1. Python Crash Course Intro, scripts
Bachelors
V1.0 dd
Hour 5

2. Why Python? Modern scripting languages: Ease of use
Python, Perl, Ruby, IDL, Matlab, …
High-level
Interactive interpreter
Ease of use
Speed of development
Encourages scripting, rather than one-off analysis
Permanent record
Repeatability

3. Why not python?
If you want fastest possible performance
Highly parallel code
Need low-level control

4. Why Python is great
Designed to be easy to learn and use – clear syntax
Well documented
Powerful, flexible, fully-featured programming language
‘Batteries included’
Comprehensive scientific tools
Fast
Interpreter, introspection
Runs everywhere
Completely free
You already have it

5. Why learn Python? Less stress Get more science done
Widely used and growing popularity
Throughout academia and industry
NASA, AstraZeneca, Google, Industrial Light & Magic, Philips,…
Web services, engineering, science, air traffic control, quantitative finance, games, education, data management, …
Python programmers in demand
Easy introduction to general programming concepts
Why not?
Existing code for your project in another language, but still…

6. Python in optical astronomy
STScI PyRAF (IRAF) + additional Python only routines
ESO PyMIDAS (MIDAS)
STScI PyFITS (access to FITS files)
Astro-WISE (widefield imaging system)
Pyephem - solar system ephemeris
LSST will use Python/C+ …

7. Python in radio astronomy
CasaPy (Casa) - AIPS++, default system for EVLA and ALMA data analysis.
ParselTongue - call AIPS tasks from Python
PYGILDAS (GILDAS) - IRAM data analysis software ported to Python
BoA (Bolometer Analysis Package) for LABOCA on APEX and other bolometers
APECS (APEX control software)
KAT-7 CMS is in Python
Presto - pulsar search and analysis suite; most recent routines in Pytho

8. Computational physics
Python in physics
CERN
PyROOT (research engine for high energy physics)
PyMad (simulate particle accelerators)
Computational physics
ALPS (Algorithms and Libraries for Physics Simulations) …

9. Introduction to language - start
Linux
At command line: python myscript.py
With script: chmod, #!/usr/bin/env python
At python prompt: execfile(’somefile.py’)
At ipython prompt: %run somefile.py

10. Introduction to language - start
Windows
Files that have the extension .py are known as Python scripts. In Windows and Mac OS, these files will appear to be "clickable", i.e. will appear to be files that you can open by clicking them with the mouse. It is not recommended that you open these files by clicking on them. Why? Because quite often the result can be unpredictable. Instead, start IDLE and open Python scripts inside an IDLE session.

11. Introduction to language - startup
pczaal2: python
Python (default, Nov , 14:26:24)
[GCC (Red Hat )] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 2+2 4
>>> # This is a comment
>>> # and a comment on the same line as code
4.0
>>> (50-5*6)/4 5
>>> width = 20 # assignment, no type declaration
>>> height = 5*9
>>> width * height
900
>>> x = y = z = 0 # zero x, y and z
>>> y
>>> n
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'n' is not defined

12. Introduction to language - scripts
2+2
# This is a comment
# and a comment on the same line as code
(50-5*6)/4
width = 20 # assignment, no type declaration
height = 5*9
width * height
x = y = z = 0 # zero x, y and z y
• Can write in a text editor and copy and paste into interpreter
Can save and execute from command line:
$ python test.py
Can save and use interactively in future sessions (import)

13. Python script
Start an editor and type some python commands. Save your file as: myfirst.py
On the Unix command line type: python myfirst.py
We want to be able to start the program by only typing its name. To make it executable use chmod u+x myfirst.py or chmod +x myfirst.py if you want to allow everybody on the system to execute your program
Run it with: ./myfirst.py The dot slash part is necessary to force execution if your current directory is not included in the settings for your path!
If you type command echo $path on the command line, then a list is displayed with directories with the paths to these directories included. If you type the name of an executable file on the command line then all the directories in the list are visited to look for the wanted executable. If the name is found, it will be executed. If not, then you get a warning.
Now we get an error message. Remember that we created a script and the first line of a script should contain the so called shebang line which defines the path to the application that has to execute the script
Add in your script a shebang line as the first line: #!/usr/bin/env python
Run it with: ./myfirst.py It should give you the right answer.

