Changeset: 019e5733100a for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=019e5733100a
Added Files:
sql/backends/monet5/k3m/3dtree.c
sql/backends/monet5/k3m/3dtree.h
sql/backends/monet5/k3m/67_k3m.mal
sql/backends/monet5/k3m/67_k3m.sql
sql/backends/monet5/k3m/Makefile.ag
sql/backends/monet5/k3m/Tests/All
sql/backends/monet5/k3m/Tests/k3m.sql
sql/backends/monet5/k3m/k3m.c
sql/backends/monet5/k3m/k3m.mal
sql/backends/monet5/k3m/k3match.h
sql/backends/monet5/k3m/median.c
sql/backends/monet5/k3m/median.h
sql/backends/monet5/k3m/point.c
sql/backends/monet5/k3m/point.h
Modified Files:
configure.ag
sql/backends/monet5/Makefile.ag
Branch: default
Log Message:
K3Match support
diffs (truncated from 920 to 300 lines):
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2209,6 +2209,17 @@ if test "x$have_valgrind" != xno; then
[if test "x$have_valgrind" = xyes; then AC_MSG_ERROR([no
valgrind support found]); fi])
fi
+org_have_k3m=no
+have_k3m=$org_have_k3m
+AC_ARG_WITH(k3m,
+ AS_HELP_STRING([--with-k3m],
+ [include Pim Schellart's K3Match library (default=no)]),
+ have_k3m=$withval)
+if test "x$have_k3m" != xno; then
+ AC_DEFINE(HAVE_K3M, 1, [Define if you want to use the K3Match library])
+fi
+AM_CONDITIONAL(HAVE_K3M, test x"$have_k3m" != xno)
+
# check for sphinxclient
org_have_sphinxclient="auto"
have_sphinxclient=$org_have_sphinxclient
@@ -3454,6 +3465,7 @@ for comp in \
'java ' \
'java_control ' \
'java_jdbc ' \
+ 'k3m ' \
'liblas ' \
'libxml2 ' \
'lidar ' \
diff --git a/sql/backends/monet5/Makefile.ag b/sql/backends/monet5/Makefile.ag
--- a/sql/backends/monet5/Makefile.ag
+++ b/sql/backends/monet5/Makefile.ag
@@ -4,7 +4,7 @@
#
# Copyright 1997 - July 2008 CWI, August 2008 - 2016 MonetDB B.V.
-SUBDIRS = NOT_WIN32?vaults UDF LSST HAVE_GSL?gsl generator
+SUBDIRS = NOT_WIN32?vaults UDF LSST HAVE_GSL?gsl generator HAVE_K3M?k3m
INCLUDES = ../../include ../../common ../../storage ../../server \
../../../monetdb5/modules/atoms \
diff --git a/sql/backends/monet5/k3m/3dtree.c b/sql/backends/monet5/k3m/3dtree.c
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/k3m/3dtree.c
@@ -0,0 +1,230 @@
+/**************************************************************************
+ * This file is part of the K3Match library. *
+ * Copyright (C) 2010 Pim Schellart <p.schell...@astro.ru.nl> *
+ * *
+ * This library 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 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This library 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 library. If not, see <http://www.gnu.org/licenses/>. *
+ **************************************************************************/
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "k3match.h"
+
+#define SQUARE(x) ((x) * (x))
+
+void k3m_build_balanced_tree(node_t *tree, point_t **points, int_t npoints,
int axis, int_t *npool)
+{
+ node_t *current = tree+(*npool);
+
+ int next_axis = (axis + 1) % 3;
+
+ int_t nleft, nright;
+
+ current->left = NULL;
+ current->right = NULL;
+ current->axis = axis;
+
+ current->point = k3m_median(points, npoints, current->axis);
+
+ nright = npoints / 2;
+ nleft = nright - (1 - npoints % 2);
+
+ if (nleft > 0)
+ {
+ (*npool)++;
+ current->left = tree+(*npool);
+ current->left->parent = &(*current);
+ k3m_build_balanced_tree(tree, points, nleft, next_axis, npool);
+ }
+
+ if (nright > 0)
+ {
+ (*npool)++;
+ current->right = tree+(*npool);
+ current->right->parent = &(*current);
+ k3m_build_balanced_tree(tree, points+nleft+1, nright, next_axis, npool);
+ }
+}
+
+void k3m_print_tree(node_t *tree)
+{
+ if (!tree) return;
+
+ k3m_print_tree(tree->left);
+ printf("%lu %f %f %f\n", (unsigned long)tree->point->id,
tree->point->value[0], tree->point->value[1], tree->point->value[2]);
+ k3m_print_tree(tree->right);
+}
+
+void k3m_print_dot_tree(node_t *tree)
+{
+ if (!tree) return;
+
+ if (tree->left != NULL)
+ {
+ printf("%lu -> %lu;\n", (unsigned long)tree->point->id, (unsigned
