HashedId::HashedId(const Eigen::Vector3i&pos,const int&edgeLen,const int&no) {
_id[0]=edgeLen;
_id[1]=pos.x();
_id[2]=pos.y();
_id[3]=pos.z();
_no=no;
}
void WorldDownloadManager::findExtraCubesForBoundingBox(const Eigen::Vector3f& current_cube_min,
const Eigen::Vector3f& current_cube_max,const Eigen::Vector3f& bbox_min,const Eigen::Vector3f& bbox_max,Vector3fVector& cubes_centers,
bool& extract_current)
{
const Eigen::Vector3f & cube_size = current_cube_max - current_cube_min;
cubes_centers.clear();
extract_current = false;
const Eigen::Vector3f relative_act_bbox_min = bbox_min - current_cube_min;
const Eigen::Vector3f relative_act_bbox_max = bbox_max - current_cube_min;
const Eigen::Vector3i num_cubes_plus = Eigen::Vector3f(floor3f(Eigen::Vector3f(relative_act_bbox_max.array() / cube_size.array())
- (Eigen::Vector3f::Ones() * 0.0001))).cast<int>();
const Eigen::Vector3i num_cubes_minus = Eigen::Vector3f(floor3f(Eigen::Vector3f(relative_act_bbox_min.array() / cube_size.array())
+ (Eigen::Vector3f::Ones() * 0.0001))).cast<int>();
for (int z = num_cubes_minus.z(); z <= num_cubes_plus.z(); z++)
for (int y = num_cubes_minus.y(); y <= num_cubes_plus.y(); y++)
for (int x = num_cubes_minus.x(); x <= num_cubes_plus.x(); x++)
{
const Eigen::Vector3i cube_index(x,y,z);
if ((cube_index.array() == Eigen::Vector3i::Zero().array()).all())
{
extract_current = true;
continue;
}
const Eigen::Vector3f relative_cube_origin = cube_index.cast<float>().array() * cube_size.array();
const Eigen::Vector3f cube_center = relative_cube_origin + current_cube_min + (cube_size * 0.5);
cubes_centers.push_back(cube_center);
}
}
/** \brief Constructor
* param[in] volume_size size of the volume in mm
* param[in] volume_res volume grid resolution (typically device::VOLUME_X x device::VOLUME_Y x device::VOLUME_Z)
*/
DeviceVolume (const Eigen::Vector3f &volume_size, const Eigen::Vector3i &volume_res)
: volume_size_ (volume_size)
{
// initialize GPU
device_volume_.create (volume_res[1] * volume_res[2], volume_res[0]); // (device::VOLUME_Y * device::VOLUME_Z, device::VOLUME_X)
pcl::device::initVolume (device_volume_);
// truncation distance
Eigen::Vector3f voxel_size = volume_size.array() / volume_res.array().cast<float>();
trunc_dist_ = max ((float)min_trunc_dist, 2.1f * max (voxel_size[0], max (voxel_size[1], voxel_size[2])));
};
template <typename VoxelT, typename WeightT> bool
pcl::TSDFVolume<VoxelT, WeightT>::extractNeighborhood (const Eigen::Vector3i &voxel_coord, int neighborhood_size,
VoxelTVec &neighborhood) const
{
// point_index is at the center of a cube of scale_ x scale_ x scale_ voxels
int shift = (neighborhood_size - 1) / 2;
Eigen::Vector3i min_index = voxel_coord.array() - shift;
Eigen::Vector3i max_index = voxel_coord.array() + shift;
// check that index is within range
if (getLinearVoxelIndex(min_index) < 0 || getLinearVoxelIndex(max_index) >= (int)size())
{
pcl::console::print_info ("[extractNeighborhood] Skipping voxel with coord (%d, %d, %d).\n", voxel_coord(0), voxel_coord(1), voxel_coord(2));
return false;
}
static const int descriptor_size = neighborhood_size*neighborhood_size*neighborhood_size;
neighborhood.resize (descriptor_size);
const Eigen::RowVector3i offset_vector (1, neighborhood_size, neighborhood_size*neighborhood_size);
// loop over all voxels in 3D neighborhood
#pragma omp parallel for
for (int z = min_index(2); z <= max_index(2); ++z)
{
for (int y = min_index(1); y <= max_index(1); ++y)
{
for (int x = min_index(0); x <= max_index(0); ++x)
{
