include/dai/alldai.h

   1 /*  This file is part of libDAI - http://www.libdai.org/
   2  *
   3  *  Copyright (c) 2006-2011, The libDAI authors. All rights reserved.
   4  *
   5  *  Use of this source code is governed by a BSD-style license that can be found in the LICENSE file.
   6  */
   7
   8
   9 /** \file
  10  *  \brief Main libDAI header file. It \#includes all other libDAI headers.
  11  *
  12  *  \todo Replace VarSets by SmallSet<size_t> where appropriate, in order to minimize the use of FactorGraph::findVar().
  13  *
  14  *  \todo Improve SWIG interfaces and merge their build process with the main build process
  15  */
  16
  17
  18 #ifndef __defined_libdai_alldai_h
  19 #define __defined_libdai_alldai_h
  20
  21
  22 #include <dai/dai_config.h>
  23 #include <string>
  24 #include <dai/daialg.h>
  25 #include <dai/properties.h>
  26 #include <dai/exactinf.h>
  27 #include <dai/evidence.h>
  28 #include <dai/emalg.h>
  29 #ifdef DAI_WITH_BP
  30     #include <dai/bp.h>
  31 #endif
  32 #ifdef DAI_WITH_FBP
  33     #include <dai/fbp.h>
  34 #endif
  35 #ifdef DAI_WITH_TRWBP
  36     #include <dai/trwbp.h>
  37 #endif
  38 #ifdef DAI_WITH_MF
  39     #include <dai/mf.h>
  40 #endif
  41 #ifdef DAI_WITH_HAK
  42     #include <dai/hak.h>
  43 #endif
  44 #ifdef DAI_WITH_LC
  45     #include <dai/lc.h>
  46 #endif
  47 #ifdef DAI_WITH_TREEEP
  48     #include <dai/treeep.h>
  49 #endif
  50 #ifdef DAI_WITH_JTREE
  51     #include <dai/jtree.h>
  52 #endif
  53 #ifdef DAI_WITH_MR
  54     #include <dai/mr.h>
  55 #endif
  56 #ifdef DAI_WITH_GIBBS
  57     #include <dai/gibbs.h>
  58 #endif
  59 #ifdef DAI_WITH_CBP
  60     #include <dai/cbp.h>
  61 #endif
  62 #ifdef DAI_WITH_DECMAP
  63     #include <dai/decmap.h>
  64 #endif
  65 #ifdef DAI_WITH_GLC
  66     #include <dai/glc.h>
  67 #endif
  68
  69
  70 /// Namespace for libDAI
  71 namespace dai {
  72
  73
  74 /// Returns a map that contains for each built-in inference algorithm its name and a pointer to an object of that type
  75 /** \obsolete This functionality is obsolete and will be removed in future versions of libDAI
  76  */
  77 std::map<std::string, InfAlg *>& builtinInfAlgs();
  78
  79
  80 /// Returns a set of names of all available inference algorithms
  81 /*  These are the names of the algorithms that were compiled in and can be
  82  *  given to \ref newInfAlg and \ref newInfAlgFromString.
  83  *  \return A set of strings, each one corresponding with the name of an available inference algorithm.
  84  *  \note The set is returned by value because it will be reasonably small
  85  *  enough and this function is expected to be called infrequently.
  86  */
  87 std::set<std::string> builtinInfAlgNames();
  88
  89
  90 /// Constructs a new inference algorithm.
  91 /** \param name The name of the inference algorithm.
  92  *  \param fg The FactorGraph that the algorithm should be applied to.
  93  *  \param opts A PropertySet specifying the options for the algorithm.
  94  *  \return Returns a pointer to the new InfAlg object; it is the responsibility of the caller to delete it later.
  95  *  \throw UNKNOWN_DAI_ALGORITHM if the requested name is not known/compiled in.
  96  */
  97 InfAlg *newInfAlg( const std::string &name, const FactorGraph &fg, const PropertySet &opts );
  98
  99
 100 /// Constructs a new inference algorithm.
 101 /** \param nameOpts The name and options of the inference algorithm (should be in the format "name[key1=val1,key2=val2,...,keyn=valn]").
 102  *  \param fg The FactorGraph that the algorithm should be applied to.
 103  *  \return Returns a pointer to the new InfAlg object; it is the responsibility of the caller to delete it later.
 104  *  \throw UNKNOWN_DAI_ALGORITHM if the requested name is not known/compiled in.
 105  */
 106 InfAlg *newInfAlgFromString( const std::string &nameOpts, const FactorGraph &fg );
 107
 108
 109 /// Constructs a new inference algorithm.
 110 /** \param nameOpts The name and options of the inference algorithm (should be in the format "name[key1=val1,key2=val2,...,keyn=valn]").
 111  *  \param fg The FactorGraph that the algorithm should be applied to.
 112  *  \param aliases Maps names to strings in the format "name[key1=val1,key2=val2,...,keyn=valn]"; if not empty, alias substitution
 113  *  will be performed when parsing \a nameOpts by invoking parseNameProperties(const std::string &,const std::map<std::string,std::string> &)
 114  *  \see newInfAlgFromString(const std::string &, const FactorGraph &)
 115  */
 116 InfAlg *newInfAlgFromString( const std::string &nameOpts, const FactorGraph &fg, const std::map<std::string,std::string> &aliases );
 117
 118
 119 /// Extracts the name and property set from a string \a s in the format "name[key1=val1,key2=val2,...]" or "name"
 120 std::pair<std::string, PropertySet> parseNameProperties( const std::string &s );
 121
 122
 123 /// Extracts the name and property set from a string \a s in the format "name[key1=val1,key2=val2,...]" or "name", performing alias substitution
 124 /** Alias substitution is performed as follows: as long as name appears as a key in \a aliases,
 125  *  it is substituted by its value. Properties in \a s override those of the alias (in case of
 126  *  recursion, the "outer" properties override those of the "inner" aliases).
 127  */
 128 std::pair<std::string, PropertySet> parseNameProperties( const std::string &s, const std::map<std::string,std::string> &aliases );
 129
 130
 131 /// Reads aliases from file named \a filename
 132 /** \param filename Name of the alias file
 133  *  \return A map that maps aliases to the strings they should be substituted with.
 134  *  \see \ref fileformats-aliases
 135  */
 136 std::map<std::string,std::string> readAliasesFile( const std::string &filename );
 137
 138
 139 } // end of namespace dai
 140
 141
 142 /** \example example.cpp
 143  *  This example illustrates how to read a factor graph from a file and how to
 144  *  run several inference algorithms (junction tree, loopy belief propagation,
 145  *  and the max-product algorithm) on it.
 146  */
 147
 148
 149 /** \example example_imagesegmentation.cpp
 150  *  This example shows how one can use approximate inference in factor graphs
 151  *  on a simple vision task: given two images, identify smooth regions where these
 152  *  two images differ more than some threshold. This can be used to seperate
 153  *  foreground from background if one image contains the background and the other
 154  *  one the combination of background and foreground.
 155  *
 156  *  \note In order to build this example, a recent version of CImg needs to be installed.
 157  */
 158
 159
 160 /** \example uai2010-aie-solver.cpp
 161  *  This example contains the full source code of the solver that was one of the
 162  *  winners (the 'libDAI2' solver) in the UAI 2010 Approximate Inference Challenge
 163  *  (see http://www.cs.huji.ac.il/project/UAI10/ for more information).
 164  */
 165
 166
 167 #endif