14. Introduction to language - numbers
>>> 13
>>> 7
>>> 10 * 3 30
>>> 10 / 3 3
>>> 10 // 3
>>> 10 % 3 1
>>> 10**3
1000
>>> * 5 # *,/ then +,- 25
>>> (10 + 3) * 5 65
>>> -1**2 # -(1**2) -1
>>>
13.0
>>>
7.0
>>> 10.0 * 3
30.0
>>> 10.0 / 3
>>> 10.0 // 3
3.0
>>> 10.0 % 3.0
1.0
>>> 10.0**3
1000.0
>>>
>>> 4.2 * 3.14

15. Introduction to language - numbers
Integer division is weird!
Integer division truncates
Floating point division produces floating point numbers
>>> 10 / 2 5
>>> 9 / 2 4
>>> 99 / 100
>>> 10.0 / 2.0
5.0
>>> 99.0 / 100.0
0.99
Mixing Integer and Floating
When you perform an operation where one operand is an integer and the other operand is a floating point the result is a floating point
The integer is converted to a floating point before the operation
>>> 99 / 100
>>> 99 / 100.0
0.99
>>> 99.0 / 100
>>> * 3 /
-2.5

16. Arithmetic Operators
Assume variable a holds 10 and variable b holds 20 then:
Operator
Description
Example +
Addition - Adds values on either side of the operator
a + b will give 30 -
Subtraction - Subtracts right hand operand from left hand operand
a - b will give -10 *
Multiplication - Multiplies values on either side of the operator
a * b will give 200 /
Division - Divides left hand operand by right hand operand
b / a will give 2 %
Modulus - Divides left hand operand by right hand operand and returns remainder
b % a will give 0 **
Exponent - Performs exponential (power) calculation on operators
a**b will give 10 to the power 20 //
Floor Division - The division of operands where the result is the quotient in which the digits after the decimal point are removed.
9//2 is equal to 4 and 9.0//2.0 is equal to 4.0

17. Arithmetic Operators Precedence
Highest precedence rule to lowest precedence rule
Parenthesis are always respected
Exponentiation (raise to a power)
Multiplication, Division, and Remainder
Addition and Subtraction
Left to right
Parenthesis
Power
Multiplication
Addition
Left to Right
1 + 2 ** 3 / 4 * 5
1 + 8 / 4 * 5
1 + 2 * 5
1 + 10 11

18. Numerical types Integers: Long integers: Complex numbers: Floats:
>>> 2
>>> 0
>>> -4711
>>> 07, 022 # Octal tuple
>>> 0x9, 0xa, 0XF # Hexadecimal tuple
>>> # Expression
>>> 0xa - 2
>>> 23 ** (2+3) # Power
>>> 7 / 2, 7 / -2 # Int division
>>> from __future__ import division
>>> 7/2
Long integers:
>>> 2**1000
>>> 2L, 3l
>>>
>>> float(2), float(2**1000)
>>> int(2.3), int(-2.3)
>>> int(2**1000), long(2), str(2)
Complex numbers:
>>> 2.+3j, 2-3J # complex literals
>>> j # will not work
>>> 1J # but this will
>>> complex(1,2)
>>> # Watch operator precedence:
>>> 1+1j*2, (1+1j)*2
>>> (2.+3j).real, (2+3j).imag
>>> type(2-3j)
Floats:
>>> 2.3
>>> -4.
>>> 0.1, .1
>>> 2.99E10, e-27, -1e10
>>>
>>>
>>> 7./2., 7./2, 7/2.

19. Introduction to language - variables
>>> x = 2 # Assign variable
>>> x # Display
>>> x + 3 # Use variable
>>> y = x + 3 # New variable
>>> x = x + 1 # Assign new value
>>> x += 1 # Shorthand; but no x++
>>> x = j # Change type
>>> x **= 2j
>>> xy, Xy = 2, 3 # Case sensitive
>>> 9x = 2 # Not allowed, must begin w. letter
>>> x9 = 2 # ok
>>> _x = 2 # ok, but special
>>> if = 2 # must not be keyword
Reserved keywords:
and del from not while
as elif global or with
assert else if pass yield
break except import print
class exec in raise
continue finally is return
def for lambda try
None
as with
Some tricks:
>>> x, y = 2, 3
>>> x, y = y, x # No temporary variables needed
>>> x = y = z = 1

20. Introduction to language - type
Python knows what “type” everything is
Some operations are prohibited
You cannot “add 1” to a string
We can ask Python what type something is by using the type() function.
>>> eee = 'hello ' + 'there‘
>>> eee = eee + 1
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: cannot concatenate 'str' and 'int' objects
>>> type(eee)
<type 'str'>
>>> type('hello')
>>> type(1)
<type 'int'>

21. Assignment Operators
Assume variable a holds 10 and variable b holds 20 then:
Operator
Description
Example =
Simple assignment operator, Assigns values from right side operands to left side operand
c = a + b will assigne value of a + b into c +=
Add AND assignment operator, It adds right operand to the left operand and assign the result to left operand
c += a is equivalent to c = c + a -=
Subtract AND assignment operator, It subtracts right operand from the left operand and assign the result to left operand
c -= a is equivalent to c = c - a *=
Multiply AND assignment operator, It multiplies right operand with the left operand and assign the result to left operand
c *= a is equivalent to c = c * a /=
Divide AND assignment operator, It divides left operand with the right operand and assign the result to left operand
c /= a is equivalent to c = c / a %=
Modulus AND assignment operator, It takes modulus using two operands and assign the result to left operand
c %= a is equivalent to c = c % a
**=
Exponent AND assignment operator, Performs exponential (power) calculation on operators and assign value to the left operand
c **= a is equivalent to c = c ** a
//=
Floor Dividion and assigns a value, Performs floor division on operators and assign value to the left operand
c //= a is equivalent to c = c // a

