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b9a5be5a2d
* Remove accidentally tracked files and unset x flag * Ignore ComicNeue * Unify test tag to `reader` * Trivial destructors * Bump CMAKE_CXX_STANDARD to 14 (#4165)
362 lines
9.9 KiB
C++
362 lines
9.9 KiB
C++
//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef __RD_SYMM_MATRIX_H__
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#define __RD_SYMM_MATRIX_H__
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#include "Matrix.h"
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#include "SquareMatrix.h"
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#include <cstring>
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#include <boost/smart_ptr.hpp>
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//#ifndef INVARIANT_SILENT_METHOD
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//#define INVARIANT_SILENT_METHOD
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//#endif
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namespace RDNumeric {
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//! A symmetric matrix class
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/*!
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The data is stored as the lower triangle, so
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A[i,j] = data[i*(i+1) + j] when i >= j and
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A[i,j] = data[j*(j+1) + i] when i < j
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*/
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template <class TYPE>
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class SymmMatrix {
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public:
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typedef boost::shared_array<TYPE> DATA_SPTR;
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explicit SymmMatrix(unsigned int N) : d_size(N), d_dataSize(N * (N + 1) / 2) {
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TYPE *data = new TYPE[d_dataSize];
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memset(static_cast<void *>(data), 0, d_dataSize * sizeof(TYPE));
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d_data.reset(data);
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}
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SymmMatrix(unsigned int N, TYPE val)
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: d_size(N), d_dataSize(N * (N + 1) / 2) {
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TYPE *data = new TYPE[d_dataSize];
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unsigned int i;
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for (i = 0; i < d_dataSize; i++) {
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data[i] = val;
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}
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d_data.reset(data);
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}
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SymmMatrix(unsigned int N, DATA_SPTR data)
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: d_size(N), d_dataSize(N * (N + 1) / 2) {
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d_data = data;
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}
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SymmMatrix(const SymmMatrix<TYPE> &other)
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: d_size(other.numRows()), d_dataSize(other.getDataSize()) {
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TYPE *data = new TYPE[d_dataSize];
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const TYPE *otherData = other.getData();
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memcpy(static_cast<void *>(data), static_cast<const void *>(otherData),
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d_dataSize * sizeof(TYPE));
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d_data.reset(data);
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}
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~SymmMatrix() = default;
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//! returns the number of rows
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inline unsigned int numRows() const { return d_size; }
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//! returns the number of columns
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inline unsigned int numCols() const { return d_size; }
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inline unsigned int getDataSize() const { return d_dataSize; }
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void setToIdentity() {
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TYPE *data = d_data.get();
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memset(static_cast<void *>(data), 0, d_dataSize * sizeof(TYPE));
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for (unsigned int i = 0; i < d_size; i++) {
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data[i * (i + 3) / 2] = (TYPE)1.0;
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}
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}
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TYPE getVal(unsigned int i, unsigned int j) const {
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URANGE_CHECK(i, d_size);
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URANGE_CHECK(j, d_size);
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unsigned int id;
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if (i >= j) {
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id = i * (i + 1) / 2 + j;
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} else {
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id = j * (j + 1) / 2 + i;
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}
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return d_data[id];
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}
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void setVal(unsigned int i, unsigned int j, TYPE val) {
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URANGE_CHECK(i, d_size);
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URANGE_CHECK(j, d_size);
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unsigned int id;
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if (i >= j) {
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id = i * (i + 1) / 2 + j;
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} else {
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id = j * (j + 1) / 2 + i;
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}
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d_data[id] = val;
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}
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void getRow(unsigned int i, Vector<TYPE> &row) {
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CHECK_INVARIANT(d_size == row.size(), "");
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TYPE *rData = row.getData();
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TYPE *data = d_data.get();
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for (unsigned int j = 0; j < d_size; j++) {
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unsigned int id;
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if (j <= i) {
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id = i * (i + 1) / 2 + j;
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} else {
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id = j * (j + 1) / 2 + i;
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}
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rData[j] = data[id];
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}
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}
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void getCol(unsigned int i, Vector<TYPE> &col) {
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CHECK_INVARIANT(d_size == col.size(), "");
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TYPE *rData = col.getData();
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TYPE *data = d_data.get();
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for (unsigned int j = 0; j < d_size; j++) {
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unsigned int id;
