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/** \mainpage VIGRA Reference Manual
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref Installation
<BR> <em>how to get started</em>
<LI> \ref Tutorial
<BR> <em>first steps with VIGRA</em>
<LI> \ref Concepts
<BR> <em>generic interface definitions</em>
<LI> \ref Utilities
<BR> <em>Basic helper functionality needed throughout</em>
<LI> \ref ErrorReporting
<BR> <em>Exceptions and assertions</em>
<LI> \ref MathFunctionality
<BR> <em>Number types, mathematical constants and functions, linear algebra etc.</em>
<LI> \ref PixelTypes
<BR> <em>Non-scalar types such as RGBValue and TinyVector</em>
<LI> \ref ImageDataStructures
<BR> <em>Images, image iterators, and supporting types and functions</em>
<LI> \ref MultiDimensionalArrays
<BR> <em>Arrays, iterators, and supporting types and functions
for arbitrary dimensions</em>
<LI> \ref ChunkedArrayClasses
<BR> <em>Store big data (potentially larger than RAM) as a collection of rectangular blocks</em>
<LI> \ref GraphDataStructures
<BR> <em>Graph-based algorithms (e.g. segmentation) and underlying graph classes (e.g. grid graphs for arbitrary dimensions)</em>
<LI> \ref ImportExport
<BR> <em>Conversion from and to other image data types</em>
<LI> \ref ColorConversions
<BR> <em>Convert between RGB and other color spaces, such as L*u*v*, Y'PbPr</em>
<LI> \ref ImageProcessing
<BR> <em>Point operators, image arithmetic, convolution, morphology</em>
<LI> \ref Registration
<BR> <em>Transforming different images into a common coordinate system</em>
<LI> \ref ImageAnalysis
<BR> <em>Segmentation and feature extraction algorithms</em>
<LI> \ref MachineLearning
<BR> <em>Classification algorithms</em>
<LI> \ref ExampleList
<BR> <em>Demonstration programs for VIGRA's usage </em>
<LI> \ref VigraMatlab
<BR> <em>VIGRA Matlab bindings</em>
<LI> <b><a href="/usr/share/doc/python-vigra-doc/html/index.html">vigranumpy</a></b>
<BR> <em>VIGRA Python bindings</em>
<LI> \ref CreditsChangelog
<BR> <em>Who contributed what?</em>
</UL>
\anchor _details
<CENTER>
\section Main VIGRA - Vision with Generic Algorithms
Version \vigra_version
by <a href="http://hci.iwr.uni-heidelberg.de/people/ukoethe/">Ullrich Köthe</a>
</CENTER>
VIGRA is a computer vision library that puts its main emphasis on
<em>flexible algorithms</em>, because
algorithms represent the principle know-how of this field.
The library was consequently built
using <em>generic programming</em> as introduced by Stepanov
and Musser and exemplified in the C++
<a href=\stl_link>Standard Template Library</a>.
By writing a few adapters (image iterators and accessors)
you can use VIGRA's algorithms on top of
<em>your</em> data structures, within <em>your</em> environment. Alternatively,
you can also use the data structures provided within VIGRA, which can
be easily adapted to a wide range of applications. VIGRA's flexibility
comes almost for free: Since the design uses compile-time polymorphism
(templates), performance of the compiled program approaches that
of a traditional, hand tuned, inflexible, solution.
VIGRA's design is documented in the chapter <em>"Reusable Software in
Computer Vision"</em> by
<a href="http://hci.iwr.uni-heidelberg.de/people/ukoethe/">Ullrich Köthe</a>,
in: B. Jähne, H. Haußecker, P. Geißler: "Handbook on
Computer Vision and Applications", volume 3, Academic Press, 1999.
