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Introduction to Python
Heavily based on presentations by
Matt Huenerfauth (Penn State)
Guido van Rossum (Google)
Richard P. Muller (Caltech)
...
Monday, October 19, 2009
• Open source general-purpose language.
• Object Oriented, Procedural, Functional
• Easy to interface with C/ObjC/Java/Fortran
• Easy-ish to interface with C++ (via SWIG)
• Great interactive environment
• Downloads: http://www.python.org
• Documentation: http://www.python.org/doc/
• Free book: http://www.diveintopython.org
Python
Monday, October 19, 2009
2.5.x / 2.6.x / 3.x ???
• “Current” version is 2.6.x
• “Mainstream” version is 2.5.x
• The new kid on the block is 3.x
You probably want 2.5.x unless you are starting from
scratch. Then maybe 3.x
Monday, October 19, 2009
Technical Issues
Installing & Running Python
Monday, October 19, 2009
Binaries
• Python comes pre-installed with Mac OS X and
Linux.
• Windows binaries from http://python.org/
• You might not have to do anything!
Monday, October 19, 2009
The Python Interpreter
• Interactive interface to Python
% python
Python 2.5 (r25:51908, May 25 2007, 16:14:04)
[GCC 4.1.2 20061115 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
• Python interpreter evaluates inputs:
>>> 3*(7+2)
27
• Python prompts with ‘>>>’.
• To exit Python:
• CTRL-D
Monday, October 19, 2009
Running Programs on UNIX
% python filename.py
You could make the *.py file executable and add the
following #!/usr/bin/env python to the top to make it
runnable.
Monday, October 19, 2009
Batteries Included
• Large collection of proven modules included in the
standard distribution.
http://docs.python.org/modindex.html
Monday, October 19, 2009
numpy
• Offers Matlab-ish capabilities within Python
• Fast array operations
• 2D arrays, multi-D arrays, linear algebra etc.
• Downloads: http://numpy.scipy.org/
• Tutorial: http://www.scipy.org/
Tentative_NumPy_Tutorial
Monday, October 19, 2009
matplotlib
• High quality plotting library.
• Downloads: http://matplotlib.sourceforge.net/
#!/usr/bin/env python
import numpy as np
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
mu, sigma = 100, 15
x = mu + sigma*np.random.randn(10000)
# the histogram of the data
n, bins, patches = plt.hist(x, 50, normed=1, facecolor='green',
alpha=0.75)
# add a 'best fit' line
y = mlab.normpdf( bins, mu, sigma)
l = plt.plot(bins, y, 'r--', linewidth=1)
plt.xlabel('Smarts')
plt.ylabel('Probability')
plt.title(r'$mathrm{Histogram of IQ:} mu=100, sigma=15$')
plt.axis([40, 160, 0, 0.03])
plt.grid(True)
plt.show()
Monday, October 19, 2009
PyFITS
• FITS I/O made simple:
• Downloads: http://www.stsci.edu/resources/
software_hardware/pyfits
>>> import pyfits
>>> hdulist = pyfits.open(’input.fits’)
>>> hdulist.info()
Filename: test1.fits
No. Name Type Cards Dimensions Format
0 PRIMARY PrimaryHDU 220 () Int16
1 SCI ImageHDU 61 (800, 800) Float32
2 SCI ImageHDU 61 (800, 800) Float32
3 SCI ImageHDU 61 (800, 800) Float32
4 SCI ImageHDU 61 (800, 800) Float32
>>> hdulist[0].header[’targname’]
’NGC121’
>>> scidata = hdulist[1].data
>>> scidata.shape
(800, 800)
>>> scidata.dtype.name ’float32’
>>> scidata[30:40,10:20] = scidata[1,4] = 999
Monday, October 19, 2009
pyds9 / python-sao
• Interaction with DS9
• Display Python 1-D and 2-D arrays in DS9
• Display FITS files in DS9
• Downloads: Ask Eric Mandel :-)
• Downloads: http://code.google.com/p/python-sao/
Monday, October 19, 2009
Wrappers for Astronomical Packages
• CasaPy (Casa)
• PYGILDAS (GILDAS)
• ParselTongue (AIPS)
• PyRAF (IRAF)
• PyMIDAS (MIDAS)
• PyIMSL (IMSL)
Monday, October 19, 2009
Custom Distributions
• Python(x,y): http://www.pythonxy.com/
• Python(x,y) is a free scientific and engineering development
software for numerical computations, data analysis and data
visualization
• Sage: http://www.sagemath.org/
• Sage is a free open-source mathematics software system
licensed under the GPL. It combines the power of many existing
open-source packages into a common Python-based interface.
Monday, October 19, 2009
Extra Astronomy Links
• iPython (better shell, distributed computing):
http://ipython.scipy.org/
• SciPy (collection of science tools): http://
www.scipy.org/
• Python Astronomy Modules: http://
astlib.sourceforge.net/
• Python Astronomer Wiki: http://macsingularity.org/
astrowiki/tiki-index.php?page=python
• AstroPy: http://www.astro.washington.edu/users/
rowen/AstroPy.html
• Python for Astronomers: http://www.iac.es/
sieinvens/siepedia/pmwiki.php?
n=HOWTOs.EmpezandoPython
Monday, October 19, 2009
The Basics
Monday, October 19, 2009
A Code Sample
x = 34 - 23 # A comment.
y = “Hello” # Another one.
z = 3.45
if z == 3.45 or y == “Hello”:
x = x + 1
y = y + “ World” # String concat.
print x
print y
Monday, October 19, 2009
Enough to Understand the Code
• Assignment uses = and comparison uses ==.
• For numbers + - * / % are as expected.
• Special use of + for string concatenation.
• Special use of % for string formatting (as with printf in C)
• Logical operators are words (and, or, not)
not symbols
• The basic printing command is print.
• The first assignment to a variable creates it.
• Variable types don’t need to be declared.
• Python figures out the variable types on its own.
Monday, October 19, 2009
Basic Datatypes
• Integers (default for numbers)
z = 5 / 2 # Answer is 2, integer division.
• Floats
x = 3.456
• Strings
• Can use “” or ‘’ to specify.
“abc” ‘abc’ (Same thing.)
• Unmatched can occur within the string.
“matt’s”
• Use triple double-quotes for multi-line strings or strings than contain both ‘
and “ inside of them:
“““a‘b“c”””
Monday, October 19, 2009
Whitespace
Whitespace is meaningful in Python: especially
indentation and placement of newlines.
• Use a newline to end a line of code.
• Use  when must go to next line prematurely.
• No braces { } to mark blocks of code in Python…
Use consistent indentation instead.
• The first line with less indentation is outside of the block.
• The first line with more indentation starts a nested block
• Often a colon appears at the start of a new block.
(E.g. for function and class definitions.)
Monday, October 19, 2009
Comments
• Start comments with # – the rest of line is ignored.
• Can include a “documentation string” as the first line of any
new function or class that you define.
• The development environment, debugger, and other tools use
it: it’s good style to include one.
def my_function(x, y):
“““This is the docstring. This
function does blah blah blah.”””
# The code would go here...
Monday, October 19, 2009
Assignment
• Binding a variable in Python means setting a name to hold a
reference to some object.
