Considering multiple neighboring triangles for support point normals

src/eigen/unsupported/Eigen/SparseExtra

@@ -0,0 +1,53 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2008-2009 Gael Guennebaud <g.gael@free.fr>
+//
+// 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_SPARSE_EXTRA_MODULE_H
+#define EIGEN_SPARSE_EXTRA_MODULE_H
+
+#include "../../Eigen/Sparse"
+
+#include "../../Eigen/src/Core/util/DisableStupidWarnings.h"
+
+#include <vector>
+#include <map>
+#include <cstdlib>
+#include <cstring>
+#include <algorithm>
+#include <fstream>
+#include <sstream>
+
+#ifdef EIGEN_GOOGLEHASH_SUPPORT
+  #include <google/dense_hash_map>
+#endif
+
+/**
+  * \defgroup SparseExtra_Module SparseExtra module
+  *
+  * This module contains some experimental features extending the sparse module.
+  *
+  * \code
+  * #include <Eigen/SparseExtra>
+  * \endcode
+  */
+
+
+#include "src/SparseExtra/DynamicSparseMatrix.h"
+#include "src/SparseExtra/BlockOfDynamicSparseMatrix.h"
+#include "src/SparseExtra/RandomSetter.h"
+
+#include "src/SparseExtra/MarketIO.h"
+
+#if !defined(_WIN32)
+#include <dirent.h>
+#include "src/SparseExtra/MatrixMarketIterator.h"
+#endif
+
+#include "../../Eigen/src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_SPARSE_EXTRA_MODULE_H

src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h

@@ -0,0 +1,122 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
+//
+// 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_SPARSE_BLOCKFORDYNAMICMATRIX_H
+#define EIGEN_SPARSE_BLOCKFORDYNAMICMATRIX_H
+
+namespace Eigen { 
+
+#if 0
+
+// NOTE Have to be reimplemented as a specialization of BlockImpl< DynamicSparseMatrix<_Scalar, _Options, _Index>, ... >
+// See SparseBlock.h for an example
+
+
+/***************************************************************************
+* specialisation for DynamicSparseMatrix
+***************************************************************************/
+
+template<typename _Scalar, int _Options, typename _Index, int Size>
+class SparseInnerVectorSet<DynamicSparseMatrix<_Scalar, _Options, _Index>, Size>
+  : public SparseMatrixBase<SparseInnerVectorSet<DynamicSparseMatrix<_Scalar, _Options, _Index>, Size> >
+{
+    typedef DynamicSparseMatrix<_Scalar, _Options, _Index> MatrixType;
+  public:
+
+    enum { IsRowMajor = internal::traits<SparseInnerVectorSet>::IsRowMajor };
+
+    EIGEN_SPARSE_PUBLIC_INTERFACE(SparseInnerVectorSet)
+    class InnerIterator: public MatrixType::InnerIterator
+    {
+      public:
+        inline InnerIterator(const SparseInnerVectorSet& xpr, Index outer)
+          : MatrixType::InnerIterator(xpr.m_matrix, xpr.m_outerStart + outer), m_outer(outer)
+        {}
+        inline Index row() const { return IsRowMajor ? m_outer : this->index(); }
+        inline Index col() const { return IsRowMajor ? this->index() : m_outer; }
+      protected:
+        Index m_outer;
+    };
+
+    inline SparseInnerVectorSet(const MatrixType& matrix, Index outerStart, Index outerSize)
+      : m_matrix(matrix), m_outerStart(outerStart), m_outerSize(outerSize)
+    {
+      eigen_assert( (outerStart>=0) && ((outerStart+outerSize)<=matrix.outerSize()) );
+    }
+
+    inline SparseInnerVectorSet(const MatrixType& matrix, Index outer)
+      : m_matrix(matrix), m_outerStart(outer), m_outerSize(Size)
+    {
+      eigen_assert(Size!=Dynamic);
+      eigen_assert( (outer>=0) && (outer<matrix.outerSize()) );
+    }
+
+    template<typename OtherDerived>
+    inline SparseInnerVectorSet& operator=(const SparseMatrixBase<OtherDerived>& other)
+    {
+      if (IsRowMajor != ((OtherDerived::Flags&RowMajorBit)==RowMajorBit))
+      {
+        // need to transpose => perform a block evaluation followed by a big swap
+        DynamicSparseMatrix<Scalar,IsRowMajor?RowMajorBit:0> aux(other);
+        *this = aux.markAsRValue();
+      }
+      else
+      {
+        // evaluate/copy vector per vector
+        for (Index j=0; j<m_outerSize.value(); ++j)
+        {
+          SparseVector<Scalar,IsRowMajor ? RowMajorBit : 0> aux(other.innerVector(j));
+          m_matrix.const_cast_derived()._data()[m_outerStart+j].swap(aux._data());
+        }
+      }
+      return *this;
+    }
+
+    inline SparseInnerVectorSet& operator=(const SparseInnerVectorSet& other)
+    {
+      return operator=<SparseInnerVectorSet>(other);
+    }
+
+    Index nonZeros() const
+    {
+      Index count = 0;
+      for (Index j=0; j<m_outerSize.value(); ++j)
+        count += m_matrix._data()[m_outerStart+j].size();
+      return count;
+    }
+
+    const Scalar& lastCoeff() const
+    {
+      EIGEN_STATIC_ASSERT_VECTOR_ONLY(SparseInnerVectorSet);
+      eigen_assert(m_matrix.data()[m_outerStart].size()>0);
+      return m_matrix.data()[m_outerStart].vale(m_matrix.data()[m_outerStart].size()-1);
+    }
+
+//     template<typename Sparse>
+//     inline SparseInnerVectorSet& operator=(const SparseMatrixBase<OtherDerived>& other)
+//     {
+//       return *this;
+//     }
+
+    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(); }
+
+  protected:
+
+    const typename MatrixType::Nested m_matrix;
+    Index m_outerStart;
+    const internal::variable_if_dynamic<Index, Size> m_outerSize;
+
+};
+
+#endif
+
+} // end namespace Eigen
+
+#endif // EIGEN_SPARSE_BLOCKFORDYNAMICMATRIX_H

