ShapeFactory.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 +
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
 
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidGeometry/Instrument/Container.h"
#include "MantidGeometry/Objects/CSGObject.h"
#include "MantidGeometry/Rendering/GeometryHandler.h"
#include "MantidGeometry/Rendering/ShapeInfo.h"
#include "MantidGeometry/Surfaces/Cone.h"
#include "MantidGeometry/Surfaces/Cylinder.h"
#include "MantidGeometry/Surfaces/Plane.h"
#include "MantidGeometry/Surfaces/Quadratic.h"
#include "MantidGeometry/Surfaces/Sphere.h"
#include "MantidGeometry/Surfaces/Surface.h"
#include "MantidGeometry/Surfaces/Torus.h"
 
#include "MantidKernel/Logger.h"
#include "MantidKernel/Quat.h"
 
#include <Poco/AutoPtr.h>
#include <Poco/DOM/DOMParser.h>
#include <Poco/DOM/DOMWriter.h>
#include <Poco/DOM/Document.h>
#include <Poco/DOM/Element.h>
#include <Poco/DOM/NodeList.h>
 
#include "boost/make_shared.hpp"
 
#include <algorithm>
 
using Poco::XML::Document;
using Poco::XML::DOMParser;
using Poco::XML::DOMWriter;
using Poco::XML::Element;
using Poco::XML::Node;
using Poco::XML::NodeList;
 
namespace Mantid::Geometry {
 
using namespace Kernel;
 
namespace {
const V3D DEFAULT_CENTRE(0, 0, 0);
const V3D DEFAULT_AXIS(0, 0, 1);
 
Logger g_log("ShapeFactory");
} // namespace
 
namespace {
std::vector<double> DegreesToRadians(const std::vector<double> &anglesDegrees) {
  std::vector<double> anglesRadians;
  std::transform(anglesDegrees.cbegin(), anglesDegrees.cend(), std::back_inserter(anglesRadians),
                 [](const auto angle) { return angle * M_PI / 180.0; });
  return anglesRadians;
}
} // namespace
 
std::shared_ptr<CSGObject> ShapeFactory::createShape(std::string shapeXML, bool addTypeTag) {
  // wrap in a type tag
  if (addTypeTag)
    shapeXML = "<type name=\"userShape\"> " + shapeXML + " </type>";
 
  // Set up the DOM parser and parse xml string
  DOMParser pParser;
  Poco::AutoPtr<Document> pDoc;
  try {
    pDoc = pParser.parseString(shapeXML);
  } catch (...) {
    g_log.warning("Unable to parse XML string " + shapeXML + " . Empty geometry Object is returned.");
 
    return std::make_shared<CSGObject>();
  }
  // Get pointer to root element
  Element *pRootElem = pDoc->documentElement();
 
  // convert into a Geometry object
  return createShape(pRootElem);
}
 
std::shared_ptr<CSGObject> ShapeFactory::createShape(Poco::XML::Element *pElem) {
  // Write the definition to a string to store in the final object
  std::stringstream xmlstream;
  DOMWriter writer;
  writer.writeNode(xmlstream, pElem);
  std::string shapeXML = xmlstream.str();
  auto retVal = std::make_shared<CSGObject>(shapeXML);
 
  // if no <algebra> element then use default algebra
  bool defaultAlgebra(false);
  // get algebra string
  Poco::AutoPtr<NodeList> pNL_algebra = pElem->getElementsByTagName("algebra");
  std::string algebraFromUser;
  if (pNL_algebra->length() == 0) {
    defaultAlgebra = true;
  } else if (pNL_algebra->length() == 1) {
    auto *pElemAlgebra = static_cast<Element *>(pNL_algebra->item(0));
    algebraFromUser = pElemAlgebra->getAttribute("val");
  } else {
    g_log.warning() << "More than one algebra string defined for this shape. "
                    << "Maximum one allowed. Therefore empty shape is returned.";
    return retVal;
  }
 
  Poco::AutoPtr<NodeList> pNL_gonio = pElem->getElementsByTagName("goniometer");
  auto *pElemGonio = static_cast<Element *>(pNL_gonio->item(0));
  m_gonioRotateMatrix.identityMatrix();
  if (pElemGonio) {
    // Parse the rotate matrix, defined in units of radians
    for (size_t i = 0; i < 3; ++i) {
      for (size_t j = 0; j < 3; ++j) {
        m_gonioRotateMatrix[i][j] = getDoubleAttribute(pElemGonio, "a" + std::to_string(i + 1) + std::to_string(j + 1));
      }
    }
  }
 
  Poco::AutoPtr<NodeList> pNL_rotate_all = pElem->getElementsByTagName("rotate-all");
  auto *pElemRotateAll = static_cast<Element *>(pNL_rotate_all->item(0));
  m_rotateAllMatrix.identityMatrix();
  if (pElemRotateAll) {
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElemRotateAll));
    m_rotateAllMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
  }
 
  // match id given to a shape by the user to
  // id understandable by Mantid code
  std::map<std::string, std::string> idMatching;
 
  // loop over all the sub-elements of pElem
  Poco::AutoPtr<NodeList> pNL = pElem->childNodes(); // get all child nodes
  unsigned long pNL_length = pNL->length();
  int numPrimitives = 0;
  // stores the primitives that will be
  // used to build final shape
  std::map<int, std::shared_ptr<Surface>> primitives;
  // used to build up unique id's for each shape added. Must start
  // from int > zero.
  int l_id = 1;
  // Element of fixed complete object
  Element *lastElement = nullptr;
  for (unsigned int i = 0; i < pNL_length; i++) {
    if ((pNL->item(i))->nodeType() == Node::ELEMENT_NODE) {
      auto *pE = static_cast<Element *>(pNL->item(i));
 
      // assume for now that if sub-element has attribute id then it is a shape
      // element
      if (pE->hasAttribute("id")) {
        std::string idFromUser = pE->getAttribute("id"); // get id
 
