Merge remote-tracking branch 'origin/develop' into feature/ImuFactorPush2

Conflicts:
	gtsam/navigation/tests/testImuFactor.cpp

CMakeLists.txt

@@ -131,7 +131,7 @@ endif()
 
 if(NOT (${Boost_VERSION} LESS 105600))
 	message("Ignoring Boost restriction on optional lvalue assignment from rvalues")
-	add_definitions(-DBOOST_OPTIONAL_ALLOW_BINDING_TO_RVALUES)
+	add_definitions(-DBOOST_OPTIONAL_ALLOW_BINDING_TO_RVALUES -DBOOST_OPTIONAL_CONFIG_ALLOW_BINDING_TO_RVALUES)
 endif()
 
 ###############################################################################

cmake/GtsamBuildTypes.cmake

@@ -34,19 +34,19 @@ if(NOT FIRST_PASS_DONE)
     set(CMAKE_MODULE_LINKER_FLAGS_PROFILING "${CMAKE_MODULE_LINKER_FLAGS_RELEASE}" CACHE STRING "Linker flags during profiling builds." FORCE)
     mark_as_advanced(CMAKE_C_FLAGS_PROFILING CMAKE_CXX_FLAGS_PROFILING CMAKE_EXE_LINKER_FLAGS_PROFILING CMAKE_SHARED_LINKER_FLAGS_PROFILING CMAKE_MODULE_LINKER_FLAGS_PROFILING)
   else()
-    set(CMAKE_C_FLAGS_DEBUG            "${CMAKE_C_FLAGS_DEBUG} -fno-inline -Wall -DEIGEN_INITIALIZE_MATRICES_BY_NAN" CACHE STRING "Flags used by the compiler during debug builds." FORCE)
+    set(CMAKE_C_FLAGS_DEBUG            "${CMAKE_C_FLAGS_DEBUG} -std=c11 -fno-inline -Wall -DEIGEN_INITIALIZE_MATRICES_BY_NAN" CACHE STRING "Flags used by the compiler during debug builds." FORCE)
-    set(CMAKE_CXX_FLAGS_DEBUG          "${CMAKE_CXX_FLAGS_DEBUG} -fno-inline -Wall -DEIGEN_INITIALIZE_MATRICES_BY_NAN" CACHE STRING "Flags used by the compiler during debug builds." FORCE)
+    set(CMAKE_CXX_FLAGS_DEBUG          "${CMAKE_CXX_FLAGS_DEBUG} -std=c++11 -fno-inline -Wall -DEIGEN_INITIALIZE_MATRICES_BY_NAN" CACHE STRING "Flags used by the compiler during debug builds." FORCE)
-    set(CMAKE_C_FLAGS_RELWITHDEBINFO   "-g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during relwithdebinfo builds." FORCE)
+    set(CMAKE_C_FLAGS_RELWITHDEBINFO   "-std=c11 -g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during relwithdebinfo builds." FORCE)
-    set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during relwithdebinfo builds." FORCE)
+    set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-std=c++11 -g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during relwithdebinfo builds." FORCE)
-    set(CMAKE_C_FLAGS_RELEASE          "-O3 -Wall -DNDEBUG -Wall" CACHE STRING "Flags used by the compiler during release builds." FORCE)
+    set(CMAKE_C_FLAGS_RELEASE          "-std=c11 -O3 -Wall -DNDEBUG -Wall" CACHE STRING "Flags used by the compiler during release builds." FORCE)
-    set(CMAKE_CXX_FLAGS_RELEASE        "-O3 -Wall -DNDEBUG -Wall" CACHE STRING "Flags used by the compiler during release builds." FORCE)
+    set(CMAKE_CXX_FLAGS_RELEASE        "-std=c++11 -O3 -Wall -DNDEBUG -Wall" CACHE STRING "Flags used by the compiler during release builds." FORCE)
     set(CMAKE_C_FLAGS_TIMING           "${CMAKE_C_FLAGS_RELEASE} -DENABLE_TIMING" CACHE STRING "Flags used by the compiler during timing builds." FORCE)
     set(CMAKE_CXX_FLAGS_TIMING         "${CMAKE_CXX_FLAGS_RELEASE} -DENABLE_TIMING" CACHE STRING "Flags used by the compiler during timing builds." FORCE)
     set(CMAKE_EXE_LINKER_FLAGS_TIMING  "${CMAKE_EXE_LINKER_FLAGS_RELEASE}" CACHE STRING "Linker flags during timing builds." FORCE)
     set(CMAKE_SHARED_LINKER_FLAGS_TIMING  "${CMAKE_EXE_LINKER_FLAGS_RELEASE}" CACHE STRING "Linker flags during timing builds." FORCE)
     mark_as_advanced(CMAKE_C_FLAGS_TIMING CMAKE_CXX_FLAGS_TIMING CMAKE_EXE_LINKER_FLAGS_TIMING CMAKE_SHARED_LINKER_FLAGS_TIMING)
-    set(CMAKE_C_FLAGS_PROFILING        "-g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during profiling builds." FORCE)
+    set(CMAKE_C_FLAGS_PROFILING        "-std=c11 -g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during profiling builds." FORCE)
-    set(CMAKE_CXX_FLAGS_PROFILING      "-g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during profiling builds." FORCE)
+    set(CMAKE_CXX_FLAGS_PROFILING      "-std=c++11 -g -O3 -Wall -DNDEBUG" CACHE STRING "Flags used by the compiler during profiling builds." FORCE)
     set(CMAKE_EXE_LINKER_FLAGS_PROFILING "${CMAKE_EXE_LINKER_FLAGS_RELEASE}" CACHE STRING "Linker flags during profiling builds." FORCE)
 	set(CMAKE_SHARED_LINKER_FLAGS_PROFILING "${CMAKE__LINKER_FLAGS_RELEASE}" CACHE STRING "Linker flags during profiling builds." FORCE)
     mark_as_advanced(CMAKE_C_FLAGS_PROFILING CMAKE_CXX_FLAGS_PROFILING CMAKE_EXE_LINKER_FLAGS_PROFILING CMAKE_SHARED_LINKER_FLAGS_PROFILING)

gtsam/3rdparty/Eigen/.hg_archival.txt

@@ -1,4 +1,4 @@
 repo: 8a21fd850624c931e448cbcfb38168cb2717c790
-node: 10219c95fe653d4962aa9db4946f6fbea96dd740
+node: b30b87236a1b1552af32ac34075ee5696a9b5a33
 branch: 3.2
-tag: 3.2.4
+tag: 3.2.7

gtsam/3rdparty/Eigen/.hgtags

@@ -27,3 +27,6 @@ ffa86ffb557094721ca71dcea6aed2651b9fd610 3.2.0
 6b38706d90a9fe182e66ab88477b3dbde34b9f66 3.2.1
 1306d75b4a21891e59ff9bd96678882cf831e39f 3.2.2
 36fd1ba04c120cfdd90f3e4cede47f43b21d19ad 3.2.3
+10219c95fe653d4962aa9db4946f6fbea96dd740 3.2.4
+bdd17ee3b1b3a166cd5ec36dcad4fc1f3faf774a 3.2.5
+c58038c56923e0fd86de3ded18e03df442e66dfb 3.2.6

gtsam/3rdparty/Eigen/CMakeLists.txt

@@ -301,7 +301,7 @@ if(EIGEN_INCLUDE_INSTALL_DIR)
   )
 else()
   set(INCLUDE_INSTALL_DIR
-    "${CMAKE_INSTALL_PREFIX}/include/eigen3"
+    "include/eigen3"
     CACHE INTERNAL
     "The directory where we install the header files (internal)"
   )
@@ -404,7 +404,7 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "make install  | Install to ${CMAKE_INSTALL_PREFIX}. To change that:")
   message(STATUS "              |     cmake . -DCMAKE_INSTALL_PREFIX=yourpath")
   message(STATUS "              |   Eigen headers will then be installed to:")
-  message(STATUS "              |     ${INCLUDE_INSTALL_DIR}")
+  message(STATUS "              |     ${CMAKE_INSTALL_PREFIX}/${INCLUDE_INSTALL_DIR}")
   message(STATUS "              |   To install Eigen headers to a separate location, do:")
   message(STATUS "              |     cmake . -DEIGEN_INCLUDE_INSTALL_DIR=yourpath")
   message(STATUS "make doc      | Generate the API documentation, requires Doxygen & LaTeX")

gtsam/3rdparty/Eigen/Eigen/Core

@@ -123,7 +123,7 @@
     #undef bool
     #undef vector
     #undef pixel
-  #elif defined  __ARM_NEON__
+  #elif defined  __ARM_NEON
     #define EIGEN_VECTORIZE
     #define EIGEN_VECTORIZE_NEON
     #include <arm_neon.h>

gtsam/3rdparty/Eigen/Eigen/SparseCore

@@ -14,7 +14,7 @@
 /** 
   * \defgroup SparseCore_Module SparseCore module
   *
-  * This module provides a sparse matrix representation, and basic associatd matrix manipulations
+  * This module provides a sparse matrix representation, and basic associated matrix manipulations
   * and operations.
   *
   * See the \ref TutorialSparse "Sparse tutorial"

gtsam/3rdparty/Eigen/Eigen/src/Cholesky/LDLT.h

@@ -235,6 +235,11 @@ template<typename _MatrixType, int _UpLo> class LDLT
     }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
 
     /** \internal
       * Used to compute and store the Cholesky decomposition A = L D L^* = U^* D U.
@@ -434,6 +439,8 @@ template<typename MatrixType> struct LDLT_Traits<MatrixType,Upper>
 template<typename MatrixType, int _UpLo>
 LDLT<MatrixType,_UpLo>& LDLT<MatrixType,_UpLo>::compute(const MatrixType& a)
 {
+  check_template_parameters();
+  
   eigen_assert(a.rows()==a.cols());
   const Index size = a.rows();
 
@@ -457,7 +464,7 @@ LDLT<MatrixType,_UpLo>& LDLT<MatrixType,_UpLo>::compute(const MatrixType& a)
   */
 template<typename MatrixType, int _UpLo>
 template<typename Derived>
-LDLT<MatrixType,_UpLo>& LDLT<MatrixType,_UpLo>::rankUpdate(const MatrixBase<Derived>& w, const typename NumTraits<typename MatrixType::Scalar>::Real& sigma)
+LDLT<MatrixType,_UpLo>& LDLT<MatrixType,_UpLo>::rankUpdate(const MatrixBase<Derived>& w, const typename LDLT<MatrixType,_UpLo>::RealScalar& sigma)
 {
   const Index size = w.rows();
   if (m_isInitialized)

gtsam/3rdparty/Eigen/Eigen/src/Cholesky/LLT.h

@@ -174,6 +174,12 @@ template<typename _MatrixType, int _UpLo> class LLT
     LLT rankUpdate(const VectorType& vec, const RealScalar& sigma = 1);
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     /** \internal
       * Used to compute and store L
       * The strict upper part is not used and even not initialized.
@@ -283,7 +289,7 @@ template<typename Scalar> struct llt_inplace<Scalar, Lower>
         return k;
       mat.coeffRef(k,k) = x = sqrt(x);
       if (k>0 && rs>0) A21.noalias() -= A20 * A10.adjoint();
-      if (rs>0) A21 *= RealScalar(1)/x;
+      if (rs>0) A21 /= x;
     }
     return -1;
   }
@@ -384,6 +390,8 @@ template<typename MatrixType> struct LLT_Traits<MatrixType,Upper>
 template<typename MatrixType, int _UpLo>
 LLT<MatrixType,_UpLo>& LLT<MatrixType,_UpLo>::compute(const MatrixType& a)
 {
+  check_template_parameters();
+  
   eigen_assert(a.rows()==a.cols());
   const Index size = a.rows();
   m_matrix.resize(size, size);

gtsam/3rdparty/Eigen/Eigen/src/Cholesky/LLT_MKL.h

@@ -60,7 +60,7 @@ template<> struct mkl_llt<EIGTYPE> \
     lda = m.outerStride(); \
 \
     info = LAPACKE_##MKLPREFIX##potrf( matrix_order, uplo, size, (MKLTYPE*)a, lda ); \
-    info = (info==0) ? -1 : 1; \
+    info = (info==0) ? -1 : info>0 ? info-1 : size; \
     return info; \
   } \
 }; \

gtsam/3rdparty/Eigen/Eigen/src/CholmodSupport/CholmodSupport.h

@@ -78,7 +78,7 @@ cholmod_sparse viewAsCholmod(SparseMatrix<_Scalar,_Options,_Index>& mat)
   {
     res.itype = CHOLMOD_INT;
   }
-  else if (internal::is_same<_Index,UF_long>::value)
+  else if (internal::is_same<_Index,SuiteSparse_long>::value)
   {
     res.itype = CHOLMOD_LONG;
   }
@@ -395,7 +395,7 @@ class CholmodSimplicialLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimpl
     CholmodSimplicialLLT(const MatrixType& matrix) : Base()
     {
       init();
-      compute(matrix);
+      Base::compute(matrix);
     }
 
     ~CholmodSimplicialLLT() {}
@@ -442,7 +442,7 @@ class CholmodSimplicialLDLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimp
     CholmodSimplicialLDLT(const MatrixType& matrix) : Base()
     {
       init();
-      compute(matrix);
+      Base::compute(matrix);
     }
 
     ~CholmodSimplicialLDLT() {}
@@ -487,7 +487,7 @@ class CholmodSupernodalLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSuper
     CholmodSupernodalLLT(const MatrixType& matrix) : Base()
     {
       init();
-      compute(matrix);
+      Base::compute(matrix);
     }
 
     ~CholmodSupernodalLLT() {}
@@ -534,7 +534,7 @@ class CholmodDecomposition : public CholmodBase<_MatrixType, _UpLo, CholmodDecom
     CholmodDecomposition(const MatrixType& matrix) : Base()
     {
       init();
-      compute(matrix);
+      Base::compute(matrix);
     }
 
     ~CholmodDecomposition() {}

gtsam/3rdparty/Eigen/Eigen/src/Core/Array.h

@@ -124,6 +124,21 @@ class Array
     }
 #endif
 
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
+    Array(Array&& other)
+      : Base(std::move(other))
+    {
+      Base::_check_template_params();
+      if (RowsAtCompileTime!=Dynamic && ColsAtCompileTime!=Dynamic)
+        Base::_set_noalias(other);
+    }
+    Array& operator=(Array&& other)
+    {
+      other.swap(*this);
+      return *this;
+    }
+#endif
+
     /** Constructs a vector or row-vector with given dimension. \only_for_vectors
       *
       * Note that this is only useful for dynamic-size vectors. For fixed-size vectors,

gtsam/3rdparty/Eigen/Eigen/src/Core/ArrayBase.h

@@ -46,9 +46,6 @@ template<typename Derived> class ArrayBase
 
     typedef ArrayBase Eigen_BaseClassForSpecializationOfGlobalMathFuncImpl;
 
-    using internal::special_scalar_op_base<Derived,typename internal::traits<Derived>::Scalar,
-                typename NumTraits<typename internal::traits<Derived>::Scalar>::Real>::operator*;
-
     typedef typename internal::traits<Derived>::StorageKind StorageKind;
     typedef typename internal::traits<Derived>::Index Index;
     typedef typename internal::traits<Derived>::Scalar Scalar;
@@ -56,6 +53,7 @@ template<typename Derived> class ArrayBase
     typedef typename NumTraits<Scalar>::Real RealScalar;
 
     typedef DenseBase<Derived> Base;
+    using Base::operator*;
     using Base::RowsAtCompileTime;
     using Base::ColsAtCompileTime;
     using Base::SizeAtCompileTime;

gtsam/3rdparty/Eigen/Eigen/src/Core/Assign.h

@@ -439,19 +439,26 @@ struct assign_impl<Derived1, Derived2, SliceVectorizedTraversal, NoUnrolling, Ve
   typedef typename Derived1::Index Index;
   static inline void run(Derived1 &dst, const Derived2 &src)
   {
-    typedef packet_traits<typename Derived1::Scalar> PacketTraits;
+    typedef typename Derived1::Scalar Scalar;
+    typedef packet_traits<Scalar> PacketTraits;
     enum {
       packetSize = PacketTraits::size,
       alignable = PacketTraits::AlignedOnScalar,
-      dstAlignment = alignable ? Aligned : int(assign_traits<Derived1,Derived2>::DstIsAligned) ,
+      dstIsAligned = assign_traits<Derived1,Derived2>::DstIsAligned,
+      dstAlignment = alignable ? Aligned : int(dstIsAligned),
       srcAlignment = assign_traits<Derived1,Derived2>::JointAlignment
     };
+    const Scalar *dst_ptr = &dst.coeffRef(0,0);
+    if((!bool(dstIsAligned)) && (size_t(dst_ptr) % sizeof(Scalar))>0)
+    {
+      // the pointer is not aligend-on scalar, so alignment is not possible
+      return assign_impl<Derived1,Derived2,DefaultTraversal,NoUnrolling>::run(dst, src);
+    }
     const Index packetAlignedMask = packetSize - 1;
     const Index innerSize = dst.innerSize();
     const Index outerSize = dst.outerSize();
     const Index alignedStep = alignable ? (packetSize - dst.outerStride() % packetSize) & packetAlignedMask : 0;
-    Index alignedStart = ((!alignable) || assign_traits<Derived1,Derived2>::DstIsAligned) ? 0
+    Index alignedStart = ((!alignable) || bool(dstIsAligned)) ? 0 : internal::first_aligned(dst_ptr, innerSize);
-                       : internal::first_aligned(&dst.coeffRef(0,0), innerSize);
 
     for(Index outer = 0; outer < outerSize; ++outer)
     {

gtsam/3rdparty/Eigen/Eigen/src/Core/Block.h

@@ -66,8 +66,9 @@ struct traits<Block<XprType, BlockRows, BlockCols, InnerPanel> > : traits<XprTyp
                          : ColsAtCompileTime != Dynamic ? int(ColsAtCompileTime)
                          : int(traits<XprType>::MaxColsAtCompileTime),
     XprTypeIsRowMajor = (int(traits<XprType>::Flags)&RowMajorBit) != 0,
-    IsRowMajor = (MaxRowsAtCompileTime==1&&MaxColsAtCompileTime!=1) ? 1
+    IsDense = is_same<StorageKind,Dense>::value,
-               : (MaxColsAtCompileTime==1&&MaxRowsAtCompileTime!=1) ? 0
+    IsRowMajor = (IsDense&&MaxRowsAtCompileTime==1&&MaxColsAtCompileTime!=1) ? 1
+               : (IsDense&&MaxColsAtCompileTime==1&&MaxRowsAtCompileTime!=1) ? 0
                : XprTypeIsRowMajor,
     HasSameStorageOrderAsXprType = (IsRowMajor == XprTypeIsRowMajor),
     InnerSize = IsRowMajor ? int(ColsAtCompileTime) : int(RowsAtCompileTime),

gtsam/3rdparty/Eigen/Eigen/src/Core/CommaInitializer.h.orig

@@ -1,154 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_COMMAINITIALIZER_H
-#define EIGEN_COMMAINITIALIZER_H
-
-namespace Eigen { 
-
-/** \class CommaInitializer
-  * \ingroup Core_Module
-  *
-  * \brief Helper class used by the comma initializer operator
-  *
-  * This class is internally used to implement the comma initializer feature. It is
-  * the return type of MatrixBase::operator<<, and most of the time this is the only
-  * way it is used.
-  *
-  * \sa \ref MatrixBaseCommaInitRef "MatrixBase::operator<<", CommaInitializer::finished()
-  */
-template<typename XprType>
-struct CommaInitializer
-{
-  typedef typename XprType::Scalar Scalar;
-  typedef typename XprType::Index Index;
-
-  inline CommaInitializer(XprType& xpr, const Scalar& s)
-    : m_xpr(xpr), m_row(0), m_col(1), m_currentBlockRows(1)
-  {
-    m_xpr.coeffRef(0,0) = s;
-  }
-
-  template<typename OtherDerived>
-  inline CommaInitializer(XprType& xpr, const DenseBase<OtherDerived>& other)
-    : m_xpr(xpr), m_row(0), m_col(other.cols()), m_currentBlockRows(other.rows())
-  {
-    m_xpr.block(0, 0, other.rows(), other.cols()) = other;
-  }
-
-  /* Copy/Move constructor which transfers ownership. This is crucial in 
-   * absence of return value optimization to avoid assertions during destruction. */
-  // FIXME in C++11 mode this could be replaced by a proper RValue constructor
-  inline CommaInitializer(const CommaInitializer& o)
-  : m_xpr(o.m_xpr), m_row(o.m_row), m_col(o.m_col), m_currentBlockRows(o.m_currentBlockRows) {
-    // Mark original object as finished. In absence of R-value references we need to const_cast:
-    const_cast<CommaInitializer&>(o).m_row = m_xpr.rows();
-    const_cast<CommaInitializer&>(o).m_col = m_xpr.cols();
-    const_cast<CommaInitializer&>(o).m_currentBlockRows = 0;
-  }
-
-  /* inserts a scalar value in the target matrix */
-  CommaInitializer& operator,(const Scalar& s)
-  {
-    if (m_col==m_xpr.cols())
-    {
-      m_row+=m_currentBlockRows;
-      m_col = 0;
-      m_currentBlockRows = 1;
-      eigen_assert(m_row<m_xpr.rows()
-        && "Too many rows passed to comma initializer (operator<<)");
-    }
-    eigen_assert(m_col<m_xpr.cols()
-      && "Too many coefficients passed to comma initializer (operator<<)");
-    eigen_assert(m_currentBlockRows==1);
-    m_xpr.coeffRef(m_row, m_col++) = s;
-    return *this;
-  }
-
-  /* inserts a matrix expression in the target matrix */
-  template<typename OtherDerived>
-  CommaInitializer& operator,(const DenseBase<OtherDerived>& other)
-  {
-    if(other.cols()==0 || other.rows()==0)
-      return *this;
-    if (m_col==m_xpr.cols())
-    {
-      m_row+=m_currentBlockRows;
-      m_col = 0;
-      m_currentBlockRows = other.rows();
-      eigen_assert(m_row+m_currentBlockRows<=m_xpr.rows()
-        && "Too many rows passed to comma initializer (operator<<)");
-    }
-    eigen_assert(m_col<m_xpr.cols()
-      && "Too many coefficients passed to comma initializer (operator<<)");
-    eigen_assert(m_currentBlockRows==other.rows());
-    if (OtherDerived::SizeAtCompileTime != Dynamic)
-      m_xpr.template block<OtherDerived::RowsAtCompileTime != Dynamic ? OtherDerived::RowsAtCompileTime : 1,
-                              OtherDerived::ColsAtCompileTime != Dynamic ? OtherDerived::ColsAtCompileTime : 1>
-                    (m_row, m_col) = other;
-    else
-      m_xpr.block(m_row, m_col, other.rows(), other.cols()) = other;
-    m_col += other.cols();
-    return *this;
-  }
-
-  inline ~CommaInitializer()
-  {
-    eigen_assert((m_row+m_currentBlockRows) == m_xpr.rows()
-         && m_col == m_xpr.cols()
-         && "Too few coefficients passed to comma initializer (operator<<)");
-  }
-
-  /** \returns the built matrix once all its coefficients have been set.
-    * Calling finished is 100% optional. Its purpose is to write expressions
-    * like this:
-    * \code
-    * quaternion.fromRotationMatrix((Matrix3f() << axis0, axis1, axis2).finished());
-    * \endcode
-    */
-  inline XprType& finished() { return m_xpr; }
-
-  XprType& m_xpr;   // target expression
-  Index m_row;              // current row id
-  Index m_col;              // current col id
-  Index m_currentBlockRows; // current block height
-};
-
-/** \anchor MatrixBaseCommaInitRef
-  * Convenient operator to set the coefficients of a matrix.
-  *
-  * The coefficients must be provided in a row major order and exactly match
-  * the size of the matrix. Otherwise an assertion is raised.
-  *
-  * Example: \include MatrixBase_set.cpp
-  * Output: \verbinclude MatrixBase_set.out
-  * 
-  * \note According the c++ standard, the argument expressions of this comma initializer are evaluated in arbitrary order.
-  *
-  * \sa CommaInitializer::finished(), class CommaInitializer
-  */
-template<typename Derived>
-inline CommaInitializer<Derived> DenseBase<Derived>::operator<< (const Scalar& s)
-{
-  return CommaInitializer<Derived>(*static_cast<Derived*>(this), s);
-}
-
-/** \sa operator<<(const Scalar&) */
-template<typename Derived>
-template<typename OtherDerived>
-inline CommaInitializer<Derived>
-DenseBase<Derived>::operator<<(const DenseBase<OtherDerived>& other)
-{
-  return CommaInitializer<Derived>(*static_cast<Derived *>(this), other);
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_COMMAINITIALIZER_H

gtsam/3rdparty/Eigen/Eigen/src/Core/CwiseBinaryOp.h

@@ -81,7 +81,8 @@ struct traits<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
         )
      ),
     Flags = (Flags0 & ~RowMajorBit) | (LhsFlags & RowMajorBit),
-    CoeffReadCost = LhsCoeffReadCost + RhsCoeffReadCost + functor_traits<BinaryOp>::Cost
+    Cost0 = EIGEN_ADD_COST(LhsCoeffReadCost,RhsCoeffReadCost),
+    CoeffReadCost = EIGEN_ADD_COST(Cost0,functor_traits<BinaryOp>::Cost)
   };
 };
 } // end namespace internal

gtsam/3rdparty/Eigen/Eigen/src/Core/CwiseUnaryOp.h

@@ -47,7 +47,7 @@ struct traits<CwiseUnaryOp<UnaryOp, XprType> >
     Flags = _XprTypeNested::Flags & (
       HereditaryBits | LinearAccessBit | AlignedBit
       | (functor_traits<UnaryOp>::PacketAccess ? PacketAccessBit : 0)),
-    CoeffReadCost = _XprTypeNested::CoeffReadCost + functor_traits<UnaryOp>::Cost
+    CoeffReadCost = EIGEN_ADD_COST(_XprTypeNested::CoeffReadCost, functor_traits<UnaryOp>::Cost)
   };
 };
 }

gtsam/3rdparty/Eigen/Eigen/src/Core/DenseBase.h

@@ -41,14 +41,13 @@ static inline void check_DenseIndex_is_signed() {
 template<typename Derived> class DenseBase
 #ifndef EIGEN_PARSED_BY_DOXYGEN
   : public internal::special_scalar_op_base<Derived,typename internal::traits<Derived>::Scalar,
-                                     typename NumTraits<typename internal::traits<Derived>::Scalar>::Real>
+                                            typename NumTraits<typename internal::traits<Derived>::Scalar>::Real,
+                                            DenseCoeffsBase<Derived> >
 #else
   : public DenseCoeffsBase<Derived>
 #endif // not EIGEN_PARSED_BY_DOXYGEN
 {
   public:
-    using internal::special_scalar_op_base<Derived,typename internal::traits<Derived>::Scalar,
-                typename NumTraits<typename internal::traits<Derived>::Scalar>::Real>::operator*;
 
     class InnerIterator;
 
