
class tridiag:
def __init__(self,n):
self.A = Numeric.zeros(n,Numeric.Float)
self.B = Numeric.zeros(n,Numeric.Float)
self.C = Numeric.zeros(n,Numeric.Float)

1.4. ADVANCED PYTHON TOPICS

def __getitem__(self,key):
# key is a list of arguments passed within square
# brackets when an indexing operation is performed
# on an instance of the object. In this case,
# key is expected to be a two element list.
if key[0] < key[1] - 1:
return 0.
if key[0] > key[1] + 1:
return 0.
if key[0] == key[1] -1:
return self.A[key[1]] #Below the diagonal case
if key[0] == key[1]:
return self.B[key[1]] #Diagonal case
if key[0] == key[1]+1:
return self.C[key[1]] #Above the diagonal case
def __setitem__(self,key,value):
# key is a list of arguments passed within square
# brackets when an indexing operation is performed
# on an instance of the object. In this case,
# key is expected to be a two element list.
#
# value is the value to which the element is to be set.
# It is taken from the right hand side of the equal
# sign in an expression like M[i,j] = 1., where M
# is an instance of the object.
#
if key[0] < key[1] - 1:
print "Out of bounds"
if key[0] > key[1] + 1:
print "Out of bounds"
if key[0] == key[1] -1:
self.A[key[1]] = value #Below the diagonal case
if key[0] == key[1]:
self.B[key[1]] = value #Diagonal case
if key[0] == key[1]+1:
self.C[key[1]] = value #Above the diagonal case
The object could be used as follows:
M = tridiag(10)
for i in range(10):

31

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CHAPTER 1. GETTING STARTED

M[i-1,i] = 1.
M[i,i] = -2.
M[i,i+1] = 1.

print M[9,9],M[2,2],M[2,3]
Square brackets are used in indexing operations. If the square brackets contain only
a single item, that item is passed to getitem and setitem as key. If the
brackets contain a sequence of elements separated by commas, they are passed as a
list, whence key has to be treated as a list, as in the example above. This example
uses integers for indexing, but the indexing model in Python is completely general.
Any Python objects may be used for indexing, including floats, complex numbers,
strings, and even objects you have defined yourself.
One of the most powerful features of object-oriented programming is that you
can define, or overload all the arithmetic operators so that they have the behavior
you want when applied to your own objects. This allows you to design customized
data types that allow you to condense very complicated operations into compact
and simple statements. As a very simple example, lets create a gaussian integer
data type, which behaves like a complex number, but uses long integers so as to
allow unlimited precision. Python does not provide this as a native data type, but
the following example allows us to do it ourselves:
class gaussInt:
def __init__(self,real,imag):
self.real = real
self.imag = imag
def __add__(self,other):
if (type(other) == type(1)) or (type(other) == type(1L)):
return gaussInt(other+self.real,other+self.imag)
else:
return gaussInt(other.real+self.real,other.imag+self.imag)
def __mul__(self,other):
if (type(other) == type(1)) or (type(other) == type(1L)):
return gaussInt(other*self.real,other*self.imag)
else:
return gaussInt(other.real*self.real-other.imag*self.imag,
other.imag*self.real + other.real*self.imag)
def __repr__(self):
return "%d + %d i"%(self.real,self.imag)
Note that the arithmetic methods create a new gaussInt object to return. Note

1.4. ADVANCED PYTHON TOPICS

33

also the type-checking, which allows arithmetic to be performed between Gaussian

integers and regular integers. The class would be used as follows:
x = gaussInt(3,5)
y = gaussInt(7,1)
x*3 + y*y
z = 1
for i in range(50):
z = x*z
print z
The repr method in this example makes the object print out nicely when you
type its name or use it in a print statement. Try leaving it out, and see what
happens when you type the objects name, or perform an arithmetic operation.
We have defined addition and multiplication for our Gaussian integers, but
attempts to use subtraction, negation, mod,exponentiation or division will cause
an error message, because these operations have not been defined. Each of these
operations, and many more, have their own reserved method names that can be
defined. There is no need to stick to uses of the operator symbols that resemble
their customary use. Youre free to redefine addition as multiplication and multiplication as addition, if you want. More usefully, if you need a special symbol to
represent matrix multiplication, you can redefine the mod operature % to mean matrix multiplication, leaving * to mean pointwise multiplication. Or, if you mostly
use matrix multiplication, you can define * to mean matrix multiplication and % to
mean pointwise multiplication.
A commutative operator (say, *) is one for which x y = y x. Many
operations, most commonly matrix multiplication, are non-commutative; one needs
to keep track of the order of operation. All the binary operators can be made
non-commutative in Python. In the Gaussian integer example, we didnt need to
think much about which operand in x*y was self and which one was other,
because the operation being implemented is commutative. To implement a noncommutative operation, you only need to pay attention to which operand is self
and which is other. The rule in Python is that in a binary operation such as
x*y, the first operand (x) is self and the second (y) is other. As a simple
example, lets implement * as string concatenation, which is a non-commutative
operation. For strings, Python already implements concatenation as the meaning of
the operator +, so the only point of this example is to fix in the mind the somewhat
confusing matter of which operand is self and which is other. We define the
class nonCommutative:
class nonCommutative:

