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Day one : 22 February 2013
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************
Introduction
************

Two different modes of working:

* interactive
* building code

Today is interactive. As before we'll be using the `IPython notebook`_.

Next week we'll be building code.

The idea of software carpentry:

* Learning how to use tools.
* Homework for this week: editors.

See :ref:`choosing-editor-2013` for a review of some choices.

**********************
The Python environment
**********************

* Python itself comes with many useful modules in the `Python standard library`_
    * ``os, sys, shutil, glob, tempfile``
    * ``urllib2``, ``HTMLParser``, ``xml``, many other web libraries
    * ``math, decimal`` (very high precision numbers), ``random``
    * ``csv``, database access with ``sqlite3`` and others
    * ``tarfile, zipfile, gzip`` and other compression formats

  Along with debugging, documentation tools, testing tools and much else.

* Numpy_ is a Python library defining arrays of data, with many routines for
  manipulating arrays including basic linear algebra, random number generation
  and Fourier transforms.  Python + Numpy gets you most of what MATLAB can do.

* Scipy_ adds a large library of scientific code built on top of Numpy.  It is a
  collection of many different kinds of routines including:

    * ``scipy.io``: Read / write of scientific data formats including MATLAB
      ``.mat`` files
    * ``scipy.ndimage``: processing tools such as smoothing and convolution,
      resampling for N-D (2D, 3D, 4D etc) arrays.
    * ``scipy.linalg``: expanded linear algebra tools with interfaces to much of
      the highly optimized LAPACK linear algebra libraries.
    * ``scipy.optimize``: tools for finding optimum values in functions
    * ``scipy.sparse``: working with sparse arrays
    * ``scipy.interpolate``: routines for interpolating data points
    * ``scipy.stats``: routines for statistical distributions, fitting and
      tests.

  Please see the `scipy reference guide`_ for more detail.

* Matplotlib_ provides 2D and some 3D plotting, with an interface modeled after
  MATLAB. See the `matplotlib gallery`_ for a taster of the kind of things you
  can do.

* Cython_: write Python code but with the ability to optimize and compile it
  down to the C level, often giving very large increases in execution speed.

* Sympy_: a library for symbolic mathematics.  It is a computer algebra system
  like Mathematica or Maple that allows you to manipulate mathematical symbols
  and functions.  It is useful for such things as defining and simplifying and
  solving equations, finding integrals and differentials.

* Pandas_: high-level fast data analysis using R-like data frames to hold and
  manipulate data.

* scikit-learn_: an extensive machine learning library, containing algorithms
  such as independent component analysis, support vector machines among many
  others.

* scikit-image_: 2D image processing

* statsmodels_: statistical models defined and estimated.

There are many other libraries, including some specific to neuroimaging.  We'll
meet one of those next week, nibabel_.

********************
The Python libraries
********************

* `The Python libraries raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/python_libraries.ipynb>`_
  notebook file for downloading.
* `The Python libraries web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/python_libraries.ipynb>`_
  notebook presented nicely as a web page.

**********************
Introduction to python
**********************

Continuing on from last week:

* `Introduction to Python raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/introduction_to_python.ipynb>`_
  notebook file for downloading.
* `Introduction to Python web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/introduction_to_python.ipynb>`_
  notebook presented nicely as a web page.

.. include:: links_names.inc