@@ -63,8 +62,9 @@ template<typename Derived> class DenseBase
     typedef typename internal::traits<Derived>::Scalar Scalar;
     typedef typename internal::packet_traits<Scalar>::type PacketScalar;
     typedef typename NumTraits<Scalar>::Real RealScalar;
+    typedef internal::special_scalar_op_base<Derived,Scalar,RealScalar, DenseCoeffsBase<Derived> > Base;
 
-    typedef DenseCoeffsBase<Derived> Base;
+    using Base::operator*;
     using Base::derived;
     using Base::const_cast_derived;
     using Base::rows;
@@ -183,10 +183,6 @@ template<typename Derived> class DenseBase
     /** \returns the number of nonzero coefficients which is in practice the number
       * of stored coefficients. */
     inline Index nonZeros() const { return size(); }
-    /** \returns true if either the number of rows or the number of columns is equal to 1.
-      * In other words, this function returns
-      * \code rows()==1 || cols()==1 \endcode
-      * \sa rows(), cols(), IsVectorAtCompileTime. */
 
     /** \returns the outer size.
       *
@@ -266,11 +262,13 @@ template<typename Derived> class DenseBase
     template<typename OtherDerived>
     Derived& operator=(const ReturnByValue<OtherDerived>& func);
 
-#ifndef EIGEN_PARSED_BY_DOXYGEN
+    /** \internal Copies \a other into *this without evaluating other. \returns a reference to *this. */
-    /** Copies \a other into *this without evaluating other. \returns a reference to *this. */
     template<typename OtherDerived>
     Derived& lazyAssign(const DenseBase<OtherDerived>& other);
-#endif // not EIGEN_PARSED_BY_DOXYGEN
+
+    /** \internal Evaluates \a other into *this. \returns a reference to *this. */
+    template<typename OtherDerived>
+    Derived& lazyAssign(const ReturnByValue<OtherDerived>& other);
 
     CommaInitializer<Derived> operator<< (const Scalar& s);
 

gtsam/3rdparty/Eigen/Eigen/src/Core/DenseStorage.h

@@ -122,33 +122,41 @@ template<typename T, int Size, int _Rows, int _Cols, int _Options> class DenseSt
 {
     internal::plain_array<T,Size,_Options> m_data;
   public:
-    inline DenseStorage() {}
+    DenseStorage() {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert)
+    DenseStorage(internal::constructor_without_unaligned_array_assert)
       : m_data(internal::constructor_without_unaligned_array_assert()) {}
-    inline DenseStorage(DenseIndex,DenseIndex,DenseIndex) {}
+    DenseStorage(const DenseStorage& other) : m_data(other.m_data) {}
-    inline void swap(DenseStorage& other) { std::swap(m_data,other.m_data); }
+    DenseStorage& operator=(const DenseStorage& other)
-    static inline DenseIndex rows(void) {return _Rows;}
+    {
-    static inline DenseIndex cols(void) {return _Cols;}
+      if (this != &other) m_data = other.m_data;
-    inline void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {}
+      return *this;
-    inline void resize(DenseIndex,DenseIndex,DenseIndex) {}
+    }
-    inline const T *data() const { return m_data.array; }
+    DenseStorage(DenseIndex,DenseIndex,DenseIndex) {}
-    inline T *data() { return m_data.array; }
+    void swap(DenseStorage& other) { std::swap(m_data,other.m_data); }
+    static DenseIndex rows(void) {return _Rows;}
+    static DenseIndex cols(void) {return _Cols;}
+    void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {}
+    void resize(DenseIndex,DenseIndex,DenseIndex) {}
+    const T *data() const { return m_data.array; }
+    T *data() { return m_data.array; }
 };
 
 // null matrix
 template<typename T, int _Rows, int _Cols, int _Options> class DenseStorage<T, 0, _Rows, _Cols, _Options>
 {
   public:
-    inline DenseStorage() {}
+    DenseStorage() {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert) {}
+    DenseStorage(internal::constructor_without_unaligned_array_assert) {}
-    inline DenseStorage(DenseIndex,DenseIndex,DenseIndex) {}
+    DenseStorage(const DenseStorage&) {}
-    inline void swap(DenseStorage& ) {}
+    DenseStorage& operator=(const DenseStorage&) { return *this; }
-    static inline DenseIndex rows(void) {return _Rows;}
+    DenseStorage(DenseIndex,DenseIndex,DenseIndex) {}
-    static inline DenseIndex cols(void) {return _Cols;}
+    void swap(DenseStorage& ) {}
-    inline void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {}
+    static DenseIndex rows(void) {return _Rows;}
-    inline void resize(DenseIndex,DenseIndex,DenseIndex) {}
+    static DenseIndex cols(void) {return _Cols;}
-    inline const T *data() const { return 0; }
+    void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {}
-    inline T *data() { return 0; }
+    void resize(DenseIndex,DenseIndex,DenseIndex) {}
+    const T *data() const { return 0; }
+    T *data() { return 0; }
 };
 
 // more specializations for null matrices; these are necessary to resolve ambiguities
@@ -168,18 +176,29 @@ template<typename T, int Size, int _Options> class DenseStorage<T, Size, Dynamic
     DenseIndex m_rows;
     DenseIndex m_cols;
   public:
-    inline DenseStorage() : m_rows(0), m_cols(0) {}
+    DenseStorage() : m_rows(0), m_cols(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert)
+    DenseStorage(internal::constructor_without_unaligned_array_assert)
       : m_data(internal::constructor_without_unaligned_array_assert()), m_rows(0), m_cols(0) {}
-    inline DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) : m_rows(nbRows), m_cols(nbCols) {}
+    DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_rows(other.m_rows), m_cols(other.m_cols) {}
-    inline void swap(DenseStorage& other)
+    DenseStorage& operator=(const DenseStorage& other)
+    {
+      if (this != &other)
+      {
+        m_data = other.m_data;
+        m_rows = other.m_rows;
+        m_cols = other.m_cols;
+      }
+      return *this;
+    }
+    DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) : m_rows(nbRows), m_cols(nbCols) {}
+    void swap(DenseStorage& other)
     { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); std::swap(m_cols,other.m_cols); }
-    inline DenseIndex rows() const {return m_rows;}
+    DenseIndex rows() const {return m_rows;}
-    inline DenseIndex cols() const {return m_cols;}
+    DenseIndex cols() const {return m_cols;}
-    inline void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; }
+    void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; }
-    inline void resize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; }
+    void resize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; }
-    inline const T *data() const { return m_data.array; }
+    const T *data() const { return m_data.array; }
-    inline T *data() { return m_data.array; }
+    T *data() { return m_data.array; }
 };
 
 // dynamic-size matrix with fixed-size storage and fixed width
@@ -188,17 +207,27 @@ template<typename T, int Size, int _Cols, int _Options> class DenseStorage<T, Si
     internal::plain_array<T,Size,_Options> m_data;
     DenseIndex m_rows;
   public:
-    inline DenseStorage() : m_rows(0) {}
+    DenseStorage() : m_rows(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert)
+    DenseStorage(internal::constructor_without_unaligned_array_assert)
       : m_data(internal::constructor_without_unaligned_array_assert()), m_rows(0) {}
-    inline DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex) : m_rows(nbRows) {}
+    DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_rows(other.m_rows) {}
-    inline void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); }
+    DenseStorage& operator=(const DenseStorage& other)
-    inline DenseIndex rows(void) const {return m_rows;}
+    {
-    inline DenseIndex cols(void) const {return _Cols;}
+      if (this != &other)
-    inline void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; }
+      {
-    inline void resize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; }
+        m_data = other.m_data;
-    inline const T *data() const { return m_data.array; }
+        m_rows = other.m_rows;
-    inline T *data() { return m_data.array; }
+      }
+      return *this;
+    }
+    DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex) : m_rows(nbRows) {}
+    void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); }
+    DenseIndex rows(void) const {return m_rows;}
+    DenseIndex cols(void) const {return _Cols;}
+    void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; }
+    void resize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; }
+    const T *data() const { return m_data.array; }
+    T *data() { return m_data.array; }
 };
 
 // dynamic-size matrix with fixed-size storage and fixed height
@@ -207,17 +236,27 @@ template<typename T, int Size, int _Rows, int _Options> class DenseStorage<T, Si
     internal::plain_array<T,Size,_Options> m_data;
     DenseIndex m_cols;
   public:
-    inline DenseStorage() : m_cols(0) {}
+    DenseStorage() : m_cols(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert)
+    DenseStorage(internal::constructor_without_unaligned_array_assert)
       : m_data(internal::constructor_without_unaligned_array_assert()), m_cols(0) {}
-    inline DenseStorage(DenseIndex, DenseIndex, DenseIndex nbCols) : m_cols(nbCols) {}
+    DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_cols(other.m_cols) {}
-    inline void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); }
+    DenseStorage& operator=(const DenseStorage& other)
-    inline DenseIndex rows(void) const {return _Rows;}
+    {
-    inline DenseIndex cols(void) const {return m_cols;}
+      if (this != &other)
-    inline void conservativeResize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; }
+      {
-    inline void resize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; }
+        m_data = other.m_data;
-    inline const T *data() const { return m_data.array; }
+        m_cols = other.m_cols;
-    inline T *data() { return m_data.array; }
+      }
+      return *this;
+    }
+    DenseStorage(DenseIndex, DenseIndex, DenseIndex nbCols) : m_cols(nbCols) {}
+    void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); }
+    DenseIndex rows(void) const {return _Rows;}
+    DenseIndex cols(void) const {return m_cols;}
+    void conservativeResize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; }
+    void resize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; }
+    const T *data() const { return m_data.array; }
+    T *data() { return m_data.array; }
 };
 
 // purely dynamic matrix.
@@ -227,18 +266,35 @@ template<typename T, int _Options> class DenseStorage<T, Dynamic, Dynamic, Dynam
     DenseIndex m_rows;
     DenseIndex m_cols;
   public:
-    inline DenseStorage() : m_data(0), m_rows(0), m_cols(0) {}
+    DenseStorage() : m_data(0), m_rows(0), m_cols(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert)
+    DenseStorage(internal::constructor_without_unaligned_array_assert)
        : m_data(0), m_rows(0), m_cols(0) {}
-    inline DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols)
+    DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols)
       : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_rows(nbRows), m_cols(nbCols)
     { EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN }
-    inline ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, m_rows*m_cols); }
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
-    inline void swap(DenseStorage& other)
+    DenseStorage(DenseStorage&& other)
+      : m_data(std::move(other.m_data))
+      , m_rows(std::move(other.m_rows))
+      , m_cols(std::move(other.m_cols))
+    {
+      other.m_data = nullptr;
+    }
+    DenseStorage& operator=(DenseStorage&& other)
+    {
+      using std::swap;
+      swap(m_data, other.m_data);
+      swap(m_rows, other.m_rows);
+      swap(m_cols, other.m_cols);
+      return *this;
+    }
+#endif
+    ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, m_rows*m_cols); }
+    void swap(DenseStorage& other)
     { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); std::swap(m_cols,other.m_cols); }
-    inline DenseIndex rows(void) const {return m_rows;}
+    DenseIndex rows(void) const {return m_rows;}
-    inline DenseIndex cols(void) const {return m_cols;}
+    DenseIndex cols(void) const {return m_cols;}
-    inline void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols)
+    void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols)
     {
       m_data = internal::conditional_aligned_realloc_new_auto<T,(_Options&DontAlign)==0>(m_data, size, m_rows*m_cols);
       m_rows = nbRows;
@@ -258,8 +314,11 @@ template<typename T, int _Options> class DenseStorage<T, Dynamic, Dynamic, Dynam
       m_rows = nbRows;
       m_cols = nbCols;
     }
-    inline const T *data() const { return m_data; }
+    const T *data() const { return m_data; }
-    inline T *data() { return m_data; }
+    T *data() { return m_data; }
+  private:
+    DenseStorage(const DenseStorage&);
+    DenseStorage& operator=(const DenseStorage&);
 };
 
 // matrix with dynamic width and fixed height (so that matrix has dynamic size).
@@ -268,15 +327,30 @@ template<typename T, int _Rows, int _Options> class DenseStorage<T, Dynamic, _Ro
     T *m_data;
     DenseIndex m_cols;
   public:
-    inline DenseStorage() : m_data(0), m_cols(0) {}
+    DenseStorage() : m_data(0), m_cols(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_cols(0) {}
+    DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_cols(0) {}
-    inline DenseStorage(DenseIndex size, DenseIndex, DenseIndex nbCols) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_cols(nbCols)
+    DenseStorage(DenseIndex size, DenseIndex, DenseIndex nbCols) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_cols(nbCols)
     { EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN }
-    inline ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, _Rows*m_cols); }
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
-    inline void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); }
+    DenseStorage(DenseStorage&& other)
-    static inline DenseIndex rows(void) {return _Rows;}
+      : m_data(std::move(other.m_data))
-    inline DenseIndex cols(void) const {return m_cols;}
+      , m_cols(std::move(other.m_cols))
-    inline void conservativeResize(DenseIndex size, DenseIndex, DenseIndex nbCols)
+    {
+      other.m_data = nullptr;
+    }
+    DenseStorage& operator=(DenseStorage&& other)
+    {
+      using std::swap;
+      swap(m_data, other.m_data);
+      swap(m_cols, other.m_cols);
+      return *this;
+    }
+#endif
+    ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, _Rows*m_cols); }
+    void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); }
+    static DenseIndex rows(void) {return _Rows;}
+    DenseIndex cols(void) const {return m_cols;}
+    void conservativeResize(DenseIndex size, DenseIndex, DenseIndex nbCols)
     {
       m_data = internal::conditional_aligned_realloc_new_auto<T,(_Options&DontAlign)==0>(m_data, size, _Rows*m_cols);
       m_cols = nbCols;
@@ -294,8 +368,11 @@ template<typename T, int _Rows, int _Options> class DenseStorage<T, Dynamic, _Ro
       }
       m_cols = nbCols;
     }
-    inline const T *data() const { return m_data; }
+    const T *data() const { return m_data; }
-    inline T *data() { return m_data; }
+    T *data() { return m_data; }
+  private:
+    DenseStorage(const DenseStorage&);
+    DenseStorage& operator=(const DenseStorage&);
 };
 
 // matrix with dynamic height and fixed width (so that matrix has dynamic size).
@@ -304,15 +381,30 @@ template<typename T, int _Cols, int _Options> class DenseStorage<T, Dynamic, Dyn
     T *m_data;
     DenseIndex m_rows;
   public:
-    inline DenseStorage() : m_data(0), m_rows(0) {}
+    DenseStorage() : m_data(0), m_rows(0) {}
-    inline DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_rows(0) {}
+    DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_rows(0) {}
-    inline DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_rows(nbRows)
+    DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_rows(nbRows)
     { EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN }
-    inline ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, _Cols*m_rows); }
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
-    inline void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); }
+    DenseStorage(DenseStorage&& other)
-    inline DenseIndex rows(void) const {return m_rows;}
+      : m_data(std::move(other.m_data))
-    static inline DenseIndex cols(void) {return _Cols;}
+      , m_rows(std::move(other.m_rows))
-    inline void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex)
+    {
+      other.m_data = nullptr;
+    }
+    DenseStorage& operator=(DenseStorage&& other)
+    {
+      using std::swap;
+      swap(m_data, other.m_data);
+      swap(m_rows, other.m_rows);
+      return *this;
+    }
+#endif
+    ~DenseStorage() { internal::conditional_aligned_delete_auto<T,(_Options&DontAlign)==0>(m_data, _Cols*m_rows); }
+    void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); }
+    DenseIndex rows(void) const {return m_rows;}
+    static DenseIndex cols(void) {return _Cols;}
+    void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex)
     {
       m_data = internal::conditional_aligned_realloc_new_auto<T,(_Options&DontAlign)==0>(m_data, size, m_rows*_Cols);
       m_rows = nbRows;
@@ -330,8 +422,11 @@ template<typename T, int _Cols, int _Options> class DenseStorage<T, Dynamic, Dyn
       }
       m_rows = nbRows;
     }
-    inline const T *data() const { return m_data; }
+    const T *data() const { return m_data; }
-    inline T *data() { return m_data; }
+    T *data() { return m_data; }
+  private:
+    DenseStorage(const DenseStorage&);
+    DenseStorage& operator=(const DenseStorage&);
 };
 
 } // end namespace Eigen

gtsam/3rdparty/Eigen/Eigen/src/Core/DiagonalProduct.h

@@ -34,8 +34,9 @@ struct traits<DiagonalProduct<MatrixType, DiagonalType, ProductOrder> >
     _Vectorizable = bool(int(MatrixType::Flags)&PacketAccessBit) && _SameTypes && (_ScalarAccessOnDiag || (bool(int(DiagonalType::DiagonalVectorType::Flags)&PacketAccessBit))),
     _LinearAccessMask = (RowsAtCompileTime==1 || ColsAtCompileTime==1) ? LinearAccessBit : 0,
 
-    Flags = ((HereditaryBits|_LinearAccessMask) & (unsigned int)(MatrixType::Flags)) | (_Vectorizable ? PacketAccessBit : 0) | AlignedBit,//(int(MatrixType::Flags)&int(DiagonalType::DiagonalVectorType::Flags)&AlignedBit),
+    Flags = ((HereditaryBits|_LinearAccessMask|AlignedBit) & (unsigned int)(MatrixType::Flags)) | (_Vectorizable ? PacketAccessBit : 0),//(int(MatrixType::Flags)&int(DiagonalType::DiagonalVectorType::Flags)&AlignedBit),
-    CoeffReadCost = NumTraits<Scalar>::MulCost + MatrixType::CoeffReadCost + DiagonalType::DiagonalVectorType::CoeffReadCost
+    Cost0 = EIGEN_ADD_COST(NumTraits<Scalar>::MulCost, MatrixType::CoeffReadCost),
+    CoeffReadCost = EIGEN_ADD_COST(Cost0,DiagonalType::DiagonalVectorType::CoeffReadCost)
   };
 };
 }

gtsam/3rdparty/Eigen/Eigen/src/Core/Functors.h

@@ -259,6 +259,47 @@ template<> struct functor_traits<scalar_boolean_or_op> {
   };
 };
 
+/** \internal
+  * \brief Template functors for comparison of two scalars
+  * \todo Implement packet-comparisons
+  */
+template<typename Scalar, ComparisonName cmp> struct scalar_cmp_op;
+
+template<typename Scalar, ComparisonName cmp>
+struct functor_traits<scalar_cmp_op<Scalar, cmp> > {
+  enum {
+    Cost = NumTraits<Scalar>::AddCost,
+    PacketAccess = false
+  };
+};
+
+template<ComparisonName Cmp, typename Scalar>
+struct result_of<scalar_cmp_op<Scalar, Cmp>(Scalar,Scalar)> {
+  typedef bool type;
+};
+
+
+template<typename Scalar> struct scalar_cmp_op<Scalar, cmp_EQ> {
+  EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op)
+  EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a==b;}
+};
+template<typename Scalar> struct scalar_cmp_op<Scalar, cmp_LT> {
+  EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op)
+  EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a<b;}
+};
+template<typename Scalar> struct scalar_cmp_op<Scalar, cmp_LE> {
+  EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op)
+  EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a<=b;}
+};
+template<typename Scalar> struct scalar_cmp_op<Scalar, cmp_UNORD> {
+  EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op)
+  EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return !(a<=b || b<=a);}
+};
+template<typename Scalar> struct scalar_cmp_op<Scalar, cmp_NEQ> {
+  EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op)
+  EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a!=b;}
+};
+
 // unary functors:
 
 /** \internal

gtsam/3rdparty/Eigen/Eigen/src/Core/GeneralProduct.h

@@ -257,7 +257,7 @@ template<typename Lhs, typename Rhs>
 class GeneralProduct<Lhs, Rhs, OuterProduct>
   : public ProductBase<GeneralProduct<Lhs,Rhs,OuterProduct>, Lhs, Rhs>
 {
-    template<typename T> struct IsRowMajor : internal::conditional<(int(T::Flags)&RowMajorBit), internal::true_type, internal::false_type>::type {};
+    template<typename T> struct is_row_major : internal::conditional<(int(T::Flags)&RowMajorBit), internal::true_type, internal::false_type>::type {};
     
   public:
     EIGEN_PRODUCT_PUBLIC_INTERFACE(GeneralProduct)
@@ -281,22 +281,22 @@ class GeneralProduct<Lhs, Rhs, OuterProduct>
     
     template<typename Dest>
     inline void evalTo(Dest& dest) const {
-      internal::outer_product_selector_run(*this, dest, set(), IsRowMajor<Dest>());
+      internal::outer_product_selector_run(*this, dest, set(), is_row_major<Dest>());
     }
     
     template<typename Dest>
     inline void addTo(Dest& dest) const {
-      internal::outer_product_selector_run(*this, dest, add(), IsRowMajor<Dest>());
+      internal::outer_product_selector_run(*this, dest, add(), is_row_major<Dest>());
     }
 
     template<typename Dest>
     inline void subTo(Dest& dest) const {
-      internal::outer_product_selector_run(*this, dest, sub(), IsRowMajor<Dest>());
+      internal::outer_product_selector_run(*this, dest, sub(), is_row_major<Dest>());
     }
 
     template<typename Dest> void scaleAndAddTo(Dest& dest, const Scalar& alpha) const
     {
-      internal::outer_product_selector_run(*this, dest, adds(alpha), IsRowMajor<Dest>());
+      internal::outer_product_selector_run(*this, dest, adds(alpha), is_row_major<Dest>());
     }
 };
 

gtsam/3rdparty/Eigen/Eigen/src/Core/MapBase.h

@@ -123,7 +123,7 @@ template<typename Derived> class MapBase<Derived, ReadOnlyAccessors>
       return internal::ploadt<PacketScalar, LoadMode>(m_data + index * innerStride());
     }
 
-    inline MapBase(PointerType dataPtr) : m_data(dataPtr), m_rows(RowsAtCompileTime), m_cols(ColsAtCompileTime)
+    explicit inline MapBase(PointerType dataPtr) : m_data(dataPtr), m_rows(RowsAtCompileTime), m_cols(ColsAtCompileTime)
     {
       EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived)
       checkSanity();
@@ -157,7 +157,7 @@ template<typename Derived> class MapBase<Derived, ReadOnlyAccessors>
                                         internal::inner_stride_at_compile_time<Derived>::ret==1),
                           PACKET_ACCESS_REQUIRES_TO_HAVE_INNER_STRIDE_FIXED_TO_1);
       eigen_assert(EIGEN_IMPLIES(internal::traits<Derived>::Flags&AlignedBit, (size_t(m_data) % 16) == 0)
-                   && "data is not aligned");
+                   && "input pointer is not aligned on a 16 byte boundary");
     }
 
     PointerType m_data;

gtsam/3rdparty/Eigen/Eigen/src/Core/MathFunctions.h

@@ -294,7 +294,7 @@ struct hypot_impl
     RealScalar _x = abs(x);
     RealScalar _y = abs(y);
     RealScalar p = (max)(_x, _y);
-    if(p==RealScalar(0)) return 0;
+    if(p==RealScalar(0)) return RealScalar(0);
     RealScalar q = (min)(_x, _y);
     RealScalar qp = q/p;
     return p * sqrt(RealScalar(1) + qp*qp);

gtsam/3rdparty/Eigen/Eigen/src/Core/Matrix.h

@@ -211,6 +211,21 @@ class Matrix
       : Base(internal::constructor_without_unaligned_array_assert())
     { Base::_check_template_params(); EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED }
 
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
+    Matrix(Matrix&& other)
+      : Base(std::move(other))
+    {
+      Base::_check_template_params();
+      if (RowsAtCompileTime!=Dynamic && ColsAtCompileTime!=Dynamic)
+        Base::_set_noalias(other);
+    }
+    Matrix& operator=(Matrix&& other)
+    {
+      other.swap(*this);
+      return *this;
+    }
+#endif
+
     /** \brief Constructs a vector or row-vector with given dimension. \only_for_vectors
       *
       * Note that this is only useful for dynamic-size vectors. For fixed-size vectors,

gtsam/3rdparty/Eigen/Eigen/src/Core/MatrixBase.h

@@ -159,13 +159,11 @@ template<typename Derived> class MatrixBase
     template<typename OtherDerived>
     Derived& operator=(const ReturnByValue<OtherDerived>& other);
 
