Python Scripting for Computational Science

Transcription

1 Hans Petter Langtangen Python Scripting for Computational Science Third Edition With 62 Figures 43 Springer

2 Table of Contents 1 Introduction Scripting versus Traditional Programming Why Scripting is Useful in Computational Science Classification of Programming Languages Productive Pairs of Programming Languages Gluing Existing Applications Scripting Yields Shorter Code Efficiency Type-Specification (Declaration) of Variables Flexible Function Interfaces Interactive Computing Creating Code at Run Time Nested Heterogeneous Data Structures GUI Programming Mixed Language Programming When to Choose a Dynamically Typed Language Why Python? Script or Program? Preparations for Working with This Book Getting Started with Python Scripting A Scientific Hello World Script Executing Python Scripts Dissection of the Scientific Hello World Script Working with Files and Data Problem Specification The Complete Code Dissection Working with Files in Memory Array Computing Interactive Computing and Debugging Efficiency Measurements Exercises Gluing Stand-Alone Applications The Simulation Code Using Gnuplot to Visualize Curves Functionality of the Script The Complete Code Dissection Exercises Conducting Numerical Experiments Wrapping a Loop Around Another Script... 59

3 XII Table of Contents Generating an HTML Report Making Animations Varying Any Parameter File Format Conversion A Simple Read/Write Script Storing Data in Dictionaries and Lists Making a Module with Functions Exercises Basic Python Introductory Topics Recommended Python Documentation Control Statements Running Applications File Reading and Writing Output Formatting Variables of Different Types Boolean Types The None Variable Numbers and Numerical Expressions Lists and Tuples Dictionaries Splitting and Joining Text String Operations Text Processing The Basics of a Python Class Copy and Assignment Determining a Variable's Type Exercises Functions Keyword Arguments Doc Strings Variable Number of Arguments Call by Reference Treatment of Input and Output Arguments Function Objects Working with Files and Directories Listing Files in a Directory Testing File Types Removing Files and Directories Copying and Renaming Files Splitting Pathnames Creating and Moving to Directories Traversing Directory Trees Exercises

4 Table of Contents XIII 4 Numerical Computing in Python A Quick NumPy Primer Creating Arrays Array Indexing Loops over Arrays Array Computations More Array Functionality Type Testing Matrix Objects Exercises Vectorized Algorithms From Scalar to Array in Function Arguments Slicing Exercises More Advanced Array Computing Random Numbers Linear Algebra Plotting Example: Curve Fitting Arrays an Structured Grids File I/O with NumPy Arrays Functionality in the Numpyutils Module Exercises Other Tools for Numerical Computations The ScientificPython Package The SciPy Package The Python-Matlab Interface Symbolic Computing in Python Some Useful Python Modules Combining Python with Fortran, C, and C About Mixed Language Programming Applications of Mixed Language Programming Calling C from Python Automatic Generation of Wrapper Code Scientific Hello World Examples Combining Python and Fortran Combining Python and C Combining Python and C++ Functions Combining Python and C++ Classes Exercises A Simple Computational Steering Example Modified Time Loop for Repeated Simulations Creating a Python Interface The Steering Python Script Equipping the Steering Script with a GUI Scripting Interfaces to Large Libraries

5 XIV Table of Contents 6 Introduction to GUI Programming Scientific Hello World GUI Introductory Topics The First Python/Tkinter Encounter Binding Events Changing the Layout The Final Scientific Hello World GUI An Alternative to Tkinter Variables About the Pack Command An Introduction to the Grid Geometry Manager Implementing a GUI as a Class A Simple Graphical Function Evaluator Exercises Adding GUIs to Scripts A Simulation and Visualization Script with a GUI Improving the Layout Exercises A List of Common Widget Operations Frame Label Button Text Entry Balloon Help Option Menu Slider Check Button Making a Simple Megawidget Menu Bar List Data Listbox Radio Button Combo Box Message Box User-Defined Dialogs Color-Picker Dialogs File Selection Dialogs Toplevel Some Other Types of Widgets Adapting Widgets to the User's Resize Actions Customizing Fonts and Colors Widget Overview Exercises

6 `Fable of Contents XV 7 Web Interfaces and CGI Programming Introductory CGI Scripts Web Forms and CGI Scripts Generating Forms in CGI Scripts Debugging CGI Scripts A General Shell Script Wrapper for CGI Scripts Security Issues Adding Web Interfaces to Scripts A Class for Form Parameters Calling Other Programs Running Simulations Getting a CGI Script to Work Using Web Applications from Scripts Exercises Advanced Python Miscellaneous Topics Parsing Command-Line Arguments Platform-Dependent Operations Run-Time Generation of Code Exercises Regular Expressions and Text Processing Motivation Special Characters Regular Expressions for Real Numbers Using Groups to Extract Parts of a Text Extracting Interval Limits Extracting Multiple Matches Splitting Text Pattern-Matching Modifiers Substitution and Backreferences Example: Swapping Arguments in Function Calls A General Substitution Script Debugging Regular Expressions Exercises Tools for Handling Data in Files Writing and Reading Python Data Structures Pickling Objects Shelving Objects Writing and Reading Zip and Tar Archive Files Downloading Internet Files Binary Input/Output Exercises A Database for NumPy Arrays The Structure of the Database Pickling Formatted ASCII Storage

