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3dpcp/include/slam6d/Boctree.h
josch 0281b65175 initial commit
2012-09-16 14:33:11 +02:00

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/**
* @file
* @brief Efficient representation of an octree
* @author Jan Elsberg. Automation Group, Jacobs University Bremen gGmbH, Germany.
* @author Kai Lingemann. Institute of Computer Science, University of Osnabrueck, Germany.
* @author Andreas Nuechter. Institute of Computer Science, University of Osnabrueck, Germany.
*/
#ifndef BOCTREE_H
#define BOCTREE_H
#include "searchTree.h"
#include "point_type.h"
#include "data_types.h"
#include "allocator.h"
#include "limits.h"
#include "nnparams.h"
#include "globals.icc"
#include <stdio.h>
#include <vector>
using std::vector;
#include <deque>
using std::deque;
#include <set>
using std::set;
#include <list>
using std::list;
#include <iostream>
#include <fstream>
#include <string>
#if __GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
#define POPCOUNT(mask) __builtin_popcount(mask)
#else
#define POPCOUNT(mask) _my_popcount_3(mask)
#endif
#include <boost/interprocess/offset_ptr.hpp> // to avoid ifdeffing for offset_ptr.get(), use &(*ptr)
namespace { namespace ip = boost::interprocess; }
// forward declaration
template <class T> union bitunion;
/**
* This is our preferred representation for the leaf nodes (as it is the most compact).
* BOctTree makes an array of this, the first containing the number of points (not the
* number of coordinates) stored.
*/
template <class T> union dunion {
T v;
unsigned int length;
dunion() : length(0) {};
};
// typedefs in combination with templates are weird
//typedef dunion<T> pointrep<T>;
#define pointrep union dunion<T>
/**
* This struct represents the nodes of the octree
*
* child_pointer is a relative pointer to the first child of this node, as it is only
* 48 bit this will cause issues on systems with more than 268 TB of memory. All children
* of this node must be stored sequentially. If one of the children is a leaf, that
* child will be a pointer to however a set of points is represented (pointrep *).
*
* valid is a bitmask describing whether the corresponding buckets are filled.
*
* leaf is a bitmask describing whether the correpsonding bucket is a leaf node.
*
* The representation of the bitmask is somewhat inefficient. We use 16 bits for only
* 3^8 possible states, so in essence we could save 3 bits by compression.
*
*/
class bitoct{
public:
#ifdef _MSC_VER
__int64 child_pointer : 48;
unsigned valid : 8;
unsigned leaf : 8;
#else
signed long child_pointer : 48;
unsigned valid : 8;
unsigned leaf : 8;
#endif
/**
* sets the child pointer of parent so it points to child
*/
template <class T>
static inline void link(bitoct &parent, bitunion<T> *child) {
parent.child_pointer = (long)((char*)child - (char*)&parent);
}
/**
* Returns the children of this node (given as parent).
*/
template <class T>
static inline void getChildren(const bitoct &parent, bitunion<T>* &children) {
children = (bitunion<T>*)((char*)&parent + parent.child_pointer);
}
template <class T>
inline bitunion<T>* getChild(unsigned char index) {
bitunion<T> *children = (bitunion<T>*)((char*)this + this->child_pointer);
for (unsigned char i = 0; i < index; i++) {
if ( ( 1 << i ) & valid ) { // if ith node exists
children++;
}
}
return children;
}
};
/**
* This union combines an octree node with a pointer to a set of points. This allows
* us to use both nodes and leaves interchangeably.
*
* points is a pointer to the point representation in use
*
* node is simply the octree node
*
*/
template <class T> union bitunion {
pointrep *points;
//union dunion<T> *points;
bitoct node;
bitunion(pointrep *p) : points(p) {};
bitunion(bitoct b) : node(b) {};
bitunion() : points(0) {
node.child_pointer = 0;
node.valid = 0;
node.leaf = 0;
}; // needed for new []
//! Leaf node: links a pointrep array [length+values] to this union, saved as an offset pointer
static inline void link(bitunion<T>* leaf, pointrep* points) {
// use node child_pointer as offset_ptr, not pointrep
leaf->node.child_pointer = (long)((char*)points - (char*)leaf);
}
//! Leaf node: points in the array
inline T* getPoints() const {
// absolute pointer
//return &(this->points[1].v);
// offset pointer
return reinterpret_cast<T*>(
reinterpret_cast<pointrep*>((char*)this + node.child_pointer) + 1
);
}
//! Leaf node: length in the array
inline unsigned int getLength() const {
// absolute pointer
//return this->points[0].length;
// offset pointer
return (reinterpret_cast<pointrep*>((char*)this + node.child_pointer))[0].length;
}
//! Leaf node: all points
inline pointrep* getPointreps() const {
return reinterpret_cast<pointrep*>((char*)this + node.child_pointer);
}
inline bitunion<T>* getChild(unsigned char index) const {