-#ifndef EIGEN_PARSED_BY_DOXYGEN
     template<typename ProductDerived, typename Lhs, typename Rhs>
     Derived& lazyAssign(const ProductBase<ProductDerived, Lhs,Rhs>& other);
 
     template<typename MatrixPower, typename Lhs, typename Rhs>
     Derived& lazyAssign(const MatrixPowerProduct<MatrixPower, Lhs,Rhs>& other);
-#endif // not EIGEN_PARSED_BY_DOXYGEN
 
     template<typename OtherDerived>
     Derived& operator+=(const MatrixBase<OtherDerived>& other);
@@ -442,6 +440,15 @@ template<typename Derived> class MatrixBase
     template<typename OtherScalar>
     void applyOnTheRight(Index p, Index q, const JacobiRotation<OtherScalar>& j);
 
+///////// SparseCore module /////////
+
+    template<typename OtherDerived>
+    EIGEN_STRONG_INLINE const typename SparseMatrixBase<OtherDerived>::template CwiseProductDenseReturnType<Derived>::Type
+    cwiseProduct(const SparseMatrixBase<OtherDerived> &other) const
+    {
+      return other.cwiseProduct(derived());
+    }
+
 ///////// MatrixFunctions module /////////
 
     typedef typename internal::stem_function<Scalar>::type StemFunction;

gtsam/3rdparty/Eigen/Eigen/src/Core/PermutationMatrix.h

@@ -250,6 +250,35 @@ class PermutationBase : public EigenBase<Derived>
     template<typename Other> friend
     inline PlainPermutationType operator*(const Transpose<PermutationBase<Other> >& other, const PermutationBase& perm)
     { return PlainPermutationType(internal::PermPermProduct, other.eval(), perm); }
+    
+    /** \returns the determinant of the permutation matrix, which is either 1 or -1 depending on the parity of the permutation.
+      *
+      * This function is O(\c n) procedure allocating a buffer of \c n booleans.
+      */
+    Index determinant() const
+    {
+      Index res = 1;
+      Index n = size();
+      Matrix<bool,RowsAtCompileTime,1,0,MaxRowsAtCompileTime> mask(n);
+      mask.fill(false);
+      Index r = 0;
+      while(r < n)
+      {
+        // search for the next seed
+        while(r<n && mask[r]) r++;
+        if(r>=n)
+          break;
+        // we got one, let's follow it until we are back to the seed
+        Index k0 = r++;
+        mask.coeffRef(k0) = true;
+        for(Index k=indices().coeff(k0); k!=k0; k=indices().coeff(k))
+        {
+          mask.coeffRef(k) = true;
+          res = -res;
+        }
+      }
+      return res;
+    }
 
   protected:
 

gtsam/3rdparty/Eigen/Eigen/src/Core/PlainObjectBase.h

@@ -437,6 +437,36 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     }
 #endif
 
+#ifdef EIGEN_HAVE_RVALUE_REFERENCES
+    PlainObjectBase(PlainObjectBase&& other)
+      : m_storage( std::move(other.m_storage) )
+    {
+    }
+
+    PlainObjectBase& operator=(PlainObjectBase&& other)
+    {
+      using std::swap;
+      swap(m_storage, other.m_storage);
+      return *this;
+    }
+#endif
+
+    /** Copy constructor */
+    EIGEN_STRONG_INLINE PlainObjectBase(const PlainObjectBase& other)
+      : m_storage()
+    {
+      _check_template_params();
+      lazyAssign(other);
+    }
+
+    template<typename OtherDerived>
+    EIGEN_STRONG_INLINE PlainObjectBase(const DenseBase<OtherDerived> &other)
+      : m_storage()
+    {
+      _check_template_params();
+      lazyAssign(other);
+    }
+
     EIGEN_STRONG_INLINE PlainObjectBase(Index a_size, Index nbRows, Index nbCols)
       : m_storage(a_size, nbRows, nbCols)
     {
@@ -573,6 +603,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
                  : (rows() == other.rows() && cols() == other.cols())))
         && "Size mismatch. Automatic resizing is disabled because EIGEN_NO_AUTOMATIC_RESIZING is defined");
       EIGEN_ONLY_USED_FOR_DEBUG(other);
+      if(this->size()==0)
+        resizeLike(other);
       #else
       resizeLike(other);
       #endif

gtsam/3rdparty/Eigen/Eigen/src/Core/Redux.h

@@ -247,8 +247,9 @@ struct redux_impl<Func, Derived, LinearVectorizedTraversal, NoUnrolling>
   }
 };
 
-template<typename Func, typename Derived>
+// NOTE: for SliceVectorizedTraversal we simply bypass unrolling
-struct redux_impl<Func, Derived, SliceVectorizedTraversal, NoUnrolling>
+template<typename Func, typename Derived, int Unrolling>
+struct redux_impl<Func, Derived, SliceVectorizedTraversal, Unrolling>
 {
   typedef typename Derived::Scalar Scalar;
   typedef typename packet_traits<Scalar>::type PacketScalar;

gtsam/3rdparty/Eigen/Eigen/src/Core/Ref.h

@@ -108,7 +108,8 @@ struct traits<Ref<_PlainObjectType, _Options, _StrideType> >
       OuterStrideMatch = Derived::IsVectorAtCompileTime
                       || int(StrideType::OuterStrideAtCompileTime)==int(Dynamic) || int(StrideType::OuterStrideAtCompileTime)==int(Derived::OuterStrideAtCompileTime),
       AlignmentMatch = (_Options!=Aligned) || ((PlainObjectType::Flags&AlignedBit)==0) || ((traits<Derived>::Flags&AlignedBit)==AlignedBit),
-      MatchAtCompileTime = HasDirectAccess && StorageOrderMatch && InnerStrideMatch && OuterStrideMatch && AlignmentMatch
+      ScalarTypeMatch = internal::is_same<typename PlainObjectType::Scalar, typename Derived::Scalar>::value,
+      MatchAtCompileTime = HasDirectAccess && StorageOrderMatch && InnerStrideMatch && OuterStrideMatch && AlignmentMatch && ScalarTypeMatch
     };
     typedef typename internal::conditional<MatchAtCompileTime,internal::true_type,internal::false_type>::type type;
   };
@@ -187,9 +188,11 @@ protected:
 template<typename PlainObjectType, int Options, typename StrideType> class Ref
   : public RefBase<Ref<PlainObjectType, Options, StrideType> >
 {
+  private:
     typedef internal::traits<Ref> Traits;
     template<typename Derived>
-    inline Ref(const PlainObjectBase<Derived>& expr);
+    inline Ref(const PlainObjectBase<Derived>& expr,
+               typename internal::enable_if<bool(Traits::template match<Derived>::MatchAtCompileTime),Derived>::type* = 0);
   public:
 
     typedef RefBase<Ref> Base;
@@ -198,13 +201,15 @@ template<typename PlainObjectType, int Options, typename StrideType> class Ref
 
     #ifndef EIGEN_PARSED_BY_DOXYGEN
     template<typename Derived>
-    inline Ref(PlainObjectBase<Derived>& expr)
+    inline Ref(PlainObjectBase<Derived>& expr,
+               typename internal::enable_if<bool(Traits::template match<Derived>::MatchAtCompileTime),Derived>::type* = 0)
     {
       EIGEN_STATIC_ASSERT(static_cast<bool>(Traits::template match<Derived>::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
       Base::construct(expr.derived());
     }
     template<typename Derived>
-    inline Ref(const DenseBase<Derived>& expr)
+    inline Ref(const DenseBase<Derived>& expr,
+               typename internal::enable_if<bool(Traits::template match<Derived>::MatchAtCompileTime),Derived>::type* = 0)
     #else
     template<typename Derived>
     inline Ref(DenseBase<Derived>& expr)
@@ -231,13 +236,23 @@ template<typename TPlainObjectType, int Options, typename StrideType> class Ref<
     EIGEN_DENSE_PUBLIC_INTERFACE(Ref)
 
     template<typename Derived>
-    inline Ref(const DenseBase<Derived>& expr)
+    inline Ref(const DenseBase<Derived>& expr,
+               typename internal::enable_if<bool(Traits::template match<Derived>::ScalarTypeMatch),Derived>::type* = 0)
     {
 //      std::cout << match_helper<Derived>::HasDirectAccess << "," << match_helper<Derived>::OuterStrideMatch << "," << match_helper<Derived>::InnerStrideMatch << "\n";
 //      std::cout << int(StrideType::OuterStrideAtCompileTime) << " - " << int(Derived::OuterStrideAtCompileTime) << "\n";
 //      std::cout << int(StrideType::InnerStrideAtCompileTime) << " - " << int(Derived::InnerStrideAtCompileTime) << "\n";
       construct(expr.derived(), typename Traits::template match<Derived>::type());
     }
+    
+    inline Ref(const Ref& other) : Base(other) {
+      // copy constructor shall not copy the m_object, to avoid unnecessary malloc and copy
+    }
+
+    template<typename OtherRef>
+    inline Ref(const RefBase<OtherRef>& other) {
+      construct(other.derived(), typename Traits::template match<OtherRef>::type());
+    }
 
   protected:
 

gtsam/3rdparty/Eigen/Eigen/src/Core/ReturnByValue.h

@@ -72,6 +72,8 @@ template<typename Derived> class ReturnByValue
     const Unusable& coeff(Index,Index) const { return *reinterpret_cast<const Unusable*>(this); }
     Unusable& coeffRef(Index) { return *reinterpret_cast<Unusable*>(this); }
     Unusable& coeffRef(Index,Index) { return *reinterpret_cast<Unusable*>(this); }
+    template<int LoadMode>  Unusable& packet(Index) const;
+    template<int LoadMode>  Unusable& packet(Index, Index) const;
 #endif
 };
 
@@ -83,6 +85,15 @@ Derived& DenseBase<Derived>::operator=(const ReturnByValue<OtherDerived>& other)
   return derived();
 }
 
+template<typename Derived>
+template<typename OtherDerived>
+Derived& DenseBase<Derived>::lazyAssign(const ReturnByValue<OtherDerived>& other)
+{
+  other.evalTo(derived());
+  return derived();
+}
+
+
 } // end namespace Eigen
 
 #endif // EIGEN_RETURNBYVALUE_H

gtsam/3rdparty/Eigen/Eigen/src/Core/SelfCwiseBinaryOp.h

@@ -180,15 +180,9 @@ inline Derived& DenseBase<Derived>::operator*=(const Scalar& other)
 template<typename Derived>
 inline Derived& DenseBase<Derived>::operator/=(const Scalar& other)
 {
-  typedef typename internal::conditional<NumTraits<Scalar>::IsInteger,
-                                        internal::scalar_quotient_op<Scalar>,
-                                        internal::scalar_product_op<Scalar> >::type BinOp;
   typedef typename Derived::PlainObject PlainObject;
-  SelfCwiseBinaryOp<BinOp, Derived, typename PlainObject::ConstantReturnType> tmp(derived());
+  SelfCwiseBinaryOp<internal::scalar_quotient_op<Scalar>, Derived, typename PlainObject::ConstantReturnType> tmp(derived());
-  Scalar actual_other;
+  tmp = PlainObject::Constant(rows(),cols(), other);
-  if(NumTraits<Scalar>::IsInteger)  actual_other = other;
-  else                              actual_other = Scalar(1)/other;
-  tmp = PlainObject::Constant(rows(),cols(), actual_other);
   return derived();
 }
 

gtsam/3rdparty/Eigen/Eigen/src/Core/arch/NEON/PacketMath.h

@@ -384,6 +384,7 @@ template<> EIGEN_STRONG_INLINE int predux_max<Packet4i>(const Packet4i& a)
   a_lo = vget_low_s32(a);
   a_hi = vget_high_s32(a);
   max = vpmax_s32(a_lo, a_hi);
+  max = vpmax_s32(max, max);
 
   return vget_lane_s32(max, 0);
 }

gtsam/3rdparty/Eigen/Eigen/src/Core/arch/SSE/MathFunctions.h

@@ -126,7 +126,7 @@ Packet4f pexp<Packet4f>(const Packet4f& _x)
   _EIGEN_DECLARE_CONST_Packet4f(cephes_exp_p4, 1.6666665459E-1f);
   _EIGEN_DECLARE_CONST_Packet4f(cephes_exp_p5, 5.0000001201E-1f);
 
-  Packet4f tmp = _mm_setzero_ps(), fx;
+  Packet4f tmp, fx;
   Packet4i emm0;
 
   // clamp x
@@ -195,7 +195,7 @@ Packet2d pexp<Packet2d>(const Packet2d& _x)
   _EIGEN_DECLARE_CONST_Packet2d(cephes_exp_C2, 1.42860682030941723212e-6);
   static const __m128i p4i_1023_0 = _mm_setr_epi32(1023, 1023, 0, 0);
 
-  Packet2d tmp = _mm_setzero_pd(), fx;
+  Packet2d tmp, fx;
   Packet4i emm0;
 
   // clamp x
@@ -279,7 +279,7 @@ Packet4f psin<Packet4f>(const Packet4f& _x)
   _EIGEN_DECLARE_CONST_Packet4f(coscof_p2,  4.166664568298827E-002f);
   _EIGEN_DECLARE_CONST_Packet4f(cephes_FOPI, 1.27323954473516f); // 4 / M_PI
 
-  Packet4f xmm1, xmm2 = _mm_setzero_ps(), xmm3, sign_bit, y;
+  Packet4f xmm1, xmm2, xmm3, sign_bit, y;
 
   Packet4i emm0, emm2;
   sign_bit = x;
@@ -378,7 +378,7 @@ Packet4f pcos<Packet4f>(const Packet4f& _x)
   _EIGEN_DECLARE_CONST_Packet4f(coscof_p2,  4.166664568298827E-002f);
   _EIGEN_DECLARE_CONST_Packet4f(cephes_FOPI, 1.27323954473516f); // 4 / M_PI
 
-  Packet4f xmm1, xmm2 = _mm_setzero_ps(), xmm3, y;
+  Packet4f xmm1, xmm2, xmm3, y;
   Packet4i emm0, emm2;
 
   x = pabs(x);

gtsam/3rdparty/Eigen/Eigen/src/Core/products/CoeffBasedProduct.h

@@ -134,7 +134,7 @@ class CoeffBasedProduct
     };
 
     typedef internal::product_coeff_impl<CanVectorizeInner ? InnerVectorizedTraversal : DefaultTraversal,
-                                   Unroll ? (InnerSize==0 ? 0 : InnerSize-1) : Dynamic,
+                                   Unroll ? InnerSize : Dynamic,
                                    _LhsNested, _RhsNested, Scalar> ScalarCoeffImpl;
 
     typedef CoeffBasedProduct<LhsNested,RhsNested,NestByRefBit> LazyCoeffBasedProductType;
@@ -185,7 +185,7 @@ class CoeffBasedProduct
     {
       PacketScalar res;
       internal::product_packet_impl<Flags&RowMajorBit ? RowMajor : ColMajor,
-                              Unroll ? (InnerSize==0 ? 0 : InnerSize-1) : Dynamic,
+                              Unroll ? InnerSize : Dynamic,
                               _LhsNested, _RhsNested, PacketScalar, LoadMode>
         ::run(row, col, m_lhs, m_rhs, res);
       return res;
@@ -243,7 +243,17 @@ struct product_coeff_impl<DefaultTraversal, UnrollingIndex, Lhs, Rhs, RetScalar>
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, RetScalar &res)
   {
     product_coeff_impl<DefaultTraversal, UnrollingIndex-1, Lhs, Rhs, RetScalar>::run(row, col, lhs, rhs, res);
-    res += lhs.coeff(row, UnrollingIndex) * rhs.coeff(UnrollingIndex, col);
+    res += lhs.coeff(row, UnrollingIndex-1) * rhs.coeff(UnrollingIndex-1, col);
+  }
+};
+
+template<typename Lhs, typename Rhs, typename RetScalar>
+struct product_coeff_impl<DefaultTraversal, 1, Lhs, Rhs, RetScalar>
+{
+  typedef typename Lhs::Index Index;
+  static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, RetScalar &res)
+  {
+    res = lhs.coeff(row, 0) * rhs.coeff(0, col);
   }
 };
 
@@ -251,9 +261,9 @@ template<typename Lhs, typename Rhs, typename RetScalar>
 struct product_coeff_impl<DefaultTraversal, 0, Lhs, Rhs, RetScalar>
 {
   typedef typename Lhs::Index Index;
-  static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, RetScalar &res)
+  static EIGEN_STRONG_INLINE void run(Index /*row*/, Index /*col*/, const Lhs& /*lhs*/, const Rhs& /*rhs*/, RetScalar &res)
   {
-    res = lhs.coeff(row, 0) * rhs.coeff(0, col);
+    res = RetScalar(0);
   }
 };
 
@@ -293,6 +303,16 @@ struct product_coeff_vectorized_unroller<0, Lhs, Rhs, Packet>
   }
 };
 
+template<typename Lhs, typename Rhs, typename RetScalar>
+struct product_coeff_impl<InnerVectorizedTraversal, 0, Lhs, Rhs, RetScalar>
+{
+  typedef typename Lhs::Index Index;
+  static EIGEN_STRONG_INLINE void run(Index /*row*/, Index /*col*/, const Lhs& /*lhs*/, const Rhs& /*rhs*/, RetScalar &res)
+  {
+    res = 0;
+  }
+};
+
 template<int UnrollingIndex, typename Lhs, typename Rhs, typename RetScalar>
 struct product_coeff_impl<InnerVectorizedTraversal, UnrollingIndex, Lhs, Rhs, RetScalar>
 {
@@ -302,8 +322,7 @@ struct product_coeff_impl<InnerVectorizedTraversal, UnrollingIndex, Lhs, Rhs, Re
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, RetScalar &res)
   {
     Packet pres;
-    product_coeff_vectorized_unroller<UnrollingIndex+1-PacketSize, Lhs, Rhs, Packet>::run(row, col, lhs, rhs, pres);
+    product_coeff_vectorized_unroller<UnrollingIndex-PacketSize, Lhs, Rhs, Packet>::run(row, col, lhs, rhs, pres);
-    product_coeff_impl<DefaultTraversal,UnrollingIndex,Lhs,Rhs,RetScalar>::run(row, col, lhs, rhs, res);
     res = predux(pres);
   }
 };
@@ -371,7 +390,7 @@ struct product_packet_impl<RowMajor, UnrollingIndex, Lhs, Rhs, Packet, LoadMode>
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet &res)
   {
     product_packet_impl<RowMajor, UnrollingIndex-1, Lhs, Rhs, Packet, LoadMode>::run(row, col, lhs, rhs, res);
-    res =  pmadd(pset1<Packet>(lhs.coeff(row, UnrollingIndex)), rhs.template packet<LoadMode>(UnrollingIndex, col), res);
+    res =  pmadd(pset1<Packet>(lhs.coeff(row, UnrollingIndex-1)), rhs.template packet<LoadMode>(UnrollingIndex-1, col), res);
   }
 };
 
@@ -382,12 +401,12 @@ struct product_packet_impl<ColMajor, UnrollingIndex, Lhs, Rhs, Packet, LoadMode>
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet &res)
   {
     product_packet_impl<ColMajor, UnrollingIndex-1, Lhs, Rhs, Packet, LoadMode>::run(row, col, lhs, rhs, res);
-    res =  pmadd(lhs.template packet<LoadMode>(row, UnrollingIndex), pset1<Packet>(rhs.coeff(UnrollingIndex, col)), res);
+    res =  pmadd(lhs.template packet<LoadMode>(row, UnrollingIndex-1), pset1<Packet>(rhs.coeff(UnrollingIndex-1, col)), res);
   }
 };
 
 template<typename Lhs, typename Rhs, typename Packet, int LoadMode>
-struct product_packet_impl<RowMajor, 0, Lhs, Rhs, Packet, LoadMode>
+struct product_packet_impl<RowMajor, 1, Lhs, Rhs, Packet, LoadMode>
 {
   typedef typename Lhs::Index Index;
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet &res)
@@ -397,7 +416,7 @@ struct product_packet_impl<RowMajor, 0, Lhs, Rhs, Packet, LoadMode>
 };
 
 template<typename Lhs, typename Rhs, typename Packet, int LoadMode>
-struct product_packet_impl<ColMajor, 0, Lhs, Rhs, Packet, LoadMode>
+struct product_packet_impl<ColMajor, 1, Lhs, Rhs, Packet, LoadMode>
 {
   typedef typename Lhs::Index Index;
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet &res)
@@ -406,16 +425,35 @@ struct product_packet_impl<ColMajor, 0, Lhs, Rhs, Packet, LoadMode>
   }
 };
 
+template<typename Lhs, typename Rhs, typename Packet, int LoadMode>
+struct product_packet_impl<RowMajor, 0, Lhs, Rhs, Packet, LoadMode>
+{
+  typedef typename Lhs::Index Index;
+  static EIGEN_STRONG_INLINE void run(Index /*row*/, Index /*col*/, const Lhs& /*lhs*/, const Rhs& /*rhs*/, Packet &res)
+  {
+    res = pset1<Packet>(0);
+  }
+};
+
+template<typename Lhs, typename Rhs, typename Packet, int LoadMode>
+struct product_packet_impl<ColMajor, 0, Lhs, Rhs, Packet, LoadMode>
+{
+  typedef typename Lhs::Index Index;
+  static EIGEN_STRONG_INLINE void run(Index /*row*/, Index /*col*/, const Lhs& /*lhs*/, const Rhs& /*rhs*/, Packet &res)
+  {
+    res = pset1<Packet>(0);
+  }
+};
+
 template<typename Lhs, typename Rhs, typename Packet, int LoadMode>
 struct product_packet_impl<RowMajor, Dynamic, Lhs, Rhs, Packet, LoadMode>
 {
   typedef typename Lhs::Index Index;
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet& res)
   {
-    eigen_assert(lhs.cols()>0 && "you are using a non initialized matrix");
+    res = pset1<Packet>(0);
-    res = pmul(pset1<Packet>(lhs.coeff(row, 0)),rhs.template packet<LoadMode>(0, col));
+    for(Index i = 0; i < lhs.cols(); ++i)
-      for(Index i = 1; i < lhs.cols(); ++i)
+      res =  pmadd(pset1<Packet>(lhs.coeff(row, i)), rhs.template packet<LoadMode>(i, col), res);
-        res =  pmadd(pset1<Packet>(lhs.coeff(row, i)), rhs.template packet<LoadMode>(i, col), res);
   }
 };
 
@@ -425,10 +463,9 @@ struct product_packet_impl<ColMajor, Dynamic, Lhs, Rhs, Packet, LoadMode>
   typedef typename Lhs::Index Index;
   static EIGEN_STRONG_INLINE void run(Index row, Index col, const Lhs& lhs, const Rhs& rhs, Packet& res)
   {
-    eigen_assert(lhs.cols()>0 && "you are using a non initialized matrix");
+    res = pset1<Packet>(0);
-    res = pmul(lhs.template packet<LoadMode>(row, 0), pset1<Packet>(rhs.coeff(0, col)));
+    for(Index i = 0; i < lhs.cols(); ++i)
-      for(Index i = 1; i < lhs.cols(); ++i)
+      res =  pmadd(lhs.template packet<LoadMode>(row, i), pset1<Packet>(rhs.coeff(i, col)), res);
-        res =  pmadd(lhs.template packet<LoadMode>(row, i), pset1<Packet>(rhs.coeff(i, col)), res);
   }
 };
 

gtsam/3rdparty/Eigen/Eigen/src/Core/products/Parallelizer.h

@@ -125,19 +125,22 @@ void parallelize_gemm(const Functor& func, Index rows, Index cols, bool transpos
   if(transpose)
     std::swap(rows,cols);
 
-  Index blockCols = (cols / threads) & ~Index(0x3);
-  Index blockRows = (rows / threads) & ~Index(0x7);
-  
   GemmParallelInfo<Index>* info = new GemmParallelInfo<Index>[threads];
 
-  #pragma omp parallel for schedule(static,1) num_threads(threads)
+  #pragma omp parallel num_threads(threads)
-  for(Index i=0; i<threads; ++i)
   {
+    Index i = omp_get_thread_num();
+    // Note that the actual number of threads might be lower than the number of request ones.
+    Index actual_threads = omp_get_num_threads();
+    
+    Index blockCols = (cols / actual_threads) & ~Index(0x3);
+    Index blockRows = (rows / actual_threads) & ~Index(0x7);
+    
     Index r0 = i*blockRows;
-    Index actualBlockRows = (i+1==threads) ? rows-r0 : blockRows;
+    Index actualBlockRows = (i+1==actual_threads) ? rows-r0 : blockRows;
 
