template<typename PointT> void
OutofcoreOctreeRamContainer<PointT>::readRange (const boost::uint64_t start, const boost::uint64_t count,
AlignedPointTVector& v)
{
v.resize (count);
memcpy (v.data (), container_.data () + start, count * sizeof(PointT));
}
template<typename PointT, typename LeafT, typename BranchT, typename OctreeT> int
pcl::octree::OctreePointCloud<PointT, LeafT, BranchT, OctreeT>::getApproxIntersectedVoxelCentersBySegment (
const Eigen::Vector3f& origin,
const Eigen::Vector3f& end,
AlignedPointTVector &voxel_center_list,
float precision)
{
Eigen::Vector3f direction = end - origin;
float norm = direction.norm ();
direction.normalize ();
const float step_size = static_cast<const float> (resolution_) * precision;
// Ensure we get at least one step for the first voxel.
const int nsteps = std::max (1, static_cast<int> (norm / step_size));
OctreeKey prev_key;
bool bkeyDefined = false;
// Walk along the line segment with small steps.
for (int i = 0; i < nsteps; ++i)
{
Eigen::Vector3f p = origin + (direction * step_size * static_cast<const float> (i));
PointT octree_p;
octree_p.x = p.x ();
octree_p.y = p.y ();
octree_p.z = p.z ();
OctreeKey key;
this->genOctreeKeyforPoint (octree_p, key);
// Not a new key, still the same voxel.
if ((key == prev_key) && (bkeyDefined) )
continue;
prev_key = key;
bkeyDefined = true;
PointT center;
genLeafNodeCenterFromOctreeKey (key, center);
voxel_center_list.push_back (center);
}
OctreeKey end_key;
PointT end_p;
end_p.x = end.x ();
end_p.y = end.y ();
end_p.z = end.z ();
this->genOctreeKeyforPoint (end_p, end_key);
if (!(end_key == prev_key))
{
PointT center;
genLeafNodeCenterFromOctreeKey (end_key, center);
voxel_center_list.push_back (center);
}
return (static_cast<int> (voxel_center_list.size ()));
}
template<typename PointT> void
OutofcoreOctreeRamContainer<PointT>::insertRange (const PointT* const * start, const boost::uint64_t count)
{
AlignedPointTVector temp;
temp.resize (count);
for (boost::uint64_t i = 0; i < count; i++)
{
temp[i] = *start[i];
}
container_.insert (container_.end (), temp.begin (), temp.end ());
}
template<typename ContainerT, typename PointT> void
OutofcoreOctreeBase<ContainerT, PointT>::queryBBIncludes_subsample (const Eigen::Vector3d& min, const Eigen::Vector3d& max, const size_t query_depth, const double percent, AlignedPointTVector& dst) const
{
boost::shared_lock < boost::shared_mutex > lock (read_write_mutex_);
dst.clear ();
root_->queryBBIncludes_subsample (min, max, query_depth, percent, dst);
}
void point_test(octree_disk& t)
{
boost::mt19937 rng(rngseed);
boost::uniform_real<float> dist(0,1);
double query_box_min[3];
double qboxmax[3];
for(int i = 0; i < 10; i++)
{
//std::cout << "query test round " << i << std::endl;
for(int j = 0; j < 3; j++)
{
query_box_min[j] = dist(rng);
qboxmax[j] = dist(rng);
if(qboxmax[j] < query_box_min[j])
{
std::swap(query_box_min[j], qboxmax[j]);
}
}
//query the trees
AlignedPointTVector p_ot;
t.queryBBIncludes(query_box_min, qboxmax, t.getDepth(), p_ot);
//query the list
AlignedPointTVector pointsinregion;
for(AlignedPointTVector::iterator pointit = points.begin (); pointit != points.end (); ++pointit)
{
if((query_box_min[0] <= pointit->x) && (pointit->x < qboxmax[0]) && (query_box_min[1] < pointit->y) && (pointit->y < qboxmax[1]) && (query_box_min[2] <= pointit->z) && (pointit->z < qboxmax[2]))
{
pointsinregion.push_back(*pointit);
}
}
EXPECT_EQ (p_ot.size (), pointsinregion.size ());
//very slow exhaustive comparison
while( !p_ot.empty () )
{
AlignedPointTVector::iterator it;
