Volumes#

VDB-backed volumes and loaders used with attribute / grid workflows.

Typedefs

using FloatVDBVolume = VDBVolume<openvdb::FloatGrid>#
typedef openvdb::Grid<openvdb::tree::Tree4<openvdb::Vec2s, 5, 4, 3>::Type> Vec2sGrid#
using Vec2sVDBVolume = VDBVolume<Vec2sGrid>#
using Vec3sVDBVolume = VDBVolume<openvdb::Vec3SGrid>#
typedef openvdb::Grid<openvdb::tree::Tree4<openvdb::Vec4s, 5, 4, 3>::Type> Vec4sGrid#
using Vec4sVDBVolume = VDBVolume<Vec4sGrid>#
template<typename GridType>
class VDBVolume#
#include <vdb_volume.h>

Public Types

using GridPtr = typename GridType::Ptr#
using ValueType = typename GridType::ValueType#

Public Functions

inline std::pair<glm::vec3, glm::vec3> bounding_box() const#
inline std::shared_ptr<VDBVolume<GridType>> clone() const#
inline GridPtr grid() const#
inline std::string grid_type() const#
inline ValueType sample(const double x, const double y, const double z) const#
inline void set_transform(const openvdb::math::Transform &transform)#
inline VDBVolume()#
inline explicit VDBVolume(GridPtr grid, bool center = false)#

Private Members

std::shared_ptr<typename GridType::Accessor> m_accessor#
GridPtr m_grid#
openvdb::tools::GridSampler<GridType, openvdb::tools::BoxSampler>::Ptr m_sampler#
namespace VDB_Loader#

Functions

std::shared_ptr<Vec3sVDBVolume> load_vdb_vec3s_volume_from_grid(const std::string &file_path, const std::string &grid_name, bool center = false)#
std::shared_ptr<Vec4sVDBVolume> load_vdb_vec4s_volume_from_grid(const std::string &file_path, const std::string &grid_name, bool center = false)#
std::shared_ptr<FloatVDBVolume> load_vdb_volume_from_grid(const std::string &file_path, const std::string &grid_name, bool center = false)#
class DICOMLoader#
#include <dicom_loader.h>

Public Functions

std::shared_ptr<FloatVDBVolume> as_volume()#
DICOMLoader(const std::string &directory, bool center = false, double rescale_slope = -std::numeric_limits<double>::infinity(), double rescale_intercept = -std::numeric_limits<double>::infinity(), double slice_thickness = -std::numeric_limits<double>::infinity(), double x_pixel_spacing = -std::numeric_limits<double>::infinity(), double y_pixel_spacing = -std::numeric_limits<double>::infinity())#

Construct a DICOM volume from the given directory.

Parameters:

  • directory – The directory containing the DICOM stack.

  • center – Whether to center the volume at the origin. Default is false.

  • rescale_slope – The rescale slope to apply to the pixel values. If not provided, it will be read from the DICOM metadata.

  • rescale_intercept – The rescale intercept to apply to the pixel values. If not provided, it will be read from the DICOM metadata.

  • slice_thickness – The slice thickness in mm. If not provided, it will be read from the DICOM metadata.

  • x_pixel_spacing – The pixel spacing in the x direction in mm. If not provided, it will be read from the DICOM metadata.

  • y_pixel_spacing – The pixel spacing in the y direction in mm. If not provided, it will be read from the DICOM metadata.

inline std::pair<glm::vec3, glm::vec3> get_bounding_box() const#
inline glm::vec3 get_dimensions() const#
inline std::pair<double, double> get_min_max_hu() const#
inline double get_rescale_intercept() const#
inline double get_rescale_slope() const#
inline glm::vec3 get_voxel_size() const#

Private Types

using GridType = openvdb::FloatGrid#

Private Functions

std::vector<std::vector<double>> load_dicom_image(const std::string &file_path)#

Load a single DICOM image from the given file path and return the pixel data as a 2D vector.

void load_dicom_stack(const std::string &directory)#

Load a DICOM stack from the given directory into an OpenVDB volume.

Parameters:

directory – The directory containing the DICOM stack.

Private Members

bool m_center = false#
double m_hu_max = std::numeric_limits<double>::min()#
double m_hu_min = std::numeric_limits<double>::max()#
double m_rescale_intercept = -std::numeric_limits<double>::infinity()#
double m_rescale_slope = -std::numeric_limits<double>::infinity()#
openvdb::tools::GridSampler<GridType, openvdb::tools::BoxSampler>::Ptr m_sampler#
GridType::Ptr m_volume#
double m_x_size = 0#
double m_x_spacing = -std::numeric_limits<double>::infinity()#
double m_y_size = 0#
double m_y_spacing = -std::numeric_limits<double>::infinity()#
double m_z_size = 0#
double m_z_spacing = -std::numeric_limits<double>::infinity()#

Private Static Functions

static DICOM_Meta_Data GetDICOMMetaData(const std::string &file_path)#

Get the metadata for a DICOM image from the given file path.

static glm::mat4 GetDICOMRigidTransform(DcmDataset *dataset)#
static double GetRescaledValue(Uint16 pixel_value, double rescale_slope, double rescale_intercept)#
struct DICOM_Meta_Data#

Public Members

bool found_rescale_intercept = false#
bool found_rescale_slope = false#
bool found_thickness = false#
bool found_width_and_height = false#
bool found_xy_spacing = false#
size_t height = 0#
double rescale_intercept = 0.0#
double rescale_slope = 1.0#
glm::mat4 rigid_transform = glm::mat4(1.0f)#
double slice_thickness = 1#
size_t width = 0#
double x_pixel_spacing = -1#
double y_pixel_spacing = -1#