src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h

@@ -0,0 +1,392 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
+//
+// 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_DYNAMIC_SPARSEMATRIX_H
+#define EIGEN_DYNAMIC_SPARSEMATRIX_H
+
+namespace Eigen { 
+
+/** \deprecated use a SparseMatrix in an uncompressed mode
+  *
+  * \class DynamicSparseMatrix
+  *
+  * \brief A sparse matrix class designed for matrix assembly purpose
+  *
+  * \param _Scalar the scalar type, i.e. the type of the coefficients
+  *
+  * Unlike SparseMatrix, this class provides a much higher degree of flexibility. In particular, it allows
+  * random read/write accesses in log(rho*outer_size) where \c rho is the probability that a coefficient is
+  * nonzero and outer_size is the number of columns if the matrix is column-major and the number of rows
+  * otherwise.
+  *
+  * Internally, the data are stored as a std::vector of compressed vector. The performances of random writes might
+  * decrease as the number of nonzeros per inner-vector increase. In practice, we observed very good performance
+  * till about 100 nonzeros/vector, and the performance remains relatively good till 500 nonzeros/vectors.
+  *
+  * \see SparseMatrix
+  */
+
+namespace internal {
+template<typename _Scalar, int _Options, typename _StorageIndex>
+struct traits<DynamicSparseMatrix<_Scalar, _Options, _StorageIndex> >
+{
+  typedef _Scalar Scalar;
+  typedef _StorageIndex StorageIndex;
+  typedef Sparse StorageKind;
+  typedef MatrixXpr XprKind;
+  enum {
+    RowsAtCompileTime = Dynamic,
+    ColsAtCompileTime = Dynamic,
+    MaxRowsAtCompileTime = Dynamic,
+    MaxColsAtCompileTime = Dynamic,
+    Flags = _Options | NestByRefBit | LvalueBit,
+    CoeffReadCost = NumTraits<Scalar>::ReadCost,
+    SupportedAccessPatterns = OuterRandomAccessPattern
+  };
+};
+}
+
+template<typename _Scalar, int _Options, typename _StorageIndex>
+ class  DynamicSparseMatrix
+  : public SparseMatrixBase<DynamicSparseMatrix<_Scalar, _Options, _StorageIndex> >
+{
+    typedef SparseMatrixBase<DynamicSparseMatrix> Base;
+    using Base::convert_index;
+  public:
+    EIGEN_SPARSE_PUBLIC_INTERFACE(DynamicSparseMatrix)
+    // FIXME: why are these operator already alvailable ???
+    // EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(DynamicSparseMatrix, +=)
+    // EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(DynamicSparseMatrix, -=)
+    typedef MappedSparseMatrix<Scalar,Flags> Map;
+    using Base::IsRowMajor;
+    using Base::operator=;
+    enum {
+      Options = _Options
+    };
+
+  protected:
+
+    typedef DynamicSparseMatrix<Scalar,(Flags&~RowMajorBit)|(IsRowMajor?RowMajorBit:0), StorageIndex> TransposedSparseMatrix;
+
+    Index m_innerSize;
+    std::vector<internal::CompressedStorage<Scalar,StorageIndex> > m_data;
+
+  public:
+
+    inline Index rows() const { return IsRowMajor ? outerSize() : m_innerSize; }
+    inline Index cols() const { return IsRowMajor ? m_innerSize : outerSize(); }
+    inline Index innerSize() const { return m_innerSize; }
+    inline Index outerSize() const { return convert_index(m_data.size()); }
+    inline Index innerNonZeros(Index j) const { return m_data[j].size(); }
+
+    std::vector<internal::CompressedStorage<Scalar,StorageIndex> >& _data() { return m_data; }
+    const std::vector<internal::CompressedStorage<Scalar,StorageIndex> >& _data() const { return m_data; }
+
+    /** \returns the coefficient value at given position \a row, \a col
+      * This operation involes a log(rho*outer_size) binary search.
+      */
+    inline Scalar coeff(Index row, Index col) const
+    {
+      const Index outer = IsRowMajor ? row : col;
+      const Index inner = IsRowMajor ? col : row;
+      return m_data[outer].at(inner);
+    }
+
+    /** \returns a reference to the coefficient value at given position \a row, \a col
+      * This operation involes a log(rho*outer_size) binary search. If the coefficient does not
+      * exist yet, then a sorted insertion into a sequential buffer is performed.
+      */
+    inline Scalar& coeffRef(Index row, Index col)
+    {
+      const Index outer = IsRowMajor ? row : col;
+      const Index inner = IsRowMajor ? col : row;
+      return m_data[outer].atWithInsertion(inner);
+    }
+
+    class InnerIterator;
+    class ReverseInnerIterator;
+
+    void setZero()
+    {
+      for (Index j=0; j<outerSize(); ++j)
+        m_data[j].clear();
+    }
+
+    /** \returns the number of non zero coefficients */
+    Index nonZeros() const
+    {
+      Index res = 0;
+      for (Index j=0; j<outerSize(); ++j)
+        res += m_data[j].size();
+      return res;
+    }
+
+
+
+    void reserve(Index reserveSize = 1000)
+    {
+      if (outerSize()>0)
+      {
+        Index reserveSizePerVector = (std::max)(reserveSize/outerSize(),Index(4));
+        for (Index j=0; j<outerSize(); ++j)
+        {
+          m_data[j].reserve(reserveSizePerVector);
+        }
+      }
+    }
+
+    /** Does nothing: provided for compatibility with SparseMatrix */
+    inline void startVec(Index /*outer*/) {}
+
+    /** \returns a reference to the non zero coefficient at position \a row, \a col assuming that:
+      * - the nonzero does not already exist
+      * - the new coefficient is the last one of the given inner vector.
+      *
+      * \sa insert, insertBackByOuterInner */
+    inline Scalar& insertBack(Index row, Index col)
+    {
+      return insertBackByOuterInner(IsRowMajor?row:col, IsRowMajor?col:row);
+    }
+
+    /** \sa insertBack */
+    inline Scalar& insertBackByOuterInner(Index outer, Index inner)
+    {
+      eigen_assert(outer<Index(m_data.size()) && inner<m_innerSize && "out of range");
+      eigen_assert(((m_data[outer].size()==0) || (m_data[outer].index(m_data[outer].size()-1)<inner))
+                && "wrong sorted insertion");
+      m_data[outer].append(0, inner);
+      return m_data[outer].value(m_data[outer].size()-1);
+    }
+
+    inline Scalar& insert(Index row, Index col)
+    {
+      const Index outer = IsRowMajor ? row : col;
+      const Index inner = IsRowMajor ? col : row;
+
+      Index startId = 0;
+      Index id = static_cast<Index>(m_data[outer].size()) - 1;
+      m_data[outer].resize(id+2,1);
+
+      while ( (id >= startId) && (m_data[outer].index(id) > inner) )
+      {
+        m_data[outer].index(id+1) = m_data[outer].index(id);
+        m_data[outer].value(id+1) = m_data[outer].value(id);
+        --id;
+      }
+      m_data[outer].index(id+1) = inner;
+      m_data[outer].value(id+1) = 0;
+      return m_data[outer].value(id+1);
+    }
+
+    /** Does nothing: provided for compatibility with SparseMatrix */
+    inline void finalize() {}
+