If you don't have the book, you may read a
<a href="http://hci.iwr.uni-heidelberg.de/vigra/documents/GenericProg2D.ps">draft of this article</a>. A shorter
article <em><a href="http://hci.iwr.uni-heidelberg.de/people/ukoethe/papers/index.php#cite_GenericProg2DCppReport">STL Style Generic Programming with Images</a></em>
describing some of the
ideas has appeared in the January 2000 issue of
<a href="http://www.creport.com/">C++ Report Magazine</a>. The most comprehensive source of information is
U. Köthe's PhD thesis <em><a href="http://hci.iwr.uni-heidelberg.de/people/ukoethe/papers/index.php#cite_PhD">Generische Programmierung für die Bildverarbeitung</a></em>, but this is written in German.
VIGRA is subject to this <a href="LICENSE.txt">LICENSE</a>.
You can also subscribe to the <a href="https://mailhost.informatik.uni-hamburg.de/mailman/listinfo/vigra">VIGRA Mailing List</a> to get instant information about new releases, discuss VIGRA's features and development, and ask the experts for help.
*/
/** \page Concepts Concepts
<DL>
<DT>
Description of the generic interface concepts used within VIGRA.
<DD>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref AlgebraicConcepts
<BR> <em>Requirements for types that implement arithmetic operations</em>
<LI> \ref ImageIterators
<BR> <em>Requirements for 2D iterators</em>
<LI> \ref MultiIteratorPage
<BR> <em>Iterators for multi-dimensional arrays</em>
<LI> \ref DataAccessors
<BR> <em>Requirements for data accessors</em>
<LI> \ref vigra::FunctorTraits
<BR> <em>Requirements for functor traits</em>
<LI> \ref CrackEdgeImage
</UL>
</DL>
*/
/** \page MathFunctionality Mathematical Tools
<b>Number types, mathematical constants, special functions, linear algebra</b>
<p>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref AlgebraicConcepts
<BR> <em>Requirements for types that implement arithmetic operations</em>
<LI> \ref NumericPromotionTraits
<BR> <em>Meta-information about arithmetic types</em>
<LI> \ref MathConstants
<BR> <em>M_PI, M_SQRT2</em>
<LI> <b>Grid Neighborhood Specification</b>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref PixelNeighborhood "2-dimensional" (4- and 8-neighborhood)
<LI> \ref VoxelNeighborhood "3-dimensional" (6- and 26-neighborhood)
</UL>
<LI> <b>Number Types</b>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::Rational
<LI> \ref vigra::TinyVector
<LI> \ref vigra::autodiff::DualVector
<LI> \ref vigra::FFTWComplex
<LI> \ref vigra::FixedPoint16
<LI> \ref vigra::Quaternion
</UL>
<LI> \ref RandomNumberGeneration
<BR> <em>Mersenne twister class and random number functors</em>
<LI> \ref Polynomials
<BR> <em>Polynomials and root determination</em>
<LI> \ref MathFunctions
<BR> <em>and functors</em>
<LI> \ref vigra::linalg::Matrix "Matrix class"
<BR> <em>the matrix class</em>
<LI> \ref LinearAlgebraModule "Linear Algebra"
<BR> <em>matrix algebra, solution of linear systems, eigenvalue calculation etc.</em>
<LI> \ref Unsupervised_Decomposition "Unsupervised Decomposition"
<BR> <em>Unsupervised matrix decomposition methods (pLSA)</em>
<LI> \ref Optimization "Optimization and Regression"
<BR> <em>ordinary and non-negative least squares, ridge regression, least angle regression (LARS and LASSO)</em>
</UL>
*/
/** \page PixelTypes Pixel Types
<DL>
<DT>
<b>Scalar types</b>
<DD>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref FixedSizeInt
<LI> \ref vigra::Rational
<LI> \ref vigra::FixedPoint
<LI> \ref vigra::FixedPoint16
</UL>
<p>
<DT>
<b>RGB colors and related functionality</b>
<DD>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::RGBValue
<LI> \ref RGBValueTraits
<LI> \ref RGBValueOperators
<LI> \ref RGBValueAccessors
</UL>
<p>
<DT>
<b>Fixed-size vectors and related functionality</b>
<DD>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::TinyVector
<LI> \ref vigra::TinyVectorView
