Duplicate nodes when removing from kdtree - c

Question

I am writing an algorithm that requires me to search nearest neighbors of points. I found the kdtree library from this post (Using Google's C KD Tree Library) but it does not have a function to delete individual nodes from the tree. So I started to implement my own using
www (dot) geeksforgeeks.org/k-dimensional-tree-set-3-delete/
as a template. It all runs through but unfortunately sometimes nodes get duplicated.
My test case is the following:
#include <stdio.h>
#include <assert.h>
#include <stdlib.h>
#include <math.h>
#include <errno.h>
#include <string.h>
#include <stdarg.h>
#include "kdtree.h"
/* (hopefully) platform independent directory creation */
#if defined(_WIN32) || defined(WIN32) /* this should be defined under windows, regardless of 64 or 32 bit*/
#include <direct.h>
#include <sys/stat.h>
#define GetWorkingDir _getcwd
#define MakeDir(str) _mkdir(str)
#else /* unix based system */
#include <unistd.h>
#include <sys/stat.h>
#define GetWorkingDir getcwd
#define MakeDir(str) mkdir(str, 0777)
#endif
#ifndef MAX_PATH
#define MAX_PATH 260
#endif
void GetLogDir(char* strPath, int nBufSize)
{
if(GetWorkingDir(strPath, nBufSize))
{
strncat(strPath, "/log/", 5);
MakeDir(strPath);
}
else
{
fprintf(stderr, "Could not get working directory");
exit(ENOENT);
}
}
FILE* GetOpenFileHandle(const char* strFilenamePlusPath, const char* strOpenMode)
{
if(strOpenMode == NULL) // too bad we dont have default arguments in C :(
{
strOpenMode = "a+";
}
return(fopen(strFilenamePlusPath, strOpenMode));
}
int CloseFile(FILE* pFile)
{
if(pFile != NULL)
{
fprintf(pFile, "\r\n"); // append a new line before closing!
return(fclose(pFile));
}
fprintf(stderr, "Invalid file handle");
exit(EFAULT);
}
void NodeLabelToFile(FILE* pFile, kdnode* node, const char* strName)
{
fprintf(pFile, "%s [label=\"(%.3f, %.3f)\"] \n", strName, node->pos[0], node->pos[1]);
}
char* NodeToString(kdnode* node, int* num)
{
char* strName = (char*) malloc(MAX_PATH);
if(*num == 0)
{
sprintf(strName, "%s","root");
}
else
{
sprintf(strName, "node%d", *num);
}
return strName;
}
void NodesToFile(FILE* pFile, kdnode* node, const char* strParentname, int* num)
{
if(node && pFile)
{
char* strLeft = NULL;
char* strRight = NULL;
if(node->left)
{
(*num)++;
strLeft = NodeToString(node->left, num);
NodeLabelToFile(pFile, node->left, strLeft);
fprintf(pFile, "%s -> %s \n", strParentname, strLeft);
}
if(node->right)
{
(*num)++;
strRight = NodeToString(node->right, num); // name of the current node
NodeLabelToFile(pFile, node->right, strRight);
fprintf(pFile, "%s -> %s \n", strParentname, strRight);
}
if(strLeft)
{
NodesToFile(pFile, node->left, strLeft, num);
free(strLeft);
}
if(strRight)
{
// (*num)++;
NodesToFile(pFile, node->right, strRight, num);
free(strRight);
}
}
}
FILE* MakeOpenLogFile(const char* strFilename, const char* strOpenMode)
{
if(strOpenMode == NULL)
{
strOpenMode = "a+";
}
char* strFilenamePlusPath = (char*) malloc(MAX_PATH);
GetLogDir(strFilenamePlusPath, MAX_PATH);
strncat(strFilenamePlusPath, strFilename, strlen(strFilename));
FILE* pFile = GetOpenFileHandle(strFilenamePlusPath, strOpenMode);
free(strFilenamePlusPath);
return(pFile);
}
void KDTreeToDotFile(kdtree* Tree, const char* strFilename)
{
if(Tree)
{
FILE* pFile = MakeOpenLogFile(strFilename, "w");
fprintf(pFile, "%s", "digraph d { \n"); // print opening statement for the graph in dot language
// traverse the tree and print the nodes
int* num = (int*) malloc(sizeof(int)); // make this a unique location to make sure numbers can't occur twice
*num = 0;
char* strRoot = NodeToString(Tree->root, num);
NodeLabelToFile(pFile, Tree->root, strRoot);
NodesToFile(pFile, Tree->root, "root", num);
if(strRoot)
{
free(strRoot);
}
free(num);
fprintf(pFile,"%s", "}"); // close the digraph environment
CloseFile(pFile);
}
}
int main(int argc, const char * argv[])
{
int numel = 20;
int toRemove = 19;
double dMax = 3000;
int nNumDim = 2;
printf("init rng");
srand(1234); // seed the rng // srand((unsigned) time(&t));
printf("creating kdtree");
kdtree* TreeRoot = kd_create(nNumDim); // construct the kd tree for the nearest neighbor search
kd_data_destructor(TreeRoot, free); // set free as data destructor
double* pos = (double*) malloc(nNumDim * numel * sizeof(double));
int retval;
for (int ii = 0; ii < numel; ii++)
{