• Assignment creates references, not copies
• Names in Python do not have an intrinsic type. Objects have
types.
• Python determines the type of the reference automatically based on the
data object assigned to it.
• You create a name the first time it appears on the left side of
an assignment expression:
! x = 3
• A reference is deleted via garbage collection after any names
bound to it have passed out of scope.
Monday, October 19, 2009
Accessing Non-Existent Names
• If you try to access a name before it’s been properly created
(by placing it on the left side of an assignment), you’ll get an
error.
>>> y
Traceback (most recent call last):
File "<pyshell#16>", line 1, in -toplevel-
y
NameError: name ‘y' is not defined
>>> y = 3
>>> y
3
Monday, October 19, 2009
Multiple Assignment
• You can also assign to multiple names at the same time.
>>> x, y = 2, 3
>>> x
2
>>> y
3
Monday, October 19, 2009
Naming Rules
• Names are case sensitive and cannot start with a number.
They can contain letters, numbers, and underscores.
bob Bob _bob _2_bob_ bob_2 BoB
• There are some reserved words:
and, assert, break, class, continue, def, del, elif,
else, except, exec, finally, for, from, global, if,
import, in, is, lambda, not, or, pass, print, raise,
return, try, while
Monday, October 19, 2009
Understanding Reference Semantics in
Python
Monday, October 19, 2009
Understanding Reference Semantics
• Assignment manipulates references
—x = y does not make a copy of the object y references
—x = y makes x reference the object y references
• Very useful; but beware!
• Example:
>>> a = [1, 2, 3] # a now references the list [1, 2, 3]
>>> b = a # b now references what a references
>>> a.append(4) # this changes the list a references
>>> print b # if we print what b references,
[1, 2, 3, 4] # SURPRISE! It has changed…
Why??
Monday, October 19, 2009
Understanding Reference Semantics II
• There is a lot going on when we type:
x = 3
• First, an integer 3 is created and stored in memory
• A name x is created
• An reference to the memory location storing the 3 is then
assigned to the name x
• So: When we say that the value of x is 3
• we mean that x now refers to the integer 3
Type: Integer
Data: 3
Name: x
Ref: <address1>
name list memory
Monday, October 19, 2009
Understanding Reference Semantics III
• The data 3 we created is of type integer. In Python, the
datatypes integer, float, and string (and tuple) are
“immutable.”
• This doesn’t mean we can’t change the value of x, i.e. change
what x refers to …
• For example, we could increment x:
>>> x = 3
>>> x = x + 1
>>> print x
4
Monday, October 19, 2009
Understanding Reference Semantics IV
• If we increment x, then what’s really happening is:
1. The reference of name x is looked up.
2. The value at that reference is retrieved.
Type: Integer
Data: 3Name: x
Ref: <address1>
>>> x = x + 1
Monday, October 19, 2009
Understanding Reference Semantics IV
• If we increment x, then what’s really happening is:
1. The reference of name x is looked up.
2. The value at that reference is retrieved.
3. The 3+1 calculation occurs, producing a new data element 4 which is
assigned to a fresh memory location with a new reference.
Type: Integer
Data: 3Name: x
Ref: <address1>
Type: Integer
Data: 4
>>> x = x + 1
Monday, October 19, 2009
Understanding Reference Semantics IV
• If we increment x, then what’s really happening is:
1. The reference of name x is looked up.
2. The value at that reference is retrieved.
3. The 3+1 calculation occurs, producing a new data element 4 which is
assigned to a fresh memory location with a new reference.
4. The name x is changed to point to this new reference.
Type: Integer
Data: 3Name: x
Ref: <address1>
Type: Integer
Data: 4
>>> x = x + 1
Monday, October 19, 2009
Understanding Reference Semantics IV
• If we increment x, then what’s really happening is:
1. The reference of name x is looked up.
2. The value at that reference is retrieved.
3. The 3+1 calculation occurs, producing a new data element 4 which is
assigned to a fresh memory location with a new reference.
4. The name x is changed to point to this new reference.
5. The old data 3 is garbage collected if no name still refers to it.
Name: x
Ref: <address1>
Type: Integer
Data: 4
>>> x = x + 1
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Type: Integer
Data: 3
Name: x
Ref: <address1>
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Type: Integer
Data: 3
Name: x
Ref: <address1>
Name: y
Ref: <address1>
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Type: Integer
Data: 3
Name: x
Ref: <address1>
Type: Integer
Data: 4
Name: y
Ref: <address1>
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Type: Integer
Data: 3
Name: x
Ref: <address1>
Type: Integer
Data: 4
Name: y
Ref: <address2>
Monday, October 19, 2009
Assignment 1
• So, for simple built-in datatypes (integers, floats, strings),
assignment behaves as you would expect:
>>> x = 3 # Creates 3, name x refers to 3
>>> y = x # Creates name y, refers to 3.
>>> y = 4 # Creates ref for 4. Changes y.
>>> print x # No effect on x, still ref 3.
3
Type: Integer
Data: 3
Name: x
Ref: <address1>
Type: Integer
Data: 4
Name: y
Ref: <address2>
Monday, October 19, 2009
Assignment 2
• For other data types (lists, dictionaries, user-defined types), assignment
works differently.
• These datatypes are “mutable.”
• When we change these data, we do it in place.
• We don’t copy them into a new memory address each time.
• If we type y=x and then modify y, both x and y are changed.
>>> x = 3 x = some mutable object
>>> y = x y = x
>>> y = 4 make a change to y
>>> print x look at x
3 x will be changed as well
immutable mutable
Monday, October 19, 2009
a
1 2 3
b
a
1 2 3
b
4
a = [1, 2, 3]
a.append(4)
b = a
a 1 2 3
Why? Changing a Shared List
Monday, October 19, 2009
Our surprising example surprising no more...
• So now, here’s our code:
>>> a = [1, 2, 3] # a now references the list [1, 2, 3]
>>> b = a # b now references what a references
>>> a.append(4) # this changes the list a references
>>> print b # if we print what b references,
[1, 2, 3, 4] # SURPRISE! It has changed…
Monday, October 19, 2009
Sequence types:
Tuples, Lists, and Strings
Monday, October 19, 2009
Sequence Types
1. Tuple
• A simple immutable ordered sequence of items
• Items can be of mixed types, including collection types
2. Strings
• Immutable
• Conceptually very much like a tuple
3. List
• Mutable ordered sequence of items of mixed types
Monday, October 19, 2009
Similar Syntax
• All three sequence types (tuples, strings, and lists)
share much of the same syntax and functionality.
• Key difference:
• Tuples and strings are immutable
• Lists are mutable
• The operations shown in this section can be
applied to all sequence types
• most examples will just show the operation
performed on one
Monday, October 19, 2009
Sequence Types 1
• Tuples are defined using parentheses (and commas).
>>> tu = (23, ‘abc’, 4.56, (2,3), ‘def’)
• Lists are defined using square brackets (and commas).
>>> li = [“abc”, 34, 4.34, 23]
• Strings are defined using quotes (“, ‘, or “““).
>>> st = “Hello World”
>>> st = ‘Hello World’
>>> st = “““This is a multi-line
string that uses triple quotes.”””