+    /** Suppress all nonzeros which are smaller than \a reference under the tolerence \a epsilon */
+    void prune(Scalar reference, RealScalar epsilon = NumTraits<RealScalar>::dummy_precision())
+    {
+      for (Index j=0; j<outerSize(); ++j)
+        m_data[j].prune(reference,epsilon);
+    }
+
+    /** Resize the matrix without preserving the data (the matrix is set to zero)
+      */
+    void resize(Index rows, Index cols)
+    {
+      const Index outerSize = IsRowMajor ? rows : cols;
+      m_innerSize = convert_index(IsRowMajor ? cols : rows);
+      setZero();
+      if (Index(m_data.size()) != outerSize)
+      {
+        m_data.resize(outerSize);
+      }
+    }
+
+    void resizeAndKeepData(Index rows, Index cols)
+    {
+      const Index outerSize = IsRowMajor ? rows : cols;
+      const Index innerSize = IsRowMajor ? cols : rows;
+      if (m_innerSize>innerSize)
+      {
+        // remove all coefficients with innerCoord>=innerSize
+        // TODO
+        //std::cerr << "not implemented yet\n";
+        exit(2);
+      }
+      if (m_data.size() != outerSize)
+      {
+        m_data.resize(outerSize);
+      }
+    }
+
+    /** The class DynamicSparseMatrix is deprectaed */
+    EIGEN_DEPRECATED inline DynamicSparseMatrix()
+      : m_innerSize(0), m_data(0)
+    {
+      eigen_assert(innerSize()==0 && outerSize()==0);
+    }
+
+    /** The class DynamicSparseMatrix is deprectaed */
+    EIGEN_DEPRECATED inline DynamicSparseMatrix(Index rows, Index cols)
+      : m_innerSize(0)
+    {
+      resize(rows, cols);
+    }
+
+    /** The class DynamicSparseMatrix is deprectaed */
+    template<typename OtherDerived>
+    EIGEN_DEPRECATED explicit inline DynamicSparseMatrix(const SparseMatrixBase<OtherDerived>& other)
+      : m_innerSize(0)
+    {
+    Base::operator=(other.derived());
+    }
+
+    inline DynamicSparseMatrix(const DynamicSparseMatrix& other)
+      : Base(), m_innerSize(0)
+    {
+      *this = other.derived();
+    }
+
+    inline void swap(DynamicSparseMatrix& other)
+    {
+      //EIGEN_DBG_SPARSE(std::cout << "SparseMatrix:: swap\n");
+      std::swap(m_innerSize, other.m_innerSize);
+      //std::swap(m_outerSize, other.m_outerSize);
+      m_data.swap(other.m_data);
+    }
+
+    inline DynamicSparseMatrix& operator=(const DynamicSparseMatrix& other)
+    {
+      if (other.isRValue())
+      {
+        swap(other.const_cast_derived());
+      }
+      else
+      {
+        resize(other.rows(), other.cols());
+        m_data = other.m_data;
+      }
+      return *this;
+    }
+
+    /** Destructor */
+    inline ~DynamicSparseMatrix() {}
+
+  public:
+
+    /** \deprecated
+      * Set the matrix to zero and reserve the memory for \a reserveSize nonzero coefficients. */
+    EIGEN_DEPRECATED void startFill(Index reserveSize = 1000)
+    {
+      setZero();
+      reserve(reserveSize);
+    }
+
+    /** \deprecated use insert()
+      * inserts a nonzero coefficient at given coordinates \a row, \a col and returns its reference assuming that:
+      *  1 - the coefficient does not exist yet
+      *  2 - this the coefficient with greater inner coordinate for the given outer coordinate.
+      * In other words, assuming \c *this is column-major, then there must not exists any nonzero coefficient of coordinates
+      * \c i \c x \a col such that \c i >= \a row. Otherwise the matrix is invalid.
+      *
+      * \see fillrand(), coeffRef()
+      */
+    EIGEN_DEPRECATED Scalar& fill(Index row, Index col)
+    {
+      const Index outer = IsRowMajor ? row : col;
+      const Index inner = IsRowMajor ? col : row;
+      return insertBack(outer,inner);
+    }
+
+    /** \deprecated use insert()
+      * Like fill() but with random inner coordinates.
+      * Compared to the generic coeffRef(), the unique limitation is that we assume
+      * the coefficient does not exist yet.
+      */
+    EIGEN_DEPRECATED Scalar& fillrand(Index row, Index col)
+    {
+      return insert(row,col);
+    }
+
+    /** \deprecated use finalize()
+      * Does nothing. Provided for compatibility with SparseMatrix. */
+    EIGEN_DEPRECATED void endFill() {}
+    
+#   ifdef EIGEN_DYNAMICSPARSEMATRIX_PLUGIN
+#     include EIGEN_DYNAMICSPARSEMATRIX_PLUGIN
+#   endif
+ };
+
+template<typename Scalar, int _Options, typename _StorageIndex>
+class DynamicSparseMatrix<Scalar,_Options,_StorageIndex>::InnerIterator : public SparseVector<Scalar,_Options,_StorageIndex>::InnerIterator
+{
+    typedef typename SparseVector<Scalar,_Options,_StorageIndex>::InnerIterator Base;
+  public:
+    InnerIterator(const DynamicSparseMatrix& mat, Index outer)
+      : Base(mat.m_data[outer]), m_outer(outer)
+    {}
+
+    inline Index row() const { return IsRowMajor ? m_outer : Base::index(); }
+    inline Index col() const { return IsRowMajor ? Base::index() : m_outer; }
+    inline Index outer() const { return m_outer; }
+
+  protected:
+    const Index m_outer;
+};
+
+template<typename Scalar, int _Options, typename _StorageIndex>
+class DynamicSparseMatrix<Scalar,_Options,_StorageIndex>::ReverseInnerIterator : public SparseVector<Scalar,_Options,_StorageIndex>::ReverseInnerIterator
+{
+    typedef typename SparseVector<Scalar,_Options,_StorageIndex>::ReverseInnerIterator Base;
+  public:
+    ReverseInnerIterator(const DynamicSparseMatrix& mat, Index outer)
+      : Base(mat.m_data[outer]), m_outer(outer)
+    {}
+
+    inline Index row() const { return IsRowMajor ? m_outer : Base::index(); }
+    inline Index col() const { return IsRowMajor ? Base::index() : m_outer; }
+    inline Index outer() const { return m_outer; }
+
+  protected:
+    const Index m_outer;
+};
+
+namespace internal {
+
+template<typename _Scalar, int _Options, typename _StorageIndex>
+struct evaluator<DynamicSparseMatrix<_Scalar,_Options,_StorageIndex> >
+  : evaluator_base<DynamicSparseMatrix<_Scalar,_Options,_StorageIndex> >
+{
+  typedef _Scalar Scalar;
+  typedef DynamicSparseMatrix<_Scalar,_Options,_StorageIndex> SparseMatrixType;
+  typedef typename SparseMatrixType::InnerIterator InnerIterator;
+  typedef typename SparseMatrixType::ReverseInnerIterator ReverseInnerIterator;
+  
+  enum {
+    CoeffReadCost = NumTraits<_Scalar>::ReadCost,
+    Flags = SparseMatrixType::Flags
+  };
+  
+  evaluator() : m_matrix(0) {}
+  evaluator(const SparseMatrixType &mat) : m_matrix(&mat) {}
+  
+  operator SparseMatrixType&() { return m_matrix->const_cast_derived(); }
+  operator const SparseMatrixType&() const { return *m_matrix; }
+  
+  Scalar coeff(Index row, Index col) const { return m_matrix->coeff(row,col); }
+  
+  Index nonZerosEstimate() const { return m_matrix->nonZeros(); }
+
+  const SparseMatrixType *m_matrix;
+};
+
+}
+
+} // end namespace Eigen
+
+#endif // EIGEN_DYNAMIC_SPARSEMATRIX_H

