wiki-legacy-tags.txt

This is a legacy file for providing tags for the notebooks, based on
the sections they were categorized in the wiki.

It's not meant to be edited. Instead, include tag specifications to
the cookbook files themselves (see README.md)


Outdated
========

* [[Cookbook/xplt]]
* [[Cookbook/A_Numerical_Agnostic_Pyrex_Class]]
* [[Cookbook/ArrayStruct_and_Pyrex]]
* [[Cookbook/DataFrame]]
* [[Cookbook/dbase]]
* [[Cookbook/FortranIO_FortranFile]]
* [[Cookbook/TimeSeries_FAQ]]
* [[Cookbook/PIL_example]]
* [[Cookbook/MayaVi_InstallPythonStuffFromSource]]

Numpy
=====

* [[Cookbook/BuildingArrays|Building Arrays]] Introduction to numerical arrays.
* [[Cookbook/Indexing|Indexing]] Indexing numpy arrays, from simple to complicated.
* [[Cookbook/MultiDot|Multiplying multiple arguments]] Generalizing `dot(a,b)` to the case of N arguments.
* [[Cookbook/SegmentAxis|Segment axis]] Devious trick using strides to allow general operations (like convolution) on successive, overlapping pieces of an array
* [[Cookbook/GameOfLifeStrides|Stride tricks for the Game of Life]] This is similar to [[Cookbook/SegmentAxis|Segment axis]], but for 2D arrays with 2D windows.
* [[Cookbook/MetaArray|MetaArray]] Class for storing per-axis meta [[http://open.salon.com/blog/smebs/2011/05/16/marketing_data_box_-_complete_strategy_guide_for_smbs|data]] information with an array (axis names, column names, units, etc.)
* [[Cookbook/Obarray|Obarray]] Trick for avoiding object arrays when dealing with arrays of objects.
* [[Cookbook/Recarray|Recarray]] Accessing array columns with structured arrays and recarrays.
* [[Cookbook/AccumarrayLike|accumarray-like function]] A function that behaves like MATLAB's accumarray.

* [[Cookbook/ViewsVsCopies|Views vs Copies]] A quick introduction to array views and some caveats on situations where you should expect a [[http://open.salon.com/blog/smebs/2011/05/16/marketing_data_box_-_complete_strategy_guide_for_smbs|data]] view or a data copy.

Linear Algebra
==============

* [[Cookbook/RankNullspace|Rank and nullspace]] of a matrix.

Interpolation
=============

* [[Cookbook/Interpolation|Interpolation]] Examples of interpolation (see also [[Cookbook/Matplotlib/Gridding_irregularly_spaced_data|Gridding irregularly spaced data]]).
* [[Cookbook/RadialBasisFunctions|Radial Basis Functions]] Using radial basis functions for smoothing/interpolation

Optimization and fitting
========================

* [[Cookbook/OptimizationDemo1|Optimization]] Quick example of fminbound with plot.
* [[Cookbook/OptimizationAndFitDemo1|Optimization with fit]] Similar to above with spline fit and chaco plot.
* [[Cookbook/FittingData|Fitting Data]] Day to day work in the lab: fitting experimental data.
* [[Cookbook/LinearRegression|Linear regression]] Simple Linear regression example.
* [[Cookbook/OLS|Fit statistics]] Estimates a multi-variate regression model and provides various fit statistics.
* [[Cookbook/Least_Squares_Circle|Least Squares Circle]] Fitting the least squares circle from a series of 2D points
* [[Cookbook/RANSAC|RANSAC algorithm]] Implementation of the robust estimation method.

Ordinary differential equations
===============================

* [[Cookbook/Zombie_Apocalypse_ODEINT|Zombie Apocalypse ODE Modeling]] Modeling a Zombie Apocalypse by solving a system of ordinary differential equations using the SciPy routine, ''odeint''.
* [[Cookbook/CoupledSpringMassSystem|A coupled spring-mass system]] Another example of solving differential equations.
* [[LoktaVolterraTutorial|Lotka-Volterra Tutorial]] Solving ordinary differential equations with Scipy
* [[Cookbook/KdV|KdV]] Solving the Korteweg-deVries equation on a periodic domain using the pseudo-spectral method with the method of lines.
* [[Cookbook/Theoretical_Ecology/Hastings_and_Powell|Hastings and Powell food chain model]]

Root finding
============

* [[Cookbook/SphericalBesselZeros|Spherical Bessel Zeros]] Finding the zeros of the spherical Bessel functions and its derivative
* [[Cookbook/Intersection|Intersection of functions]] Compute the points at which two given functions intersect.