        std::string primitiveName = pE->tagName(); // get name of primitive
 
        // if there are any error thrown while parsing the XML string for a
        // given shape
        // write out a warning to the user that this shape is ignored. If all
        // shapes are ignored
        // this way an empty object is returned to the user.
        try {
          if (primitiveName == "sphere") {
            lastElement = pE;
            idMatching[idFromUser] = parseSphere(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "infinite-plane") {
            idMatching[idFromUser] = parseInfinitePlane(pE, primitives, l_id);
            retVal->setFiniteGeometryFlag(false);
            numPrimitives++;
          } else if (primitiveName == "infinite-cylinder") {
            idMatching[idFromUser] = parseInfiniteCylinder(pE, primitives, l_id);
            retVal->setFiniteGeometryFlag(false);
            numPrimitives++;
          } else if (primitiveName == "cylinder") {
            lastElement = pE;
            idMatching[idFromUser] = parseCylinder(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "hollow-cylinder") {
            lastElement = pE;
            idMatching[idFromUser] = parseHollowCylinder(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "cuboid") {
            lastElement = pE;
            idMatching[idFromUser] = parseCuboid(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "infinite-cone") {
            idMatching[idFromUser] = parseInfiniteCone(pE, primitives, l_id);
            retVal->setFiniteGeometryFlag(false);
            numPrimitives++;
          } else if (primitiveName == "cone") {
            lastElement = pE;
            idMatching[idFromUser] = parseCone(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "hexahedron") {
            lastElement = pE;
            idMatching[idFromUser] = parseHexahedron(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "tapered-guide") {
            idMatching[idFromUser] = parseTaperedGuide(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "torus") {
            idMatching[idFromUser] = parseTorus(pE, primitives, l_id);
            numPrimitives++;
          } else if (primitiveName == "slice-of-cylinder-ring") {
            idMatching[idFromUser] = parseSliceOfCylinderRing(pE, primitives, l_id);
            numPrimitives++;
          } else {
            g_log.warning(primitiveName + " not a recognised geometric shape. This shape is ignored.");
          }
        } catch (std::invalid_argument &e) {
          g_log.warning() << e.what() << " <" << primitiveName << "> shape is ignored.";
        } catch (std::runtime_error &e) {
          g_log.warning() << e.what() << " <" << primitiveName << "> shape is ignored.";
        } catch (...) {
          g_log.warning() << " Problem with parsing XML string for <" << primitiveName << ">. This shape is ignored.";
        }
      }
    }
  }
 
  if (!defaultAlgebra) {
    // Translate algebra string defined by the user into something Mantid can
    // understand
 
    // std::string algebra;  // to hold algebra in a way Mantid can understand
    std::map<std::string, std::string>::iterator iter;
    std::map<size_t, std::string, std::greater<size_t>> allFound;
    for (iter = idMatching.begin(); iter != idMatching.end(); ++iter) {
      size_t found = algebraFromUser.find(iter->first);
 
      if (found == std::string::npos) {
        defaultAlgebra = true;
        g_log.warning() << "Algebra shape Warning: " + iter->first +
                               " not found in algebra string: " + algebraFromUser + "\n" +
                               ". Default to equal shape to intersection of those defined.";
        break;
      } else {
        allFound[found] = iter->first;
      }
    }
 
    // Here do the actually swapping of strings
    // but only if the algebra containes all the shapes
    if (allFound.size() == idMatching.size()) {
      std::map<size_t, std::string, std::greater<size_t>>::iterator iter2;
      for (iter2 = allFound.begin(); iter2 != allFound.end(); ++iter2) {
        // std::string  kuse = iter2->second;
        algebraFromUser.replace(iter2->first, (iter2->second).size(), idMatching[iter2->second]);
      }
    }
  }
  if (defaultAlgebra) {
    algebraFromUser = ""; // reset in case we are overwriten invalid string
    std::map<std::string, std::string>::iterator iter;
    for (iter = idMatching.begin(); iter != idMatching.end(); ++iter) {
      algebraFromUser.append(iter->second + " "); // default is intersection
    }
  }
 
  // check to see if there actually were any primitives in 'type' xml element
  // and if yes then return empty Object. Otherwise populate Object with the
  // primitives
 
  if (numPrimitives == 0)
    return retVal;
  else {
    retVal->setObject(21, algebraFromUser);
    retVal->populate(primitives);
    // check whether there is only one surface/closed surface
    if (numPrimitives == 1 && lastElement != nullptr) // special case
    {
      // parse the primitive and create a Geometry handler for the object
      createGeometryHandler(lastElement, retVal);
    }
 
    // get bounding box string
    Poco::AutoPtr<NodeList> pNL_boundingBox = pElem->getElementsByTagName("bounding-box");
    if (pNL_boundingBox->length() != 1) // should probably throw an error if
                                        // more than 1 bounding box is
                                        // defined...
      return retVal;
 
    double xmin = std::stod((getShapeElement(pElem, "x-min"))->getAttribute("val"));
    double ymin = std::stod((getShapeElement(pElem, "y-min"))->getAttribute("val"));
    double zmin = std::stod((getShapeElement(pElem, "z-min"))->getAttribute("val"));
    double xmax = std::stod((getShapeElement(pElem, "x-max"))->getAttribute("val"));
    double ymax = std::stod((getShapeElement(pElem, "y-max"))->getAttribute("val"));
    double zmax = std::stod((getShapeElement(pElem, "z-max"))->getAttribute("val"));
 
    retVal->defineBoundingBox(xmax, ymax, zmax, xmin, ymin, zmin);
 
    return retVal;
  }
}
 
std::string ShapeFactory::parseSphere(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                      int &l_id) {
  Element *pElemCentre = getOptionalShapeElement(pElem, "centre");
  Element *pElemRadius = getShapeElement(pElem, "radius");
  const double radius = getDoubleAttribute(pElemRadius, "val");
  V3D centre = pElemCentre ? parsePosition(pElemCentre) : DEFAULT_CENTRE;
 
  // Only rotate the normal vector by the rotate-all and goniometer tags
  // Special case: do not obey rotate tag as rotation around the centre of sphere is unneccessary
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    centre.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    centre.rotate(m_gonioRotateMatrix);
  }
 
  prim[l_id] = std::make_shared<Sphere>(centre, radius);
  const auto algebra = sphereAlgebra(l_id);
  l_id++;
  return algebra;
}
 
std::string ShapeFactory::sphereAlgebra(const int surfaceID) { return "(-" + std::to_string(surfaceID) + ")"; }
 
std::string ShapeFactory::parseInfinitePlane(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                             int &l_id) {
  Element *pElemPip = getShapeElement(pElem, "point-in-plane");
  Element *pElemNormal = getShapeElement(pElem, "normal-to-plane");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  V3D normVec = normalize(parsePosition(pElemNormal));
  V3D centre = parsePosition(pElemPip);
 
  // Rotate the normal vector by the rotate, rotate-all and goniometer tags
  // Rotate the centre by the rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    normVec.rotate(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    centre.rotate(m_rotateAllMatrix);
    normVec.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    centre.rotate(m_gonioRotateMatrix);
    normVec.rotate(m_gonioRotateMatrix);
  }
 
  // create infinite-plane
  auto pPlane = std::make_shared<Plane>();
  pPlane->setPlane(centre, normVec);
  prim[l_id] = pPlane;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(" << l_id << ")";
  l_id++;
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseInfiniteCylinder(Poco::XML::Element *pElem,
                                                std::map<int, std::shared_ptr<Surface>> &prim, int &l_id) {
  Element *pElemCentre = getShapeElement(pElem, "centre");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemRadius = getShapeElement(pElem, "radius");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  // getDoubleAttribute can throw - put the calls above any new
  const double radius = getDoubleAttribute(pElemRadius, "val");
  V3D normVec = normalize(parsePosition(pElemAxis));
  V3D centre = parsePosition(pElemCentre);
 
