sequenzo 0.1.18__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h

@@ -1,431 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 20010-2011 Hauke Heibel <hauke.heibel@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_SPLINE_FITTING_H
-#define EIGEN_SPLINE_FITTING_H
-
-#include <algorithm>
-#include <functional>
-#include <numeric>
-#include <vector>
-
-#include "SplineFwd.h"
-
-#include "../../../../Eigen/LU"
-#include "../../../../Eigen/QR"
-
-namespace Eigen
-{
-  /**
-   * \brief Computes knot averages.
-   * \ingroup Splines_Module
-   *
-   * The knots are computed as
-   * \f{align*}
-   *  u_0 & = \hdots = u_p = 0 \\
-   *  u_{m-p} & = \hdots = u_{m} = 1 \\
-   *  u_{j+p} & = \frac{1}{p}\sum_{i=j}^{j+p-1}\bar{u}_i \quad\quad j=1,\hdots,n-p
-   * \f}
-   * where \f$p\f$ is the degree and \f$m+1\f$ the number knots
-   * of the desired interpolating spline.
-   *
-   * \param[in] parameters The input parameters. During interpolation one for each data point.
-   * \param[in] degree The spline degree which is used during the interpolation.
-   * \param[out] knots The output knot vector.
-   *
-   * \sa Les Piegl and Wayne Tiller, The NURBS book (2nd ed.), 1997, 9.2.1 Global Curve Interpolation to Point Data
-   **/
-  template <typename KnotVectorType>
-  void KnotAveraging(const KnotVectorType& parameters, DenseIndex degree, KnotVectorType& knots)
-  {
-    knots.resize(parameters.size()+degree+1);      
-
-    for (DenseIndex j=1; j<parameters.size()-degree; ++j)
-      knots(j+degree) = parameters.segment(j,degree).mean();
-
-    knots.segment(0,degree+1) = KnotVectorType::Zero(degree+1);
-    knots.segment(knots.size()-degree-1,degree+1) = KnotVectorType::Ones(degree+1);
-  }
-
-  /**
-   * \brief Computes knot averages when derivative constraints are present.
-   * Note that this is a technical interpretation of the referenced article
-   * since the algorithm contained therein is incorrect as written.
-   * \ingroup Splines_Module
-   *
-   * \param[in] parameters The parameters at which the interpolation B-Spline
-   *            will intersect the given interpolation points. The parameters
-   *            are assumed to be a non-decreasing sequence.
-   * \param[in] degree The degree of the interpolating B-Spline. This must be
-   *            greater than zero.
-   * \param[in] derivativeIndices The indices corresponding to parameters at
-   *            which there are derivative constraints. The indices are assumed
-   *            to be a non-decreasing sequence.
-   * \param[out] knots The calculated knot vector. These will be returned as a
-   *             non-decreasing sequence
-   *
-   * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
-   * Curve interpolation with directional constraints for engineering design. 
-   * Engineering with Computers
-   **/
-  template <typename KnotVectorType, typename ParameterVectorType, typename IndexArray>
-  void KnotAveragingWithDerivatives(const ParameterVectorType& parameters,
-                                    const unsigned int degree,
-                                    const IndexArray& derivativeIndices,
-                                    KnotVectorType& knots)
-  {
-    typedef typename ParameterVectorType::Scalar Scalar;
-
-    DenseIndex numParameters = parameters.size();
-    DenseIndex numDerivatives = derivativeIndices.size();
-
-    if (numDerivatives < 1)
-    {
-      KnotAveraging(parameters, degree, knots);
-      return;
-    }
-
-    DenseIndex startIndex;
-    DenseIndex endIndex;
-  
-    DenseIndex numInternalDerivatives = numDerivatives;
-    
-    if (derivativeIndices[0] == 0)
-    {
-      startIndex = 0;
-      --numInternalDerivatives;
-    }
-    else
-    {
-      startIndex = 1;
-    }
-    if (derivativeIndices[numDerivatives - 1] == numParameters - 1)
-    {
-      endIndex = numParameters - degree;
-      --numInternalDerivatives;
-    }
-    else
-    {
-      endIndex = numParameters - degree - 1;
-    }
-
-    // There are (endIndex - startIndex + 1) knots obtained from the averaging
-    // and 2 for the first and last parameters.
