MeshObject.cpp

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidGeometry/Objects/MeshObject.h"
#include "MantidGeometry/Objects/MeshObjectCommon.h"
#include "MantidGeometry/Objects/Track.h"
#include "MantidGeometry/RandomPoint.h"
#include "MantidGeometry/Rendering/GeometryHandler.h"
#include "MantidGeometry/Rendering/vtkGeometryCacheReader.h"
#include "MantidGeometry/Rendering/vtkGeometryCacheWriter.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/Material.h"
#include "MantidNexus/NexusFile.h"
 
#include <algorithm>
#include <memory>
#include <utility>
 
namespace Mantid::Geometry {
 
MeshObject::MeshObject(std::vector<uint32_t> faces, std::vector<Kernel::V3D> vertices, const Kernel::Material &material)
    : m_boundingBox(), m_id("MeshObject"), m_triangles(std::move(faces)), m_vertices(std::move(vertices)),
      m_material(material) {
 
  initialize();
}
 
MeshObject::MeshObject(std::vector<uint32_t> &&faces, std::vector<Kernel::V3D> &&vertices,
                       const Kernel::Material &&material)
    : m_boundingBox(), m_id("MeshObject"), m_triangles(std::move(faces)), m_vertices(std::move(vertices)),
      m_material(material) {
 
  initialize();
}
 
// Do things that need to be done in constructor
void MeshObject::initialize() {
 
  MeshObjectCommon::checkVertexLimit(m_vertices.size());
  m_handler = std::make_shared<GeometryHandler>(*this);
}
 
const Kernel::Material &MeshObject::material() const { return m_material; }
 
void MeshObject::setMaterial(const Kernel::Material &material) { m_material = material; }
 
bool MeshObject::hasValidShape() const {
  // May enclose volume if there are at
  // at least 4 triangles and 4 vertices (Tetrahedron)
  return (numberOfTriangles() >= 4 && numberOfVertices() >= 4);
}
 
bool MeshObject::isValid(const Kernel::V3D &point) const {
 
  BoundingBox bb = getBoundingBox();
  if (!bb.isPointInside(point)) {
    return false;
  }
 
  Kernel::V3D direction(0.0, 0.0, 1.0); // direction to look for intersections
  std::vector<Kernel::V3D> intersectionPoints;
  std::vector<TrackDirection> entryExitFlags;
 
  getIntersections(point, direction, intersectionPoints, entryExitFlags);
 
  if (intersectionPoints.empty()) {
    return false;
  }
 
  // True if point is on surface
  const auto it = std::find_if(
      intersectionPoints.cbegin(), intersectionPoints.cend(),
      [this, &point](const auto &intersectionPoint) { return point.distance(intersectionPoint) < M_TOLERANCE; });
  if (it != intersectionPoints.cend())
    return true;
 
  // Look for nearest point then check its entry-exit flag
  double nearestPointDistance = point.distance(intersectionPoints[0]);
  size_t nearestPointIndex = 0;
  for (size_t i = 1; i < intersectionPoints.size(); ++i) {
    if (point.distance(intersectionPoints[i]) < nearestPointDistance) {
      nearestPointDistance = point.distance(intersectionPoints[i]);
      nearestPointIndex = i;
    }
  }
  return (entryExitFlags[nearestPointIndex] == TrackDirection::LEAVING);
}
 
bool MeshObject::isOnSide(const Kernel::V3D &point) const {
 
  BoundingBox bb = getBoundingBox();
  if (!bb.isPointInside(point)) {
    return false;
  }
 
  const std::vector<Kernel::V3D> directions = {Kernel::V3D{0, 0, 1}, Kernel::V3D{0, 1, 0},
                                               Kernel::V3D{1, 0, 0}}; // directions to look for intersections
  // We have to look in several directions in case a point is on a face
  // or edge parallel to the first direction or also the second direction.
  for (const auto &direction : directions) {
    std::vector<Kernel::V3D> intersectionPoints;
    std::vector<TrackDirection> entryExitFlags;
 
    getIntersections(point, direction, intersectionPoints, entryExitFlags);
 