bitunion<T> *children = (bitunion<T>*)((char*)this + this->node.child_pointer);
for (unsigned char i = 0; i < index; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
children++;
}
}
return children;
}
inline bool isValid(unsigned char index) {
return ( ( 1 << index ) & node.valid );
}
/*
inline pointrep* getChild(unsigned char index) {
bitunion<T> *children = (bitunion<T>*)((char*)this + this->node.child_pointer);
return children[index].points;
}*/
inline bool childIsLeaf(unsigned char index) {
return ( ( 1 << index ) & node.leaf ); // if ith node is leaf get center
}
};
// initialized in Boctree.cc, sequence intialized on startup
extern char amap[8][8];
extern char imap[8][8];
extern char sequence2ci[8][256][8]; // maps preference to index in children array for every valid_mask and every case
/**
* @brief Octree
*
* A cubic bounding box is calculated
* from the given 3D points. Then it
* is recusivly subdivided into smaller
* subboxes
*/
template <typename T>
class BOctTree : public SearchTree {
public:
BOctTree() {
}
template <class P>
BOctTree(P * const* pts, int n, T voxelSize, PointType _pointtype = PointType(), bool _earlystop = false ) : pointtype(_pointtype), earlystop(_earlystop)
{
alloc = new PackedChunkAllocator;
this->voxelSize = voxelSize;
this->POINTDIM = pointtype.getPointDim();
mins = alloc->allocate<T>(POINTDIM);
maxs = alloc->allocate<T>(POINTDIM);
// initialising
for (unsigned int i = 0; i < POINTDIM; i++) {
mins[i] = pts[0][i];
maxs[i] = pts[0][i];
}
for (unsigned int i = 0; i < POINTDIM; i++) {
for (int j = 1; j < n; j++) {
mins[i] = min(mins[i], (T)pts[j][i]);
maxs[i] = max(maxs[i], (T)pts[j][i]);
}
}
center[0] = 0.5 * (mins[0] + maxs[0]);
center[1] = 0.5 * (mins[1] + maxs[1]);
center[2] = 0.5 * (mins[2] + maxs[2]);
size = max(max(0.5 * (maxs[0] - mins[0]), 0.5 * (maxs[1] - mins[1])), 0.5 * (maxs[2] - mins[2]));
size += 1.0; // for numerical reasons we increase size
// calculate new buckets
T newcenter[8][3];
T sizeNew = size / 2.0;
for (unsigned char i = 0; i < 8; i++) {
childcenter(center, newcenter[i], size, i);
}
// set up values
uroot = alloc->allocate<bitunion<T> >();
root = &uroot->node;
countPointsAndQueueFast(pts, n, newcenter, sizeNew, *root, center);
init();
}
BOctTree(std::string filename) {
alloc = new PackedChunkAllocator;
deserialize(filename);
init();
}
template <class P>
BOctTree(vector<P *> &pts, T voxelSize, PointType _pointtype = PointType(), bool _earlystop = false) : earlystop(_earlystop)
{
alloc = new PackedChunkAllocator;
this->voxelSize = voxelSize;
this->POINTDIM = pointtype.getPointDim();
mins = alloc->allocate<T>(POINTDIM);
maxs = alloc->allocate<T>(POINTDIM);
// initialising
for (unsigned int i = 0; i < POINTDIM; i++) {
mins[i] = pts[0][i];
maxs[i] = pts[0][i];
}
for (unsigned int i = 0; i < POINTDIM; i++) {
for (unsigned int j = 1; j < pts.size(); j++) {
mins[i] = min(mins[i], pts[j][i]);
maxs[i] = max(maxs[i], pts[j][i]);
}
}
center[0] = 0.5 * (mins[0] + maxs[0]);
center[1] = 0.5 * (mins[1] + maxs[1]);
center[2] = 0.5 * (mins[2] + maxs[2]);
size = max(max(0.5 * (maxs[0] - mins[0]), 0.5 * (maxs[1] - mins[1])), 0.5 * (maxs[2] - mins[2]));
size += 1.0; // for numerical reasons we increase size
// calculate new buckets
T newcenter[8][3];
T sizeNew = size / 2.0;
for (unsigned char i = 0; i < 8; i++) {
childcenter(center, newcenter[i], size, i);
}
// set up values
uroot = alloc->allocate<bitunion<T> >();
root = &uroot->node;
countPointsAndQueue(pts, newcenter, sizeNew, *root, center);
}
virtual ~BOctTree()
{
if(alloc) {
delete alloc;
}
}
void init() {
// compute maximal depth as well as the size of the smalles leaf
real_voxelSize = size;
max_depth = 1;
while (real_voxelSize > voxelSize) {
real_voxelSize = real_voxelSize/2.0;
max_depth++;
}
child_bit_depth = alloc->allocate<unsigned int>(max_depth);
child_bit_depth_inv = alloc->allocate<unsigned int>(max_depth);
for(int d=0; d < max_depth; d++) {
child_bit_depth[d] = 1 << (max_depth - d - 1);
child_bit_depth_inv[d] = ~child_bit_depth[d];
}
mult = 1.0/real_voxelSize;
add[0] = -center[0] + size;
add[1] = -center[1] + size;
add[2] = -center[2] + size;
largest_index = child_bit_depth[0] * 2 -1;
}
protected:
/**
* Serialization critical variables
*/
//! the root of the octree
ip::offset_ptr<bitoct> root;
ip::offset_ptr<bitunion<T> > uroot;
//! storing the center
T center[3];
//! storing the dimension
T size;
//! storing the voxel size
T voxelSize;
//! The real voxelsize of the leaves
T real_voxelSize;
//! Offset and real voxelsize inverse factor for manipulation points
T add[3];
T mult;
//! Dimension of each point: 3 (xyz) + N (attributes)
unsigned int POINTDIM;
//! storing minimal and maximal values for all dimensions
ip::offset_ptr<T> mins;
ip::offset_ptr<T> maxs;
//! Details of point attributes
PointType pointtype;
//! ?
