UNIX intro

1
UNIX intro

• Well use the command line windows are for
  wimps.
• The unix shell
• This is what lets you send commands to the
  system.
• Generally bash or csh.
• Do printenv SHELL to find out yours.
• Some differences at the lt 10 level.
• bash is more professional.

Unix and linux look very similar to the user so
I will use the terms interchangeably.
2
The UNIX file structure

• The prompt
• ims_at_server2 - this is what UNIX shows you when
  it is ready to receive a new command.
• Directory, file and path
• Directory names often have /s. Eg /home/ims
• File names dont. Eg clever_code.py
• File names may have a dot then a 2- to 4-letter
  suffix which gives you a hint about the file
  type.
• It is not a good idea to include spaces in Unix
  file or directory names. Use an underscore
  instead.
• The full name for a file includes the directory
  where it is located, and is called a path name.
  Eg
• /home/ims/clever_code.py

3
UNIX shell commands

• pwd
• present working directory - tells you where you
  are in the file system.
• cd ltnamegt
• change pwd to directory name.
• mkdir ltnamegt
• makes a new directory.
• rmdir ltnamegt
• removes (deletes) the named directory.

4
UNIX shell commands

• ls
• list the files in the pwd.
• cp ltnamegt ltdestinationgt
• copies the named file.
• mv ltnamegt ltdestinationgt
• equals cp followed by rm. But mv can also move
  directories.
• rm ltnamegt
• removes (deletes) the named file.

Note that each of the last three can erase files
so Back up your work!
5
UNIX shell commands

• ssh ltuser namegt_at_ltcomputer namegt
• How to log in (securely!) to another computer.
• exit, logout
• How to log out (pretty obvious).
• scp, rsync
• ways to transfer files from one computer to
  another.
• man ltname of commandgt
• gives you a manual, ie a lot of documentation
  (sometimes more than you really wanted!) for the
  named command.

6
Other interesting UNIX topics

• Environment variables (eg SHELL, PYTHONPATH)
• The file named .bashrc (note the dot).
• Try more .bashrc
• Wild cards - and ?.
• Try
• touch fred
• touch bert
• touch mary
• ls e
• Should list all files which have names matching
  the pattern anything, then an e, then anything.
  This will get fred and bert but not mary.

7
File types
ASCII
Binary
8
FITS Flexible Image Transport System
This will be the default data format for this
course. See http//fits.gsfc.nasa.gov/fits_standa
rd.html
Cards
2880-byte blocks
1
80
1
Header
2
3
4
Header

36
KEYWORD VALUE / UNIT COMMENT
etc
Unused cards of last header block filled with
spaces (ASCII 32)
Binary table
Data
Data
or
Image
Data
Data
etc
Unused bytes of last data block filled with
spaces (ASCII 32)
9
Text editors

• vi
• non-windows, but abstruse commands.
• pico
• non-windows, fairly user-friendly.
• emacs, xemacs
• the editor of choice for many, but I dont like
  it.
• gedit
• my favourite.
• IDE for python coding maybe ok

Whichever you choose Back up your work!!

10
Python
11
Python

• is a scripting language, which roughly
  translated means
• python code doesnt have to be compiled
• its pretty slow.
• is an object-oriented (OO) language. Some OO
  code can look pretty wacky. But relax! you wont
  have to write any.
• !/usr/bin/env python huh..?

probably not, anyway.
12
Python

• Python insists on block indenting. This means
  if you start any block, like an if statement, or
  a for loop, you have to indent within the block.
  The relaxation of this indenting is the way
  python recognizes the end of the block.
• You dont have to run python as a script, you can
  also use it interactively. Type python at your
  normal unix prompt and youll get a new
  sergeant prompt gtgtgt. You can enter your python
  statements then line by line. Type control-d to
  get out when youre finished.

13
Large chunks of python

• The script you run on the command line, which
  consists of a single ascii file, is the main
  program. Obviously you need a main to get
  anything done. But if your program is long, you
  may want to disperse some your code into
  subsidiary files, which are called from the main
  program. These secondary files are known as
  modules. They are called via the import statement.

14
How python finds your modules

• Suppose you have some neat code in a module named
  huge_brane.py which you keep in a directory named
  /home/me/src. You want a separate program
  slogger.py to be able to make use of this module.
  At the command line, do
• Within your code slogger.py include the line
• Note that you leave off the .py bit.

export PYTHONPATH/home/me/src
from huge_brane import
15
Smaller chunks of python

• Within a module the largest chunks are functions.
  The syntax of a typical function is
• Note the and the indenting typical for any
  block in python. Relax the indenting for the 1st
  statement after the end of the function.
• You call the function from the main code like

def myfunction(foo, bar, bert) some stuff
here return some value optional
newvar myfunction(foo, bar, bert)
16
Python variables

• Python scalar data types
• real
• integer
• string
• boolean (True or False)
• object (ie something with internal structure)
• BUT the python philosophy is to ignore this
  distinction as far as possible. Variables are not
  declared as with other languages. Python sets
  (or resets, if necessary) the type of a variable
  to fit whatever data you try to load into it.

17
Python variables

• Ways to arrange several objects
• A single one is called a scalar.
• A list elements numbered, data types can be
  different.
• A tuple similar to a list but written with round
  brackets rather than square.
• A dictionary elements accessed by a key, data
  types can be different curly brackets.
• These groupings are themselves objects.

Python numbering starts from zero.
18
Python operations

• They are mostly pretty standard.
• Change in place can be a trap. Eg, type
  python at the prompt, then try
• This should print 4. Now try
• Youll get 999,2,3. Cf mutability

gtgtgta4 gtgtgtba gtgtgta3 gtgtgtprint b
gtgtgtaa1,2,3 gtgtgtbbaa gtgtgtaa0999 gtgtgtprint bb
19
Trouble with change in place
20
OO

• OO programming is the business of constructing
  objects. This is done via the class statement.
  You probably wont need to use this. However,
  objects themselves are inescapable in python if
  you dont make them, someone else will.
• In fact, almost everything in python is an object.

21
OO

• Objects have two extra features
• Attributes, which have names separated from the
  object name by a dot, eg fred.height is an
  attribute named height which belongs to object
  type of which fred is an example.
• Methods these are attributes which are
  functions. Like any function they can accept
  arguments, and must still be written with empty
  brackets even if there are no arguments. Eg the
  append() method of lists and the copy() method of
  dictionaries.

22
Python control structures
if lttest1gt do some stuff elif lttest2gt you
can have 0 or more of these do some other
stuff else you can have 0 or 1 of these
third lot of stuff

• There is NO goto statement in python. This is a
  feature.
• Anything after a is a comment.

while lttestgt do loop stuff break
optional dumps out and avoids the else.
continue like goto while. else optional -
processing after normal loop exit. stuff to
do after normal loop exit for ltitemgt in ltlistgt
etc
23
Python ins and outs

• Were going to mostly read our data from FITS
  files, using a module called pyfits.
• http//www.stsci.edu/resources/software_hardware/p
  yfits
• Well crunch up the data using a module called
  numpy.
• http//numpy.scipy.org/
• For graphical output well use module ppgplot, (2
  ps) which is a (fairly crude) wrapper to a
  package called PGPLOT.
• http//efault.net/npat/hacks/ppgplot/
• http//www.astro.caltech.edu/tjp/pgplot/