Ver el código de «Tutorial Python Alex 19-10-12»

<div id="Python Tutorial" class="note">

= Python Tutorial =

Author: Alex, October 19th, 2012 

* '''Install the software'''
 Base OS: [http://www.ubuntu.com/ Ubuntu 12.04.1]

For Ubuntu repository versions:
 <font face="monospace">
 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
 </font>

For updated versions we can use [http://pypi.python.org/pypi Python Package Index (PyPI)]:
 <font face="monospace">
 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
 </font>

Neuroimaging:
 [http://nipy.sourceforge.net/ Nipy]
 <font face="monospace">
 sudo pip install -U sympy
 sudo pip install -U nibabel nipype nipy
 sudo pip install -U dipy nitime
 </font>


* '''Download the data'''
***  [[Media:Python alex docs.zip | docs]]
***  [http://www.ehu.es/ccwintco/groupware/webdav.php/apps/phpbrain/648/nisl_data.tar.gz nisl_data.tar.gz]
***  [http://db.tt/e4oouc2R nisl_data.tar.gz]

* '''Python'''<strike> </strike>
** [http://python.about.com/od/gettingstarted/ss/helloworld_all.htm '''Hello World!''']
** Tutorials:
*** [http://docs.python.org/tutorial/index.html <font color="#3465A4">http://docs.python.org/tutorial/index.html</font>]
*** [http://docs.python.org/tutorial/controlflow.html <font color="#3465A4">http://docs.python.org/tutorial/controlflow.html</font>]
*** [http://docs.python.org/tutorial/datastructures.html <font color="#3465A4">http://docs.python.org/tutorial/datastructures.html</font>]
*** [http://docs.python.org/tutorial/datastructures.html#looping-techniques <font color="#3465A4">http://docs.python.org/tutorial/datastructures.html#looping-techniques</font>]
*** [http://docs.python.org/tutorial/datastructures.html#dictionaries <font color="#3465A4">http://docs.python.org/tutorial/datastructures.html#dictionaries</font>]

* '''IDEs'''
** [http://ipython.org <font color="#3465A4">http://ipython.org</font>]
** [http://www.sagemath.org/ <font color="#3465A4">Sage</font>]
** [http://code.google.com/p/pythonxy/ <font color="#3465A4">http://code.google.com/p/pythonxy/</font>]
** [http://spyder-ide.blogspot.com.es/ <font color="#3465A4">http://spyder-ide.blogspot.com.es</font>]
** [http://eric-ide.python-projects.org/ Eric Python IDE]
** [http://www.reinteract.org/addons.html Reinteract]

How to install a few of them:
 <font face="monospace">
 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
 </font>

* '''Installing libraries'''
** Ubuntu repositories
** [http://pypi.python.org/pypi <font color="#3465A4">http://pypi.python.org/pypi</font>]

* '''Numpy'''<strike> </strike>
** [http://numpy.scipy.org/ <font color="#3465A4">http://numpy.scipy.org/</font>]
** [http://www.scipy.org/Tentative_NumPy_Tutorial <font color="#3465A4">http://www.scipy.org/Tentative_NumPy_Tutorial</font>]
** Numpy for Matlab users
*** [http://www.scipy.org/NumPy_for_Matlab_Users <font color="#3465A4">http://www.scipy.org/NumPy_for_Matlab_Users</font>]
** Tutorials:
*** [http://www.scipy.org/Tentative_NumPy_Tutorial#head-864862d3f2bb4c32f04260fac61eb4ef34788c4c <font color="#3465A4">http://www.scipy.org/Tentative_NumPy_Tutorial#head-864862d3f2bb4c32f04260fac61eb4ef34788c4c</font>]
*** [http://www.scipy.org/Tentative_NumPy_Tutorial#head-d55e594d46b4f347c20efe1b4c65c92779f06268 <font color="#3465A4">http://www.scipy.org/Tentative_NumPy_Tutorial#head-d55e594d46b4f347c20efe1b4c65c92779f06268</font>]
*** [http://www.scipy.org/Tentative_NumPy_Tutorial#head-aa75ec76530ff51a2e98071adb7224a4b793519e <font color="#3465A4">http://www.scipy.org/Tentative_NumPy_Tutorial#head-aa75ec76530ff51a2e98071adb7224a4b793519e</font>]

* '''Scipy'''
** [http://www.scipy.org/Cookbook <font color="#3465A4">http://www.scipy.org/Cookbook</font>]
** [http://scipy-central.org/ <font color="#3465A4">http://scipy-central.org/</font>]
** [http://docs.scipy.org/doc/scipy/reference/index.html <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/index.html</font>]
** Tutorials:
*** [http://www.scipy.org/Cookbook/Interpolation <font color="#3465A4">http://www.scipy.org/Cookbook/Interpolation</font>]
*** [http://www.scipy.org/Cookbook/Watershed <font color="#3465A4">http://www.scipy.org/Cookbook/Watershed</font>]
*** [http://www.scipy.org/Cookbook/RadialBasisFunctions <font color="#3465A4">http://www.scipy.org/Cookbook/RadialBasisFunctions</font>]
*** [http://www.scipy.org/Cookbook/LinearRegression <font color="#3465A4">http://www.scipy.org/Cookbook/LinearRegression</font>]

