--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancStone/Sources/Toolbox/DicomStructureSet.cpp	Tue Jul 07 16:21:02 2020 +0200
@@ -0,0 +1,1067 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2020 Osimis S.A., Belgium
+ *
+ * This program 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.
+ *
+ * This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "DicomStructureSet.h"
+#include "DicomStructureSetUtils.h"
+
+#include "../Toolbox/GeometryToolbox.h"
+#include "OrthancDatasets/DicomDatasetReader.h"
+
+#include <Logging.h>
+#include <OrthancException.h>
+#include <Toolbox.h>
+
+#if defined(_MSC_VER)
+#  pragma warning(push)
+#  pragma warning(disable:4244)
+#endif
+
+#include <limits>
+#include <stdio.h>
+#include <boost/geometry.hpp>
+#include <boost/geometry/geometries/point_xy.hpp>
+#include <boost/geometry/geometries/polygon.hpp>
+#include <boost/geometry/multi/geometries/multi_polygon.hpp>
+
+#if defined(_MSC_VER)
+#  pragma warning(pop)
+#endif
+
+#if ORTHANC_ENABLE_DCMTK == 1
+#  include "ParsedDicomDataset.h"
+#endif
+
+
+typedef boost::geometry::model::d2::point_xy<double> BoostPoint;
+typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon;
+typedef boost::geometry::model::multi_polygon<BoostPolygon>  BoostMultiPolygon;
+
+
+static void Union(BoostMultiPolygon& output,
+                  std::vector<BoostPolygon>& input)
+{
+  for (size_t i = 0; i < input.size(); i++)
+  {
+    boost::geometry::correct(input[i]);
+  }
+  
+  if (input.size() == 0)
+  {
+    output.clear();
+  }
+  else if (input.size() == 1)
+  {
+    output.resize(1);
+    output[0] = input[0];
+  }
+  else
+  {
+    boost::geometry::union_(input[0], input[1], output);
+
+    for (size_t i = 0; i < input.size(); i++)
+    {
+      BoostMultiPolygon tmp;
+      boost::geometry::union_(output, input[i], tmp);
+      output = tmp;
+    }
+  }
+}
+
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+
+static BoostPolygon CreateRectangle(float x1, float y1,
+                                    float x2, float y2)
+{
+  BoostPolygon r;
+  boost::geometry::append(r, BoostPoint(x1, y1));
+  boost::geometry::append(r, BoostPoint(x1, y2));
+  boost::geometry::append(r, BoostPoint(x2, y2));
+  boost::geometry::append(r, BoostPoint(x2, y1));
+  return r;
+}
+
+#else
+
+namespace OrthancStone
+{
+  static RtStructRectangleInSlab CreateRectangle(float x1, float y1,
+                                                 float x2, float y2)
+  {
+    RtStructRectangleInSlab rect;
+    rect.xmin = std::min(x1, x2);
+    rect.xmax = std::max(x1, x2);
+    rect.ymin = std::min(y1, y2);
+    rect.ymax = std::max(y1, y2);
+    return rect;
+  }
+
+  bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, const std::pair<RtStructRectangleInSlab, double>& r2)
+  {
+    return r1.second < r2.second;
+  }
+
+  bool CompareSlabsY(const RtStructRectanglesInSlab& r1, const RtStructRectanglesInSlab& r2)
+  {
+    if ((r1.size() == 0) || (r2.size() == 0))
+      return false;
+
+    return r1[0].ymax < r2[0].ymax;
+  }
+}
+
+#endif
+
+namespace OrthancStone
+{
+  static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
+  static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
+  static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
+  static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
+  static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
+  static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
+  static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
+  static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
+  static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
+  static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
+  static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
+  static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
+
+
+  static uint8_t ConvertColor(double v)
+  {
+    if (v < 0)
+    {
+      return 0;
+    }
+    else if (v >= 255)
+    {
+      return 255;
+    }
+    else
+    {
+      return static_cast<uint8_t>(v);
+    }
+  }
+
+
+  static bool ParseVector(Vector& target,
+                          const IDicomDataset& dataset,
+                          const DicomPath& tag)
+  {
+    std::string value;
+    return (dataset.GetStringValue(value, tag) &&
+            LinearAlgebra::ParseVector(target, value));
+  }
+
+  void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const
+  {
+    if (hasSlice_)
+    {
+      double magnitude =
+        GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal());
