# HG changeset patch
# User Dmitriy Morozov <dmitriy@mrzv.org>
# Date 1336690012 25200
# Node ID 45589223382c54c14e7812aa4709c19c9952b3d8
# Parent ad3aefb5a0e037270aec5b8ca7d292b5b243ec37
Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp
diff -r ad3aefb5a0e0 -r 45589223382c bindings/python/CMakeLists.txt
--- a/bindings/python/CMakeLists.txt Thu May 10 15:42:21 2012 -0700
+++ b/bindings/python/CMakeLists.txt Thu May 10 15:46:52 2012 -0700
@@ -18,7 +18,6 @@
cohomology-persistence.cpp
rips.cpp
distances.cpp
- ../../include/utilities/munkres/munkres.cpp
)
set (bindings_libraries ${libraries})
diff -r ad3aefb5a0e0 -r 45589223382c include/utilities/munkres/matrix.cpp
--- a/include/utilities/munkres/matrix.cpp Thu May 10 15:42:21 2012 -0700
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,231 +0,0 @@
-/*
- * 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];
-}
diff -r ad3aefb5a0e0 -r 45589223382c include/utilities/munkres/matrix.hpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/include/utilities/munkres/matrix.hpp Thu May 10 15:46:52 2012 -0700
@@ -0,0 +1,231 @@
+/*
+ * 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];
+}
diff -r ad3aefb5a0e0 -r 45589223382c include/utilities/munkres/munkres.h
--- a/include/utilities/munkres/munkres.h Thu May 10 15:42:21 2012 -0700
+++ b/include/utilities/munkres/munkres.h Thu May 10 15:46:52 2012 -0700
@@ -46,4 +46,7 @@
int saverow, savecol;
};
+// DM: This is dangerous, but will do for now
+#include "munkres.cpp"
+
#endif /* !defined(_MUNKRES_H_) */