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rdkit/Code/Numerics/Matrix.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.
//
#ifndef __RD_MATRIX_H__
#define __RD_MATRIX_H__
#include <RDGeneral/Invariant.h>
#include "Vector.h"
#include <iostream>
#include <iomanip>
#include <cstring>
#include <boost/smart_ptr.hpp>
//#ifndef INVARIANT_SILENT_METHOD
//#define INVARIANT_SILENT_METHOD
//#endif
namespace RDNumeric {
//! A matrix class for general, non-square matrices
template <class TYPE> class Matrix {
public:
typedef boost::shared_array<TYPE> DATA_SPTR;
//! Initialize with a size.
Matrix(unsigned int nRows, unsigned int nCols) :
d_nRows(nRows), d_nCols(nCols), d_dataSize(nRows*nCols) {
TYPE *data = new TYPE[d_dataSize];
memset(static_cast<void *>(data),0,d_dataSize*sizeof(TYPE));
d_data.reset(data);
};
//! Initialize with a size and default value.
Matrix(unsigned int nRows, unsigned int nCols, TYPE val) :
d_nRows(nRows), d_nCols(nCols), d_dataSize(nRows*nCols) {
TYPE *data = new TYPE[d_dataSize];
unsigned int i;
for (i = 0; i < d_dataSize; i++) {
data[i] = val;
}
d_data.reset(data);
}
//! Initialize from a pointer.
/*!
<b>NOTE:</b> this does not take ownership of the data,
if you delete the data externally, this Matrix will be sad.
*/
Matrix(unsigned int nRows, unsigned int nCols, DATA_SPTR data) :
d_nRows(nRows), d_nCols(nCols), d_dataSize(nRows*nCols) {
d_data = data;
}
//! copy constructor
/*! We make a copy of the other vector's data.
*/
Matrix(const Matrix<TYPE> &other) :
d_nRows(other.numRows()), d_nCols(other.numCols()), d_dataSize(d_nRows*d_nCols) {
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);
}
virtual ~Matrix() {
}
//! returns the number of rows
inline unsigned int numRows() const {
return d_nRows;
}
//! returns the number of columns
inline unsigned int numCols() const {
return d_nCols;
}
inline unsigned int getDataSize() const {
return d_dataSize;
}
//! returns a particular element of the matrix
inline virtual TYPE getVal(unsigned int i, unsigned int j) const {
PRECONDITION(i<d_nRows,"bad index");
PRECONDITION(j<d_nCols,"bad index");
unsigned int id = i*d_nCols + j;
return d_data[id];
}
//! sets a particular element of the matrix
inline virtual void setVal(unsigned int i, unsigned int j, TYPE val) {
PRECONDITION(i<d_nRows,"bad index");
PRECONDITION(j<d_nCols,"bad index");
unsigned int id = i*d_nCols + j;
d_data[id] = val;
}
//! returns a copy of a row of the matrix
inline virtual void getRow(unsigned int i, Vector<TYPE> &row) const {
PRECONDITION(i<d_nRows,"bad index");
PRECONDITION(d_nCols == row.size(), "");
unsigned int id = i*d_nCols;
TYPE *rData = row.getData();
TYPE *data = d_data.get();
memcpy(static_cast<void *>(rData), static_cast<void *>(&data[id]), d_nCols*sizeof(TYPE));
}
//! returns a copy of a column of the matrix
inline virtual void getCol(unsigned int i, Vector<TYPE> &col) const {
PRECONDITION(i<d_nCols,"bad index");
PRECONDITION(d_nRows == col.size(), "");
unsigned int j,id;
TYPE *rData = col.getData();
TYPE *data = d_data.get();
for (j = 0; j < d_nRows; j++) {
id = j*d_nCols + i;
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();
}
//! Copy operator.
/*! We make a copy of the other Matrix's data.
*/
Matrix<TYPE>& assign(const Matrix<TYPE> &other) {
PRECONDITION(d_nRows == other.numRows(), "Num rows mismatch in matrix copying");
PRECONDITION(d_nCols == other.numCols(), "Num cols mismatch in matrix copying");
const TYPE *otherData = other.getData();
TYPE *data = d_data.get();
memcpy(static_cast<void *>(data), static_cast<const void *>(otherData), d_dataSize*sizeof(TYPE));
return *this;
}
//! Matrix addition.
/*! Perform a element by element addition of other Matrix to this Matrix
*/
virtual Matrix<TYPE>& operator+=(const Matrix<TYPE> &other) {
PRECONDITION(d_nRows == other.numRows(), "Num rows mismatch in matrix addition");
PRECONDITION(d_nCols == other.numCols(), "Num cols mismatch in matrix addition");
const TYPE *oData = other.getData();
unsigned int i;
TYPE *data = d_data.get();
for (i = 0; i < d_dataSize; i++) {
data[i] += oData[i];
}
return *this;
}
//! Matrix subtraction.