Monday, October 19, 2009
Sequence Types 2
• We can access individual members of a tuple, list, or string
using square bracket “array” notation.
• Note that all are 0 based…
>>> tu = (23, ‘abc’, 4.56, (2,3), ‘def’)
>>> tu[1] # Second item in the tuple.
‘abc’
>>> li = [“abc”, 34, 4.34, 23]
>>> li[1] # Second item in the list.
34
>>> st = “Hello World”
>>> st[1] # Second character in string.
‘e’
Monday, October 19, 2009
Positive and negative indices
>>> t = (23, ‘abc’, 4.56, (2,3), ‘def’)
Positive index: count from the left, starting with 0.
>>> t[1]
‘abc’
Negative lookup: count from right, starting with –1.
>>> t[-3]
4.56
Monday, October 19, 2009
Slicing: Return Copy of a Subset 1
>>> t = (23, ‘abc’, 4.56, (2,3), ‘def’)
Return a copy of the container with a subset of the original
members. Start copying at the first index, and stop copying
before the second index.
>>> t[1:4]
(‘abc’, 4.56, (2,3))
You can also use negative indices when slicing.
>>> t[1:-1]
(‘abc’, 4.56, (2,3))
Monday, October 19, 2009
Slicing: Return Copy of a Subset 2
>>> t = (23, ‘abc’, 4.56, (2,3), ‘def’)
Omit the first index to make a copy starting from the beginning
of the container.
>>> t[:2]
(23, ‘abc’)
Omit the second index to make a copy starting at the first index
and going to the end of the container.
>>> t[2:]
(4.56, (2,3), ‘def’)
Monday, October 19, 2009
Copying the Whole Sequence
To make a copy of an entire sequence, you can use [:].
>>> t[:]
(23, ‘abc’, 4.56, (2,3), ‘def’)
Note the difference between these two lines for mutable
sequences:
>>> list2 = list1 # 2 names refer to 1 ref
# Changing one affects both
>>> list2 = list1[:] # Two independent copies, two refs
Monday, October 19, 2009
The ‘in’ Operator
• Boolean test whether a value is inside a container:
>>> t = [1, 2, 4, 5]
>>> 3 in t
False
>>> 4 in t
True
>>> 4 not in t
False
• For strings, tests for substrings
>>> a = 'abcde'
>>> 'c' in a
True
>>> 'cd' in a
True
>>> 'ac' in a
False
• Be careful: the in keyword is also used in the syntax of
for loops and list comprehensions.
Monday, October 19, 2009
The + Operator
• The + operator produces a new tuple, list, or string whose
value is the concatenation of its arguments.
>>> (1, 2, 3) + (4, 5, 6)
(1, 2, 3, 4, 5, 6)
>>> [1, 2, 3] + [4, 5, 6]
[1, 2, 3, 4, 5, 6]
>>> “Hello” + “ ” + “World”
‘Hello World’
Monday, October 19, 2009
The * Operator
• The * operator produces a new tuple, list, or string that
“repeats” the original content.
>>> (1, 2, 3) * 3
(1, 2, 3, 1, 2, 3, 1, 2, 3)
>>> [1, 2, 3] * 3
[1, 2, 3, 1, 2, 3, 1, 2, 3]
>>> “Hello” * 3
‘HelloHelloHello’
Monday, October 19, 2009
Mutability:
Tuples vs. Lists
Monday, October 19, 2009
Tuples: Immutable
>>> t = (23, ‘abc’, 4.56, (2,3), ‘def’)
>>> t[2] = 3.14
Traceback (most recent call last):
File "<pyshell#75>", line 1, in -toplevel-
tu[2] = 3.14
TypeError: object doesn't support item assignment
You can’t change a tuple.
You can make a fresh tuple and assign its reference to a previously used
name.
>>> t = (23, ‘abc’, 3.14, (2,3), ‘def’)
Monday, October 19, 2009
Lists: Mutable
>>> li = [‘abc’, 23, 4.34, 23]
>>> li[1] = 45
>>> li
[‘abc’, 45, 4.34, 23]
• We can change lists in place.
• Name li still points to the same memory reference when we’re
done.
• The mutability of lists means that they aren’t as fast as tuples.
Monday, October 19, 2009
Operations on Lists Only 1
>>> li = [1, 11, 3, 4, 5]
>>> li.append(‘a’) # Our first exposure to method syntax
>>> li
[1, 11, 3, 4, 5, ‘a’]
>>> li.insert(2, ‘i’)
>>>li
[1, 11, ‘i’, 3, 4, 5, ‘a’]
Monday, October 19, 2009
The extend method vs the + operator.
• + creates a fresh list (with a new memory reference)
• extend operates on list li in place.
>>> li.extend([9, 8, 7])
>>>li
[1, 2, ‘i’, 3, 4, 5, ‘a’, 9, 8, 7]
Confusing:
• Extend takes a list as an argument.
• Append takes a singleton as an argument.
>>> li.append([10, 11, 12])
>>> li
[1, 2, ‘i’, 3, 4, 5, ‘a’, 9, 8, 7, [10, 11, 12]]
Monday, October 19, 2009
Operations on Lists Only 3
>>> li = [‘a’, ‘b’, ‘c’, ‘b’]
>>> li.index(‘b’) # index of first occurrence
1
>>> li.count(‘b’) # number of occurrences
2
>>> li.remove(‘b’) # remove first occurrence
>>> li
[‘a’, ‘c’, ‘b’]
Monday, October 19, 2009
Operations on Lists Only 4
>>> li = [5, 2, 6, 8]
>>> li.reverse() # reverse the list *in place*
>>> li
[8, 6, 2, 5]
>>> li.sort() # sort the list *in place*
>>> li
[2, 5, 6, 8]
>>> li.sort(some_function)
# sort in place using user-defined comparison
Monday, October 19, 2009
Tuples vs. Lists
• Lists slower but more powerful than tuples.
• Lists can be modified, and they have lots of handy operations we can
perform on them.
• Tuples are immutable and have fewer features.
• To convert between tuples and lists use the list() and tuple()
functions:
li = list(tu)
tu = tuple(li)
Monday, October 19, 2009
Dictionaries
63
Monday, October 19, 2009
Dictionaries: A Mapping type
• Dictionaries store a mapping between a set of keys
and a set of values.
• Keys can be any immutable type.
• Values can be any type
• A single dictionary can store values of different types
• You can define, modify, view, lookup, and delete
the key-value pairs in the dictionary.
Monday, October 19, 2009
Using dictionaries
>>> d = {‘user’:‘bozo’, ‘pswd’:1234}
>>> d[‘user’]
‘bozo’
>>> d[‘pswd’]
1234
>>> d[‘bozo’]
Traceback (innermost last):
File ‘<interactive input>’ line 1, in ?
KeyError: bozo
>>> d = {‘user’:‘bozo’, ‘pswd’:1234}
>>> d[‘user’] = ‘clown’
>>> d
{‘user’:‘clown’, ‘pswd’:1234}
>>> d[‘id’] = 45
>>> d
{‘user’:‘clown’, ‘id’:45, ‘pswd’:1234}
>>> d = {‘user’:‘bozo’, ‘p’:1234, ‘i’:34}
>>> del d[‘user’] # Remove one.
