borglab · varunagrawal · Oct 26, 2022 · Jul 26, 2022 · Jul 26, 2022 · Jul 26, 2022
diff --git a/INSTALL.md b/INSTALL.md
@@ -50,7 +50,7 @@ will run up to 10x faster in Release mode! See the end of this document for
 additional debugging tips.
 
 3. GTSAM has Doxygen documentation. To generate, run 'make doc' from your
-build directory.
+build directory after setting the `GTSAM_BUILD_DOCS` and `GTSAM_BUILD_[HTML|LATEX]` cmake flags.
 
 4. The instructions below install the library to the default system install path and
 build all components. From a terminal, starting in the root library folder,

diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
@@ -26,14 +26,14 @@ if (GTSAM_BUILD_DOCS)
         gtsam/basis 
         gtsam/discrete
         gtsam/geometry
+        gtsam/hybrid
         gtsam/inference
         gtsam/linear
         gtsam/navigation
         gtsam/nonlinear
         gtsam/sam
         gtsam/sfm
         gtsam/slam
-        gtsam/smart
         gtsam/symbolic
         gtsam
     )
@@ -42,10 +42,12 @@ if (GTSAM_BUILD_DOCS)
     set(gtsam_unstable_doc_subdirs
         gtsam_unstable/base
         gtsam_unstable/discrete
+        gtsam_unstable/dynamics
+        gtsam_unstable/geometry
         gtsam_unstable/linear
-        gtsam_unstable/nonlinear 
-        gtsam_unstable/slam 
-        gtsam_unstable/dynamics 
+        gtsam_unstable/nonlinear
+        gtsam_unstable/partition
+        gtsam_unstable/slam
         gtsam_unstable
     )
 

diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
diff --git a/doc/DoxygenLayout.xml b/doc/DoxygenLayout.xml
@@ -18,7 +18,6 @@
       <tab type="files" visible="yes" title="" intro=""/>
       <tab type="globals" visible="yes" title="" intro=""/>
     </tab>
-    <tab type="dirs" visible="yes" title="" intro=""/>
     <tab type="examples" visible="yes" title="" intro=""/>  
   </navindex>
 

diff --git a/gtsam/base/ConcurrentMap.h b/gtsam/base/ConcurrentMap.h
@@ -62,7 +62,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename KEY, typename VALUE>
 class ConcurrentMap : public ConcurrentMapBase<KEY,VALUE> {

diff --git a/gtsam/base/DSFMap.h b/gtsam/base/DSFMap.h
@@ -28,7 +28,7 @@ namespace gtsam {
 /**
  * Disjoint set forest using an STL map data structure underneath
  * Uses rank compression and union by rank, iterator version
- * @addtogroup base
+ * @ingroup base
  */
 template <class KEY>
 class DSFMap {

diff --git a/gtsam/base/DSFVector.h b/gtsam/base/DSFVector.h
@@ -33,7 +33,7 @@ namespace gtsam {
  * A fast implementation of disjoint set forests that uses vector as underly data structure.
  * This is the absolute minimal DSF data structure, and only allows size_t keys
  * Uses rank compression but not union by rank :-(
- * @addtogroup base
+ * @ingroup base
  */
 class GTSAM_EXPORT DSFBase {
 
@@ -59,7 +59,7 @@ class GTSAM_EXPORT DSFBase {
 
 /**
  * DSFVector additionally keeps a vector of keys to support more expensive operations
- * @addtogroup base
+ * @ingroup base
  */
 class GTSAM_EXPORT DSFVector: public DSFBase {
 

diff --git a/gtsam/base/FastList.h b/gtsam/base/FastList.h
@@ -34,7 +34,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
-   * @addtogroup base
+   * @ingroup base
  */
 template<typename VALUE>
 class FastList: public std::list<VALUE, typename internal::FastDefaultAllocator<VALUE>::type> {

diff --git a/gtsam/base/FastMap.h b/gtsam/base/FastMap.h
@@ -31,7 +31,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename KEY, typename VALUE>
 class FastMap : public std::map<KEY, VALUE, std::less<KEY>,

diff --git a/gtsam/base/FastSet.h b/gtsam/base/FastSet.h
@@ -43,7 +43,7 @@ namespace gtsam {
  * fast_pool_allocator instead of the default STL allocator.  This is just a
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several %.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename VALUE>
 class FastSet: public std::set<VALUE, std::less<VALUE>,

