template <typename VoxelT, typename WeightT> template <typename PointT> void
pcl::TSDFVolume<VoxelT, WeightT>::getVoxelCoord (const PointT &point, Eigen::Vector3i &coord) const
{
static Eigen::Array3f voxel_size = voxelSize().array();
// point coordinates in world coordinate frame and voxel coordinates
Eigen::Array3f point_coord (point.x, point.y, point.z);
Eigen::Array3f voxel_coord = (point_coord / voxel_size) - 0.5f; // 0.5f offset due to voxel center vs grid
coord(0) = round(voxel_coord(0));
coord(1) = round(voxel_coord(1));
coord(2) = round(voxel_coord(2));
}
sender(async::dispatcher &worker,
const t_syncRadiusList& syncRadien,
t_terrainAccessor* tiles)
: m_syncRadien(syncRadien)
{
BASSERT(tiles != nullptr);
BASSERT(tiles->getNumLod() <= (int32)syncRadien.size());
real voxelSize(1.);
for (int32 indLod = 0; indLod < tiles->getNumLod(); ++indLod)
{
const auto callback(boost::bind(&sender::isInRange, this, _1, _2, indLod));
t_simpleAccessor* toWork(tiles->getLod(indLod));
t_multipleTilesPtr lod(new t_multipleTiles(worker, voxelSize, callback, toWork));
voxelSize*=2.;
m_multipleTiles.push_back(lod);
lod->signalSendTileData()->connect(boost::bind(&sender::lodWantsToSendTileData, this, _1, _2, indLod));
}
}
void ItkReader::ReadImageDirect(DataContainer& data) {
typedef itk::ImageIOBase::IOComponentType ScalarPixelType;
itk::ImageIOBase::Pointer imageIO =
itk::ImageIOFactory::CreateImageIO(p_url.getValue().c_str(), itk::ImageIOFactory::ReadMode);
if (imageIO.IsNotNull())
{
WeaklyTypedPointer wtp;
imageIO->SetFileName(p_url.getValue());
imageIO->ReadImageInformation();
const ScalarPixelType pixelType = imageIO->GetComponentType();
const size_t numDimensions = imageIO->GetNumberOfDimensions();
LDEBUG("Reading Image with Reader " << imageIO->GetNameOfClass());
LDEBUG("Pixel Type is " << imageIO->GetComponentTypeAsString(pixelType));
LDEBUG("numDimensions: " << numDimensions);
if (numDimensions > 3) {
LERROR("Error: Dimensions higher than 3 not supported!");
return;
}
itk::ImageIORegion ioRegion(numDimensions);
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
cgt::vec3 imageOffset(0.f);
cgt::vec3 voxelSize(1.f);
cgt::ivec3 size_i(1);
//we assured above that numDimensions is < 3
for (int i = 0; i < static_cast<int>(numDimensions); i++) {
size_i[i] = imageIO->GetDimensions(i);
imageOffset[i] = imageIO->GetOrigin(i);
voxelSize[i] = imageIO->GetSpacing(i);
ioStart[i] = 0;
ioSize[i] = size_i[i];
}
cgt::svec3 size(size_i);
size_t dimensionality = (size_i[2] == 1) ? ((size_i[1] == 1) ? 1 : 2) : 3;
LDEBUG("Image Size is " << size);
LDEBUG("Voxel Size is " << voxelSize);
LDEBUG("Image Offset is " << imageOffset);
LDEBUG("component size: " << imageIO->GetComponentSize());
LDEBUG("components: " << imageIO->GetNumberOfComponents());
LDEBUG("pixel type (string): " << imageIO->GetPixelTypeAsString(imageIO->GetPixelType())); // 'vector'
LDEBUG("pixel type: " << imageIO->GetPixelType()); // '5'
switch (pixelType) {
case itk::ImageIOBase::CHAR:
wtp._baseType = WeaklyTypedPointer::INT8; break;
case itk::ImageIOBase::UCHAR:
wtp._baseType = WeaklyTypedPointer::UINT8; break;
case itk::ImageIOBase::SHORT:
wtp._baseType = WeaklyTypedPointer::INT16; break;
case itk::ImageIOBase::USHORT:
wtp._baseType = WeaklyTypedPointer::UINT16; break;