<LI> \ref TinyVectorTraits
<LI> \ref TinyVectorOperators
</UL>
<p>
<DT>
<b>Complex Numbers</b>
<DD>
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::FFTWComplex
<LI> \ref FFTWComplexTraits
<LI> \ref FFTWComplexOperators
<LI> \ref FFTWComplexAccessors
</UL>
</DL>
*/
/** \page ImageDataStructures Image Data Structures and Iterators
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::BasicImage
<BR> <em>Fundamental class template for images </em>
<LI> \ref vigra::BasicImageView
<BR> <em>Class template for images that use external memory</em>
<LI> \ref StandardImageTypes
<BR> <em>The most common instantiations of \ref vigra::BasicImage</em>
<LI> \ref vigra::SplineImageView
<BR> <em>Wrap a discrete image as a continous function</em>
<LI> \ref VigraImpex
<BR> <em>Image import/export</em>
<LI> \ref ImageContainers
<BR> <em>Classes to manage multiple images (ImageArray..)</em>
<LI> \ref PixelNeighborhood
<BR> <em>Easy access to the 4- and 8-neighbors of a pixel</em>
<LI> \ref ImageIterators
<BR> <em>Basic image iterator implementations </em>
<LI> \ref ImageIteratorAdapters
<BR> <em>Iterate over rows, columns, and other image subsets </em>
<LI> \ref DataAccessors
<BR> <em>Basic templates to encapsulate access to the data of an iterator</em>
<LI> \ref ArgumentObjectFactories
<BR> <em>Factory functions to create argument objects which simplify long argument lists </em>
</UL>
*/
/** \page MultiDimensionalArrays Multi-Dimensional Arrays and Iterators
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref vigra::MultiArrayView
<BR> <em>Interface for multi-dimensional arrays </em>
<LI> \ref vigra::MultiArray
<BR> <em>Array class that holds the actual memory</em>
<LI> \ref MultiMathModule
<BR> <em>Arithmetic and algebraic expressions for multi-dimensional arrays</em>
<LI> \ref MultiArrayTags
<BR> <em>Meta-programming tags to mark array's as strided or unstrided</em>
<LI> \ref MultiIteratorPage
<BR> <em>Iterators for multi-dimensional arrays</em>
<LI> \ref vigra::MultiArrayNavigator
<BR> <em>Navigator utility for multi-dimensional arrays</em>
<LI> \ref VolumeImpex
<BR> <em>Import/export of volume data.</em>
<LI> \ref MultiPointoperators
<BR> <em>Point operators on multi-dimensional arrays</em>
<LI> \ref MultiArrayConvolutionFilters
<BR> <em>Convolution filters in arbitrary dimensions</em>
<LI> \ref FourierTransform
<BR> <em>Fast Fourier transform for arrays of arbitrary dimension</em>
<LI> \ref resizeMultiArraySplineInterpolation()
<BR> <em>Interpolation of arrays in arbitrary dimensions</em>
<LI> \ref MultiArrayDistanceTransform
<BR> <em>Separable distance transform for arrays of arbitrary dimension</em>
<LI> \ref MultiArrayMorphology
<BR> <em>Separable morphology with parabola structuring function for arrays of arbitrary dimension</em>
<LI> \ref labelVolume(), \ref seededRegionGrowing3D(), \ref watersheds3D(), \ref localMinima3D(), \ref localMaxima3D(),
<BR> <em>3-dimensional image (i.e. volume) analysis</em>
<LI> \ref VoxelNeighborhood
<BR> <em>Easy access to the 6- and 26-neighbors of a voxel</em>
<LI> \ref vigra::NumpyArray and \ref vigra::NumpyAnyArray
<BR> <em>Provide the VIGRA multi array interface Python arrays</em>
</UL>
*/
/** \page ImportExport Image Import and Export
Conversion from and to other image data types
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref VigraImpex
<BR> <em>VIGRA's highlevel image import/export interface</em>
<LI> \ref VolumeImpex
<BR> <em>Import/export interface for volume data</em>
<LI> \ref VigraHDF5Impex
<BR> <em>Import/export of images and arrays in
<a href="http://www.hdfgroup.org/HDF5/">HDF5</a> format</em>
<LI> \ref TIFFImpex
<BR> <em>image import/export interface if you want to call libtiff functions directly</em>
</UL>
There are two fundamentally different approaches to interfacing between VIGRA and the rest of the world.