src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h

@@ -0,0 +1,275 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2011 Gael Guennebaud <gael.guennebaud@inria.fr>
+// Copyright (C) 2012 Desire NUENTSA WAKAM <desire.nuentsa_wakam@inria.fr>
+//
+// 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_SPARSE_MARKET_IO_H
+#define EIGEN_SPARSE_MARKET_IO_H
+
+#include <iostream>
+
+namespace Eigen { 
+
+namespace internal 
+{
+  template <typename Scalar>
+  inline bool GetMarketLine (std::stringstream& line, Index& M, Index& N, Index& i, Index& j, Scalar& value)
+  {
+    line >> i >> j >> value;
+    i--;
+    j--;
+    if(i>=0 && j>=0 && i<M && j<N)
+    {
+      return true; 
+    }
+    else
+      return false;
+  }
+  template <typename Scalar>
+  inline bool GetMarketLine (std::stringstream& line, Index& M, Index& N, Index& i, Index& j, std::complex<Scalar>& value)
+  {
+    Scalar valR, valI;
+    line >> i >> j >> valR >> valI;
+    i--;
+    j--;
+    if(i>=0 && j>=0 && i<M && j<N)
+    {
+      value = std::complex<Scalar>(valR, valI);
+      return true; 
+    }
+    else
+      return false;
+  }
+
+  template <typename RealScalar>
+  inline void  GetVectorElt (const std::string& line, RealScalar& val)
+  {
+    std::istringstream newline(line);
+    newline >> val;  
+  }
+
+  template <typename RealScalar>
+  inline void GetVectorElt (const std::string& line, std::complex<RealScalar>& val)
+  {
+    RealScalar valR, valI; 
+    std::istringstream newline(line);
+    newline >> valR >> valI; 
+    val = std::complex<RealScalar>(valR, valI);
+  }
+  
+  template<typename Scalar>
+  inline void putMarketHeader(std::string& header,int sym)
+  {
+    header= "%%MatrixMarket matrix coordinate ";
+    if(internal::is_same<Scalar, std::complex<float> >::value || internal::is_same<Scalar, std::complex<double> >::value)
+    {
+      header += " complex"; 
+      if(sym == Symmetric) header += " symmetric";
+      else if (sym == SelfAdjoint) header += " Hermitian";
+      else header += " general";
+    }
+    else
+    {
+      header += " real"; 
+      if(sym == Symmetric) header += " symmetric";
+      else header += " general";
+    }
+  }
+
+  template<typename Scalar>
+  inline void PutMatrixElt(Scalar value, int row, int col, std::ofstream& out)
+  {
+    out << row << " "<< col << " " << value << "\n";
+  }
+  template<typename Scalar>
+  inline void PutMatrixElt(std::complex<Scalar> value, int row, int col, std::ofstream& out)
+  {
+    out << row << " " << col << " " << value.real() << " " << value.imag() << "\n";
+  }
+
+
+  template<typename Scalar>
+  inline void putVectorElt(Scalar value, std::ofstream& out)
+  {
+    out << value << "\n"; 
+  }
+  template<typename Scalar>
+  inline void putVectorElt(std::complex<Scalar> value, std::ofstream& out)
+  {
+    out << value.real << " " << value.imag()<< "\n"; 
+  }
+
+} // end namepsace internal
+
+inline bool getMarketHeader(const std::string& filename, int& sym, bool& iscomplex, bool& isvector)
+{
+  sym = 0; 
+  iscomplex = false;
+  isvector = false;
+  std::ifstream in(filename.c_str(),std::ios::in);
+  if(!in)
+    return false;
+  
+  std::string line; 
+  // The matrix header is always the first line in the file 
+  std::getline(in, line); eigen_assert(in.good());
+  
+  std::stringstream fmtline(line); 
+  std::string substr[5];
+  fmtline>> substr[0] >> substr[1] >> substr[2] >> substr[3] >> substr[4];
+  if(substr[2].compare("array") == 0) isvector = true;
+  if(substr[3].compare("complex") == 0) iscomplex = true;
+  if(substr[4].compare("symmetric") == 0) sym = Symmetric;
+  else if (substr[4].compare("Hermitian") == 0) sym = SelfAdjoint;
+  
+  return true;
+}
+  
+template<typename SparseMatrixType>
+bool loadMarket(SparseMatrixType& mat, const std::string& filename)
+{
+  typedef typename SparseMatrixType::Scalar Scalar;
+  typedef typename SparseMatrixType::Index Index;
+  std::ifstream input(filename.c_str(),std::ios::in);
+  if(!input)
+    return false;
+  
+  const int maxBuffersize = 2048;
+  char buffer[maxBuffersize];
+  
+  bool readsizes = false;
+
+  typedef Triplet<Scalar,Index> T;
+  std::vector<T> elements;
+  
+  Index M(-1), N(-1), NNZ(-1);
+  Index count = 0;
+  while(input.getline(buffer, maxBuffersize))
+  {
+    // skip comments   
+    //NOTE An appropriate test should be done on the header to get the  symmetry
+    if(buffer[0]=='%')
+      continue;
+    
+    std::stringstream line(buffer);
+    
+    if(!readsizes)
+    {
+      line >> M >> N >> NNZ;
+      if(M > 0 && N > 0 && NNZ > 0) 
+      {
+        readsizes = true;
+        //std::cout << "sizes: " << M << "," << N << "," << NNZ << "\n";
+        mat.resize(M,N);
+        mat.reserve(NNZ);
+      }
+    }
+    else
+    { 
+      Index i(-1), j(-1);
+      Scalar value; 
+      if( internal::GetMarketLine(line, M, N, i, j, value) ) 
+      {
+        ++ count;
+        elements.push_back(T(i,j,value));
+      }
+      else 
+        std::cerr << "Invalid read: " << i << "," << j << "\n";        
+    }
+  }
+  mat.setFromTriplets(elements.begin(), elements.end());
+  if(count!=NNZ)
+    std::cerr << count << "!=" << NNZ << "\n";
+  
+  input.close();
+  return true;
+}
+
+template<typename VectorType>
+bool loadMarketVector(VectorType& vec, const std::string& filename)
+{
+   typedef typename VectorType::Scalar Scalar;
+  std::ifstream in(filename.c_str(), std::ios::in);
+  if(!in)
+    return false;
+  
+  std::string line; 
+  int n(0), col(0); 
+  do 
+  { // Skip comments
+    std::getline(in, line); eigen_assert(in.good());
+  } while (line[0] == '%');
+  std::istringstream newline(line);
+  newline  >> n >> col; 
+  eigen_assert(n>0 && col>0);
+  vec.resize(n);
+  int i = 0; 
+  Scalar value; 
+  while ( std::getline(in, line) && (i < n) ){
+    internal::GetVectorElt(line, value); 
+    vec(i++) = value; 
+  }
+  in.close();
+  if (i!=n){
+    std::cerr<< "Unable to read all elements from file " << filename << "\n";
+    return false;
+  }
+  return true;
+}
+
+template<typename SparseMatrixType>
+bool saveMarket(const SparseMatrixType& mat, const std::string& filename, int sym = 0)
+{
+  typedef typename SparseMatrixType::Scalar Scalar;
+  std::ofstream out(filename.c_str(),std::ios::out);
+  if(!out)
+    return false;
+  
+  out.flags(std::ios_base::scientific);
+  out.precision(64);
+  std::string header; 
+  internal::putMarketHeader<Scalar>(header, sym); 
+  out << header << std::endl; 
+  out << mat.rows() << " " << mat.cols() << " " << mat.nonZeros() << "\n";
+  int count = 0;
+  for(int j=0; j<mat.outerSize(); ++j)
+    for(typename SparseMatrixType::InnerIterator it(mat,j); it; ++it)
+    {
+      ++ count;
+      internal::PutMatrixElt(it.value(), it.row()+1, it.col()+1, out);
+      // out << it.row()+1 << " " << it.col()+1 << " " << it.value() << "\n";
+    }
+  out.close();
+  return true;
+}
+
+template<typename VectorType>
+bool saveMarketVector (const VectorType& vec, const std::string& filename)
+{
+ typedef typename VectorType::Scalar Scalar; 
+ std::ofstream out(filename.c_str(),std::ios::out);
+  if(!out)
+    return false;
+  
+  out.flags(std::ios_base::scientific);
+  out.precision(64);
+  if(internal::is_same<Scalar, std::complex<float> >::value || internal::is_same<Scalar, std::complex<double> >::value)
+      out << "%%MatrixMarket matrix array complex general\n"; 
+  else
+    out << "%%MatrixMarket matrix array real general\n"; 
+  out << vec.size() << " "<< 1 << "\n";
+  for (int i=0; i < vec.size(); i++){
+    internal::putVectorElt(vec(i), out); 
+  }
+  out.close();
+  return true; 
+}
+
+} // end namespace Eigen
+
+#endif // EIGEN_SPARSE_MARKET_IO_H