unsigned char max_depth;
ip::offset_ptr<unsigned int> child_bit_depth;
ip::offset_ptr<unsigned int> child_bit_depth_inv;
int largest_index;
/**
* Serialization uncritical, runtime relevant variables
*/
//! Threadlocal storage of parameters used in SearchTree operations
static NNParams params[100];
/**
* Serialization uncritical, runtime irrelevant variables (constructor-stuff)
*/
//! Whether to stop subdividing at N<10 nodes or not
bool earlystop;
//! Allocator used for creating nodes in the constructor
Allocator* alloc;
public:
inline const T* getMins() const { return &(*mins); }
inline const T* getMaxs() const { return &(*maxs); }
inline const T* getCenter() const { return center; }
inline T getSize() const { return size; }
inline unsigned int getPointdim() const { return POINTDIM; }
inline const bitoct& getRoot() const { return *root; }
inline unsigned int getMaxDepth() const { return max_depth; }
inline void getCenter(double _center[3]) const {
_center[0] = center[0];
_center[1] = center[1];
_center[2] = center[2];
}
void GetOctTreeCenter(vector<T*>&c) { GetOctTreeCenter(c, *root, center, size); }
void GetOctTreeRandom(vector<T*>&c) { GetOctTreeRandom(c, *root); }
void GetOctTreeRandom(vector<T*>&c, unsigned int ptspervoxel) { GetOctTreeRandom(c, ptspervoxel, *root); }
void AllPoints(vector<T *> &vp) { AllPoints(*BOctTree<T>::root, vp); }
long countNodes() { return 1 + countNodes(*root); } // computes number of inner nodes
long countLeaves() { return countLeaves(*root); } // computes number of leaves + points
long countOctLeaves() { return countOctLeaves(*root); } // computes number of leaves
void deserialize(std::string filename ) {
char buffer[sizeof(T) * 20];
T *p = reinterpret_cast<T*>(buffer);
std::ifstream file;
file.open (filename.c_str(), std::ios::in | std::ios::binary);
// read magic bits
file.read(buffer, 2);
if ( buffer[0] != 'X' || buffer[1] != 'T') {
std::cerr << "Not an octree file!!" << endl;
file.close();
return;
}
// read header
pointtype = PointType::deserialize(file);
file.read(buffer, 5 * sizeof(T));
voxelSize = p[0];
center[0] = p[1];
center[1] = p[2];
center[2] = p[3];
size = p[4];
file.read(buffer, sizeof(int));
int *ip = reinterpret_cast<int*>(buffer);
POINTDIM = *ip;
mins = alloc->allocate<T>(POINTDIM);
maxs = alloc->allocate<T>(POINTDIM);
file.read(reinterpret_cast<char*>(&(*mins)), POINTDIM * sizeof(T));
file.read(reinterpret_cast<char*>(&(*maxs)), POINTDIM * sizeof(T));
// read root node
uroot = alloc->allocate<bitunion<T> >();
root = &uroot->node;
deserialize(file, *root);
file.close();
}
static void deserialize(std::string filename, vector<Point> &points ) {
char buffer[sizeof(T) * 20];
std::ifstream file;
file.open (filename.c_str(), std::ios::in | std::ios::binary);
// read magic bits
file.read(buffer, 2);
if ( buffer[0] != 'X' || buffer[1] != 'T') {
std::cerr << "Not an octree file!!" << endl;
file.close();
return;
}
// read header
PointType pointtype = PointType::deserialize(file);
file.read(buffer, 5 * sizeof(T)); // read over voxelsize, center and size
file.read(buffer, sizeof(int));
int *ip = reinterpret_cast<int*>(buffer);
unsigned int POINTDIM = *ip;
file.read(buffer, POINTDIM * sizeof(T));
file.read(buffer, POINTDIM * sizeof(T));
// read root node
deserialize(file, points, pointtype);
file.close();
}
void serialize(std::string filename) {
char buffer[sizeof(T) * 20];
T *p = reinterpret_cast<T*>(buffer);
std::ofstream file;
file.open (filename.c_str(), std::ios::out | std::ios::binary);
// write magic bits
buffer[0] = 'X';
buffer[1] = 'T';
file.write(buffer, 2);
// write header
pointtype.serialize(file);
p[0] = voxelSize;
p[1] = center[0];
p[2] = center[1];
p[3] = center[2];
p[4] = size;
int *ip = reinterpret_cast<int*>(&(buffer[5 * sizeof(T)]));
*ip = POINTDIM;
file.write(buffer, 5 * sizeof(T) + sizeof(int));
for (unsigned int i = 0; i < POINTDIM; i++) {
p[i] = mins[i];
}
for (unsigned int i = 0; i < POINTDIM; i++) {
p[i+POINTDIM] = maxs[i];
}
file.write(buffer, 2*POINTDIM * sizeof(T));
// write root node
serialize(file, *root);
file.close();
}
static PointType readType(std::string filename ) {
char buffer[sizeof(T) * 20];
std::ifstream file;
file.open (filename.c_str(), std::ios::in | std::ios::binary);
// read magic bits
file.read(buffer, 2);
if ( buffer[0] != 'X' || buffer[1] != 'T') {
std::cerr << "Not an octree file!!" << endl;
file.close();
return PointType();
}
// read header
PointType pointtype = PointType::deserialize(file);
file.close();
return pointtype;
}
/**
* Picks the first point in depth first order starting from the given node
*
*/
T* pickPoint(bitoct &node) {
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
// absolute pointer
//return &(children->points[1].v);
// offset pointer
return children->getPoints();
} else { // recurse
return pickPoint(children->node);
}
++children; // next child
}
}
return 0;
}
static void childcenter(const T *pcenter, T *ccenter, T size, unsigned char i) {
switch (i) {
case 0: // 000
ccenter[0] = pcenter[0] - size / 2.0;
ccenter[1] = pcenter[1] - size / 2.0;
ccenter[2] = pcenter[2] - size / 2.0;
break;
case 1: // 001
ccenter[0] = pcenter[0] + size / 2.0;