  // Rotate the normal vector by the rotate, rotate-all and goniometer tags
  // Rotate the centre by the rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    normVec.rotate(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    centre.rotate(m_rotateAllMatrix);
    normVec.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    centre.rotate(m_gonioRotateMatrix);
    normVec.rotate(m_gonioRotateMatrix);
  }
 
  // create infinite-cylinder
  auto pCylinder = std::make_shared<Cylinder>();
  pCylinder->setNorm(normVec);
  pCylinder->setCentre(centre);
 
  pCylinder->setRadius(radius);
  prim[l_id] = pCylinder;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(-" << l_id << ")";
  l_id++;
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseCylinder(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                        int &l_id) {
  Element *pElemBase = getShapeElement(pElem, "centre-of-bottom-base");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemRadius = getShapeElement(pElem, "radius");
  Element *pElemHeight = getShapeElement(pElem, "height");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  V3D normVec = normalize(parsePosition(pElemAxis));
 
  // getDoubleAttribute can throw - put the calls above any new
  const double radius = getDoubleAttribute(pElemRadius, "val");
  const double height = getDoubleAttribute(pElemHeight, "val");
 
  // add infinite cylinder
  auto pCylinder = std::make_shared<Cylinder>();
  V3D centreOfBottomBase = parsePosition(pElemBase);
  V3D centre = centreOfBottomBase + normVec * (0.5 * height);
  pCylinder->setRadius(radius);
 
  // Rotate the normal vector by the rotate, rotate-all and goniometer tags
  // Rotate the centre by the rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    normVec.rotate(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    centre.rotate(m_rotateAllMatrix);
    normVec.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    centre.rotate(m_gonioRotateMatrix);
    normVec.rotate(m_gonioRotateMatrix);
  }
 
  pCylinder->setNorm(normVec);
  pCylinder->setCentre(centre);
 
  prim[l_id] = pCylinder;
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(-" << l_id << " ";
  l_id++;
 
  // add top plane
  auto pPlaneTop = std::make_shared<Plane>();
  // to get point in top plane
  V3D pointInPlaneTop = centre + (normVec * height * 0.5);
  pPlaneTop->setPlane(pointInPlaneTop, normVec);
  prim[l_id] = pPlaneTop;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add bottom plane
  auto pPlaneBottom = std::make_shared<Plane>();
  V3D pointInPlaneBottom = centre - (normVec * height * 0.5);
  pPlaneBottom->setPlane(pointInPlaneBottom, normVec);
  prim[l_id] = pPlaneBottom;
  retAlgebraMatch << "" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseHollowCylinder(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                              int &l_id) {
  Element *pElemBase = getShapeElement(pElem, "centre-of-bottom-base");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemInnerRadius = getShapeElement(pElem, "inner-radius");
  Element *pElemOuterRadius = getShapeElement(pElem, "outer-radius");
  Element *pElemHeight = getShapeElement(pElem, "height");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  const double innerRadius = getDoubleAttribute(pElemInnerRadius, "val");
  if (innerRadius <= 0.0) {
    throw std::runtime_error("ShapeFactory::parseHollowCylinder(): inner-radius < 0.0");
  }
  const double outerRadius = getDoubleAttribute(pElemOuterRadius, "val");
  if (outerRadius <= 0.0) {
    throw std::runtime_error("ShapeFactory::parseHollowCylinder(): outer-radius < 0.0");
  }
  if (innerRadius > outerRadius) {
    throw std::runtime_error("ShapeFactory::parseHollowCylinder(): inner-radius > outer-radius.");
  }
  const double height = getDoubleAttribute(pElemHeight, "val");
  if (height <= 0.0) {
    throw std::runtime_error("ShapeFactory::parseHollowCylinder(): height < 0.0");
  }
  V3D centreOfBottomBase = parsePosition(pElemBase);
  V3D normVec = normalize(parsePosition(pElemAxis));
  V3D centre = centreOfBottomBase + normVec * (0.5 * height);
 
  // Rotate the normal vector by the rotate, rotate-all and goniometer tags
  // Rotate the centre by the rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    normVec.rotate(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    centre.rotate(m_rotateAllMatrix);
    normVec.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    centre.rotate(m_gonioRotateMatrix);
    normVec.rotate(m_gonioRotateMatrix);
  }
 
  // add outer infinite cylinder surface
  auto outerCylinder = std::make_shared<Cylinder>();
  outerCylinder->setCentre(centre);
  outerCylinder->setNorm(normVec);
  outerCylinder->setRadius(outerRadius);
  prim[l_id] = outerCylinder;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(-" << l_id << " ";
  l_id++;
 
  // add inner infinite cylinder surface
  auto innerCylinder = std::make_shared<Cylinder>();
  innerCylinder->setCentre(centre);
  innerCylinder->setNorm(normVec);
  innerCylinder->setRadius(innerRadius);
  prim[l_id] = innerCylinder;
  retAlgebraMatch << l_id << " ";
  l_id++;
 
  // add top plane
  auto pPlaneTop = std::make_shared<Plane>();
  // to get point in top plane
  V3D pointInPlaneTop = centre + (normVec * height * 0.5);
  pPlaneTop->setPlane(pointInPlaneTop, normVec);
  prim[l_id] = pPlaneTop;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add bottom plane
  auto pPlaneBottom = std::make_shared<Plane>();
  V3D pointInPlaneBottom = centre - (normVec * height * 0.5);
  pPlaneBottom->setPlane(pointInPlaneBottom, normVec);
  prim[l_id] = pPlaneBottom;
  retAlgebraMatch << "" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
CuboidCorners ShapeFactory::parseCuboid(Poco::XML::Element *pElem) {
  // Users have two syntax options when defining cuboids:
 
  // A - "Point" syntax.
  Element *pElem_lfb = getOptionalShapeElement(pElem, "left-front-bottom-point");
  Element *pElem_lft = getOptionalShapeElement(pElem, "left-front-top-point");
  Element *pElem_lbb = getOptionalShapeElement(pElem, "left-back-bottom-point");
  Element *pElem_rfb = getOptionalShapeElement(pElem, "right-front-bottom-point");
 
  // B - "Alternate" syntax.
  Element *pElem_height = getOptionalShapeElement(pElem, "height");
  Element *pElem_width = getOptionalShapeElement(pElem, "width");
  Element *pElem_depth = getOptionalShapeElement(pElem, "depth");
  Element *pElem_centre = getOptionalShapeElement(pElem, "centre");
  Element *pElem_axis = getOptionalShapeElement(pElem, "axis");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  const bool usingPointSyntax = pElem_lfb && pElem_lft && pElem_lbb && pElem_rfb;
  const bool usingAlternateSyntax = pElem_height && pElem_width && pElem_depth;
 
  const bool usedPointSyntaxField = pElem_lfb || pElem_lft || pElem_lbb || pElem_rfb;
  const bool usedAlternateSyntaxField =
      pElem_height || pElem_width || pElem_depth || pElem_centre || pElem_axis || pElem_rot;
 
  const std::string SYNTAX_ERROR_MSG = "XML element: <" + pElem->tagName() +
                                       "> may contain EITHER corner points (LFB, LFT, LBB and RFB) OR " +
                                       "height, width, depth, centre and axis values.";
 