>>> d
{‘p’:1234, ‘i’:34}
>>> d.clear() # Remove all.
>>> d
{}
>>> d = {‘user’:‘bozo’, ‘p’:1234, ‘i’:34}
>>> d.keys() # List of keys.
[‘user’, ‘p’, ‘i’]
>>> d.values() # List of values.
[‘bozo’, 1234, 34]
>>> d.items() # List of item tuples.
[(‘user’,‘bozo’), (‘p’,1234), (‘i’,34)]
Monday, October 19, 2009
Functions
Monday, October 19, 2009
Functions
• def creates a function and assigns it a name
• return sends a result back to the caller
• Arguments are passed by assignment
• Arguments and return types are not declared
def <name>(arg1, arg2, ..., argN):
! <statements>
! return <value>
def times(x,y):
! return x*y
Monday, October 19, 2009
Passing Arguments to Functions
• Arguments are passed by assignment
• Passed arguments are assigned to local names
• Assignment to argument names don't affect the
caller
• Changing a mutable argument may affect the caller
def changer (x,y):
! x = 2! ! ! # changes local value of x only
! y[0] = 'hi'!! # changes shared object
Monday, October 19, 2009
Optional Arguments
• Can define defaults for arguments that need not be
passed
def func(a, b, c=10, d=100):
! print a, b, c, d
>>> func(1,2)
1 2 10 100
>>> func(1,2,3,4)
1,2,3,4
Monday, October 19, 2009
Gotchas
• All functions in Python have a return value
• even if no return line inside the code.
• Functions without a return return the special value
None.
• There is no function overloading in Python.
• Two different functions can’t have the same name, even if they
have different arguments.
• Functions can be used as any other data type.
They can be:
• Arguments to function
• Return values of functions
• Assigned to variables
• Parts of tuples, lists, etc
Monday, October 19, 2009
Control of Flow
71
Monday, October 19, 2009
Examples
if x == 3:
print “X equals 3.”
elif x == 2:
print “X equals 2.”
else:
print “X equals something else.”
print “This is outside the ‘if’.”
x = 3
while x < 10:
if x > 7:
x += 2
continue
x = x + 1
print “Still in the loop.”
if x == 8:
break
print “Outside of the loop.”
assert(number_of_players < 5)
for x in range(10):
if x > 7:
x += 2
continue
x = x + 1
print “Still in the loop.”
if x == 8:
break
print “Outside of the loop.”
Monday, October 19, 2009
Modules
Monday, October 19, 2009
Why Use Modules?
• Code reuse
• Routines can be called multiple times within a program
• Routines can be used from multiple programs
• Namespace partitioning
• Group data together with functions used for that data
• Implementing shared services or data
• Can provide global data structure that is accessed by multiple
subprograms
Monday, October 19, 2009
Modules
• Modules are functions and variables defined in
separate files
• Items are imported using from or import
from module import function
function()
import module
module.function()
• Modules are namespaces
• Can be used to organize variable names, i.e.
atom.position = atom.position - molecule.position
Monday, October 19, 2009
Classes and Objects
Monday, October 19, 2009
What is an Object?
• A software item that contains variables and
methods
• Object Oriented Design focuses on
• Encapsulation:
—dividing the code into a public interface, and a private implementation
of that interface
• Polymorphism:
—the ability to overload standard operators so that they have appropriate
behavior based on their context
• Inheritance:
—the ability to create subclasses that contain specializations of their
parents
Monday, October 19, 2009
Example
class atom(object):
! def __init__(self,atno,x,y,z):
! ! self.atno = atno
! ! self.position = (x,y,z)
! def symbol(self): # a class method
! ! return Atno_to_Symbol[atno]
! def __repr__(self): # overloads printing
! ! return '%d %10.4f %10.4f %10.4f' %
! ! ! (self.atno, self.position[0],
! ! ! self.position[1],self.position[2])
>>> at = atom(6,0.0,1.0,2.0)
>>> print at
6 0.0000 1.0000 2.0000
>>> at.symbol()
'C'
Monday, October 19, 2009
Atom Class
• Overloaded the default constructor
• Defined class variables (atno,position) that are
persistent and local to the atom object
• Good way to manage shared memory:
• instead of passing long lists of arguments, encapsulate some of
this data into an object, and pass the object.
• much cleaner programs result
• Overloaded the print operator
• We now want to use the atom class to build
molecules...
Monday, October 19, 2009
Molecule Class
class molecule:
! def __init__(self,name='Generic'):
! ! self.name = name
! ! self.atomlist = []
! def addatom(self,atom):
! ! self.atomlist.append(atom)
! def __repr__(self):
! ! str = 'This is a molecule named %sn' % self.name
! ! str = str+'It has %d atomsn' % len(self.atomlist)
! ! for atom in self.atomlist:
! ! ! str = str + `atom` + 'n'
! ! return str
Monday, October 19, 2009
Using Molecule Class
>>> mol = molecule('Water')
>>> at = atom(8,0.,0.,0.)
>>> mol.addatom(at)
>>> mol.addatom(atom(1,0.,0.,1.))
>>> mol.addatom(atom(1,0.,1.,0.))
>>> print mol
This is a molecule named Water
It has 3 atoms
8 0.000 0.000 0.000
1 0.000 0.000 1.000
1 0.000 1.000 0.000
• Note that the print function calls the atoms print
function
• Code reuse: only have to type the code that prints an atom
once; this means that if you change the atom specification, you
only have one place to update.
Monday, October 19, 2009
Inheritance
class qm_molecule(molecule):
def addbasis(self):
self.basis = []
for atom in self.atomlist:
self.basis = add_bf(atom,self.basis)
• __init__, __repr__, and __addatom__ are taken
from the parent class (molecule)
• Added a new function addbasis() to add a basis set
• Another example of code reuse
• Basic functions don't have to be retyped, just inherited
• Less to rewrite when specifications change
Monday, October 19, 2009
Overloading
class qm_molecule(molecule):
def __repr__(self):
! ! str = 'QM Rules!n'
! ! for atom in self.atomlist:
! ! ! str = str + `atom` + 'n'
! ! return str
• Now we only inherit __init__ and addatom from the
parent
• We define a new version of __repr__ specially for
QM
Monday, October 19, 2009
Adding to Parent Functions
• Sometimes you want to extend, rather than
replace, the parent functions.
class qm_molecule(molecule):
! def __init__(self,name="Generic",basis="6-31G**"):
! ! self.basis = basis
! ! super(qm_molecule, self).__init__(name)
Monday, October 19, 2009
Public and Private Data
• In Python anything with two leading underscores
is private
__a, __my_variable
• Anything with one leading underscore is semi-
private, and you should feel guilty accessing this
data directly.
_b
• Sometimes useful as an intermediate step to making data
private
Monday, October 19, 2009
The Extra Stuff...
86
Monday, October 19, 2009
File I/O, Strings, Exceptions...
fileptr = open(‘filename’)
somestring = fileptr.read()
for line in fileptr:
print line
fileptr.close()
>>> a = 1
>>> b = 2.4
>>> c = 'Tom'
>>> '%s has %d coins worth a total of $%.02f' % (c, a, b)
'Tom has 1 coins worth a total of $2.40'
>>> try:
... 1 / 0
... except:
... print('That was silly!')