+      if(!LinearAlgebra::IsNear(
+           magnitude,
+           projectionAlongNormal_,
+           sliceThickness_ / 2.0 /* in mm */ ))
+      {
+        LOG(ERROR) << "This RT-STRUCT contains a point that is off the "
+                   << "slice of its instance | "
+                   << "magnitude = " << magnitude << " | "
+                   << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
+                   << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
+
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+      }
+    }
+  }
+
+  bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const
+  {
+    if (hasSlice_)
+    {
+      double magnitude = 
+        GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal());
+      bool onSlice = LinearAlgebra::IsNear(
+        magnitude,
+        projectionAlongNormal_,
+        sliceThickness_ / 2.0 /* in mm */);
+      if (!onSlice)
+      {
+        LOG(WARNING) << "This RT-STRUCT contains a point that is off the "
+                     << "slice of its instance | "
+                     << "magnitude = " << magnitude << " | "
+                     << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
+                     << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
+      }
+      return onSlice;
+    }
+    else
+    {
+      return true;
+    }
+  }
+
+  void DicomStructureSet::Polygon::AddPoint(const Vector& v)
+  {
+#if 1
+    // BGO 2019-09-03
+    if (IsPointOnSliceIfAny(v))
+    {
+      points_.push_back(v);
+    }
+#else
+    CheckPoint(v);
+    points_.push_back(v);
+#endif 
+  }
+
+
+  bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
+  {
+    if (hasSlice_)
+    {
+      return true;
+    }
+    else
+    {
+      ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
+      
+      if (it == slices.end())
+      {
+        return false;
+      }
+      else
+      {
+        const CoordinateSystem3D& geometry = it->second.geometry_;
+        
+        hasSlice_ = true;
+        geometry_ = geometry;
+        projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal());
+        sliceThickness_ = it->second.thickness_;
+
+        extent_.Reset();
+        
+        for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it)
+        {
+          if (IsPointOnSliceIfAny(*it))
+          {
+            double x, y;
+            geometry.ProjectPoint2(x, y, *it);
+            extent_.AddPoint(x, y);
+          }
+        }
+        return true;
+      }
+    }
+  }
+
+  bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
+  {
+    bool isOpposite = false;
+
+    if (points_.empty() ||
+        !hasSlice_ ||
+        !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal()))
+    {
+      return false;
+    }
+    
+    double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal());
+
+    return (LinearAlgebra::IsNear(d, projectionAlongNormal_,
+                                  sliceThickness_ / 2.0));
+  }
+    
+  bool DicomStructureSet::Polygon::Project(double& x1,
+                                           double& y1,
+                                           double& x2,
+                                           double& y2,
+                                           const CoordinateSystem3D& slice) const
+  {
+    // TODO: optimize this method using a sweep-line algorithm for polygons
+    
+    if (!hasSlice_ ||
+        points_.size() <= 1)
+    {
+      return false;
+    }
+
+    double x, y;
+    geometry_.ProjectPoint2(x, y, slice.GetOrigin());
+      
+    bool isOpposite;
+    if (GeometryToolbox::IsParallelOrOpposite
+        (isOpposite, slice.GetNormal(), geometry_.GetAxisY()))
+    {
+      // plane is constant Y
+
+      if (y < extent_.GetY1() ||
+          y > extent_.GetY2())
+      {
+        // The polygon does not intersect the input slice
+        return false;
+      }
+        
+      bool isFirst = true;
+      double xmin = std::numeric_limits<double>::infinity();
+      double xmax = -std::numeric_limits<double>::infinity();
+
+      double prevX, prevY;
+      geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]);
+        
+      for (size_t i = 0; i < points_.size(); i++)
+      {
+        // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py
+        double curX, curY;
+        geometry_.ProjectPoint2(curX, curY, points_[i]);
+
+        // if prev* and cur* are on opposite sides of y, this means that the
+        // segment intersects the plane.