/*! Perform a element by element subtraction of other Matrix from this Matrix
*/
virtual Matrix<TYPE>& operator-=(const Matrix<TYPE> &other) {
PRECONDITION(d_nRows == other.numRows(), "Num rows mismatch in matrix addition");
PRECONDITION(d_nCols == other.numCols(), "Num cols mismatch in matrix addition");
const TYPE *oData = other.getData();
unsigned int i;
TYPE *data = d_data.get();
for (i = 0; i < d_dataSize; i++) {
data[i] -= oData[i];
}
return *this;
}
//! Multiplication by a scalar
virtual Matrix<TYPE>& operator*=(TYPE scale) {
unsigned int i;
TYPE *data = d_data.get();
for (i = 0; i < d_dataSize; i++) {
data[i] *= scale;
}
return *this;
}
//! division by a scalar
virtual Matrix<TYPE>& operator/=(TYPE scale) {
unsigned int i;
TYPE *data = d_data.get();
for (i = 0; i < d_dataSize; i++) {
data[i] /= scale;
}
return *this;
}
//! copies the transpose of this Matrix into another, returns the result
/*!
\param transpose the Matrix to store the results
\return the transpose of this matrix.
This is just a reference to the argument.
*/
virtual Matrix<TYPE>& transpose(Matrix<TYPE> &transpose) const {
unsigned int tRows = transpose.numRows();
unsigned int tCols = transpose.numCols();
PRECONDITION(d_nCols == tRows, "Size mismatch during transposing");
PRECONDITION(d_nRows == tCols, "Size mismatch during transposing");
unsigned int i, j;
unsigned int idA, idAt, idT;
TYPE *tData = transpose.getData();
TYPE *data = d_data.get();
for (i = 0; i < d_nRows; i++) {
idA = i*d_nCols;
for (j = 0; j < d_nCols; j++) {
idAt = idA + j;
idT = j*tCols + i;
tData[idT] = data[idAt];
}
}
return transpose;
}
protected:
Matrix() : d_nRows(0), d_nCols(0), d_dataSize(0), d_data(){} ;
unsigned int d_nRows;
unsigned int d_nCols;
unsigned int d_dataSize;
DATA_SPTR d_data;
private:
Matrix<TYPE>& operator=(const Matrix<TYPE> &other);
};
//! Matrix multiplication
/*!
Multiply a Matrix A with a second Matrix B
so the result is C = A*B
\param A the the first Matrix used in the multiplication
\param B the Matrix by which to multiply
\param C Matrix to use for the results
\return the results of multiplying A by B.
This is just a reference to C.
*/
template <class TYPE>
Matrix<TYPE>& multiply(const Matrix<TYPE> &A, const Matrix<TYPE> &B,
Matrix<TYPE> &C) {
unsigned int aRows = A.numRows();
unsigned int aCols = A.numCols();
unsigned int cRows = C.numRows();
unsigned int cCols = C.numCols();
unsigned int bRows = B.numRows();
unsigned int bCols = B.numCols();
CHECK_INVARIANT(aCols == bRows, "Size mismatch during multiplication");
CHECK_INVARIANT(aRows == cRows, "Size mismatch during multiplication");
CHECK_INVARIANT(bCols == cCols, "Size mismatch during multiplication");
// we have the sizes check do do the multiplication
TYPE *cData = C.getData();
const TYPE *bData = B.getData();
const TYPE *aData = A.getData();
unsigned int i, j, k;
unsigned int idA, idAt, idB, idC, idCt;
for (i = 0; i < aRows; i++) {
idC = i*cCols;
idA = i*aCols;
for (j = 0; j < cCols; j++) {
idCt = idC + j;
cData[idCt] = (TYPE)0.0;
for (k = 0; k < aCols; k++) {
idAt = idA + k;
idB = k*bCols + j;
cData[idCt] += (aData[idAt]*bData[idB]);
}
}
}
return C;
};
//! Matrix-Vector multiplication
/*!
Multiply a Matrix A with a Vector x
so the result is y = A*x
\param A the matrix used in the multiplication
\param x the Vector by which to multiply
\param y Vector to use for the results
\return the results of multiplying x by this
This is just a reference to y.
*/
template <class TYPE>
Vector<TYPE>& multiply(const Matrix<TYPE> &A, const Vector<TYPE> &x,
Vector<TYPE> &y) {
unsigned int aRows = A.numRows();
unsigned int aCols = A.numCols();
unsigned int xSiz = x.size();
unsigned int ySiz = y.size();
CHECK_INVARIANT(aCols == xSiz, "Size mismatch during multiplication");
CHECK_INVARIANT(aRows == ySiz, "Size mismatch during multiplication");
unsigned int i, j;
unsigned int idA, idAt;
const TYPE *xData = x.getData();
const TYPE *aData = A.getData();
TYPE *yData = y.getData();
for (i = 0; i < aRows; i++) {
idA = i*aCols;
yData[i] = (TYPE)(0.0);
for (j = 0; j < aCols; j++) {
idAt = idA + j;
yData[i] += (aData[idAt]*xData[j]);
}
}
return y;
};
typedef Matrix<double> DoubleMatrix;
};
//! ostream operator for Matrix's
template <class TYPE > std::ostream & operator<<(std::ostream& target,
const RDNumeric::Matrix<TYPE> &mat) {
unsigned int nr = mat.numRows();
unsigned int nc = mat.numCols();
target << "Rows: " << mat.numRows() << " Columns: " << mat.numCols() << "\n";
unsigned int i, j;
for (i = 0; i < nr; i++) {
for (j = 0; j < nc; j++) {
target << std::setw(7) << std::setprecision(3) << mat.getVal(i, j);
}
target << "\n";
}
return target;
}
#endif
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