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CHAPTER 1. GETTING STARTED

def __init__(self,x):
#x should be a string
self.val = x
def __mul__(self,other):
return nonCommutative(self.val + other.val) #Concatenate strings
def __repr__(self):
return self.val

Now, if we create some instances:

x = nonCommutative(a)
y = nonCommutative(b)
then x*y will evaluate to ab and y*x will evaluate to ba. Thus, to implement a
noncommutative operation, you only need to keep in mind that self is the operand
on the left and other is the operand on the right, in binary operations like add
or mul .
Since matrix multiplication is non-commutative, you would need to pay attention to this if you wanted to overload multiplication of Numeric arrays so that
* meant matrix multiplication instead of point-by-point multiplication. You dont
need to pay much attention, though, since the basic lesson is that if you keep the
operands in the natural order, everything will work out fine. The following defines a new class of matrices, for which * is matrix multiplication and % is pointwise
multiplication:
class BetterArray:
def __init__(self,array):
self.array = array
def __mul__(self,other):
return BetterArray(Numeric.matrixmultiply(self.array,other.array))
def __mod__(self,other):
return BetterArray(self.array*other.array)
The array handed to init should be a Numeric array, though this class doesnt
check to make sure that is the case. To try this out, letx multiply the matrices




0 1
0 1
(1.1)
X=
,Y =
1 0
1 0
To create and multiply these arrays, and print out the result, type the following:
import Numeric

1.4. ADVANCED PYTHON TOPICS

35

X = BetterArray(Numeric.array([[0,1],[1,0]]))
Y = BetterArray(Numeric.array([[0,1],[-1,0]]))
Z = X*Y
print Z.array
Z1 = Y*X
print Z1.array
Multiply out the arrays by hand to make sure our implementation of BetterArray
handles the non-commutativity properly. Note that to get the results in the above
example, we needed to do things like print Z.array, because we didnt go through
the bother of writing a repr method for BetterArray. Without this, simply
typing X*Y performs the operation, but tells us nothing useful about the result.
Z.arrayis a Numeric array, which knows how to print itself. 1
As an exercise, complete the definition of the BetterArray class by defining
addition, subtraction and negation, and try out the object. You can further extend
the class by adding some type-checking of other so that the operations can handle the case of multiplication by a scalar. If you are really ambitious, you could
even define matrix division, by incorporating a matrix inversion method for square
matrices.
Python also provides methods for right versions of the binary operations, e.g.
rmul and radd . If y has an rmul method and x has no mul method,
then x*y translates into a call to the rmul of the object y in which y is self and
x is other, i.e. y. rmul (x). It works similarly for other binary operations. As
weve already seen, you do not need to use the right versions to make operations
non-commutative. So what are the right versions good for? Our gaussint class
provides an example of a case where you would need rmul and radd . If z is a
gaussInt then z*3 returns the correct answer because z has a mul method and
this method checks if other is an integer and proceeds accordingly. However, 3*z
raises an error, because the integer has no way of knowing how to multiply itself by
a gaussInt. The way out of this problem is to give the gaussInt class an rmul
method:
class gaussInt:
... #Same stuff as before here
def __rmul__(self,other):
if (type(other) == type(1)) or (type(other) == type(1L)):
return gaussInt(other*self.real,other*self.imag)
else:
1

Unfortunately, the repr method of Numeric arrays is buried in the compiled level of the
implementation, and cant easily be gotten at.