    if (intersectionPoints.empty()) {
      return false;
    }
 
    const auto it = std::find_if(
        intersectionPoints.cbegin(), intersectionPoints.cend(),
        [this, &point](const auto &intersectionPoint) { return point.distance(intersectionPoint) < M_TOLERANCE; });
    if (it != intersectionPoints.cend())
      return true;
  }
  return false;
}
 
int MeshObject::interceptSurface(Geometry::Track &UT) const {
  int originalCount = UT.count(); // Number of intersections original track
  BoundingBox bb = getBoundingBox();
  if (!bb.doesLineIntersect(UT)) {
    return 0;
  }
 
  std::vector<Kernel::V3D> intersectionPoints;
  std::vector<TrackDirection> entryExit;
 
  getIntersections(UT.startPoint(), UT.direction(), intersectionPoints, entryExit);
  if (intersectionPoints.empty())
    return 0; // Quit if no intersections found
 
  // For a 3D mesh, a ray may intersect several segments
  for (size_t i = 0; i < intersectionPoints.size(); ++i) {
    UT.addPoint(entryExit[i], intersectionPoints[i], *this);
  }
  UT.buildLink();
 
  return UT.count() - originalCount;
}
 
double MeshObject::distance(const Track &track) const {
  Kernel::V3D vertex1, vertex2, vertex3, intersection;
  TrackDirection unused;
  for (size_t i = 0; getTriangle(i, vertex1, vertex2, vertex3); ++i) {
    if (MeshObjectCommon::rayIntersectsTriangle(track.startPoint(), track.direction(), vertex1, vertex2, vertex3,
                                                intersection, unused)) {
      return track.startPoint().distance(intersection);
    }
  }
  std::ostringstream os;
  os << "Unable to find intersection with object with track starting at " << track.startPoint() << " in direction "
     << track.direction() << "\n";
  throw std::runtime_error(os.str());
}
 
void MeshObject::getIntersections(const Kernel::V3D &start, const Kernel::V3D &direction,
                                  std::vector<Kernel::V3D> &intersectionPoints,
                                  std::vector<TrackDirection> &entryExitFlags) const {
 
  Kernel::V3D vertex1, vertex2, vertex3, intersection;
  TrackDirection entryExit;
  for (size_t i = 0; getTriangle(i, vertex1, vertex2, vertex3); ++i) {
    if (MeshObjectCommon::rayIntersectsTriangle(start, direction, vertex1, vertex2, vertex3, intersection, entryExit)) {
      intersectionPoints.emplace_back(intersection);
      entryExitFlags.emplace_back(entryExit);
    }
  }
  // still need to deal with edge cases
}
 
/*
 * Get a triangle - useful for iterating over triangles
 * @param index :: Index of triangle in MeshObject
 * @param v1 :: First vertex of triangle
 * @param v2 :: Second vertex of triangle
 * @param v3 :: Third vertex of triangle
 * @returns true if the specified triangle exists
 */
bool MeshObject::getTriangle(const size_t index, Kernel::V3D &vertex1, Kernel::V3D &vertex2,
                             Kernel::V3D &vertex3) const {
  bool triangleExists = index < m_triangles.size() / 3;
  if (triangleExists) {
    vertex1 = m_vertices[m_triangles[3 * index]];
    vertex2 = m_vertices[m_triangles[3 * index + 1]];
    vertex3 = m_vertices[m_triangles[3 * index + 2]];
  }
  return triangleExists;
}
 
int MeshObject::calcValidType(const Kernel::V3D &point, const Kernel::V3D &uVec) const {
  const Kernel::V3D shift(uVec * Kernel::Tolerance * 25.0);
  const Kernel::V3D testA(point - shift);
  const Kernel::V3D testB(point + shift);
  const int flagA = isValid(testA);
  const int flagB = isValid(testB);
  if (!(flagA ^ flagB))
    return 0;
  return (flagA) ? -1 : 1;
}
 
void MeshObject::getBoundingBox(double &xmax, double &ymax, double &zmax, double &xmin, double &ymin,
                                double &zmin) const {
  return MeshObjectCommon::getBoundingBox(m_vertices, m_boundingBox, xmax, ymax, zmax, xmin, ymin, zmin);
}
 