... finally:
... print('This gets executed no matter what')
...
That was silly!
This gets executed no matter what
Monday, October 19, 2009

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Python

  • 1. Introduction to Python Heavily based on presentations by Matt Huenerfauth (Penn State) Guido van Rossum (Google) Richard P. Muller (Caltech) ... Monday, October 19, 2009
  • 2. • Open source general-purpose language. • Object Oriented, Procedural, Functional • Easy to interface with C/ObjC/Java/Fortran • Easy-ish to interface with C++ (via SWIG) • Great interactive environment • Downloads: http://www.python.org • Documentation: http://www.python.org/doc/ • Free book: http://www.diveintopython.org Python Monday, October 19, 2009
  • 3. 2.5.x / 2.6.x / 3.x ??? • “Current” version is 2.6.x • “Mainstream” version is 2.5.x • The new kid on the block is 3.x You probably want 2.5.x unless you are starting from scratch. Then maybe 3.x Monday, October 19, 2009
  • 4. Technical Issues Installing & Running Python Monday, October 19, 2009
  • 5. Binaries • Python comes pre-installed with Mac OS X and Linux. • Windows binaries from http://python.org/ • You might not have to do anything! Monday, October 19, 2009
  • 6. The Python Interpreter • Interactive interface to Python % python Python 2.5 (r25:51908, May 25 2007, 16:14:04) [GCC 4.1.2 20061115 (prerelease) (SUSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> • Python interpreter evaluates inputs: >>> 3*(7+2) 27 • Python prompts with ‘>>>’. • To exit Python: • CTRL-D Monday, October 19, 2009
  • 7. Running Programs on UNIX % python filename.py You could make the *.py file executable and add the following #!/usr/bin/env python to the top to make it runnable. Monday, October 19, 2009
  • 8. Batteries Included • Large collection of proven modules included in the standard distribution. http://docs.python.org/modindex.html Monday, October 19, 2009
  • 9. numpy • Offers Matlab-ish capabilities within Python • Fast array operations • 2D arrays, multi-D arrays, linear algebra etc. • Downloads: http://numpy.scipy.org/ • Tutorial: http://www.scipy.org/ Tentative_NumPy_Tutorial Monday, October 19, 2009
  • 10. matplotlib • High quality plotting library. • Downloads: http://matplotlib.sourceforge.net/ #!/usr/bin/env python import numpy as np import matplotlib.mlab as mlab import matplotlib.pyplot as plt mu, sigma = 100, 15 x = mu + sigma*np.random.randn(10000) # the histogram of the data n, bins, patches = plt.hist(x, 50, normed=1, facecolor='green', alpha=0.75) # add a 'best fit' line y = mlab.normpdf( bins, mu, sigma) l = plt.plot(bins, y, 'r--', linewidth=1) plt.xlabel('Smarts') plt.ylabel('Probability') plt.title(r'$mathrm{Histogram of IQ:} mu=100, sigma=15$') plt.axis([40, 160, 0, 0.03]) plt.grid(True) plt.show() Monday, October 19, 2009
  • 11. PyFITS • FITS I/O made simple: • Downloads: http://www.stsci.edu/resources/ software_hardware/pyfits >>> import pyfits >>> hdulist = pyfits.open(’input.fits’) >>> hdulist.info() Filename: test1.fits No. Name Type Cards Dimensions Format 0 PRIMARY PrimaryHDU 220 () Int16 1 SCI ImageHDU 61 (800, 800) Float32 2 SCI ImageHDU 61 (800, 800) Float32 3 SCI ImageHDU 61 (800, 800) Float32 4 SCI ImageHDU 61 (800, 800) Float32 >>> hdulist[0].header[’targname’] ’NGC121’ >>> scidata = hdulist[1].data >>> scidata.shape (800, 800) >>> scidata.dtype.name ’float32’ >>> scidata[30:40,10:20] = scidata[1,4] = 999 Monday, October 19, 2009
  • 12. pyds9 / python-sao • Interaction with DS9 • Display Python 1-D and 2-D arrays in DS9 • Display FITS files in DS9 • Downloads: Ask Eric Mandel :-) • Downloads: http://code.google.com/p/python-sao/ Monday, October 19, 2009
  • 13. Wrappers for Astronomical Packages • CasaPy (Casa) • PYGILDAS (GILDAS) • ParselTongue (AIPS) • PyRAF (IRAF) • PyMIDAS (MIDAS) • PyIMSL (IMSL) Monday, October 19, 2009
  • 14. Custom Distributions • Python(x,y): http://www.pythonxy.com/ • Python(x,y) is a free scientific and engineering development software for numerical computations, data analysis and data visualization • Sage: http://www.sagemath.org/ • Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. Monday, October 19, 2009
  • 15. Extra Astronomy Links • iPython (better shell, distributed computing): http://ipython.scipy.org/ • SciPy (collection of science tools): http:// www.scipy.org/ • Python Astronomy Modules: http:// astlib.sourceforge.net/ • Python Astronomer Wiki: http://macsingularity.org/ astrowiki/tiki-index.php?page=python • AstroPy: http://www.astro.washington.edu/users/ rowen/AstroPy.html • Python for Astronomers: http://www.iac.es/ sieinvens/siepedia/pmwiki.php? n=HOWTOs.EmpezandoPython Monday, October 19, 2009
  • 17. A Code Sample x = 34 - 23 # A comment. y = “Hello” # Another one. z = 3.45 if z == 3.45 or y == “Hello”: x = x + 1 y = y + “ World” # String concat. print x print y Monday, October 19, 2009
  • 18. Enough to Understand the Code • Assignment uses = and comparison uses ==. • For numbers + - * / % are as expected. • Special use of + for string concatenation. • Special use of % for string formatting (as with printf in C) • Logical operators are words (and, or, not) not symbols • The basic printing command is print. • The first assignment to a variable creates it. • Variable types don’t need to be declared. • Python figures out the variable types on its own. Monday, October 19, 2009
  • 19. Basic Datatypes • Integers (default for numbers) z = 5 / 2 # Answer is 2, integer division. • Floats x = 3.456 • Strings • Can use “” or ‘’ to specify. “abc” ‘abc’ (Same thing.) • Unmatched can occur within the string. “matt’s” • Use triple double-quotes for multi-line strings or strings than contain both ‘ and “ inside of them: “““a‘b“c””” Monday, October 19, 2009
  • 20. Whitespace Whitespace is meaningful in Python: especially indentation and placement of newlines. • Use a newline to end a line of code. • Use when must go to next line prematurely. • No braces { } to mark blocks of code in Python… Use consistent indentation instead. • The first line with less indentation is outside of the block. • The first line with more indentation starts a nested block • Often a colon appears at the start of a new block. (E.g. for function and class definitions.) Monday, October 19, 2009
  • 21. Comments • Start comments with # – the rest of line is ignored. • Can include a “documentation string” as the first line of any new function or class that you define. • The development environment, debugger, and other tools use it: it’s good style to include one. def my_function(x, y): “““This is the docstring. This function does blah blah blah.””” # The code would go here... Monday, October 19, 2009
