SymmMatrix.h

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//
//  Copyright (C) 2004-2006 Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_SYMM_MATRIX_H__
#define __RD_SYMM_MATRIX_H__
 
#include "Matrix.h"
#include "SquareMatrix.h"
#include <cstring>
#include <boost/smart_ptr.hpp>
 
// #ifndef INVARIANT_SILENT_METHOD
// #define INVARIANT_SILENT_METHOD
// #endif
namespace RDNumeric {
//! A symmetric matrix class
/*!
  The data is stored as the lower triangle, so
   A[i,j] = data[i*(i+1) + j] when i >= j and
   A[i,j] = data[j*(j+1) + i] when i < j
*/
template <class TYPE>
class SymmMatrix {
 public:
  typedef boost::shared_array<TYPE> DATA_SPTR;
 
  explicit SymmMatrix(unsigned int N) : d_size(N), d_dataSize(N * (N + 1) / 2) {
    TYPE *data = new TYPE[d_dataSize];
    memset(static_cast<void *>(data), 0, d_dataSize * sizeof(TYPE));
    d_data.reset(data);
  }
 
  SymmMatrix(unsigned int N, TYPE val)
      : d_size(N), d_dataSize(N * (N + 1) / 2) {
    TYPE *data = new TYPE[d_dataSize];
    unsigned int i;
    for (i = 0; i < d_dataSize; i++) {
      data[i] = val;
    }
    d_data.reset(data);
  }
 
  SymmMatrix(unsigned int N, DATA_SPTR data)
      : d_size(N), d_dataSize(N * (N + 1) / 2) {
    d_data = data;
  }
 
  SymmMatrix(const SymmMatrix<TYPE> &other)
      : d_size(other.numRows()), d_dataSize(other.getDataSize()) {
    TYPE *data = new TYPE[d_dataSize];
    const TYPE *otherData = other.getData();
 
    memcpy(static_cast<void *>(data), static_cast<const void *>(otherData),
           d_dataSize * sizeof(TYPE));
    d_data.reset(data);
  }
 
  ~SymmMatrix() = default;
 
  //! returns the number of rows
  inline unsigned int numRows() const { return d_size; }
 
  //! returns the number of columns
  inline unsigned int numCols() const { return d_size; }
 
  inline unsigned int getDataSize() const { return d_dataSize; }
 
  void setToIdentity() {
    TYPE *data = d_data.get();
    memset(static_cast<void *>(data), 0, d_dataSize * sizeof(TYPE));
    for (unsigned int i = 0; i < d_size; i++) {
      data[i * (i + 3) / 2] = (TYPE)1.0;
    }
  }
 
  TYPE getVal(unsigned int i, unsigned int j) const {
    URANGE_CHECK(i, d_size);
    URANGE_CHECK(j, d_size);
    unsigned int id;
    if (i >= j) {
      id = i * (i + 1) / 2 + j;
    } else {
      id = j * (j + 1) / 2 + i;
    }
    return d_data[id];
  }
 
  void setVal(unsigned int i, unsigned int j, TYPE val) {
    URANGE_CHECK(i, d_size);
    URANGE_CHECK(j, d_size);
    unsigned int id;
    if (i >= j) {
      id = i * (i + 1) / 2 + j;
    } else {
      id = j * (j + 1) / 2 + i;
    }
    d_data[id] = val;
  }
 
  void getRow(unsigned int i, Vector<TYPE> &row) {
    CHECK_INVARIANT(d_size == row.size(), "");
    TYPE *rData = row.getData();
    TYPE *data = d_data.get();
    for (unsigned int j = 0; j < d_size; j++) {
      unsigned int id;
      if (j <= i) {
        id = i * (i + 1) / 2 + j;
      } else {
        id = j * (j + 1) / 2 + i;
      }
      rData[j] = data[id];
    }
  }
 
  void getCol(unsigned int i, Vector<TYPE> &col) {
    CHECK_INVARIANT(d_size == col.size(), "");
    TYPE *rData = col.getData();
    TYPE *data = d_data.get();
    for (unsigned int j = 0; j < d_size; j++) {
      unsigned int id;
      if (i <= j) {
        id = j * (j + 1) / 2 + i;
      } else {
        id = i * (i + 1) / 2 + j;
      }
      rData[j] = data[id];
    }
  }
 