  CuboidCorners result;
 
  if (usingPointSyntax && !usingAlternateSyntax) {
    if (usedAlternateSyntaxField)
      throw std::invalid_argument(SYNTAX_ERROR_MSG);
 
    result.lfb = parsePosition(pElem_lfb);
    result.lft = parsePosition(pElem_lft);
    result.lbb = parsePosition(pElem_lbb);
    result.rfb = parsePosition(pElem_rfb);
  } else if (usingAlternateSyntax && !usingPointSyntax) {
    if (usedPointSyntaxField)
      throw std::invalid_argument(SYNTAX_ERROR_MSG);
 
    const double deltaH = getDoubleAttribute(pElem_height, "val") / 2;
    const double deltaW = getDoubleAttribute(pElem_width, "val") / 2;
    const double deltaD = getDoubleAttribute(pElem_depth, "val") / 2;
 
    V3D centre = pElem_centre ? parsePosition(pElem_centre) : DEFAULT_CENTRE;
 
    result.lfb = V3D(-deltaW, -deltaH, -deltaD);
    result.lft = V3D(-deltaW, deltaH, -deltaD);
    result.lbb = V3D(-deltaW, -deltaH, deltaD);
    result.rfb = V3D(deltaW, -deltaH, -deltaD);
 
    if (pElem_axis) {
      // Use a quarternion to do a rotate for us, with respect to the default
      // axis.  Our "Quat" implementation requires that the vectors passed to
      // it be normalised.
      const V3D axis = normalize(parsePosition(pElem_axis));
      const Quat rotate(DEFAULT_AXIS, axis);
 
      rotate.rotate(result.lfb);
      rotate.rotate(result.lft);
      rotate.rotate(result.lbb);
      rotate.rotate(result.rfb);
    }
 
    // Rotate the points by the rotate, rotate-all and goniometer tags
    // Rotate the centre by the rotate-all and goniometer tags
    if (pElem_rot) {
      // Apply manual rotation supplied to rotate tag
      std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
      const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
      result.rotatePoints(rotateMatrix);
    }
    if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
      // Apply automatic rotation due to the rotate-all tag
      result.rotatePoints(m_rotateAllMatrix);
      centre.rotate(m_rotateAllMatrix);
    }
    if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
      // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
      result.rotatePoints(m_gonioRotateMatrix);
      centre.rotate(m_gonioRotateMatrix);
    }
 
    result.lfb += centre;
    result.lft += centre;
    result.lbb += centre;
    result.rfb += centre;
  } else {
    throw std::invalid_argument(SYNTAX_ERROR_MSG);
  }
 
  return result;
}
 
std::string ShapeFactory::parseCuboid(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                      int &l_id) {
  auto corners = parseCuboid(pElem);
 
  const V3D pointTowardBack = normalize(corners.lbb - corners.lfb);
 
  // add front plane cutoff
  auto pPlaneFrontCutoff = std::make_shared<Plane>();
  try {
    pPlaneFrontCutoff->setPlane(corners.lfb, pointTowardBack);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneFrontCutoff;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(" << l_id << " ";
  l_id++;
 
  // add back plane cutoff
  auto pPlaneBackCutoff = std::make_shared<Plane>();
  try {
    pPlaneBackCutoff->setPlane(corners.lbb, pointTowardBack);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneBackCutoff;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  const V3D pointTowardRight = normalize(corners.rfb - corners.lfb);
 
  // add left plane cutoff
  auto pPlaneLeftCutoff = std::make_shared<Plane>();
  try {
    pPlaneLeftCutoff->setPlane(corners.lfb, pointTowardRight);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneLeftCutoff;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // add right plane cutoff
  auto pPlaneRightCutoff = std::make_shared<Plane>();
  try {
    pPlaneRightCutoff->setPlane(corners.rfb, pointTowardRight);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneRightCutoff;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  const V3D pointTowardTop = normalize(corners.lft - corners.lfb);
 
  // add bottom plane cutoff
  auto pPlaneBottomCutoff = std::make_shared<Plane>();
  try {
    pPlaneBottomCutoff->setPlane(corners.lfb, pointTowardTop);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneBottomCutoff;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // add top plane cutoff
  auto pPlaneTopCutoff = std::make_shared<Plane>();
  try {
    pPlaneTopCutoff->setPlane(corners.lft, pointTowardTop);
  } catch (std::invalid_argument &) {
    throw;
  }
  prim[l_id] = pPlaneTopCutoff;
  retAlgebraMatch << "-" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseInfiniteCone(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                            int &l_id) {
  Element *pElemTipPoint = getShapeElement(pElem, "tip-point");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemAngle = getShapeElement(pElem, "angle");
 
  const V3D normVec = normalize(parsePosition(pElemAxis));
 
  // getDoubleAttribute can throw - put the calls above any new
  const double angle = getDoubleAttribute(pElemAngle, "val");
 
  // add infinite double cone
  auto pCone = std::make_shared<Cone>();
  pCone->setCentre(parsePosition(pElemTipPoint));
  pCone->setNorm(normVec);
  pCone->setAngle(angle);
  prim[l_id] = pCone;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(" << l_id << " ";
  l_id++;
 
  // plane top cut of top part of double cone
  auto pPlaneBottom = std::make_shared<Plane>();
  pPlaneBottom->setPlane(parsePosition(pElemTipPoint), normVec);
  prim[l_id] = pPlaneBottom;
  retAlgebraMatch << "-" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseCone(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                    int &l_id) {
  Element *pElemTipPoint = getShapeElement(pElem, "tip-point");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemAngle = getShapeElement(pElem, "angle");
  Element *pElemHeight = getShapeElement(pElem, "height");
 
  const V3D normVec = normalize(parsePosition(pElemAxis));
 
  // getDoubleAttribute can throw - put the calls above any new
  const double angle = getDoubleAttribute(pElemAngle, "val");
  const double height = getDoubleAttribute(pElemHeight, "val");
 
  // add infinite double cone
  auto pCone = std::make_shared<Cone>();
  pCone->setCentre(parsePosition(pElemTipPoint));
  pCone->setNorm(normVec);
  pCone->setAngle(angle);
  prim[l_id] = pCone;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(" << l_id << " ";
  l_id++;
 