+        if ((prevY < y && curY > y) ||
+            (prevY > y && curY < y))
+        {
+          double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY);
+          xmin = std::min(xmin, p);
+          xmax = std::max(xmax, p);
+          isFirst = false;
+
+          // xmin and xmax represent the extent of the rectangle along the 
+          // intersection between the plane and the polygon geometry
+
+        }
+
+        prevX = curX;
+        prevY = curY;
+      }
+        
+      // if NO segment intersects the plane
+      if (isFirst)
+      {
+        return false;
+      }
+      else
+      {
+        // y is the plane y coord in the polygon geometry
+        // xmin and xmax are ALSO expressed in the polygon geometry
+
+        // let's convert them to 3D world geometry...
+        Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) +
+                     sliceThickness_ / 2.0 * geometry_.GetNormal());
+        Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) -
+                     sliceThickness_ / 2.0 * geometry_.GetNormal());
+          
+        // then to the cutting plane geometry...
+        slice.ProjectPoint2(x1, y1, p1);
+        slice.ProjectPoint2(x2, y2, p2);
+        return true;
+      }
+    }
+    else if (GeometryToolbox::IsParallelOrOpposite
+             (isOpposite, slice.GetNormal(), geometry_.GetAxisX()))
+    {
+      // plane is constant X => Sagittal view (remember that in the
+      // sagittal projection, the normal must be swapped)
+
+      
+      /*
+        Please read the comments in the section above, by taking into account
+        the fact that, in this case, the plane has a constant X, not Y (in 
+        polygon geometry_ coordinates)
+      */
+
+      if (x < extent_.GetX1() ||
+          x > extent_.GetX2())
+      {
+        return false;
+      }
+
+      bool isFirst = true;
+      double ymin = std::numeric_limits<double>::infinity();
+      double ymax = -std::numeric_limits<double>::infinity();
+
+      double prevX, prevY;
+      geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]);
+        
+      for (size_t i = 0; i < points_.size(); i++)
+      {
+        // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py
+        double curX, curY;
+        geometry_.ProjectPoint2(curX, curY, points_[i]);
+
+        if ((prevX < x && curX > x) ||
+            (prevX > x && curX < x))
+        {
+          double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX);
+          ymin = std::min(ymin, p);
+          ymax = std::max(ymax, p);
+          isFirst = false;
+        }
+
+        prevX = curX;
+        prevY = curY;
+      }
+        
+      if (isFirst)
+      {
+        return false;
+      }
+      else
+      {
+        Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) +
+                     sliceThickness_ / 2.0 * geometry_.GetNormal());
+        Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) -
+                     sliceThickness_ / 2.0 * geometry_.GetNormal());
+
+        slice.ProjectPoint2(x1, y1, p1);
+        slice.ProjectPoint2(x2, y2, p2);
+
+        return true;
+      }
+    }
+    else
+    {
+      // Should not happen
+      return false;
+    }
+  }
+
+  
+  const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
+  {
+    if (index >= structures_.size())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    return structures_[index];
+  }
+
+
+  DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index)
+  {
+    if (index >= structures_.size())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    return structures_[index];
+  }
+
+  void DicomStructureSet::Setup(const IDicomDataset& tags)
+  {
+    DicomDatasetReader reader(tags);
+    
+    size_t count, tmp;
+    if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
+        !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
+        tmp != count ||
+        !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
+        tmp != count)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+
+    structures_.resize(count);
+    for (size_t i = 0; i < count; i++)
+    {
+      structures_[i].interpretation_ = reader.GetStringValue
+        (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
+                   DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
+         "No interpretation");
+
+      structures_[i].name_ = reader.GetStringValue
+        (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
+                   DICOM_TAG_ROI_NAME),
+         "No name");
+
+      Vector color;
+      if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                             DICOM_TAG_ROI_DISPLAY_COLOR)) &&
+          color.size() == 3)
+      {