  //! returns a pointer to our data array
  inline TYPE *getData() { return d_data.get(); }
 
  //! returns a const pointer to our data array
  inline const TYPE *getData() const { return d_data.get(); }
 
  SymmMatrix<TYPE> &operator*=(TYPE scale) {
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_dataSize; i++) {
      data[i] *= scale;
    }
    return *this;
  }
 
  SymmMatrix<TYPE> &operator/=(TYPE scale) {
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_dataSize; i++) {
      data[i] /= scale;
    }
    return *this;
  }
 
  SymmMatrix<TYPE> &operator+=(const SymmMatrix<TYPE> &other) {
    CHECK_INVARIANT(d_size == other.numRows(),
                    "Sizes don't match in the addition");
    const TYPE *oData = other.getData();
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_dataSize; i++) {
      data[i] += oData[i];
    }
    return *this;
  }
 
  SymmMatrix<TYPE> &operator-=(const SymmMatrix<TYPE> &other) {
    CHECK_INVARIANT(d_size == other.numRows(),
                    "Sizes don't match in the addition");
    const TYPE *oData = other.getData();
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_dataSize; i++) {
      data[i] -= oData[i];
    }
    return *this;
  }
 
  //! in-place matrix multiplication
  SymmMatrix<TYPE> &operator*=(const SymmMatrix<TYPE> &B) {
    CHECK_INVARIANT(d_size == B.numRows(),
                    "Size mismatch during multiplication");
    TYPE *cData = new TYPE[d_dataSize];
    const TYPE *bData = B.getData();
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_size; i++) {
      unsigned int idC = i * (i + 1) / 2;
      for (unsigned int j = 0; j < i + 1; j++) {
        unsigned int idCt = idC + j;
        cData[idCt] = (TYPE)0.0;
        for (unsigned int k = 0; k < d_size; k++) {
          unsigned int idA, idB;
          if (k <= i) {
            idA = i * (i + 1) / 2 + k;
          } else {
            idA = k * (k + 1) / 2 + i;
          }
          if (k <= j) {
            idB = j * (j + 1) / 2 + k;
          } else {
            idB = k * (k + 1) / 2 + j;
          }
          cData[idCt] += (data[idA] * bData[idB]);
        }
      }
    }
 
    for (unsigned int i = 0; i < d_dataSize; i++) {
      data[i] = cData[i];
    }
    delete[] cData;
    return (*this);
  }
 
  /* Transpose will basically return a copy of itself
   */
  SymmMatrix<TYPE> &transpose(SymmMatrix<TYPE> &transpose) const {
    CHECK_INVARIANT(d_size == transpose.numRows(),
                    "Size mismatch during transposing");
    TYPE *tData = transpose.getData();
    TYPE *data = d_data.get();
    for (unsigned int i = 0; i < d_dataSize; i++) {
      tData[i] = data[i];
    }
    return transpose;
  }
 
  SymmMatrix<TYPE> &transposeInplace() {
    // nothing to be done we are symmetric
    return (*this);
  }
 
 protected:
  SymmMatrix() : d_data(0) {}
  unsigned int d_size{0};
  unsigned int d_dataSize{0};
  DATA_SPTR d_data;
 
 private:
  SymmMatrix<TYPE> &operator=(const SymmMatrix<TYPE> &other);
};
 
//! SymmMatrix-SymmMatrix multiplication
/*!
  Multiply SymmMatrix A with a second SymmMatrix B
  and write the result to C = A*B
 
  \param A  the first SymmMatrix
  \param B  the second SymmMatrix to multiply
  \param C  SymmMatrix to use for the results
 
  \return the results of multiplying A by B.
  This is just a reference to C.
 