-    DenseIndex numAverageKnots = endIndex - startIndex + 3;
-    KnotVectorType averageKnots(numAverageKnots);
-    averageKnots[0] = parameters[0];
-
-    int newKnotIndex = 0;
-    for (DenseIndex i = startIndex; i <= endIndex; ++i)
-      averageKnots[++newKnotIndex] = parameters.segment(i, degree).mean();
-    averageKnots[++newKnotIndex] = parameters[numParameters - 1];
-
-    newKnotIndex = -1;
-  
-    ParameterVectorType temporaryParameters(numParameters + 1);
-    KnotVectorType derivativeKnots(numInternalDerivatives);
-    for (DenseIndex i = 0; i < numAverageKnots - 1; ++i)
-    {
-      temporaryParameters[0] = averageKnots[i];
-      ParameterVectorType parameterIndices(numParameters);
-      int temporaryParameterIndex = 1;
-      for (DenseIndex j = 0; j < numParameters; ++j)
-      {
-        Scalar parameter = parameters[j];
-        if (parameter >= averageKnots[i] && parameter < averageKnots[i + 1])
-        {
-          parameterIndices[temporaryParameterIndex] = j;
-          temporaryParameters[temporaryParameterIndex++] = parameter;
-        }
-      }
-      temporaryParameters[temporaryParameterIndex] = averageKnots[i + 1];
-
-      for (int j = 0; j <= temporaryParameterIndex - 2; ++j)
-      {
-        for (DenseIndex k = 0; k < derivativeIndices.size(); ++k)
-        {
-          if (parameterIndices[j + 1] == derivativeIndices[k]
-              && parameterIndices[j + 1] != 0
-              && parameterIndices[j + 1] != numParameters - 1)
-          {
-            derivativeKnots[++newKnotIndex] = temporaryParameters.segment(j, 3).mean();
-            break;
-          }
-        }
-      }
-    }
-    
-    KnotVectorType temporaryKnots(averageKnots.size() + derivativeKnots.size());
-
-    std::merge(averageKnots.data(), averageKnots.data() + averageKnots.size(),
-               derivativeKnots.data(), derivativeKnots.data() + derivativeKnots.size(),
-               temporaryKnots.data());
-
-    // Number of knots (one for each point and derivative) plus spline order.
-    DenseIndex numKnots = numParameters + numDerivatives + degree + 1;
-    knots.resize(numKnots);
-
-    knots.head(degree).fill(temporaryKnots[0]);
-    knots.tail(degree).fill(temporaryKnots.template tail<1>()[0]);
-    knots.segment(degree, temporaryKnots.size()) = temporaryKnots;
-  }
-
-  /**
-   * \brief Computes chord length parameters which are required for spline interpolation.
-   * \ingroup Splines_Module
-   *
-   * \param[in] pts The data points to which a spline should be fit.
-   * \param[out] chord_lengths The resulting chord length vector.
-   *
-   * \sa Les Piegl and Wayne Tiller, The NURBS book (2nd ed.), 1997, 9.2.1 Global Curve Interpolation to Point Data
-   **/   
-  template <typename PointArrayType, typename KnotVectorType>
-  void ChordLengths(const PointArrayType& pts, KnotVectorType& chord_lengths)
-  {
-    typedef typename KnotVectorType::Scalar Scalar;
-
-    const DenseIndex n = pts.cols();
-
-    // 1. compute the column-wise norms
-    chord_lengths.resize(pts.cols());
-    chord_lengths[0] = 0;
-    chord_lengths.rightCols(n-1) = (pts.array().leftCols(n-1) - pts.array().rightCols(n-1)).matrix().colwise().norm();
-
-    // 2. compute the partial sums
-    std::partial_sum(chord_lengths.data(), chord_lengths.data()+n, chord_lengths.data());
-
-    // 3. normalize the data
-    chord_lengths /= chord_lengths(n-1);
-    chord_lengths(n-1) = Scalar(1);
-  }
-
-  /**
-   * \brief Spline fitting methods.
-   * \ingroup Splines_Module
-   **/     
-  template <typename SplineType>
-  struct SplineFitting
-  {
-    typedef typename SplineType::KnotVectorType KnotVectorType;
-    typedef typename SplineType::ParameterVectorType ParameterVectorType;
-
-    /**
-     * \brief Fits an interpolating Spline to the given data points.
-     *
-     * \param pts The points for which an interpolating spline will be computed.
-     * \param degree The degree of the interpolating spline.