it = std::find_first_of(p_ot.begin(), p_ot.end(), pointsinregion.begin (), pointsinregion.end (), compPt);
if(it != p_ot.end())
{
p_ot.erase(it);
}
else
{
FAIL () << "Dropped Point from tree1!" << std::endl;
break;
}
}
EXPECT_TRUE(p_ot.empty());
}
}
template<typename PointT, typename LeafT, typename BranchT, typename OctreeT> int
pcl::octree::OctreePointCloud<PointT, LeafT, BranchT, OctreeT>::getOccupiedVoxelCenters (
AlignedPointTVector &voxelCenterList_arg) const
{
OctreeKey key;
key.x = key.y = key.z = 0;
voxelCenterList_arg.clear ();
return getOccupiedVoxelCentersRecursive (this->rootNode_, key, voxelCenterList_arg);
}
TEST (PCL, Outofcore_Octree_Build)
{
boost::filesystem::remove_all (filename_otreeA.parent_path ());
boost::filesystem::remove_all (filename_otreeB.parent_path ());
Eigen::Vector3d min (-32.0, -32.0, -32.0);
Eigen::Vector3d max (32.0, 32.0, 32.0);
// Build two trees using each constructor
// depth of treeA will be same as B because 1/2^3 > .1 and 1/2^4 < .1
// depth really affects performance
octree_disk treeA (min, max, .1, filename_otreeA, "ECEF");
octree_disk treeB (4, min, max, filename_otreeB, "ECEF");
// Equidistributed uniform pseudo-random number generator
boost::mt19937 rng(rngseed);
// For testing sparse
//boost::uniform_real<double> dist(0,1);
// For testing less sparse
boost::normal_distribution<float> dist (0.5f, .1f);
// Create a point
PointT p;
points.resize (numPts);
//ignore these fields from the UR point for now
// p.r = p.g = p.b = 0;
// p.nx = p.ny = p.nz = 1;
// p.cameraCount = 0;
// p.error = 0;
// p.triadID = 0;
// Radomize it's position in space
for (size_t i = 0; i < numPts; i++)
{
p.x = dist (rng);
p.y = dist (rng);
p.z = dist (rng);
points[i] = p;
}
// Add to tree
treeA.addDataToLeaf (points);
// Add to tree
treeB.addDataToLeaf (points);
}
template<typename Container, typename PointT> boost::uint64_t
octree_base<Container, PointT>::addDataToLeaf (const AlignedPointTVector& p)
{
boost::unique_lock < boost::shared_mutex > lock (read_write_mutex_);
const bool _FORCE_BB_CHECK = true;
uint64_t pt_added = root_->addDataToLeaf (p, _FORCE_BB_CHECK);
assert (p.size () == pt_added);
return (pt_added);
}
template<typename PointT, typename LeafT, typename BranchT, typename OctreeT> int
pcl::octree::OctreePointCloud<PointT, LeafT, BranchT, OctreeT>::getOccupiedVoxelCentersRecursive (
const BranchNode* node_arg,
const OctreeKey& key_arg,
AlignedPointTVector &voxelCenterList_arg) const
{
// child iterator
unsigned char childIdx;
int voxelCount = 0;
// iterate over all children
for (childIdx = 0; childIdx < 8; childIdx++)
{
if (!this->branchHasChild (*node_arg, childIdx))
continue;
const OctreeNode * childNode;
childNode = this->getBranchChildPtr (*node_arg, childIdx);
// generate new key for current branch voxel
OctreeKey newKey;
newKey.x = (key_arg.x << 1) | (!!(childIdx & (1 << 2)));
newKey.y = (key_arg.y << 1) | (!!(childIdx & (1 << 1)));
newKey.z = (key_arg.z << 1) | (!!(childIdx & (1 << 0)));
switch (childNode->getNodeType ())
{
case BRANCH_NODE:
{
// recursively proceed with indexed child branch
voxelCount += getOccupiedVoxelCentersRecursive (static_cast<const BranchNode*> (childNode), newKey, voxelCenterList_arg);
break;
}
case LEAF_NODE:
{
PointT newPoint;
genLeafNodeCenterFromOctreeKey (newKey, newPoint);
voxelCenterList_arg.push_back (newPoint);
voxelCount++;
break;
}
default:
break;
}
}
return (voxelCount);
}
template<typename PointT, typename LeafT, typename OctreeT> int
pcl::octree::OctreePointCloudSearch<PointT, LeafT, OctreeT>::getIntersectedVoxelCenters (