  • 22. Assignment • Binding a variable in Python means setting a name to hold a reference to some object. • Assignment creates references, not copies • Names in Python do not have an intrinsic type. Objects have types. • Python determines the type of the reference automatically based on the data object assigned to it. • You create a name the first time it appears on the left side of an assignment expression: ! x = 3 • A reference is deleted via garbage collection after any names bound to it have passed out of scope. Monday, October 19, 2009
  • 23. Accessing Non-Existent Names • If you try to access a name before it’s been properly created (by placing it on the left side of an assignment), you’ll get an error. >>> y Traceback (most recent call last): File "<pyshell#16>", line 1, in -toplevel- y NameError: name ‘y' is not defined >>> y = 3 >>> y 3 Monday, October 19, 2009
  • 24. Multiple Assignment • You can also assign to multiple names at the same time. >>> x, y = 2, 3 >>> x 2 >>> y 3 Monday, October 19, 2009
  • 25. Naming Rules • Names are case sensitive and cannot start with a number. They can contain letters, numbers, and underscores. bob Bob _bob _2_bob_ bob_2 BoB • There are some reserved words: and, assert, break, class, continue, def, del, elif, else, except, exec, finally, for, from, global, if, import, in, is, lambda, not, or, pass, print, raise, return, try, while Monday, October 19, 2009
  • 26. Understanding Reference Semantics in Python Monday, October 19, 2009
  • 27. Understanding Reference Semantics • Assignment manipulates references —x = y does not make a copy of the object y references —x = y makes x reference the object y references • Very useful; but beware! • Example: >>> a = [1, 2, 3] # a now references the list [1, 2, 3] >>> b = a # b now references what a references >>> a.append(4) # this changes the list a references >>> print b # if we print what b references, [1, 2, 3, 4] # SURPRISE! It has changed… Why?? Monday, October 19, 2009
  • 28. Understanding Reference Semantics II • There is a lot going on when we type: x = 3 • First, an integer 3 is created and stored in memory • A name x is created • An reference to the memory location storing the 3 is then assigned to the name x • So: When we say that the value of x is 3 • we mean that x now refers to the integer 3 Type: Integer Data: 3 Name: x Ref: <address1> name list memory Monday, October 19, 2009
  • 29. Understanding Reference Semantics III • The data 3 we created is of type integer. In Python, the datatypes integer, float, and string (and tuple) are “immutable.” • This doesn’t mean we can’t change the value of x, i.e. change what x refers to … • For example, we could increment x: >>> x = 3 >>> x = x + 1 >>> print x 4 Monday, October 19, 2009
  • 30. Understanding Reference Semantics IV • If we increment x, then what’s really happening is: 1. The reference of name x is looked up. 2. The value at that reference is retrieved. Type: Integer Data: 3Name: x Ref: <address1> >>> x = x + 1 Monday, October 19, 2009
  • 31. Understanding Reference Semantics IV • If we increment x, then what’s really happening is: 1. The reference of name x is looked up. 2. The value at that reference is retrieved. 3. The 3+1 calculation occurs, producing a new data element 4 which is assigned to a fresh memory location with a new reference. Type: Integer Data: 3Name: x Ref: <address1> Type: Integer Data: 4 >>> x = x + 1 Monday, October 19, 2009
  • 32. Understanding Reference Semantics IV • If we increment x, then what’s really happening is: 1. The reference of name x is looked up. 2. The value at that reference is retrieved. 3. The 3+1 calculation occurs, producing a new data element 4 which is assigned to a fresh memory location with a new reference. 4. The name x is changed to point to this new reference. Type: Integer Data: 3Name: x Ref: <address1> Type: Integer Data: 4 >>> x = x + 1 Monday, October 19, 2009
  • 33. Understanding Reference Semantics IV • If we increment x, then what’s really happening is: 1. The reference of name x is looked up. 2. The value at that reference is retrieved. 3. The 3+1 calculation occurs, producing a new data element 4 which is assigned to a fresh memory location with a new reference. 4. The name x is changed to point to this new reference. 5. The old data 3 is garbage collected if no name still refers to it. Name: x Ref: <address1> Type: Integer Data: 4 >>> x = x + 1 Monday, October 19, 2009
  • 34. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Monday, October 19, 2009
  • 35. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Type: Integer Data: 3 Name: x Ref: <address1> Monday, October 19, 2009
  • 36. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Type: Integer Data: 3 Name: x Ref: <address1> Name: y Ref: <address1> Monday, October 19, 2009
  • 37. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Type: Integer Data: 3 Name: x Ref: <address1> Type: Integer Data: 4 Name: y Ref: <address1> Monday, October 19, 2009
  • 38. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Type: Integer Data: 3 Name: x Ref: <address1> Type: Integer Data: 4 Name: y Ref: <address2> Monday, October 19, 2009
  • 39. Assignment 1 • So, for simple built-in datatypes (integers, floats, strings), assignment behaves as you would expect: >>> x = 3 # Creates 3, name x refers to 3 >>> y = x # Creates name y, refers to 3. >>> y = 4 # Creates ref for 4. Changes y. >>> print x # No effect on x, still ref 3. 3 Type: Integer Data: 3 Name: x Ref: <address1> Type: Integer Data: 4 Name: y Ref: <address2> Monday, October 19, 2009
  • 40. Assignment 2 • For other data types (lists, dictionaries, user-defined types), assignment works differently. • These datatypes are “mutable.” • When we change these data, we do it in place. • We don’t copy them into a new memory address each time. • If we type y=x and then modify y, both x and y are changed. >>> x = 3 x = some mutable object >>> y = x y = x >>> y = 4 make a change to y >>> print x look at x 3 x will be changed as well immutable mutable Monday, October 19, 2009
  • 41. a 1 2 3 b a 1 2 3 b 4 a = [1, 2, 3] a.append(4) b = a a 1 2 3 Why? Changing a Shared List Monday, October 19, 2009
  • 42. Our surprising example surprising no more... • So now, here’s our code: >>> a = [1, 2, 3] # a now references the list [1, 2, 3] >>> b = a # b now references what a references >>> a.append(4) # this changes the list a references >>> print b # if we print what b references, [1, 2, 3, 4] # SURPRISE! It has changed… Monday, October 19, 2009
  • 43. Sequence types: Tuples, Lists, and Strings Monday, October 19, 2009
  • 44. Sequence Types 1. Tuple • A simple immutable ordered sequence of items • Items can be of mixed types, including collection types 2. Strings • Immutable • Conceptually very much like a tuple 3. List • Mutable ordered sequence of items of mixed types Monday, October 19, 2009