diff --git a/gtsam/base/FastVector.h b/gtsam/base/FastVector.h
@@ -27,7 +27,7 @@ namespace gtsam {
 /**
  * FastVector is a type alias to a std::vector with a custom memory allocator.
  * The particular allocator depends on GTSAM's cmake configuration.
- * @addtogroup base
+ * @ingroup base
  */
 template <typename T>
 using FastVector =

diff --git a/gtsam/base/SymmetricBlockMatrix.h b/gtsam/base/SymmetricBlockMatrix.h
@@ -47,7 +47,7 @@ namespace gtsam {
   * matrix view.  firstBlock() determines the block that appears to have index 0 for all operations
   * (except re-setting firstBlock()).
   *
-  * @addtogroup base */
+  * @ingroup base */
   class GTSAM_EXPORT SymmetricBlockMatrix
   {
   public:

diff --git a/gtsam/base/Testable.h b/gtsam/base/Testable.h
@@ -51,7 +51,7 @@ namespace gtsam {
    * tests and in generic algorithms.
    *
    * See macros for details on using this structure
-   * @addtogroup base
+   * @ingroup base
    * @tparam T is the objectype this constrains to be testable - assumes print() and equals()
    */
   template <class T>

diff --git a/gtsam/base/ThreadsafeException.h b/gtsam/base/ThreadsafeException.h
@@ -14,7 +14,7 @@
  * @brief    Base exception type that uses tbb_allocator if GTSAM is compiled with TBB
  * @author   Richard Roberts
  * @date     Aug 21, 2010
- * @addtogroup base
+ * @ingroup base
  */
 
 #pragma once

diff --git a/gtsam/base/VerticalBlockMatrix.h b/gtsam/base/VerticalBlockMatrix.h
@@ -38,7 +38,7 @@ namespace gtsam {
    * row for all operations.  To include all rows, rowEnd() should be set to the number of rows in
    * the matrix (i.e. one after the last true row index).
    *
-   * @addtogroup base */
+   * @ingroup base */
   class GTSAM_EXPORT VerticalBlockMatrix
   {
   public:

diff --git a/gtsam/base/make_shared.h b/gtsam/base/make_shared.h
@@ -26,7 +26,7 @@
 #include <type_traits>
 
 namespace gtsam {
-  /// An shorthand alias for accessing the ::type inside std::enable_if that can be used in a template directly
+  /// An shorthand alias for accessing the \::type inside std::enable_if that can be used in a template directly
   template<bool B, class T = void>
   using enable_if_t = typename std::enable_if<B, T>::type;
 }

diff --git a/gtsam/base/timing.h b/gtsam/base/timing.h
@@ -147,7 +147,7 @@ namespace gtsam {
       size_t id_;
       size_t t_;
       size_t tWall_;
-      double t2_ ; ///< cache the \sum t_i^2
+      double t2_ ; ///< cache the \f$ \sum t_i^2 \f$
       size_t tIt_;
       size_t tMax_;
       size_t tMin_;

diff --git a/gtsam/base/types.cpp b/gtsam/base/types.cpp
@@ -14,7 +14,7 @@
  * @brief    Functions for handling type information
  * @author   Varun Agrawal
  * @date     May 18, 2020
- * @addtogroup base
+ * @ingroup base
  */
 
 #include <gtsam/base/types.h>

diff --git a/gtsam/base/types.h b/gtsam/base/types.h
@@ -14,7 +14,7 @@
  * @brief    Typedefs for easier changing of types
  * @author   Richard Roberts
  * @date     Aug 21, 2010
- * @addtogroup base
+ * @ingroup base
  */
 
 #pragma once

diff --git a/gtsam/basis/Basis.h b/gtsam/basis/Basis.h
@@ -78,6 +78,8 @@ using Weights = Eigen::Matrix<double, 1, -1>; /* 1xN vector */
  * @tparam M Size of the identity matrix.
  * @param w The weights of the polynomial.
  * @return Mx(M*N) kronecker product [w(0)*I, w(1)*I, ..., w(N-1)*I]
+ *
+ * @ingroup basis
  */
 template <size_t M>
 Matrix kroneckerProductIdentity(const Weights& w) {
@@ -90,7 +92,10 @@ Matrix kroneckerProductIdentity(const Weights& w) {
   return result;
 }
 