     Index c0 = i*blockCols;
-    Index actualBlockCols = (i+1==threads) ? cols-c0 : blockCols;
+    Index actualBlockCols = (i+1==actual_threads) ? cols-c0 : blockCols;
 
     info[i].rhs_start = c0;
     info[i].rhs_length = actualBlockCols;

gtsam/3rdparty/Eigen/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h

@@ -109,7 +109,7 @@ struct product_triangular_matrix_matrix_trmm<EIGTYPE,Index,Mode,true, \
 /* Non-square case - doesn't fit to MKL ?TRMM. Fall to default triangular product or call MKL ?GEMM*/ \
    if (rows != depth) { \
 \
-     int nthr = mkl_domain_get_max_threads(MKL_BLAS); \
+     int nthr = mkl_domain_get_max_threads(EIGEN_MKL_DOMAIN_BLAS); \
 \
      if (((nthr==1) && (((std::max)(rows,depth)-diagSize)/(double)diagSize < 0.5))) { \
      /* Most likely no benefit to call TRMM or GEMM from MKL*/ \
@@ -223,7 +223,7 @@ struct product_triangular_matrix_matrix_trmm<EIGTYPE,Index,Mode,false, \
 /* Non-square case - doesn't fit to MKL ?TRMM. Fall to default triangular product or call MKL ?GEMM*/ \
    if (cols != depth) { \
 \
-     int nthr = mkl_domain_get_max_threads(MKL_BLAS); \
+     int nthr = mkl_domain_get_max_threads(EIGEN_MKL_DOMAIN_BLAS); \
 \
      if ((nthr==1) && (((std::max)(cols,depth)-diagSize)/(double)diagSize < 0.5)) { \
      /* Most likely no benefit to call TRMM or GEMM from MKL*/ \

gtsam/3rdparty/Eigen/Eigen/src/Core/products/TriangularSolverMatrix.h

@@ -302,9 +302,12 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheRight,Mode,Conj
                 for (Index i=0; i<actual_mc; ++i)
                   r[i] -= a[i] * b;
               }
-              Scalar b = (Mode & UnitDiag) ? Scalar(1) : Scalar(1)/conj(rhs(j,j));
+              if((Mode & UnitDiag)==0)
-              for (Index i=0; i<actual_mc; ++i)
+              {
-                r[i] *= b;
+                Scalar b = conj(rhs(j,j));
+                for (Index i=0; i<actual_mc; ++i)
+                  r[i] /= b;
+              }
             }
 
             // pack the just computed part of lhs to A

gtsam/3rdparty/Eigen/Eigen/src/Core/util/Constants.h

@@ -433,6 +433,19 @@ struct MatrixXpr {};
 /** The type used to identify an array expression */
 struct ArrayXpr {};
 
+namespace internal {
+  /** \internal
+  * Constants for comparison functors
+  */
+  enum ComparisonName {
+    cmp_EQ = 0,
+    cmp_LT = 1,
+    cmp_LE = 2,
+    cmp_UNORD = 3,
+    cmp_NEQ = 4
+  };
+}
+
 } // end namespace Eigen
 
 #endif // EIGEN_CONSTANTS_H

gtsam/3rdparty/Eigen/Eigen/src/Core/util/ForwardDeclarations.h

@@ -235,6 +235,9 @@ template<typename Scalar> class Rotation2D;
 template<typename Scalar> class AngleAxis;
 template<typename Scalar,int Dim> class Translation;
 
+// Sparse module:
+template<typename Derived> class SparseMatrixBase;
+
 #ifdef EIGEN2_SUPPORT
 template<typename Derived, int _Dim> class eigen2_RotationBase;
 template<typename Lhs, typename Rhs> class eigen2_Cross;

gtsam/3rdparty/Eigen/Eigen/src/Core/util/MKL_support.h

@@ -76,6 +76,38 @@
 #include <mkl_lapacke.h>
 #define EIGEN_MKL_VML_THRESHOLD 128
 
+/* MKL_DOMAIN_BLAS, etc are defined only in 10.3 update 7 */
+/* MKL_BLAS, etc are not defined in 11.2 */
+#ifdef MKL_DOMAIN_ALL
+#define EIGEN_MKL_DOMAIN_ALL MKL_DOMAIN_ALL
+#else
+#define EIGEN_MKL_DOMAIN_ALL MKL_ALL
+#endif
+
+#ifdef MKL_DOMAIN_BLAS
+#define EIGEN_MKL_DOMAIN_BLAS MKL_DOMAIN_BLAS
+#else
+#define EIGEN_MKL_DOMAIN_BLAS MKL_BLAS
+#endif
+
+#ifdef MKL_DOMAIN_FFT
+#define EIGEN_MKL_DOMAIN_FFT MKL_DOMAIN_FFT
+#else
+#define EIGEN_MKL_DOMAIN_FFT MKL_FFT
+#endif
+
+#ifdef MKL_DOMAIN_VML
+#define EIGEN_MKL_DOMAIN_VML MKL_DOMAIN_VML
+#else
+#define EIGEN_MKL_DOMAIN_VML MKL_VML
+#endif
+
+#ifdef MKL_DOMAIN_PARDISO
+#define EIGEN_MKL_DOMAIN_PARDISO MKL_DOMAIN_PARDISO
+#else
+#define EIGEN_MKL_DOMAIN_PARDISO MKL_PARDISO
+#endif
+
 namespace Eigen {
 
 typedef std::complex<double> dcomplex;

gtsam/3rdparty/Eigen/Eigen/src/Core/util/Macros.h

@@ -13,7 +13,7 @@
 
 #define EIGEN_WORLD_VERSION 3
 #define EIGEN_MAJOR_VERSION 2
-#define EIGEN_MINOR_VERSION 4
+#define EIGEN_MINOR_VERSION 7
 
 #define EIGEN_VERSION_AT_LEAST(x,y,z) (EIGEN_WORLD_VERSION>x || (EIGEN_WORLD_VERSION>=x && \
                                       (EIGEN_MAJOR_VERSION>y || (EIGEN_MAJOR_VERSION>=y && \
@@ -96,6 +96,20 @@
 #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
 #endif
 
+// A Clang feature extension to determine compiler features.
+// We use it to determine 'cxx_rvalue_references'
+#ifndef __has_feature
+# define __has_feature(x) 0
+#endif
+
+// Do we support r-value references?
+#if (__has_feature(cxx_rvalue_references) || \
+     defined(__GXX_EXPERIMENTAL_CXX0X__) || \
+     (defined(_MSC_VER) && _MSC_VER >= 1600))
+  #define EIGEN_HAVE_RVALUE_REFERENCES
+#endif
+
+
 // Cross compiler wrapper around LLVM's __has_builtin
 #ifdef __has_builtin
 #  define EIGEN_HAS_BUILTIN(x) __has_builtin(x)
@@ -278,6 +292,7 @@ namespace Eigen {
   #error Please tell me what is the equivalent of __attribute__((aligned(n))) for your compiler
 #endif
 
+#define EIGEN_ALIGN8  EIGEN_ALIGN_TO_BOUNDARY(8)
 #define EIGEN_ALIGN16 EIGEN_ALIGN_TO_BOUNDARY(16)
 
 #if EIGEN_ALIGN_STATICALLY
@@ -332,8 +347,11 @@ namespace Eigen {
   }
 #endif
 
-#define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) \
+/** \internal
-  EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived)
+ * \brief Macro to manually inherit assignment operators.
+ * This is necessary, because the implicitly defined assignment operator gets deleted when a custom operator= is defined.
+ */
+#define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived)
 
 /**
 * Just a side note. Commenting within defines works only by documenting
@@ -405,6 +423,8 @@ namespace Eigen {
 #define EIGEN_SIZE_MAX(a,b) (((int)a == Dynamic || (int)b == Dynamic) ? Dynamic \
                            : ((int)a >= (int)b) ? (int)a : (int)b)
 
+#define EIGEN_ADD_COST(a,b) int(a)==Dynamic || int(b)==Dynamic ? Dynamic : int(a)+int(b)
+
 #define EIGEN_LOGICAL_XOR(a,b) (((a) || (b)) && !((a) && (b)))
 
 #define EIGEN_IMPLIES(a,b) (!(a) || (b))

gtsam/3rdparty/Eigen/Eigen/src/Core/util/Memory.h

@@ -523,7 +523,7 @@ template<typename T> struct smart_copy_helper<T,false> {
 // you can overwrite Eigen's default behavior regarding alloca by defining EIGEN_ALLOCA
 // to the appropriate stack allocation function
 #ifndef EIGEN_ALLOCA
-  #if (defined __linux__)
+  #if (defined __linux__) || (defined __APPLE__) || (defined alloca)
     #define EIGEN_ALLOCA alloca
   #elif defined(_MSC_VER)
     #define EIGEN_ALLOCA _alloca

gtsam/3rdparty/Eigen/Eigen/src/Core/util/XprHelper.h

@@ -366,17 +366,17 @@ struct dense_xpr_base<Derived, ArrayXpr>
 
 /** \internal Helper base class to add a scalar multiple operator
   * overloads for complex types */
-template<typename Derived,typename Scalar,typename OtherScalar,
+template<typename Derived, typename Scalar, typename OtherScalar, typename BaseType,
          bool EnableIt = !is_same<Scalar,OtherScalar>::value >
-struct special_scalar_op_base : public DenseCoeffsBase<Derived>
+struct special_scalar_op_base : public BaseType
 {
   // dummy operator* so that the
   // "using special_scalar_op_base::operator*" compiles
   void operator*() const;
 };
 
-template<typename Derived,typename Scalar,typename OtherScalar>
+template<typename Derived,typename Scalar,typename OtherScalar, typename BaseType>
-struct special_scalar_op_base<Derived,Scalar,OtherScalar,true>  : public DenseCoeffsBase<Derived>
+struct special_scalar_op_base<Derived,Scalar,OtherScalar,BaseType,true>  : public BaseType
 {
   const CwiseUnaryOp<scalar_multiple2_op<Scalar,OtherScalar>, Derived>
   operator*(const OtherScalar& scalar) const

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h

@@ -234,6 +234,12 @@ template<typename _MatrixType> class ComplexEigenSolver
     }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     EigenvectorType m_eivec;
     EigenvalueType m_eivalues;
     ComplexSchur<MatrixType> m_schur;
@@ -251,6 +257,8 @@ template<typename MatrixType>
 ComplexEigenSolver<MatrixType>& 
 ComplexEigenSolver<MatrixType>::compute(const MatrixType& matrix, bool computeEigenvectors)
 {
+  check_template_parameters();
+  
   // this code is inspired from Jampack
   eigen_assert(matrix.cols() == matrix.rows());
 

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/EigenSolver.h

@@ -298,6 +298,13 @@ template<typename _MatrixType> class EigenSolver
     void doComputeEigenvectors();
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+      EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL);
+    }
+    
     MatrixType m_eivec;
     EigenvalueType m_eivalues;
     bool m_isInitialized;
@@ -364,6 +371,8 @@ template<typename MatrixType>
 EigenSolver<MatrixType>& 
 EigenSolver<MatrixType>::compute(const MatrixType& matrix, bool computeEigenvectors)
 {
+  check_template_parameters();
+  
   using std::sqrt;
   using std::abs;
   eigen_assert(matrix.cols() == matrix.rows());

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h

@@ -263,6 +263,13 @@ template<typename _MatrixType> class GeneralizedEigenSolver
     }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+      EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL);
+    }
+    
     MatrixType m_eivec;
     ComplexVectorType m_alphas;
     VectorType m_betas;
@@ -290,6 +297,8 @@ template<typename MatrixType>
 GeneralizedEigenSolver<MatrixType>&
 GeneralizedEigenSolver<MatrixType>::compute(const MatrixType& A, const MatrixType& B, bool computeEigenvectors)
 {
+  check_template_parameters();
+  
   using std::sqrt;
   using std::abs;
   eigen_assert(A.cols() == A.rows() && B.cols() == A.rows() && B.cols() == B.rows());

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/RealQZ.h

@@ -240,10 +240,10 @@ namespace Eigen {
             m_S.coeffRef(i,j) = Scalar(0.0);
             m_S.rightCols(dim-j-1).applyOnTheLeft(i-1,i,G.adjoint());
             m_T.rightCols(dim-i+1).applyOnTheLeft(i-1,i,G.adjoint());
+            // update Q
+            if (m_computeQZ)
+              m_Q.applyOnTheRight(i-1,i,G);
           }
-          // update Q
-          if (m_computeQZ)
-            m_Q.applyOnTheRight(i-1,i,G);
           // kill T(i,i-1)
           if(m_T.coeff(i,i-1)!=Scalar(0))
           {
@@ -251,10 +251,10 @@ namespace Eigen {
             m_T.coeffRef(i,i-1) = Scalar(0.0);
             m_S.applyOnTheRight(i,i-1,G);
             m_T.topRows(i).applyOnTheRight(i,i-1,G);
+            // update Z
+            if (m_computeQZ)
+              m_Z.applyOnTheLeft(i,i-1,G.adjoint());
           }
-          // update Z
-          if (m_computeQZ)
-            m_Z.applyOnTheLeft(i,i-1,G.adjoint());
         }
       }
     }

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/RealSchur.h

@@ -234,7 +234,7 @@ template<typename _MatrixType> class RealSchur
     typedef Matrix<Scalar,3,1> Vector3s;
 
     Scalar computeNormOfT();
-    Index findSmallSubdiagEntry(Index iu, const Scalar& norm);
+    Index findSmallSubdiagEntry(Index iu);
     void splitOffTwoRows(Index iu, bool computeU, const Scalar& exshift);
     void computeShift(Index iu, Index iter, Scalar& exshift, Vector3s& shiftInfo);
     void initFrancisQRStep(Index il, Index iu, const Vector3s& shiftInfo, Index& im, Vector3s& firstHouseholderVector);
@@ -286,7 +286,7 @@ RealSchur<MatrixType>& RealSchur<MatrixType>::computeFromHessenberg(const HessMa
   {
     while (iu >= 0)
     {
-      Index il = findSmallSubdiagEntry(iu, norm);
+      Index il = findSmallSubdiagEntry(iu);
 
       // Check for convergence
       if (il == iu) // One root found
@@ -343,16 +343,14 @@ inline typename MatrixType::Scalar RealSchur<MatrixType>::computeNormOfT()
 
 /** \internal Look for single small sub-diagonal element and returns its index */
 template<typename MatrixType>
-inline typename MatrixType::Index RealSchur<MatrixType>::findSmallSubdiagEntry(Index iu, const Scalar& norm)
+inline typename MatrixType::Index RealSchur<MatrixType>::findSmallSubdiagEntry(Index iu)
 {
   using std::abs;
   Index res = iu;
   while (res > 0)
   {
     Scalar s = abs(m_matT.coeff(res-1,res-1)) + abs(m_matT.coeff(res,res));
-    if (s == 0.0)
+    if (abs(m_matT.coeff(res,res-1)) <= NumTraits<Scalar>::epsilon() * s)
-      s = norm;
-    if (abs(m_matT.coeff(res,res-1)) < NumTraits<Scalar>::epsilon() * s)
       break;
     res--;
   }
@@ -457,9 +455,7 @@ inline void RealSchur<MatrixType>::initFrancisQRStep(Index il, Index iu, const V
     const Scalar lhs = m_matT.coeff(im,im-1) * (abs(v.coeff(1)) + abs(v.coeff(2)));
     const Scalar rhs = v.coeff(0) * (abs(m_matT.coeff(im-1,im-1)) + abs(Tmm) + abs(m_matT.coeff(im+1,im+1)));
     if (abs(lhs) < NumTraits<Scalar>::epsilon() * rhs)
-    {
       break;
-    }
   }
 }
 

gtsam/3rdparty/Eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h

@@ -80,6 +80,8 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
     /** \brief Scalar type for matrices of type \p _MatrixType. */
     typedef typename MatrixType::Scalar Scalar;
     typedef typename MatrixType::Index Index;
+    
+    typedef Matrix<Scalar,Size,Size,ColMajor,MaxColsAtCompileTime,MaxColsAtCompileTime> EigenvectorsType;
 
     /** \brief Real scalar type for \p _MatrixType.
       *
@@ -225,7 +227,7 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
       *
       * \sa eigenvalues()
       */
-    const MatrixType& eigenvectors() const
+    const EigenvectorsType& eigenvectors() const
     {
       eigen_assert(m_isInitialized && "SelfAdjointEigenSolver is not initialized.");
       eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
@@ -351,7 +353,12 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
     #endif // EIGEN2_SUPPORT
 
   protected:
-    MatrixType m_eivec;
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
+    EigenvectorsType m_eivec;
     RealVectorType m_eivalues;
     typename TridiagonalizationType::SubDiagonalType m_subdiag;
     ComputationInfo m_info;
@@ -376,7 +383,7 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
   * "implicit symmetric QR step with Wilkinson shift"
   */
 namespace internal {
-template<int StorageOrder,typename RealScalar, typename Scalar, typename Index>
+template<typename RealScalar, typename Scalar, typename Index>
 static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n);
 }
 
@@ -384,6 +391,8 @@ template<typename MatrixType>
 SelfAdjointEigenSolver<MatrixType>& SelfAdjointEigenSolver<MatrixType>
 ::compute(const MatrixType& matrix, int options)
 {
+  check_template_parameters();
+  
   using std::abs;
   eigen_assert(matrix.cols() == matrix.rows());
   eigen_assert((options&~(EigVecMask|GenEigMask))==0
@@ -406,7 +415,7 @@ SelfAdjointEigenSolver<MatrixType>& SelfAdjointEigenSolver<MatrixType>
 
   // declare some aliases
   RealVectorType& diag = m_eivalues;
-  MatrixType& mat = m_eivec;
+  EigenvectorsType& mat = m_eivec;
 
   // map the matrix coefficients to [-1:1] to avoid over- and underflow.
   mat = matrix.template triangularView<Lower>();
@@ -442,7 +451,7 @@ SelfAdjointEigenSolver<MatrixType>& SelfAdjointEigenSolver<MatrixType>
     while (start>0 && m_subdiag[start-1]!=0)
       start--;
 
-    internal::tridiagonal_qr_step<MatrixType::Flags&RowMajorBit ? RowMajor : ColMajor>(diag.data(), m_subdiag.data(), start, end, computeEigenvectors ? m_eivec.data() : (Scalar*)0, n);
+    internal::tridiagonal_qr_step(diag.data(), m_subdiag.data(), start, end, computeEigenvectors ? m_eivec.data() : (Scalar*)0, n);
   }
 
   if (iter <= m_maxIterations * n)
@@ -490,7 +499,13 @@ template<typename SolverType> struct direct_selfadjoint_eigenvalues<SolverType,3
   typedef typename SolverType::MatrixType MatrixType;
   typedef typename SolverType::RealVectorType VectorType;
   typedef typename SolverType::Scalar Scalar;
+  typedef typename MatrixType::Index Index;
+  typedef typename SolverType::EigenvectorsType EigenvectorsType;
   
+  /** \internal
+   * Computes the roots of the characteristic polynomial of \a m.
+   * For numerical stability m.trace() should be near zero and to avoid over- or underflow m should be normalized.
+   */
   static inline void computeRoots(const MatrixType& m, VectorType& roots)
   {
     using std::sqrt;
@@ -510,158 +525,123 @@ template<typename SolverType> struct direct_selfadjoint_eigenvalues<SolverType,3
     // Construct the parameters used in classifying the roots of the equation
     // and in solving the equation for the roots in closed form.
     Scalar c2_over_3 = c2*s_inv3;
-    Scalar a_over_3 = (c1 - c2*c2_over_3)*s_inv3;
+    Scalar a_over_3 = (c2*c2_over_3 - c1)*s_inv3;
-    if (a_over_3 > Scalar(0))
+    if(a_over_3<Scalar(0))
       a_over_3 = Scalar(0);
 
     Scalar half_b = Scalar(0.5)*(c0 + c2_over_3*(Scalar(2)*c2_over_3*c2_over_3 - c1));
 
-    Scalar q = half_b*half_b + a_over_3*a_over_3*a_over_3;
+    Scalar q = a_over_3*a_over_3*a_over_3 - half_b*half_b;
-    if (q > Scalar(0))
+    if(q<Scalar(0))
       q = Scalar(0);
 
     // Compute the eigenvalues by solving for the roots of the polynomial.
-    Scalar rho = sqrt(-a_over_3);
+    Scalar rho = sqrt(a_over_3);
-    Scalar theta = atan2(sqrt(-q),half_b)*s_inv3;
+    Scalar theta = atan2(sqrt(q),half_b)*s_inv3;  // since sqrt(q) > 0, atan2 is in [0, pi] and theta is in [0, pi/3]
     Scalar cos_theta = cos(theta);
     Scalar sin_theta = sin(theta);
-    roots(0) = c2_over_3 + Scalar(2)*rho*cos_theta;
+    // roots are already sorted, since cos is monotonically decreasing on [0, pi]
-    roots(1) = c2_over_3 - rho*(cos_theta + s_sqrt3*sin_theta);
+    roots(0) = c2_over_3 - rho*(cos_theta + s_sqrt3*sin_theta); // == 2*rho*cos(theta+2pi/3)
-    roots(2) = c2_over_3 - rho*(cos_theta - s_sqrt3*sin_theta);
+    roots(1) = c2_over_3 - rho*(cos_theta - s_sqrt3*sin_theta); // == 2*rho*cos(theta+ pi/3)
-
+    roots(2) = c2_over_3 + Scalar(2)*rho*cos_theta;
-    // Sort in increasing order.
-    if (roots(0) >= roots(1))
-      std::swap(roots(0),roots(1));
-    if (roots(1) >= roots(2))
-    {
-      std::swap(roots(1),roots(2));
-      if (roots(0) >= roots(1))
-        std::swap(roots(0),roots(1));
-    }
   }
-  
+
+  static inline bool extract_kernel(MatrixType& mat, Ref<VectorType> res, Ref<VectorType> representative)
+  {
+    using std::abs;
+    Index i0;
+    // Find non-zero column i0 (by construction, there must exist a non zero coefficient on the diagonal):
+    mat.diagonal().cwiseAbs().maxCoeff(&i0);
+    // mat.col(i0) is a good candidate for an orthogonal vector to the current eigenvector,
+    // so let's save it:
+    representative = mat.col(i0);
+    Scalar n0, n1;
+    VectorType c0, c1;
+    n0 = (c0 = representative.cross(mat.col((i0+1)%3))).squaredNorm();
+    n1 = (c1 = representative.cross(mat.col((i0+2)%3))).squaredNorm();
+    if(n0>n1) res = c0/std::sqrt(n0);
+    else      res = c1/std::sqrt(n1);
+
+    return true;
+  }
+
   static inline void run(SolverType& solver, const MatrixType& mat, int options)
   {
-    using std::sqrt;
     eigen_assert(mat.cols() == 3 && mat.cols() == mat.rows());
     eigen_assert((options&~(EigVecMask|GenEigMask))==0
             && (options&EigVecMask)!=EigVecMask
             && "invalid option parameter");
     bool computeEigenvectors = (options&ComputeEigenvectors)==ComputeEigenvectors;
     
-    MatrixType& eivecs = solver.m_eivec;
+    EigenvectorsType& eivecs = solver.m_eivec;
     VectorType& eivals = solver.m_eivalues;
   
-    // map the matrix coefficients to [-1:1] to avoid over- and underflow.
+    // Shift the matrix to the mean eigenvalue and map the matrix coefficients to [-1:1] to avoid over- and underflow.
-    Scalar scale = mat.cwiseAbs().maxCoeff();
+    Scalar shift = mat.trace() / Scalar(3);
-    MatrixType scaledMat = mat / scale;
+    // TODO Avoid this copy. Currently it is necessary to suppress bogus values when determining maxCoeff and for computing the eigenvectors later
+    MatrixType scaledMat = mat.template selfadjointView<Lower>();
+    scaledMat.diagonal().array() -= shift;
+    Scalar scale = scaledMat.cwiseAbs().maxCoeff();
+    if(scale > 0) scaledMat /= scale;   // TODO for scale==0 we could save the remaining operations
 
     // compute the eigenvalues
     computeRoots(scaledMat,eivals);
 
-    // compute the eigen vectors
+    // compute the eigenvectors
     if(computeEigenvectors)
     {
-      Scalar safeNorm2 = Eigen::NumTraits<Scalar>::epsilon();
       if((eivals(2)-eivals(0))<=Eigen::NumTraits<Scalar>::epsilon())
       {
+        // All three eigenvalues are numerically the same
         eivecs.setIdentity();
       }
       else
       {
-        scaledMat = scaledMat.template selfadjointView<Lower>();
         MatrixType tmp;
         tmp = scaledMat;
 
+        // Compute the eigenvector of the most distinct eigenvalue
         Scalar d0 = eivals(2) - eivals(1);
         Scalar d1 = eivals(1) - eivals(0);
-        int k =  d0 > d1 ? 2 : 0;
+        Index k(0), l(2);
-        d0 = d0 > d1 ? d0 : d1;
+        if(d0 > d1)
-
-        tmp.diagonal().array () -= eivals(k);
-        VectorType cross;
-        Scalar n;
-        n = (cross = tmp.row(0).cross(tmp.row(1))).squaredNorm();
-
-        if(n>safeNorm2)
         {
-          eivecs.col(k) = cross / sqrt(n);
+          std::swap(k,l);
+          d0 = d1;
+        }
+
+        // Compute the eigenvector of index k
+        {
+          tmp.diagonal().array () -= eivals(k);
+          // By construction, 'tmp' is of rank 2, and its kernel corresponds to the respective eigenvector.
+          extract_kernel(tmp, eivecs.col(k), eivecs.col(l));
+        }
+
+        // Compute eigenvector of index l
+        if(d0<=2*Eigen::NumTraits<Scalar>::epsilon()*d1)
+        {
+          // If d0 is too small, then the two other eigenvalues are numerically the same,
+          // and thus we only have to ortho-normalize the near orthogonal vector we saved above.
+          eivecs.col(l) -= eivecs.col(k).dot(eivecs.col(l))*eivecs.col(l);
+          eivecs.col(l).normalize();
         }
         else
         {
-          n = (cross = tmp.row(0).cross(tmp.row(2))).squaredNorm();
+          tmp = scaledMat;
+          tmp.diagonal().array () -= eivals(l);
 