+        structures_[i].red_ = ConvertColor(color[0]);
+        structures_[i].green_ = ConvertColor(color[1]);
+        structures_[i].blue_ = ConvertColor(color[2]);
+      }
+      else
+      {
+        structures_[i].red_ = 255;
+        structures_[i].green_ = 0;
+        structures_[i].blue_ = 0;
+      }
+
+      size_t countSlices;
+      if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                                       DICOM_TAG_CONTOUR_SEQUENCE)))
+      {
+        countSlices = 0;
+      }
+
+      LOG(INFO) << "New RT structure: \"" << structures_[i].name_ 
+                << "\" with interpretation \"" << structures_[i].interpretation_
+                << "\" containing " << countSlices << " slices (color: " 
+                << static_cast<int>(structures_[i].red_) << "," 
+                << static_cast<int>(structures_[i].green_) << ","
+                << static_cast<int>(structures_[i].blue_) << ")";
+
+      // These temporary variables avoid allocating many vectors in the loop below
+      DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                DICOM_TAG_CONTOUR_SEQUENCE, 0,
+                                DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
+
+      DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                  DICOM_TAG_CONTOUR_SEQUENCE, 0,
+                                  DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
+      
+      DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                  DICOM_TAG_CONTOUR_SEQUENCE, 0,
+                                  DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
+
+      // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
+      DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                       DICOM_TAG_CONTOUR_SEQUENCE, 0,
+                                       DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
+                                       DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
+
+      DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
+                                DICOM_TAG_CONTOUR_SEQUENCE, 0,
+                                DICOM_TAG_CONTOUR_DATA);
+
+      for (size_t j = 0; j < countSlices; j++)
+      {
+        unsigned int countPoints;
+
+        countPointsPath.SetPrefixIndex(1, j);
+        if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
+        {
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+        }
+            
+        //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
+
+        geometricTypePath.SetPrefixIndex(1, j);
+        std::string type = reader.GetMandatoryStringValue(geometricTypePath);
+        if (type != "CLOSED_PLANAR")
+        {
+          LOG(WARNING) << "Ignoring contour with geometry type: " << type;
+          continue;
+        }
+
+        size_t size;
+
+        imageSequencePath.SetPrefixIndex(1, j);
+        if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
+        {
+          LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);          
+        }
+
+        referencedInstancePath.SetPrefixIndex(1, j);
+        std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
+
+        contourDataPath.SetPrefixIndex(1, j);        
+        std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
+
+        Vector points;
+        if (!LinearAlgebra::ParseVector(points, slicesData) ||
+            points.size() != 3 * countPoints)
+        {
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);          
+        }
+
+        // seen in real world
+        if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") 
+        {
+          LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)";
+        }
+
+        Polygon polygon(sopInstanceUid);
+        polygon.Reserve(countPoints);
+
+        for (size_t k = 0; k < countPoints; k++)
+        {
+          Vector v(3);
+          v[0] = points[3 * k];
+          v[1] = points[3 * k + 1];
+          v[2] = points[3 * k + 2];
+          polygon.AddPoint(v);
+        }
+
+        structures_[i].polygons_.push_back(polygon);
+      }
+    }
+  }
+
+
+#if ORTHANC_ENABLE_DCMTK == 1
+  DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance)
+  {
+    ParsedDicomDataset dataset(instance);
+    Setup(dataset);
+  }
+#endif
+  
+
+  Vector DicomStructureSet::GetStructureCenter(size_t index) const
+  {
+    const Structure& structure = GetStructure(index);
+
+    Vector center;
+    LinearAlgebra::AssignVector(center, 0, 0, 0);
+    if (structure.polygons_.empty())
+    {
+      return center;
+    }
+
+    double n = static_cast<double>(structure.polygons_.size());
+
+    for (Polygons::const_iterator polygon = structure.polygons_.begin();