pos[nNumDim * ii] = floor((double)rand()/(double)(RAND_MAX/dMax));
pos[nNumDim * ii + 1] = floor((double)rand()/(double)(RAND_MAX/dMax));
int* randint = (int*) malloc(sizeof(int));
*randint = rand();
retval = kd_insert2(TreeRoot,
pos[nNumDim * ii],
pos[nNumDim * ii + 1],
randint, sizeof(int));
assert(retval == 0);
}
KDTreeToDotFile(TreeRoot, "original.dot");
double* dRemovePos = (double*) malloc(sizeof(double)*nNumDim);
for (int ii = 0; ii < toRemove; ii++)
{
dRemovePos[0] = pos[2*ii];
dRemovePos[1] = pos[2*ii + 1];
kd_remove(TreeRoot, dRemovePos);
}
KDTreeToDotFile(TreeRoot, "removed.dot");
kd_free(TreeRoot); // free kdtree
return 0;
}
and the functions to remove the nodes are implemented like this:
(I don't think if it is too much code, so I only will post my changes to the kd library. If I should add the rest of the code, which is more than 1000 lines unfortunately, just tell me in the comments.)
int kd_remove(kdtree* tree, const double* pos)
{
printf("removing node %.3f, %.3f \n", pos[0], pos[1]);
if(tree->root != NULL)
{
assert(tree->dim != 0); // prevent division by 0 (error code 136)
assert(pos != NULL); // make sure a valid position is passed
tree->root = remove_rec(tree->root, pos, tree->dim, tree->destr, 0);
}
return(0);
}
kdnode* remove_rec(kdnode* node, const double* pos, int dim, void (*destr)(void*), int depth)
{
if(node == NULL)
{
return(NULL);
}
int curdim = depth % dim;
if(same_pos(node->pos, pos, dim))
{
// we found the droid we're looking for
if(node->right)
{
// find the minimum in the right subtree
kdnode* node_min = find_min(node->right, curdim, dim);
if(node_min)
{
copy_node_data(node_min, node, dim);
node->right = remove_rec(node->right, node_min->pos, dim, destr, depth + 1);
}
}
else if(node->left)
{
// find the minimum in the left subtree
kdnode* node_min = find_min(node->left, curdim, dim);
if(node_min)
{
copy_node_data(node_min, node, dim);
node->left = remove_rec(node->left, node_min->pos, dim, destr, depth + 1);
}
}
else
{
// no subtrees -> delete the found node
clear_rec(node, destr);
return(NULL);
}
return node; // return the newly filled node to the recursion step one "above"
}
else
{
// points are not the same, look further
if(pos[curdim] < node->pos[curdim])
{
// position we're looking for is smaller -> go left
node->left = remove_rec(node->left, pos, dim, destr, depth + 1);
}
else
{
// go right, position we're looking for is greater
node->right = remove_rec(node->right, pos, dim, destr, depth + 1);
}
return node;
}
}
void copy_node_data(const kdnode* src, kdnode* dst, int dim)
{
if(src && dst)
{
int nNumBytes = dim * sizeof(double);
memcpy(dst->pos, src->pos, nNumBytes);
if(dst->data != NULL)
{
free(dst->data);
dst->data = malloc(src->databytes);
}
memcpy(dst->data, src->data, src->databytes);
dst->databytes = src->databytes;
}
}
int same_pos(const double* pos1, const double* pos2, int dim)
{
for (int i = 0; i < dim; ++i)
{
if(pos1[i] != pos2[i])
{
return 0; // false
}
}
return 1; // true
}
kdnode* find_min(kdnode* node, int dir, int numdim)
{
return find_min_rec(node, dir, 0, numdim);
}
kdnode* find_min_rec(kdnode* node, int dir, int depth, int numdim)
{
if(!node)
{
return NULL;
}
if(node->left == NULL && node->right == NULL)
{
return node; // is leaf node
}
int curdim = depth % numdim;
if(curdim == numdim)
{
if(node->left == NULL)
{
// no smaller node in tree
return node;
}
else
{
// left subtree is populated -> we need to go deeper
return find_min_rec(node->left, node->dir, depth + 1, numdim);;
}
}
// we have to search both subtrees and find the smallest value compared to the current node
return min_node(node, find_min_rec(node->left, node->dir, depth + 1, numdim),
find_min_rec(node->right, node->dir, depth + 1, numdim), node->dir);
}
kdnode* min_node(kdnode* a, kdnode* left, kdnode* right, int dir)
{
if(a == NULL)
{
// node a is the only one that can't be NULL!
fprintf(stderr, "Error: invalid node passed! \n");
exit(EFAULT);
}
kdnode* result = a;
if(left != NULL)
{
if(left->pos[dir] < result->pos[dir])
{
result = left;
}
}
if(right != NULL)
{
if(right->pos[dir] < result->pos[dir])
{
result = right;
}
}
return result;
}
original.dot looks like this and removed.dot like that.
I've been debugging this since yesterday and I have the feeling it is something really obvious that I am missing here...
Thanks in advance to anyone willing to help :)