  • 45. Similar Syntax • All three sequence types (tuples, strings, and lists) share much of the same syntax and functionality. • Key difference: • Tuples and strings are immutable • Lists are mutable • The operations shown in this section can be applied to all sequence types • most examples will just show the operation performed on one Monday, October 19, 2009
  • 46. Sequence Types 1 • Tuples are defined using parentheses (and commas). >>> tu = (23, ‘abc’, 4.56, (2,3), ‘def’) • Lists are defined using square brackets (and commas). >>> li = [“abc”, 34, 4.34, 23] • Strings are defined using quotes (“, ‘, or “““). >>> st = “Hello World” >>> st = ‘Hello World’ >>> st = “““This is a multi-line string that uses triple quotes.””” Monday, October 19, 2009
  • 47. Sequence Types 2 • We can access individual members of a tuple, list, or string using square bracket “array” notation. • Note that all are 0 based… >>> tu = (23, ‘abc’, 4.56, (2,3), ‘def’) >>> tu[1] # Second item in the tuple. ‘abc’ >>> li = [“abc”, 34, 4.34, 23] >>> li[1] # Second item in the list. 34 >>> st = “Hello World” >>> st[1] # Second character in string. ‘e’ Monday, October 19, 2009
  • 48. Positive and negative indices >>> t = (23, ‘abc’, 4.56, (2,3), ‘def’) Positive index: count from the left, starting with 0. >>> t[1] ‘abc’ Negative lookup: count from right, starting with –1. >>> t[-3] 4.56 Monday, October 19, 2009
  • 49. Slicing: Return Copy of a Subset 1 >>> t = (23, ‘abc’, 4.56, (2,3), ‘def’) Return a copy of the container with a subset of the original members. Start copying at the first index, and stop copying before the second index. >>> t[1:4] (‘abc’, 4.56, (2,3)) You can also use negative indices when slicing. >>> t[1:-1] (‘abc’, 4.56, (2,3)) Monday, October 19, 2009
  • 50. Slicing: Return Copy of a Subset 2 >>> t = (23, ‘abc’, 4.56, (2,3), ‘def’) Omit the first index to make a copy starting from the beginning of the container. >>> t[:2] (23, ‘abc’) Omit the second index to make a copy starting at the first index and going to the end of the container. >>> t[2:] (4.56, (2,3), ‘def’) Monday, October 19, 2009
  • 51. Copying the Whole Sequence To make a copy of an entire sequence, you can use [:]. >>> t[:] (23, ‘abc’, 4.56, (2,3), ‘def’) Note the difference between these two lines for mutable sequences: >>> list2 = list1 # 2 names refer to 1 ref # Changing one affects both >>> list2 = list1[:] # Two independent copies, two refs Monday, October 19, 2009
  • 52. The ‘in’ Operator • Boolean test whether a value is inside a container: >>> t = [1, 2, 4, 5] >>> 3 in t False >>> 4 in t True >>> 4 not in t False • For strings, tests for substrings >>> a = 'abcde' >>> 'c' in a True >>> 'cd' in a True >>> 'ac' in a False • Be careful: the in keyword is also used in the syntax of for loops and list comprehensions. Monday, October 19, 2009
  • 53. The + Operator • The + operator produces a new tuple, list, or string whose value is the concatenation of its arguments. >>> (1, 2, 3) + (4, 5, 6) (1, 2, 3, 4, 5, 6) >>> [1, 2, 3] + [4, 5, 6] [1, 2, 3, 4, 5, 6] >>> “Hello” + “ ” + “World” ‘Hello World’ Monday, October 19, 2009
  • 54. The * Operator • The * operator produces a new tuple, list, or string that “repeats” the original content. >>> (1, 2, 3) * 3 (1, 2, 3, 1, 2, 3, 1, 2, 3) >>> [1, 2, 3] * 3 [1, 2, 3, 1, 2, 3, 1, 2, 3] >>> “Hello” * 3 ‘HelloHelloHello’ Monday, October 19, 2009
  • 56. Tuples: Immutable >>> t = (23, ‘abc’, 4.56, (2,3), ‘def’) >>> t[2] = 3.14 Traceback (most recent call last): File "<pyshell#75>", line 1, in -toplevel- tu[2] = 3.14 TypeError: object doesn't support item assignment You can’t change a tuple. You can make a fresh tuple and assign its reference to a previously used name. >>> t = (23, ‘abc’, 3.14, (2,3), ‘def’) Monday, October 19, 2009
  • 57. Lists: Mutable >>> li = [‘abc’, 23, 4.34, 23] >>> li[1] = 45 >>> li [‘abc’, 45, 4.34, 23] • We can change lists in place. • Name li still points to the same memory reference when we’re done. • The mutability of lists means that they aren’t as fast as tuples. Monday, October 19, 2009
  • 58. Operations on Lists Only 1 >>> li = [1, 11, 3, 4, 5] >>> li.append(‘a’) # Our first exposure to method syntax >>> li [1, 11, 3, 4, 5, ‘a’] >>> li.insert(2, ‘i’) >>>li [1, 11, ‘i’, 3, 4, 5, ‘a’] Monday, October 19, 2009
  • 59. The extend method vs the + operator. • + creates a fresh list (with a new memory reference) • extend operates on list li in place. >>> li.extend([9, 8, 7]) >>>li [1, 2, ‘i’, 3, 4, 5, ‘a’, 9, 8, 7] Confusing: • Extend takes a list as an argument. • Append takes a singleton as an argument. >>> li.append([10, 11, 12]) >>> li [1, 2, ‘i’, 3, 4, 5, ‘a’, 9, 8, 7, [10, 11, 12]] Monday, October 19, 2009
  • 60. Operations on Lists Only 3 >>> li = [‘a’, ‘b’, ‘c’, ‘b’] >>> li.index(‘b’) # index of first occurrence 1 >>> li.count(‘b’) # number of occurrences 2 >>> li.remove(‘b’) # remove first occurrence >>> li [‘a’, ‘c’, ‘b’] Monday, October 19, 2009
  • 61. Operations on Lists Only 4 >>> li = [5, 2, 6, 8] >>> li.reverse() # reverse the list *in place* >>> li [8, 6, 2, 5] >>> li.sort() # sort the list *in place* >>> li [2, 5, 6, 8] >>> li.sort(some_function) # sort in place using user-defined comparison Monday, October 19, 2009
  • 62. Tuples vs. Lists • Lists slower but more powerful than tuples. • Lists can be modified, and they have lots of handy operations we can perform on them. • Tuples are immutable and have fewer features. • To convert between tuples and lists use the list() and tuple() functions: li = list(tu) tu = tuple(li) Monday, October 19, 2009
  • 64. Dictionaries: A Mapping type • Dictionaries store a mapping between a set of keys and a set of values. • Keys can be any immutable type. • Values can be any type • A single dictionary can store values of different types • You can define, modify, view, lookup, and delete the key-value pairs in the dictionary. Monday, October 19, 2009
  • 65. Using dictionaries >>> d = {‘user’:‘bozo’, ‘pswd’:1234} >>> d[‘user’] ‘bozo’ >>> d[‘pswd’] 1234 >>> d[‘bozo’] Traceback (innermost last): File ‘<interactive input>’ line 1, in ? KeyError: bozo >>> d = {‘user’:‘bozo’, ‘pswd’:1234} >>> d[‘user’] = ‘clown’ >>> d {‘user’:‘clown’, ‘pswd’:1234} >>> d[‘id’] = 45 >>> d {‘user’:‘clown’, ‘id’:45, ‘pswd’:1234} >>> d = {‘user’:‘bozo’, ‘p’:1234, ‘i’:34} >>> del d[‘user’] # Remove one. >>> d {‘p’:1234, ‘i’:34} >>> d.clear() # Remove all. >>> d {} >>> d = {‘user’:‘bozo’, ‘p’:1234, ‘i’:34} >>> d.keys() # List of keys. [‘user’, ‘p’, ‘i’] >>> d.values() # List of values. [‘bozo’, 1234, 34] >>> d.items() # List of item tuples. [(‘user’,‘bozo’), (‘p’,1234), (‘i’,34)] Monday, October 19, 2009