7 XVI Table of Contents Shelving... Comparing the Various Techniques Scripts Involving Local and Remote Hosts Secure Shell Commands Distributed Simulation and Visualization Client/Server Programming Threads Classes Class Programming Checking the Class Type Private Data Static Data Special Attributes Special Methods Multiple Inheritance Using a Class as a C-like Structure Attribute Access via String Names New-Style Classes Implementing Get/Set Functions via Properties Subclassing Built-in Types Building Class Interfaces at Run Time Building Flexible Class Interfaces Exercises Scope of Variables Global, Local, and Class Variables Nested Functions Dictionaries of Variables in Namespaces Exceptions Handling Exceptions Raising Exceptions Iterators Constructing an Iterator A Pointwise Grid Iterator A Vectorized Grid Iterator Generators Some Aspects of Generic Programming Exercises Investigating Efficiency CPU-Time Measurements Profiling Python Scripts Optimization of Python Code Case Study an Numerical Efficiency

8 XVIII Table of Contents Table of Contents XVII 9 Fortran Programming with NumPy Arrays Problem Definition Filling an Array in Fortran The Fortran Subroutine Building and Inspecting the Extension Module Array Storage Issues Generating an Erroneous Interface Array Storage in C and Fortran Input and Output Arrays as Function Arguments F2PY Interface Files Hiding Work Arrays Increasing Callback Efficiency Callbacks to Vectorized Python Functions Avoiding Callbacks to Python Compiled Inline Callback Functions Summary Exercises C and C++ Programming with NumPy Arrays Automatic Interfacing of C/C++ Code Using F2PY Using Instant Using Weave C Programming with NumPy Arrays The Basics of the NumPy C API The Handwritten Extension Code Sending Arguments from Python to C Consistency Checks Computing Array Values Returning an Output Array Convenient Macros Module Initialization Extension Module Template Compiling, Linking, and Debugging the Module Writing a Wrapper for a C Function C++ Programming with NumPy Arrays Wrapping a NumPy Array in a C++ Object Using SCXX NumPy C++ Class Conversion Comparison of the Implementations Efficiency Error Handling Summary Exercises

9 XVIII Table of Contents 11 More Advanced GUI Programming Adding Plot Areas in GUIs The BLT Graph Widget Animation of Functions in BLT Graph Widgets Other Tools for Making GUIs with Plots Exercises Event Bindings Binding Events to Functions with Arguments A Text Widget with Tailored Keyboard Bindings A Fancy List Widget Animated Graphics with Canvas Widgets The First Canvas Encounter Coordinate Systems The Mathematical Model Class The Planet Class Drawing and Moving Planets Dragging Planets to New Positions Using Pmw's Scrolled Canvas Widget Simulation and Visualization Scripts Restructuring the Script Representing a Parameter by a Class Improved Command-Line Script Improved GUI Script Improved CGI Script Parameters with Physical Dimensions Adding a Curve Plot Area Automatic Generation of Scripts Applications of the Tools Allowing Physical Units in Input Files Converting Input Files to GUIs Tools and Examples Running Series of Computer Experiments Multiple Values of Input Parameters Implementation Details Further Applications Tools for Representing Functions Functions Defined by String Formulas A Unified Interface to Functions Interactive Drawing of Functions A Notebook for Selecting Functions Solving Partial Differential Equations Numerical Methods for 1D Wave Equations Implementations of 1D Wave Equations Classes for Solving 1D Wave Equations A Problem Solving Environment Numerical Methods for 2D Wave Equations

10 Table of Contents XIX Implementations of 2D Wave Equations Exercises A Setting up the Required Software Environment A.1 Installation on Unix Systems A.1.1 A Suggested Directory Structure A.1.2 Setting Some Environment Variables A.1.3 Installing Tcl/Tk and Additional Modules A.1.4 Installing Python A.1.5 Installing Python Modules A.1.6 Installing Gnuplot A.1.7 Installing SWIG A.1.8 Summary of Environment Variables A.1.9 Testing the Installation of Scripting Utilities A.2 Installation on Windows Systems B Elements of Software Engineering B.1 Building and Using Modules B.1.1 Single-File Modules B.1.2 Multi-File Modules B.1.3 Debugging and Troubleshooting B.2 Tools for Documenting Python Software B.2.1 Doc Strings B.2.2 Tools for Automatic Documentation B.3 Coding Standards B.3.1 Style Guide B.3.2 Pythonic Programming B.4 Verification of Scripts B.4.1 Automating Regression Tests B.4.2 Implementing a Tool for Regression Tests B.4.3 Writing a Test Script B.4.4 Verifying Output from Numerical Computations B.4.5 Automatic Doc String Testing B.4.6 Unit Testing B.5 Version Control Management B.5.1 Mercurial B.5.2 Subversion B.6 Exercises Bibliography Index