ccenter[1] = pcenter[1] - size / 2.0;
ccenter[2] = pcenter[2] - size / 2.0;
break;
case 2: // 010
ccenter[0] = pcenter[0] - size / 2.0;
ccenter[1] = pcenter[1] + size / 2.0;
ccenter[2] = pcenter[2] - size / 2.0;
break;
case 3: // 011
ccenter[0] = pcenter[0] + size / 2.0;
ccenter[1] = pcenter[1] + size / 2.0;
ccenter[2] = pcenter[2] - size / 2.0;
break;
case 4: // 100
ccenter[0] = pcenter[0] - size / 2.0;
ccenter[1] = pcenter[1] - size / 2.0;
ccenter[2] = pcenter[2] + size / 2.0;
break;
case 5: // 101
ccenter[0] = pcenter[0] + size / 2.0;
ccenter[1] = pcenter[1] - size / 2.0;
ccenter[2] = pcenter[2] + size / 2.0;
break;
case 6: // 110
ccenter[0] = pcenter[0] - size / 2.0;
ccenter[1] = pcenter[1] + size / 2.0;
ccenter[2] = pcenter[2] + size / 2.0;
break;
case 7: // 111
ccenter[0] = pcenter[0] + size / 2.0;
ccenter[1] = pcenter[1] + size / 2.0;
ccenter[2] = pcenter[2] + size / 2.0;
break;
default:
break;
}
}
static void childcenter(int x, int y, int z, int &cx, int &cy, int &cz, char i, int size) {
switch (i) {
case 0: // 000
cx = x - size ;
cy = y - size ;
cz = z - size ;
break;
case 1: // 001
cx = x + size ;
cy = y - size ;
cz = z - size ;
break;
case 2: // 010
cx = x - size ;
cy = y + size ;
cz = z - size ;
break;
case 3: // 011
cx = x + size ;
cy = y + size ;
cz = z - size ;
break;
case 4: // 100
cx = x - size ;
cy = y - size ;
cz = z + size ;
break;
case 5: // 101
cx = x + size ;
cy = y - size ;
cz = z + size ;
break;
case 6: // 110
cx = x - size ;
cy = y + size ;
cz = z + size ;
break;
case 7: // 111
cx = x + size ;
cy = y + size ;
cz = z + size ;
break;
default:
break;
}
}
protected:
void AllPoints( bitoct &node, vector<T*> &vp) {
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf get center
// absolute pointer
//pointrep *points = children->points;
// offset pointer
pointrep* points = children->getPointreps();
unsigned int length = points[0].length;
T *point = &(points[1].v); // first point
for(unsigned int iterator = 0; iterator < length; iterator++ ) {
//T *p = new T[BOctTree<T>::POINTDIM];
// T *p = new T[3];
// p[0] = point[0]; p[1] = point[1]; p[2] = point[2];
T *p = new T[BOctTree<T>::POINTDIM];
for (unsigned int k = 0; k < BOctTree<T>::POINTDIM; k++)
p[k] = point[k];
vp.push_back(p);
//glVertex3f( point[0], point[1], point[2]);
point+=BOctTree<T>::POINTDIM;
}
} else { // recurse
AllPoints( children->node, vp);
}
++children; // next child
}
}
}
static void deserialize(std::ifstream &f, vector<Point> &vpoints, PointType &pointtype) {
char buffer[2];
pointrep *point = new pointrep[pointtype.getPointDim()];
f.read(buffer, 2);
bitoct node;
node.valid = buffer[0];
node.leaf = buffer[1];
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf read points
pointrep first;
f.read(reinterpret_cast<char*>(&first), sizeof(pointrep));
unsigned int length = first.length; // read first element, which is the length
for (unsigned int k = 0; k < length; k++) {
f.read(reinterpret_cast<char*>(point), sizeof(pointrep) * pointtype.getPointDim()); // read the points
vpoints.push_back( pointtype.createPoint( &(point->v ) ) );
}
} else { // write child
deserialize(f, vpoints, pointtype);
}
}
}
delete [] point;
}
void deserialize(std::ifstream &f, bitoct &node) {
char buffer[2];
f.read(buffer, 2);
node.valid = buffer[0];
node.leaf = buffer[1];
unsigned short n_children = POPCOUNT(node.valid);
// create children
bitunion<T> *children = alloc->allocate<bitunion<T> >(n_children);
bitoct::link(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf read points
pointrep first;
f.read(reinterpret_cast<char*>(&first), sizeof(pointrep));
unsigned int length = first.length; // read first element, which is the length
pointrep *points = alloc->allocate<pointrep> (POINTDIM*length + 1);
// absolute pointer
//children->points = points;
// offset pointer
bitunion<T>::link(children, points);
points[0] = first;
points++;
f.read(reinterpret_cast<char*>(points), sizeof(pointrep) * length * POINTDIM); // read the points
} else { // write child
deserialize(f, children->node);
}
++children; // next child
}
}
}
void serialize(std::ofstream &of, bitoct &node) {
char buffer[2];
buffer[0] = node.valid;
buffer[1] = node.leaf;
of.write(buffer, 2);
// write children
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf write points
// absolute pointer
//pointrep *points = children->points;
// offset pointer
pointrep* points = children->getPointreps();
unsigned int length = points[0].length;
of.write(reinterpret_cast<char*>(points), sizeof(pointrep) * (length * POINTDIM +1));
} else { // write child
serialize(of, children->node);
}
++children; // next child
}
}
}
void GetOctTreeCenter(vector<T*>&c, bitoct &node, T *center, T size) {
T ccenter[3];
bitunion<T> *children;
bitoct::getChildren(node, children);
for (unsigned char i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
childcenter(center, ccenter, size, i); // childrens center
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf get center
T * cp = new T[3];
for (unsigned int iterator = 0; iterator < 3; iterator++) {
cp[iterator] = ccenter[iterator];
}
c.push_back(cp);
} else { // recurse
GetOctTreeCenter(c, children->node, ccenter, size/2.0);
}