Answer 1

You are creating 40 elements
int numel = 20;
int nNumDim = 2;
double* pos = (double*) malloc(nNumDim * numel * sizeof(double)); // Don't cast
but removing only 38
int toRemove = 19;
for (int ii = 0; ii < toRemove; ii++)
{
dRemovePos[0] = pos[nNumDim * ii];
dRemovePos[1] = pos[nNumDim * ii + 1];
kd_remove(TreeRoot, dRemovePos);
}
In the last iteration:
pos[nNumDim * ii]; = pos[2 * 18]; = pos[36];
pos[nNumDim * ii + 1]; = pos[2 * 18 + 1]; = pos[37];
pos[38] and pos[39] are still there.
Change to int toRemove = 20;.
Your code is obfuscated due to the flat array, why don't you declare some type like
struct data {
double el1;
double el2;
};
or
typedef double data[2];
and then
data *value = malloc(numel * sizeof(*value));

Answer 2

So, I know this probably won't be read by anyone but I found the bug after not touching the code for a while and for completeness here is how:
In the find_min() function I start the recursion with depth = 0.
This can cause the split dimension to get messed up and therefore not access all the nodes.
I modified the function to take depth as an argument and pass the recursion depth of remove_rec() like this:
kdnode* node_min = find_min(node->right, curdim, dim, depth + 1);
and
kdnode* node_min = find_min(node->left, curdim, dim, depth + 1);
respectively.