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if (i <= j) {
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id = j * (j + 1) / 2 + i;
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} else {
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id = i * (i + 1) / 2 + j;
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}
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rData[j] = data[id];
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}
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}
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//! returns a pointer to our data array
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inline TYPE *getData() { return d_data.get(); }
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//! returns a const pointer to our data array
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inline const TYPE *getData() const { return d_data.get(); }
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SymmMatrix<TYPE> &operator*=(TYPE scale) {
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_dataSize; i++) {
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data[i] *= scale;
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}
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return *this;
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}
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SymmMatrix<TYPE> &operator/=(TYPE scale) {
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_dataSize; i++) {
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data[i] /= scale;
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}
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return *this;
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}
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SymmMatrix<TYPE> &operator+=(const SymmMatrix<TYPE> &other) {
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CHECK_INVARIANT(d_size == other.numRows(),
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"Sizes don't match in the addition");
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const TYPE *oData = other.getData();
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_dataSize; i++) {
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data[i] += oData[i];
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}
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return *this;
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}
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SymmMatrix<TYPE> &operator-=(const SymmMatrix<TYPE> &other) {
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CHECK_INVARIANT(d_size == other.numRows(),
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"Sizes don't match in the addition");
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const TYPE *oData = other.getData();
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_dataSize; i++) {
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data[i] -= oData[i];
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}
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return *this;
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}
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//! in-place matrix multiplication
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SymmMatrix<TYPE> &operator*=(const SymmMatrix<TYPE> &B) {
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CHECK_INVARIANT(d_size == B.numRows(),
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"Size mismatch during multiplication");
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TYPE *cData = new TYPE[d_dataSize];
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const TYPE *bData = B.getData();
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_size; i++) {
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unsigned int idC = i * (i + 1) / 2;
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for (unsigned int j = 0; j < i + 1; j++) {
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unsigned int idCt = idC + j;
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cData[idCt] = (TYPE)0.0;
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for (unsigned int k = 0; k < d_size; k++) {
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unsigned int idA, idB;
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if (k <= i) {
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idA = i * (i + 1) / 2 + k;
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} else {
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idA = k * (k + 1) / 2 + i;
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}
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if (k <= j) {
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idB = j * (j + 1) / 2 + k;
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} else {
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idB = k * (k + 1) / 2 + j;
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}
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cData[idCt] += (data[idA] * bData[idB]);
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}
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}
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}
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for (unsigned int i = 0; i < d_dataSize; i++) {
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data[i] = cData[i];
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}
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delete[] cData;
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return (*this);
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}
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/* Transpose will basically return a copy of itself
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*/
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SymmMatrix<TYPE> &transpose(SymmMatrix<TYPE> &transpose) const {
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CHECK_INVARIANT(d_size == transpose.numRows(),
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"Size mismatch during transposing");
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TYPE *tData = transpose.getData();
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TYPE *data = d_data.get();
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for (unsigned int i = 0; i < d_dataSize; i++) {
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tData[i] = data[i];
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}
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return transpose;
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}
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SymmMatrix<TYPE> &transposeInplace() {
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// nothing to be done we are symmetric
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return (*this);
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}
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protected:
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SymmMatrix() : d_data(0) {}
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unsigned int d_size{0};
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unsigned int d_dataSize{0};
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DATA_SPTR d_data;
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private:
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SymmMatrix<TYPE> &operator=(const SymmMatrix<TYPE> &other);
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};
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//! SymmMatrix-SymmMatrix multiplication
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/*!
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Multiply SymmMatrix A with a second SymmMatrix B
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and write the result to C = A*B
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\param A the first SymmMatrix
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\param B the second SymmMatrix to multiply
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\param C SymmMatrix to use for the results
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\return the results of multiplying A by B.