double MeshObject::solidAngle(const SolidAngleParams &params) const {
  double solidAngleSum(0), solidAngleNegativeSum(0);
  Kernel::V3D vertex1, vertex2, vertex3;
  for (size_t i = 0; this->getTriangle(i, vertex1, vertex2, vertex3); ++i) {
    double sa = MeshObjectCommon::getTriangleSolidAngle(vertex1, vertex2, vertex3, params.observer());
    if (sa > 0.0) {
      solidAngleSum += sa;
    } else {
      solidAngleNegativeSum += sa;
    }
  }
  /*
    Same implementation as CSGObject. Assumes a convex closed mesh with
    solidAngleSum == -solidAngleNegativeSum
 
    Average is used to bypass issues with winding order. Surface normal
    affects magnitude of solid angle. See CSGObject.
  */
  return 0.5 * (solidAngleSum - solidAngleNegativeSum);
}
 
double MeshObject::solidAngle(const SolidAngleParams &params, const Kernel::V3D &scaleFactor) const {
  std::vector<Kernel::V3D> scaledVertices;
  scaledVertices.reserve(m_vertices.size());
  std::transform(m_vertices.cbegin(), m_vertices.cend(), std::back_inserter(scaledVertices),
                 [&scaleFactor](const auto &vertex) { return scaleFactor * vertex; });
  MeshObject meshScaled(m_triangles, scaledVertices, m_material);
  return meshScaled.solidAngle(params);
}
 
double MeshObject::volume() const {
  // Select centre of bounding box as centre point.
  // For each triangle calculate the signed volume of
  // the tetrahedron formed by the triangle and the
  // centre point. Then add to total.
 
  BoundingBox bb = getBoundingBox();
  double cX = 0.5 * (bb.xMax() + bb.xMin());
  double cY = 0.5 * (bb.yMax() + bb.yMin());
  double cZ = 0.5 * (bb.zMax() + bb.zMin());
  Kernel::V3D centre(cX, cY, cZ);
 
  double volumeTimesSix(0.0);
 
  Kernel::V3D vertex1, vertex2, vertex3;
  for (size_t i = 0; getTriangle(i, vertex1, vertex2, vertex3); ++i) {
    Kernel::V3D a = vertex1 - centre;
    Kernel::V3D b = vertex2 - centre;
    Kernel::V3D c = vertex3 - centre;
    volumeTimesSix += a.scalar_prod(b.cross_prod(c));
  }
 
  return volumeTimesSix / 6.0;
}
 
const BoundingBox &MeshObject::getBoundingBox() const {
  return MeshObjectCommon::getBoundingBox(m_vertices, m_boundingBox);
}
 
int MeshObject::getPointInObject(Kernel::V3D &point) const {
 
  Kernel::V3D testPt(0, 0, 0);
  // Try centre of bounding box as initial guess, if we have one.
  const BoundingBox &boundingBox = getBoundingBox();
  if (boundingBox.isNonNull()) {
    testPt = boundingBox.centrePoint();
    if (searchForObject(testPt)) {
      point = testPt;
      return 1;
    }
  }
 
  return 0;
}
 
std::optional<Kernel::V3D> MeshObject::generatePointInObject(Kernel::PseudoRandomNumberGenerator &rng,
                                                             const size_t maxAttempts) const {
  const auto &bbox = getBoundingBox();
  if (bbox.isNull()) {
    throw std::runtime_error("Object::generatePointInObject() - Invalid "
                             "bounding box. Cannot generate new point.");
  }
  return generatePointInObject(rng, bbox, maxAttempts);
}
 
std::optional<Kernel::V3D> MeshObject::generatePointInObject(Kernel::PseudoRandomNumberGenerator &rng,
                                                             const BoundingBox &activeRegion,
                                                             const size_t maxAttempts) const {
 
  const auto point = RandomPoint::bounded(*this, rng, activeRegion, maxAttempts);
 
