Python for Scientific Programming Jim Pulokas, Research Programmer Automated Molecular Imaging Group

1
Python for Scientific ProgrammingJim Pulokas,
Research ProgrammerAutomated Molecular Imaging
Group
2
Introduction to Python

• Interpreted, interactive, object-oriented
• Portable (compiled from C)
• Easy to extend and embed
• Features dynamic typing, garbage collection

3
Learning Python

• Books I used while learning Python
• Learning Python
• Python in a Nutshell
• www.python.org - complete and well organized
  documentation
• The joy of interpreted languages You can
  experiment without the pain of compiling and
  debugging
• My demo...

4
Python Demo

• The usual Python is a calculator
• Types int, float, long, string, list, tuple,
  dict, function
• Control flow
• Modules
• Exceptions

5
Numerical Python Module (Numeric, numarray)

• http//www.stsci.edu/resources/software_hardware/n
  umarray
• Modules for working with multi-dimensional
  numerical arrays
• Contains functions similar to Matlab
• Array operations implemented using C arrays, so
  faster than Python's built in sequence types
• Can be extended just like Python
• Demo later (with references to Matlab)

6
Numeric Demo (references to Matlab)
7
DemoExtending Python and Numeric
8
Other Modules PyMat

• Allows Python to start and interact with a Matlab
  engine.
• Numeric arrays can be passed into and out of
  Matlab arrays
• Matlab functions can be executed by passing
  strings to the Matlab engine.
• sourceforge.net/projects/pymat

9
Other Modules ScientificPython

• Geometry vectors, tensors, transformations
• Interpolation
• Polynomials
• Least Squares Fit
• starship.python.net/hinsen/ScientificPython/

10
Other Modules SciPy

• More complete set of functions than
  ScientificPython
• FFT, integration, interpolation, signal
  processing, filters, optimization, statistics...
• www.scipy.org

11
Other Modules fftw-numpy

• Wrapper around fftw C library
• Calculate fft of Numeric arrays
• Faster than FFT module that comes with Numeric
• pylab.sourceforge.net/

12
Python Imaging Library

• Similar to ImageMagick functions
• Image visualization, scaling, rotation, etc.
• Not very science oriented
• www.pythonware.com/products/pil

13
Developed Using Python Leginon

• Framework for creating TEM data acquisition
  applications
• Modular architecture
• Python features used threading, sockets, memory
  management
• External modules used Numeric, MySQLdb,
  wxPython, PIL
• It's running right now, let's watch...