++children; // next child
}
}
}
void GetOctTreeRandom(vector<T*>&c, bitoct &node) {
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
// absolute pointer
//pointrep *points = children->points;
// offset pointer
pointrep* points = children->getPointreps();
// new version to ignore leaves with less than 3 points
/*
if(points[0].length > 2) {
for(int tmp = 0; tmp < points[0].length; tmp++) {
T *point = &(points[POINTDIM*tmp+1].v);
c.push_back(point);
}
}
*/
//old version
int tmp = rand(points[0].length);
T *point = &(points[POINTDIM*tmp+1].v);
c.push_back(point);
} else { // recurse
GetOctTreeRandom(c, children->node);
}
++children; // next child
}
}
}
void GetOctTreeRandom(vector<T*>&c, unsigned int ptspervoxel, bitoct &node) {
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
// absolute pointer
//pointrep *points = children->points;
// offset pointer
pointrep* points = children->getPointreps();
unsigned int length = points[0].length;
if (ptspervoxel >= length) {
for (unsigned int j = 0; j < length; j++)
c.push_back(&(points[POINTDIM*j+1].v));
++children; // next child
continue;
}
set<int> indices;
while(indices.size() < ptspervoxel) {
int tmp = rand(length-1);
indices.insert(tmp);
}
for(set<int>::iterator it = indices.begin(); it != indices.end(); it++)
c.push_back(&(points[POINTDIM*(*it)+1].v));
} else { // recurse
GetOctTreeRandom(c, ptspervoxel, children->node);
}
++children; // next child
}
}
}
long countNodes(bitoct &node) {
long result = 0;
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
//++result;
} else { // recurse
result += countNodes(children->node) + 1;
}
++children; // next child
}
}
return result;
}
long countLeaves(bitoct &node) {
long result = 0;
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
long nrpts = children->getLength();
result += POINTDIM*nrpts;
} else { // recurse
result += countLeaves(children->node);
}
++children; // next child
}
}
return result;
}
long countOctLeaves(bitoct &node) {
long result = 0;
bitunion<T> *children;
bitoct::getChildren(node, children);
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
result ++;
} else { // recurse
result += countTrueLeaves(children->node);
}
++children; // next child
}
}
return result;
}
// TODO: is this still needed? nodes and pointreps are all in the Allocator
void deletetNodes(bitoct &node) {
bitunion<T> *children;
bitoct::getChildren(node, children);
bool haschildren = false;
for (short i = 0; i < 8; i++) {
if ( ( 1 << i ) & node.valid ) { // if ith node exists
if ( ( 1 << i ) & node.leaf ) { // if ith node is leaf
// absolute pointer
//delete [] children->points;
// offset pointer
delete [] children->getPointreps();
} else { // recurse
deletetNodes(children->node);
}
++children; // next child
haschildren = true;
}
}
// delete children
if (haschildren) {
bitoct::getChildren(node, children);
}
}
template <class P>
void* branch( bitoct &node, P * const * splitPoints, int n, T _center[3], T _size) {
// if bucket is too small stop building tree
// -----------------------------------------
if ((_size <= voxelSize) || (earlystop && n <= 10) ) {
// copy points
pointrep *points = alloc->allocate<pointrep> (POINTDIM*n + 1);
points[0].length = n;
int i = 1;
for (int j = 0; j < n; j++) {
for (unsigned int iterator = 0; iterator < POINTDIM; iterator++) {
points[i++].v = splitPoints[j][iterator];
}
}
return points;
}
// calculate new buckets
T newcenter[8][3];
T sizeNew;
sizeNew = _size / 2.0;
for (unsigned char i = 0; i < 8; i++) {
childcenter(_center, newcenter[i], _size, i);
}
countPointsAndQueueFast(splitPoints, n, newcenter, sizeNew, node, _center);
return 0;
}
template <class P>
void* branch( bitoct &node, vector<P*> &splitPoints, T _center[3], T _size) {
// if bucket is too small stop building tree
// -----------------------------------------
if ((_size <= voxelSize) || (earlystop && splitPoints.size() <= 10) ) {
// copy points
pointrep *points = alloc->allocate<pointrep> (POINTDIM*splitPoints.size() + 1);
points[0].length = splitPoints.size();
int i = 1;
for (typename vector<P *>::iterator itr = splitPoints.begin();
itr != splitPoints.end(); itr++) {
for (unsigned int iterator = 0; iterator < POINTDIM; iterator++) {
points[i++].v = (*itr)[iterator];
}
}
return points;
}
// calculate new buckets
T newcenter[8][3];
T sizeNew;
sizeNew = _size / 2.0;
for (unsigned char i = 0; i < 8; i++) {
childcenter(_center, newcenter[i], _size, i);
}
countPointsAndQueue(splitPoints, newcenter, sizeNew, node, _center);
return 0;
}
template <class P>
void countPointsAndQueue(vector<P*> &i_points, T center[8][3], T size, bitoct &parent, T *pcenter) {
vector<P*> points[8];
int n_children = 0;
for (typename vector<P *>::iterator itr = i_points.begin(); itr != i_points.end(); itr++) {
points[childIndex<P>(pcenter, *itr)].push_back( *itr );
}
i_points.clear();
vector<P*>().swap(i_points);
for (int j = 0; j < 8; j++) {
if (!points[j].empty()) {
parent.valid = ( 1 << j ) | parent.valid;
++n_children;
}
}
// create children
bitunion<T> *children = alloc->allocate<bitunion<T> >(n_children);
bitoct::link(parent, children);
int count = 0;
for (int j = 0; j < 8; j++) {
if (!points[j].empty()) {