* '''Statistics and Pattern analysis'''
** [http://pypi.python.org/pypi/statsmodels <font color="#3465A4">http://pypi.python.org/pypi/statsmodels</font>]
** [http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/tutorial/stats.html</font>]
** [http://www.pymvpa.org/ <font color="#3465A4">http://www.pymvpa.org/</font>]
** [http://www.shogun-toolbox.org/ <font color="#3465A4">http://www.shogun-toolbox.org/</font>]
*** [http://www.shogun-toolbox.org/doc/en/current/methods.html <font color="#3465A4">http://www.shogun-toolbox.org/doc/en/current/methods.html</font>]
** [http://scikit-learn.org/stable/ <font color="#3465A4">http://scikit-learn.org/stable/</font>]
** [http://scikits.appspot.com/scikits <font color="#3465A4">http://scikits.appspot.com/scikits</font>]
** Tutorial scipy.stats:
*** [http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind</font>]
*** [http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr</font>]
** Tutorial scikit-learn:
'''Download data:'''
 [http://www.ehu.es/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes <font color="#3465A4">http://www.ehu.es/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes</font>]
 [http://www.ehu.es/ccwintco/uploads/a/a3/Salinas_corrected.mat <font color="#3465A4">http://www.ehu.es/ccwintco/uploads/a/a3/Salinas_corrected.mat</font>]
 [http://www.ehu.es/ccwintco/uploads/f/fa/Salinas_gt.mat <font color="#3465A4">http://www.ehu.es/ccwintco/uploads/f/fa/Salinas_gt.mat</font>]
 sklearn_on_salinas.py in zip file

* '''Neuroimaging with Scikit-learn'''
** [http://nisl.github.com/index.html <font color="#3465A4">http://nisl.github.com/index.html</font>]
** [http://nisl.github.com/auto_examples/index.html <font color="#3465A4">http://nisl.github.com/auto_examples/index.html</font>]
** Tutorial:
<font face="monospace">
  $ git clone [https://github.com/nisl/tutorial.git <font color="#3465A4">https://github.com/nisl/tutorial.git</font>]
  $ 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 <font color="#3465A4">http://nisl.github.com/auto_examples/plot_ica_resting_state.html#example-tutorial-plot-ica-resting-state-py</font>]
</font>

<strike> </strike>

* '''Imaging'''
** [http://docs.scipy.org/doc/scipy/reference/ndimage.html <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/ndimage.html</font>]
** [http://www.pythonware.com/products/pil/ <font color="#3465A4">http://www.pythonware.com/products/pil/</font>]
** [http://scikit-image.org/ <font color="#3465A4">http://scikit-image.org/</font>]
** [http://opencv.willowgarage.com/wiki/ <font color="#3465A4">http://opencv.willowgarage.com/wiki/</font>]
** Imagemagick API
** Nifti images: [http://nipy.sourceforge.net/nibabel/ <font color="#3465A4">http://nipy.sourceforge.net/nibabel/</font>]
** Tutorials:
*** [http://scikit-image.org/docs/dev/auto_examples/plot_gabors_from_lena.html <font color="#3465A4">http://scikit-image.org/docs/dev/auto_examples/plot_gabors_from_lena.html</font>]
*** [http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html <font color="#3465A4">http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html</font>]

* '''Hyperspectral Imaging'''
** [http://www.orfeo-toolbox.org/otb/ <font color="#3465A4">http://www.orfeo-toolbox.org/otb/</font>]
** [http://spectralpython.sourceforge.net/ <font color="#3465A4">http://spectralpython.sourceforge.net/</font>]

* '''Interfaces with other softwares'''
** [http://docs.scipy.org/doc/scipy/reference/io.html <font color="#3465A4">http://docs.scipy.org/doc/scipy/reference/io.html</font>]
** [http://forge.scilab.org/index.php/p/sciscipy/ <font color="#3465A4">http://forge.scilab.org/index.php/p/sciscipy/</font>]
** [http://rpy.sourceforge.net/rpy2.html <font color="#3465A4">http://rpy.sourceforge.net/rpy2.html</font>]
** [http://www.boost.org/doc/libs/1_51_0/libs/python/doc/index.html Boost.python]
** [http://cython.org/ <font color="#3465A4">http://cython.org/</font>]

* '''Plotting'''
** [http://matplotlib.org/ <font color="#3465A4">http://matplotlib.org/</font>]
** [http://code.enthought.com/projects/mayavi/ <font color="#3465A4">http://code.enthought.com/projects/mayavi/</font>]
** [http://cairoplot.sourceforge.net <font color="#3465A4">http://cairoplot.sourceforge.net</font>]
** [http://luke.campagnola.me/code/pyqtgraph/ <font color="#3465A4">http://luke.campagnola.me/code/pyqtgraph/</font>]

* '''Others'''
** [http://igraph.sourceforge.net/ <font color="#3465A4">http://igraph.sourceforge.net/</font>]
** [http://networkx.lanl.gov/ <font color="#3465A4">http://networkx.lanl.gov/</font>]
** [http://nltk.org/ <font color="#3465A4">http://nltk.org/</font>]
** [http://sympy.org/en/index.html <font color="#3465A4">http://sympy.org/en/index.html</font>]
** Machine Learning, Stephen Marsland: link, book, python source code

* '''Added later'''
** [http://www.pymvpa.org/ PyMVPA]
** [http://scikit-learn.org/stable/ scikit-learn]
** [http://statsmodels.sourceforge.net/ scikit-statsmodels]
** [http://scikit-image.org/ scikit-image]
** [http://pybrain.org/pages/features PyBrain]
** [http://mlpy.sourceforge.net/ mlpy]
** [http://pyml.sourceforge.net/index.html PyML]
** [http://luispedro.org/software/pymorph pymorph]
** [http://luispedro.org/software/mahotas mahotas]


* '''Cleanup before leaving... ?'''
<font face="monospace">
 sudo pip uninstall nisl 
 rm -r tutorial
</font>