-     *
-     * \returns A spline interpolating the initially provided points.
-     **/
-    template <typename PointArrayType>
-    static SplineType Interpolate(const PointArrayType& pts, DenseIndex degree);
-
-    /**
-     * \brief Fits an interpolating Spline to the given data points.
-     *
-     * \param pts The points for which an interpolating spline will be computed.
-     * \param degree The degree of the interpolating spline.
-     * \param knot_parameters The knot parameters for the interpolation.
-     *
-     * \returns A spline interpolating the initially provided points.
-     **/
-    template <typename PointArrayType>
-    static SplineType Interpolate(const PointArrayType& pts, DenseIndex degree, const KnotVectorType& knot_parameters);
-
-    /**
-     * \brief Fits an interpolating spline to the given data points and
-     * derivatives.
-     * 
-     * \param points The points for which an interpolating spline will be computed.
-     * \param derivatives The desired derivatives of the interpolating spline at interpolation
-     *                    points.
-     * \param derivativeIndices An array indicating which point each derivative belongs to. This
-     *                          must be the same size as @a derivatives.
-     * \param degree The degree of the interpolating spline.
-     *
-     * \returns A spline interpolating @a points with @a derivatives at those points.
-     *
-     * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
-     * Curve interpolation with directional constraints for engineering design. 
-     * Engineering with Computers
-     **/
-    template <typename PointArrayType, typename IndexArray>
-    static SplineType InterpolateWithDerivatives(const PointArrayType& points,
-                                                 const PointArrayType& derivatives,
-                                                 const IndexArray& derivativeIndices,
-                                                 const unsigned int degree);
-
-    /**
-     * \brief Fits an interpolating spline to the given data points and derivatives.
-     * 
-     * \param points The points for which an interpolating spline will be computed.
-     * \param derivatives The desired derivatives of the interpolating spline at interpolation points.
-     * \param derivativeIndices An array indicating which point each derivative belongs to. This
-     *                          must be the same size as @a derivatives.
-     * \param degree The degree of the interpolating spline.
-     * \param parameters The parameters corresponding to the interpolation points.
-     *
-     * \returns A spline interpolating @a points with @a derivatives at those points.
-     *
-     * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
-     * Curve interpolation with directional constraints for engineering design. 
-     * Engineering with Computers
-     */
-    template <typename PointArrayType, typename IndexArray>
-    static SplineType InterpolateWithDerivatives(const PointArrayType& points,
-                                                 const PointArrayType& derivatives,
-                                                 const IndexArray& derivativeIndices,
-                                                 const unsigned int degree,
-                                                 const ParameterVectorType& parameters);
-  };
-
-  template <typename SplineType>
-  template <typename PointArrayType>
-  SplineType SplineFitting<SplineType>::Interpolate(const PointArrayType& pts, DenseIndex degree, const KnotVectorType& knot_parameters)
-  {
-    typedef typename SplineType::KnotVectorType::Scalar Scalar;      
-    typedef typename SplineType::ControlPointVectorType ControlPointVectorType;      
-
-    typedef Matrix<Scalar,Dynamic,Dynamic> MatrixType;
-
-    KnotVectorType knots;
-    KnotAveraging(knot_parameters, degree, knots);
-
-    DenseIndex n = pts.cols();
-    MatrixType A = MatrixType::Zero(n,n);
-    for (DenseIndex i=1; i<n-1; ++i)
-    {
-      const DenseIndex span = SplineType::Span(knot_parameters[i], degree, knots);
-
-      // The segment call should somehow be told the spline order at compile time.
-      A.row(i).segment(span-degree, degree+1) = SplineType::BasisFunctions(knot_parameters[i], degree, knots);
-    }
-    A(0,0) = 1.0;
-    A(n-1,n-1) = 1.0;
-
-    HouseholderQR<MatrixType> qr(A);
-
-    // Here, we are creating a temporary due to an Eigen issue.