  return point;
}
 
bool MeshObject::searchForObject(Kernel::V3D &point) const {
  //
  // Method - check if point in object, if not search directions along
  // principle axes using interceptSurface
  //
  if (isValid(point))
    return true;
  for (const auto &dir : {Kernel::V3D(1., 0., 0.), Kernel::V3D(-1., 0., 0.), Kernel::V3D(0., 1., 0.),
                          Kernel::V3D(0., -1., 0.), Kernel::V3D(0., 0., 1.), Kernel::V3D(0., 0., -1.)}) {
    Geometry::Track tr(point, dir);
    if (this->interceptSurface(tr) > 0) {
      point = tr.cbegin()->entryPoint;
      return true;
    }
  }
  return false;
}
 
void MeshObject::setGeometryHandler(const std::shared_ptr<GeometryHandler> &h) {
  if (h == nullptr)
    return;
  m_handler = h;
}
 
void MeshObject::draw() const {
  if (m_handler == nullptr)
    return;
  // Render the Object
  m_handler->render();
}
 
void MeshObject::initDraw() const {
  if (m_handler == nullptr)
    return;
  // Render the Object
  m_handler->initialize();
}
 
std::shared_ptr<GeometryHandler> MeshObject::getGeometryHandler() const {
  // Check if the geometry handler is upto dated with the cache, if not then
  // cache it now.
  return m_handler;
}
 
void MeshObject::rotate(const Kernel::Matrix<double> &rotationMatrix) {
  std::for_each(m_vertices.begin(), m_vertices.end(),
                [&rotationMatrix](auto &vertex) { vertex.rotate(rotationMatrix); });
}
 
void MeshObject::bakeGoniometerRotation(const Kernel::Matrix<double> &rotationMatrix) {
  rotate(rotationMatrix);
  m_appliedRotation = rotationMatrix * m_appliedRotation;
}
 
void MeshObject::setAppliedGoniometerRotation(const Kernel::Matrix<double> &bakedRotation) {
  m_appliedRotation = bakedRotation;
}
 
void MeshObject::translate(const Kernel::V3D &translationVector) {
  std::transform(m_vertices.cbegin(), m_vertices.cend(), m_vertices.begin(),
                 [&translationVector](const auto &vertex) { return vertex + translationVector; });
}
 
void MeshObject::scale(const double scaleFactor) {
  std::transform(m_vertices.cbegin(), m_vertices.cend(), m_vertices.begin(),
                 [&scaleFactor](const auto &vertex) { return vertex * scaleFactor; });
}
 
void MeshObject::multiply(const Kernel::Matrix<double> &matrix) {
  if ((matrix.numCols() != 4) || (matrix.numRows() != 4)) {
    throw std::invalid_argument("Transformation matrix must be 4 x 4");
  }
 
  // create homogenous coordinates for the input vector with 4th element
  // equal to 1 (position)
  for (Kernel::V3D &vertex : m_vertices) {
    std::vector<double> vertexin(4);
    vertexin[0] = vertex.X();
    vertexin[1] = vertex.Y();
    vertexin[2] = vertex.Z();
    vertexin[3] = 1;
    std::vector<double> vertexout(4);
    matrix.multiplyPoint(vertexin, vertexout);
    Kernel::V3D newvertex(vertexout[0], vertexout[1], vertexout[2]);
    vertex = newvertex;
  }
}
 
void MeshObject::updateGeometryHandler() {
  return; // Hopefully nothing necessary here
}
 
size_t MeshObject::numberOfTriangles() const { return m_triangles.size() / 3; }
 
const std::vector<uint32_t> &MeshObject::getTriangles() const { return m_triangles; }
 
size_t MeshObject::numberOfVertices() const { return m_vertices.size(); }
 
std::vector<double> MeshObject::getVertices() const { return MeshObjectCommon::getVertices(m_vertices); }
 
const std::vector<Kernel::V3D> &MeshObject::getV3Ds() const { return m_vertices; }
 
detail::ShapeInfo::GeometryShape MeshObject::shape() const { return detail::ShapeInfo::GeometryShape::NOSHAPE; }
 
const detail::ShapeInfo &MeshObject::shapeInfo() const {
  throw std::runtime_error("MeshObject::shapeInfo() is not implemented");
}
 