// linear voxel index in volume and index in descriptor vector
Eigen::Vector3i point (x,y,z);
int volume_idx = getLinearVoxelIndex (point);
int descr_idx = offset_vector * (point - min_index);
/* std::cout << "linear index " << volume_idx << std::endl;
std::cout << "weight " << weights_->at (volume_idx) << std::endl;
std::cout << "volume " << volume_->at (volume_idx) << std::endl;
std::cout << "descr " << neighborhood.rows() << "x" << neighborhood.cols() << ", val = " << neighborhood << std::endl;
std::cout << "descr index = " << descr_idx << std::endl;
*/
// get the TSDF value and store as descriptor entry
if (weights_->at (volume_idx) != 0)
neighborhood (descr_idx) = volume_->at (volume_idx);
else
neighborhood (descr_idx) = -1.0; // if never visited we assume inside of object (outside captured and thus filled with positive values)
}
}
}
return true;
}
template <typename VoxelT, typename WeightT> bool
pcl::TSDFVolume<VoxelT, WeightT>::addNeighborhood (const Eigen::Vector3i &voxel_coord, int neighborhood_size,
const VoxelTVec &neighborhood, WeightT voxel_weight)
{
// point_index is at the center of a cube of scale_ x scale_ x scale_ voxels
int shift = (neighborhood_size - 1) / 2;
Eigen::Vector3i min_index = voxel_coord.array() - shift;
Eigen::Vector3i max_index = voxel_coord.array() + shift;
// check that index is within range
if (getLinearVoxelIndex(min_index) < 0 || getLinearVoxelIndex(max_index) >= (int)size())
{
pcl::console::print_info ("[addNeighborhood] Skipping voxel with coord (%d, %d, %d).\n", voxel_coord(0), voxel_coord(1), voxel_coord(2));
return false;
}
// static const int descriptor_size = neighborhood_size*neighborhood_size*neighborhood_size;
const Eigen::RowVector3i offset_vector (1, neighborhood_size, neighborhood_size*neighborhood_size);
Eigen::Vector3i index = min_index;
// loop over all voxels in 3D neighborhood
#pragma omp parallel for
for (int z = min_index(2); z <= max_index(2); ++z)
{
for (int y = min_index(1); y <= max_index(1); ++y)
{
for (int x = min_index(0); x <= max_index(0); ++x)
{
// linear voxel index in volume and index in descriptor vector
Eigen::Vector3i point (x,y,z);
int volume_idx = getLinearVoxelIndex (point);
int descr_idx = offset_vector * (point - min_index);
// add the descriptor entry to the volume
VoxelT &voxel = volume_->at (volume_idx);
WeightT &weight = weights_->at (volume_idx);
// TODO check that this simple lock works correctly!!
#pragma omp atomic
voxel += neighborhood (descr_idx);
#pragma omp atomic
weight += voxel_weight;
}
}
}
return true;
}
IntBoundingBox3D::IntBoundingBox3D(const Eigen::Vector3i& a, const Eigen::Vector3i& b)
{
Eigen::Vector3i bl, tr;
for (unsigned i = 0; i < a.size(); ++i)
{
bl[i] = std::min(a[i], b[i]);
tr[i] = std::max(a[i], b[i]);
}
elems[0] = static_cast<int> (bl[0]);
elems[1] = static_cast<int> (tr[0]);
elems[2] = static_cast<int> (bl[1]);
elems[3] = static_cast<int> (tr[1]);
elems[4] = static_cast<int> (bl[2]);
elems[5] = static_cast<int> (tr[2]);
}
// Create root cells and connect their nodes accordingly
void OctreeGrid::createRootCells() {
// Clear current octree
m_Nodes.clear();
m_Cells.clear();
// Anisotropic grids: we need multiple root cells
int minFineCellSize = m_CellGridSize.minCoeff();
Eigen::Vector3i coarseCellGridSize = m_CellGridSize / minFineCellSize;
Eigen::Vector3i coarseNodeGridSize = coarseCellGridSize.array() + 1;
// Create coarse grid nodes and set up adjacency relations
for (int i = 0; i < coarseNodeGridSize.prod(); ++i) {
Node newNode;
Eigen::Vector3i coarsePos = Layout3D::toGrid(i, coarseNodeGridSize);