Eigen::Vector3f origin, Eigen::Vector3f direction, AlignedPointTVector &voxelCenterList) const
{
OctreeKey key;
key.x = key.y = key.z = 0;
voxelCenterList.clear ();
voxelCenterList.reserve (this->leafCount_);
// Voxel childIdx remapping
unsigned char a = 0;
double minX, minY, minZ, maxX, maxY, maxZ;
initIntersectedVoxel (origin, direction, minX, minY, minZ, maxX, maxY, maxZ, a);
if (max (max (minX, minY), minZ) < min (min (maxX, maxY), maxZ))
return getIntersectedVoxelCentersRecursive (minX, minY, minZ, maxX, maxY, maxZ, a, this->rootNode_, key,
voxelCenterList);
return (0);
}
TEST (PCL, Outofcore_Octree_Build_LOD)
{
boost::filesystem::remove_all (filename_otreeA_LOD.parent_path ());
boost::filesystem::remove_all (filename_otreeB_LOD.parent_path ());
Eigen::Vector3d min (0.0, 0.0, 0.0);
Eigen::Vector3d max (1.0, 1.0, 1.0);
// Build two trees using each constructor
octree_disk treeA (min, max, .1, filename_otreeA_LOD, "ECEF");
octree_disk treeB (4, min, max, filename_otreeB_LOD, "ECEF");
// Equidistributed uniform pseudo-random number generator
boost::mt19937 rng (rngseed);
// For testing sparse
//boost::uniform_real<double> dist(0,1);
// For testing less sparse
boost::normal_distribution<float> dist (0.5f, .1f);
// Create a point
PointT p;
/*
p.r = p.g = p.b = 0;
p.nx = p.ny = p.nz = 1;
p.cameraCount = 0;
p.error = 0;
p.triadID = 0;
*/
points.resize (numPts);
// Radomize it's position in space
for (size_t i = 0; i < numPts; i++)
{
p.x = dist (rng);
p.y = dist (rng);
p.z = dist (rng);
points[i] = p;
}
// Add to tree
treeA.addDataToLeaf_and_genLOD (points);
// Add to tree
treeB.addDataToLeaf_and_genLOD (points);
}
template<typename PointT> void
OutofcoreOctreeRamContainer<PointT>::readRangeSubSample (const boost::uint64_t start,
const boost::uint64_t count,
const double percent,
AlignedPointTVector& v)
{
/** \todo change the subsampling technique to use built in PCL sampling */
boost::uint64_t samplesize = static_cast<boost::uint64_t> (percent * static_cast<double> (count));
boost::mutex::scoped_lock lock (rng_mutex_);
boost::uniform_int < boost::uint64_t > buffdist (start, start + count);
boost::variate_generator<boost::mt19937&, boost::uniform_int<boost::uint64_t> > buffdie (rand_gen_, buffdist);
for (boost::uint64_t i = 0; i < samplesize; i++)
{
boost::uint64_t buffstart = buffdie ();
v.push_back (container_[buffstart]);
}
}
template<typename PointT, typename LeafContainerT, typename BranchContainerT> int
pcl::octree::OctreePointCloudSearch<PointT, LeafContainerT, BranchContainerT>::getIntersectedVoxelCenters (
Eigen::Vector3f origin, Eigen::Vector3f direction, AlignedPointTVector &voxel_center_list,
int max_voxel_count) const
{
OctreeKey key;
key.x = key.y = key.z = 0;
voxel_center_list.clear ();
// Voxel child_idx remapping
unsigned char a = 0;
double min_x, min_y, min_z, max_x, max_y, max_z;
initIntersectedVoxel (origin, direction, min_x, min_y, min_z, max_x, max_y, max_z, a);
if (std::max (std::max (min_x, min_y), min_z) < std::min (std::min (max_x, max_y), max_z))
return getIntersectedVoxelCentersRecursive (min_x, min_y, min_z, max_x, max_y, max_z, a, this->root_node_, key,
voxel_center_list, max_voxel_count);
return (0);
}
//loads chunks of up to 2e9 pts at a time; this is a completely arbitrary number
template<typename Container, typename PointT> void
octree_base<Container, PointT>::buildLOD (octree_base_node<Container, PointT>** current_branch, const int current_dims)
{
//stop if this brach DNE
if (!current_branch[current_dims - 1])
{
return;
}
if ((current_branch[current_dims - 1]->numchildren () == 0)