pointrep *c = (pointrep*)branch(children[count].node, points[j], center[j], size); // leaf node
if (c) {
// absolute pointer
//children[count].points = c; // set this child to deque of points
// offset pointer
bitunion<T>::link(&children[count], c);
parent.leaf = ( 1 << j ) | parent.leaf; // remember this is a leaf
}
points[j].clear();
vector<P*>().swap(points[j]);
++count;
}
}
}
template <class P>
void countPointsAndQueueFast(P * const* points, int n, T center[8][3], T size, bitoct &parent, T pcenter[3]) {
P * const *blocks[9];
blocks[0] = points;
blocks[8] = points + n;
fullsort(points, n, pcenter, blocks+1);
int n_children = 0;
for (int j = 0; j < 8; j++) {
// if non-empty set valid flag for this child
if (blocks[j+1] - blocks[j] > 0) {
parent.valid = ( 1 << j ) | parent.valid;
++n_children;
}
}
// create children
bitunion<T> *children = alloc->allocate<bitunion<T> >(n_children);
bitoct::link(parent, children);
int count = 0;
for (int j = 0; j < 8; j++) {
if (blocks[j+1] - blocks[j] > 0) {
pointrep *c = (pointrep*)branch(children[count].node, blocks[j], blocks[j+1] - blocks[j], center[j], size); // leaf node
if (c) {
// absolute pointer
//children[count].points = c; // set this child to vector of points
// offset pointer
bitunion<T>::link(&children[count], c); // set this child to vector of points
parent.leaf = ( 1 << j ) | parent.leaf; // remember this is a leaf
}
++count;
}
}
}
void getByIndex(T *point, T *&points, unsigned int &length) {
unsigned int x,y,z;
x = (point[0] + add[0]) * mult;
y = (point[1] + add[1]) * mult;
z = (point[2] + add[2]) * mult;
bitunion<T> *node = uroot;
unsigned char child_index;
unsigned int child_bit;
unsigned int depth = 0;
while (true) {
child_bit = child_bit_depth[depth];
child_index = ((x & child_bit )!=0) | (((y & child_bit )!=0 )<< 1) | (((z & child_bit )!=0) << 2);
if (node->childIsLeaf(child_index) ) {
node = node->getChild(child_index);
points = node->getPoints();
length = node->getLength();
return;
} else {
node = node->getChild(child_index);
}
depth++;
}
}
template <class P>
inline unsigned char childIndex(const T *center, const P *point) {
return (point[0] > center[0] ) | ((point[1] > center[1] ) << 1) | ((point[2] > center[2] ) << 2) ;
}
/**
* Given a leaf node, this function looks for the closest point to params[threadNum].closest
* in the list of points.
*/
inline void findClosestInLeaf(bitunion<T> *node, int threadNum) const {
if (params[threadNum].count >= params[threadNum].max_count) return;
params[threadNum].count++;
T* points = node->getPoints();
unsigned int length = node->getLength();
for(unsigned int iterator = 0; iterator < length; iterator++ ) {
double myd2 = Dist2(params[threadNum].p, points);
if (myd2 < params[threadNum].closest_d2) {
params[threadNum].closest_d2 = myd2;
params[threadNum].closest = points;
if (myd2 <= 0.0001) {
params[threadNum].closest_v = 0; // the search radius in units of voxelSize
} else {
params[threadNum].closest_v = sqrt(myd2) * mult + 1; // the search radius in units of voxelSize
}
}
points+=BOctTree<T>::POINTDIM;
}
}
/**
* This function finds the closest point in the octree given a specified
* radius. This implementation is quit complex, although it is already
* simplified. The simplification incurs a significant loss in speed, as
* several calculations have to be performed repeatedly and a high number of
* unnecessary jumps are executed.
*/
double *FindClosest(double *point, double maxdist2, int threadNum) const
{
params[threadNum].closest = 0; // no point found currently
params[threadNum].closest_d2 = maxdist2;
params[threadNum].p = point;
params[threadNum].x = (point[0] + add[0]) * mult;
params[threadNum].y = (point[1] + add[1]) * mult;
params[threadNum].z = (point[2] + add[2]) * mult;
params[threadNum].closest_v = sqrt(maxdist2) * mult + 1; // the search radius in units of voxelSize
params[threadNum].count = 0;
params[threadNum].max_count = 10000; // stop looking after this many buckets
// box within bounds in voxel coordinates
int xmin, ymin, zmin, xmax, ymax, zmax;
xmin = max(params[threadNum].x-params[threadNum].closest_v, 0);
ymin = max(params[threadNum].y-params[threadNum].closest_v, 0);
zmin = max(params[threadNum].z-params[threadNum].closest_v, 0);
// int largest_index = child_bit_depth[0] * 2 -1;
xmax = min(params[threadNum].x+params[threadNum].closest_v, largest_index);
ymax = min(params[threadNum].y+params[threadNum].closest_v, largest_index);
zmax = min(params[threadNum].z+params[threadNum].closest_v, largest_index);
unsigned char depth = 0;
unsigned int child_bit;
unsigned int child_index_min;
unsigned int child_index_max;
bitunion<T> *node = &(*uroot);
int cx, cy, cz;
child_bit = child_bit_depth[depth];
cx = child_bit_depth[depth];
cy = child_bit_depth[depth];
cz = child_bit_depth[depth];
while (true) { // find the first node where branching is required
child_index_min = ((xmin & child_bit )!=0) | (((ymin & child_bit )!=0 )<< 1) | (((zmin & child_bit )!=0) << 2);
child_index_max = ((xmax & child_bit )!=0) | (((ymax & child_bit )!=0 )<< 1) | (((zmax & child_bit )!=0) << 2);
// if these are the same, go there
// TODO: optimization: also traverse if only single child...