newNode.position = (1 << m_MaxDepth) * coarsePos;
for (int axis = 0; axis < 3; ++axis) {
for (int c = 0; c < 2; ++c) {
Eigen::Vector3i q = coarsePos;
q[axis] += (c ? 1 : -1);
q = Layout3D::clamp(q, coarseNodeGridSize);
int j = Layout3D::toIndex(q, coarseNodeGridSize);
newNode.neighNodeId[2*axis+c] = (j != i ? j : -1);
}
}
m_Nodes.emplace_back(newNode);
}
// Create coarse grid cells
for (int e = 0; e < coarseCellGridSize.prod(); ++e) {
Cell newCell;
Eigen::Vector3i lowerCorner = Layout3D::toGrid(e, coarseCellGridSize);
for (int k = 0; k < 8; ++k) {
Eigen::Vector3i currentCorner = lowerCorner + Cube::delta(k);
int i = Layout3D::toIndex(currentCorner, coarseNodeGridSize);
newCell.setCorner(k, i);
}
m_Cells.emplace_back(newCell);
}
m_NumRootCells = (int) m_Cells.size();
// Link adjacent cells together
for (int i = 0; i < coarseCellGridSize.prod(); ++i) {
Eigen::Vector3i coarsePos = Layout3D::toGrid(i, coarseCellGridSize);
for (int axis = 0; axis < 3; ++axis) {
for (int c = 0; c < 2; ++c) {
Eigen::Vector3i q = coarsePos;
q[axis] += (c ? 1 : -1);
q = Layout3D::clamp(q, coarseCellGridSize);
int j = Layout3D::toIndex(q, coarseCellGridSize);
m_Cells[i].neighCellId[2*axis+c] = (j != i ? j : -1);
}
}
}
}
OctreeGrid::OctreeGrid(Eigen::Vector3i fineCellGridSize, int maxNodeGuess, int maxCellGuess)
: m_NodeGridSize(fineCellGridSize.array() + 1)
, m_CellGridSize(fineCellGridSize)
, m_NumRootCells(0)
{
m_Nodes.reserve(maxNodeGuess);
m_Cells.reserve(maxCellGuess);
// Some sanity checks
oct_assert(Math::isPowerOfTwo(fineCellGridSize[0]));
oct_assert(Math::isPowerOfTwo(fineCellGridSize[1]));
oct_assert(Math::isPowerOfTwo(fineCellGridSize[2]));
// Max depth depends on fineCellGridSize
int minFineCellSize = m_CellGridSize.minCoeff();
m_MaxDepth = 0;
while ( m_MaxDepth < 64 && (1 << m_MaxDepth) < minFineCellSize) { ++m_MaxDepth; }
// logger_debug("OctreeGrid", "MaxDepth: %s", m_MaxDepth);
// Create root cells
createRootCells();
}
//==============================================================================
std::string toString(const Eigen::Vector3i& _v)
{
return boost::lexical_cast<std::string>(_v.transpose());
}
void CollisionSpace::propagatePositive(
std::vector<std::vector<CollisionSpaceCell*> >& bucket_queue) {
double max_distance_sq = getMaxtDistSq();
// now process the queue:
cout << "process the Queue : " << bucket_queue.size() << endl;
for (unsigned int i = 0; i < bucket_queue.size(); ++i) {
std::vector<CollisionSpaceCell*>::iterator list_it =
bucket_queue[i].begin();
while (list_it != bucket_queue[i].end()) {
CollisionSpaceCell* vptr = *list_it;
// TODO: no idea why this happens
if (vptr == NULL) {
continue;
}
// Get the cell location in grid
Eigen::Vector3i loc = getCellCoord(vptr);
int D = i;
if (D > 1) D = 1;
// avoid a possible segfault situation:
if (vptr->m_UpdateDirection < 0 || vptr->m_UpdateDirection > 26) {
cout << "Invalid update direction detected: " << vptr->m_UpdateDirection
<< endl;
++list_it;
continue;
}
// select the neighborhood list based on the update direction:
std::vector<std::vector<int> >& neighborhood =
m_Neighborhoods[D][vptr->m_UpdateDirection];
// Look in the neighbouring cells and update distance
for (unsigned int n = 0; n < neighborhood.size(); n++) {
Eigen::Vector3i direction;
direction.x() = neighborhood[n][0];
direction.y() = neighborhood[n][1];
direction.z() = neighborhood[n][2];
Eigen::Vector3i neigh_loc = loc + direction;
CollisionSpaceCell* neighbour = getCellSpaceCell(neigh_loc);
if (!neighbour) continue;
double new_distance_sq_float =