Signal processing
=================
* [[Cookbook/KalmanFiltering|Kalman Filtering]] Example from the Welch & Bishop [[http://www.cs.unc.edu/~welch/kalman/kalmanIntro.html|Introduction to the Kalman Filter]].
* [[Cookbook/CommTheory|Comm Theory]] Example of BPSK simulation.
* [[Cookbook/SignalSmooth|Smoothing a signal]] Performing smoothing of 1D and 2D signals by convolving them with a window.
* [[Cookbook/ButterworthBandpass|Butterworth Bandpass Filter]] Create and apply a Butterworth bandpass filter.
* [[Cookbook/FIRFilter|FIR Filter Design]] Design a low-pass FIR filter using the window method.
* [[Cookbook/ApplyFIRFilter|How to apply a FIR filter:]] signal.convolve, signal.fftconvolve, ndimage.convolve1d or signal.lfilter?
* [[Cookbook/FiltFilt|A zero phase delay filter]] Sample code for a null phase delay filter that processes the signal in the forward and backward direction removing the phase delay.
* [[Cookbook/SavitzkyGolay|Savitzky Golay filtering of data]] Sample code for Savitzky Golay filtering.
* [[Cookbook/FrequencySweptDemo|Frequency-swept signals]] Generating frequency-swept signals with chirp() and sweep_poly() from scipy.signal (SciPy 0.8)

Other examples
==============

* [[Cookbook/LineIntegralConvolution|Line Integral Convolution]] code in cython for visualizing vector fields
* [[Cookbook/Rebinning|Data rebinning]] Examples of rebinning data to produce smaller arrays with and without interpolation.
* [[Cookbook/Histograms|Histograms]] 2D histograms with variable bin width
* [[Cookbook/Finding_Convex_Hull|Convex Hull]] Finds the convex hull around a set of data points.
* [[Cookbook/Finding_Convex_Hull_Minimum_Point|Minimum Point of a Convex Hull]] Finds the minimum point of the convex hull of a finite set of points.
* [[Cookbook/Multithreading|Multithreading]] Easy multithreading for embarrassingly parallel problems
* [[Cookbook/KDTree_example|KDTree]] Searching multidimensional space using kd-trees.
* [[Cookbook/ParticleFilter|Particle Filter]] A simple particle filter algorithm for tracking objects in a video sequence.
* [[Cookbook/BrownianMotion|Brownian Motion]] Compute Brownian motion (i.e. the Wiener process).
* [[Cookbook/CorrelatedRandomSamples|Correlated Random Samples]] Generate correlated normally distributed random samples.
* [[Cookbook/Solving_Large_Markov_Chains|Large Markov Chains]] Find the stationary distribution of a large Markov chain; the M/M/1 tandem queue
* [[Cookbook/Watershed|Watershed algorithm]] Apply the watershed algorithm in order to split an array into distinct components (e.g. for the segmentation of an image into objects).
* [[Cookbook/LinearClassification|Linear Classification]] Fisher's discriminant function and Probabilistic Generative model
* [[Cookbook/EyeDiagram| Plot an eye diagram]] using numpy and matplotlib.

Scientific Scripts
===================================
* [[Cookbook/Theoretical_Ecology|Theoretical Ecology]]
* [[Cookbook/SchrodingerFDTD|Schrödinger's equation]]: a 1-d FDTD solver that animates the time evolution of a gaussian wave packet interacting with simple potentials.

Input & Output
==============
* [[Cookbook/hdf5_in_Matlab|Loading hdf5 in Matlab]]
* [[Cookbook/Reading_mat_files|Reading Matlab .mat files]]
* [[Cookbook/DataFrame|DataFrames]] A useful class for storing alphanumerical data, similar to GNU R's data frames.
* [[Cookbook/Data_Acquisition_with_PyUL|Data acquisition with PyUniversalLibrary]] A series of examples using an inexpensive USB data acquisition device from Measurement Computing.
* [[Cookbook/Data_Acquisition_with_NIDAQmx|Data acquisition with Ni-DAQmx]] A simple example of using ctypes and numpy to access data acquisition devices from National Instruments.
* [[Cookbook/InputOutput|input/output]] Reading and writing a !NumPy array from/to an ascii/binary file.
* [[Cookbook/FortranIO|Fortran I/O]] Reading FORTRAN record-structured binary files (if you don't know what these are, thank your stars and you don't need this).
* [[Cookbook/Reading_SPE_files|Reading SPE files]] Reading SPE binary files produced by CCD cameras (Princeton and like).
* [[Cookbook/LASReader|Reading LAS files]] Reading LAS (Log ASCII Standard) well log files.