src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h

@@ -0,0 +1,247 @@
+
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2012 Desire NUENTSA WAKAM <desire.nuentsa_wakam@inria.fr>
+//
+// 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_BROWSE_MATRICES_H
+#define EIGEN_BROWSE_MATRICES_H
+
+namespace Eigen {
+
+enum {
+  SPD = 0x100,
+  NonSymmetric = 0x0
+}; 
+
+/** 
+ * @brief Iterator to browse matrices from a specified folder
+ * 
+ * This is used to load all the matrices from a folder. 
+ * The matrices should be in Matrix Market format
+ * It is assumed that the matrices are named as matname.mtx
+ * and matname_SPD.mtx if the matrix is Symmetric and positive definite (or Hermitian)
+ * The right hand side vectors are loaded as well, if they exist.
+ * They should be named as matname_b.mtx. 
+ * Note that the right hand side for a SPD matrix is named as matname_SPD_b.mtx
+ * 
+ * Sometimes a reference solution is available. In this case, it should be named as matname_x.mtx
+ * 
+ * Sample code
+ * \code
+ * 
+ * \endcode
+ * 
+ * \tparam Scalar The scalar type 
+ */
+template <typename Scalar>
+class MatrixMarketIterator 
+{
+    typedef typename NumTraits<Scalar>::Real RealScalar;
+  public:
+    typedef Matrix<Scalar,Dynamic,1> VectorType; 
+    typedef SparseMatrix<Scalar,ColMajor> MatrixType; 
+  
+  public:
+    MatrixMarketIterator(const std::string &folder)
+      : m_sym(0), m_isvalid(false), m_matIsLoaded(false), m_hasRhs(false), m_hasrefX(false), m_folder(folder)
+    {
+      m_folder_id = opendir(folder.c_str());
+      if(m_folder_id)
+        Getnextvalidmatrix();
+    }
+    
+    ~MatrixMarketIterator()
+    {
+      if (m_folder_id) closedir(m_folder_id); 
+    }
+    
+    inline MatrixMarketIterator& operator++()
+    {
+      m_matIsLoaded = false;
+      m_hasrefX = false;
+      m_hasRhs = false;
+      Getnextvalidmatrix();
+      return *this;
+    }
+    inline operator bool() const { return m_isvalid;}
+    
+    /** Return the sparse matrix corresponding to the current file */
+    inline MatrixType& matrix() 
+    { 
+      // Read the matrix
+      if (m_matIsLoaded) return m_mat;
+      
+      std::string matrix_file = m_folder + "/" + m_matname + ".mtx";
+      if ( !loadMarket(m_mat, matrix_file)) 
+      {
+        std::cerr << "Warning loadMarket failed when loading \"" << matrix_file << "\"" << std::endl;
+        m_matIsLoaded = false;
+        return m_mat;
+      }
+      m_matIsLoaded = true; 
+
+      if (m_sym != NonSymmetric) 
+      {
+        // Check whether we need to restore a full matrix:
+        RealScalar diag_norm  = m_mat.diagonal().norm();
+        RealScalar lower_norm = m_mat.template triangularView<Lower>().norm();
+        RealScalar upper_norm = m_mat.template triangularView<Upper>().norm();
+        if(lower_norm>diag_norm && upper_norm==diag_norm)
+        {
+          // only the lower part is stored
+          MatrixType tmp(m_mat);
+          m_mat = tmp.template selfadjointView<Lower>();
+        }
+        else if(upper_norm>diag_norm && lower_norm==diag_norm)
+        {
+          // only the upper part is stored
+          MatrixType tmp(m_mat);
+          m_mat = tmp.template selfadjointView<Upper>();
+        }
+      }
+      return m_mat; 
+    }
+    
+    /** Return the right hand side corresponding to the current matrix. 
+     * If the rhs file is not provided, a random rhs is generated
+     */
+    inline VectorType& rhs() 
+    { 
+       // Get the right hand side
+      if (m_hasRhs) return m_rhs;
+      
+      std::string rhs_file;
+      rhs_file = m_folder + "/" + m_matname + "_b.mtx"; // The pattern is matname_b.mtx
+      m_hasRhs = Fileexists(rhs_file);
+      if (m_hasRhs)
+      {
+        m_rhs.resize(m_mat.cols());
+        m_hasRhs = loadMarketVector(m_rhs, rhs_file);
+      }
+      if (!m_hasRhs)
+      {
+        // Generate a random right hand side
+        if (!m_matIsLoaded) this->matrix(); 
+        m_refX.resize(m_mat.cols());
+        m_refX.setRandom();
+        m_rhs = m_mat * m_refX;
+        m_hasrefX = true;
+        m_hasRhs = true;
+      }
+      return m_rhs; 
+    }
+    
+    /** Return a reference solution
+     * If it is not provided and if the right hand side is not available
+     * then refX is randomly generated such that A*refX = b 
+     * where A and b are the matrix and the rhs. 
+     * Note that when a rhs is provided, refX is not available 
+     */
+    inline VectorType& refX() 
+    { 
+      // Check if a reference solution is provided
+      if (m_hasrefX) return m_refX;
+      
+      std::string lhs_file;
+      lhs_file = m_folder + "/" + m_matname + "_x.mtx"; 
+      m_hasrefX = Fileexists(lhs_file);
+      if (m_hasrefX)
+      {
+        m_refX.resize(m_mat.cols());
+        m_hasrefX = loadMarketVector(m_refX, lhs_file);
+      }
+      else
+        m_refX.resize(0);
+      return m_refX; 
+    }
+    
+    inline std::string& matname() { return m_matname; }
+    
+    inline int sym() { return m_sym; }
+    
+    bool hasRhs() {return m_hasRhs; }
+    bool hasrefX() {return m_hasrefX; }
+    bool isFolderValid() { return bool(m_folder_id); }
+    
+  protected:
+    
+    inline bool Fileexists(std::string file)
+    {
+      std::ifstream file_id(file.c_str());
+      if (!file_id.good() ) 
+      {
+        return false;
+      }
+      else 
+      {
+        file_id.close();
+        return true;
+      }
+    }
+    
+    void Getnextvalidmatrix( )
+    {
+      m_isvalid = false;
+      // Here, we return with the next valid matrix in the folder
+      while ( (m_curs_id = readdir(m_folder_id)) != NULL) {
+        m_isvalid = false;
+        std::string curfile;
+        curfile = m_folder + "/" + m_curs_id->d_name;
+        // Discard if it is a folder
+        if (m_curs_id->d_type == DT_DIR) continue; //FIXME This may not be available on non BSD systems
+//         struct stat st_buf; 
+//         stat (curfile.c_str(), &st_buf);
+//         if (S_ISDIR(st_buf.st_mode)) continue;
+        
+        // Determine from the header if it is a matrix or a right hand side 
+        bool isvector,iscomplex=false;
+        if(!getMarketHeader(curfile,m_sym,iscomplex,isvector)) continue;
+        if(isvector) continue;
+        if (!iscomplex)
+        {
+          if(internal::is_same<Scalar, std::complex<float> >::value || internal::is_same<Scalar, std::complex<double> >::value)
+            continue; 
+        }
+        if (iscomplex)
+        {
+          if(internal::is_same<Scalar, float>::value || internal::is_same<Scalar, double>::value)
+            continue; 
+        }
+        
+        
+        // Get the matrix name
+        std::string filename = m_curs_id->d_name;
+        m_matname = filename.substr(0, filename.length()-4); 
+        
+        // Find if the matrix is SPD 
+        size_t found = m_matname.find("SPD");
+        if( (found!=std::string::npos) && (m_sym != NonSymmetric) )
+          m_sym = SPD;
+       
+        m_isvalid = true;
+        break; 
+      }
+    }
+    int m_sym; // Symmetry of the matrix
+    MatrixType m_mat; // Current matrix  
+    VectorType m_rhs;  // Current vector
+    VectorType m_refX; // The reference solution, if exists
+    std::string m_matname; // Matrix Name
+    bool m_isvalid; 
+    bool m_matIsLoaded; // Determine if the matrix has already been loaded from the file
+    bool m_hasRhs; // The right hand side exists
+    bool m_hasrefX; // A reference solution is provided
+    std::string m_folder;
+    DIR * m_folder_id;
+    struct dirent *m_curs_id; 
+    
+};
+
+} // end namespace Eigen
+
+#endif