(vptr->m_ClosestPoint - neigh_loc).squaredNorm();
int new_distance_sq = new_distance_sq_float;
if (new_distance_sq > max_distance_sq) {
cout << "new_distance_sq : " << new_distance_sq << endl;
continue;
}
if (new_distance_sq < neighbour->m_DistanceSquare) {
neighbour->m_DistanceSquare = new_distance_sq;
neighbour->m_ClosestPoint = vptr->m_ClosestPoint;
neighbour->m_UpdateDirection =
getDirectionNumber(direction[0], direction[1], direction[2]);
// and put it in the queue
bucket_queue[new_distance_sq].push_back(neighbour);
}
}
++list_it;
}
bucket_queue[i].clear();
}
}
vtkVolume * VTKDialog::cubeVolume(Cube *cube)
{
qDebug() << "Cube dimensions: " << cube->dimensions().x()
<< cube->dimensions().y() << cube->dimensions().z();
qDebug() << "min/max:" << cube->minValue() << cube->maxValue();
qDebug() << cube->data()->size();
vtkNew<vtkImageData> data;
data->SetNumberOfScalarComponents(1);
Eigen::Vector3i dim = cube->dimensions();
data->SetExtent(0, dim.x()-1, 0, dim.y()-1, 0, dim.z()-1);
data->SetOrigin(cube->min().x(), cube->min().y(), cube->min().z());
data->SetSpacing(cube->spacing().data());
data->SetScalarTypeToDouble();
data->AllocateScalars();
data->Update();
double *dataPtr = static_cast<double *>(data->GetScalarPointer());
std::vector<double> *cubePtr = cube->data();
for (int i = 0; i < dim.x(); ++i)
for (int j = 0; j < dim.y(); ++j)
for (int k = 0; k < dim.z(); ++k) {
dataPtr[(k * dim.y() + j) * dim.x() + i] =
(*cubePtr)[(i * dim.y() + j) * dim.z() + k];
}
double range[2];
data->Update();
range[0] = data->GetScalarRange()[0];
range[1] = data->GetScalarRange()[1];
// a->GetRange(range);
qDebug() << "ImageData range: " << range[0] << range[1];
vtkNew<vtkImageShiftScale> t;
t->SetInput(data.GetPointer());
t->SetShift(-range[0]);
double magnitude = range[1] - range[0];
if(magnitude == 0.0)
{
magnitude = 1.0;
}
t->SetScale(255.0/magnitude);
t->SetOutputScalarTypeToDouble();
qDebug() << "magnitude: " << magnitude;
t->Update();
vtkNew<vtkSmartVolumeMapper> volumeMapper;
vtkNew<vtkVolumeProperty> volumeProperty;
vtkVolume *volume = vtkVolume::New();
volumeMapper->SetBlendModeToComposite();
// volumeMapper->SetBlendModeToComposite(); // composite first
volumeMapper->SetInputConnection(t->GetOutputPort());
volumeProperty->ShadeOff();
volumeProperty->SetInterpolationTypeToLinear();
vtkNew<vtkPiecewiseFunction> compositeOpacity;
vtkNew<vtkColorTransferFunction> color;
if (cube->cubeType() == Cube::MO) {
compositeOpacity->AddPoint( 0.00, 0.0);
compositeOpacity->AddPoint( 63.75, 0.5);
compositeOpacity->AddPoint(127.50, 0.0);
compositeOpacity->AddPoint(192.25, 0.5);
compositeOpacity->AddPoint(255.00, 0.0);
color->AddRGBPoint( 0.00, 0.0, 0.0, 0.0);
color->AddRGBPoint( 63.75, 1.0, 0.0, 0.0);
color->AddRGBPoint(127.50, 0.0, 0.2, 0.0);
color->AddRGBPoint(191.25, 0.0, 0.0, 1.0);
color->AddRGBPoint(255.00, 0.0, 0.0, 0.0);
}
else {
compositeOpacity->AddPoint( 0.00, 0.00);
compositeOpacity->AddPoint( 1.75, 0.30);
compositeOpacity->AddPoint( 2.50, 0.50);
compositeOpacity->AddPoint(192.25, 0.85);
compositeOpacity->AddPoint(255.00, 0.90);
color->AddRGBPoint( 0.00, 0.0, 0.0, 1.0);
color->AddRGBPoint( 63.75, 0.0, 0.0, 0.8);
color->AddRGBPoint(127.50, 0.0, 0.0, 0.5);
color->AddRGBPoint(191.25, 0.0, 0.0, 0.2);
color->AddRGBPoint(255.00, 0.0, 0.0, 0.0);
}
volumeProperty->SetScalarOpacity(compositeOpacity.GetPointer()); // composite first.
volumeProperty->SetColor(color.GetPointer());
volume->SetMapper(volumeMapper.GetPointer());
volume->SetProperty(volumeProperty.GetPointer());
return volume;
}