22. A variable is a memory location used to store a value (0.6)
Assignment Operators
A variable is a memory location used to store a value (0.6) x
0.6
0.6
0.6
x = * x * ( x )
0.4
Right side is an expression. Once expression is evaluated, the result is placed in (assigned to) X..
0.93

23. Assignment Operators x 0.93 x = 3.9 * x * ( 1 - x ) 0.6 0.93
A variable is a memory location used to store a value. The value stored in a variable can be updated by replacing the old value (0.6) with a new value (0.93). x
x = * x * ( x )
Right side is an expression. Once expression is evaluated, the result is placed in (assigned to) the variable on the left side (i.e. x).
0.93

24. Python environment PYTHONSTARTUP PYTHONPATH
Personal startup file defined in startup file:
setenv PYTHONSTARTUP /home/personal/mystartup.py
all code in startup file will be executed upon start
PYTHONPATH
tells the Python interpreter where to locate the module files you import into a program
setenv PYTHONPATH
“/usr/lib64/python2.7/site-packages:/home/personal/python/site-packages”
$ls /usr/lib64/python2.7/site-packages
abrt_exception_handler.py
abrt_exception_handler.pyc
abrt_exception_handler.pyo
abrt.pth
acutilmodule.so*
audit.py
audit.pyc
audit.pyo
_audit.so*
auparse.so*
Avogadro.so*
basemap py2.7.egg-info
_blueman.so*
Brlapi py2.7.egg-info
brlapi.so*
cairo/
...

25. ipython
What is it
interactive shell for the Python programming language that offers enhanced introspection, additional shell syntax, tab completion and rich history.
Why
default interactive Python shell can sometimes feel to basic
gives you all that you get in the basic interpreter but with a lot extra (line numbers, advanced editing, more functions, help functions etc)
Python (default, Nov , 14:26:24)
Type "copyright", "credits" or "license" for more information.
IPython An enhanced Interactive Python.
? > Introduction and overview of IPython's features.
%quickref -> Quick reference.
help > Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
From .ipython starup env
In [1]:

26. Python environment PYTHONSTARTUP Profile
Personal startup file defined in startup file:
setenv PYTHONSTARTUP /home/personal/mystartup.py
all code in startup file will be executed upon start
Profile
~/.ipython directory structure
all scripts in .ipython/profile_default/startup are executed upon start
new profile can be created using:
$ ipython profile create profile_name
and used:
$ ipython --profile=profile_name
.ipython/:
db/
history
profile_default/
.ipython/db:
shadowhist/
shadowhist_idx
.ipython/db/shadowhist: 05 21 2e 61 7a 90 95 b4 f3
.ipython/profile_default:
history.sqlite
log/
pid/
security/
startup/
.ipython/profile_default/db:
rootmodules
.ipython/profile_default/log:
.ipython/profile_default/pid:
.ipython/profile_default/security:
.ipython/profile_default/startup:
README

27. ipython TAB completion
especially for attributes, is a convenient way to explore the structure of any object you’re dealing with
besides Python objects and keywords, tab completion also works on file and directory names
In [4]: x.__
x.__abs__ x.__hash__ x.__reduce__
x.__add__ x.__init__ x.__reduce_ex__
x.__class__ x.__int__ x.__repr__
x.__coerce__ x.__le__ x.__rfloordiv__
x.__delattr__ x.__long__ x.__rmod__
x.__div__ x.__lt__ x.__rmul__
x.__divmod__ x.__mod__ x.__rpow__
x.__doc__ x.__mul__ x.__rsub__
x.__eq__ x.__ne__ x.__rtruediv__
x.__float__ x.__neg__ x.__setattr__
x.__floordiv__ x.__new__ x.__setformat__
x.__format__ x.__nonzero__ x.__sizeof__
x.__ge__ x.__pos__ x.__str__
x.__getattribute__ x.__pow__ x.__sub__
x.__getformat__ x.__radd__ x.__subclasshook__
x.__getnewargs__ x.__rdiv__ x.__truediv__
x.__gt__ x.__rdivmod__ x.__trunc__
In [1]: from sys import std
stderr stdin stdout
In [1]: from urllib2 import url
url2pathname urlopen urlparse