+         polygon != structure.polygons_.end(); ++polygon)
+    {
+      if (!polygon->GetPoints().empty())
+      {
+        center += polygon->GetPoints().front() / n;
+      }
+    }
+
+    return center;
+  }
+
+
+  const std::string& DicomStructureSet::GetStructureName(size_t index) const
+  {
+    return GetStructure(index).name_;
+  }
+
+
+  const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
+  {
+    return GetStructure(index).interpretation_;
+  }
+
+
+  Color DicomStructureSet::GetStructureColor(size_t index) const
+  {
+    const Structure& s = GetStructure(index);
+    return Color(s.red_, s.green_, s.blue_);
+  }
+  
+    
+  void DicomStructureSet::GetStructureColor(uint8_t& red,
+                                            uint8_t& green,
+                                            uint8_t& blue,
+                                            size_t index) const
+  {
+    const Structure& s = GetStructure(index);
+    red = s.red_;
+    green = s.green_;
+    blue = s.blue_;
+  }
+
+
+  void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances)
+  {
+    for (Structures::const_iterator structure = structures_.begin();
+         structure != structures_.end(); ++structure)
+    {
+      for (Polygons::const_iterator polygon = structure->polygons_.begin();
+           polygon != structure->polygons_.end(); ++polygon)
+      {
+        instances.insert(polygon->GetSopInstanceUid());
+      }
+    }
+  }
+
+
+  void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid,
+                                             const std::string& seriesInstanceUid,
+                                             const CoordinateSystem3D& geometry,
+                                             double thickness)
+  {
+    if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
+    {
+      // This geometry is already known
+      LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid;
+     
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      if (thickness < 0)
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+      }
+        
+      if (!referencedSlices_.empty())
+      {
+        const ReferencedSlice& reference = referencedSlices_.begin()->second;
+
+        if (reference.seriesInstanceUid_ != seriesInstanceUid)
+        {
+          LOG(ERROR) << "This RT-STRUCT refers to several different series";
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+        }
+
+        if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
+        {
+          LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+        }
+      }
+        
+      referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
+
+      for (Structures::iterator structure = structures_.begin();
+           structure != structures_.end(); ++structure)
+      {
+        for (Polygons::iterator polygon = structure->polygons_.begin();
+             polygon != structure->polygons_.end(); ++polygon)
+        {
+          polygon->UpdateReferencedSlice(referencedSlices_);
+        }
+      }
+    }
+  }
+
+
+  void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset)
+  {
+    CoordinateSystem3D slice(dataset);
+
+    double thickness = 1;  // 1 mm by default
+
+    std::string s;
+    Vector v;
+    if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
+        LinearAlgebra::ParseVector(v, s) &&
+        v.size() > 0)
+    {
+      thickness = v[0];
+    }
+
+    std::string instance, series;
+    if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
+        dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
+    {
+      AddReferencedSlice(instance, series, slice, thickness);
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+  }
+
+
+  void DicomStructureSet::CheckReferencedSlices()
+  {
+    for (Structures::iterator structure = structures_.begin();
+         structure != structures_.end(); ++structure)
+    {
+      for (Polygons::iterator polygon = structure->polygons_.begin();
+           polygon != structure->polygons_.end(); ++polygon)
+      {
+        if (!polygon->UpdateReferencedSlice(referencedSlices_))
+        {
+          std::string sopInstanceUid = polygon->GetSopInstanceUid();
+          if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
+          {
+            LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): "
+                       << " missing information about referenced instance "
+                       << "(sopInstanceUid is empty!)";
+          }
+          else
+          {
+            LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): "
+                       << " missing information about referenced instance "
+                       << "(sopInstanceUid = " << sopInstanceUid << ")";