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This is just a reference to C.
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This method is reimplemented here for efficiency reasons
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(we basically don't want to use getter and setter functions)
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*/
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template <class TYPE>
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SymmMatrix<TYPE> &multiply(const SymmMatrix<TYPE> &A, const SymmMatrix<TYPE> &B,
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SymmMatrix<TYPE> &C) {
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unsigned int aSize = A.numRows();
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CHECK_INVARIANT(B.numRows() == aSize,
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"Size mismatch in matric multiplication");
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CHECK_INVARIANT(C.numRows() == aSize,
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"Size mismatch in matric multiplication");
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TYPE *cData = C.getData();
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const TYPE *aData = A.getData();
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const TYPE *bData = B.getData();
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for (unsigned int i = 0; i < aSize; i++) {
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unsigned int idC = i * (i + 1) / 2;
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for (unsigned int j = 0; j < i + 1; j++) {
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unsigned int idCt = idC + j;
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cData[idCt] = (TYPE)0.0;
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for (unsigned int k = 0; k < aSize; k++) {
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unsigned int idA, idB;
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if (k <= i) {
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idA = i * (i + 1) / 2 + k;
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} else {
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idA = k * (k + 1) / 2 + i;
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}
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if (k <= j) {
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idB = j * (j + 1) / 2 + k;
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} else {
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idB = k * (k + 1) / 2 + j;
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}
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cData[idCt] += (aData[idA] * bData[idB]);
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}
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}
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}
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return C;
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}
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//! SymmMatrix-Vector multiplication
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/*!
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Multiply a SymmMatrix A with a Vector x
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so the result is y = A*x
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\param A the SymmMatrix for multiplication
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\param x the Vector by which to multiply
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\param y Vector to use for the results
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\return the results of multiplying x by A
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This is just a reference to y.
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This method is reimplemented here for efficiency reasons
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(we basically don't want to use getter and setter functions)
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*/
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template <class TYPE>
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Vector<TYPE> &multiply(const SymmMatrix<TYPE> &A, const Vector<TYPE> &x,
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Vector<TYPE> &y) {
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unsigned int aSize = A.numRows();
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CHECK_INVARIANT(aSize == x.size(), "Size mismatch during multiplication");
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CHECK_INVARIANT(aSize == y.size(), "Size mismatch during multiplication");
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const TYPE *xData = x.getData();
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const TYPE *aData = A.getData();
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TYPE *yData = y.getData();
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for (unsigned int i = 0; i < aSize; i++) {
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yData[i] = (TYPE)(0.0);
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unsigned int idA = i * (i + 1) / 2;
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for (unsigned int j = 0; j < i + 1; j++) {
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// idA = i*(i+1)/2 + j;
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yData[i] += (aData[idA] * xData[j]);
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idA++;
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}
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idA--;
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for (unsigned int j = i + 1; j < aSize; j++) {
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// idA = j*(j+1)/2 + i;
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idA += j;
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yData[i] += (aData[idA] * xData[j]);
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}
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}
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return y;
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}
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typedef SymmMatrix<double> DoubleSymmMatrix;
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typedef SymmMatrix<int> IntSymmMatrix;
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typedef SymmMatrix<unsigned int> UintSymmMatrix;
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} // namespace RDNumeric
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//! ostream operator for Matrix's
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template <class TYPE>
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std::ostream &operator<<(std::ostream &target,
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const RDNumeric::SymmMatrix<TYPE> &mat) {
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unsigned int nr = mat.numRows();
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unsigned int nc = mat.numCols();
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target << "Rows: " << mat.numRows() << " Columns: " << mat.numCols() << "\n";
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for (unsigned int i = 0; i < nr; i++) {
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for (unsigned int j = 0; j < nc; j++) {
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target << std::setw(7) << std::setprecision(3) << mat.getVal(i, j);
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}
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target << "\n";
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}
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return target;
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}
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#endif
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