-          if(n>safeNorm2)
+          VectorType dummy;
-          {
+          extract_kernel(tmp, eivecs.col(l), dummy);
-            eivecs.col(k) = cross / sqrt(n);
-          }
-          else
-          {
-            n = (cross = tmp.row(1).cross(tmp.row(2))).squaredNorm();
-
-            if(n>safeNorm2)
-            {
-              eivecs.col(k) = cross / sqrt(n);
-            }
-            else
-            {
-              // the input matrix and/or the eigenvaues probably contains some inf/NaN,
-              // => exit
-              // scale back to the original size.
-              eivals *= scale;
-
-              solver.m_info = NumericalIssue;
-              solver.m_isInitialized = true;
-              solver.m_eigenvectorsOk = computeEigenvectors;
-              return;
-            }
-          }
         }
 
-        tmp = scaledMat;
+        // Compute last eigenvector from the other two
-        tmp.diagonal().array() -= eivals(1);
+        eivecs.col(1) = eivecs.col(2).cross(eivecs.col(0)).normalized();
-
-        if(d0<=Eigen::NumTraits<Scalar>::epsilon())
-        {
-          eivecs.col(1) = eivecs.col(k).unitOrthogonal();
-        }
-        else
-        {
-          n = (cross = eivecs.col(k).cross(tmp.row(0))).squaredNorm();
-          if(n>safeNorm2)
-          {
-            eivecs.col(1) = cross / sqrt(n);
-          }
-          else
-          {
-            n = (cross = eivecs.col(k).cross(tmp.row(1))).squaredNorm();
-            if(n>safeNorm2)
-              eivecs.col(1) = cross / sqrt(n);
-            else
-            {
-              n = (cross = eivecs.col(k).cross(tmp.row(2))).squaredNorm();
-              if(n>safeNorm2)
-                eivecs.col(1) = cross / sqrt(n);
-              else
-              {
-                // we should never reach this point,
-                // if so the last two eigenvalues are likely to be very close to each other
-                eivecs.col(1) = eivecs.col(k).unitOrthogonal();
-              }
-            }
-          }
-
-          // make sure that eivecs[1] is orthogonal to eivecs[2]
-          // FIXME: this step should not be needed
-          Scalar d = eivecs.col(1).dot(eivecs.col(k));
-          eivecs.col(1) = (eivecs.col(1) - d * eivecs.col(k)).normalized();
-        }
-
-        eivecs.col(k==2 ? 0 : 2) = eivecs.col(k).cross(eivecs.col(1)).normalized();
       }
     }
+
     // Rescale back to the original size.
     eivals *= scale;
+    eivals.array() += shift;
     
     solver.m_info = Success;
     solver.m_isInitialized = true;
@@ -675,11 +655,12 @@ template<typename SolverType> struct direct_selfadjoint_eigenvalues<SolverType,2
   typedef typename SolverType::MatrixType MatrixType;
   typedef typename SolverType::RealVectorType VectorType;
   typedef typename SolverType::Scalar Scalar;
+  typedef typename SolverType::EigenvectorsType EigenvectorsType;
   
   static inline void computeRoots(const MatrixType& m, VectorType& roots)
   {
     using std::sqrt;
-    const Scalar t0 = Scalar(0.5) * sqrt( numext::abs2(m(0,0)-m(1,1)) + Scalar(4)*m(1,0)*m(1,0));
+    const Scalar t0 = Scalar(0.5) * sqrt( numext::abs2(m(0,0)-m(1,1)) + Scalar(4)*numext::abs2(m(1,0)));
     const Scalar t1 = Scalar(0.5) * (m(0,0) + m(1,1));
     roots(0) = t1 - t0;
     roots(1) = t1 + t0;
@@ -688,13 +669,15 @@ template<typename SolverType> struct direct_selfadjoint_eigenvalues<SolverType,2
   static inline void run(SolverType& solver, const MatrixType& mat, int options)
   {
     using std::sqrt;
+    using std::abs;
+
     eigen_assert(mat.cols() == 2 && mat.cols() == mat.rows());
     eigen_assert((options&~(EigVecMask|GenEigMask))==0
             && (options&EigVecMask)!=EigVecMask
             && "invalid option parameter");
     bool computeEigenvectors = (options&ComputeEigenvectors)==ComputeEigenvectors;
     
-    MatrixType& eivecs = solver.m_eivec;
+    EigenvectorsType& eivecs = solver.m_eivec;
     VectorType& eivals = solver.m_eivalues;
   
     // map the matrix coefficients to [-1:1] to avoid over- and underflow.
@@ -708,22 +691,29 @@ template<typename SolverType> struct direct_selfadjoint_eigenvalues<SolverType,2
     // compute the eigen vectors
     if(computeEigenvectors)
     {
-      scaledMat.diagonal().array () -= eivals(1);
+      if((eivals(1)-eivals(0))<=abs(eivals(1))*Eigen::NumTraits<Scalar>::epsilon())
-      Scalar a2 = numext::abs2(scaledMat(0,0));
-      Scalar c2 = numext::abs2(scaledMat(1,1));
-      Scalar b2 = numext::abs2(scaledMat(1,0));
-      if(a2>c2)
       {
-        eivecs.col(1) << -scaledMat(1,0), scaledMat(0,0);
+        eivecs.setIdentity();
-        eivecs.col(1) /= sqrt(a2+b2);
       }
       else
       {
-        eivecs.col(1) << -scaledMat(1,1), scaledMat(1,0);
+        scaledMat.diagonal().array () -= eivals(1);
-        eivecs.col(1) /= sqrt(c2+b2);
+        Scalar a2 = numext::abs2(scaledMat(0,0));
-      }
+        Scalar c2 = numext::abs2(scaledMat(1,1));
+        Scalar b2 = numext::abs2(scaledMat(1,0));
+        if(a2>c2)
+        {
+          eivecs.col(1) << -scaledMat(1,0), scaledMat(0,0);
+          eivecs.col(1) /= sqrt(a2+b2);
+        }
+        else
+        {
+          eivecs.col(1) << -scaledMat(1,1), scaledMat(1,0);
+          eivecs.col(1) /= sqrt(c2+b2);
+        }
 
-      eivecs.col(0) << eivecs.col(1).unitOrthogonal();
+        eivecs.col(0) << eivecs.col(1).unitOrthogonal();
+      }
     }
     
     // Rescale back to the original size.
@@ -746,7 +736,7 @@ SelfAdjointEigenSolver<MatrixType>& SelfAdjointEigenSolver<MatrixType>
 }
 
 namespace internal {
-template<int StorageOrder,typename RealScalar, typename Scalar, typename Index>
+template<typename RealScalar, typename Scalar, typename Index>
 static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n)
 {
   using std::abs;
@@ -798,8 +788,7 @@ static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index sta
     // apply the givens rotation to the unit matrix Q = Q * G
     if (matrixQ)
     {
-      // FIXME if StorageOrder == RowMajor this operation is not very efficient
+      Map<Matrix<Scalar,Dynamic,Dynamic,ColMajor> > q(matrixQ,n,n);
-      Map<Matrix<Scalar,Dynamic,Dynamic,StorageOrder> > q(matrixQ,n,n);
       q.applyOnTheRight(k,k+1,rot);
     }
   }

gtsam/3rdparty/Eigen/Eigen/src/Geometry/AlignedBox.h

@@ -19,10 +19,12 @@ namespace Eigen {
   *
   * \brief An axis aligned box
   *
-  * \param _Scalar the type of the scalar coefficients
+  * \tparam _Scalar the type of the scalar coefficients
-  * \param _AmbientDim the dimension of the ambient space, can be a compile time value or Dynamic.
+  * \tparam _AmbientDim the dimension of the ambient space, can be a compile time value or Dynamic.
   *
   * This class represents an axis aligned box as a pair of the minimal and maximal corners.
+  * \warning The result of most methods is undefined when applied to an empty box. You can check for empty boxes using isEmpty().
+  * \sa alignedboxtypedefs
   */
 template <typename _Scalar, int _AmbientDim>
 class AlignedBox
@@ -40,18 +42,21 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
   /** Define constants to name the corners of a 1D, 2D or 3D axis aligned bounding box */
   enum CornerType
   {
-    /** 1D names */
+    /** 1D names @{ */
     Min=0, Max=1,
+    /** @} */
 
-    /** Added names for 2D */
+    /** Identifier for 2D corner @{ */
     BottomLeft=0, BottomRight=1,
     TopLeft=2, TopRight=3,
+    /** @} */
 
-    /** Added names for 3D */
+    /** Identifier for 3D corner  @{ */
     BottomLeftFloor=0, BottomRightFloor=1,
     TopLeftFloor=2, TopRightFloor=3,
     BottomLeftCeil=4, BottomRightCeil=5,
     TopLeftCeil=6, TopRightCeil=7
+    /** @} */
   };
 
 
@@ -63,34 +68,33 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
   inline explicit AlignedBox(Index _dim) : m_min(_dim), m_max(_dim)
   { setEmpty(); }
 
-  /** Constructs a box with extremities \a _min and \a _max. */
+  /** Constructs a box with extremities \a _min and \a _max.
+   * \warning If either component of \a _min is larger than the same component of \a _max, the constructed box is empty. */
   template<typename OtherVectorType1, typename OtherVectorType2>
   inline AlignedBox(const OtherVectorType1& _min, const OtherVectorType2& _max) : m_min(_min), m_max(_max) {}
 
   /** Constructs a box containing a single point \a p. */
   template<typename Derived>
-  inline explicit AlignedBox(const MatrixBase<Derived>& a_p)
+  inline explicit AlignedBox(const MatrixBase<Derived>& p) : m_min(p), m_max(m_min)
-  {
+  { }
-    typename internal::nested<Derived,2>::type p(a_p.derived());
-    m_min = p;
-    m_max = p;
-  }
 
   ~AlignedBox() {}
 
   /** \returns the dimension in which the box holds */
   inline Index dim() const { return AmbientDimAtCompileTime==Dynamic ? m_min.size() : Index(AmbientDimAtCompileTime); }
 
-  /** \deprecated use isEmpty */
+  /** \deprecated use isEmpty() */
   inline bool isNull() const { return isEmpty(); }
 
-  /** \deprecated use setEmpty */
+  /** \deprecated use setEmpty() */
   inline void setNull() { setEmpty(); }
 
-  /** \returns true if the box is empty. */
+  /** \returns true if the box is empty.
+   * \sa setEmpty */
   inline bool isEmpty() const { return (m_min.array() > m_max.array()).any(); }
 
-  /** Makes \c *this an empty box. */
+  /** Makes \c *this an empty box.
+   * \sa isEmpty */
   inline void setEmpty()
   {
     m_min.setConstant( ScalarTraits::highest() );
@@ -159,7 +163,7 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
    * a uniform distribution */
   inline VectorType sample() const
   {
-    VectorType r;
+    VectorType r(dim());
     for(Index d=0; d<dim(); ++d)
     {
       if(!ScalarTraits::IsInteger)
@@ -175,27 +179,34 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
 
   /** \returns true if the point \a p is inside the box \c *this. */
   template<typename Derived>
-  inline bool contains(const MatrixBase<Derived>& a_p) const
+  inline bool contains(const MatrixBase<Derived>& p) const
   {
-    typename internal::nested<Derived,2>::type p(a_p.derived());
+    typename internal::nested<Derived,2>::type p_n(p.derived());
-    return (m_min.array()<=p.array()).all() && (p.array()<=m_max.array()).all();
+    return (m_min.array()<=p_n.array()).all() && (p_n.array()<=m_max.array()).all();
   }
 
   /** \returns true if the box \a b is entirely inside the box \c *this. */
   inline bool contains(const AlignedBox& b) const
   { return (m_min.array()<=(b.min)().array()).all() && ((b.max)().array()<=m_max.array()).all(); }
 
-  /** Extends \c *this such that it contains the point \a p and returns a reference to \c *this. */
+  /** \returns true if the box \a b is intersecting the box \c *this.
+   * \sa intersection, clamp */
+  inline bool intersects(const AlignedBox& b) const
+  { return (m_min.array()<=(b.max)().array()).all() && ((b.min)().array()<=m_max.array()).all(); }
+
+  /** Extends \c *this such that it contains the point \a p and returns a reference to \c *this.
+   * \sa extend(const AlignedBox&) */
   template<typename Derived>
-  inline AlignedBox& extend(const MatrixBase<Derived>& a_p)
+  inline AlignedBox& extend(const MatrixBase<Derived>& p)
   {
-    typename internal::nested<Derived,2>::type p(a_p.derived());
+    typename internal::nested<Derived,2>::type p_n(p.derived());
-    m_min = m_min.cwiseMin(p);
+    m_min = m_min.cwiseMin(p_n);
-    m_max = m_max.cwiseMax(p);
+    m_max = m_max.cwiseMax(p_n);
     return *this;
   }
 
-  /** Extends \c *this such that it contains the box \a b and returns a reference to \c *this. */
+  /** Extends \c *this such that it contains the box \a b and returns a reference to \c *this.
+   * \sa merged, extend(const MatrixBase&) */
   inline AlignedBox& extend(const AlignedBox& b)
   {
     m_min = m_min.cwiseMin(b.m_min);
@@ -203,7 +214,9 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
     return *this;
   }
 
-  /** Clamps \c *this by the box \a b and returns a reference to \c *this. */
+  /** Clamps \c *this by the box \a b and returns a reference to \c *this.
+   * \note If the boxes don't intersect, the resulting box is empty.
+   * \sa intersection(), intersects() */
   inline AlignedBox& clamp(const AlignedBox& b)
   {
     m_min = m_min.cwiseMax(b.m_min);
@@ -211,11 +224,15 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
     return *this;
   }
 
-  /** Returns an AlignedBox that is the intersection of \a b and \c *this */
+  /** Returns an AlignedBox that is the intersection of \a b and \c *this
+   * \note If the boxes don't intersect, the resulting box is empty.
+   * \sa intersects(), clamp, contains()  */
   inline AlignedBox intersection(const AlignedBox& b) const
   {return AlignedBox(m_min.cwiseMax(b.m_min), m_max.cwiseMin(b.m_max)); }
 
-  /** Returns an AlignedBox that is the union of \a b and \c *this */
+  /** Returns an AlignedBox that is the union of \a b and \c *this.
+   * \note Merging with an empty box may result in a box bigger than \c *this. 
+   * \sa extend(const AlignedBox&) */
   inline AlignedBox merged(const AlignedBox& b) const
   { return AlignedBox(m_min.cwiseMin(b.m_min), m_max.cwiseMax(b.m_max)); }
 
@@ -231,20 +248,20 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
 
   /** \returns the squared distance between the point \a p and the box \c *this,
     * and zero if \a p is inside the box.
-    * \sa exteriorDistance()
+    * \sa exteriorDistance(const MatrixBase&), squaredExteriorDistance(const AlignedBox&)
     */
   template<typename Derived>
-  inline Scalar squaredExteriorDistance(const MatrixBase<Derived>& a_p) const;
+  inline Scalar squaredExteriorDistance(const MatrixBase<Derived>& p) const;
 
   /** \returns the squared distance between the boxes \a b and \c *this,
     * and zero if the boxes intersect.
-    * \sa exteriorDistance()
+    * \sa exteriorDistance(const AlignedBox&), squaredExteriorDistance(const MatrixBase&)
     */
   inline Scalar squaredExteriorDistance(const AlignedBox& b) const;
 
   /** \returns the distance between the point \a p and the box \c *this,
     * and zero if \a p is inside the box.
-    * \sa squaredExteriorDistance()
+    * \sa squaredExteriorDistance(const MatrixBase&), exteriorDistance(const AlignedBox&)
     */
   template<typename Derived>
   inline NonInteger exteriorDistance(const MatrixBase<Derived>& p) const
@@ -252,7 +269,7 @@ EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
 
   /** \returns the distance between the boxes \a b and \c *this,
     * and zero if the boxes intersect.
-    * \sa squaredExteriorDistance()
+    * \sa squaredExteriorDistance(const AlignedBox&), exteriorDistance(const MatrixBase&)
     */
   inline NonInteger exteriorDistance(const AlignedBox& b) const
   { using std::sqrt; return sqrt(NonInteger(squaredExteriorDistance(b))); }

gtsam/3rdparty/Eigen/Eigen/src/Geometry/AngleAxis.h

@@ -131,7 +131,7 @@ public:
     m_angle = Scalar(other.angle());
   }
 
-  static inline const AngleAxis Identity() { return AngleAxis(0, Vector3::UnitX()); }
+  static inline const AngleAxis Identity() { return AngleAxis(Scalar(0), Vector3::UnitX()); }
 
   /** \returns \c true if \c *this is approximately equal to \a other, within the precision
     * determined by \a prec.
@@ -165,8 +165,8 @@ AngleAxis<Scalar>& AngleAxis<Scalar>::operator=(const QuaternionBase<QuatDerived
   Scalar n2 = q.vec().squaredNorm();
   if (n2 < NumTraits<Scalar>::dummy_precision()*NumTraits<Scalar>::dummy_precision())
   {
-    m_angle = 0;
+    m_angle = Scalar(0);
-    m_axis << 1, 0, 0;
+    m_axis << Scalar(1), Scalar(0), Scalar(0);
   }
   else
   {

gtsam/3rdparty/Eigen/Eigen/src/Geometry/Homogeneous.h

@@ -79,7 +79,7 @@ template<typename MatrixType,int _Direction> class Homogeneous
     {
       if(  (int(Direction)==Vertical   && row==m_matrix.rows())
         || (int(Direction)==Horizontal && col==m_matrix.cols()))
-        return 1;
+        return Scalar(1);
       return m_matrix.coeff(row, col);
     }
 

gtsam/3rdparty/Eigen/Eigen/src/Geometry/Quaternion.h

@@ -102,11 +102,11 @@ public:
   /** \returns a quaternion representing an identity rotation
     * \sa MatrixBase::Identity()
     */
-  static inline Quaternion<Scalar> Identity() { return Quaternion<Scalar>(1, 0, 0, 0); }
+  static inline Quaternion<Scalar> Identity() { return Quaternion<Scalar>(Scalar(1), Scalar(0), Scalar(0), Scalar(0)); }
 
   /** \sa QuaternionBase::Identity(), MatrixBase::setIdentity()
     */
-  inline QuaternionBase& setIdentity() { coeffs() << 0, 0, 0, 1; return *this; }
+  inline QuaternionBase& setIdentity() { coeffs() << Scalar(0), Scalar(0), Scalar(0), Scalar(1); return *this; }
 
   /** \returns the squared norm of the quaternion's coefficients
     * \sa QuaternionBase::norm(), MatrixBase::squaredNorm()
@@ -161,7 +161,7 @@ public:
   { return coeffs().isApprox(other.coeffs(), prec); }
 
 	/** return the result vector of \a v through the rotation*/
-  EIGEN_STRONG_INLINE Vector3 _transformVector(Vector3 v) const;
+  EIGEN_STRONG_INLINE Vector3 _transformVector(const Vector3& v) const;
 
   /** \returns \c *this with scalar type casted to \a NewScalarType
     *
@@ -231,7 +231,7 @@ class Quaternion : public QuaternionBase<Quaternion<_Scalar,_Options> >
 public:
   typedef _Scalar Scalar;
 
-  EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Quaternion)
+  EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Quaternion)
   using Base::operator*=;
 
   typedef typename internal::traits<Quaternion>::Coefficients Coefficients;
@@ -341,7 +341,7 @@ class Map<const Quaternion<_Scalar>, _Options >
   public:
     typedef _Scalar Scalar;
     typedef typename internal::traits<Map>::Coefficients Coefficients;
-    EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Map)
+    EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Map)
     using Base::operator*=;
 
     /** Constructs a Mapped Quaternion object from the pointer \a coeffs
@@ -378,7 +378,7 @@ class Map<Quaternion<_Scalar>, _Options >
   public:
     typedef _Scalar Scalar;
     typedef typename internal::traits<Map>::Coefficients Coefficients;
-    EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Map)
+    EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Map)
     using Base::operator*=;
 
     /** Constructs a Mapped Quaternion object from the pointer \a coeffs
@@ -461,7 +461,7 @@ EIGEN_STRONG_INLINE Derived& QuaternionBase<Derived>::operator*= (const Quaterni
   */
 template <class Derived>
 EIGEN_STRONG_INLINE typename QuaternionBase<Derived>::Vector3
-QuaternionBase<Derived>::_transformVector(Vector3 v) const
+QuaternionBase<Derived>::_transformVector(const Vector3& v) const
 {
     // Note that this algorithm comes from the optimization by hand
     // of the conversion to a Matrix followed by a Matrix/Vector product.
@@ -637,7 +637,7 @@ inline Quaternion<typename internal::traits<Derived>::Scalar> QuaternionBase<Der
 {
   // FIXME should this function be called multiplicativeInverse and conjugate() be called inverse() or opposite()  ??
   Scalar n2 = this->squaredNorm();
-  if (n2 > 0)
+  if (n2 > Scalar(0))
     return Quaternion<Scalar>(conjugate().coeffs() / n2);
   else
   {
@@ -667,12 +667,10 @@ template <class OtherDerived>
 inline typename internal::traits<Derived>::Scalar
 QuaternionBase<Derived>::angularDistance(const QuaternionBase<OtherDerived>& other) const
 {
-  using std::acos;
+  using std::atan2;
   using std::abs;
-  Scalar d = abs(this->dot(other));
+  Quaternion<Scalar> d = (*this) * other.conjugate();
-  if (d>=Scalar(1))
+  return Scalar(2) * atan2( d.vec().norm(), abs(d.w()) );
-    return Scalar(0);
-  return Scalar(2) * acos(d);
 }
 
  
@@ -712,7 +710,7 @@ QuaternionBase<Derived>::slerp(const Scalar& t, const QuaternionBase<OtherDerive
     scale0 = sin( ( Scalar(1) - t ) * theta) / sinTheta;
     scale1 = sin( ( t * theta) ) / sinTheta;
   }
-  if(d<0) scale1 = -scale1;
+  if(d<Scalar(0)) scale1 = -scale1;
 
   return Quaternion<Scalar>(scale0 * coeffs() + scale1 * other.coeffs());
 }

gtsam/3rdparty/Eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h

@@ -65,10 +65,10 @@ class DiagonalPreconditioner
       {
         typename MatType::InnerIterator it(mat,j);
         while(it && it.index()!=j) ++it;
-        if(it && it.index()==j)
+        if(it && it.index()==j && it.value()!=Scalar(0))
           m_invdiag(j) = Scalar(1)/it.value();
         else
-          m_invdiag(j) = 0;
+          m_invdiag(j) = Scalar(1);
       }
       m_isInitialized = true;
       return *this;

gtsam/3rdparty/Eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h

@@ -151,20 +151,7 @@ struct traits<BiCGSTAB<_MatrixType,_Preconditioner> >
   * \endcode
   * 
   * By default the iterations start with x=0 as an initial guess of the solution.
-  * One can control the start using the solveWithGuess() method. Here is a step by
+  * One can control the start using the solveWithGuess() method.
-  * step execution example starting with a random guess and printing the evolution
-  * of the estimated error:
-  * * \code
-  * x = VectorXd::Random(n);
-  * solver.setMaxIterations(1);
-  * int i = 0;
-  * do {
-  *   x = solver.solveWithGuess(b,x);
-  *   std::cout << i << " : " << solver.error() << std::endl;
-  *   ++i;
-  * } while (solver.info()!=Success && i<100);
-  * \endcode
-  * Note that such a step by step excution is slightly slower.
   * 
   * \sa class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
   */
@@ -199,7 +186,8 @@ public:
     * this class becomes invalid. Call compute() to update it with the new
     * matrix A, or modify a copy of A.
     */
-  BiCGSTAB(const MatrixType& A) : Base(A) {}
+  template<typename MatrixDerived>
+  explicit BiCGSTAB(const EigenBase<MatrixDerived>& A) : Base(A.derived()) {}
 
   ~BiCGSTAB() {}
   

gtsam/3rdparty/Eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h

@@ -112,9 +112,9 @@ struct traits<ConjugateGradient<_MatrixType,_UpLo,_Preconditioner> >
   * This class allows to solve for A.x = b sparse linear problems using a conjugate gradient algorithm.
   * The sparse matrix A must be selfadjoint. The vectors x and b can be either dense or sparse.
   *
-  * \tparam _MatrixType the type of the sparse matrix A, can be a dense or a sparse matrix.
+  * \tparam _MatrixType the type of the matrix A, can be a dense or a sparse matrix.
-  * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower
+  * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower,
-  *               or Upper. Default is Lower.
+  *               Upper, or Lower|Upper in which the full matrix entries will be considered. Default is Lower.
   * \tparam _Preconditioner the type of the preconditioner. Default is DiagonalPreconditioner
   *
   * The maximal number of iterations and tolerance value can be controlled via the setMaxIterations()
@@ -137,20 +137,7 @@ struct traits<ConjugateGradient<_MatrixType,_UpLo,_Preconditioner> >
   * \endcode
   * 
   * By default the iterations start with x=0 as an initial guess of the solution.
-  * One can control the start using the solveWithGuess() method. Here is a step by
+  * One can control the start using the solveWithGuess() method.
-  * step execution example starting with a random guess and printing the evolution
-  * of the estimated error:
-  * * \code
-  * x = VectorXd::Random(n);
-  * cg.setMaxIterations(1);
-  * int i = 0;
-  * do {
-  *   x = cg.solveWithGuess(b,x);
-  *   std::cout << i << " : " << cg.error() << std::endl;
-  *   ++i;
-  * } while (cg.info()!=Success && i<100);
-  * \endcode
-  * Note that such a step by step excution is slightly slower.
   * 
   * \sa class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
   */
@@ -189,7 +176,8 @@ public:
     * this class becomes invalid. Call compute() to update it with the new
     * matrix A, or modify a copy of A.
     */
-  ConjugateGradient(const MatrixType& A) : Base(A) {}
+  template<typename MatrixDerived>
+  explicit ConjugateGradient(const EigenBase<MatrixDerived>& A) : Base(A.derived()) {}
 