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CHAPTER 1. GETTING STARTED

return gaussInt(other.real*self.real-other.imag*self.imag,
other.imag*self.real + other.real*self.imag)

Now, 3*z works, because z has an rmul method that Python can use. Note that,
because we want i*z to give the same result as z*i, where i is an integer, we didnt
really need to copy the whole definition of mul int rmul , as we did above. As
a shortcut, we could have written simply
class gaussInt:
... #Same stuff as before here
def __rmul__(self,other):
return self.__mul__(other)
Note that we invoke the mul method as self. mul (other) not as self. mul (self,other).
That is because the special self argument is only used in Python when we are
defining a method, and never when we are just invoking (calling) it. As an exercise,
extend the arithmetic of gaussInt further by adding an radd method.
Basically, the right versions of the binary operations are never needed if
you only want to define operations between objects of the same type. You only
need them to deal with operations between objects of differing types. Now here
comes the confusing part. Suppose x has an add method and y has an radd
method. How is x+y interpreted? Is it x. add (y) or y. radd (x)? The answer
is that Python will implement the operation as x. add (y). There is an important
exception to this rule. Namely, certain very well-constructed objects will go on to
try y. radd (x) if x. add (y) creates an error (and similarly for other binary
operations). This is how Python was able to make sense of 3*z, in our gaussInt
example, even though integers already have a mul method, which youd think
would raise an error, since they dont know how to multiply an algebraic integer by
themselves. This kind of error trapping doesnt happen automatically. It has to be
built into the object. Integers, long integers, floats, complex numbers, strings, lists
and Numeric arrays are all well constructed objects in this sense.
In the case of the class BetterArray, it is a considerable nuisance that it is
necessary to provide definitions of all the operations you want the object to handle,
even if you dont need to change their behavior (as in the case of addition and
subtraction). Object oriented languages like Python provide a powerful way to
handle this issue, in the form of inheritance. 2 Use of inheritance to build daughter
2

Unfortunately, you cant actually use inheritance with Numeric arrays in this way, since the
classes used in these arrays are implemented in efficient, compiled code. These object definitions
are not accessible to the Python interpreter, and so most their methods cannot be inherited by
objects defined at the Python level.

1.4. ADVANCED PYTHON TOPICS

37

classes from existing ones will not be treated here. Other advanced object concepts
we are leaving out include introspection and polymorphism. The eager student who
wishes to dig deeper into object oriented programming can find excellent treatments
of these subjects in virtually any complete Python programming handbook.

1.4.2

Dictionaries

1.4.3

Writing text data to files

The data writing and reading capabilities provided by the Curve object will probably
take care of all the input-output needed to get through this course. At some point,
you may be faced with the need for writing or reading files of a more general form.
This section and the next covers the basics of how that is done.
First you need to open the file. To do this, you type
myfile = open(test.out,w)
where myfile is the object by which you will refer to the file in your Python program. You can use any variable name you want for this. Similarly, you can replace
test.out with whatever you want the file to be called. The second argument of
open says that we want to create a new file, if necessary, and allow the program to
write to it.
You can only write a string to a file, so first you have to convert your data to
a string. You have already learned how to do this. The following example serves as
a reminder, and also shows how you can skip to a new line at the end of the string.
a = 1.
b=2.
outstring = %f %f\n%(a,b)
outstring
The definition of outstring tells Python to make a string converting the elements
of the tuple from floats to characters, with a space in between and a carriage return
(newline) at the end of the line.
Files are objects in Python, so to write the string to the file, you just do
myfile.write(outstring).
Now you have everything you need to write space-delimited data to a file, except that when you are done, you need to close the file by executing myfile.close().

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CHAPTER 1. GETTING STARTED

Using what you have learned write a table of the functions x/(1 + x) and
x2 /(1 + x2 ) vs. x to a file. You can take a look at the resulting file in any text
editor, or load the file into the program of your choice for plotting.

1.4.4

Reading text data from a file

To read text data from a file, you need to read in a line of text, and then convert
the items into numbers, if that is what they represent. In order to do the conversion, it is necessary to know what kinds of items are in the file, although strings
have various methods that can help you identify whether an item is a number or
not. Conversion is done by string-to-number routines found in the module string.
Strings representing integers can be converted to float numbers, but if you try to
convert a string representing a float to an integer, you will get an error.
The following example reads a single line from a file, which may consist of
integers or floats separated by white-space characters, and converts it into a list of
values. To read the rest of the file, you would repeat the procedure until the end of
the file is reached.
import string
f = open("myfile.txt")
buff = f.readline()
items = buff.split() # Or, do it all at once with items = f.readline().split()
values = [string.atof(item) for item in items]