case itk::ImageIOBase::INT:
wtp._baseType = WeaklyTypedPointer::INT32; break;
case itk::ImageIOBase::UINT:
wtp._baseType = WeaklyTypedPointer::UINT32; break;
case itk::ImageIOBase::DOUBLE:
LWARNING("Pixel Type is DOUBLE. Conversion to float may result in loss of precision!");
case itk::ImageIOBase::FLOAT:
wtp._baseType = WeaklyTypedPointer::FLOAT; break;
default:
LERROR("Error while loading ITK image: unsupported type: " << pixelType);
return;
}
wtp._numChannels = imageIO->GetNumberOfComponents();
//Setup the image region to read
ioRegion.SetIndex(ioStart);
ioRegion.SetSize(ioSize);
imageIO->SetIORegion(ioRegion);
if (pixelType != itk::ImageIOBase::DOUBLE) {
//Finally, allocate buffer and read the image data
wtp._pointer = new uint8_t[imageIO->GetImageSizeInBytes()];
imageIO->Read(wtp._pointer);
}
else {
//convert float volume to double volume
double * inputBuf = new double[imageIO->GetImageSizeInComponents()];
wtp._pointer = new uint8_t[imageIO->GetImageSizeInComponents() * sizeof(float)];
imageIO->Read(inputBuf);
double * dptr = inputBuf;
float * fptr = static_cast<float*>(wtp._pointer);
for (int i = 0, s = imageIO->GetImageSizeInComponents(); i < s; ++i) {
*fptr = *dptr;
fptr++;
dptr++;
}
delete[] inputBuf;
}
ImageData* image = new ImageData(dimensionality, size, wtp._numChannels);
ImageRepresentationLocal::create(image, wtp);
image->setMappingInformation(ImageMappingInformation(size, imageOffset/* + p_imageOffset.getValue()*/, voxelSize /** p_voxelSize.getValue()*/));
data.addData(p_targetImageID.getValue(), image);
}
else {
LWARNING("Unable to create ImageIO Instance; No suitable reader found!");
}
}
void ItkReader::ReadImageSeries(DataContainer& data) {
typedef itk::ImageIOBase::IOComponentType ScalarPixelType;
std::vector<std::string> imageFileNames = GetImageFileNames();
if (!imageFileNames.size())
return;
itk::ImageIOBase::Pointer imageIO =
itk::ImageIOFactory::CreateImageIO(imageFileNames[0].c_str(), itk::ImageIOFactory::ReadMode);
const int numSlices = imageFileNames.size();
if (imageIO.IsNotNull())
{
WeaklyTypedPointer wtp;
imageIO->SetFileName(imageFileNames[0]);
imageIO->ReadImageInformation();
const ScalarPixelType pixelType = imageIO->GetComponentType();
const size_t numDimensions = imageIO->GetNumberOfDimensions();
LDEBUG("Reading Image with Reader " << imageIO->GetNameOfClass());
LDEBUG("Pixel Type is " << imageIO->GetComponentTypeAsString(pixelType));
LDEBUG("numDimensions: " << numDimensions);
if (numDimensions > 3) {
LERROR("Error: Dimensions higher than 3 not supported!");
return;
}
itk::ImageIORegion ioRegion(numDimensions);
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
cgt::vec3 imageOffset(0.f);
cgt::vec3 voxelSize(1.f);
cgt::ivec3 size_i(1);
//we assured above that numDimensions is < 3
for (int i = 0; i < static_cast<int>(numDimensions); i++) {
size_i[i] = imageIO->GetDimensions(i);
imageOffset[i] = imageIO->GetOrigin(i);
voxelSize[i] = imageIO->GetSpacing(i);
ioStart[i] = 0;
ioSize[i] = size_i[i];
}
cgt::svec3 size(size_i);
size_t dimensionality = (size_i[2] == 1) ? ((size_i[1] == 1) ? 1 : 2) : 3;
if (dimensionality > 2) {
LERROR("Error: Cannot load image series with more than two dimensions!");
return;
}
LDEBUG("Image Size is " << size);
