Tutorial Python Alex 19-10-12

Python Tutorial

Author: Alex, October 19th, 2012

• Install the software

Base OS: Ubuntu 12.04.1

For Ubuntu repository versions:

sudo apt-get install ipython python-numpy python-scipy python-mvpa2 python-matplotlib git python-pip python-nibabel cython python-statsmodels python-sklearn python-skimage

For updated versions we can use Python Package Index (PyPI):

sudo apt-get install python-pip python-dev build-essential 
sudo pip install -U pip
sudo pip install -U ipython
sudo pip install -U cython
sudo pip install -U numpy 
sudo apt-get install build-essential gfortran libblas-dev liblapack-dev libumfpack5.4.0
sudo pip install -U scipy 
sudo pip install -U pandas
sudo pip install -U scikit-image scikit-learn statsmodels

Neuroimaging:

Nipy

sudo pip install -U sympy
sudo pip install -U nibabel nipype nipy
sudo pip install -U dipy nitime

• Download the data
  • • docs
    • nisl_data.tar.gz
    • nisl_data.tar.gz

• Python
  • Hello World!
  • Tutorials:
    • http://docs.python.org/tutorial/index.html
    • http://docs.python.org/tutorial/controlflow.html
    • http://docs.python.org/tutorial/datastructures.html
    • http://docs.python.org/tutorial/datastructures.html#looping-techniques
    • http://docs.python.org/tutorial/datastructures.html#dictionaries

• IDEs
  • http://ipython.org
  • Sage
  • http://code.google.com/p/pythonxy/
  • http://spyder-ide.blogspot.com.es
  • Eric Python IDE
  • Reinteract

How to install a few of them:

sudo apt-get install ipython
sudo apt-get install ipython-qtconsole
sudo apt-get install spyder
sudo apt-get install eric
sudo apt-get install reinteract

• Installing libraries
  • Ubuntu repositories
  • http://pypi.python.org/pypi

• Numpy
  • http://numpy.scipy.org/
  • http://www.scipy.org/Tentative_NumPy_Tutorial
  • Numpy for Matlab users
    • http://www.scipy.org/NumPy_for_Matlab_Users
  • Tutorials:
    • http://www.scipy.org/Tentative_NumPy_Tutorial#head-864862d3f2bb4c32f04260fac61eb4ef34788c4c
    • http://www.scipy.org/Tentative_NumPy_Tutorial#head-d55e594d46b4f347c20efe1b4c65c92779f06268
    • http://www.scipy.org/Tentative_NumPy_Tutorial#head-aa75ec76530ff51a2e98071adb7224a4b793519e

• Scipy
  • http://www.scipy.org/Cookbook
  • http://scipy-central.org/
  • http://docs.scipy.org/doc/scipy/reference/index.html
  • Tutorials:
    • http://www.scipy.org/Cookbook/Interpolation
    • http://www.scipy.org/Cookbook/Watershed
    • http://www.scipy.org/Cookbook/RadialBasisFunctions
    • http://www.scipy.org/Cookbook/LinearRegression

• Statistics and Pattern analysis
  • http://pypi.python.org/pypi/statsmodels
  • http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html
  • http://www.pymvpa.org/
  • http://www.shogun-toolbox.org/
    • http://www.shogun-toolbox.org/doc/en/current/methods.html
  • http://scikit-learn.org/stable/
  • http://scikits.appspot.com/scikits
  • Tutorial scipy.stats:
    • http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind
    • http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr
  • Tutorial scikit-learn:

Download data:

http://www.ehu.es/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes
http://www.ehu.es/ccwintco/uploads/a/a3/Salinas_corrected.mat
http://www.ehu.es/ccwintco/uploads/f/fa/Salinas_gt.mat
sklearn_on_salinas.py in zip file

• Neuroimaging with Scikit-learn
  • http://nisl.github.com/index.html
  • http://nisl.github.com/auto_examples/index.html
  • Tutorial:

 $ git clone https://github.com/nisl/tutorial.git
 $ cd tutorial
 $ sudo python setup.py install
 $ ipython
 http://nisl.github.com/auto_examples/plot_ica_resting_state.html#example-tutorial-plot-ica-resting-state-py

• Imaging
  • http://docs.scipy.org/doc/scipy/reference/ndimage.html
  • http://www.pythonware.com/products/pil/
  • http://scikit-image.org/
  • http://opencv.willowgarage.com/wiki/
  • Imagemagick API
  • Nifti images: http://nipy.sourceforge.net/nibabel/
  • Tutorials:
    • http://scikit-image.org/docs/dev/auto_examples/plot_gabors_from_lena.html
    • http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html

• Hyperspectral Imaging
  • http://www.orfeo-toolbox.org/otb/
  • http://spectralpython.sourceforge.net/

• Interfaces with other softwares
  • http://docs.scipy.org/doc/scipy/reference/io.html
  • http://forge.scilab.org/index.php/p/sciscipy/
  • http://rpy.sourceforge.net/rpy2.html
  • Boost.python
  • http://cython.org/

• Plotting
  • http://matplotlib.org/
  • http://code.enthought.com/projects/mayavi/
  • http://cairoplot.sourceforge.net
  • http://luke.campagnola.me/code/pyqtgraph/

• Others
  • http://igraph.sourceforge.net/
  • http://networkx.lanl.gov/
  • http://nltk.org/
  • http://sympy.org/en/index.html
  • Machine Learning, Stephen Marsland: link, book, python source code

• Added later
  • PyMVPA
  • scikit-learn
  • scikit-statsmodels
  • scikit-image
  • PyBrain
  • mlpy
  • PyML
  • pymorph
  • mahotas

• Cleanup before leaving... ?

sudo pip uninstall nisl 
rm -r tutorial