-/// CRTP Base class for function bases
+/**
+ * CRTP Base class for function bases
+ *  @ingroup basis
+ */
 template <typename DERIVED>
 class Basis {
  public:

diff --git a/gtsam/basis/BasisFactors.h b/gtsam/basis/BasisFactors.h
@@ -32,6 +32,8 @@ namespace gtsam {
  *
  * Example, degree 8 Chebyshev polynomial measured at x=0.5:
  *  EvaluationFactor<Chebyshev2> factor(key, measured, model, 8, 0.5);
+ *
+ * @ingroup basis
  */
 template <class BASIS>
 class EvaluationFactor : public FunctorizedFactor<double, Vector> {
@@ -86,6 +88,8 @@ class EvaluationFactor : public FunctorizedFactor<double, Vector> {
  *
  * @param BASIS: The basis class to use e.g. Chebyshev2
  * @param M: Size of the evaluated state vector.
+ *
+ * @ingroup basis
  */
 template <class BASIS, int M>
 class VectorEvaluationFactor
@@ -149,6 +153,8 @@ class VectorEvaluationFactor
  *  VectorComponentFactor<BASIS, P> controlPrior(key, measured, model,
  *                                               N, i, t, a, b);
  *  where N is the degree and i is the component index.
+ *
+ * @ingroup basis
  */
 template <class BASIS, size_t P>
 class VectorComponentFactor

diff --git a/gtsam/basis/ParameterMatrix.h b/gtsam/basis/ParameterMatrix.h
@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file ParamaterMatrix.h
+ * @file ParameterMatrix.h
  * @brief Define ParameterMatrix class which is used to store values at
  * interpolation points.
  * @author Varun Agrawal, Frank Dellaert

diff --git a/gtsam/discrete/AlgebraicDecisionTree.h b/gtsam/discrete/AlgebraicDecisionTree.h
@@ -31,6 +31,8 @@ namespace gtsam {
    * Algebraic Decision Trees fix the range to double
    * Just has some nice constructors and some syntactic sugar
    * TODO: consider eliminating this class altogether?
+   *
+   * @ingroup discrete
    */
   template <typename L>
   class GTSAM_EXPORT AlgebraicDecisionTree : public DecisionTree<L, double> {

diff --git a/gtsam/discrete/Assignment.h b/gtsam/discrete/Assignment.h
@@ -31,6 +31,7 @@ namespace gtsam {
  * An assignment from labels to value index (size_t).
  * Assigns to each label a value. Implemented as a simple map.
  * A discrete factor takes an Assignment and returns a value.
+ * @ingroup discrete
  */
 template <class L>
 class Assignment : public std::map<L, size_t> {

diff --git a/gtsam/discrete/DecisionTree.h b/gtsam/discrete/DecisionTree.h
@@ -38,6 +38,8 @@ namespace gtsam {
    * Decision Tree
    * L = label for variables
    * Y = function range (any algebra), e.g., bool, int, double
+   *
+   * @ingroup discrete
    */
   template<typename L, typename Y>
   class DecisionTree {

diff --git a/gtsam/discrete/DecisionTreeFactor.h b/gtsam/discrete/DecisionTreeFactor.h
@@ -36,7 +36,9 @@ namespace gtsam {
   class DiscreteConditional;
 
   /**
-   * A discrete probabilistic factor
+   * A discrete probabilistic factor.
+   *
+   * @ingroup discrete
    */
   class GTSAM_EXPORT DecisionTreeFactor : public DiscreteFactor,
                                           public AlgebraicDecisionTree<Key> {

diff --git a/gtsam/discrete/DiscreteBayesNet.h b/gtsam/discrete/DiscreteBayesNet.h
@@ -33,7 +33,7 @@ namespace gtsam {
 
 /** 
  * A Bayes net made from discrete conditional distributions. 
- * @addtogroup discrete
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteBayesNet: public BayesNet<DiscreteConditional> {
  public:

diff --git a/gtsam/discrete/DiscreteBayesTree.h b/gtsam/discrete/DiscreteBayesTree.h
@@ -62,7 +62,10 @@ class GTSAM_EXPORT DiscreteBayesTreeClique
 };
 