-    ControlPointVectorType ctrls = qr.solve(MatrixType(pts.transpose())).transpose();
-
-    return SplineType(knots, ctrls);
-  }
-
-  template <typename SplineType>
-  template <typename PointArrayType>
-  SplineType SplineFitting<SplineType>::Interpolate(const PointArrayType& pts, DenseIndex degree)
-  {
-    KnotVectorType chord_lengths; // knot parameters
-    ChordLengths(pts, chord_lengths);
-    return Interpolate(pts, degree, chord_lengths);
-  }
-  
-  template <typename SplineType>
-  template <typename PointArrayType, typename IndexArray>
-  SplineType 
-  SplineFitting<SplineType>::InterpolateWithDerivatives(const PointArrayType& points,
-                                                        const PointArrayType& derivatives,
-                                                        const IndexArray& derivativeIndices,
-                                                        const unsigned int degree,
-                                                        const ParameterVectorType& parameters)
-  {
-    typedef typename SplineType::KnotVectorType::Scalar Scalar;      
-    typedef typename SplineType::ControlPointVectorType ControlPointVectorType;
-
-    typedef Matrix<Scalar, Dynamic, Dynamic> MatrixType;
-
-    const DenseIndex n = points.cols() + derivatives.cols();
-    
-    KnotVectorType knots;
-
-    KnotAveragingWithDerivatives(parameters, degree, derivativeIndices, knots);
-    
-    // fill matrix
-    MatrixType A = MatrixType::Zero(n, n);
-
-    // Use these dimensions for quicker populating, then transpose for solving.
-    MatrixType b(points.rows(), n);
-
-    DenseIndex startRow;
-    DenseIndex derivativeStart;
-
-    // End derivatives.
-    if (derivativeIndices[0] == 0)
-    {
-      A.template block<1, 2>(1, 0) << -1, 1;
-      
-      Scalar y = (knots(degree + 1) - knots(0)) / degree;
-      b.col(1) = y*derivatives.col(0);
-      
-      startRow = 2;
-      derivativeStart = 1;
-    }
-    else
-    {
-      startRow = 1;
-      derivativeStart = 0;
-    }
-    if (derivativeIndices[derivatives.cols() - 1] == points.cols() - 1)
-    {
-      A.template block<1, 2>(n - 2, n - 2) << -1, 1;
-
-      Scalar y = (knots(knots.size() - 1) - knots(knots.size() - (degree + 2))) / degree;
-      b.col(b.cols() - 2) = y*derivatives.col(derivatives.cols() - 1);
-    }
-    
-    DenseIndex row = startRow;
-    DenseIndex derivativeIndex = derivativeStart;
-    for (DenseIndex i = 1; i < parameters.size() - 1; ++i)
-    {
-      const DenseIndex span = SplineType::Span(parameters[i], degree, knots);
-
-      if (derivativeIndex < derivativeIndices.size() && derivativeIndices[derivativeIndex] == i)
-      {
-        A.block(row, span - degree, 2, degree + 1)
-          = SplineType::BasisFunctionDerivatives(parameters[i], 1, degree, knots);
-
-        b.col(row++) = points.col(i);
-        b.col(row++) = derivatives.col(derivativeIndex++);
-      }
-      else
-      {
-        A.row(row).segment(span - degree, degree + 1)
-          = SplineType::BasisFunctions(parameters[i], degree, knots);
-        b.col(row++) = points.col(i);
-      }
-    }
-    b.col(0) = points.col(0);
-    b.col(b.cols() - 1) = points.col(points.cols() - 1);
-    A(0,0) = 1;
-    A(n - 1, n - 1) = 1;
-    
-    // Solve
-    FullPivLU<MatrixType> lu(A);
-    ControlPointVectorType controlPoints = lu.solve(MatrixType(b.transpose())).transpose();
-
-    SplineType spline(knots, controlPoints);
-    
-    return spline;
-  }
-  
-  template <typename SplineType>
-  template <typename PointArrayType, typename IndexArray>
-  SplineType
-  SplineFitting<SplineType>::InterpolateWithDerivatives(const PointArrayType& points,
-                                                        const PointArrayType& derivatives,
-                                                        const IndexArray& derivativeIndices,
-                                                        const unsigned int degree)
-  {
-    ParameterVectorType parameters;
-    ChordLengths(points, parameters);
-    return InterpolateWithDerivatives(points, derivatives, derivativeIndices, degree, parameters);
-  }
-}
-
-#endif // EIGEN_SPLINE_FITTING_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h

@@ -1,93 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 20010-2011 Hauke Heibel <hauke.heibel@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_SPLINES_FWD_H
-#define EIGEN_SPLINES_FWD_H
-
-#include "../../../../Eigen/Core"
-
-namespace Eigen
-{
-    template <typename Scalar, int Dim, int Degree = Dynamic> class Spline;
-
-    template < typename SplineType, int DerivativeOrder = Dynamic > struct SplineTraits {};
-
-    /**
-     * \ingroup Splines_Module
-     * \brief Compile-time attributes of the Spline class for Dynamic degree.