&& (!current_branch[current_dims - 1]->hasUnloadedChildren ()))//at leaf: subsample, remove, and copy to higher nodes
{
//this node's idx is (current_dims-1)
octree_base_node<Container, PointT>* leaf = current_branch[current_dims - 1];
boost::uint64_t leaf_start_size = leaf->payload->size ();
if (leaf_start_size > 0)//skip empty
{
for (boost::uint64_t startp = 0; startp < leaf_start_size; startp += LOAD_COUNT_)
{
//there are (current_dims-1) nodes above this one, indexed 0 thru (current_dims-2)
for (size_t level = (current_dims - 1); level >= 1; level--)
{
//the target
octree_base_node<Container, PointT>* target_parent = current_branch[level - 1];
//the percent to copy
//each level up the chain gets sample_precent^l of the leaf's data
double percent = pow (double (octree_base_node<Container, PointT>::sample_precent), double (current_dims - level));
//read in percent of node
AlignedPointTVector v;
if ((startp + LOAD_COUNT_) < leaf_start_size)
{
leaf->payload->readRangeSubSample (startp, LOAD_COUNT_, percent, v);
}
else
{
leaf->payload->readRangeSubSample (startp, leaf_start_size - startp, percent, v);
}
//write to the target
if (!v.empty ())
{
target_parent->payload->insertRange ( v );
// target_parent->payload->insertRange (&(v.front ()), v.size ());
this->incrementPointsInLOD (target_parent->depth, v.size ());
}
}
}
}
}
else//not at leaf, keep going down
{
//clear this node, in case we are updating the LOD
current_branch[current_dims - 1]->payload->clear ();
const int next_dims = current_dims + 1;
octree_base_node<Container, PointT>** next_branch = new octree_base_node<Container, PointT>*[next_dims];
memcpy (next_branch, current_branch, current_dims * sizeof(octree_base_node<Container, PointT>**));
size_t numchild = current_branch[current_dims - 1]->numchildren ();
if ((numchild != 8) && (current_branch[current_dims - 1]->hasUnloadedChildren ()))
{
current_branch[current_dims - 1]->loadChildren (false);
numchild = current_branch[current_dims - 1]->numchildren ();
}
for (size_t i = 0; i < numchild; i++)
{
next_branch[next_dims - 1] = next_branch[current_dims - 1]->children[i];
buildLOD (next_branch, next_dims);
}
delete[] next_branch;
}
}
TEST (PCL, Outofcore_Ram_Tree)
{
Eigen::Vector3d min (0.0,0.0,0.0);
Eigen::Vector3d max (1.0, 1.0, 1.0);
const boost::filesystem::path filename_otreeA = "ram_tree/ram_tree.oct_idx";
octree_ram t (min, max, .1, filename_otreeA, "ECEF");
boost::mt19937 rng (rngseed);
//boost::uniform_real<double> dist(0,1);//for testing sparse
boost::normal_distribution<float> dist (0.5f, .1f);//for testing less sparse
PointT p;
points.resize (numPts);
for (size_t i = 0; i < numPts; i++)
{
p.x = dist(rng);
p.y = dist(rng);
p.z = dist(rng);
points[i] = p;
}
t.addDataToLeaf_and_genLOD (points);
//t.addDataToLeaf(points);
Eigen::Vector3d qboxmin;
Eigen::Vector3d qboxmax;
for (int i = 0; i < 10; i++)
{
//std::cout << "query test round " << i << std::endl;
for (int j = 0; j < 3; j++)
{
qboxmin[j] = dist (rng);
qboxmax[j] = dist (rng);
if (qboxmax[j] < qboxmin[j])
{
std::swap (qboxmin[j], qboxmax[j]);
}
}
//query the trees
AlignedPointTVector p_ot1;
t.queryBBIncludes (qboxmin, qboxmax, t.getDepth (), p_ot1);
//query the list
AlignedPointTVector pointsinregion;
BOOST_FOREACH(const PointT& p, points)
{
if ((qboxmin[0] <= p.x) && (p.x <= qboxmax[0]) && (qboxmin[1] <= p.y) && (p.y <= qboxmax[1]) && (qboxmin[2] <= p.z) && (p.z <= qboxmax[2]))
{
pointsinregion.push_back (p);
}
}
EXPECT_EQ (p_ot1.size (), pointsinregion.size ());
//very slow exhaustive comparison
while (!p_ot1.empty ())
{
AlignedPointTVector::iterator it;