if (child_index_min == child_index_max) {
if (node->childIsLeaf(child_index_min) ) { // luckily, no branching is required
findClosestInLeaf(node->getChild(child_index_min), threadNum);
return static_cast<double*>(params[threadNum].closest);
} else {
if (node->isValid(child_index_min) ) { // only descend when there is a child
childcenter(cx,cy,cz, cx,cy,cz, child_index_min, child_bit/2 );
node = node->getChild(child_index_min);
child_bit /= 2;
} else { // there is no child containing the bounding box => no point is close enough
return 0;
}
}
} else {
// if min and max are not in the same child we must branch
break;
}
}
// node contains all box-within-bounds cells, now begin best bin first search
_FindClosest(threadNum, node->node, child_bit/2, cx, cy, cz);
return static_cast<double*>(params[threadNum].closest);
}
/**
* This is the heavy duty search function doing most of the (theoretically unneccesary) work. The tree is recursively searched.
* Depending on which of the 8 child-voxels is closer to the query point, the children are examined in a special order.
* This order is defined in map, imap is its inverse and sequence2ci is a speedup structure for faster access to the child indices.
*/
void _FindClosest(int threadNum, bitoct &node, int size, int x, int y, int z) const
{
// Recursive case
// compute which child is closest to the query point
unsigned char child_index = ((params[threadNum].x - x) >= 0) |
(((params[threadNum].y - y) >= 0) << 1) |
(((params[threadNum].z - z) >= 0) << 2);
char *seq2ci = sequence2ci[child_index][node.valid]; // maps preference to index in children array
char *mmap = amap[child_index]; // maps preference to area index
bitunion<T> *children;
bitoct::getChildren(node, children);
int cx, cy, cz;
cx = cy = cz = 0; // just to shut up the compiler warnings
for (unsigned char i = 0; i < 8; i++) { // in order of preference
child_index = mmap[i]; // the area index of the node
if ( ( 1 << child_index ) & node.valid ) { // if ith node exists
childcenter(x,y,z, cx,cy,cz, child_index, size);
if ( params[threadNum].closest_v == 0 || max(max(abs( cx - params[threadNum].x ),
abs( cy - params[threadNum].y )),
abs( cz - params[threadNum].z )) - size
> params[threadNum].closest_v ) {
continue;
}
// find the closest point in leaf seq2ci[i]
if ( ( 1 << child_index ) & node.leaf ) { // if ith node is leaf
findClosestInLeaf( &children[seq2ci[i]], threadNum);
} else { // recurse
_FindClosest(threadNum, children[seq2ci[i]].node, size/2, cx, cy, cz);
}
}
}
}
/**
* This function shows the possible speedup that can be gained by using the
* octree for nearest neighbour search, if a more sophisticated
* implementation were given. Here, only the bucket in which the query point
* falls is looked up. If doing the same thing in the kd-tree search, this
* function is about 3-5 times as fast
*/
double *FindClosestInBucket(double *point, double maxdist2, int threadNum) {
params[threadNum].closest = 0;
params[threadNum].closest_d2 = maxdist2;
params[threadNum].p = point;
unsigned int x,y,z;
x = (point[0] + add[0]) * mult;
y = (point[1] + add[1]) * mult;
z = (point[2] + add[2]) * mult;
T * points;
unsigned int length;
bitunion<T> *node = uroot;
unsigned char child_index;
unsigned int child_bit = child_bit_depth[0];
while (true) {
child_index = ((x & child_bit )!=0) | (((y & child_bit )!=0 )<< 1) | (((z & child_bit )!=0) << 2);
if (node->childIsLeaf(child_index) ) {
node = node->getChild(child_index);
points = node->getPoints();
length = node->getLength();
for(unsigned int iterator = 0; iterator < length; iterator++ ) {
double myd2 = Dist2(params[threadNum].p, points);
if (myd2 < params[threadNum].closest_d2) {
params[threadNum].closest_d2 = myd2;
params[threadNum].closest = points;
}
points+=BOctTree<T>::POINTDIM;
}
return static_cast<double*>(params[threadNum].closest);
} else {
if (node->isValid(child_index) ) {
node = node->getChild(child_index);
} else {
return 0;
}
}
child_bit >>= 1;
}
return static_cast<double*>(params[threadNum].closest);
}
template <class P>
void fullsort(P * const * points, int n, T splitval[3], P * const * blocks[9]) {
P* const * L0;
P* const * L1;
P* const * L2;
unsigned int n0L, n0R, n1L, n1R ;
// sort along Z
L0 = sort(points, n, splitval[2], 2);
n0L = L0 - points;
// sort along Y (left of Z) points -- L0
L1 = sort(points, n0L, splitval[1], 1);
n1L = L1 - points;
// sort along X (left of Y) points -- L1
L2 = sort(points, n1L, splitval[0], 0);
blocks[0] = L2;
n1R = n0L - n1L;
// sort along X (right of Y) // L1 -- L0
L2 = sort(L1, n1R, splitval[0], 0);