<b>If you already have an image data type in your system:</b>
Then I recommend using VIGRA's algorithms directly on top of your data type.
To do this, you simply wrap your data in an \ref vigra::ImageIterator and/or
\ref vigra::MultiArrayView (depending on the functions you want to call). If
your data have some exotic properties, that prevent this solution from working,
you can still implement your own versions or subclasses of the interface classe,
which isn't very difficult.
Alternatively, you may use the data structures provided within VIGRA
and convert your data type into one of them. Take a look at \ref tiffToScalarImage() and
\ref createScalarTiffImage() to see how this might be done.
<b>If you don't have an image data type in your system:</b>
Use the data structures provided within VIGRA and use one of the import/export facilities above.
*/
/** \page ImageProcessing Image Processing
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref PointOperators
<BR> <em>algorithms and functors for image arithmetic, inspection, transformations etc.</em>
<LI> \ref MultiMathModule
<BR> <em>Arithmetic and algebraic expressions for multi-dimensional arrays</em>
<LI> \ref FunctorExpressions
<BR> <em>Expression templates for automated functor creation</em>
<LI> \ref GeometricTransformations "Resize and Other Geometric Image Transformations"
<BR> <em>resize and interpolation, image mirroring, rotation, arbitrary affine transformations</em>
<LI> \ref vigra::SplineImageView
<BR> <em>Wrap a discrete image as a continous function</em>
<LI> \ref Convolution
<BR> <em>1D, 2D, and nD filters, including separable and recursive convolution</em>
<LI> \ref NonLinearDiffusion
<BR> <em>Edge-preserving smoothing and denoising</em>
<LI> \ref Correlation
<BR> <em>Fast and slow algorithms to estimate the correlation between images</em>
<LI> \ref Registration
<BR> <em>Transforming different images into a common coordinate system</em>
<LI> \ref FourierTransform
<BR> <em>forward and backward FFT, cosine transform, and related
functionality</em>
<LI> \ref GaborFilter
<BR> <em>Gabor filter generation and related
functionality</em>
<LI> \ref TensorImaging
<BR> <em>Tensor image processing</em>
<LI> \ref Morphology
<BR> <em>erosion, dilation, and median with disc structuring functions</em>
<LI> \ref NoiseNormalization
<BR> <em>transform intensity-dependent noise into additive Gaussian noise</em>
<LI> \ref SlantedEdgeMTF
<BR> <em>determine the magnitude transfer function (MTF) of a camera using the slanted edge method</em>
</UL>
*/
/** \page ImageAnalysis Image Analysis
<UL style="list-style-image:url(documents/bullet.gif)">
<LI> \ref InspectAlgo and \ref InspectFunctor
<BR> <em>Statistical analysis of images and regions</em>
<LI> \ref FeatureAccumulators
<BR> <em>Computation of global and per-region statistics of multi arrays via accumulators framework</em>
<LI> \ref vigra::Threshold
<BR> <em>Good old thresholding</em>
<LI> \ref Labeling
<BR> <em>Connected components labeling using 4 or 8 connectivity </em>
<LI> \ref LocalMinMax
<BR> <em>Including extremal plateaus larger than 1 pixel</em>
<LI> \ref DistanceTransform
<BR> <em>Distance transform using Euclidean, Manhattan, or chessboard metrics </em>
<LI> \ref TensorImaging
<BR> <em>Tensor image analysis</em>
<LI> \ref EdgeDetection
<BR> <em>Edge detectors based on first and second derivatives</em>
<LI> \ref CornerDetection
<BR> <em>Measure the 'cornerness' at each pixel </em>
<LI> \ref SymmetryDetection
<BR> <em>Measure the local symmetry at each pixel </em>
<LI> \ref SeededRegionGrowing
<BR> <em>Region growing, watersheds, and voronoi tesselation</em>
</UL>
*/
/** \page AlgebraicConcepts Algebraic Concepts
The algebraic concepts describe requirements for algebraic types, that is
for types that support arithmetic operations. The built-in types are concepts
of \ref AlgebraicField and \ref DivisionAlgebra.
