voxel_grid.h

#ifndef VOXELGRID_H
#define VOXELGRID_H
 
#include <vector>
#include "voxel.h"
#include "interaction_data.h"
#include <Eigen/Dense>
#include <pybind11/embed.h>
#include <pybind11/numpy.h>
#include <unordered_map>
#include <iostream>
#include <utility>
 
namespace py = pybind11;
 
namespace VoxelGridHelpers {
    template <typename T, std::size_t N>
    Eigen::Vector<T, N> pyTupleToEigenVector(const py::tuple &tuple);
    double covertUnitNameToCm(const std::string& unitName);
    int dimensionStringToIndex(const std::string& dimension);
}
 
class VoxelGrid {
public:
    VoxelGrid() = default;
 
    explicit VoxelGrid(std::string  filename, bool is_python_environment = false);
 
    Voxel& getVoxel(const Eigen::Vector3i& voxel_index);
 
    void setVoxel(const Eigen::Vector3i& voxel_index, Voxel& value);
 
    Eigen::Vector3d getVoxelPosition(const Eigen::Vector3i& voxel_index);
 
    bool withinGrid(const Eigen::Vector3d& position) const;
 
    Eigen::Vector3i getVoxelIndex(const Eigen::Vector3d& position) const;
 
    std::vector<std::string> getMaterialNames() const;
 
    double getTotalEnergyDeposited();
 
    std::unordered_map<int, VectorValue> getEnergyDepositedInMaterials();
 
    void addExit() {
        numExits_++;
    }
 
    int getNumExits() const {
        return numExits_;
    }
 
    Eigen::Vector3d getDimSpace() const {
        return dim_space_;
    }
 
private:
    Eigen::Vector3i dim_vox_;
    Eigen::Vector3d spacing_; // in cm
    Eigen::Vector3d dim_space_; // in cm
    int numOfVoxels_ = 0;
    int numExits_ = 0;
    std::vector<Voxel> voxels_;
    std::string filename_;
    double units_ = 1.0; // in cm
    bool is_python_environment_;
 
    // initialize voxels according to the nifti file
    void initializeVoxels();
 
    // calculate the index of the voxel at (i, j, k)
    int voxelNumber(const Eigen::Vector3i& voxel_index) const;
 
    void handleOutOfBounds(const Eigen::Vector3d& position) const;
 
    void setVoxelProperties(const py::array_t<uint8_t>& array, const py::object &header);
 
    static py::array_t<uint8_t> getNumPyArrayFromImg(const py::object& img);
    void setDimVox(const py::array_t<uint8_t>& array);
    void setUnits(const py::object& header);
    void setSpacing(const py::object& header);
    void setNumOfVoxels();
    void setDimSpace();
    void setVoxelMaterialIDs(const py::array_t<uint8_t>& array);
};
 
#endif // VOXELGRID_H