Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in adaptor.py
/*
* Copyright (c) 2007 John Weaver
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include "matrix.h"
#include <cassert>
#include <cstdlib>
#include <algorithm>
/*export*/ template <class T>
Matrix<T>::Matrix() {
m_rows = 0;
m_columns = 0;
m_matrix = NULL;
}
/*export*/ template <class T>
Matrix<T>::Matrix(const Matrix<T> &other) {
if ( other.m_matrix != NULL ) {
// copy arrays
m_matrix = NULL;
resize(other.m_rows, other.m_columns);
for ( int i = 0 ; i < m_rows ; i++ )
for ( int j = 0 ; j < m_columns ; j++ )
m_matrix[i][j] = other.m_matrix[i][j];
} else {
m_matrix = NULL;
m_rows = 0;
m_columns = 0;
}
}
/*export*/ template <class T>
Matrix<T>::Matrix(int rows, int columns) {
m_matrix = NULL;
resize(rows, columns);
}
/*export*/ template <class T>
Matrix<T> &
Matrix<T>::operator= (const Matrix<T> &other) {
if ( other.m_matrix != NULL ) {
// copy arrays
resize(other.m_rows, other.m_columns);
for ( int i = 0 ; i < m_rows ; i++ )
for ( int j = 0 ; j < m_columns ; j++ )
m_matrix[i][j] = other.m_matrix[i][j];
} else {
// free arrays
for ( int i = 0 ; i < m_columns ; i++ )
delete [] m_matrix[i];
delete [] m_matrix;
m_matrix = NULL;
m_rows = 0;
m_columns = 0;
}
return *this;
}
/*export*/ template <class T>
Matrix<T>::~Matrix() {
if ( m_matrix != NULL ) {
// free arrays
for ( int i = 0 ; i < m_rows ; i++ )
delete [] m_matrix[i];
delete [] m_matrix;
}
m_matrix = NULL;
}
/*export*/ template <class T>
void
Matrix<T>::resize(int rows, int columns) {
if ( m_matrix == NULL ) {
// alloc arrays
m_matrix = new T*[rows]; // rows
for ( int i = 0 ; i < rows ; i++ )
m_matrix[i] = new T[columns]; // columns
m_rows = rows;
m_columns = columns;
clear();
} else {
// save array pointer
T **new_matrix;
// alloc new arrays
new_matrix = new T*[rows]; // rows
for ( int i = 0 ; i < rows ; i++ ) {
new_matrix[i] = new T[columns]; // columns
for ( int j = 0 ; j < columns ; j++ )
new_matrix[i][j] = 0;
}
// copy data from saved pointer to new arrays
int minrows = std::min<int>(rows, m_rows);
int mincols = std::min<int>(columns, m_columns);
for ( int x = 0 ; x < minrows ; x++ )
for ( int y = 0 ; y < mincols ; y++ )
new_matrix[x][y] = m_matrix[x][y];
// delete old arrays
if ( m_matrix != NULL ) {
for ( int i = 0 ; i < m_rows ; i++ )
delete [] m_matrix[i];
delete [] m_matrix;
}
m_matrix = new_matrix;
}
m_rows = rows;
m_columns = columns;
}
/*export*/ template <class T>
void
Matrix<T>::identity() {
assert( m_matrix != NULL );
clear();
int x = std::min<int>(m_rows, m_columns);
for ( int i = 0 ; i < x ; i++ )
m_matrix[i][i] = 1;
}
/*export*/ template <class T>
void
Matrix<T>::clear() {
assert( m_matrix != NULL );
for ( int i = 0 ; i < m_rows ; i++ )
for ( int j = 0 ; j < m_columns ; j++ )
m_matrix[i][j] = 0;
}
/*export*/ template <class T>
T
Matrix<T>::trace() {
assert( m_matrix != NULL );
T value = 0;
int x = std::min<int>(m_rows, m_columns);
for ( int i = 0 ; i < x ; i++ )
value += m_matrix[i][i];
return value;
}
/*export*/ template <class T>
Matrix<T>&
Matrix<T>::transpose() {
assert( m_rows > 0 );
assert( m_columns > 0 );
int new_rows = m_columns;
int new_columns = m_rows;
if ( m_rows != m_columns ) {
// expand matrix
int m = std::max<int>(m_rows, m_columns);
resize(m,m);
}
for ( int i = 0 ; i < m_rows ; i++ ) {
for ( int j = i+1 ; j < m_columns ; j++ ) {
T tmp = m_matrix[i][j];
m_matrix[i][j] = m_matrix[j][i];
m_matrix[j][i] = tmp;
}
}
if ( new_columns != new_rows ) {
// trim off excess.
resize(new_rows, new_columns);
}
return *this;
}
/*export*/ template <class T>
Matrix<T>
Matrix<T>::product(Matrix<T> &other) {
assert( m_matrix != NULL );
assert( other.m_matrix != NULL );
assert ( m_columns == other.m_rows );
Matrix<T> out(m_rows, other.m_columns);
for ( int i = 0 ; i < out.m_rows ; i++ ) {
for ( int j = 0 ; j < out.m_columns ; j++ ) {
for ( int x = 0 ; x < m_columns ; x++ ) {
out(i,j) += m_matrix[i][x] * other.m_matrix[x][j];
}
}
}
return out;
}
/*export*/ template <class T>
T&
Matrix<T>::operator ()(int x, int y) {
assert ( x >= 0 );
assert ( y >= 0 );
assert ( x < m_rows );
assert ( y < m_columns );
assert ( m_matrix != NULL );
return m_matrix[x][y];
}