\anchor AlgebraicRing
<h3>Algebraic Ring</h3>
<ul>
<li>A model of Algebraic Ring implements <tt>Assignable</TT>, <tt>Default Constructible</TT>,
<tt>Equality Comparable</TT> and <tt>Strict Weakly Comparable</TT>
as defined in the C++ standard (cf. the
<a href=\stl_link>Standard Template Library documentation</a>).
<li>A model of Algebraic Ring implements addition, subtraction and unary negation. The associated
\link NumericTraits NumericTraits \endlink define a 'zero' element, the type of the
result of addition and subtraction, and a type conversion function.
Addition must be commutative.
\code
ModelOfAlgebraicRing a, b;
NumericTraits<ModelOfAlgebraicRing>::Promote c;
ModelOfAlgebraicRing zero = NumericTraits<ModelOfAlgebraicRing>::zero();
b += a;
b -= a;
b = -a;
c = a + b;
c = a - b;
c = a;
a = NumericTraits<ModelOfAlgebraicRing>::fromPromote(c);
assert(a + zero == a);
assert(a + b == b + a);
assert(a - b == a + (-b));
\endcode
<li>If mixed-type addition and subtraction are supported,
\link PromoteTraits PromoteTraits \endlink define the result type:
\code
ModelOfAlgebraicRing1 a;
ModelOfAlgebraicRing2 b;
PromoteTraits<ModelOfAlgebraicRing1, ModelOfAlgebraicRing2>::Promote c;
c = a + b;
\endcode
<li>A model of Algebraic Ring implements multiplication. The associated
\link NumericTraits NumericTraits \endlink define a 'one' element, the type of the
result of multiplication, and a type conversion function.
\code
ModelOfAlgebraicRing a, b;
NumericTraits<ModelOfAlgebraicRing>::RealPromote c;
ModelOfAlgebraicRing one = NumericTraits<ModelOfAlgebraicRing>::one();
b *= a;
c = a * b;
c = a;
a = NumericTraits<ModelOfAlgebraicRing>::fromRealPromote(c);
assert(a * one == a);
\endcode
</ul>
\anchor AlgebraicField
<h3>Algebraic Field</h3>
<ul>
<li>A model of Algebraic Field implements \ref AlgebraicRing as defined above.
<li>A model of Algebraic Field implements division. Division is undefined if
and only if the right operand is 'zero'.
\code
ModelOfAlgebraicField a, b;
typename NumericTraits<ModelOfAlgebraicField>::RealPromote c;
ModelOfAlgebraicField zero = NumericTraits<ModelOfAlgebraicField>::zero();
if(a != zero) b /= a;
if(a != zero) c = b / a;
\endcode
</ul>
\anchor LinearSpace
<h3>Linear Space</h3>
<ul>
<li>A model of Linear Space implements <tt>Assignable</TT>, <tt>Default Constructible</TT>
and <tt>Equality Comparable</TT>
as defined in the C++ standard (cf. the
<a href=\stl_link>Standard Template Library documentation</a>).