Graphics
========

There are several packages available to produce interactive screen
graphics (use the mouse to zoom, orient, and fine-tune) and
publication-quality printed plots, in 2D, 3D, and 4D (animations).
These packages have releases more frequently than SciPy.  Rather than
bundling out-of-date packages with SciPy, the plotting packages are
released separately.  However, their developers work closely with the
SciPy developers to ensure compatibility.

* [[Cookbook/Matplotlib|Matplotlib cookbook]].  Matplotlib is the preferred package for 2D graphics.
* [[Cookbook/PIL_example|Python Imaging Library]]. Create/manipulate images as numpy array's.
* [[Cookbook/xplt|Plotting with xplt]].  xplt is very fast but less flexible than matplotlib.  It allows simple 3-d surface visualizations as well. It is based on pygist (included) and is available under the sandbox directory in SVN scipy.
* [[WilnaDuToit|Mat3d]]. Simple 3D plotting using an OpenGL backend.
* [[Cookbook/OldMatplotlib|Old Matplotlib recipes]]. The recipes on this page are being contributed to the Matplotlib project and will eventually be deleted from this Wiki.

Mayavi
======

* [[Cookbook/MayaVi|3D plotting with Mayavi]]. Advanced 3D data visualization with !MayaVi2 (and TVTK): a very powerful interactive scientific data visualizer.

* [[Cookbook/MayaVi|3D plotting with Mayavi]]. Advanced 3D data visualization with !MayaVi2 (and TVTK): a very powerful interactive scientific data visualizer.

* [[Cookbook/MayaVi/RunningMayavi2| Running MayaVi2]] on the command line.

* [[Cookbook/MayaVi/ScriptingMayavi2| Scripting MayaVi2]] in Python.

* [[Cookbook/MayaVi/ScriptingMayavi2/BasicModules]]
* [[Cookbook/MayaVi/ScriptingMayavi2/Filters]]
* [[Cookbook/MayaVi/ScriptingMayavi2/MainModules]]

* [[Cookbook/MayaVi/examples| Scripting Examples]] (all provided in !MayaVi2 svn tree):

* Using Contour Module (contour.py)

    * Using Glyph Module (glyph.py)

    * Using Mayavi2 without GUI (nongui.py)

    * A 3D array as numerical source (numeric_source.py)

    * Using Streamline Module (streamline.py)

    * Using !ImagePlaneWidget Module (test.py)

    * Plotting a surface from a matrix (surf_regular_mlab.py). See also [[Cookbook/MayaVi/Surf]]

* [[Cookbook/MayaVi/Tips| Tips]]: General tips for !MayaVi2 and around.
* [[Cookbook/MayaVi_examples]]


* [[Cookbook/MayaVi/mlab| Mlab]]: module allowing to drive VTK from Python to do 3D plots ala matlab.

* [[Cookbook/MayaVi/tvtk| tvtk]]: Traited VTK, including iVTK


Matplotlib
==========

The cookbook is a place for community contributions of recipes, howtos and examples.

Complete documentation and tutorials for matplotlib can be found at [[http://matplotlib.sourceforge.net/|matplotlib's webpage]]

<<BR>> <<TableOfContents>>

Simple Plotting
---------------

* [[Cookbook/Matplotlib/SigmoidalFunctions|Sigmoidal Functions]] - plotting simple functions
  . {{attachment:sigmoids_small.png}}
* [[Cookbook/Matplotlib/MultilinePlots|Multiline Plots]] - how to plot multiple lines over one another
  . {{attachment:multiline.png}}
* [[Cookbook/Matplotlib/BarCharts|Bar Charts]] - how to make a bar chart
  . {{attachment:barchartscaled.png}}
* [[Cookbook/Matplotlib/Common_Errors|Common Errors]] - Compilation of common errors that can cause erroneous behavior. Check before emailing mailing lists.
* [[Matplotlib/Animations]] - how to animate your figures.
* [[Cookbook/Matplotlib/MulticoloredLine|Multicolored Line]] - different colors for different parts of a line
  . {{attachment:colored_line.png}}
* [[Cookbook/Matplotlib/ShadedRegions|Shaded Regions]] - how to plot grey shaded regions using transparency.
  . {{attachment:shaded_small.png}}
* [[Matplotlib/Arrows]] - how to plot arrows
  . {{attachment:plot_arrow_small.png}}
* [[Cookbook/Matplotlib/UnfilledHistograms|Unfilled Histograms]] - how to plot histograms that are un-filled and don't look like bar charts.
  . {{attachment:hist_outline_small.png}}
* [[Cookbook/Histograms]] - 2D histograms with variable bin width.
  . {{attachment:Cookbook/Histograms/histogram2d.png}}
* [[Cookbook/Matplotlib/CustomLogLabels|Custom Log Plot Labels]] - plotting log plots with custom tick labels that are formatted as integer numbers rather than exponents as is the default.
  . {{attachment:log_labels_small.png}}
* [[Cookbook/Matplotlib/ThickAxes|Thick Axes]] - how to make thick axes lines and bold fonts.
  . {{attachment:thick_axes.png}}
* [[Matplotlib/Maps]] - how to plot data on map projections
  . {{attachment:basemap1.png}}
* [[Cookbook/Matplotlib/Plotting_values_with_masked_arrays|Plotting values with masked arrays]] - How to plot only selected values of an array, because some values are meaningless (detector malfunction), out of range, etc. etc.
* [[Matplotlib/Transformations]] - Using transformations to convert between different coordinate systems.
* [[Matplotlib/TreeMap]] - classic treemap style plots
* [[Matplotlib/Legend]] - Adding a legend to your plot
* [[Cookbook/Matplotlib/HintonDiagrams|Hinton Diagrams]] - A way of visualizing weight matrices
  . {{attachment:hinton-small.png}}
* [[Cookbook/Matplotlib_TreeMap]]