LDEBUG("Voxel Size is " << voxelSize);
LDEBUG("Image Offset is " << imageOffset);
LDEBUG("component size: " << imageIO->GetComponentSize());
LDEBUG("components: " << imageIO->GetNumberOfComponents());
LDEBUG("pixel type (string): " << imageIO->GetPixelTypeAsString(imageIO->GetPixelType()));
LDEBUG("pixel type: " << imageIO->GetPixelType());
switch (pixelType) {
case itk::ImageIOBase::CHAR:
wtp._baseType = WeaklyTypedPointer::INT8; break;
case itk::ImageIOBase::UCHAR:
wtp._baseType = WeaklyTypedPointer::UINT8; break;
case itk::ImageIOBase::SHORT:
wtp._baseType = WeaklyTypedPointer::INT16; break;
case itk::ImageIOBase::USHORT:
wtp._baseType = WeaklyTypedPointer::UINT16; break;
case itk::ImageIOBase::INT:
wtp._baseType = WeaklyTypedPointer::INT32; break;
case itk::ImageIOBase::UINT:
wtp._baseType = WeaklyTypedPointer::UINT32; break;
case itk::ImageIOBase::DOUBLE:
LWARNING("Pixel Type is DOUBLE. Conversion to float may result in loss of precision!");
case itk::ImageIOBase::FLOAT:
wtp._baseType = WeaklyTypedPointer::FLOAT; break;
default:
LERROR("Error while loading ITK image: unsupported type: " << pixelType);
return;
}
wtp._numChannels = imageIO->GetNumberOfComponents();
//Setup the image region to read
ioRegion.SetIndex(ioStart);
ioRegion.SetSize(ioSize);
imageIO->SetIORegion(ioRegion);
//allocate a temporary buffer if necessary
double* inputBuf = (pixelType == itk::ImageIOBase::DOUBLE) ? new double[imageIO->GetImageSizeInComponents()] : nullptr;
size_t sliceSize = (pixelType == itk::ImageIOBase::DOUBLE) ? imageIO->GetImageSizeInComponents() * sizeof(float) : imageIO->GetImageSizeInBytes();
wtp._pointer = new uint8_t[numSlices * sliceSize];
for (int idx = 0; idx < numSlices; ++idx) {
itk::ImageIOBase::Pointer fileIO = imageIO;
//itk::ImageIOFactory::CreateImageIO(imageFileNames[idx].c_str(), itk::ImageIOFactory::ReadMode);
fileIO->SetFileName(imageFileNames[idx]);
fileIO->ReadImageInformation();
fileIO->SetIORegion(ioRegion);
size_t currentSliceSize = (pixelType == itk::ImageIOBase::DOUBLE) ? imageIO->GetImageSizeInComponents() * sizeof(float) : fileIO->GetImageSizeInBytes();
if (currentSliceSize != sliceSize) {
LERROR("Image " << imageFileNames[idx] << " has different dimensionality or data type!");
delete static_cast<uint8_t*>(wtp._pointer);
delete inputBuf;
wtp._pointer = nullptr;
return;
}
uint8_t* sliceBuffer = static_cast<uint8_t*>(wtp._pointer) + idx * sliceSize;
if (pixelType != itk::ImageIOBase::DOUBLE) {
// directly read slice into buffer
fileIO->Read(sliceBuffer);
}
else {
//convert float volume to double volume
fileIO->Read(inputBuf);
double* dptr = inputBuf;
float* fptr = reinterpret_cast<float*>(sliceBuffer);
for (int i = 0, s = fileIO->GetImageSizeInComponents(); i < s; ++i) {
*fptr = static_cast<float>(*dptr);
fptr++;
dptr++;
}
}
}
delete[] inputBuf;
size[2] = numSlices;
//series adds one dimension
ImageData* image = new ImageData(dimensionality+1, size, wtp._numChannels);
ImageRepresentationLocal::create(image, wtp);
image->setMappingInformation(ImageMappingInformation(size, imageOffset/* + p_imageOffset.getValue()*/, voxelSize /** p_voxelSize.getValue()*/));
data.addData(p_targetImageID.getValue(), image);
}
else {
LWARNING("Unable to create ImageIO Instance; No suitable reader found!");
}
}
