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| </style></head><body><div class="note" id="Python Tutorial"><a name="python tutorial"></a><h1>Python Tutorial</h1>
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| - Alexandre Savio, October 19th, 2012
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| <span style="font-family:monospace">sudo apt-get install ipython python-numpy python-scipy python-mvpa2 python-setuptools python-matplotlib python-mvpa2-tutorialdata git python-pip python-nibabel
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|
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| sudo pip install -U scikit-image scikit-learn statsmodels</span>
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|
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| <ul><li dir="ltr"><b>Python</b><strike>
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| </strike><ul><li dir="ltr"><b>Hello World!</b>
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| </li><li dir="ltr">Tutorials:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://docs.python.org/tutorial/index.html">http://docs.python.org/tutorial/index.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.python.org/tutorial/controlflow.html">http://docs.python.org/tutorial/controlflow.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.python.org/tutorial/datastructures.html">http://docs.python.org/tutorial/datastructures.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.python.org/tutorial/datastructures.html#looping-techniques">http://docs.python.org/tutorial/datastructures.html#looping-techniques</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.python.org/tutorial/datastructures.html#dictionaries">http://docs.python.org/tutorial/datastructures.html#dictionaries</a></li></ul></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>IDEs</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://ipython.org">http://ipython.org</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://code.google.com/p/pythonxy/">http://code.google.com/p/pythonxy/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://spyder-ide.blogspot.com.es/">http://spyder-ide.blogspot.com.es/</a>
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| </li></ul></li><li dir="ltr">
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| </li><li dir="ltr"><b>Installing libraries</b>
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| <ul><li dir="ltr">Ubuntu repositories
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://pypi.python.org/pypi">http://pypi.python.org/pypi</a></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Numpy</b><strike>
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| </strike><ul><li dir="ltr"><a style="color:#3465A4" href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Tentative_NumPy_Tutorial">http://www.scipy.org/Tentative_NumPy_Tutorial</a>
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| </li><li dir="ltr">Numpy for Matlab users
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/NumPy_for_Matlab_Users">http://www.scipy.org/NumPy_for_Matlab_Users</a>
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| </li></ul></li><li dir="ltr">Tutorials:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Tentative_NumPy_Tutorial#head-864862d3f2bb4c32f04260fac61eb4ef34788c4c">http://www.scipy.org/Tentative_NumPy_Tutorial#head-864862d3f2bb4c32f04260fac61eb4ef34788c4c</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Tentative_NumPy_Tutorial#head-d55e594d46b4f347c20efe1b4c65c92779f06268">http://www.scipy.org/Tentative_NumPy_Tutorial#head-d55e594d46b4f347c20efe1b4c65c92779f06268</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Tentative_NumPy_Tutorial#head-aa75ec76530ff51a2e98071adb7224a4b793519e">http://www.scipy.org/Tentative_NumPy_Tutorial#head-aa75ec76530ff51a2e98071adb7224a4b793519e</a></li></ul></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Scipy</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Cookbook">http://www.scipy.org/Cookbook</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://scipy-central.org/">http://scipy-central.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.scipy.org/doc/scipy/reference/index.html">http://docs.scipy.org/doc/scipy/reference/index.html</a>
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| </li><li dir="ltr">Tutorials:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Cookbook/Interpolation">http://www.scipy.org/Cookbook/Interpolation</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Cookbook/Watershed">http://www.scipy.org/Cookbook/Watershed</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Cookbook/RadialBasisFunctions">http://www.scipy.org/Cookbook/RadialBasisFunctions</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.scipy.org/Cookbook/LinearRegression">http://www.scipy.org/Cookbook/LinearRegression</a></li></ul></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Statistics and Pattern analysis</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://pypi.python.org/pypi/statsmodels">http://pypi.python.org/pypi/statsmodels</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html">http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.pymvpa.org/">http://www.pymvpa.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.shogun-toolbox.org/">http://www.shogun-toolbox.org/</a>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.shogun-toolbox.org/doc/en/current/methods.html">http://www.shogun-toolbox.org/doc/en/current/methods.html</a>
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| </li></ul></li><li dir="ltr"><a style="color:#3465A4" href="http://scikit-learn.org/stable/">http://scikit-learn.org/stable/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://scikits.appspot.com/scikits">http://scikits.appspot.com/scikits</a>
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| </li><li dir="ltr">Tutorial scipy.stats:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="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.ttest_ind.html#scipy.stats.ttest_ind</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr</a>
