sequenzo 0.1.17__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl

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

@@ -1,247 +0,0 @@
-
-// 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

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

@@ -1,349 +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>
-//
-// 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
-
-#if defined(EIGEN_GOOGLEHASH_SUPPORT)
-// Ensure the ::google namespace exists, required for checking existence of 
-// ::google::dense_hash_map and ::google::sparse_hash_map.
-namespace google {}
-#endif
-
-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
-
-#if defined(EIGEN_GOOGLEHASH_SUPPORT)
-
-namespace google {
-  
-// Namespace work-around, since sometimes dense_hash_map and sparse_hash_map
-// are in the global namespace, and other times they are under ::google.
-using namespace ::google;
-
-template<typename KeyType, typename Scalar>
-struct DenseHashMap {
-  typedef dense_hash_map<KeyType, Scalar> type;
-};
-
-template<typename KeyType, typename Scalar>
-struct SparseHashMap {
-  typedef sparse_hash_map<KeyType, Scalar> type;
-};
-
-} // namespace google
-
-/** Represents a google::dense_hash_map
-  *
-  * \see RandomSetter
-  */
-template<typename Scalar> struct GoogleDenseHashMapTraits
-{
-  typedef int KeyType;
-  typedef typename google::DenseHashMap<KeyType,Scalar>::type Type;
-  enum {
-    IsSorted = 0
-  };
-
-  static void setInvalidKey(Type& map, const KeyType& k)
-  { map.set_empty_key(k); }
-};
-
-/** Represents a google::sparse_hash_map
-  *
-  * \see RandomSetter
-  */
-template<typename Scalar> struct GoogleSparseHashMapTraits
-{
-  typedef int KeyType;
-  typedef typename google::SparseHashMap<KeyType,Scalar>::type 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
-  * Google's hash_map implementations. To enable the support for them, you must define
-  * EIGEN_GOOGLEHASH_SUPPORT. This will include both <google/dense_hash_map> and
-  * <google/sparse_hash_map> for you.
-  *
-  * \see https://github.com/sparsehash/sparsehash
-  */
-template<typename SparseMatrixType,
-         template <typename T> class MapTraits =
-#if defined(EIGEN_GOOGLEHASH_SUPPORT)
-          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
-        StorageIndex count = 0;
-        for (Index j=0; j<mp_target->outerSize(); ++j)
-        {
-          StorageIndex 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] = internal::convert_index<StorageIndex>(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