Python for Scientists

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1. The Python Environment

Starting Python

If the interpreter is not in your PATHs

Using the interpreter

Trying a few commands

The help() function

Running a Python script

Python scripts on UNIX

Python editors and IDEs

2. Getting Started

Using variables

Keywors

Built-in functions

Strings

Single-quoted string literals

Triple-quoted string literals

Raw string literals

Unicode literals

String operators and expressions

Converting among types

Writing to the screen

String formatting

Legacy string formatting

Command line parameters

Reading from the keyboard

3. Flow Control

What’s with the w hite space?

if and elif

Conditional expressions

Relational and Boolean operators

while loops

Alternate ways to exit as loop

4. Lists and Tuples

About Sequences

Lists

Tuples

Indexing and slicing

Iterating through a sequence

Functions for all sequences

Using enumerate()

Operators and keywords for sequences

The xrange() function

Nested sequences

List comprehensions

Generator expressions

5. Working with Files

Text file I/O

Opening a text file

The with block

Reading a text file

Writing a text file

About flow control

“Binary” (raw, or non -delimited) data

6. Dictionaries and Sets

About dictionaries

When to use dictionaries

Creating dictionaries

Getting dictionary values

Iterating through a dictionary

Reading file data into a dictionary

Counting with dictionaries

About sets

Creating sets

Working with sets

7. Functions

Defining a function

Function parameters

Global variables

Variable scope

Returning values

8. Exception Handling

Syntax errors

Exceptions

Handling exceptions with try

Handling multiple exceptions

Handling generic exceptions

Ignoring exceptions

Using else

Cleaning up with finally

Re-raising exceptions

Raising a new exception

The standard exception hierarchy

9. OS Services

The os module

Environment variables

Launching external processes

Paths, directories, and filenames

Walking directory trees

Dates and times

Sending email

10. Pythonic Idioms

The Zen of Python

Common Python idioms

Packing and unpacking

Lambda functions

List comprehensions

Generators vs. iterators

Generator expressions

String tricks

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11. Modules and Packages

What is a module?

The import statement

Where did the .pyc file come from?

Module search path

Zipped libraries

Creating Modules

Packages

Module aliases

When the batteries aren’t included

12. Classes

Defining classes

Instance objects

Instance attributes

Methods

__init__

Properties

Class data

Inheritance

Multiple Inheritance

Base classes

Special methods

Pseudo-private variables

Static methods

13. Developer Tools

Program development

Comments

pylint

Customizing pylint

Unit testing

The unittest module

Creating a test class

Establishing success or failure

Startup and Cleanup

Running the tests

The Python debugger

Starting debug mode

Stepping through a program

Setting breakpoints

Debugging command reference

Benchmarking

14. XML and JSON

About XML

Normal approaches to XML

Which module to use?

Getting started with ElementTree

How ElementTree works

Creating a new XML Document

Parsing an XML Document

Navigating the XML Document

Using XPath

Advanced XPath

15. iPython

About iPython

Features of iPython

Starting iPython

Tab completion

Magic commands

Benchmarking

External commands

Enhanced help

Notebooks

16. numpy

Python’s scientific stack

numpy overview

Creating arrays

Creating ranges

Working with arrays

Shapes

Slicing and indexing

Indexing with Booleans

Stacking

Iterating

Tricks with arrays

Matrices

Data types

numpy functions

17. scipy

About scipy

Polynomials

Vectorizing functions

Subpackages

fftpack

integrate

interpolate

io

linalg

ndimage

odr

optimize

signal

sparse

spatial

special

stats

19. pandas

About pandas

Pandas architecture

Series

DataFrames

Data Alignment

Index

Objects

Basic Indexing

Broadcasting

Removing entries

Time series

Reading Data

20. matplotlib

About matplotlib

matplotlib architecture

matplotlib Terminology

matplotlib keeps state

What else can you do?

21. Python Imaging Library

The PIL

Supported image file types

The Image class

Reading and writing

Creating thumbnails

Coordinate system

Cropping and pasting

Rotating, resizing, and flipping Enhancing

Getting help

Weave

18. A Tour of scipy subpackages

cluster

constants