egs_mesh.h

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/*
###############################################################################
#
#  EGSnrc egs++ mesh geometry library headers.
#  Copyright (C) 2020 Mevex Corporation
#
#  This file is part of EGSnrc.
#
#  EGSnrc is free software: you can redistribute it and/or modify it under
#  the terms of the GNU Affero General Public License as published by the
#  Free Software Foundation, either version 3 of the License, or (at your
#  option) any later version.
#
#  EGSnrc is distributed in the hope that it will be useful, but WITHOUT ANY
#  WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
#  FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for
#  more details.
#
#  You should have received a copy of the GNU Affero General Public License
#  along with EGSnrc. If not, see <http://www.gnu.org/licenses/>.
#
###############################################################################
#
#  Authors:         Dave Macrillo, 2020
#                   Matt Ronan,
#                   Nigel Vezeau,
#                   Lou Thompson,
#                   Max Orok
#
#  Contributors:    Pascal Michaud
#                   Reid Townson
#
###############################################################################
#
#  The original EGS_Mesh geometry started as a product of many people's hard
#  work at Mevex Corporation. Thank you to the entire team. Special thanks to
#  Dave Brown and Emily Craven for their support in releasing this work
#  under a public licence.
#
#  The EGS_Mesh library was then extended and refactored significantly by
#  Max Orok, as the subject of his Masters degree in Applied Science at the
#  University of Ottawa, in the department of Mechanical Engineering and under
#  the supervision of Professor James McDonald.
#
###############################################################################
*/
 
#ifndef EGS_MESH
#define EGS_MESH
 
#include <algorithm>
#include <chrono>
#include <cstdint>
#include <iostream>
#include <iomanip>
#include <memory>
#include <sstream>
#include <vector>
#include <array>
 
#include "egs_base_geometry.h"
#include "egs_vector.h"
 
#ifdef WIN32
 
    #ifdef BUILD_EGS_MESH_DLL
        #define EGS_MESH_EXPORT __declspec(dllexport)
    #else
        #define EGS_MESH_EXPORT __declspec(dllimport)
    #endif
    #define EGS_MESH_LOCAL
 
#else
 
    #ifdef HAVE_VISIBILITY
        #define EGS_MESH_EXPORT __attribute__ ((visibility ("default")))
        #define EGS_MESH_LOCAL  __attribute__ ((visibility ("hidden")))
    #else
        #define EGS_MESH_EXPORT
        #define EGS_MESH_LOCAL
    #endif
 
#endif
 
// exclude from doxygen
class EGS_Mesh_Octree;
 
class EGS_MESH_EXPORT EGS_MeshSpec {
public:
 
    struct Tetrahedron {
        Tetrahedron(int tag, int medium_tag, int a, int b, int c, int d) :
            tag(tag), medium_tag(medium_tag), a(a), b(b), c(c), d(d) {}
        int tag = -1;
        int medium_tag = -1;
        // nodes
        int a = -1;
        int b = -1;
        int c = -1;
        int d = -1;
    };
 
    struct Node {
        Node(int tag, double x, double y, double z) :
            tag(tag), x(x), y(y), z(z) {}
        int tag = -1;
        double x = 0.0;
        double y = 0.0;
        double z = 0.0;
    };
 
    struct Medium {
        Medium(int tag, std::string medium_name) :
            tag(tag), medium_name(medium_name) {}
        int tag = -1;
        std::string medium_name;
    };
 
    EGS_MeshSpec() = default;
    EGS_MeshSpec(std::vector<Tetrahedron> elements, std::vector<Node> nodes,
                 std::vector<Medium> media) : elements(std::move(elements)),
        nodes(std::move(nodes)), media(std::move(media)) {}
    EGS_MeshSpec(const EGS_MeshSpec &) = delete;
    EGS_MeshSpec &operator=(const EGS_MeshSpec &) = delete;
    // EGS_MeshSpec is move-only
    EGS_MeshSpec(EGS_MeshSpec &&) = default;
    EGS_MeshSpec &operator=(EGS_MeshSpec &&) = default;
    ~EGS_MeshSpec() = default;
 
    void checkValid() const;
 
    void scale(EGS_Float factor) {
        for (auto &node: nodes) {
            node.x *= factor;
            node.y *= factor;
            node.z *= factor;
        }
    }
 