 /* ************************************************************************* */
-/** A Bayes tree representing a Discrete density */
+/**
+ * @brief A Bayes tree representing a Discrete density.
+ * @ingroup discrete
+ */
 class GTSAM_EXPORT DiscreteBayesTree
     : public BayesTree<DiscreteBayesTreeClique> {
  private:

diff --git a/gtsam/discrete/DiscreteConditional.h b/gtsam/discrete/DiscreteConditional.h
@@ -32,6 +32,8 @@ namespace gtsam {
 /**
  * Discrete Conditional Density
  * Derives from DecisionTreeFactor
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteConditional
     : public DecisionTreeFactor,

diff --git a/gtsam/discrete/DiscreteDistribution.h b/gtsam/discrete/DiscreteDistribution.h
@@ -27,6 +27,8 @@ namespace gtsam {
 /**
  * A prior probability on a set of discrete variables.
  * Derives from DiscreteConditional
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteDistribution : public DiscreteConditional {
  public:

diff --git a/gtsam/discrete/DiscreteEliminationTree.h b/gtsam/discrete/DiscreteEliminationTree.h
@@ -24,6 +24,10 @@
 
 namespace gtsam {
 
+  /**
+   * @brief Elimination tree for discrete factors.
+   * @ingroup discrete
+   */
   class GTSAM_EXPORT DiscreteEliminationTree :
     public EliminationTree<DiscreteBayesNet, DiscreteFactorGraph>
   {

diff --git a/gtsam/discrete/DiscreteFactor.h b/gtsam/discrete/DiscreteFactor.h
@@ -31,6 +31,8 @@ class DiscreteConditional;
 /**
  * Base class for discrete probabilistic factors
  * The most general one is the derived DecisionTreeFactor
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteFactor: public Factor {
 

diff --git a/gtsam/discrete/DiscreteFactorGraph.h b/gtsam/discrete/DiscreteFactorGraph.h
@@ -40,7 +40,14 @@ class DiscreteEliminationTree;
 class DiscreteBayesTree;
 class DiscreteJunctionTree;
 
-/** Main elimination function for DiscreteFactorGraph */
+/**
+ * @brief Main elimination function for DiscreteFactorGraph.
+ * 
+ * @param factors 
+ * @param keys 
+ * @return GTSAM_EXPORT
+ * @ingroup discrete
+ */
 GTSAM_EXPORT std::pair<boost::shared_ptr<DiscreteConditional>, DecisionTreeFactor::shared_ptr>
 EliminateDiscrete(const DiscreteFactorGraph& factors, const Ordering& keys);
 
@@ -64,6 +71,7 @@ template<> struct EliminationTraits<DiscreteFactorGraph>
 /**
  * A Discrete Factor Graph is a factor graph where all factors are Discrete, i.e.
  *   Factor == DiscreteFactor
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteFactorGraph
     : public FactorGraph<DiscreteFactor>,

diff --git a/gtsam/discrete/DiscreteJunctionTree.h b/gtsam/discrete/DiscreteJunctionTree.h
@@ -44,7 +44,8 @@ namespace gtsam {
    * The tree structure and elimination method are exactly analogous to the EliminationTree,
    * except that in the JunctionTree, at each node multiple variables are eliminated at a time.
    *
-   * \addtogroup Multifrontal
+   * \ingroup Multifrontal
+   * @ingroup discrete
    * \nosubgrouping
    */
   class GTSAM_EXPORT DiscreteJunctionTree :

diff --git a/gtsam/discrete/DiscreteKey.h b/gtsam/discrete/DiscreteKey.h
@@ -31,6 +31,7 @@ namespace gtsam {
   /**
    * Key type for discrete variables.
    * Includes Key and cardinality.
+   * @ingroup discrete
    */
   using DiscreteKey = std::pair<Key,size_t>;
 

diff --git a/gtsam/discrete/DiscreteLookupDAG.h b/gtsam/discrete/DiscreteLookupDAG.h
@@ -32,6 +32,7 @@ class DiscreteBayesNet;
 
 /**
  * @brief DiscreteLookupTable table for max-product
+ * @ingroup discrete
  *
  * Inherits from discrete conditional for convenience, but is not normalized.
  * Is used in the max-product algorithm.