Pseudo Color Plots
------------------

* [[Cookbook/Matplotlib/Loading_a_colormap_dynamically|Loading a colormap dynamically]] - How to load a color map from a GMT (Generic Mapping Tools) file.
* [[Cookbook/Matplotlib/Show_colormaps|Show colormaps]] - Small script to display all of the Matplotlib colormaps, and an exampleshowing how to create a new one.
* [[Cookbook/Matplotlib/converting_a_matrix_to_a_raster_image|Converting a matrix to a raster image]] - A replacement for scipy's imsave command
* [[Cookbook/Matplotlib/Gridding_irregularly_spaced_data|Gridding irregularly spaced data]] - how to grid scattered data points in order to make a contour or image plot.
* [[Cookbook/Matplotlib/Plotting_Images_with_Special_Values|Plotting Images with Special Values]] - how to plot an image with special values mapped to specific colors, e.g. missing values or data extrema
  . {{attachment:sentinel.png}}
* [[Cookbook/Matplotlib/ColormapTransformations|Transformations on Colormaps]] - how to apply a function to the look up table of a colormap and turn it into another one.

Typesetting
-----------

* [[Cookbook/Matplotlib/UsingTex|Using TeX]] - formatting matplotlib text with LaTeX
  . {{attachment:tex_demo.png}}
* [[Cookbook/Matplotlib/LaTeX_Examples|LaTeX Examples]] - Complete examples for generating publication quality figures using LaTeX.

3D Plotting
-----------

||'''NOTE:''' '''''Experimental work has been going on to integrate 3D plotting functionality into matplotlib'''''. Please see the related [[http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/index.html?highlight-mplot3d|mplot3d documentation]] or take a look at [[http://matplotlib.sourceforge.net/gallery.html|matplotlib gallery]] for example 3D plots. For a more sophisticated 3D visualization and plotting interface, you can try [[http://code.enthought.com/projects/mayavi/|Mayavi]] which is actively maintained and features an 'mlab' interface similar to matplotlib's 'pylab'. ||

* [[Cookbook/Matplotlib/mplot3D|3D plots]] - Simple 3D plots using matplotlibs built-in 3D functions (which were originally provided by John Porter's mplot3d add-on module).
  . {{attachment:contourf3D.jpg}}
* [[Cookbook/Matplotlib/VTK_Integration|VTK Integration]] - How to import plots into VTK.
  . {{attachment:mpl_vtk.png}}

Embedding Plots in Apps
-----------------------

* [[Cookbook/Matplotlib/EmbeddingInWx|Embedding in WX]] - Advice on how to embed matplotlib figures in [[http://www.wxpython.org|wxPython]] applications.
* [[http://agni.phys.iit.edu/~kmcivor/wxmpl|WxMpl]] - Python module for integrating matplotlib into wxPython GUIs.
* [[Cookbook/Matplotlib/ScrollingPlot]] - Demonstrates how to control a matplotlib plot embedded in a wxPython application with scrollbars.
* [[http://code.enthought.com/projects/traits/docs/html/tutorials/traits_ui_scientific_app.html|Gael Varoquax's scientific GUI tutorial]] - Includes an instructive example of embedding matplotlib in a [[http://code.enthought.com/projects/traits_gui/|Traits GUI]].
* [[Cookbook/Matplotlib/PySide]] - Demonstrates how to display a matplotlib plot embedded in a PySide (Qt) application
* [[Cookbook/EmbeddingInTraitsGUI]]
* [[Cookbook/Matplotlib_Drag_n_Drop_Text_Example]]