    // Public members
 
    std::vector<EGS_MeshSpec::Tetrahedron> elements;
    std::vector<EGS_MeshSpec::Node> nodes;
    std::vector<EGS_MeshSpec::Medium> media;
};
 
class EGS_MESH_EXPORT EGS_Mesh : public EGS_BaseGeometry {
public:
    explicit EGS_Mesh(EGS_MeshSpec spec);
 
    // EGS_Mesh is move-only
    EGS_Mesh(const EGS_Mesh &) = delete;
    EGS_Mesh &operator=(const EGS_Mesh &) = delete;
 
    // Declare move constructor, move assignment, and destructor without
    // defining them. We can't define them yet because of the unique_ptr to
    // forward declared EGS_Mesh_Octree members.
    EGS_Mesh(EGS_Mesh &&);
    EGS_Mesh &operator=(EGS_Mesh &&);
    ~EGS_Mesh();
 
    int num_elements() const {
        return elt_tags_.size();
    }
 
    int num_nodes() const {
        return nodes_.size();
    }
 
    const std::array<int, 4> &element_neighbours(int i) const {
        return neighbours_.at(i);
    }
 
    EGS_Float element_volume(int i) const {
        const auto &n = element_nodes(i);
        return std::abs((n.A - n.D) * ((n.B - n.D) % (n.C - n.D))) / 6.0;
    }
 
    EGS_Float element_density(int i) const {
        return EGS_BaseGeometry::getMediumRho(medium_indices_.at(i));
    }
 
    int element_tag(int i) const {
        return elt_tags_.at(i);
    }
 
    inline bool is_boundary(int reg) const {
        return boundary_faces_[4*reg] || boundary_faces_[4*reg + 1] ||
               boundary_faces_[4*reg + 2] || boundary_faces_[4*reg + 3];
    }
 
    void printElement(int i, std::ostream &elt_info = std::cout) const {
        const auto &n = element_nodes(i);
        elt_info << " Tetrahedron " << i << ":\n"
                 << " \tNode coordinates (cm):\n"
                 << " \t0: " << n.A.x << " " << n.A.y << " " << n.A.z << "\n"
                 << " \t1: " << n.B.x << " " << n.B.y << " " << n.B.z << "\n"
                 << " \t2: " << n.C.x << " " << n.C.y << " " << n.C.z << "\n"
                 << " \t3: " << n.D.x << " " << n.C.y << " " << n.C.z << "\n"
                 << " \tNeighbour elements:\n"
                 << " \t\tOn face 0: " << neighbours_[i][0] << "\n"
                 << " \t\tOn face 1: " << neighbours_[i][1] << "\n"
                 << " \t\tOn face 2: " << neighbours_[i][2] << "\n"
                 << " \t\tOn face 3: " << neighbours_[i][3] << "\n"
                 << std::boolalpha
                 << " \tBoundary element: " << is_boundary(i) << "\n"
                 << " \tMedia index: "<< medium_indices_[i] << "\n";
    }
 
    // EGS_BaseGeometry interface
    const std::string &getType() const override {
        return type;
    }
    bool isInside(const EGS_Vector &x) override;
    int inside(const EGS_Vector &x) override;
    int medium(int ireg) const override;
    int isWhere(const EGS_Vector &x) override;
    int howfar(int ireg, const EGS_Vector &x, const EGS_Vector &u,
               EGS_Float &t, int *newmed=0, EGS_Vector *normal=0) override;
    EGS_Float hownear(int ireg, const EGS_Vector &x) override;
    void printInfo() const override;
 
    bool insideElement(int i, const EGS_Vector &x);
 
    // exclude from doxygen, should be private but used by EGS_Mesh_Octree::Node
    struct Intersection {
        Intersection(EGS_Float dist, int face_index)
            : dist(dist), face_index(face_index) {}
        EGS_Float dist;
        int face_index;
    };
 