  // Plane to cut off cone from below
  auto pPlaneTop = std::make_shared<Plane>();
  V3D pointInPlane = parsePosition(pElemTipPoint);
  pointInPlane -= (normVec * height);
  pPlaneTop->setPlane(pointInPlane, normVec);
  prim[l_id] = pPlaneTop;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // plane top cut of top part of double cone
  auto pPlaneBottom = std::make_shared<Plane>();
  pPlaneBottom->setPlane(parsePosition(pElemTipPoint), normVec);
  prim[l_id] = pPlaneBottom;
  retAlgebraMatch << "-" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseHexahedronFromStruct(const Hexahedron &hex,
                                                    std::map<int, std::shared_ptr<Surface>> &prim, int &l_id) {
  // add front face
  auto pPlaneFrontCutoff = std::make_shared<Plane>();
  auto normal = (hex.rfb - hex.lfb).cross_prod(hex.lft - hex.lfb);
 
  // V3D jjj = (normal*(rfb-rbb));
  if (normal.scalar_prod(hex.rfb - hex.rbb) < 0)
    normal *= -1.0;
  pPlaneFrontCutoff->setPlane(hex.lfb, normal);
  prim[l_id] = pPlaneFrontCutoff;
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(-" << l_id << " ";
  l_id++;
 
  // add back face
  auto pPlaneBackCutoff = std::make_shared<Plane>();
  normal = (hex.rbb - hex.lbb).cross_prod(hex.lbt - hex.lbb);
  if (normal.scalar_prod(hex.rfb - hex.rbb) < 0)
    normal *= -1.0;
  pPlaneBackCutoff->setPlane(hex.lbb, normal);
  prim[l_id] = pPlaneBackCutoff;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // add left face
  auto pPlaneLeftCutoff = std::make_shared<Plane>();
  normal = (hex.lbb - hex.lfb).cross_prod(hex.lft - hex.lfb);
  if (normal.scalar_prod(hex.rfb - hex.lfb) < 0)
    normal *= -1.0;
  pPlaneLeftCutoff->setPlane(hex.lfb, normal);
  prim[l_id] = pPlaneLeftCutoff;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // add right face
  auto pPlaneRightCutoff = std::make_shared<Plane>();
  normal = (hex.rbb - hex.rfb).cross_prod(hex.rft - hex.rfb);
  if (normal.scalar_prod(hex.rfb - hex.lfb) < 0)
    normal *= -1.0;
  pPlaneRightCutoff->setPlane(hex.rfb, normal);
  prim[l_id] = pPlaneRightCutoff;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add top face
  auto pPlaneTopCutoff = std::make_shared<Plane>();
  normal = (hex.rft - hex.lft).cross_prod(hex.lbt - hex.lft);
  if (normal.scalar_prod(hex.rft - hex.rfb) < 0)
    normal *= -1.0;
  pPlaneTopCutoff->setPlane(hex.lft, normal);
  prim[l_id] = pPlaneTopCutoff;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add bottom face
  auto pPlaneBottomCutoff = std::make_shared<Plane>();
  normal = (hex.rfb - hex.lfb).cross_prod(hex.lbb - hex.lfb);
  if (normal.scalar_prod(hex.rft - hex.rfb) < 0)
    normal *= -1.0;
  pPlaneBottomCutoff->setPlane(hex.lfb, normal);
  prim[l_id] = pPlaneBottomCutoff;
  retAlgebraMatch << "" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
Hexahedron ShapeFactory::parseHexahedron(Poco::XML::Element *pElem) {
  Element *pElem_lfb = getShapeElement(pElem, "left-front-bottom-point");
  Element *pElem_lft = getShapeElement(pElem, "left-front-top-point");
  Element *pElem_lbb = getShapeElement(pElem, "left-back-bottom-point");
  Element *pElem_lbt = getShapeElement(pElem, "left-back-top-point");
  Element *pElem_rfb = getShapeElement(pElem, "right-front-bottom-point");
  Element *pElem_rft = getShapeElement(pElem, "right-front-top-point");
  Element *pElem_rbb = getShapeElement(pElem, "right-back-bottom-point");
  Element *pElem_rbt = getShapeElement(pElem, "right-back-top-point");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  const bool isValid =
      pElem_lfb && pElem_lft && pElem_lbb && pElem_lbt && pElem_rfb && pElem_rft && pElem_rbb && pElem_rbt;
 
  std::ostringstream ERROR_MSG;
  ERROR_MSG << "XML element: <" + pElem->tagName() + ""
            << "> contains invalid syntax for defining hexahedron. The "
               "following points have not been defined:\n\n";
 
  if (!pElem_lfb)
    ERROR_MSG << "left-front-bottom-point\n";
  if (!pElem_lft)
    ERROR_MSG << "left-front-top-point\n";
  if (!pElem_lbb)
    ERROR_MSG << "left-back-bottom-point\n";
  if (!pElem_lbt)
    ERROR_MSG << "left-back-top-point\n";
  if (!pElem_rfb)
    ERROR_MSG << "right-front-bottom-point\n";
  if (!pElem_rft)
    ERROR_MSG << "right-front-top-point\n";
  if (!pElem_rbb)
    ERROR_MSG << "right-back-bottom-point\n";
  if (!pElem_rbt)
    ERROR_MSG << "right-back-top-point\n";
 
  if (!isValid)
    throw std::invalid_argument(ERROR_MSG.str());
 
  Hexahedron hex;
  hex.lfb = parsePosition(pElem_lfb);
  hex.lft = parsePosition(pElem_lft);
  hex.lbb = parsePosition(pElem_lbb);
  hex.lbt = parsePosition(pElem_lbt);
  hex.rfb = parsePosition(pElem_rfb);
  hex.rft = parsePosition(pElem_rft);
  hex.rbb = parsePosition(pElem_rbb);
  hex.rbt = parsePosition(pElem_rbt);
 
  // Rotate the points by the rotate, rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    hex.rotatePoints(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    hex.rotatePoints(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    hex.rotatePoints(m_gonioRotateMatrix);
  }
 
  return hex;
}
 
std::string ShapeFactory::parseHexahedron(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                          int &l_id) {
  Hexahedron hex = parseHexahedron(pElem);
 
  return parseHexahedronFromStruct(hex, prim, l_id);
}
 
std::string ShapeFactory::parseTaperedGuide(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                            int &l_id) {
  Element *pElemApertureStart = getShapeElement(pElem, "aperture-start");
  Element *pElemLength = getShapeElement(pElem, "length");
  Element *pElemApertureEnd = getShapeElement(pElem, "aperture-end");
  Element *pElemCentre = getOptionalShapeElement(pElem, "centre");
  Element *pElemAxis = getOptionalShapeElement(pElem, "axis");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  // For centre and axis we allow defaults.
  V3D centre = pElemCentre ? parsePosition(pElemCentre) : DEFAULT_CENTRE;
  // Quat requires normalised axes.
  const V3D axis = normalize(pElemAxis ? parsePosition(pElemAxis) : DEFAULT_AXIS);
 
  const double apertureStartWidth = getDoubleAttribute(pElemApertureStart, "width");
  const double apertureStartHeight = getDoubleAttribute(pElemApertureStart, "height");
  const double length = getDoubleAttribute(pElemLength, "val");
  const double apertureEndWidth = getDoubleAttribute(pElemApertureEnd, "width");
  const double apertureEndHeight = getDoubleAttribute(pElemApertureEnd, "height");
 
  const double halfSW = apertureStartWidth / 2;
  const double halfSH = apertureStartHeight / 2;
  const double halfEW = apertureEndWidth / 2;
  const double halfEH = apertureEndHeight / 2;
 