<li>A model of Algebraic Ring implements addition, subtraction and unary negation. The associated
\link NumericTraits NumericTraits \endlink define a 'zero' element, the type of the
result of addition and subtraction, and a type conversion function.
Addition must be commutative. (This part of the requirements is identical to
\ref AlgebraicRing above.)
\code
ModelOfAlgebraicRing a, b;
NumericTraits<ModelOfAlgebraicRing>::Promote c;
ModelOfAlgebraicRing zero = NumericTraits<ModelOfAlgebraicRing>::zero();
b += a;
b -= a;
b = -a;
c = a + b;
c = a - b;
c = a;
a = NumericTraits<ModelOfAlgebraicRing>::fromPromote(c);
assert(a + zero == a);
assert(a + b == b + a);
assert(a - b == a + (-b));
\endcode
<li>If mixed-type addition and subtraction are supported,
\link PromoteTraits PromoteTraits \endlink define the result type:
\code
ModelOfAlgebraicRing1 a;
ModelOfAlgebraicRing2 b;
PromoteTraits<ModelOfAlgebraicRing1, ModelOfAlgebraicRing2>::Promote c;
c = a + b;
\endcode
<li>A model of Algebraic Ring implements multiplication and division with 'double'.
(Note that the outer product could be defined with an arbitrary model of
\ref AlgebraicField. For simplicity, VIGRA restricts this to only 'double'.)
The associated \link NumericTraits NumericTraits \endlink define the type of the
results, and a type conversion function.
\code
ModelOfAlgebraicRing a;
double f;
NumericTraits<ModelOfAlgebraicRing>::RealPromote c;
a *= f;
c = a * f;
c = f * a;
if(f != 0.0) a /= f;
if(f != 0.0) c = a / f;
c = a;
a = NumericTraits<ModelOfAlgebraicRing>::fromRealPromote(c);
\endcode
</ul>
\anchor LinearAlgebraConcept
<h3>Linear Algebra</h3>
<ul>
<li>A model of Linear Algebra implements \ref LinearSpace and
\ref AlgebraicRing as defined above.
</ul>
\anchor DivisionAlgebra
<h3>Division Algebra</h3>
<ul>
<li>A model of Division Algebra implements \ref LinearSpace and
\ref AlgebraicField as defined above.
</ul>
*/
/** \page VigraMatlab Vigra Matlab
Matlab bindings (mex-files) for the most important VIGRA functions are located
<tt>[vigra_src_dir]/src/matlab</tt>. To compile and install them, start Matlab,
go into that directory and call the function buildVigraExtensions:
\code
buildVigraExtensions('install_path')
\endcode
If the compilation fails because includes or libraries are not found, you can
provide additional search directories like this:
\code
buildVigraExtensions('install_path', 'all', struct('flags', '-I/path/to/includes -L/path/to/libs'))
\endcode
Additional compiler flags are specified in the same way. Suggestions about typical settings on Linux and
Windows can be found in the individual .cpp files. For example, on Windows we usually need
\code
buildVigraExtensions('install_path', 'all', ...
struct('flags', '-I[HDF5PATH]/include -L[HDF5PATH]/lib -lhdf5dll -lhdf5_hldll -D_HDF5USEDLL_ -DHDF5CPP_USEDLL'))
\endcode
After successful compilation, you can obtain a list of the available VIGRA functions by calling
\code
help vigraIndex
\endcode
In the same way, you get documentation for the individual functions. More
information about the glue code behind the bindings is available in
<a href="http://hci.iwr.uni-heidelberg.de/vigra/documents/tutorial_reference.pdf">this report</a>.
*/
/** \namespace vigra
all VIGRA functionality is located in namespace vigra
*/
#if 0
//@{
//Include: ../include/vigra/morphological_appropriate_scale.hxx
//Include: ../include/vigra/feature_adjacency_graph.hxx
//@}
#endif
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