.. AUTO-GENERATED FILE -- DO NOT EDIT!

.. _example_smellit:


Simple Data-Exploration
=======================

Example showing some possibilities of data exploration
(i.e. to 'smell' data).

::

  from mvpa2.suite import *

  # load example fmri dataset
  ds = load_example_fmri_dataset()

  # only use the first 5 chunks to save some cpu-cycles
  ds = ds[ds.chunks < 5]

  # take a look at the distribution of the feature values in all
  # sample categories and chunks
  plot_feature_hist(ds, chunks_attr='chunks', bins=20, normed=True,
                  xlim=(0, ds.samples.max()))

  # next only works with floating point data
  ds.samples = ds.samples.astype('float')

  # look at sample similiarity
  # Note, the decreasing similarity with increasing temporal distance
  # of the samples
  pl.figure()
  pl.subplot(121)
  plot_samples_distance(ds, sortbyattr='chunks')
  pl.title('Sample distances (sorted by chunks)')

  # similar distance plot, but now samples sorted by their
  # respective targets, i.e. samples with same targets are plotted
  # in adjacent columns/rows.
  # Note, that the first and largest group corresponds to the
  # 'rest' condition in the dataset
  pl.subplot(122)
  plot_samples_distance(ds, sortbyattr='targets')
  pl.title('Sample distances (sorted by targets)')

  # z-score features individually per chunk
  print 'Detrending data'
  poly_detrend(ds, polyord=2, chunks_attr='chunks')
  print 'Z-Scoring data'
  zscore(ds)

  pl.figure()
  pl.subplot(121)
  plot_samples_distance(ds, sortbyattr='chunks')
  pl.title('Distances: z-scored, detrended (sorted by chunks)')
  pl.subplot(122)
  plot_samples_distance(ds, sortbyattr='targets')
  pl.title('Distances: z-scored, detrended (sorted by targets)')
  # XXX add some more, maybe show effect of preprocessing


Outputs of the example script. Data prior to preprocessing

.. image:: ../pics/ex_smellit2.*
   :align: center
   :alt: Data prior preprocessing

Data after minimal preprocessing

.. image:: ../pics/ex_smellit3.*
   :align: center
   :alt: Data after z-scoring and detrending


.. seealso::
  The full source code of this example is included in the PyMVPA source distribution (`doc/examples/smellit.py`).