    // `howfar` helper: Determine the closest boundary face intersection
    Intersection closest_boundary_face(int ireg, const EGS_Vector &x, const EGS_Vector &u);
 
    struct Nodes {
        const EGS_Vector &A;
        const EGS_Vector &B;
        const EGS_Vector &C;
        const EGS_Vector &D;
    };
 
    Nodes element_nodes(int element) const {
        const auto &node_indices = elt_node_indices_.at(element);
        return Nodes {
            nodes_.at(node_indices[0]),
            nodes_.at(node_indices[1]),
            nodes_.at(node_indices[2]),
            nodes_.at(node_indices[3])
        };
    }
 
    const EGS_Vector &node_coordinates(int node_offset) const {
        return nodes_.at(node_offset);
    }
 
    const std::array<int, 4> &element_node_offsets(int element) const {
        return elt_node_indices_.at(element);
    }
 
    static EGS_Float get_min_step_size() {
        return EGS_Mesh::min_step_size;
    }
 
private:
    // `hownear` helper method
    // Given a tetrahedron ireg, find the minimum distance to a face in any direction.
    EGS_Float min_interior_face_dist(int ireg, const EGS_Vector &x);
 
    // `hownear` helper method
    // Outside the mesh, find the minimum distance to the mesh in any direction (ireg = -1)
    EGS_Float min_exterior_face_dist(const EGS_Vector &x);
 
    // `howfar` helper method inside a given tetrahedron
    int howfar_interior(int ireg, const EGS_Vector &x, const EGS_Vector &u,
                        EGS_Float &t, int *newmed, EGS_Vector *normal);
 
    // `howfar_interior` helper methods
 
    struct PointLocation {
        PointLocation() = default;
        PointLocation(EGS_Float direction_dot_normal, EGS_Float signed_distance)
            : direction_dot_normal(direction_dot_normal), signed_distance(
                  signed_distance) {}
 
        EGS_Float direction_dot_normal = 0.0;
        EGS_Float signed_distance = 0.0;
    };
 
    PointLocation find_point_location(const EGS_Vector &x, const
                                      EGS_Vector &u, const EGS_Vector &plane_point, const EGS_Vector &
                                      plane_normal);
 
    Intersection find_interior_intersection(
        const std::array<PointLocation, 4> &ixs);
 
    int howfar_interior_thick_plane(
        const std::array<PointLocation, 4> &intersect_tests, int ireg,
        const EGS_Vector &x, const EGS_Vector &u, EGS_Float &t, int *newmed,
        EGS_Vector *normal);
 
    // If the particle is lost, try to recover transport by shifting the
    // particle along a small step.
    int howfar_interior_recover_lost_particle(int ireg, const EGS_Vector &x,
            const EGS_Vector &u, EGS_Float &t, int *newmed);
 
    // `howfar` helper method outside the mesh
    int howfar_exterior(const EGS_Vector &x, const EGS_Vector &u, EGS_Float &t,
                        int *newmed, EGS_Vector *normal);
 
    inline void update_medium(int newreg, int *newmed) const {
        if (!newmed) {
            return;
        }
        if (newreg == -1) {
            // vacuum
            *newmed = -1;
        }
        else {
            *newmed = medium(newreg);
        }
    }
 
    inline void update_normal(const EGS_Vector &face_normal,
                              const EGS_Vector &u_norm, EGS_Vector *normal) const {
        if (!normal) {
            return;
        }
        // egs++ convention is normal pointing opposite view ray
        if (face_normal * u_norm > 0.0) {
            *normal = -1.0 * face_normal;
        }
        else {
            *normal = face_normal;
        }
    }
 
    // Can only be called after initializeElements (for num_elements())
    EGS_InfoFunction get_logger() const {
        if (num_elements() < 50000) {
            // don't log for small meshes since loading is near instantaneous
            return nullptr;
        }
        return egsInformation;
    }
 
    // Constructor helper methods:
    //
    // Each logical piece is a separate function to help reduce peak memory
    // usage. For large meshes, having temporaries around until the end of the
    // constructor, including during intense operations like constructing the
    // octrees, etc. can raise the peak memory usage far above the steady state
    // requirements.
 