+          }
+          //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+        }
+      }
+    }
+  }
+
+
+  Vector DicomStructureSet::GetNormal() const
+  {
+    if (referencedSlices_.empty())
+    {
+      Vector v;
+      LinearAlgebra::AssignVector(v, 0, 0, 1);
+      return v;
+    }
+    else
+    {
+      return referencedSlices_.begin()->second.geometry_.GetNormal();
+    }
+  }
+
+  bool DicomStructureSet::ProjectStructure(
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+    std::vector< std::vector<Point2D> >& polygons,
+#else
+    std::vector< std::pair<Point2D, Point2D> >& segments,
+#endif
+    const Structure& structure,
+    const CoordinateSystem3D& sourceSlice) const
+  {
+    const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice);
+    
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+    polygons.clear();
+#else
+    segments.clear();
+#endif
+
+    Vector normal = GetNormal();
+    
+    bool isOpposite;    
+    if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
+    {
+      // This is an axial projection
+
+      for (Polygons::const_iterator polygon = structure.polygons_.begin();
+           polygon != structure.polygons_.end(); ++polygon)
+      {
+        if (polygon->IsOnSlice(slice))
+        {
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+          polygons.push_back(std::vector<Point2D>());
+          
+          for (Points::const_iterator p = polygon->GetPoints().begin();
+               p != polygon->GetPoints().end(); ++p)
+          {
+            double x, y;
+            slice.ProjectPoint2(x, y, *p);
+            polygons.back().push_back(Point2D(x, y));
+          }
+#else
+          // we need to add all the segments corresponding to this polygon
+          const std::vector<Vector>& points3D = polygon->GetPoints();
+          if (points3D.size() >= 3)
+          {
+            Point2D prev2D;
+            {
+              Vector prev = points3D[0];
+              double prevX, prevY;
+              slice.ProjectPoint2(prevX, prevY, prev);
+              prev2D = Point2D(prevX, prevY);
+            }
+
+            size_t pointCount = points3D.size();
+            for (size_t ipt = 1; ipt < pointCount; ++ipt)
+            {
+              Vector next = points3D[ipt];
+              double nextX, nextY;
+              slice.ProjectPoint2(nextX, nextY, next);
+              Point2D next2D(nextX, nextY);
+              segments.push_back(std::pair<Point2D, Point2D>(prev2D, next2D));
+              prev2D = next2D;
+            }
+          }
+          else
+          {
+            LOG(ERROR) << "Contour with less than 3 points!";
+            // !!!
+          }
+#endif
+        }
+      }
+
+      return true;
+    }
+    else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
+             GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
+    {
+#if 1
+      // Sagittal or coronal projection
+
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+      std::vector<BoostPolygon> projected;
+
+      for (Polygons::const_iterator polygon = structure.polygons_.begin();
+           polygon != structure.polygons_.end(); ++polygon)
+      {
+        double x1, y1, x2, y2;
+
+        if (polygon->Project(x1, y1, x2, y2, slice))
+        {
+          projected.push_back(CreateRectangle(x1, y1, x2, y2));
+        }
+      }
+#else
+      // this will contain the intersection of the polygon slab with
+      // the cutting plane, projected on the cutting plane coord system 
+      // (that yields a rectangle) + the Z coordinate of the polygon 
+      // (this is required to group polygons with the same Z later)
+      std::vector<std::pair<RtStructRectangleInSlab, double> > projected;
+
+      for (Polygons::const_iterator polygon = structure.polygons_.begin();
+           polygon != structure.polygons_.end(); ++polygon)
+      {
+        double x1, y1, x2, y2;
+
+        if (polygon->Project(x1, y1, x2, y2, slice))
+        {
+          double curZ = polygon->GetGeometryOrigin()[2];
+
+          // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane 
+          // geometry)
+          projected.push_back(std::make_pair(CreateRectangle(
+                                               static_cast<float>(x1), 
+                                               static_cast<float>(y1), 
+                                               static_cast<float>(x2), 
+                                               static_cast<float>(y2)),curZ));
+        }
+      }
+#endif
+
+#if USE_BOOST_UNION_FOR_POLYGONS != 1
+      // projected contains a set of rectangles specified by two opposite
+      // corners (x1,y1,x2,y2)
+      // we need to merge them 
+      // each slab yields ONE polygon!