  This method is reimplemented here for efficiency reasons
  (we basically don't want to use getter and setter functions)
 
*/
template <class TYPE>
SymmMatrix<TYPE> &multiply(const SymmMatrix<TYPE> &A, const SymmMatrix<TYPE> &B,
                           SymmMatrix<TYPE> &C) {
  unsigned int aSize = A.numRows();
  CHECK_INVARIANT(B.numRows() == aSize,
                  "Size mismatch in matric multiplication");
  CHECK_INVARIANT(C.numRows() == aSize,
                  "Size mismatch in matric multiplication");
  TYPE *cData = C.getData();
  const TYPE *aData = A.getData();
  const TYPE *bData = B.getData();
  for (unsigned int i = 0; i < aSize; i++) {
    unsigned int idC = i * (i + 1) / 2;
    for (unsigned int j = 0; j < i + 1; j++) {
      unsigned int idCt = idC + j;
      cData[idCt] = (TYPE)0.0;
      for (unsigned int k = 0; k < aSize; k++) {
        unsigned int idA, idB;
        if (k <= i) {
          idA = i * (i + 1) / 2 + k;
        } else {
          idA = k * (k + 1) / 2 + i;
        }
        if (k <= j) {
          idB = j * (j + 1) / 2 + k;
        } else {
          idB = k * (k + 1) / 2 + j;
        }
        cData[idCt] += (aData[idA] * bData[idB]);
      }
    }
  }
  return C;
}
 
//! SymmMatrix-Vector multiplication
/*!
  Multiply a SymmMatrix A with a Vector x
  so the result is y = A*x
 
  \param A  the SymmMatrix for multiplication
  \param x  the Vector by which to multiply
  \param y  Vector to use for the results
 
  \return the results of multiplying x by A
  This is just a reference to y.
 
  This method is reimplemented here for efficiency reasons
  (we basically don't want to use getter and setter functions)
 
*/
template <class TYPE>
Vector<TYPE> &multiply(const SymmMatrix<TYPE> &A, const Vector<TYPE> &x,
                       Vector<TYPE> &y) {
  unsigned int aSize = A.numRows();
  CHECK_INVARIANT(aSize == x.size(), "Size mismatch during multiplication");
  CHECK_INVARIANT(aSize == y.size(), "Size mismatch during multiplication");
  const TYPE *xData = x.getData();
  const TYPE *aData = A.getData();
  TYPE *yData = y.getData();
  for (unsigned int i = 0; i < aSize; i++) {
    yData[i] = (TYPE)(0.0);
    unsigned int idA = i * (i + 1) / 2;
    for (unsigned int j = 0; j < i + 1; j++) {
      // idA = i*(i+1)/2 + j;
      yData[i] += (aData[idA] * xData[j]);
      idA++;
    }
    idA--;
    for (unsigned int j = i + 1; j < aSize; j++) {
      // idA = j*(j+1)/2 + i;
      idA += j;
      yData[i] += (aData[idA] * xData[j]);
    }
  }
  return y;
}
 
typedef SymmMatrix<double> DoubleSymmMatrix;
typedef SymmMatrix<int> IntSymmMatrix;
typedef SymmMatrix<unsigned int> UintSymmMatrix;
}  // namespace RDNumeric
 
//! ostream operator for Matrix's
template <class TYPE>
std::ostream &operator<<(std::ostream &target,
                         const RDNumeric::SymmMatrix<TYPE> &mat) {
  unsigned int nr = mat.numRows();
  unsigned int nc = mat.numCols();
  target << "Rows: " << mat.numRows() << " Columns: " << mat.numCols() << "\n";
 
  for (unsigned int i = 0; i < nr; i++) {
    for (unsigned int j = 0; j < nc; j++) {
      target << std::setw(7) << std::setprecision(3) << mat.getVal(i, j);
    }
    target << "\n";
  }
  return target;
}
 
#endif