Misc
----

* [[Cookbook/Matplotlib/LoadImage|Load and display an image]] - shows a simple way to import a PNG image to a numpy array
* [[Cookbook/Matplotlib/Interactive_Plotting|Interactive Plotting]] - Adding mouse interaction to identify data annotations.
* [[Cookbook/Matplotlib/Matplotlib_and_Zope|Matplotlib and Zope]] - How to use Matplotlib within the application server [[http://www.zope.org|Zope]].
* [[Cookbook/Matplotlib/Qt_with_IPython_and_Designer|Qt with IPython and Designer]] - How to design a GUI using Qt's Designer tool using Matplotlib widgets, and that can be interactively controlled from the IPython command line.
* [[Cookbook/Matplotlib/CompilingMatPlotLibOnSolaris10|Compiling Matplotlib on Solaris 10]] - how to compile the thing on Solaris 10, using gcc/g++
* [[Cookbook/Matplotlib/Using_MatPlotLib_in_a_CGI_script|Using MatPlotLib in a CGI script]] - steps needed to be able to use matplotlib from a python cgi script
* [[http://www.answermysearches.com/index.php/making-dynamic-charts-and-graphs-for-your-webpage/135/|Making Dynamic Charts for your Webpage]] - Complete CGI script example.
* [[http://www.dalkescientific.com/writings/diary/archive/2005/04/23/matplotlib_without_gui.html|matplotlib without GUI]] by Andrew Dalke.
* [[http://debs.astraw.com/dapper/|Andrew Straw's Apt Repository]] - Bleeding edge deb packages for Debian, Ubuntu (also has packages for numpy/scipy etc.).
* [[Cookbook/Matplotlib/AdjustingImageSize|Adjusting Image Size]] - a brief discussion of how to adjust the size of figures -- for printing, web, etc.
* [[Cookbook/Matplotlib/DeletingAnExistingDataSeries|Deleting An Existing Data Series]] - a quick example showing how to remove one data series from an already existing plot.
* [[Cookbook/Matplotlib/Django|Embedding in Django]] - example on how to use matplotlib with Django.
* [[Cookbook/Matplotlib/Multiple_Subplots_with_One_Axis_Label|Multiple Subplots with One Axis Label]] - how to use one centered label to annotate several subplots

Interfacing With Other Languages
================================

* A [[PerformancePython|comparison]] of Weave with !NumPy, Pyrex, Psyco, Fortran and C++ using Laplace's equation as an example.
* Using [[Cookbook/Pyrex_and_NumPy|Pyrex and NumPy]] to share data between your Pyrex/C extension module and !NumPy.
* Using [[Cookbook/ArrayStruct_and_Pyrex|Pyrex and the array_struct interface]] to access array data without requiring a C dependency on Numeric, numarray, or !NumPy.
* '''!NumInd''': [[Cookbook/A_Numerical_Agnostic_Pyrex_Class|A Numerical Agnostic Pyrex Class]] to access Numeric/numarray/!NumPy arrays in an uniform way from both C and Pyrex space.
* Using [[Cookbook/SWIG_and_NumPy|SWIG and NumPy]] to access and modify !NumPy arrays in C libraries.
* '''numpy.i''': A few [[Cookbook/SWIG_NumPy_examples|SWIG and numpy.i]] basic examples.
* '''numpy.i''': Using [[Cookbook/SWIG_Memory_Deallocation|SWIG and numpy.i]] to handle automatic C memory deallocation from Python (using a modified numpy.i).
* Using [[Cookbook/F2Py|f2py]] to wrap Fortran codes.
* Using [[Cookbook/f2py_and_NumPy|f2py and Numpy]] to wrap C codes.
* Writing [[Cookbook/C_Extensions|C Extensions]].
* [[Cookbook/C_Extensions_NumPy_arrays]]
* Using [[Cookbook/Ctypes|ctypes with NumPy]].
* Using [[Cookbook/Weave]] and '''iterators''' for fast, generalized code.
* [[Cookbook/CompilingExtensionsOnWindowsWithMinGW|Compiling Extensions on Windows]] A quick tutorial on how to compile extension modules on Windows using MinGW


Scientific GUIs
===============

* [[vtkVolumeRendering|VTK volume rendering]]. This is a simple example that show how to use VTK to volume render your three dimensional numpy arrays.
* Using [[Cookbook/wxPython_dialogs|wxPython dialogs]] for simple user interaction.
* Using [[TraitsUI]] to build interactive applications.