sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h

@@ -1,153 +0,0 @@
- 
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012  Désiré 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_ORDERING_H
-#define EIGEN_ORDERING_H
-
-namespace Eigen {
-  
-#include "Eigen_Colamd.h"
-
-namespace internal {
-    
-/** \internal
-  * \ingroup OrderingMethods_Module
-  * \param[in] A the input non-symmetric matrix
-  * \param[out] symmat the symmetric pattern A^T+A from the input matrix \a A.
-  * FIXME: The values should not be considered here
-  */
-template<typename MatrixType> 
-void ordering_helper_at_plus_a(const MatrixType& A, MatrixType& symmat)
-{
-  MatrixType C;
-  C = A.transpose(); // NOTE: Could be  costly
-  for (int i = 0; i < C.rows(); i++) 
-  {
-      for (typename MatrixType::InnerIterator it(C, i); it; ++it)
-        it.valueRef() = typename MatrixType::Scalar(0);
-  }
-  symmat = C + A;
-}
-    
-}
-
-/** \ingroup OrderingMethods_Module
-  * \class AMDOrdering
-  *
-  * Functor computing the \em approximate \em minimum \em degree ordering
-  * If the matrix is not structurally symmetric, an ordering of A^T+A is computed
-  * \tparam  StorageIndex The type of indices of the matrix 
-  * \sa COLAMDOrdering
-  */
-template <typename StorageIndex>
-class AMDOrdering
-{
-  public:
-    typedef PermutationMatrix<Dynamic, Dynamic, StorageIndex> PermutationType;
-    
-    /** Compute the permutation vector from a sparse matrix
-     * This routine is much faster if the input matrix is column-major     
-     */
-    template <typename MatrixType>
-    void operator()(const MatrixType& mat, PermutationType& perm)
-    {
-      // Compute the symmetric pattern
-      SparseMatrix<typename MatrixType::Scalar, ColMajor, StorageIndex> symm;
-      internal::ordering_helper_at_plus_a(mat,symm); 
-    
-      // Call the AMD routine 
-      //m_mat.prune(keep_diag());
-      internal::minimum_degree_ordering(symm, perm);
-    }
-    
-    /** Compute the permutation with a selfadjoint matrix */
-    template <typename SrcType, unsigned int SrcUpLo> 
-    void operator()(const SparseSelfAdjointView<SrcType, SrcUpLo>& mat, PermutationType& perm)
-    { 
-      SparseMatrix<typename SrcType::Scalar, ColMajor, StorageIndex> C; C = mat;
-      
-      // Call the AMD routine 
-      // m_mat.prune(keep_diag()); //Remove the diagonal elements 
-      internal::minimum_degree_ordering(C, perm);
-    }
-};
-
-/** \ingroup OrderingMethods_Module
-  * \class NaturalOrdering
-  *
-  * Functor computing the natural ordering (identity)
-  * 
-  * \note Returns an empty permutation matrix
-  * \tparam  StorageIndex The type of indices of the matrix 
-  */
-template <typename StorageIndex>
-class NaturalOrdering
-{
-  public:
-    typedef PermutationMatrix<Dynamic, Dynamic, StorageIndex> PermutationType;
-    
-    /** Compute the permutation vector from a column-major sparse matrix */
-    template <typename MatrixType>
-    void operator()(const MatrixType& /*mat*/, PermutationType& perm)
-    {
-      perm.resize(0); 
-    }
-    
-};
-
-/** \ingroup OrderingMethods_Module
-  * \class COLAMDOrdering
-  *
-  * \tparam  StorageIndex The type of indices of the matrix 
-  * 
-  * Functor computing the \em column \em approximate \em minimum \em degree ordering 
-  * The matrix should be in column-major and \b compressed format (see SparseMatrix::makeCompressed()).
-  */
-template<typename StorageIndex>
-class COLAMDOrdering
-{
-  public:
-    typedef PermutationMatrix<Dynamic, Dynamic, StorageIndex> PermutationType; 
-    typedef Matrix<StorageIndex, Dynamic, 1> IndexVector;
-    
-    /** Compute the permutation vector \a perm form the sparse matrix \a mat
-      * \warning The input sparse matrix \a mat must be in compressed mode (see SparseMatrix::makeCompressed()).
-      */
-    template <typename MatrixType>
-    void operator() (const MatrixType& mat, PermutationType& perm)
-    {
-      eigen_assert(mat.isCompressed() && "COLAMDOrdering requires a sparse matrix in compressed mode. Call .makeCompressed() before passing it to COLAMDOrdering");
-      
-      StorageIndex m = StorageIndex(mat.rows());
-      StorageIndex n = StorageIndex(mat.cols());
-      StorageIndex nnz = StorageIndex(mat.nonZeros());
-      // Get the recommended value of Alen to be used by colamd
-      StorageIndex Alen = internal::Colamd::recommended(nnz, m, n); 
-      // Set the default parameters
-      double knobs [internal::Colamd::NKnobs]; 
-      StorageIndex stats [internal::Colamd::NStats];
-      internal::Colamd::set_defaults(knobs);
-      
-      IndexVector p(n+1), A(Alen); 
-      for(StorageIndex i=0; i <= n; i++)   p(i) = mat.outerIndexPtr()[i];
-      for(StorageIndex i=0; i < nnz; i++)  A(i) = mat.innerIndexPtr()[i];
-      // Call Colamd routine to compute the ordering 
-      StorageIndex info = internal::Colamd::compute_ordering(m, n, Alen, A.data(), p.data(), knobs, stats); 
-      EIGEN_UNUSED_VARIABLE(info);
-      eigen_assert( info && "COLAMD failed " );
-      
-      perm.resize(n);
-      for (StorageIndex i = 0; i < n; i++) perm.indices()(p(i)) = i;
-    }
-};
-
-} // end namespace Eigen
-
-#endif