  // Build the basic shape.
  Hexahedron hex;
  hex.lfb = V3D(-halfSW, -halfSH, 0);
  hex.lft = V3D(-halfSW, halfSH, 0);
  hex.lbb = V3D(-halfEW, -halfEH, length);
  hex.lbt = V3D(-halfEW, halfEH, length);
  hex.rfb = V3D(halfSW, -halfSH, 0);
  hex.rft = V3D(halfSW, halfSH, 0);
  hex.rbb = V3D(halfEW, -halfEH, length);
  hex.rbt = V3D(halfEW, halfEH, length);
 
  // Point it along the defined axis.
  if (axis != DEFAULT_AXIS) {
    const Quat q(DEFAULT_AXIS, axis);
 
    q.rotate(hex.lfb);
    q.rotate(hex.lft);
    q.rotate(hex.lbb);
    q.rotate(hex.lbt);
    q.rotate(hex.rfb);
    q.rotate(hex.rft);
    q.rotate(hex.rbb);
    q.rotate(hex.rbt);
  }
 
  // Rotate the points by the rotate, rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    hex.rotatePoints(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    hex.rotatePoints(m_rotateAllMatrix);
    centre.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    hex.rotatePoints(m_gonioRotateMatrix);
    centre.rotate(m_gonioRotateMatrix);
  }
 
  // Move it to the defined centre.
  hex.lfb += centre;
  hex.lft += centre;
  hex.lbb += centre;
  hex.lbt += centre;
  hex.rfb += centre;
  hex.rft += centre;
  hex.rbb += centre;
  hex.rbt += centre;
 
  return parseHexahedronFromStruct(hex, prim, l_id);
}
 
std::string ShapeFactory::parseTorus(Poco::XML::Element *pElem, std::map<int, std::shared_ptr<Surface>> &prim,
                                     int &l_id) {
  Element *pElemCentre = getShapeElement(pElem, "centre");
  Element *pElemAxis = getShapeElement(pElem, "axis");
  Element *pElemRadiusFromCentre = getShapeElement(pElem, "radius-from-centre-to-tube");
  Element *pElemRadiusTube = getShapeElement(pElem, "radius-tube");
 
  const V3D normVec = normalize(parsePosition(pElemAxis));
 
  // getDoubleAttribute can throw - put the calls above any new
  const double radiusCentre = getDoubleAttribute(pElemRadiusFromCentre, "val");
  const double radiusTube = getDoubleAttribute(pElemRadiusTube, "val");
 
  // add torus
  auto pTorus = std::make_shared<Torus>();
  pTorus->setCentre(parsePosition(pElemCentre));
  pTorus->setNorm(normVec);
  pTorus->setDistanceFromCentreToTube(radiusCentre);
  pTorus->setTubeRadius(radiusTube);
  prim[l_id] = pTorus;
 
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(-" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
std::string ShapeFactory::parseSliceOfCylinderRing(Poco::XML::Element *pElem,
                                                   std::map<int, std::shared_ptr<Surface>> &prim, int &l_id) {
  Element *pElemArc = getShapeElement(pElem, "arc");
  Element *pElemInnerRadius = getShapeElement(pElem, "inner-radius");
  Element *pElemOuterRadius = getShapeElement(pElem, "outer-radius");
  Element *pElemDepth = getShapeElement(pElem, "depth");
  Element *pElem_rot = getOptionalShapeElement(pElem, "rotate");
 
  const double outerRadius = getDoubleAttribute(pElemOuterRadius, "val");
  double innerRadius = getDoubleAttribute(pElemInnerRadius, "val");
  if (innerRadius <= 0.0) {
    innerRadius = outerRadius / 1000;
    g_log.warning() << "ShapeFactory::parseSliceOfCylinderRing(): inner-radius cannot be < 0.0 or = 0.0, so has been "
                       "automatically set.";
  }
  const double middleRadius = (outerRadius + innerRadius) / 2.0;
  const double depth = getDoubleAttribute(pElemDepth, "val");
  const double arc = (M_PI / 180.0) * getDoubleAttribute(pElemArc, "val");
 
  V3D normVec(0, 0, 1);
  V3D centrePoint(-middleRadius, 0, 0);
  V3D planeSlice1 = V3D(cos(arc / 2.0 + M_PI / 2.0), sin(arc / 2.0 + M_PI / 2.0), 0);
  V3D planeSlice2 = V3D(cos(-arc / 2.0 + M_PI / 2.0), sin(-arc / 2.0 + M_PI / 2.0), 0);
 
  // Rotate the normal vector and both place slices by the rotate, rotate-all and goniometer tags
  // Rotate the centre by the rotate-all and goniometer tags
  if (pElem_rot) {
    // Apply manual rotation supplied to rotate tag
    std::vector<double> rotateAngles = DegreesToRadians(parsePosition(pElem_rot));
    const std::vector<double> rotateMatrix = generateMatrix(rotateAngles[0], rotateAngles[1], rotateAngles[2]);
    normVec.rotate(rotateMatrix);
    planeSlice1.rotate(rotateMatrix);
    planeSlice2.rotate(rotateMatrix);
  }
  if (m_rotateAllMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the rotate-all tag
    normVec.rotate(m_rotateAllMatrix);
    planeSlice1.rotate(m_rotateAllMatrix);
    planeSlice2.rotate(m_rotateAllMatrix);
    centrePoint.rotate(m_rotateAllMatrix);
  }
  if (m_gonioRotateMatrix != Kernel::Matrix<double>(3, 3, true)) {
    // Apply automatic rotation due to the goniometer that should NOT be manually defined by the user
    normVec.rotate(m_gonioRotateMatrix);
    planeSlice1.rotate(m_gonioRotateMatrix);
    planeSlice2.rotate(m_gonioRotateMatrix);
    centrePoint.rotate(m_gonioRotateMatrix);
  }
 
  // add inner infinite cylinder
  auto pCylinder1 = std::make_shared<Cylinder>();
  pCylinder1->setCentre(centrePoint);
  pCylinder1->setNorm(normVec);
  pCylinder1->setRadius(innerRadius);
  prim[l_id] = pCylinder1;
  std::stringstream retAlgebraMatch;
  retAlgebraMatch << "(" << l_id << " ";
  l_id++;
 