  • 67. Functions • def creates a function and assigns it a name • return sends a result back to the caller • Arguments are passed by assignment • Arguments and return types are not declared def <name>(arg1, arg2, ..., argN): ! <statements> ! return <value> def times(x,y): ! return x*y Monday, October 19, 2009
  • 68. Passing Arguments to Functions • Arguments are passed by assignment • Passed arguments are assigned to local names • Assignment to argument names don't affect the caller • Changing a mutable argument may affect the caller def changer (x,y): ! x = 2! ! ! # changes local value of x only ! y[0] = 'hi'!! # changes shared object Monday, October 19, 2009
  • 69. Optional Arguments • Can define defaults for arguments that need not be passed def func(a, b, c=10, d=100): ! print a, b, c, d >>> func(1,2) 1 2 10 100 >>> func(1,2,3,4) 1,2,3,4 Monday, October 19, 2009
  • 70. Gotchas • All functions in Python have a return value • even if no return line inside the code. • Functions without a return return the special value None. • There is no function overloading in Python. • Two different functions can’t have the same name, even if they have different arguments. • Functions can be used as any other data type. They can be: • Arguments to function • Return values of functions • Assigned to variables • Parts of tuples, lists, etc Monday, October 19, 2009
  • 71. Control of Flow 71 Monday, October 19, 2009
  • 72. Examples if x == 3: print “X equals 3.” elif x == 2: print “X equals 2.” else: print “X equals something else.” print “This is outside the ‘if’.” x = 3 while x < 10: if x > 7: x += 2 continue x = x + 1 print “Still in the loop.” if x == 8: break print “Outside of the loop.” assert(number_of_players < 5) for x in range(10): if x > 7: x += 2 continue x = x + 1 print “Still in the loop.” if x == 8: break print “Outside of the loop.” Monday, October 19, 2009
  • 74. Why Use Modules? • Code reuse • Routines can be called multiple times within a program • Routines can be used from multiple programs • Namespace partitioning • Group data together with functions used for that data • Implementing shared services or data • Can provide global data structure that is accessed by multiple subprograms Monday, October 19, 2009
  • 75. Modules • Modules are functions and variables defined in separate files • Items are imported using from or import from module import function function() import module module.function() • Modules are namespaces • Can be used to organize variable names, i.e. atom.position = atom.position - molecule.position Monday, October 19, 2009
  • 76. Classes and Objects Monday, October 19, 2009
  • 77. What is an Object? • A software item that contains variables and methods • Object Oriented Design focuses on • Encapsulation: —dividing the code into a public interface, and a private implementation of that interface • Polymorphism: —the ability to overload standard operators so that they have appropriate behavior based on their context • Inheritance: —the ability to create subclasses that contain specializations of their parents Monday, October 19, 2009
  • 78. Example class atom(object): ! def __init__(self,atno,x,y,z): ! ! self.atno = atno ! ! self.position = (x,y,z) ! def symbol(self): # a class method ! ! return Atno_to_Symbol[atno] ! def __repr__(self): # overloads printing ! ! return '%d %10.4f %10.4f %10.4f' % ! ! ! (self.atno, self.position[0], ! ! ! self.position[1],self.position[2]) >>> at = atom(6,0.0,1.0,2.0) >>> print at 6 0.0000 1.0000 2.0000 >>> at.symbol() 'C' Monday, October 19, 2009
  • 79. Atom Class • Overloaded the default constructor • Defined class variables (atno,position) that are persistent and local to the atom object • Good way to manage shared memory: • instead of passing long lists of arguments, encapsulate some of this data into an object, and pass the object. • much cleaner programs result • Overloaded the print operator • We now want to use the atom class to build molecules... Monday, October 19, 2009
  • 80. Molecule Class class molecule: ! def __init__(self,name='Generic'): ! ! self.name = name ! ! self.atomlist = [] ! def addatom(self,atom): ! ! self.atomlist.append(atom) ! def __repr__(self): ! ! str = 'This is a molecule named %sn' % self.name ! ! str = str+'It has %d atomsn' % len(self.atomlist) ! ! for atom in self.atomlist: ! ! ! str = str + `atom` + 'n' ! ! return str Monday, October 19, 2009
  • 81. Using Molecule Class >>> mol = molecule('Water') >>> at = atom(8,0.,0.,0.) >>> mol.addatom(at) >>> mol.addatom(atom(1,0.,0.,1.)) >>> mol.addatom(atom(1,0.,1.,0.)) >>> print mol This is a molecule named Water It has 3 atoms 8 0.000 0.000 0.000 1 0.000 0.000 1.000 1 0.000 1.000 0.000 • Note that the print function calls the atoms print function • Code reuse: only have to type the code that prints an atom once; this means that if you change the atom specification, you only have one place to update. Monday, October 19, 2009
  • 82. Inheritance class qm_molecule(molecule): def addbasis(self): self.basis = [] for atom in self.atomlist: self.basis = add_bf(atom,self.basis) • __init__, __repr__, and __addatom__ are taken from the parent class (molecule) • Added a new function addbasis() to add a basis set • Another example of code reuse • Basic functions don't have to be retyped, just inherited • Less to rewrite when specifications change Monday, October 19, 2009
  • 83. Overloading class qm_molecule(molecule): def __repr__(self): ! ! str = 'QM Rules!n' ! ! for atom in self.atomlist: ! ! ! str = str + `atom` + 'n' ! ! return str • Now we only inherit __init__ and addatom from the parent • We define a new version of __repr__ specially for QM Monday, October 19, 2009
  • 84. Adding to Parent Functions • Sometimes you want to extend, rather than replace, the parent functions. class qm_molecule(molecule): ! def __init__(self,name="Generic",basis="6-31G**"): ! ! self.basis = basis ! ! super(qm_molecule, self).__init__(name) Monday, October 19, 2009
  • 85. Public and Private Data • In Python anything with two leading underscores is private __a, __my_variable • Anything with one leading underscore is semi- private, and you should feel guilty accessing this data directly. _b • Sometimes useful as an intermediate step to making data private Monday, October 19, 2009
  • 86. The Extra Stuff... 86 Monday, October 19, 2009
  • 87. File I/O, Strings, Exceptions... fileptr = open(‘filename’) somestring = fileptr.read() for line in fileptr: print line fileptr.close() >>> a = 1 >>> b = 2.4 >>> c = 'Tom' >>> '%s has %d coins worth a total of $%.02f' % (c, a, b) 'Tom has 1 coins worth a total of $2.40' >>> try: ... 1 / 0 ... except: ... print('That was silly!') ... finally: ... print('This gets executed no matter what') ... That was silly! This gets executed no matter what Monday, October 19, 2009