src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h

@@ -0,0 +1,327 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
+//
+// 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_RANDOMSETTER_H
+#define EIGEN_RANDOMSETTER_H
+
+namespace Eigen { 
+
+/** Represents a std::map
+  *
+  * \see RandomSetter
+  */
+template<typename Scalar> struct StdMapTraits
+{
+  typedef int KeyType;
+  typedef std::map<KeyType,Scalar> Type;
+  enum {
+    IsSorted = 1
+  };
+
+  static void setInvalidKey(Type&, const KeyType&) {}
+};
+
+#ifdef EIGEN_UNORDERED_MAP_SUPPORT
+/** Represents a std::unordered_map
+  *
+  * To use it you need to both define EIGEN_UNORDERED_MAP_SUPPORT and include the unordered_map header file
+  * yourself making sure that unordered_map is defined in the std namespace.
+  *
+  * For instance, with current version of gcc you can either enable C++0x standard (-std=c++0x) or do:
+  * \code
+  * #include <tr1/unordered_map>
+  * #define EIGEN_UNORDERED_MAP_SUPPORT
+  * namespace std {
+  *   using std::tr1::unordered_map;
+  * }
+  * \endcode
+  *
+  * \see RandomSetter
+  */
+template<typename Scalar> struct StdUnorderedMapTraits
+{
+  typedef int KeyType;
+  typedef std::unordered_map<KeyType,Scalar> Type;
+  enum {
+    IsSorted = 0
+  };
+
+  static void setInvalidKey(Type&, const KeyType&) {}
+};
+#endif // EIGEN_UNORDERED_MAP_SUPPORT
+
+#ifdef _DENSE_HASH_MAP_H_
+/** Represents a google::dense_hash_map
+  *
+  * \see RandomSetter
+  */
+template<typename Scalar> struct GoogleDenseHashMapTraits
+{
+  typedef int KeyType;
+  typedef google::dense_hash_map<KeyType,Scalar> Type;
+  enum {
+    IsSorted = 0
+  };
+
+  static void setInvalidKey(Type& map, const KeyType& k)
+  { map.set_empty_key(k); }
+};
+#endif
+
+#ifdef _SPARSE_HASH_MAP_H_
+/** Represents a google::sparse_hash_map
+  *
+  * \see RandomSetter
+  */
+template<typename Scalar> struct GoogleSparseHashMapTraits
+{
+  typedef int KeyType;
+  typedef google::sparse_hash_map<KeyType,Scalar> Type;
+  enum {
+    IsSorted = 0
+  };
+
+  static void setInvalidKey(Type&, const KeyType&) {}
+};
+#endif
+
+/** \class RandomSetter
+  *
+  * \brief The RandomSetter is a wrapper object allowing to set/update a sparse matrix with random access
+  *
+  * \tparam SparseMatrixType the type of the sparse matrix we are updating
+  * \tparam MapTraits a traits class representing the map implementation used for the temporary sparse storage.
+  *                  Its default value depends on the system.
+  * \tparam OuterPacketBits defines the number of rows (or columns) manage by a single map object
+  *                        as a power of two exponent.
+  *
+  * This class temporarily represents a sparse matrix object using a generic map implementation allowing for
+  * efficient random access. The conversion from the compressed representation to a hash_map object is performed
+  * in the RandomSetter constructor, while the sparse matrix is updated back at destruction time. This strategy
+  * suggest the use of nested blocks as in this example:
+  *
+  * \code
+  * SparseMatrix<double> m(rows,cols);
+  * {
+  *   RandomSetter<SparseMatrix<double> > w(m);
+  *   // don't use m but w instead with read/write random access to the coefficients:
+  *   for(;;)
+  *     w(rand(),rand()) = rand;
+  * }
+  * // when w is deleted, the data are copied back to m
+  * // and m is ready to use.
+  * \endcode
+  *
+  * Since hash_map objects are not fully sorted, representing a full matrix as a single hash_map would
+  * involve a big and costly sort to update the compressed matrix back. To overcome this issue, a RandomSetter
+  * use multiple hash_map, each representing 2^OuterPacketBits columns or rows according to the storage order.
+  * To reach optimal performance, this value should be adjusted according to the average number of nonzeros
+  * per rows/columns.
+  *
+  * The possible values for the template parameter MapTraits are:
+  *  - \b StdMapTraits: corresponds to std::map. (does not perform very well)
+  *  - \b GnuHashMapTraits: corresponds to __gnu_cxx::hash_map (available only with GCC)
+  *  - \b GoogleDenseHashMapTraits: corresponds to google::dense_hash_map (best efficiency, reasonable memory consumption)
+  *  - \b GoogleSparseHashMapTraits: corresponds to google::sparse_hash_map (best memory consumption, relatively good performance)
+  *
+  * The default map implementation depends on the availability, and the preferred order is:
+  * GoogleSparseHashMapTraits, GnuHashMapTraits, and finally StdMapTraits.
+  *
+  * For performance and memory consumption reasons it is highly recommended to use one of
+  * the Google's hash_map implementation. To enable the support for them, you have two options:
+  *  - \#include <google/dense_hash_map> yourself \b before Eigen/Sparse header
+  *  - define EIGEN_GOOGLEHASH_SUPPORT
+  * In the later case the inclusion of <google/dense_hash_map> is made for you.
+  *
+  * \see http://code.google.com/p/google-sparsehash/
+  */
+template<typename SparseMatrixType,
+         template <typename T> class MapTraits =
+#if defined _DENSE_HASH_MAP_H_
+          GoogleDenseHashMapTraits
+#elif defined _HASH_MAP
+          GnuHashMapTraits
+#else
+          StdMapTraits
+#endif
+         ,int OuterPacketBits = 6>
+class RandomSetter
+{
+    typedef typename SparseMatrixType::Scalar Scalar;
+    typedef typename SparseMatrixType::StorageIndex StorageIndex;
+
+    struct ScalarWrapper
+    {
+      ScalarWrapper() : value(0) {}
+      Scalar value;
+    };
+    typedef typename MapTraits<ScalarWrapper>::KeyType KeyType;
+    typedef typename MapTraits<ScalarWrapper>::Type HashMapType;
+    static const int OuterPacketMask = (1 << OuterPacketBits) - 1;
+    enum {
+      SwapStorage = 1 - MapTraits<ScalarWrapper>::IsSorted,
+      TargetRowMajor = (SparseMatrixType::Flags & RowMajorBit) ? 1 : 0,
+      SetterRowMajor = SwapStorage ? 1-TargetRowMajor : TargetRowMajor
+    };
+
+  public:
+
+    /** Constructs a random setter object from the sparse matrix \a target