void MeshObject::GetObjectGeom(detail::ShapeInfo::GeometryShape &type, std::vector<Kernel::V3D> &vectors,
                               double &innerRadius, double &radius, double &height) const {
  // In practice, this outputs type = -1,
  // to indicate not a "standard" object (cuboid/cone/cyl/sphere).
  // Retained for possible future use.
  type = detail::ShapeInfo::GeometryShape::NOSHAPE;
  if (m_handler == nullptr)
    return;
  m_handler->GetObjectGeom(type, vectors, innerRadius, radius, height);
}
 
void MeshObject::saveNexus(Nexus::File *file, const std::string &group) const {
  file->makeGroup(group, "NXoff_geometry", true);
  file->writeData("vertices", getVertices());
  file->writeData("winding_order", getTriangles());
 
  const size_t nTriangles = numberOfTriangles();
  std::vector<uint32_t> faceIndices(nTriangles);
  for (size_t i = 0; i < nTriangles; ++i) {
    faceIndices[i] = static_cast<uint32_t>(i * 3);
  }
  file->writeData("faces", faceIndices);
 
  // Written only when non-identity, so files of a shape in its own frame are byte-for-byte as before
  if (m_appliedRotation != Kernel::Matrix<double>(3, 3, true)) {
    file->writeData("applied_goniometer_rotation", m_appliedRotation.getVector());
  }
  file->closeGroup();
}
 
std::shared_ptr<MeshObject> MeshObject::loadNexus(Nexus::File *file, const std::string &group,
                                                  const Kernel::Material &material) {
  file->openGroup(group, "NXoff_geometry");
 
  std::vector<double> flatVertices;
  file->readData("vertices", flatVertices);
 
  std::vector<uint32_t> windingOrder;
  file->readData("winding_order", windingOrder);
 
  std::vector<uint32_t> faceIndices;
  file->readData("faces", faceIndices);
 
  // Absent for a shape in its own frame and for any file written before this was saved, both of
  // which mean identity. Has to be read before the group is closed.
  std::vector<double> appliedRotation;
  const bool hasAppliedRotation = file->hasData("applied_goniometer_rotation");
  if (hasAppliedRotation) {
    file->readData("applied_goniometer_rotation", appliedRotation);
  }
 
  file->closeGroup();
 
  // Convert flat vertex array to V3D
  const size_t nVerts = flatVertices.size() / 3;
  std::vector<Kernel::V3D> vertices;
  vertices.reserve(nVerts);
  for (size_t i = 0; i < nVerts; ++i) {
    vertices.emplace_back(flatVertices[3 * i], flatVertices[3 * i + 1], flatVertices[3 * i + 2]);
  }
 
  // Convert OFF face indices + winding order to triangle indices
  std::vector<uint32_t> triangles;
  triangles.reserve(windingOrder.size());
  for (size_t f = 0; f < faceIndices.size(); ++f) {
    const uint32_t start = faceIndices[f];
    const uint32_t end = (f + 1 < faceIndices.size()) ? faceIndices[f + 1] : static_cast<uint32_t>(windingOrder.size());
    const uint32_t nVertsInFace = end - start;
    // We assume that any polygon face is convex and that we can use a fan triangulation
    for (uint32_t v = 1; v + 1 < nVertsInFace; ++v) {
      triangles.push_back(windingOrder.at(start));
      triangles.push_back(windingOrder.at(start + v));
      triangles.push_back(windingOrder.at(start + v + 1));
    }
  }
 
  auto object = std::make_shared<MeshObject>(std::move(triangles), std::move(vertices), material);
  if (hasAppliedRotation) {
    // skipping it instead would leave the rotated vertices looking unrotated, to be rotated again
    if (appliedRotation.size() != 9) {
      throw std::invalid_argument("applied_goniometer_rotation in '" + group + "' must hold 9 values, not " +
                                  std::to_string(appliedRotation.size()));
    }
    // Record only - the vertices just read are already rotated, so baking here would double it
    object->setAppliedGoniometerRotation(Kernel::Matrix<double>(appliedRotation));
  }
  return object;
}
 
} // namespace Mantid::Geometry