   ~ConjugateGradient() {}
   
@@ -213,6 +201,10 @@ public:
   template<typename Rhs,typename Dest>
   void _solveWithGuess(const Rhs& b, Dest& x) const
   {
+    typedef typename internal::conditional<UpLo==(Lower|Upper),
+                                           const MatrixType&,
+                                           SparseSelfAdjointView<const MatrixType, UpLo>
+                                          >::type MatrixWrapperType;
     m_iterations = Base::maxIterations();
     m_error = Base::m_tolerance;
 
@@ -222,8 +214,7 @@ public:
       m_error = Base::m_tolerance;
 
       typename Dest::ColXpr xj(x,j);
-      internal::conjugate_gradient(mp_matrix->template selfadjointView<UpLo>(), b.col(j), xj,
+      internal::conjugate_gradient(MatrixWrapperType(*mp_matrix), b.col(j), xj, Base::m_preconditioner, m_iterations, m_error);
-                                   Base::m_preconditioner, m_iterations, m_error);
     }
 
     m_isInitialized = true;
@@ -234,7 +225,7 @@ public:
   template<typename Rhs,typename Dest>
   void _solve(const Rhs& b, Dest& x) const
   {
-    x.setOnes();
+    x.setZero();
     _solveWithGuess(b,x);
   }
 

gtsam/3rdparty/Eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h

@@ -150,7 +150,6 @@ class IncompleteLUT : internal::noncopyable
     {
       analyzePattern(amat); 
       factorize(amat);
-      m_isInitialized = m_factorizationIsOk;
       return *this;
     }
 
@@ -160,7 +159,7 @@ class IncompleteLUT : internal::noncopyable
     template<typename Rhs, typename Dest>
     void _solve(const Rhs& b, Dest& x) const
     {
-      x = m_Pinv * b;  
+      x = m_Pinv * b;
       x = m_lu.template triangularView<UnitLower>().solve(x);
       x = m_lu.template triangularView<Upper>().solve(x);
       x = m_P * x; 
@@ -223,18 +222,29 @@ template<typename _MatrixType>
 void IncompleteLUT<Scalar>::analyzePattern(const _MatrixType& amat)
 {
   // Compute the Fill-reducing permutation
+  // Since ILUT does not perform any numerical pivoting,
+  // it is highly preferable to keep the diagonal through symmetric permutations.
+#ifndef EIGEN_MPL2_ONLY
+  // To this end, let's symmetrize the pattern and perform AMD on it.
   SparseMatrix<Scalar,ColMajor, Index> mat1 = amat;
   SparseMatrix<Scalar,ColMajor, Index> mat2 = amat.transpose();
-  // Symmetrize the pattern
   // FIXME for a matrix with nearly symmetric pattern, mat2+mat1 is the appropriate choice.
   //       on the other hand for a really non-symmetric pattern, mat2*mat1 should be prefered...
   SparseMatrix<Scalar,ColMajor, Index> AtA = mat2 + mat1;
-  AtA.prune(keep_diag());
+  AMDOrdering<Index> ordering;
-  internal::minimum_degree_ordering<Scalar, Index>(AtA, m_P);  // Then compute the AMD ordering...
+  ordering(AtA,m_P);
-
+  m_Pinv  = m_P.inverse(); // cache the inverse permutation
-  m_Pinv  = m_P.inverse(); // ... and the inverse permutation
+#else
+  // If AMD is not available, (MPL2-only), then let's use the slower COLAMD routine.
+  SparseMatrix<Scalar,ColMajor, Index> mat1 = amat;
+  COLAMDOrdering<Index> ordering;
+  ordering(mat1,m_Pinv);
+  m_P = m_Pinv.inverse();
+#endif
 
   m_analysisIsOk = true;
+  m_factorizationIsOk = false;
+  m_isInitialized = false;
 }
 
 template <typename Scalar>
@@ -442,6 +452,7 @@ void IncompleteLUT<Scalar>::factorize(const _MatrixType& amat)
   m_lu.makeCompressed();
 
   m_factorizationIsOk = true;
+  m_isInitialized = m_factorizationIsOk;
   m_info = Success;
 }
 

gtsam/3rdparty/Eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h

@@ -49,10 +49,11 @@ public:
     * this class becomes invalid. Call compute() to update it with the new
     * matrix A, or modify a copy of A.
     */
-  IterativeSolverBase(const MatrixType& A)
+  template<typename InputDerived>
+  IterativeSolverBase(const EigenBase<InputDerived>& A)
   {
     init();
-    compute(A);
+    compute(A.derived());
   }
 
   ~IterativeSolverBase() {}
@@ -62,9 +63,11 @@ public:
     * Currently, this function mostly call analyzePattern on the preconditioner. In the future
     * we might, for instance, implement column reodering for faster matrix vector products.
     */
-  Derived& analyzePattern(const MatrixType& A)
+  template<typename InputDerived>
+  Derived& analyzePattern(const EigenBase<InputDerived>& A)
   {
-    m_preconditioner.analyzePattern(A);
+    grabInput(A.derived());
+    m_preconditioner.analyzePattern(*mp_matrix);
     m_isInitialized = true;
     m_analysisIsOk = true;
     m_info = Success;
@@ -80,11 +83,12 @@ public:
     * this class becomes invalid. Call compute() to update it with the new
     * matrix A, or modify a copy of A.
     */
-  Derived& factorize(const MatrixType& A)
+  template<typename InputDerived>
+  Derived& factorize(const EigenBase<InputDerived>& A)
   {
+    grabInput(A.derived());
     eigen_assert(m_analysisIsOk && "You must first call analyzePattern()"); 
-    mp_matrix = &A;
+    m_preconditioner.factorize(*mp_matrix);
-    m_preconditioner.factorize(A);
     m_factorizationIsOk = true;
     m_info = Success;
     return derived();
@@ -100,10 +104,11 @@ public:
     * this class becomes invalid. Call compute() to update it with the new
     * matrix A, or modify a copy of A.
     */
-  Derived& compute(const MatrixType& A)
+  template<typename InputDerived>
+  Derived& compute(const EigenBase<InputDerived>& A)
   {
-    mp_matrix = &A;
+    grabInput(A.derived());
-    m_preconditioner.compute(A);
+    m_preconditioner.compute(*mp_matrix);
     m_isInitialized = true;
     m_analysisIsOk = true;
     m_factorizationIsOk = true;
@@ -212,6 +217,28 @@ public:
   }
 
 protected:
+
+  template<typename InputDerived>
+  void grabInput(const EigenBase<InputDerived>& A)
+  {
+    // we const cast to prevent the creation of a MatrixType temporary by the compiler.
+    grabInput_impl(A.const_cast_derived());
+  }
+
+  template<typename InputDerived>
+  void grabInput_impl(const EigenBase<InputDerived>& A)
+  {
+    m_copyMatrix = A;
+    mp_matrix = &m_copyMatrix;
+  }
+
+  void grabInput_impl(MatrixType& A)
+  {
+    if(MatrixType::RowsAtCompileTime==Dynamic && MatrixType::ColsAtCompileTime==Dynamic)
+      m_copyMatrix.resize(0,0);
+    mp_matrix = &A;
+  }
+
   void init()
   {
     m_isInitialized = false;
@@ -220,6 +247,7 @@ protected:
     m_maxIterations = -1;
     m_tolerance = NumTraits<Scalar>::epsilon();
   }
+  MatrixType m_copyMatrix;
   const MatrixType* mp_matrix;
   Preconditioner m_preconditioner;
 

gtsam/3rdparty/Eigen/Eigen/src/LU/FullPivLU.h

@@ -374,6 +374,12 @@ template<typename _MatrixType> class FullPivLU
     inline Index cols() const { return m_lu.cols(); }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     MatrixType m_lu;
     PermutationPType m_p;
     PermutationQType m_q;
@@ -418,6 +424,8 @@ FullPivLU<MatrixType>::FullPivLU(const MatrixType& matrix)
 template<typename MatrixType>
 FullPivLU<MatrixType>& FullPivLU<MatrixType>::compute(const MatrixType& matrix)
 {
+  check_template_parameters();
+  
   // the permutations are stored as int indices, so just to be sure:
   eigen_assert(matrix.rows()<=NumTraits<int>::highest() && matrix.cols()<=NumTraits<int>::highest());
   

gtsam/3rdparty/Eigen/Eigen/src/LU/PartialPivLU.h

@@ -171,6 +171,12 @@ template<typename _MatrixType> class PartialPivLU
     inline Index cols() const { return m_lu.cols(); }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     MatrixType m_lu;
     PermutationType m_p;
     TranspositionType m_rowsTranspositions;
@@ -386,6 +392,8 @@ void partial_lu_inplace(MatrixType& lu, TranspositionType& row_transpositions, t
 template<typename MatrixType>
 PartialPivLU<MatrixType>& PartialPivLU<MatrixType>::compute(const MatrixType& matrix)
 {
+  check_template_parameters();
+  
   // the row permutation is stored as int indices, so just to be sure:
   eigen_assert(matrix.rows()<NumTraits<int>::highest());
   

gtsam/3rdparty/Eigen/Eigen/src/OrderingMethods/Amd.h

@@ -137,22 +137,27 @@ void minimum_degree_ordering(SparseMatrix<Scalar,ColMajor,Index>& C, Permutation
     degree[i] = len[i];                 // degree of node i
   }
   mark = internal::cs_wclear<Index>(0, 0, w, n);         /* clear w */
-  elen[n] = -2;                         /* n is a dead element */
-  Cp[n] = -1;                           /* n is a root of assembly tree */
-  w[n] = 0;                             /* n is a dead element */
   
   /* --- Initialize degree lists ------------------------------------------ */
   for(i = 0; i < n; i++)
   {
+    bool has_diag = false;
+    for(p = Cp[i]; p<Cp[i+1]; ++p)
+      if(Ci[p]==i)
+      {
+        has_diag = true;
+        break;
+      }
+   
     d = degree[i];
-    if(d == 0)                         /* node i is empty */
+    if(d == 1 && has_diag)           /* node i is empty */
     {
       elen[i] = -2;                 /* element i is dead */
       nel++;
       Cp[i] = -1;                   /* i is a root of assembly tree */
       w[i] = 0;
     }
-    else if(d > dense)                 /* node i is dense */
+    else if(d > dense || !has_diag)  /* node i is dense or has no structural diagonal element */
     {
       nv[i] = 0;                    /* absorb i into element n */
       elen[i] = -1;                 /* node i is dead */
@@ -168,6 +173,10 @@ void minimum_degree_ordering(SparseMatrix<Scalar,ColMajor,Index>& C, Permutation
     }
   }
   
+  elen[n] = -2;                         /* n is a dead element */
+  Cp[n] = -1;                           /* n is a root of assembly tree */
+  w[n] = 0;                             /* n is a dead element */
+  
   while (nel < n)                         /* while (selecting pivots) do */
   {
     /* --- Select node of minimum approximate degree -------------------- */

gtsam/3rdparty/Eigen/Eigen/src/QR/ColPivHouseholderQR.h

@@ -384,6 +384,12 @@ template<typename _MatrixType> class ColPivHouseholderQR
     }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     MatrixType m_qr;
     HCoeffsType m_hCoeffs;
     PermutationType m_colsPermutation;
@@ -422,6 +428,8 @@ typename MatrixType::RealScalar ColPivHouseholderQR<MatrixType>::logAbsDetermina
 template<typename MatrixType>
 ColPivHouseholderQR<MatrixType>& ColPivHouseholderQR<MatrixType>::compute(const MatrixType& matrix)
 {
+  check_template_parameters();
+  
   using std::abs;
   Index rows = matrix.rows();
   Index cols = matrix.cols();
@@ -463,20 +471,10 @@ ColPivHouseholderQR<MatrixType>& ColPivHouseholderQR<MatrixType>::compute(const
     // we store that back into our table: it can't hurt to correct our table.
     m_colSqNorms.coeffRef(biggest_col_index) = biggest_col_sq_norm;
 
-    // if the current biggest column is smaller than epsilon times the initial biggest column,
+    // Track the number of meaningful pivots but do not stop the decomposition to make
-    // terminate to avoid generating nan/inf values.
+    // sure that the initial matrix is properly reproduced. See bug 941.
-    // Note that here, if we test instead for "biggest == 0", we get a failure every 1000 (or so)
+    if(m_nonzero_pivots==size && biggest_col_sq_norm < threshold_helper * RealScalar(rows-k))
-    // repetitions of the unit test, with the result of solve() filled with large values of the order
-    // of 1/(size*epsilon).
-    if(biggest_col_sq_norm < threshold_helper * RealScalar(rows-k))
-    {
       m_nonzero_pivots = k;
-      m_hCoeffs.tail(size-k).setZero();
-      m_qr.bottomRightCorner(rows-k,cols-k)
-          .template triangularView<StrictlyLower>()
-          .setZero();
-      break;
-    }
 
     // apply the transposition to the columns
     m_colsTranspositions.coeffRef(k) = biggest_col_index;
@@ -505,7 +503,7 @@ ColPivHouseholderQR<MatrixType>& ColPivHouseholderQR<MatrixType>::compute(const
   }
 
   m_colsPermutation.setIdentity(PermIndexType(cols));
-  for(PermIndexType k = 0; k < m_nonzero_pivots; ++k)
+  for(PermIndexType k = 0; k < size/*m_nonzero_pivots*/; ++k)
     m_colsPermutation.applyTranspositionOnTheRight(k, PermIndexType(m_colsTranspositions.coeff(k)));
 
   m_det_pq = (number_of_transpositions%2) ? -1 : 1;
@@ -555,13 +553,15 @@ struct solve_retval<ColPivHouseholderQR<_MatrixType>, Rhs>
 
 } // end namespace internal
 
-/** \returns the matrix Q as a sequence of householder transformations */
+/** \returns the matrix Q as a sequence of householder transformations.
+  * You can extract the meaningful part only by using:
+  * \code qr.householderQ().setLength(qr.nonzeroPivots()) \endcode*/
 template<typename MatrixType>
 typename ColPivHouseholderQR<MatrixType>::HouseholderSequenceType ColPivHouseholderQR<MatrixType>
   ::householderQ() const
 {
   eigen_assert(m_isInitialized && "ColPivHouseholderQR is not initialized.");
-  return HouseholderSequenceType(m_qr, m_hCoeffs.conjugate()).setLength(m_nonzero_pivots);
+  return HouseholderSequenceType(m_qr, m_hCoeffs.conjugate());
 }
 
 /** \return the column-pivoting Householder QR decomposition of \c *this.

gtsam/3rdparty/Eigen/Eigen/src/QR/ColPivHouseholderQR_MKL.h

@@ -63,12 +63,12 @@ ColPivHouseholderQR<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynami
 \
   m_nonzero_pivots = 0; \
   m_maxpivot = RealScalar(0);\
-  m_colsPermutation.resize((int)cols); \
+  m_colsPermutation.resize(cols); \
   m_colsPermutation.indices().setZero(); \
 \
-  lapack_int lda = (lapack_int) m_qr.outerStride(), i; \
+  lapack_int lda = m_qr.outerStride(), i; \
   lapack_int matrix_order = MKLCOLROW; \
-  LAPACKE_##MKLPREFIX##geqp3( matrix_order, (lapack_int)rows, (lapack_int)cols, (MKLTYPE*)m_qr.data(), lda, (lapack_int*)m_colsPermutation.indices().data(), (MKLTYPE*)m_hCoeffs.data()); \
+  LAPACKE_##MKLPREFIX##geqp3( matrix_order, rows, cols, (MKLTYPE*)m_qr.data(), lda, (lapack_int*)m_colsPermutation.indices().data(), (MKLTYPE*)m_hCoeffs.data()); \
   m_isInitialized = true; \
   m_maxpivot=m_qr.diagonal().cwiseAbs().maxCoeff(); \
   m_hCoeffs.adjointInPlace(); \

gtsam/3rdparty/Eigen/Eigen/src/QR/FullPivHouseholderQR.h

@@ -368,6 +368,12 @@ template<typename _MatrixType> class FullPivHouseholderQR
     RealScalar maxPivot() const { return m_maxpivot; }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     MatrixType m_qr;
     HCoeffsType m_hCoeffs;
     IntDiagSizeVectorType m_rows_transpositions;
@@ -407,6 +413,8 @@ typename MatrixType::RealScalar FullPivHouseholderQR<MatrixType>::logAbsDetermin
 template<typename MatrixType>
 FullPivHouseholderQR<MatrixType>& FullPivHouseholderQR<MatrixType>::compute(const MatrixType& matrix)
 {
+  check_template_parameters();
+  
   using std::abs;
   Index rows = matrix.rows();
   Index cols = matrix.cols();

gtsam/3rdparty/Eigen/Eigen/src/QR/HouseholderQR.h

@@ -189,6 +189,12 @@ template<typename _MatrixType> class HouseholderQR
     const HCoeffsType& hCoeffs() const { return m_hCoeffs; }
 
   protected:
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
+    
     MatrixType m_qr;
     HCoeffsType m_hCoeffs;
     RowVectorType m_temp;
@@ -349,6 +355,8 @@ struct solve_retval<HouseholderQR<_MatrixType>, Rhs>
 template<typename MatrixType>
 HouseholderQR<MatrixType>& HouseholderQR<MatrixType>::compute(const MatrixType& matrix)
 {
+  check_template_parameters();
+  
   Index rows = matrix.rows();
   Index cols = matrix.cols();
   Index size = (std::min)(rows,cols);

gtsam/3rdparty/Eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h

@@ -47,7 +47,7 @@ namespace Eigen {
  * You can then apply it to a vector.
  * 
  * R is the sparse triangular factor. Use matrixQR() to get it as SparseMatrix.
- * NOTE : The Index type of R is always UF_long. You can get it with SPQR::Index
+ * NOTE : The Index type of R is always SuiteSparse_long. You can get it with SPQR::Index
  * 
  * \tparam _MatrixType The type of the sparse matrix A, must be a column-major SparseMatrix<>
  * NOTE 
@@ -59,24 +59,18 @@ class SPQR
   public:
     typedef typename _MatrixType::Scalar Scalar;
     typedef typename _MatrixType::RealScalar RealScalar;
-    typedef UF_long Index ; 
+    typedef SuiteSparse_long Index ;
     typedef SparseMatrix<Scalar, ColMajor, Index> MatrixType;
     typedef PermutationMatrix<Dynamic, Dynamic> PermutationType;
   public:
     SPQR() 
-      : m_isInitialized(false),
+      : m_isInitialized(false), m_ordering(SPQR_ORDERING_DEFAULT), m_allow_tol(SPQR_DEFAULT_TOL), m_tolerance (NumTraits<Scalar>::epsilon()), m_useDefaultThreshold(true)
-      m_ordering(SPQR_ORDERING_DEFAULT),
-      m_allow_tol(SPQR_DEFAULT_TOL),
-      m_tolerance (NumTraits<Scalar>::epsilon())
     { 
       cholmod_l_start(&m_cc);
     }
     
-    SPQR(const _MatrixType& matrix) 
+    SPQR(const _MatrixType& matrix)
-    : m_isInitialized(false),
+    : m_isInitialized(false), m_ordering(SPQR_ORDERING_DEFAULT), m_allow_tol(SPQR_DEFAULT_TOL), m_tolerance (NumTraits<Scalar>::epsilon()), m_useDefaultThreshold(true)
-      m_ordering(SPQR_ORDERING_DEFAULT),
-      m_allow_tol(SPQR_DEFAULT_TOL),
-      m_tolerance (NumTraits<Scalar>::epsilon())
     {
       cholmod_l_start(&m_cc);
       compute(matrix);
@@ -101,10 +95,26 @@ class SPQR
       if(m_isInitialized) SPQR_free();
 
       MatrixType mat(matrix);
+      
+      /* Compute the default threshold as in MatLab, see:
+       * Tim Davis, "Algorithm 915, SuiteSparseQR: Multifrontal Multithreaded Rank-Revealing
+       * Sparse QR Factorization, ACM Trans. on Math. Soft. 38(1), 2011, Page 8:3 
+       */
+      RealScalar pivotThreshold = m_tolerance;
+      if(m_useDefaultThreshold) 
+      {
+        using std::max;
+        RealScalar max2Norm = 0.0;
+        for (int j = 0; j < mat.cols(); j++) max2Norm = (max)(max2Norm, mat.col(j).norm());
+        if(max2Norm==RealScalar(0))
+          max2Norm = RealScalar(1);
+        pivotThreshold = 20 * (mat.rows() + mat.cols()) * max2Norm * NumTraits<RealScalar>::epsilon();
+      }
+      
       cholmod_sparse A; 
       A = viewAsCholmod(mat);
       Index col = matrix.cols();
-      m_rank = SuiteSparseQR<Scalar>(m_ordering, m_tolerance, col, &A, 
+      m_rank = SuiteSparseQR<Scalar>(m_ordering, pivotThreshold, col, &A, 
                              &m_cR, &m_E, &m_H, &m_HPinv, &m_HTau, &m_cc);
 
       if (!m_cR)
@@ -120,7 +130,7 @@ class SPQR
     /** 
      * Get the number of rows of the input matrix and the Q matrix
      */
-    inline Index rows() const {return m_H->nrow; }
+    inline Index rows() const {return m_cR->nrow; }
     
     /** 
      * Get the number of columns of the input matrix. 
@@ -145,16 +155,25 @@ class SPQR
     {
       eigen_assert(m_isInitialized && " The QR factorization should be computed first, call compute()");
       eigen_assert(b.cols()==1 && "This method is for vectors only");
-      
+
       //Compute Q^T * b
-      typename Dest::PlainObject y;
+      typename Dest::PlainObject y, y2;
       y = matrixQ().transpose() * b;
-        // Solves with the triangular matrix R
+      
+      // Solves with the triangular matrix R
       Index rk = this->rank();
-      y.topRows(rk) = this->matrixR().topLeftCorner(rk, rk).template triangularView<Upper>().solve(y.topRows(rk));
+      y2 = y;
-      y.bottomRows(cols()-rk).setZero();
+      y.resize((std::max)(cols(),Index(y.rows())),y.cols());
+      y.topRows(rk) = this->matrixR().topLeftCorner(rk, rk).template triangularView<Upper>().solve(y2.topRows(rk));
+
       // Apply the column permutation 
-      dest.topRows(cols()) = colsPermutation() * y.topRows(cols());
+      // colsPermutation() performs a copy of the permutation,
+      // so let's apply it manually:
+      for(Index i = 0; i < rk; ++i) dest.row(m_E[i]) = y.row(i);
+      for(Index i = rk; i < cols(); ++i) dest.row(m_E[i]).setZero();
+      
+//       y.bottomRows(y.rows()-rk).setZero();
+//       dest = colsPermutation() * y.topRows(cols());
       
       m_info = Success;
     }
@@ -197,7 +216,11 @@ class SPQR
     /// Set the fill-reducing ordering method to be used
     void setSPQROrdering(int ord) { m_ordering = ord;}
     /// Set the tolerance tol to treat columns with 2-norm < =tol as zero
-    void setPivotThreshold(const RealScalar& tol) { m_tolerance = tol; }
+    void setPivotThreshold(const RealScalar& tol)
+    {
+      m_useDefaultThreshold = false;
+      m_tolerance = tol;
+    }
     
     /** \returns a pointer to the SPQR workspace */
     cholmod_common *cholmodCommon() const { return &m_cc; }
@@ -230,6 +253,7 @@ class SPQR
     mutable cholmod_dense *m_HTau; // The Householder coefficients
     mutable Index m_rank; // The rank of the matrix
     mutable cholmod_common m_cc; // Workspace and parameters
+    bool m_useDefaultThreshold;     // Use default threshold
     template<typename ,typename > friend struct SPQR_QProduct;
 };
 

gtsam/3rdparty/Eigen/Eigen/src/SVD/JacobiSVD.h

@@ -742,6 +742,11 @@ template<typename _MatrixType, int QRPreconditioner> class JacobiSVD
 
   private:
     void allocate(Index rows, Index cols, unsigned int computationOptions);
+    
+    static void check_template_parameters()
+    {
+      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
+    }
 
   protected:
     MatrixUType m_matrixU;
@@ -818,6 +823,8 @@ template<typename MatrixType, int QRPreconditioner>
 JacobiSVD<MatrixType, QRPreconditioner>&
 JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType& matrix, unsigned int computationOptions)
 {
+  check_template_parameters();
+  
   using std::abs;
   allocate(matrix.rows(), matrix.cols(), computationOptions);
 

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseBlock.h

@@ -57,6 +57,16 @@ public:
     inline BlockImpl(const XprType& xpr, int startRow, int startCol, int blockRows, int blockCols)
       : m_matrix(xpr), m_outerStart(IsRowMajor ? startRow : startCol), m_outerSize(IsRowMajor ? blockRows : blockCols)
     {}
+    
+    inline const Scalar coeff(int row, int col) const
+    {
+      return m_matrix.coeff(row + IsRowMajor ? m_outerStart : 0, col +IsRowMajor ? 0 :  m_outerStart);
+    }
+    
+    inline const Scalar coeff(int index) const
+    {
+      return m_matrix.coeff(IsRowMajor ? m_outerStart : index, IsRowMajor ? index :  m_outerStart);
+    }
 