  // add outer infinite cylinder
  auto pCylinder2 = std::make_shared<Cylinder>();
  pCylinder2->setCentre(centrePoint);
  pCylinder2->setNorm(normVec);
  pCylinder2->setRadius(outerRadius);
  prim[l_id] = pCylinder2;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add top cutoff plane of infinite cylinder ring
  auto pPlaneTop = std::make_shared<Plane>();
  V3D pointInPlaneTop = centrePoint + (normVec * depth * 0.5);
  pPlaneTop->setPlane(pointInPlaneTop, normVec);
  prim[l_id] = pPlaneTop;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  // add bottom cutoff plane (which is assumed to face the sample)
  // which at this point will result in a cylinder ring
  auto pPlaneBottom = std::make_shared<Plane>();
  V3D pointInPlaneBottom = centrePoint - (normVec * depth * 0.5);
  pPlaneBottom->setPlane(pointInPlaneBottom, normVec);
  prim[l_id] = pPlaneBottom;
  retAlgebraMatch << "" << l_id << " ";
  l_id++;
 
  // the two planes that are going to cut a slice of the cylinder ring
 
  auto pPlaneSlice1 = std::make_shared<Plane>();
  pPlaneSlice1->setPlane(centrePoint, planeSlice1);
  prim[l_id] = pPlaneSlice1;
  retAlgebraMatch << "-" << l_id << " ";
  l_id++;
 
  auto pPlaneSlice2 = std::make_shared<Plane>();
  pPlaneSlice2->setPlane(centrePoint, planeSlice2);
  prim[l_id] = pPlaneSlice2;
  retAlgebraMatch << "" << l_id << ")";
  l_id++;
 
  return retAlgebraMatch.str();
}
 
Poco::XML::Element *ShapeFactory::getShapeElement(Poco::XML::Element *pElem, const std::string &name) {
  // check if this shape element contain an element with name specified by the
  // 2nd function argument
  Poco::AutoPtr<NodeList> pNL = pElem->getElementsByTagName(name);
  if (pNL->length() != 1) {
    throw std::invalid_argument("XML element: <" + pElem->tagName() +
                                "> must contain exactly one sub-element with name: <" + name + ">.");
  }
  auto *retVal = static_cast<Element *>(pNL->item(0));
  return retVal;
}
 
Poco::XML::Element *ShapeFactory::getOptionalShapeElement(Poco::XML::Element *pElem, const std::string &name) {
  // Allow zero or one occurances of subelements with the given name.
  Poco::AutoPtr<NodeList> pNL = pElem->getElementsByTagName(name);
  if (pNL->length() == 0)
    return nullptr;
  else if (pNL->length() > 1)
    throw std::invalid_argument("XML element: <" + pElem->tagName() +
                                "> may contain at most one sub-element with name: <" + name + ">.");
 
  auto *retVal = static_cast<Element *>(pNL->item(0));
  return retVal;
}
 
double ShapeFactory::getDoubleAttribute(Poco::XML::Element *pElem, const std::string &name) {
  if (pElem->hasAttribute(name)) {
    return std::stod(pElem->getAttribute(name));
  } else {
    throw std::invalid_argument("XML element: <" + pElem->tagName() + "> does not have the attribute: " + name + ".");
  }
}
 
V3D ShapeFactory::parsePosition(Poco::XML::Element *pElem) {
  V3D retVal;
 
  if (pElem->hasAttribute("R") || pElem->hasAttribute("theta") || pElem->hasAttribute("phi")) {
    double R = 0.0, theta = 0.0, phi = 0.0;
 
    if (pElem->hasAttribute("R"))
      R = std::stod(pElem->getAttribute("R"));
    if (pElem->hasAttribute("theta"))
      theta = std::stod(pElem->getAttribute("theta"));
    if (pElem->hasAttribute("phi"))
      phi = std::stod(pElem->getAttribute("phi"));
 
    retVal.spherical(R, theta, phi);
  } else if (pElem->hasAttribute("r") || pElem->hasAttribute("t") || pElem->hasAttribute("p"))
  // This is alternative way a user may specify sphecical coordinates
  // which may be preferred in the long run to the more verbose of
  // using R, theta and phi.
  {
    double R = 0.0, theta = 0.0, phi = 0.0;
 
    if (pElem->hasAttribute("r"))
      R = std::stod(pElem->getAttribute("r"));
    if (pElem->hasAttribute("t"))
      theta = std::stod(pElem->getAttribute("t"));
    if (pElem->hasAttribute("p"))
      phi = std::stod(pElem->getAttribute("p"));
 
    retVal.spherical(R, theta, phi);
  } else {
    double x = 0.0, y = 0.0, z = 0.0;
 
    if (pElem->hasAttribute("x"))
      x = std::stod(pElem->getAttribute("x"));
    if (pElem->hasAttribute("y"))
      y = std::stod(pElem->getAttribute("y"));
    if (pElem->hasAttribute("z"))
      z = std::stod(pElem->getAttribute("z"));
 
    retVal(x, y, z);
  }
 
  return retVal;
}
 
std::shared_ptr<CSGObject> ShapeFactory::createSphere(const Kernel::V3D &centre, double radius) {
  const int surfaceID = 1;
  const std::map<int, std::shared_ptr<Surface>> primitives{{surfaceID, std::make_shared<Sphere>(centre, radius)}};
 
  auto shape = std::make_shared<CSGObject>();
  shape->setObject(21, sphereAlgebra(surfaceID));
  shape->populate(primitives);
 
  auto handler = std::make_shared<GeometryHandler>(shape);
  shape->setGeometryHandler(handler);
  detail::ShapeInfo shapeInfo;
  shapeInfo.setSphere(centre, radius);
  handler->setShapeInfo(std::move(shapeInfo));
 
  shape->defineBoundingBox(radius, radius, radius, -radius, -radius, -radius);
  return shape;
}
 
std::shared_ptr<CSGObject> ShapeFactory::createHexahedralShape(double xlb, double xlf, double xrf, double xrb,
                                                               double ylb, double ylf, double yrf, double yrb) {
  Hexahedron hex;
  static const double ZDEPTH = 0.001;
  hex.lbb = V3D(xlb, ylb, 0);
  hex.lbt = V3D(xlb, ylb, ZDEPTH);
  hex.lfb = V3D(xlf, ylf, 0);
  hex.lft = V3D(xlf, ylf, ZDEPTH);
  hex.rbb = V3D(xrb, yrb, 0);
  hex.rbt = V3D(xrb, yrb, ZDEPTH);
  hex.rfb = V3D(xrf, yrf, 0);
  hex.rft = V3D(xrf, yrf, ZDEPTH);
 
  std::map<int, std::shared_ptr<Surface>> prim;
  int l_id = 1;
  auto algebra = parseHexahedronFromStruct(hex, prim, l_id);
 
  auto shape = std::make_shared<CSGObject>();
  shape->setObject(21, algebra);
  shape->populate(prim);
 
  auto handler = std::make_shared<GeometryHandler>(shape);
  detail::ShapeInfo shapeInfo;
  shape->setGeometryHandler(handler);
 