+      *
+      * Note that the initial value of \a target are imported. If you want to re-set
+      * a sparse matrix from scratch, then you must set it to zero first using the
+      * setZero() function.
+      */
+    inline RandomSetter(SparseMatrixType& target)
+      : mp_target(&target)
+    {
+      const Index outerSize = SwapStorage ? target.innerSize() : target.outerSize();
+      const Index innerSize = SwapStorage ? target.outerSize() : target.innerSize();
+      m_outerPackets = outerSize >> OuterPacketBits;
+      if (outerSize&OuterPacketMask)
+        m_outerPackets += 1;
+      m_hashmaps = new HashMapType[m_outerPackets];
+      // compute number of bits needed to store inner indices
+      Index aux = innerSize - 1;
+      m_keyBitsOffset = 0;
+      while (aux)
+      {
+        ++m_keyBitsOffset;
+        aux = aux >> 1;
+      }
+      KeyType ik = (1<<(OuterPacketBits+m_keyBitsOffset));
+      for (Index k=0; k<m_outerPackets; ++k)
+        MapTraits<ScalarWrapper>::setInvalidKey(m_hashmaps[k],ik);
+
+      // insert current coeffs
+      for (Index j=0; j<mp_target->outerSize(); ++j)
+        for (typename SparseMatrixType::InnerIterator it(*mp_target,j); it; ++it)
+          (*this)(TargetRowMajor?j:it.index(), TargetRowMajor?it.index():j) = it.value();
+    }
+
+    /** Destructor updating back the sparse matrix target */
+    ~RandomSetter()
+    {
+      KeyType keyBitsMask = (1<<m_keyBitsOffset)-1;
+      if (!SwapStorage) // also means the map is sorted
+      {
+        mp_target->setZero();
+        mp_target->makeCompressed();
+        mp_target->reserve(nonZeros());
+        Index prevOuter = -1;
+        for (Index k=0; k<m_outerPackets; ++k)
+        {
+          const Index outerOffset = (1<<OuterPacketBits) * k;
+          typename HashMapType::iterator end = m_hashmaps[k].end();
+          for (typename HashMapType::iterator it = m_hashmaps[k].begin(); it!=end; ++it)
+          {
+            const Index outer = (it->first >> m_keyBitsOffset) + outerOffset;
+            const Index inner = it->first & keyBitsMask;
+            if (prevOuter!=outer)
+            {
+              for (Index j=prevOuter+1;j<=outer;++j)
+                mp_target->startVec(j);
+              prevOuter = outer;
+            }
+            mp_target->insertBackByOuterInner(outer, inner) = it->second.value;
+          }
+        }
+        mp_target->finalize();
+      }
+      else
+      {
+        VectorXi positions(mp_target->outerSize());
+        positions.setZero();
+        // pass 1
+        for (Index k=0; k<m_outerPackets; ++k)
+        {
+          typename HashMapType::iterator end = m_hashmaps[k].end();
+          for (typename HashMapType::iterator it = m_hashmaps[k].begin(); it!=end; ++it)
+          {
+            const Index outer = it->first & keyBitsMask;
+            ++positions[outer];
+          }
+        }
+        // prefix sum
+        Index count = 0;
+        for (Index j=0; j<mp_target->outerSize(); ++j)
+        {
+          Index tmp = positions[j];
+          mp_target->outerIndexPtr()[j] = count;
+          positions[j] = count;
+          count += tmp;
+        }
+        mp_target->makeCompressed();
+        mp_target->outerIndexPtr()[mp_target->outerSize()] = count;
+        mp_target->resizeNonZeros(count);
+        // pass 2
+        for (Index k=0; k<m_outerPackets; ++k)
+        {
+          const Index outerOffset = (1<<OuterPacketBits) * k;
+          typename HashMapType::iterator end = m_hashmaps[k].end();
+          for (typename HashMapType::iterator it = m_hashmaps[k].begin(); it!=end; ++it)
+          {
+            const Index inner = (it->first >> m_keyBitsOffset) + outerOffset;
+            const Index outer = it->first & keyBitsMask;
+            // sorted insertion
+            // Note that we have to deal with at most 2^OuterPacketBits unsorted coefficients,
+            // moreover those 2^OuterPacketBits coeffs are likely to be sparse, an so only a
+            // small fraction of them have to be sorted, whence the following simple procedure:
+            Index posStart = mp_target->outerIndexPtr()[outer];
+            Index i = (positions[outer]++) - 1;
+            while ( (i >= posStart) && (mp_target->innerIndexPtr()[i] > inner) )
+            {
+              mp_target->valuePtr()[i+1] = mp_target->valuePtr()[i];
+              mp_target->innerIndexPtr()[i+1] = mp_target->innerIndexPtr()[i];
+              --i;
+            }
+            mp_target->innerIndexPtr()[i+1] = inner;
+            mp_target->valuePtr()[i+1] = it->second.value;
+          }
+        }
+      }
+      delete[] m_hashmaps;
+    }
+
+    /** \returns a reference to the coefficient at given coordinates \a row, \a col */
+    Scalar& operator() (Index row, Index col)
+    {
+      const Index outer = SetterRowMajor ? row : col;
+      const Index inner = SetterRowMajor ? col : row;
+      const Index outerMajor = outer >> OuterPacketBits; // index of the packet/map
+      const Index outerMinor = outer & OuterPacketMask;  // index of the inner vector in the packet
+      const KeyType key = internal::convert_index<KeyType>((outerMinor<<m_keyBitsOffset) | inner);
+      return m_hashmaps[outerMajor][key].value;
+    }
+
+    /** \returns the number of non zero coefficients
+      *
+      * \note According to the underlying map/hash_map implementation,
+      * this function might be quite expensive.
+      */
+    Index nonZeros() const
+    {
+      Index nz = 0;
+      for (Index k=0; k<m_outerPackets; ++k)
+        nz += static_cast<Index>(m_hashmaps[k].size());
+      return nz;
+    }
+
+
+  protected:
+
+    HashMapType* m_hashmaps;
+    SparseMatrixType* mp_target;
+    Index m_outerPackets;
+    unsigned char m_keyBitsOffset;
+};
+
+} // end namespace Eigen
+
+#endif // EIGEN_RANDOMSETTER_H

src/libslic3r/SLA/SLASupportTree.cpp

@@ -612,7 +612,9 @@ double ray_mesh_intersect(const Vec3d& s,
                           const Vec3d& dir,
                           const EigenMesh3D& m);
 