     EIGEN_STRONG_INLINE Index rows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
     EIGEN_STRONG_INLINE Index cols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
@@ -226,6 +236,21 @@ public:
       else
         return Map<const Matrix<Index,OuterSize,1> >(m_matrix.innerNonZeroPtr()+m_outerStart, m_outerSize.value()).sum();
     }
+    
+    inline Scalar& coeffRef(int row, int col)
+    {
+      return m_matrix.const_cast_derived().coeffRef(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 :  m_outerStart));
+    }
+    
+    inline const Scalar coeff(int row, int col) const
+    {
+      return m_matrix.coeff(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 :  m_outerStart));
+    }
+    
+    inline const Scalar coeff(int index) const
+    {
+      return m_matrix.coeff(IsRowMajor ? m_outerStart : index, IsRowMajor ? index :  m_outerStart);
+    }
 
     const Scalar& lastCoeff() const
     {
@@ -313,6 +338,16 @@ public:
       else
         return Map<const Matrix<Index,OuterSize,1> >(m_matrix.innerNonZeroPtr()+m_outerStart, m_outerSize.value()).sum();
     }
+    
+    inline const Scalar coeff(int row, int col) const
+    {
+      return m_matrix.coeff(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 :  m_outerStart));
+    }
+    
+    inline const Scalar coeff(int index) const
+    {
+      return m_matrix.coeff(IsRowMajor ? m_outerStart : index, IsRowMajor ? index :  m_outerStart);
+    }
 
     const Scalar& lastCoeff() const
     {
@@ -355,7 +390,8 @@ const typename SparseMatrixBase<Derived>::ConstInnerVectorReturnType SparseMatri
   * is col-major (resp. row-major).
   */
 template<typename Derived>
-Block<Derived,Dynamic,Dynamic,true> SparseMatrixBase<Derived>::innerVectors(Index outerStart, Index outerSize)
+typename SparseMatrixBase<Derived>::InnerVectorsReturnType
+SparseMatrixBase<Derived>::innerVectors(Index outerStart, Index outerSize)
 {
   return Block<Derived,Dynamic,Dynamic,true>(derived(),
                                              IsRowMajor ? outerStart : 0, IsRowMajor ? 0 : outerStart,
@@ -367,7 +403,8 @@ Block<Derived,Dynamic,Dynamic,true> SparseMatrixBase<Derived>::innerVectors(Inde
   * is col-major (resp. row-major). Read-only.
   */
 template<typename Derived>
-const Block<const Derived,Dynamic,Dynamic,true> SparseMatrixBase<Derived>::innerVectors(Index outerStart, Index outerSize) const
+const typename SparseMatrixBase<Derived>::ConstInnerVectorsReturnType
+SparseMatrixBase<Derived>::innerVectors(Index outerStart, Index outerSize) const
 {
   return Block<const Derived,Dynamic,Dynamic,true>(derived(),
                                                   IsRowMajor ? outerStart : 0, IsRowMajor ? 0 : outerStart,
@@ -394,8 +431,8 @@ public:
       : m_matrix(xpr),
         m_startRow( (BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) ? i : 0),
         m_startCol( (BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? i : 0),
-        m_blockRows(xpr.rows()),
+        m_blockRows(BlockRows==1 ? 1 : xpr.rows()),
-        m_blockCols(xpr.cols())
+        m_blockCols(BlockCols==1 ? 1 : xpr.cols())
     {}
 
     /** Dynamic-size constructor
@@ -497,3 +534,4 @@ public:
 } // end namespace Eigen
 
 #endif // EIGEN_SPARSE_BLOCK_H
+

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h

@@ -314,10 +314,10 @@ SparseMatrixBase<Derived>::operator+=(const SparseMatrixBase<OtherDerived>& othe
 
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE const EIGEN_SPARSE_CWISE_PRODUCT_RETURN_TYPE
+EIGEN_STRONG_INLINE const typename SparseMatrixBase<Derived>::template CwiseProductDenseReturnType<OtherDerived>::Type
 SparseMatrixBase<Derived>::cwiseProduct(const MatrixBase<OtherDerived> &other) const
 {
-  return EIGEN_SPARSE_CWISE_PRODUCT_RETURN_TYPE(derived(), other.derived());
+  return typename CwiseProductDenseReturnType<OtherDerived>::Type(derived(), other.derived());
 }
 
 } // end namespace Eigen

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseDenseProduct.h

@@ -180,7 +180,7 @@ struct sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, R
         typename Res::Scalar tmp(0);
         for(LhsInnerIterator it(lhs,j); it ;++it)
           tmp += it.value() * rhs.coeff(it.index(),c);
-        res.coeffRef(j,c) = alpha * tmp;
+        res.coeffRef(j,c) += alpha * tmp;
       }
     }
   }

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseMatrix.h

@@ -691,7 +691,8 @@ class SparseMatrix
       m_data.swap(other.m_data);
     }
 
-    /** Sets *this to the identity matrix */
+    /** Sets *this to the identity matrix.
+      * This function also turns the matrix into compressed mode, and drop any reserved memory. */
     inline void setIdentity()
     {
       eigen_assert(rows() == cols() && "ONLY FOR SQUARED MATRICES");
@@ -699,6 +700,8 @@ class SparseMatrix
       Eigen::Map<Matrix<Index, Dynamic, 1> >(&this->m_data.index(0), rows()).setLinSpaced(0, rows()-1);
       Eigen::Map<Matrix<Scalar, Dynamic, 1> >(&this->m_data.value(0), rows()).setOnes();
       Eigen::Map<Matrix<Index, Dynamic, 1> >(this->m_outerIndex, rows()+1).setLinSpaced(0, rows());
+      std::free(m_innerNonZeros);
+      m_innerNonZeros = 0;
     }
     inline SparseMatrix& operator=(const SparseMatrix& other)
     {

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseMatrixBase.h

@@ -23,7 +23,14 @@ namespace Eigen {
   * This class can be extended with the help of the plugin mechanism described on the page
   * \ref TopicCustomizingEigen by defining the preprocessor symbol \c EIGEN_SPARSEMATRIXBASE_PLUGIN.
   */
-template<typename Derived> class SparseMatrixBase : public EigenBase<Derived>
+template<typename Derived> class SparseMatrixBase
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+  : public internal::special_scalar_op_base<Derived,typename internal::traits<Derived>::Scalar,
+                                            typename NumTraits<typename internal::traits<Derived>::Scalar>::Real,
+                                            EigenBase<Derived> >
+#else
+  : public EigenBase<Derived>
+#endif // not EIGEN_PARSED_BY_DOXYGEN
 {
   public:
 
@@ -36,7 +43,6 @@ template<typename Derived> class SparseMatrixBase : public EigenBase<Derived>
                      >::type PacketReturnType;
 
     typedef SparseMatrixBase StorageBaseType;
-    typedef EigenBase<Derived> Base;
     
     template<typename OtherDerived>
     Derived& operator=(const EigenBase<OtherDerived> &other)
@@ -132,6 +138,9 @@ template<typename Derived> class SparseMatrixBase : public EigenBase<Derived>
     inline Derived& derived() { return *static_cast<Derived*>(this); }
     inline Derived& const_cast_derived() const
     { return *static_cast<Derived*>(const_cast<SparseMatrixBase*>(this)); }
+
+    typedef internal::special_scalar_op_base<Derived, Scalar, RealScalar, EigenBase<Derived> > Base;
+    using Base::operator*;
 #endif // not EIGEN_PARSED_BY_DOXYGEN
 
 #define EIGEN_CURRENT_STORAGE_BASE_CLASS Eigen::SparseMatrixBase
@@ -317,20 +326,18 @@ template<typename Derived> class SparseMatrixBase : public EigenBase<Derived>
     Derived& operator*=(const Scalar& other);
     Derived& operator/=(const Scalar& other);
 
-    #define EIGEN_SPARSE_CWISE_PRODUCT_RETURN_TYPE \
+    template<typename OtherDerived> struct CwiseProductDenseReturnType {
-      CwiseBinaryOp< \
+      typedef CwiseBinaryOp<internal::scalar_product_op<typename internal::scalar_product_traits<
-        internal::scalar_product_op< \
+                                                          typename internal::traits<Derived>::Scalar,
-          typename internal::scalar_product_traits< \
+                                                          typename internal::traits<OtherDerived>::Scalar
-            typename internal::traits<Derived>::Scalar, \
+                                                        >::ReturnType>,
-            typename internal::traits<OtherDerived>::Scalar \
+                            const Derived,
-          >::ReturnType \
+                            const OtherDerived
-        >, \
+                          > Type;
-        const Derived, \
+    };
-        const OtherDerived \
-      >
 
     template<typename OtherDerived>
-    EIGEN_STRONG_INLINE const EIGEN_SPARSE_CWISE_PRODUCT_RETURN_TYPE
+    EIGEN_STRONG_INLINE const typename CwiseProductDenseReturnType<OtherDerived>::Type
     cwiseProduct(const MatrixBase<OtherDerived> &other) const;
 
     // sparse * sparse
@@ -404,8 +411,10 @@ template<typename Derived> class SparseMatrixBase : public EigenBase<Derived>
     const ConstInnerVectorReturnType innerVector(Index outer) const;
 
     // set of inner-vectors
-    Block<Derived,Dynamic,Dynamic,true> innerVectors(Index outerStart, Index outerSize);
+    typedef Block<Derived,Dynamic,Dynamic,true> InnerVectorsReturnType;
-    const Block<const Derived,Dynamic,Dynamic,true> innerVectors(Index outerStart, Index outerSize) const;
+    typedef Block<const Derived,Dynamic,Dynamic,true> ConstInnerVectorsReturnType;
+    InnerVectorsReturnType innerVectors(Index outerStart, Index outerSize);
+    const ConstInnerVectorsReturnType innerVectors(Index outerStart, Index outerSize) const;
 
     /** \internal use operator= */
     template<typename DenseDerived>

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseUtil.h

@@ -67,7 +67,6 @@ const int InnerRandomAccessPattern  = 0x2 | CoherentAccessPattern;
 const int OuterRandomAccessPattern  = 0x4 | CoherentAccessPattern;
 const int RandomAccessPattern       = 0x8 | OuterRandomAccessPattern | InnerRandomAccessPattern;
 
-template<typename Derived> class SparseMatrixBase;
 template<typename _Scalar, int _Flags = 0, typename _Index = int>  class SparseMatrix;
 template<typename _Scalar, int _Flags = 0, typename _Index = int>  class DynamicSparseMatrix;
 template<typename _Scalar, int _Flags = 0, typename _Index = int>  class SparseVector;

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/SparseVector.h

@@ -158,6 +158,7 @@ class SparseVector
       
       Index inner = IsColVector ? row : col;
       Index outer = IsColVector ? col : row;
+      EIGEN_ONLY_USED_FOR_DEBUG(outer);
       eigen_assert(outer==0);
       return insert(inner);
     }

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/TriangularSolver.h

@@ -69,7 +69,7 @@ struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Upper,RowMajor>
       for(int i=lhs.rows()-1 ; i>=0 ; --i)
       {
         Scalar tmp = other.coeff(i,col);
-        Scalar l_ii = 0;
+        Scalar l_ii(0);
         typename Lhs::InnerIterator it(lhs, i);
         while(it && it.index()<i)
           ++it;

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU.h

@@ -268,7 +268,8 @@ class SparseLU : public internal::SparseLUImpl<typename _MatrixType::Scalar, typ
         {
           if(it.index() == j)
           {
-            det *= (std::abs)(it.value());
+            using std::abs;
+            det *= abs(it.value());
             break;
           }
         }
@@ -295,7 +296,8 @@ class SparseLU : public internal::SparseLUImpl<typename _MatrixType::Scalar, typ
            if(it.row() < j) continue;
            if(it.row() == j)
            {
-             det += (std::log)((std::abs)(it.value()));
+             using std::log; using std::abs;
+             det += log(abs(it.value()));
              break;
            }
          }
@@ -303,21 +305,64 @@ class SparseLU : public internal::SparseLUImpl<typename _MatrixType::Scalar, typ
        return det;
      }
 
-     /** \returns A number representing the sign of the determinant
+    /** \returns A number representing the sign of the determinant
-       *
+      *
-       * \sa absDeterminant(), logAbsDeterminant()
+      * \sa absDeterminant(), logAbsDeterminant()
-       */
+      */
-     Scalar signDeterminant()
+    Scalar signDeterminant()
-     {
+    {
-       eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
+      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
-       return Scalar(m_detPermR);
+      // Initialize with the determinant of the row matrix
-     }
+      Index det = 1;
+      // Note that the diagonal blocks of U are stored in supernodes,
+      // which are available in the  L part :)
+      for (Index j = 0; j < this->cols(); ++j)
+      {
+        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
+        {
+          if(it.index() == j)
+          {
+            if(it.value()<0)
+              det = -det;
+            else if(it.value()==0)
+              return 0;
+            break;
+          }
+        }
+      }
+      return det * m_detPermR * m_detPermC;
+    }
+    
+    /** \returns The determinant of the matrix.
+      *
+      * \sa absDeterminant(), logAbsDeterminant()
+      */
+    Scalar determinant()
+    {
+      eigen_assert(m_factorizationIsOk && "The matrix should be factorized first.");
+      // Initialize with the determinant of the row matrix
+      Scalar det = Scalar(1.);
+      // Note that the diagonal blocks of U are stored in supernodes,
+      // which are available in the  L part :)
+      for (Index j = 0; j < this->cols(); ++j)
+      {
+        for (typename SCMatrix::InnerIterator it(m_Lstore, j); it; ++it)
+        {
+          if(it.index() == j)
+          {
+            det *= it.value();
+            break;
+          }
+        }
+      }
+      return det * Scalar(m_detPermR * m_detPermC);
+    }
 
   protected:
     // Functions 
     void initperfvalues()
     {
-      m_perfv.panel_size = 1;
+      m_perfv.panel_size = 16;
       m_perfv.relax = 1; 
       m_perfv.maxsuper = 128; 
       m_perfv.rowblk = 16; 
@@ -345,8 +390,8 @@ class SparseLU : public internal::SparseLUImpl<typename _MatrixType::Scalar, typ
     // values for performance 
     internal::perfvalues<Index> m_perfv; 
     RealScalar m_diagpivotthresh; // Specifies the threshold used for a diagonal entry to be an acceptable pivot
-    Index m_nnzL, m_nnzU; // Nonzeros in L and U factors 
+    Index m_nnzL, m_nnzU; // Nonzeros in L and U factors
-    Index m_detPermR; // Determinant of the coefficient matrix
+    Index m_detPermR, m_detPermC; // Determinants of the permutation matrices
   private:
     // Disable copy constructor 
     SparseLU (const SparseLU& );
@@ -622,7 +667,8 @@ void SparseLU<MatrixType, OrderingType>::factorize(const MatrixType& matrix)
       }
       
       // Update the determinant of the row permutation matrix
-      if (pivrow != jj) m_detPermR *= -1;
+      // FIXME: the following test is not correct, we should probably take iperm_c into account and pivrow is not directly the row pivot.
+      if (pivrow != jj) m_detPermR = -m_detPermR;
 
       // Prune columns (0:jj-1) using column jj
       Base::pruneL(jj, m_perm_r.indices(), pivrow, nseg, segrep, repfnz_k, xprune, m_glu); 
@@ -637,10 +683,13 @@ void SparseLU<MatrixType, OrderingType>::factorize(const MatrixType& matrix)
     jcol += panel_size;  // Move to the next panel
   } // end for -- end elimination 
   
+  m_detPermR = m_perm_r.determinant();
+  m_detPermC = m_perm_c.determinant();
+  
   // Count the number of nonzeros in factors 
   Base::countnz(n, m_nnzL, m_nnzU, m_glu); 
   // Apply permutation  to the L subscripts 
-  Base::fixupL(n, m_perm_r.indices(), m_glu); 
+  Base::fixupL(n, m_perm_r.indices(), m_glu);
   
   // Create supernode matrix L 
   m_Lstore.setInfos(m, n, m_glu.lusup, m_glu.xlusup, m_glu.lsub, m_glu.xlsub, m_glu.supno, m_glu.xsup); 
@@ -700,8 +749,8 @@ struct SparseLUMatrixUReturnType : internal::no_assignment_operator
       }
       else
       {
-        Map<const Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > A( &(m_mapL.valuePtr()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
+        Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(m_mapL.valuePtr()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
+        Map< Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
         U = A.template triangularView<Upper>().solve(U);
       }
 

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLUImpl.h

@@ -21,6 +21,8 @@ class SparseLUImpl
 {
   public:
     typedef Matrix<Scalar,Dynamic,1> ScalarVector;
+    typedef Matrix<Scalar,Dynamic,Dynamic,ColMajor> ScalarMatrix;
+    typedef Map<ScalarMatrix, 0,  OuterStride<> > MappedMatrixBlock;
     typedef Matrix<Index,Dynamic,1> IndexVector; 
     typedef typename ScalarVector::RealScalar RealScalar; 
     typedef Ref<Matrix<Scalar,Dynamic,1> > BlockScalarVector;

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_Memory.h

@@ -153,8 +153,8 @@ Index SparseLUImpl<Scalar,Index>::memInit(Index m, Index n, Index annz, Index lw
 {
   Index& num_expansions = glu.num_expansions; //No memory expansions so far
   num_expansions = 0;
-  glu.nzumax = glu.nzlumax = (std::min)(fillratio * annz / n, m) * n; // estimated number of nonzeros in U 
+  glu.nzumax = glu.nzlumax = (std::min)(fillratio * (annz+1) / n, m) * n; // estimated number of nonzeros in U 
-  glu.nzlmax = (std::max)(Index(4), fillratio) * annz / 4; // estimated  nnz in L factor
+  glu.nzlmax = (std::max)(Index(4), fillratio) * (annz+1) / 4; // estimated  nnz in L factor
   // Return the estimated size to the user if necessary
   Index tempSpace;
   tempSpace = (2*panel_size + 4 + LUNoMarker) * m * sizeof(Index) + (panel_size + 1) * m * sizeof(Scalar);

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h

@@ -236,7 +236,7 @@ void MappedSuperNodalMatrix<Scalar,Index>::solveInPlace( MatrixBase<Dest>&X) con
     Index n = X.rows(); 
     Index nrhs = X.cols(); 
     const Scalar * Lval = valuePtr();                 // Nonzero values 
-    Matrix<Scalar,Dynamic,Dynamic> work(n, nrhs);     // working vector
+    Matrix<Scalar,Dynamic,Dynamic, ColMajor> work(n, nrhs);     // working vector
     work.setZero();
     for (Index k = 0; k <= nsuper(); k ++)
     {
@@ -267,12 +267,12 @@ void MappedSuperNodalMatrix<Scalar,Index>::solveInPlace( MatrixBase<Dest>&X) con
         Index lda = colIndexPtr()[fsupc+1] - luptr;
         
         // Triangular solve 
-        Map<const Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > A( &(Lval[luptr]), nsupc, nsupc, OuterStride<>(lda) ); 
+        Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(Lval[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) ); 
+        Map< Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) ); 
         U = A.template triangularView<UnitLower>().solve(U); 
         
         // Matrix-vector product 
-        new (&A) Map<const Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > ( &(Lval[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) ); 
+        new (&A) Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > ( &(Lval[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
         work.block(0, 0, nrow, nrhs) = A * U; 
         
         //Begin Scatter 

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h

@@ -162,11 +162,11 @@ Index SparseLUImpl<Scalar,Index>::column_bmod(const Index jcol, const Index nseg
     // points to the beginning of jcol in snode L\U(jsupno) 
     ufirst = glu.xlusup(jcol) + d_fsupc; 
     Index lda = glu.xlusup(jcol+1) - glu.xlusup(jcol);
-    Map<Matrix<Scalar,Dynamic,Dynamic>, 0,  OuterStride<> > A( &(glu.lusup.data()[luptr]), nsupc, nsupc, OuterStride<>(lda) ); 
+    MappedMatrixBlock A( &(glu.lusup.data()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
     VectorBlock<ScalarVector> u(glu.lusup, ufirst, nsupc); 
     u = A.template triangularView<UnitLower>().solve(u); 
     
-    new (&A) Map<Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > ( &(glu.lusup.data()[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) ); 
+    new (&A) MappedMatrixBlock ( &(glu.lusup.data()[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
     VectorBlock<ScalarVector> l(glu.lusup, ufirst+nsupc, nrow); 
     l.noalias() -= A * u;
     

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h

@@ -56,7 +56,7 @@ EIGEN_DONT_INLINE void LU_kernel_bmod<SegSizeAtCompileTime>::run(const int segsi
   // Dense triangular solve -- start effective triangle
   luptr += lda * no_zeros + no_zeros; 
   // Form Eigen matrix and vector 
-  Map<Matrix<Scalar,SegSizeAtCompileTime,SegSizeAtCompileTime>, 0, OuterStride<> > A( &(lusup.data()[luptr]), segsize, segsize, OuterStride<>(lda) );
+  Map<Matrix<Scalar,SegSizeAtCompileTime,SegSizeAtCompileTime, ColMajor>, 0, OuterStride<> > A( &(lusup.data()[luptr]), segsize, segsize, OuterStride<>(lda) );
   Map<Matrix<Scalar,SegSizeAtCompileTime,1> > u(tempv.data(), segsize);
   
   u = A.template triangularView<UnitLower>().solve(u); 
@@ -65,7 +65,7 @@ EIGEN_DONT_INLINE void LU_kernel_bmod<SegSizeAtCompileTime>::run(const int segsi
   luptr += segsize;
   const Index PacketSize = internal::packet_traits<Scalar>::size;
   Index ldl = internal::first_multiple(nrow, PacketSize);
-  Map<Matrix<Scalar,Dynamic,SegSizeAtCompileTime>, 0, OuterStride<> > B( &(lusup.data()[luptr]), nrow, segsize, OuterStride<>(lda) );
+  Map<Matrix<Scalar,Dynamic,SegSizeAtCompileTime, ColMajor>, 0, OuterStride<> > B( &(lusup.data()[luptr]), nrow, segsize, OuterStride<>(lda) );
   Index aligned_offset = internal::first_aligned(tempv.data()+segsize, PacketSize);
   Index aligned_with_B_offset = (PacketSize-internal::first_aligned(B.data(), PacketSize))%PacketSize;
   Map<Matrix<Scalar,Dynamic,1>, 0, OuterStride<> > l(tempv.data()+segsize+aligned_offset+aligned_with_B_offset, nrow, OuterStride<>(ldl) );

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h

@@ -102,7 +102,7 @@ void SparseLUImpl<Scalar,Index>::panel_bmod(const Index m, const Index w, const
     if(nsupc >= 2)
     { 
       Index ldu = internal::first_multiple<Index>(u_rows, PacketSize);
-      Map<Matrix<Scalar,Dynamic,Dynamic>, Aligned,  OuterStride<> > U(tempv.data(), u_rows, u_cols, OuterStride<>(ldu));
+      Map<ScalarMatrix, Aligned,  OuterStride<> > U(tempv.data(), u_rows, u_cols, OuterStride<>(ldu));
       
       // gather U
       Index u_col = 0;
@@ -136,17 +136,17 @@ void SparseLUImpl<Scalar,Index>::panel_bmod(const Index m, const Index w, const
       Index lda = glu.xlusup(fsupc+1) - glu.xlusup(fsupc);
       no_zeros = (krep - u_rows + 1) - fsupc;
       luptr += lda * no_zeros + no_zeros;
-      Map<Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > A(glu.lusup.data()+luptr, u_rows, u_rows, OuterStride<>(lda) );
+      MappedMatrixBlock A(glu.lusup.data()+luptr, u_rows, u_rows, OuterStride<>(lda) );
       U = A.template triangularView<UnitLower>().solve(U);
       
       // update
       luptr += u_rows;
-      Map<Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > B(glu.lusup.data()+luptr, nrow, u_rows, OuterStride<>(lda) );
+      MappedMatrixBlock B(glu.lusup.data()+luptr, nrow, u_rows, OuterStride<>(lda) );
       eigen_assert(tempv.size()>w*ldu + nrow*w + 1);
       
       Index ldl = internal::first_multiple<Index>(nrow, PacketSize);
       Index offset = (PacketSize-internal::first_aligned(B.data(), PacketSize)) % PacketSize;
-      Map<Matrix<Scalar,Dynamic,Dynamic>, 0, OuterStride<> > L(tempv.data()+w*ldu+offset, nrow, u_cols, OuterStride<>(ldl));
+      MappedMatrixBlock L(tempv.data()+w*ldu+offset, nrow, u_cols, OuterStride<>(ldl));
       
       L.setZero();
       internal::sparselu_gemm<Scalar>(L.rows(), L.cols(), B.cols(), B.data(), B.outerStride(), U.data(), U.outerStride(), L.data(), L.outerStride());

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_pivotL.h

@@ -71,13 +71,14 @@ Index SparseLUImpl<Scalar,Index>::pivotL(const Index jcol, const RealScalar& dia
   
   // Determine the largest abs numerical value for partial pivoting 
   Index diagind = iperm_c(jcol); // diagonal index 
-  RealScalar pivmax = 0.0; 
+  RealScalar pivmax(-1.0);
   Index pivptr = nsupc; 
   Index diag = emptyIdxLU; 
   RealScalar rtemp;
   Index isub, icol, itemp, k; 
   for (isub = nsupc; isub < nsupr; ++isub) {
-    rtemp = std::abs(lu_col_ptr[isub]);
+    using std::abs;
+    rtemp = abs(lu_col_ptr[isub]);
     if (rtemp > pivmax) {
       pivmax = rtemp; 
       pivptr = isub;
@@ -86,8 +87,9 @@ Index SparseLUImpl<Scalar,Index>::pivotL(const Index jcol, const RealScalar& dia
   }
   