long)tree->left->point->id);
+ }
+
+ if (tree->right != NULL)
+ {
+ printf("%lu -> %lu;\n", (unsigned long)tree->point->id, (unsigned
long)tree->right->point->id);
+ }
+
+ printf("%lu [label=\"%lu\\n %f %f %f\"];\n", (unsigned long)tree->point->id,
(unsigned long)tree->point->id,
+ tree->point->value[0], tree->point->value[1], tree->point->value[2]);
+
+ k3m_print_dot_tree(tree->left);
+ k3m_print_dot_tree(tree->right);
+}
+
+node_t* k3m_closest_leaf(node_t *tree, point_t *point)
+{
+ node_t* current = tree;
+ node_t* closest = NULL;
+
+ while (current)
+ {
+ closest = current;
+
+ if (point->value[current->axis] > current->point->value[current->axis])
+ {
+ current = current->right;
+ }
+ else
+ {
+ current = current->left;
+ }
+ }
+
+ return closest;
+}
+
+node_t* k3m_nearest_neighbour(node_t *tree, point_t *point)
+{
+ node_t* nearest = k3m_closest_leaf(tree, point);
+ node_t* current = nearest;
+ node_t* sub = NULL;
+ node_t* last = NULL;
+
+ real_t dn = k3m_distance_squared(nearest->point, point);
+ real_t dc = dn;
+ real_t ds;
+
+ while (1)
+ {
+ dc = k3m_distance_squared(current->point, point);
+ if (dc < dn)
+ {
+ nearest = current;
+ dn = dc;
+ }
+
+ if ((current->point->value[current->axis] - point->value[current->axis]) *
(current->point->value[current->axis] - point->value[current->axis]) < dn)
+ {
+ if (last == current->left && current->right != NULL)
+ {
+ sub = k3m_nearest_neighbour(current->right, point);
+
+ ds = k3m_distance_squared(sub->point, point);
+ if (ds < dn)
+ {
+ nearest = sub;
+ dn = ds;
+ }
+ }
+ else if (last == current->right && current->left != NULL)
+ {
+ sub = k3m_nearest_neighbour(current->left, point);
+
+ ds = k3m_distance_squared(sub->point, point);
+ if (ds < dn)
+ {
+ nearest = sub;
+ dn = ds;
+ }
+ }
+ }
+
+ if (current == tree)
+ {
+ break;
+ }
+ else
+ {
+ last = current;
+ current = current->parent;
+ }
+ }
+
+ if (nearest == NULL)
+ {
+ return tree;
+ }
+ else
+ {
+ return nearest;
+ }
+}
+
+int_t k3m_in_range(node_t *tree, point_t **match, point_t *search, real_t ds)
+{
+ node_t* current = tree;
+ real_t d[3] = {0, 0, 0};
+ int_t nmatch = 0;
+ real_t dc = 0;
+ int i = 0;
+
+ while (current)
+ {
+ /* calculate distance from current point to search point */
+ for (i=0; i<3; i++)
+ {
+ d[i] = SQUARE(current->point->value[i] - search->value[i]);
+ }
+ dc = d[0] + d[1] + d[2];
+
+ /* check if current point is within search radius */
+ if (dc < ds)
+ {
+ current->point->ds = dc;
+ current->point->neighbour = *match;
+ *match = &(*current->point);
+ nmatch++;
+ }
+
+ /* next point is on the same side of the partition plane as the search
point */
+ if (search->value[current->axis] > current->point->value[current->axis])
+ {
+ /* check if we need to examine the points on the opposite side */
+ if (d[current->axis] < ds)
+ {
+ nmatch += k3m_in_range(current->left, match, search, ds);
+ }
+
+ current = current->right;
+ }
+ else
+ {
+ /* check if we need to examine the points on the opposite side */
+ if (d[current->axis] < ds)
+ {
+ nmatch += k3m_in_range(current->right, match, search, ds);
+ }
+
+ current = current->left;
+ }
+ }
+
+ return nmatch;
+}
+
diff --git a/sql/backends/monet5/k3m/3dtree.h b/sql/backends/monet5/k3m/3dtree.h
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/k3m/3dtree.h
@@ -0,0 +1,45 @@
+/**************************************************************************
+ * This file is part of the K3Match library. *
+ * Copyright (C) 2010 Pim Schellart <p.schell...@astro.ru.nl> *
+ * *
+ * This library 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 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This library 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 library. If not, see <http://www.gnu.org/licenses/>. *
+ **************************************************************************/
+
+#ifndef __K3MATCH_3DTREE_H__
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