it = std::find_first_of (p_ot1.begin (), p_ot1.end (), pointsinregion.begin (), pointsinregion.end (), compPt);
if (it != p_ot1.end ())
{
p_ot1.erase(it);
}
else
{
break;
FAIL () << "Dropped Point from tree1!" << std::endl;
}
}
EXPECT_TRUE (p_ot1.empty ());
}
}
template<typename PointT, typename LeafT, typename BranchT> int
pcl::octree::OctreePointCloudSearch<PointT, LeafT, BranchT>::getIntersectedVoxelCentersRecursive (
double minX, double minY, double minZ, double maxX, double maxY, double maxZ, unsigned char a,
const OctreeNode* node, const OctreeKey& key, AlignedPointTVector &voxelCenterList, int maxVoxelCount) const
{
if (maxX < 0.0 || maxY < 0.0 || maxZ < 0.0)
return (0);
// If leaf node, get voxel center and increment intersection count
if (node->getNodeType () == LEAF_NODE)
{
PointT newPoint;
this->genLeafNodeCenterFromOctreeKey (key, newPoint);
voxelCenterList.push_back (newPoint);
return (1);
}
// Voxel intersection count for branches children
int voxelCount = 0;
// Voxel mid lines
double midX = 0.5 * (minX + maxX);
double midY = 0.5 * (minY + maxY);
double midZ = 0.5 * (minZ + maxZ);
// First voxel node ray will intersect
int currNode = getFirstIntersectedNode (minX, minY, minZ, midX, midY, midZ);
// Child index, node and key
unsigned char childIdx;
const OctreeNode *childNode;
OctreeKey childKey;
do
{
if (currNode != 0)
childIdx = static_cast<unsigned char> (currNode ^ a);
else
childIdx = a;
// childNode == 0 if childNode doesn't exist
childNode = this->getBranchChildPtr (static_cast<const BranchNode&> (*node), childIdx);
// Generate new key for current branch voxel
childKey.x = (key.x << 1) | (!!(childIdx & (1 << 2)));
childKey.y = (key.y << 1) | (!!(childIdx & (1 << 1)));
childKey.z = (key.z << 1) | (!!(childIdx & (1 << 0)));
// Recursively call each intersected child node, selecting the next
// node intersected by the ray. Children that do not intersect will
// not be traversed.
switch (currNode)
{
case 0:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (minX, minY, minZ, midX, midY, midZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (midX, midY, midZ, 4, 2, 1);
break;
case 1:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (minX, minY, midZ, midX, midY, maxZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (midX, midY, maxZ, 5, 3, 8);
break;
case 2:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (minX, midY, minZ, midX, maxY, midZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (midX, maxY, midZ, 6, 8, 3);
break;
case 3:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (minX, midY, midZ, midX, maxY, maxZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (midX, maxY, maxZ, 7, 8, 8);
break;
case 4:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (midX, minY, minZ, maxX, midY, midZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (maxX, midY, midZ, 8, 6, 5);
break;
case 5:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (midX, minY, midZ, maxX, midY, maxZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (maxX, midY, maxZ, 8, 7, 8);
break;
case 6:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (midX, midY, minZ, maxX, maxY, midZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = getNextIntersectedNode (maxX, maxY, midZ, 8, 8, 7);
break;
case 7:
if (childNode)
voxelCount += getIntersectedVoxelCentersRecursive (midX, midY, midZ, maxX, maxY, maxZ, a, childNode,
childKey, voxelCenterList, maxVoxelCount);
currNode = 8;
break;
}
} while ((currNode < 8) && (maxVoxelCount <= 0 || voxelCount < maxVoxelCount));
return (voxelCount);
}