  shapeInfo.setHexahedron(hex.lbb, hex.lfb, hex.rfb, hex.rbb, hex.lbt, hex.lft, hex.rft, hex.rbt);
 
  handler->setShapeInfo(std::move(shapeInfo));
 
  shape->defineBoundingBox(std::max(xrb, xrf), yrf, ZDEPTH, std::min(xlf, xlb), ylb, 0);
 
  return shape;
}
 
void ShapeFactory::createGeometryHandler(Poco::XML::Element *pElem, const std::shared_ptr<CSGObject> &Obj) {
 
  auto geomHandler = std::make_shared<GeometryHandler>(Obj);
  detail::ShapeInfo shapeInfo;
  Obj->setGeometryHandler(geomHandler);
 
  if (pElem->tagName() == "cuboid") {
    auto corners = parseCuboid(pElem);
    shapeInfo.setCuboid(corners.lfb, corners.lft, corners.lbb, corners.rfb);
  } else if (pElem->tagName() == "hexahedron") {
    auto corners = parseHexahedron(pElem);
    shapeInfo.setHexahedron(corners.lbb, corners.lfb, corners.rfb, corners.rbb, corners.lbt, corners.lft, corners.rft,
                            corners.rbt);
  } else if (pElem->tagName() == "sphere") {
    Element *pElemCentre = getOptionalShapeElement(pElem, "centre");
    Element *pElemRadius = getShapeElement(pElem, "radius");
    V3D centre;
    if (pElemCentre)
      centre = parsePosition(pElemCentre);
    shapeInfo.setSphere(centre, std::stod(pElemRadius->getAttribute("val")));
  } else if (pElem->tagName() == "cylinder") {
    Element *pElemCentre = getShapeElement(pElem, "centre-of-bottom-base");
    Element *pElemAxis = getShapeElement(pElem, "axis");
    Element *pElemRadius = getShapeElement(pElem, "radius");
    Element *pElemHeight = getShapeElement(pElem, "height");
    const V3D normVec = normalize(parsePosition(pElemAxis));
    shapeInfo.setCylinder(parsePosition(pElemCentre), normVec, std::stod(pElemRadius->getAttribute("val")),
                          std::stod(pElemHeight->getAttribute("val")));
  } else if (pElem->tagName() == "hollow-cylinder") {
    Element *pElemCentre = getShapeElement(pElem, "centre-of-bottom-base");
    Element *pElemAxis = getShapeElement(pElem, "axis");
    Element *pElemInnerRadius = getShapeElement(pElem, "inner-radius");
    Element *pElemOuterRadius = getShapeElement(pElem, "outer-radius");
    Element *pElemHeight = getShapeElement(pElem, "height");
    V3D normVec = parsePosition(pElemAxis);
    normVec.normalize();
    shapeInfo.setHollowCylinder(parsePosition(pElemCentre), normVec, std::stod(pElemInnerRadius->getAttribute("val")),
                                std::stod(pElemOuterRadius->getAttribute("val")),
                                std::stod(pElemHeight->getAttribute("val")));
  } else if (pElem->tagName() == "cone") {
    Element *pElemTipPoint = getShapeElement(pElem, "tip-point");
    Element *pElemAxis = getShapeElement(pElem, "axis");
    Element *pElemAngle = getShapeElement(pElem, "angle");
    Element *pElemHeight = getShapeElement(pElem, "height");
 
    const V3D normVec = normalize(parsePosition(pElemAxis));
    const double height = std::stod(pElemHeight->getAttribute("val"));
    const double radius = height * tan(M_PI * std::stod(pElemAngle->getAttribute("val")) / 180.0);
    shapeInfo.setCone(parsePosition(pElemTipPoint), normVec, radius, height);
  }
 
  geomHandler->setShapeInfo(std::move(shapeInfo));
}
 
Kernel::Matrix<double> ShapeFactory::generateMatrix(double xrotate, double yrotate, double zrotate) {
  Kernel::Matrix<double> xMatrix = generateXRotation(xrotate);
  Kernel::Matrix<double> yMatrix = generateYRotation(yrotate);
  Kernel::Matrix<double> zMatrix = generateZRotation(zrotate);
 
  return zMatrix * yMatrix * xMatrix;
}
 
Kernel::Matrix<double> ShapeFactory::generateXRotation(double xrotate) {
  const double sinX = sin(xrotate);
  const double cosX = cos(xrotate);
  std::vector<double> matrixList = {1, 0, 0, 0, cosX, -sinX, 0, sinX, cosX};
  return Kernel::Matrix<double>(matrixList);
}
 
Kernel::Matrix<double> ShapeFactory::generateYRotation(double yrotate) {
  const double sinY = sin(yrotate);
  const double cosY = cos(yrotate);
  std::vector<double> matrixList = {cosY, 0, sinY, 0, 1, 0, -sinY, 0, cosY};
  return Kernel::Matrix<double>(matrixList);
}
 
Kernel::Matrix<double> ShapeFactory::generateZRotation(double zrotate) {
  const double sinZ = sin(zrotate);
  const double cosZ = cos(zrotate);
  std::vector<double> matrixList = {cosZ, -sinZ, 0, sinZ, cosZ, 0, 0, 0, 1};
  return Kernel::Matrix<double>(matrixList);
}
 
std::string ShapeFactory::addGoniometerTag(const Kernel::Matrix<double> &rotateMatrix, std::string xml) {
 
  // Delete previous goniometer from xml
  std::size_t foundGonioTag = xml.find("<goniometer");
  if (foundGonioTag != std::string::npos) {
    std::size_t gonioTagLength = xml.find(">", foundGonioTag + 1) - foundGonioTag;
    xml.erase(foundGonioTag, gonioTagLength);
  }
 
  // Put goniometer tag in correct place in xml
  std::size_t gonioPlace;
  std::size_t foundType = xml.find("</type>");
  std::size_t foundSampleGeometry = xml.find("</samplegeometry");
 
  if (foundType != std::string::npos) {
    // Add goniometer BEFORE Type end tag
    gonioPlace = foundType;
  } else if (foundSampleGeometry != std::string::npos) {
    // If no type tag, add goniometer BEFORE SampleGeometry end tag
    gonioPlace = foundSampleGeometry;
  } else {
    // If no Type or SampleGeometry tag, add goniometer to the end
    gonioPlace = xml.size();
  }
 
  const std::vector<std::string> matrixElementNames = {"a11", "a12", "a13", "a21", "a22", "a23", "a31", "a32", "a33"};
  std::string goniometerRotate = " <goniometer ";
  for (size_t i = 0; i < rotateMatrix.numRows(); ++i) {
    for (size_t j = 0; j < rotateMatrix.numCols(); ++j) {
      goniometerRotate += matrixElementNames[3 * i + j] + " = '" + std::to_string(rotateMatrix[i][j]) + "' ";
    }
  }
  goniometerRotate += "/>";
  xml.insert(gonioPlace, goniometerRotate);
 
  return xml;
}
} // namespace Mantid::Geometry