-     **/
-    template <typename _Scalar, int _Dim, int _Degree>
-    struct SplineTraits< Spline<_Scalar, _Dim, _Degree>, Dynamic >
-    {
-      typedef _Scalar Scalar; /*!< The spline curve's scalar type. */
-      enum { Dimension = _Dim /*!< The spline curve's dimension. */ };
-      enum { Degree = _Degree /*!< The spline curve's degree. */ };
-
-      enum { OrderAtCompileTime = _Degree==Dynamic ? Dynamic : _Degree+1 /*!< The spline curve's order at compile-time. */ };
-      enum { NumOfDerivativesAtCompileTime = OrderAtCompileTime /*!< The number of derivatives defined for the current spline. */ };
-      
-      enum { DerivativeMemoryLayout = Dimension==1 ? RowMajor : ColMajor /*!< The derivative type's memory layout. */ };
-
-      /** \brief The data type used to store non-zero basis functions. */
-      typedef Array<Scalar,1,OrderAtCompileTime> BasisVectorType;
-
-      /** \brief The data type used to store the values of the basis function derivatives. */
-      typedef Array<Scalar,Dynamic,Dynamic,RowMajor,NumOfDerivativesAtCompileTime,OrderAtCompileTime> BasisDerivativeType;
-      
-      /** \brief The data type used to store the spline's derivative values. */
-      typedef Array<Scalar,Dimension,Dynamic,DerivativeMemoryLayout,Dimension,NumOfDerivativesAtCompileTime> DerivativeType;
-
-      /** \brief The point type the spline is representing. */
-      typedef Array<Scalar,Dimension,1> PointType;
-      
-      /** \brief The data type used to store knot vectors. */
-      typedef Array<Scalar,1,Dynamic> KnotVectorType;
-
-      /** \brief The data type used to store parameter vectors. */
-      typedef Array<Scalar,1,Dynamic> ParameterVectorType;
-      
-      /** \brief The data type representing the spline's control points. */
-      typedef Array<Scalar,Dimension,Dynamic> ControlPointVectorType;
-    };
-
-    /**
-     * \ingroup Splines_Module
-     * \brief Compile-time attributes of the Spline class for fixed degree.
-     *
-     * The traits class inherits all attributes from the SplineTraits of Dynamic degree.
-     **/
-    template < typename _Scalar, int _Dim, int _Degree, int _DerivativeOrder >
-    struct SplineTraits< Spline<_Scalar, _Dim, _Degree>, _DerivativeOrder > : public SplineTraits< Spline<_Scalar, _Dim, _Degree> >
-    {
-      enum { OrderAtCompileTime = _Degree==Dynamic ? Dynamic : _Degree+1 /*!< The spline curve's order at compile-time. */ };
-      enum { NumOfDerivativesAtCompileTime = _DerivativeOrder==Dynamic ? Dynamic : _DerivativeOrder+1 /*!< The number of derivatives defined for the current spline. */ };
-      
-      enum { DerivativeMemoryLayout = _Dim==1 ? RowMajor : ColMajor /*!< The derivative type's memory layout. */ };
-
-      /** \brief The data type used to store the values of the basis function derivatives. */
-      typedef Array<_Scalar,Dynamic,Dynamic,RowMajor,NumOfDerivativesAtCompileTime,OrderAtCompileTime> BasisDerivativeType;
-      
-      /** \brief The data type used to store the spline's derivative values. */      
-      typedef Array<_Scalar,_Dim,Dynamic,DerivativeMemoryLayout,_Dim,NumOfDerivativesAtCompileTime> DerivativeType;
-    };
-
-    /** \brief 2D float B-spline with dynamic degree. */
-    typedef Spline<float,2> Spline2f;
-    
-    /** \brief 3D float B-spline with dynamic degree. */
-    typedef Spline<float,3> Spline3f;
-
-    /** \brief 2D double B-spline with dynamic degree. */
-    typedef Spline<double,2> Spline2d;
-    
-    /** \brief 3D double B-spline with dynamic degree. */
-    typedef Spline<double,3> Spline3d;
-}
-
-#endif // EIGEN_SPLINES_FWD_H