   // Test for singularity
-  if ( pivmax == 0.0 ) {
+  if ( pivmax <= RealScalar(0.0) ) {
-    pivrow = lsub_ptr[pivptr];
+    // if pivmax == -1, the column is structurally empty, otherwise it is only numerically zero
+    pivrow = pivmax < RealScalar(0.0) ? diagind : lsub_ptr[pivptr];
     perm_r(pivrow) = jcol;
     return (jcol+1);
   }
@@ -101,7 +103,8 @@ Index SparseLUImpl<Scalar,Index>::pivotL(const Index jcol, const RealScalar& dia
     if (diag >= 0 ) 
     {
       // Diagonal element exists
-      rtemp = std::abs(lu_col_ptr[diag]);
+      using std::abs;
+      rtemp = abs(lu_col_ptr[diag]);
       if (rtemp != 0.0 && rtemp >= thresh) pivptr = diag;
     }
     pivrow = lsub_ptr[pivptr];

gtsam/3rdparty/Eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h

@@ -70,6 +70,43 @@ max
   return (max)(Derived::PlainObject::Constant(rows(), cols(), other));
 }
 
+
+#define EIGEN_MAKE_CWISE_COMP_OP(OP, COMPARATOR) \
+template<typename OtherDerived> \
+EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_ ## COMPARATOR>, const Derived, const OtherDerived> \
+OP(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const \
+{ \
+  return CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_ ## COMPARATOR>, const Derived, const OtherDerived>(derived(), other.derived()); \
+}\
+typedef CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_ ## COMPARATOR>, const Derived, const CwiseNullaryOp<internal::scalar_constant_op<Scalar>, PlainObject> > Cmp ## COMPARATOR ## ReturnType; \
+typedef CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_ ## COMPARATOR>, const CwiseNullaryOp<internal::scalar_constant_op<Scalar>, PlainObject>, const Derived > RCmp ## COMPARATOR ## ReturnType; \
+EIGEN_STRONG_INLINE const Cmp ## COMPARATOR ## ReturnType \
+OP(const Scalar& s) const { \
+  return this->OP(Derived::PlainObject::Constant(rows(), cols(), s)); \
+} \
+friend EIGEN_STRONG_INLINE const RCmp ## COMPARATOR ## ReturnType \
+OP(const Scalar& s, const Derived& d) { \
+  return Derived::PlainObject::Constant(d.rows(), d.cols(), s).OP(d); \
+}
+
+#define EIGEN_MAKE_CWISE_COMP_R_OP(OP, R_OP, RCOMPARATOR) \
+template<typename OtherDerived> \
+EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_##RCOMPARATOR>, const OtherDerived, const Derived> \
+OP(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const \
+{ \
+  return CwiseBinaryOp<internal::scalar_cmp_op<Scalar, internal::cmp_##RCOMPARATOR>, const OtherDerived, const Derived>(other.derived(), derived()); \
+} \
+\
+inline const RCmp ## RCOMPARATOR ## ReturnType \
+OP(const Scalar& s) const { \
+  return Derived::PlainObject::Constant(rows(), cols(), s).R_OP(*this); \
+} \
+friend inline const Cmp ## RCOMPARATOR ## ReturnType \
+OP(const Scalar& s, const Derived& d) { \
+  return d.R_OP(Derived::PlainObject::Constant(d.rows(), d.cols(), s)); \
+}
+
+
 /** \returns an expression of the coefficient-wise \< operator of *this and \a other
   *
   * Example: \include Cwise_less.cpp
@@ -77,7 +114,7 @@ max
   *
   * \sa all(), any(), operator>(), operator<=()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator<,std::less)
+EIGEN_MAKE_CWISE_COMP_OP(operator<, LT)
 
 /** \returns an expression of the coefficient-wise \<= operator of *this and \a other
   *
@@ -86,7 +123,7 @@ EIGEN_MAKE_CWISE_BINARY_OP(operator<,std::less)
   *
   * \sa all(), any(), operator>=(), operator<()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator<=,std::less_equal)
+EIGEN_MAKE_CWISE_COMP_OP(operator<=, LE)
 
 /** \returns an expression of the coefficient-wise \> operator of *this and \a other
   *
@@ -95,7 +132,7 @@ EIGEN_MAKE_CWISE_BINARY_OP(operator<=,std::less_equal)
   *
   * \sa all(), any(), operator>=(), operator<()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator>,std::greater)
+EIGEN_MAKE_CWISE_COMP_R_OP(operator>, operator<, LT)
 
 /** \returns an expression of the coefficient-wise \>= operator of *this and \a other
   *
@@ -104,7 +141,7 @@ EIGEN_MAKE_CWISE_BINARY_OP(operator>,std::greater)
   *
   * \sa all(), any(), operator>(), operator<=()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator>=,std::greater_equal)
+EIGEN_MAKE_CWISE_COMP_R_OP(operator>=, operator<=, LE)
 
 /** \returns an expression of the coefficient-wise == operator of *this and \a other
   *
@@ -118,7 +155,7 @@ EIGEN_MAKE_CWISE_BINARY_OP(operator>=,std::greater_equal)
   *
   * \sa all(), any(), isApprox(), isMuchSmallerThan()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator==,std::equal_to)
+EIGEN_MAKE_CWISE_COMP_OP(operator==, EQ)
 
 /** \returns an expression of the coefficient-wise != operator of *this and \a other
   *
@@ -132,7 +169,10 @@ EIGEN_MAKE_CWISE_BINARY_OP(operator==,std::equal_to)
   *
   * \sa all(), any(), isApprox(), isMuchSmallerThan()
   */
-EIGEN_MAKE_CWISE_BINARY_OP(operator!=,std::not_equal_to)
+EIGEN_MAKE_CWISE_COMP_OP(operator!=, NEQ)
+
+#undef EIGEN_MAKE_CWISE_COMP_OP
+#undef EIGEN_MAKE_CWISE_COMP_R_OP
 
 // scalar addition
 
@@ -209,3 +249,5 @@ operator||(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
                       THIS_METHOD_IS_ONLY_FOR_EXPRESSIONS_OF_BOOL);
   return CwiseBinaryOp<internal::scalar_boolean_or_op, const Derived, const OtherDerived>(derived(),other.derived());
 }
+
+

gtsam/3rdparty/Eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h

@@ -185,19 +185,3 @@ cube() const
 {
   return derived();
 }
-
-#define EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(METHOD_NAME,FUNCTOR) \
-  inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \
-  METHOD_NAME(const Scalar& s) const { \
-    return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \
-            (derived(), std::bind2nd(FUNCTOR<Scalar>(), s)); \
-  }
-
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==,  std::equal_to)
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=,  std::not_equal_to)
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<,   std::less)
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=,  std::less_equal)
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>,   std::greater)
-EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=,  std::greater_equal)
-
-

gtsam/3rdparty/Eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h

@@ -124,3 +124,20 @@ cwiseQuotient(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
 {
   return CwiseBinaryOp<internal::scalar_quotient_op<Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
 }
+
+typedef CwiseBinaryOp<internal::scalar_cmp_op<Scalar,internal::cmp_EQ>, const Derived, const ConstantReturnType> CwiseScalarEqualReturnType;
+
+/** \returns an expression of the coefficient-wise == operator of \c *this and a scalar \a s
+  *
+  * \warning this performs an exact comparison, which is generally a bad idea with floating-point types.
+  * In order to check for equality between two vectors or matrices with floating-point coefficients, it is
+  * generally a far better idea to use a fuzzy comparison as provided by isApprox() and
+  * isMuchSmallerThan().
+  *
+  * \sa cwiseEqual(const MatrixBase<OtherDerived> &) const
+  */
+inline const CwiseScalarEqualReturnType
+cwiseEqual(const Scalar& s) const
+{
+  return CwiseScalarEqualReturnType(derived(), Derived::Constant(rows(), cols(), s), internal::scalar_cmp_op<Scalar,internal::cmp_EQ>());
+}

gtsam/3rdparty/Eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h

@@ -50,18 +50,3 @@ cwiseSqrt() const { return derived(); }
 inline const CwiseUnaryOp<internal::scalar_inverse_op<Scalar>, const Derived>
 cwiseInverse() const { return derived(); }
 
-/** \returns an expression of the coefficient-wise == operator of \c *this and a scalar \a s
-  *
-  * \warning this performs an exact comparison, which is generally a bad idea with floating-point types.
-  * In order to check for equality between two vectors or matrices with floating-point coefficients, it is
-  * generally a far better idea to use a fuzzy comparison as provided by isApprox() and
-  * isMuchSmallerThan().
-  *
-  * \sa cwiseEqual(const MatrixBase<OtherDerived> &) const
-  */
-inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived>
-cwiseEqual(const Scalar& s) const
-{
-  return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived>
-          (derived(), std::bind1st(std::equal_to<Scalar>(), s));
-}

gtsam/3rdparty/Eigen/blas/xerbla.cpp

@@ -1,7 +1,7 @@
 
 #include <iostream>
 
-#if (defined __GNUC__)
+#if (defined __GNUC__) && (!defined __MINGW32__) && (!defined __CYGWIN__)
 #define EIGEN_WEAK_LINKING __attribute__ ((weak))
 #else
 #define EIGEN_WEAK_LINKING

gtsam/3rdparty/Eigen/cmake/EigenConfigureTesting.cmake

@@ -26,29 +26,18 @@ include(CTest)
 
 set(EIGEN_TEST_BUILD_FLAGS " " CACHE STRING "Options passed to the build command of unit tests")
 
-# overwrite default DartConfiguration.tcl
+# Overwrite default DartConfiguration.tcl such that ctest can build our unit tests.
-# The worarounds are different for each version of the MSVC IDE
+# Recall that our unit tests are not in the "all" target, so we have to explicitely ask ctest to build our custom 'buildtests' target.
-if(MSVC_IDE)
+# At this stage, we can also add custom flags to the build tool through the user defined EIGEN_TEST_BUILD_FLAGS variable.
-  if(CMAKE_MAKE_PROGRAM_SAVE MATCHES "devenv") # devenv
+file(READ  "${CMAKE_CURRENT_BINARY_DIR}/DartConfiguration.tcl" EIGEN_DART_CONFIG_FILE)
-    set(EIGEN_MAKECOMMAND_PLACEHOLDER "${CMAKE_MAKE_PROGRAM_SAVE} Eigen.sln /build \"Release\" /project buildtests ${EIGEN_TEST_BUILD_FLAGS} \n# ")    
+# try to grab the default flags
-  else() # msbuild
+string(REGEX MATCH "MakeCommand:.*-- (.*)\nDefaultCTestConfigurationType" EIGEN_DUMMY ${EIGEN_DART_CONFIG_FILE})
-    set(EIGEN_MAKECOMMAND_PLACEHOLDER "${CMAKE_MAKE_PROGRAM_SAVE} buildtests.vcxproj /p:Configuration=\${CTEST_CONFIGURATION_TYPE}  ${EIGEN_TEST_BUILD_FLAGS}\n# ")
+if(NOT CMAKE_MATCH_1)
-  endif()
+string(REGEX MATCH "MakeCommand:.*[^c]make (.*)\nDefaultCTestConfigurationType" EIGEN_DUMMY ${EIGEN_DART_CONFIG_FILE})
-else()
-  # for make and nmake
-  set(EIGEN_MAKECOMMAND_PLACEHOLDER "${CMAKE_MAKE_PROGRAM_SAVE} buildtests ${EIGEN_TEST_BUILD_FLAGS}")
 endif()
-
+string(REGEX REPLACE "MakeCommand:.*DefaultCTestConfigurationType" "MakeCommand: ${CMAKE_COMMAND} --build . --target buildtests --config \"\${CTEST_CONFIGURATION_TYPE}\" -- ${CMAKE_MATCH_1} ${EIGEN_TEST_BUILD_FLAGS}\nDefaultCTestConfigurationType"
-# copy ctest properties, which currently
+       EIGEN_DART_CONFIG_FILE2 ${EIGEN_DART_CONFIG_FILE})
-# o raise the warning levels
+file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/DartConfiguration.tcl" ${EIGEN_DART_CONFIG_FILE2})
-configure_file(${CMAKE_CURRENT_BINARY_DIR}/DartConfiguration.tcl ${CMAKE_BINARY_DIR}/DartConfiguration.tcl)
-
-# restore default CMAKE_MAKE_PROGRAM
-set(CMAKE_MAKE_PROGRAM ${CMAKE_MAKE_PROGRAM_SAVE})
-# un-set temporary variables so that it is like they never existed. 
-# CMake 2.6.3 introduces the more logical unset() syntax for this.
-set(CMAKE_MAKE_PROGRAM_SAVE) 
-set(EIGEN_MAKECOMMAND_PLACEHOLDER)
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/CTestCustom.cmake.in ${CMAKE_BINARY_DIR}/CTestCustom.cmake)
 

gtsam/3rdparty/Eigen/cmake/EigenTesting.cmake

@@ -322,22 +322,21 @@ macro(ei_get_compilerver VAR)
     endif()
   else()
     # on all other system we rely on ${CMAKE_CXX_COMPILER}
-    # supporting a "--version" flag
+    # supporting a "--version" or "/version" flag
     
-    # check whether the head command exists
+    if(WIN32 AND ${CMAKE_CXX_COMPILER_ID} EQUAL "Intel")
-    find_program(HEAD_EXE head NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_CMAKE_SYSTEM_PATH)
+      set(EIGEN_CXX_FLAG_VERSION "/version")
-    if(HEAD_EXE)
-      execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version
-                      COMMAND head -n 1
-                      OUTPUT_VARIABLE eigen_cxx_compiler_version_string OUTPUT_STRIP_TRAILING_WHITESPACE)
     else()
-      execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version
+      set(EIGEN_CXX_FLAG_VERSION "--version")
-                      OUTPUT_VARIABLE eigen_cxx_compiler_version_string OUTPUT_STRIP_TRAILING_WHITESPACE)
-      string(REGEX REPLACE "[\n\r].*"  ""  eigen_cxx_compiler_version_string  ${eigen_cxx_compiler_version_string})
     endif()
     
+    execute_process(COMMAND ${CMAKE_CXX_COMPILER}  ${EIGEN_CXX_FLAG_VERSION}
+                    OUTPUT_VARIABLE eigen_cxx_compiler_version_string OUTPUT_STRIP_TRAILING_WHITESPACE)
+    string(REGEX REPLACE "[\n\r].*"  ""  eigen_cxx_compiler_version_string  ${eigen_cxx_compiler_version_string})
+    
     ei_get_compilerver_from_cxx_version_string("${eigen_cxx_compiler_version_string}" CNAME CVER)
     set(${VAR} "${CNAME}-${CVER}")
+    
   endif()
 endmacro(ei_get_compilerver)
 

gtsam/3rdparty/Eigen/cmake/FindMetis.cmake

@@ -26,7 +26,7 @@ macro(_metis_check_version)
   string(REGEX MATCH "define[ \t]+METIS_VER_SUBMINOR[ \t]+([0-9]+)" _metis_subminor_version_match "${_metis_version_header}")
   set(METIS_SUBMINOR_VERSION "${CMAKE_MATCH_1}")
   if(NOT METIS_MAJOR_VERSION)
-    message(WARNING "Could not determine Metis version. Assuming version 4.0.0")
+    message(STATUS "Could not determine Metis version. Assuming version 4.0.0")
     set(METIS_VERSION 4.0.0)
   else()
     set(METIS_VERSION ${METIS_MAJOR_VERSION}.${METIS_MINOR_VERSION}.${METIS_SUBMINOR_VERSION})

gtsam/3rdparty/Eigen/cmake/FindSPQR.cmake

@@ -26,7 +26,12 @@ if(SPQR_LIBRARIES)
   find_library(SUITESPARSE_LIBRARY SuiteSparse PATHS $ENV{SPQRDIR} ${LIB_INSTALL_DIR})
   if (SUITESPARSE_LIBRARY)
     set(SPQR_LIBRARIES ${SPQR_LIBRARIES} ${SUITESPARSE_LIBRARY})
-  endif (SUITESPARSE_LIBRARY)
+  endif()
+
+  find_library(CHOLMOD_LIBRARY cholmod PATHS $ENV{UMFPACK_LIBDIR} $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR})
+  if(CHOLMOD_LIBRARY)
+    set(SPQR_LIBRARIES ${SPQR_LIBRARIES} ${CHOLMOD_LIBRARY})
+  endif()
   
 endif(SPQR_LIBRARIES)
 

gtsam/3rdparty/Eigen/cmake/FindUmfpack.cmake

@@ -20,24 +20,29 @@ find_library(UMFPACK_LIBRARIES umfpack PATHS $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR}
 
 if(UMFPACK_LIBRARIES)
 
-  if (NOT UMFPACK_LIBDIR)
+  if(NOT UMFPACK_LIBDIR)
     get_filename_component(UMFPACK_LIBDIR ${UMFPACK_LIBRARIES} PATH)
   endif(NOT UMFPACK_LIBDIR)
 
   find_library(COLAMD_LIBRARY colamd PATHS ${UMFPACK_LIBDIR} $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR})
-  if (COLAMD_LIBRARY)
+  if(COLAMD_LIBRARY)
     set(UMFPACK_LIBRARIES ${UMFPACK_LIBRARIES} ${COLAMD_LIBRARY})
-  endif (COLAMD_LIBRARY)
+  endif ()
   
   find_library(AMD_LIBRARY amd PATHS ${UMFPACK_LIBDIR} $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR})
-  if (AMD_LIBRARY)
+  if(AMD_LIBRARY)
     set(UMFPACK_LIBRARIES ${UMFPACK_LIBRARIES} ${AMD_LIBRARY})
-  endif (AMD_LIBRARY)
+  endif ()
 
   find_library(SUITESPARSE_LIBRARY SuiteSparse PATHS ${UMFPACK_LIBDIR} $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR})
-  if (SUITESPARSE_LIBRARY)
+  if(SUITESPARSE_LIBRARY)
     set(UMFPACK_LIBRARIES ${UMFPACK_LIBRARIES} ${SUITESPARSE_LIBRARY})
-  endif (SUITESPARSE_LIBRARY)
+  endif ()
+
+  find_library(CHOLMOD_LIBRARY cholmod PATHS $ENV{UMFPACK_LIBDIR} $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR})
+  if(CHOLMOD_LIBRARY)
+    set(UMFPACK_LIBRARIES ${UMFPACK_LIBRARIES} ${CHOLMOD_LIBRARY})
+  endif()
 
 endif(UMFPACK_LIBRARIES)
 
@@ -45,4 +50,4 @@ include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(UMFPACK DEFAULT_MSG
                                   UMFPACK_INCLUDES UMFPACK_LIBRARIES)
 
-mark_as_advanced(UMFPACK_INCLUDES UMFPACK_LIBRARIES AMD_LIBRARY COLAMD_LIBRARY SUITESPARSE_LIBRARY)
+mark_as_advanced(UMFPACK_INCLUDES UMFPACK_LIBRARIES AMD_LIBRARY COLAMD_LIBRARY CHOLMOD_LIBRARY SUITESPARSE_LIBRARY)

gtsam/3rdparty/Eigen/doc/CMakeLists.txt

@@ -91,7 +91,8 @@ add_custom_target(doc ALL
   COMMAND doxygen Doxyfile-unsupported
   COMMAND ${CMAKE_COMMAND} -E rename html eigen-doc
   COMMAND ${CMAKE_COMMAND} -E remove eigen-doc/eigen-doc.tgz
-  COMMAND ${CMAKE_COMMAND} -E tar cfz eigen-doc/eigen-doc.tgz eigen-doc
+  COMMAND ${CMAKE_COMMAND} -E tar cfz eigen-doc.tgz eigen-doc
+  COMMAND ${CMAKE_COMMAND} -E rename eigen-doc.tgz eigen-doc/eigen-doc.tgz
   COMMAND ${CMAKE_COMMAND} -E rename eigen-doc html
   WORKING_DIRECTORY ${Eigen_BINARY_DIR}/doc)
 

gtsam/3rdparty/Eigen/doc/Doxyfile.in

@@ -222,7 +222,7 @@ ALIASES                = "only_for_vectors=This is only for vectors (either row-
                          "note_about_using_kernel_to_study_multiple_solutions=If you need a complete analysis of the space of solutions, take the one solution obtained by this method and add to it elements of the kernel, as determined by kernel()." \
                          "note_about_checking_solutions=This method just tries to find as good a solution as possible. If you want to check whether a solution exists or if it is accurate, just call this function to get a result and then compute the error of this result, or use MatrixBase::isApprox() directly, for instance like this: \code bool a_solution_exists = (A*result).isApprox(b, precision); \endcode This method avoids dividing by zero, so that the non-existence of a solution doesn't by itself mean that you'll get \c inf or \c nan values." \
                          "note_try_to_help_rvo=This function returns the result by value. In order to make that efficient, it is implemented as just a return statement using a special constructor, hopefully allowing the compiler to perform a RVO (return value optimization)." \
-                         "nonstableyet=\warning This is not considered to be part of the stable public API yet. Changes may happen in future releases. See \ref Experimental \"Experimental parts of Eigen\"
+                         "nonstableyet=\warning This is not considered to be part of the stable public API yet. Changes may happen in future releases. See \ref Experimental \"Experimental parts of Eigen\""
 
 ALIASES += "eigenAutoToc=  "
 ALIASES += "eigenManualPage=\defgroup"
@@ -315,7 +315,7 @@ IDL_PROPERTY_SUPPORT   = YES
 # member in the group (if any) for the other members of the group. By default
 # all members of a group must be documented explicitly.
 
-DISTRIBUTE_GROUP_DOC   = NO
+DISTRIBUTE_GROUP_DOC   = YES
 
 # Set the SUBGROUPING tag to YES (the default) to allow class member groups of
 # the same type (for instance a group of public functions) to be put as a
@@ -365,7 +365,7 @@ TYPEDEF_HIDES_STRUCT   = NO
 # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
 # corresponding to a cache size of 2^16 = 65536 symbols.
 
-SYMBOL_CACHE_SIZE      = 0
+# SYMBOL_CACHE_SIZE      = 0
 
 # Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
 # set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
@@ -562,7 +562,7 @@ GENERATE_BUGLIST       = NO
 # disable (NO) the deprecated list. This list is created by putting
 # \deprecated commands in the documentation.
 
-GENERATE_DEPRECATEDLIST= NO
+GENERATE_DEPRECATEDLIST= YES
 
 # The ENABLED_SECTIONS tag can be used to enable conditional
 # documentation sections, marked by \if sectionname ... \endif.
@@ -1465,13 +1465,13 @@ XML_OUTPUT             = xml
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 
-XML_SCHEMA             =
+# XML_SCHEMA             =
 
 # The XML_DTD tag can be used to specify an XML DTD,
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 
-XML_DTD                =
+# XML_DTD                =
 
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
@@ -1699,7 +1699,7 @@ DOT_NUM_THREADS        = 0
 # the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
 # directory containing the font.
 
-DOT_FONTNAME           = FreeSans
+DOT_FONTNAME           = 
 
 # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
 # The default size is 10pt.

gtsam/3rdparty/Eigen/doc/Manual.dox

@@ -11,6 +11,7 @@ namespace Eigen {
   - \subpage TopicCustomizingEigen
   - \subpage TopicMultiThreading
   - \subpage TopicUsingIntelMKL
+  - \subpage TopicPitfalls
   - \subpage TopicTemplateKeyword
   - \subpage UserManual_UnderstandingEigen
 */

gtsam/3rdparty/Eigen/doc/Pitfalls.dox

@@ -0,0 +1,38 @@
+namespace Eigen {
+
+/** \page TopicPitfalls Common pitfalls
+
+\section TopicPitfalls_template_keyword Compilation error with template methods
+
+See this \link TopicTemplateKeyword page \endlink.
+
+\section TopicPitfalls_auto_keyword C++11 and the auto keyword
+
+In short: do not use the auto keywords with Eigen's expressions, unless you are 100% sure about what you are doing. In particular, do not use the auto keyword as a replacement for a Matrix<> type. Here is an example:
+
+\code
+MatrixXd A, B;
+auto C = A*B;
+for(...) { ... w = C * v;  ...}
+\endcode
+
+In this example, the type of C is not a MatrixXd but an abstract expression representing a matrix product and storing references to A and B. Therefore, the product of A*B will be carried out multiple times, once per iteration of the for loop. Moreover, if the coefficients of A or B change during the iteration, then C will evaluate to different values.
+
+Here is another example leading to a segfault:
+\code
+auto C = ((A+B).eval()).transpose();
+// do something with C
+\endcode
+The problem is that eval() returns a temporary object (in this case a MatrixXd) which is then referenced by the Transpose<> expression. However, this temporary is deleted right after the first line, and there the C expression reference a dead object. The same issue might occur when sub expressions are automatically evaluated by Eigen as in the following example:
+\code
+VectorXd u, v;
+auto C = u + (A*v).normalized();
+// do something with C
+\endcode
+where the normalized() method has to evaluate the expensive product A*v to avoid evaluating it twice. On the other hand, the following example is perfectly fine:
+\code
+auto C = (u + (A*v).normalized()).eval();
+\endcode
+In this case, C will be a regular VectorXd object.
+*/
+}

gtsam/3rdparty/Eigen/doc/TopicMultithreading.dox

@@ -17,7 +17,7 @@ You can control the number of thread that will be used using either the OpenMP A
 Unless setNbThreads has been called, Eigen uses the number of threads specified by OpenMP. You can restore this bahavior by calling \code setNbThreads(0); \endcode
 You can query the number of threads that will be used with:
 \code
-n = Eigen::nbThreads(n);
+n = Eigen::nbThreads( );
 \endcode
 You can disable Eigen's multi threading at compile time by defining the EIGEN_DONT_PARALLELIZE preprocessor token.