    // Initialize the mesh element information in the EGS_Mesh constructor.
    // Must be called before any other initialize functions.  After this method
    // is called, the following member data is initialized:
    // * EGS_Mesh::nodes_
    // * EGS_Mesh::elt_tags_
    // * EGS_Mesh::elt_node_indices_
    // * EGS_BaseGeometry::nreg
    // and member functions that depend on this data, like num_elements().
    void initializeElements(std::vector<EGS_MeshSpec::Tetrahedron> elements,
                            std::vector<EGS_MeshSpec::Node> nodes,
                            std::vector<EGS_MeshSpec::Medium> materials);
 
    // Initialize mesh element medium offsets, adding any previously undefined
    // media to the EGS_BaseGeometry media list. Responsible for initializing:
    // * EGS_Mesh::medium_indices_
    void initializeMedia(std::vector<EGS_MeshSpec::Tetrahedron> elements,
                         std::vector<EGS_MeshSpec::Medium> materials);
 
    // Initialize neigbhour and boundary information. Must be called after
    // initializeElements. Responsible for initializing:
    // * EGS_Mesh::neighbours_
    // * EGS_Mesh::boundary_faces_
    void initializeNeighbours();
 
    // Initialize the two octrees used to accelerate transport. Both
    // initializeElements and initializeNeighbours must be called to properly
    // set up the octrees. Responsible for initializing:
    // * EGS_Mesh::volume_tree_
    // * EGS_Mesh::surface_tree_
    void initializeOctrees();
 
    // Initialize the tetrahedron face normals. Must be called after
    // initializeElements. Responsible for initializing EGS_Mesh:face_normals_.
    void initializeNormals();
 
    std::vector<EGS_Vector> nodes_;
    std::vector<int> elt_tags_;
    std::vector<std::array<int, 4>> elt_node_indices_;
    // 4 * num_elts of which faces are boundaries
    // TODO: try vec<array<bool, 4>>
    std::vector<bool> boundary_faces_;
    // TODO if memory is an issue, could try storing tets as sets of faces,
    // faces as sets of edges, etc.
    std::vector<std::array<EGS_Vector, 4>> face_normals_;
    std::vector<int> medium_indices_;
 
    std::unique_ptr<EGS_Mesh_Octree> volume_tree_;
    std::unique_ptr<EGS_Mesh_Octree> surface_tree_;
 
    std::vector<std::array<int, 4>> neighbours_;
    static const std::string type;
 
    static constexpr EGS_Float min_step_size = 1e-10;
};
 
// exclude from doxygen
 
namespace egs_mesh {
 
// The egs_mesh::internal namespace is for internal API functions and may change
// without warning.
namespace internal {
 
class EGS_MESH_EXPORT PercentCounter {
public:
    // Create a new counter. This doesn't log anything or start the timer yet.
    // The counter must be activated later using `start`.
    PercentCounter(EGS_InfoFunction info, const std::string &msg);
 
    // Start the counter's progress toward the provided goal. The goal must be
    // a positive number and fit into an int. Logging and timing begin at this
    // point.
    void start(EGS_Float goal);
 
    // Advance the counter by a fraction of the goal value. Assumes delta is
    // positive.
    void step(EGS_Float delta);
 
    // After the task is finished, print a new message and the elapsed time.
    void finish(const std::string &end_msg);
 
private:
    // egsInformation-like function pointer.
    EGS_InfoFunction info_;
    // Progress message.
    std::string msg_;
    // Goal value.
    double goal_ = 0.0;
    // Progress value, percent complete = progress_ / goal_.
    double progress_ = 0.0;
    // The last progress percentage that was displayed, used to avoid redundant
    // I/O calls.
    int old_percent_ = 0;
    // The time when PercentCounter::start was called.
    std::chrono::time_point<std::chrono::system_clock> t_start_;
    // Whether to update the percentage in real time (true) or just report when
    // the task is finished (false).
    bool interactive_ = false;
};
 
} // namespace internal
 
} // namespace egs_mesh
 
 
#endif // EGS_MESH