Tutorial Python Alex 19-10-12

Python Tutorial - Alexandre Savio, October 19th, 2012

$ sudo apt-get install ipython python-numpy python-scipy python-mvpa2 python-setuptools python-matplotlib python-mvpa2-tutorialdata git python-pip python-nibabel

$ sudo pip install -U scikit-image scikit-learn statsmodels

   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
       http://code.google.com/p/pythonxy/
       http://spyder-ide.blogspot.com.es/
    
   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:
           http://nisl.github.com/introduction.html
           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
           /home/alexandre/Dropbox/Documents/phd/work/salinas/sklearn_on_salinas.py

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

   Cleanup before leaving... ?

sudo pip uninstall nisl rm -r ~/tutorial