28. ipython Magic built in commands %quickref
IPython -- An enhanced Interactive Python - Quick Reference Card
================================================================
obj?, obj?? : Get help, or more help for object (also works as
?obj, ??obj).
?foo.*abc* : List names in 'foo' containing 'abc' in them.
%magic : Information about IPython's 'magic' % functions.
Magic functions are prefixed by % or %%, and typically take their arguments
without parentheses, quotes or even commas for convenience. Line magics take a
single % and cell magics are prefixed with two %%.
Example magic function calls:
%alias d ls -F : 'd' is now an alias for 'ls -F'
alias d ls -F : Works if 'alias' not a python name
alist = %alias : Get list of aliases to 'alist'
cd /usr/share : Obvious. cd -<tab> to choose from visited dirs.
%cd?? : See help AND source for magic %cd
%timeit x= : time the 'x=10' statement with high precision.
%%timeit x=2**100
x** : time 'x*100' with a setup of 'x=2**100'; setup code is not
counted. This is an example of a cell magic.
Magic
built in commands
%quickref
In [57]: lsmagic
Available line magics:
%alias %alias_magic %autocall %autoindent %automagic %bookmark %cd %colors %config
%cpaste %debug %dhist %dirs %doctest_mode %ed %edit %env %gui %hist %history
%install_default_config %install_ext %install_profiles %killbgscripts %load %load_ext
%loadpy %logoff %logon %logstart %logstate %logstop %lsmagic %macro %magic
%notebook %page %paste %pastebin %pdb %pdef %pdoc %pfile %pinfo %pinfo2 %popd
%pprint %precision %profile %prun %psearch %psource %pushd %pwd %pycat %pylab
%quickref %recall %rehashx %reload_ext %rep %rerun %reset %reset_selective %run
%save %sc %store %sx %system %tb %time %timeit %unalias %unload_ext %who %who_ls
%whos %xdel %xmode
Available cell magics:
%%! %%bash %%capture %%file %%perl %%prun %%ruby %%script %%sh %%sx %%system
%%timeit
Automagic is ON, % prefix IS NOT needed for line magics.

29. ipython Input caching system Macros
input is saved and can be retrieved as variables
_i, previous, _ii, next previous, _iii …etc.
Macros
macros are great for executing the same code over and over
associate a name with a section of Python code so the code can be run later by referring to the name
In [1]: a=2
In [2]: b=3
In [3]: c=a+b
In [4]: print c 5
In [5]: %macro xxx 1-2 4
Macro `xxx` created. To execute, type its name (without quotes).
=== Macro contents: ===
a=2
b=3
print c
In [6]: xxx
In [1]: a=2
In [2]: b=3
In [3]: c=a+b
In [4]: _ii
Out[4]: u'b=3'
In [5]: _ih[1]
Out[5]: u'a=2‘
In [6]: In[3]
Out[6]: u'c=a+b‘
In [7]: print c
Out[6]: 5
In [8]: exec _ih[7]
Out[8]: 5

30. ipython Useful help commands %reset resets the interactive environment
%hist allows you to see any part of your input history
%hist -g somestring
Search (‘grep’) through your history by typing
In [55]: hist -g math
19: import math
55: hist -g math
%paste use text that you have in the clipboard, for example if you have copied code with Ctrl+C. The command cleans up certain characters and tries to find out how the code should be formatted.
%edit The %edit command (and its alias %ed) will invoke the editor set in your environment as EDITOR.
%who This function list objects, functions, etc. that have been added in the current namespace, as well as modules that have been imported.
In [50]: who
Interactive namespace is empty.

31. ipython
Shell access
Any input line beginning with a ! character is passed verbatim (minus the !) to the underlying operating system.
You can capture the output into a Python list, e.g.: files = !ls.
In [2]: !ping
PING ( ): 56 data bytes
64 bytes from : icmp_seq=0 ttl=49 time=6.096 ms
64 bytes from : icmp_seq=1 ttl=49 time=5.963 ms ^C

32. ipython
Aliases
All of your $PATH has been loaded as IPython aliases, so you should be able to type any normal system command and have it executed.
In [9]: %alias
Total number of aliases: 12
Out[9]:
[('cat', 'cat'),
('cp', 'cp -i'),
('ldir', 'ls -F -o --color %l | grep /$'),
('lf', 'ls -F -o --color %l | grep ^-'),
('lk', 'ls -F -o --color %l | grep ^l'),
('ll', 'ls -F -o --color'),
('ls', 'ls -F --color'),
('lx', 'ls -F -o --color %l | grep ^-..x'),
('mkdir', 'mkdir'),
('mv', 'mv -i'),
('rm', 'rm -i'),
('rmdir', 'rmdir')]

33. ipython the four most helpful commands
? Introduction and overview of IPython’s features.
%quickref Quick reference.
help Python’s own help system.
object? Details about ‘object’, use ‘object??’ for extra details.

34. Assignment Operators
End