-PointSet normals(const PointSet& points, const EigenMesh3D& mesh);
+PointSet normals(const PointSet& points, const EigenMesh3D& mesh,
+                 double eps = 0.05,  // min distance from edges
+                 std::function<void()> throw_on_cancel = [](){});
 
 inline Vec2d to_vec2(const Vec3d& v3) {
     return {v3(X), v3(Y)};
@@ -1049,7 +1051,7 @@ bool SLASupportTree::generate(const PointSet &points,
         tifcl();
 
         // calculate the normals to the triangles belonging to filtered points
-        auto nmls = sla::normals(filt_pts, mesh);
+        auto nmls = sla::normals(filt_pts, mesh, cfg.head_front_radius_mm, tifcl);
 
         head_norm.resize(count, 3);
         head_pos.resize(count, 3);

src/libslic3r/SLA/SLASupportTreeIGL.cpp

@@ -1,3 +1,4 @@
+#include <cmath>
 #include "SLA/SLASupportTree.hpp"
 #include "SLA/SLABoilerPlate.hpp"
 #include "SLA/SLASpatIndex.hpp"
@@ -9,15 +10,8 @@
 #include "boost/geometry/index/rtree.hpp"
 
 #include <igl/ray_mesh_intersect.h>
-
-//#if !defined(_MSC_VER) || defined(_WIN64)
-#if 1
-#define IGL_COMPATIBLE
-#endif
-
-#ifdef IGL_COMPATIBLE
 #include <igl/point_mesh_squared_distance.h>
-#endif
+#include <igl/remove_duplicate_vertices.h>
 
 #include "SLASpatIndex.hpp"
 #include "ClipperUtils.hpp"
@@ -84,33 +78,124 @@ size_t SpatIndex::size() const
     return m_impl->m_store.size();
 }
 
-PointSet normals(const PointSet& points, const EigenMesh3D& mesh) {
+bool point_on_edge(const Vec3d& p, const Vec3d& e1, const Vec3d& e2,
-    if(points.rows() == 0 || mesh.V.rows() == 0 || mesh.F.rows() == 0) return {};
+                   double eps = 0.05)
-#ifdef IGL_COMPATIBLE
+{
+    using Line3D = Eigen::ParametrizedLine<double, 3>;
+
+    auto line = Line3D::Through(e1, e2);
+    double d = line.distance(p);
+    return std::abs(d) < eps;
+}
+
+template<class Vec> double distance(const Vec& pp1, const Vec& pp2) {
+    auto p = pp2 - pp1;
+    return std::sqrt(p.transpose() * p);
+}
+
+PointSet normals(const PointSet& points, const EigenMesh3D& emesh,
+                 double eps,
+                 std::function<void()> throw_on_cancel) {
+    if(points.rows() == 0 || emesh.V.rows() == 0 || emesh.F.rows() == 0)
+        return {};
+
     Eigen::VectorXd dists;
     Eigen::VectorXi I;
     PointSet C;
 
+    // We need to remove duplicate vertices and have a true index triangle
+    // structure
+    EigenMesh3D  mesh;
+    Eigen::VectorXi SVI, SVJ;
+    igl::remove_duplicate_vertices(emesh.V, emesh.F, 1e-6,
+                                   mesh.V, SVI, SVJ, mesh.F);
+
     igl::point_mesh_squared_distance( points, mesh.V, mesh.F, dists, I, C);
 
     PointSet ret(I.rows(), 3);
     for(int i = 0; i < I.rows(); i++) {
+        throw_on_cancel();
         auto idx = I(i);
         auto trindex = mesh.F.row(idx);
 
-        auto& p1 = mesh.V.row(trindex(0));
+        const Vec3d& p1 = mesh.V.row(trindex(0));
-        auto& p2 = mesh.V.row(trindex(1));
+        const Vec3d& p2 = mesh.V.row(trindex(1));
-        auto& p3 = mesh.V.row(trindex(2));
+        const Vec3d& p3 = mesh.V.row(trindex(2));
 
+        // We should check if the point lies on an edge of the hosting triangle.
+        // If it does than all the other triangles using the same two points
+        // have to be searched and the final normal should be some kind of
+        // aggregation of the participating triangle normals. We should also
+        // consider the cases where the support point lies right on a vertex
+        // of its triangle. The procedure is the same, get the neighbor
+        // triangles and calculate an average normal.
+
+        const Vec3d& p = C.row(i);
+
+        // mark the vertex indices of the edge. ia and ib marks and edge ic
+        // will mark a single vertex.
+        int ia = -1, ib = -1, ic = -1;
+
+        if(std::abs(distance(p, p1)) < eps) {
+            ic = trindex(0);
+        }
+        else if(std::abs(distance(p, p2)) < eps) {
+            ic = trindex(1);
+        }
+        else if(std::abs(distance(p, p3)) < eps) {
+            ic = trindex(2);
+        }
+        else if(point_on_edge(p, p1, p2, eps)) {
+            ia = trindex(0); ib = trindex(1);
+        }
+        else if(point_on_edge(p, p2, p3, eps)) {
+            ia = trindex(1); ib = trindex(2);
+        }
+        else if(point_on_edge(p, p1, p3, eps)) {
+            ia = trindex(0); ib = trindex(2);
+        }
+
+        std::vector<Vec3i> neigh;
+        if(ic >= 0) { // The point is right on a vertex of the triangle
+            for(int n = 0; n < mesh.F.rows(); ++n) {
+                throw_on_cancel();
+                Vec3i ni = mesh.F.row(n);
+                if((ni(X) == ic || ni(Y) == ic || ni(Z) == ic))
+                    neigh.emplace_back(ni);
+            }
+        }
+        else if(ia >= 0 && ib >= 0) { // the point is on and edge
+            // now get all the neigboring triangles
+            for(int n = 0; n < mesh.F.rows(); ++n) {
+                throw_on_cancel();
+                Vec3i ni = mesh.F.row(n);
+                if((ni(X) == ia || ni(Y) == ia || ni(Z) == ia) &&
+                   (ni(X) == ib || ni(Y) == ib || ni(Z) == ib))
+                    neigh.emplace_back(ni);
+            }
+        }
+
+        if(!neigh.empty()) { // there were neighbors to count with
+            Vec3d sumnorm(0, 0, 0);
+            for(const Vec3i& tri : neigh) {
+                const Vec3d& pt1 = mesh.V.row(tri(0));
+                const Vec3d& pt2 = mesh.V.row(tri(1));
+                const Vec3d& pt3 = mesh.V.row(tri(2));
+                Eigen::Vector3d U = pt2 - pt1;
+                Eigen::Vector3d V = pt3 - pt1;
+                sumnorm += U.cross(V).normalized();
+            }
+            sumnorm /= neigh.size();
+            ret.row(i) = sumnorm;
+        }
+        else { // point lies safely within its triangle
             Eigen::Vector3d U = p2 - p1;
             Eigen::Vector3d V = p3 - p1;
             ret.row(i) = U.cross(V).normalized();
         }
+    }
 
     return ret;
-#else // TODO:  do something on 32 bit windows
-    return {};
-#endif
 }
 
 double ray_mesh_intersect(const Vec3d& s,
@@ -223,7 +308,7 @@ Segments model_boundary(const EigenMesh3D& emesh, double offs)
         pp.emplace_back(p);
     }
 
-    ExPolygons merged = union_ex(offset(pp, float(scale_(offs))), true);
+    ExPolygons merged = union_ex(Slic3r::offset(pp, float(scale_(offs))), true);
 
     for(auto& expoly : merged) {
         auto lines = expoly.lines();