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| </li></ul></li><li dir="ltr">Tutorial scikit-learn:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://nisl.github.com/introduction.html">http://nisl.github.com/introduction.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.ehu.es/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes">http://www.ehu.es/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.ehu.es/ccwintco/uploads/a/a3/Salinas_corrected.mat">http://www.ehu.es/ccwintco/uploads/a/a3/Salinas_corrected.mat</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.ehu.es/ccwintco/uploads/f/fa/Salinas_gt.mat">http://www.ehu.es/ccwintco/uploads/f/fa/Salinas_gt.mat</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="/home/alexandre/Dropbox/Documents/phd/work/salinas/sklearn_on_salinas.py">/home/alexandre/Dropbox/Documents/phd/work/salinas/sklearn_on_salinas.py</a></li></ul></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Neuroimaging with Scikit-learn</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://nisl.github.com/index.html">http://nisl.github.com/index.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://nisl.github.com/auto_examples/index.html">http://nisl.github.com/auto_examples/index.html</a>
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| </li><li dir="ltr">Tutorial:
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| <ul><li dir="ltr">cd ~
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| </li><li dir="ltr">git clone <a style="color:#3465A4" href="https://github.com/nisl/tutorial.git">https://github.com/nisl/tutorial.git</a>
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| </li><li dir="ltr">cd tutorial
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| </li><li dir="ltr">sudo python setup.py install
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| </li><li dir="ltr">ipython
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://nisl.github.com/auto_examples/plot_ica_resting_state.html#example-tutorial-plot-ica-resting-state-py">http://nisl.github.com/auto_examples/plot_ica_resting_state.html#example-tutorial-plot-ica-resting-state-py</a></li></ul></li></ul></li></ul><strike>
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| </strike>
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| <ul><li dir="ltr"><b>Imaging</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://docs.scipy.org/doc/scipy/reference/ndimage.html">http://docs.scipy.org/doc/scipy/reference/ndimage.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://www.pythonware.com/products/pil/">http://www.pythonware.com/products/pil/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://scikit-image.org/">http://scikit-image.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://opencv.willowgarage.com/wiki/">http://opencv.willowgarage.com/wiki/</a>
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| </li><li dir="ltr">Imagemagick API
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| </li><li dir="ltr">Nifti images: <a style="color:#3465A4" href="http://nipy.sourceforge.net/nibabel/">http://nipy.sourceforge.net/nibabel/</a>
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| </li><li dir="ltr">Tutorials:
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://scikit-image.org/docs/dev/auto_examples/plot_gabors_from_lena.html">http://scikit-image.org/docs/dev/auto_examples/plot_gabors_from_lena.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html">http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html</a></li></ul></li></ul></li></ul>
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| <ul><li dir="ltr"><b>Hyperspectral Imaging</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://www.orfeo-toolbox.org/otb/">http://www.orfeo-toolbox.org/otb/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://spectralpython.sourceforge.net/">http://spectralpython.sourceforge.net/</a></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Interfaces with other softwares</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://docs.scipy.org/doc/scipy/reference/io.html">http://docs.scipy.org/doc/scipy/reference/io.html</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://forge.scilab.org/index.php/p/sciscipy/">http://forge.scilab.org/index.php/p/sciscipy/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://rpy.sourceforge.net/rpy2.html">http://rpy.sourceforge.net/rpy2.html</a></li></ul></li></ul>
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| <ul><li dir="ltr"><b>Plotting</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://matplotlib.org/">http://matplotlib.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://code.enthought.com/projects/mayavi/">http://code.enthought.com/projects/mayavi/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://cairoplot.sourceforge.net">http://cairoplot.sourceforge.net</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://luke.campagnola.me/code/pyqtgraph/">http://luke.campagnola.me/code/pyqtgraph/</a></li></ul></li></ul>
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| <ul><li dir="ltr"><b>Others</b>
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| <ul><li dir="ltr"><a style="color:#3465A4" href="http://igraph.sourceforge.net/">http://igraph.sourceforge.net/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://networkx.lanl.gov/">http://networkx.lanl.gov/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://nltk.org/">http://nltk.org/</a>
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| </li><li dir="ltr"><a style="color:#3465A4" href="http://sympy.org/en/index.html">http://sympy.org/en/index.html</a></li></ul></li></ul>
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|
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| <ul><li dir="ltr"><b>Cleanup before leaving... ?</b></li></ul>
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| sudo pip uninstall nisl
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| rm -r <a style="color:#3465A4" href="~/tutorial">~/tutorial</a>
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| </nowiki>
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