blocks[1] = L1;
blocks[2] = L2;
n0R = n - n0L;
// sort along Y (right of Z) L0 -- end
L1 = sort(L0, n0R, splitval[1], 1);
n1L = L1 - L0;
// sort along X (left of Y) points -- L1
L2 = sort(L0, n1L, splitval[0], 0);
blocks[3] = L0;
blocks[4] = L2;
n1R = n0R - n1L;
// sort along X (right of Y) // L1 -- L0
L2 = sort(L1, n1R, splitval[0], 0);
blocks[5] = L1;
blocks[6] = L2;
}
template <class P>
P* const * sort(P* const * points, unsigned int n, T splitval, unsigned char index) {
if (n==0) return points;
if (n==1) {
if (points[0][index] < splitval)
return points+1;
else
return points;
}
P **left = const_cast<P**>(points);
P **right = const_cast<P**>(points + n - 1);
while (1) {
while ((*left)[index] < splitval)
{
left++;
if (right < left)
break;
}
while ((*right)[index] >= splitval)
{
right--;
if (right < left)
break;
}
if (right < left)
break;
std::swap(*left, *right);
}
return left;
}
public:
/**
* Copies another (via new constructed) octtree into cache allocated memory and makes it position independant
*/
BOctTree(const BOctTree& other, unsigned char* mem_ptr, unsigned int mem_max)
{
alloc = new SequentialAllocator(mem_ptr, mem_max);
// "allocate" space for *this
alloc->allocate<BOctTree<T> >();
// take members
unsigned int i;
for(i = 0; i < 3; ++i)
center[i] = other.center[i];
size = other.size;
voxelSize = other.voxelSize;
real_voxelSize = other.real_voxelSize;
for(i = 0; i < 3; ++i)
add[i] = other.add[i];
mult = other.mult;
POINTDIM = other.POINTDIM;
mins = alloc->allocate<T>(POINTDIM);
maxs = alloc->allocate<T>(POINTDIM);
for(i = 0; i < POINTDIM; ++i) {
mins[i] = other.mins[i];
maxs[i] = other.maxs[i];
}
pointtype = other.pointtype;
max_depth = other.max_depth;
child_bit_depth = alloc->allocate<unsigned int>(max_depth);
child_bit_depth_inv = alloc->allocate<unsigned int>(max_depth);
for(i = 0; i < max_depth; ++i) {
child_bit_depth[i] = other.child_bit_depth[i];
child_bit_depth_inv[i] = other.child_bit_depth_inv[i];
}
largest_index = other.largest_index;
// take node structure
uroot = alloc->allocate<bitunion<T> >();
root = &uroot->node;
copy_children(*other.root, *root);
// test if allocator has used up his space
//alloc->printSize();
// discard allocator, space is managed by the cache manager
delete alloc; alloc = 0;
}
private:
void copy_children(const bitoct& other, bitoct& my) {
// copy node attributes
my.valid = other.valid;
my.leaf = other.leaf;
// other children
bitunion<T>* other_children;
bitoct::getChildren(other, other_children);
// create own children
unsigned int n_children = POPCOUNT(other.valid);
bitunion<T>* my_children = alloc->allocate<bitunion<T> >(n_children);
bitoct::link(my, my_children);
// iterate over all (valid) children and copy them
for(unsigned int i = 0; i < 8; ++i) {
if((1<<i) & other.valid) {
if((1<<i) & other.leaf) {
// copy points
unsigned int length = other_children->getLength();
pointrep* other_pointreps = other_children->getPointreps();
pointrep* my_pointreps = alloc->allocate<pointrep>(POINTDIM * length + 1);
for(unsigned int j = 0; j < POINTDIM * length + 1; ++j)
my_pointreps[j] = other_pointreps[j];
// assign
bitunion<T>::link(my_children, my_pointreps);
} else {
// child is already created, copy and create children for it
copy_children(other_children->node, my_children->node);
}
++other_children;
++my_children;
}
}
}
public:
//! Size of the whole tree structure, including the main class, its serialize critical allocated variables and nodes, not the allocator
unsigned int getMemorySize()
{
return sizeof(*this) // all member variables
+ 2*POINTDIM*sizeof(T) // mins, maxs
+ 2*max_depth*sizeof(unsigned int) // child_bit_depth(_inv)
+ sizeof(bitunion<T>) // uroot
+ sizeChildren(*root); // all nodes
}
private:
//! Recursive size of a node's children
unsigned int sizeChildren(const bitoct& node) {
unsigned int s = 0;
bitunion<T>* children;
bitoct::getChildren(node, children);
// size of children allocation
unsigned int n_children = POPCOUNT(node.valid);
s += sizeof(bitunion<T>)*n_children;
// iterate over all (valid) children and sum them up
for(unsigned int i = 0; i < 8; ++i) {
if((1<<i) & node.valid) {
if((1<<i) & node.leaf) {
// leaf only accounts for its points
s += sizeof(pointrep)*(children->getLength()*POINTDIM+1);
} else {
// childe node is already accounted for, add its children
s += sizeChildren(children->node);
}
++children; // next (valid) child
}
}
return s;
}
};
typedef SingleObject<BOctTree<float> > DataOcttree;
template <class T>
NNParams BOctTree<T>::params[100];
#endif
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