+
+      // we need to sorted all the rectangles that originate from the same Z
+      // into lanes. To make sure they are grouped together in the array, we
+      // sort it.
+      std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection);
+
+      std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab;
+      rectanglesForEachSlab.reserve(projected.size());
+
+      double curZ = 0;
+      for (size_t i = 0; i < projected.size(); ++i)
+      {
+#if 0
+        rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
+#else
+        if (i == 0)
+        {
+          curZ = projected[i].second;
+          rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
+        }
+        else
+        {
+          // this check is needed to prevent creating a new slab if 
+          // the new polygon is at the same Z coord than last one
+          if (!LinearAlgebra::IsNear(curZ, projected[i].second))
+          {
+            rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
+            curZ = projected[i].second;
+          }
+        }
+#endif
+
+        rectanglesForEachSlab.back().push_back(projected[i].first);
+
+        // as long as they have the same y, we should put them into the same lane
+        // BUT in Sebastien's code, there is only one polygon per lane.
+
+        //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl;
+      }
+      
+      // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments)
+      std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY);
+
+      ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size());
+#else
+      BoostMultiPolygon merged;
+      Union(merged, projected);
+
+      polygons.resize(merged.size());
+      for (size_t i = 0; i < merged.size(); i++)
+      {
+        const std::vector<BoostPoint>& outer = merged[i].outer();
+
+        polygons[i].resize(outer.size());
+        for (size_t j = 0; j < outer.size(); j++)
+        {
+          polygons[i][j] = Point2D(outer[j].x(), outer[j].y());
+        }
+      }  
+#endif
+
+#else
+      for (Polygons::iterator polygon = structure.polygons_.begin();
+           polygon != structure.polygons_.end(); ++polygon)
+      {
+        double x1, y1, x2, y2;
+        if (polygon->Project(x1, y1, x2, y2, slice))
+        {
+          std::vector<Point2D> p(4);
+          p[0] = std::make_pair(x1, y1);
+          p[1] = std::make_pair(x2, y1);
+          p[2] = std::make_pair(x2, y2);
+          p[3] = std::make_pair(x1, y2);
+          polygons.push_back(p);
+        }
+      }
+#endif
+      
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
+  void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer,
+                                           const CoordinateSystem3D& plane,
+                                           size_t structureIndex,
+                                           const Color& color) const
+  {
+#if USE_BOOST_UNION_FOR_POLYGONS == 1
+    std::vector< std::vector<Point2D> > polygons;
+    if (ProjectStructure(polygons, structureIndex, plane))
+    {
+      for (size_t j = 0; j < polygons.size(); j++)
+      {
+        std::vector<ScenePoint2D> chain;
+        chain.reserve(polygons[j].size());
+
+        for (size_t k = 0; k < polygons[j].size(); k++)
+        {
+          chain.push_back(ScenePoint2D(polygons[j][k].x, polygons[j][k].y));
+        }
+
+        layer.AddChain(chain, true, color.GetRed(), color.GetGreen(), color.GetBlue());
+      }
+    }
+    
+#else
+    std::vector< std::pair<Point2D, Point2D> >  segments;
+
+    if (ProjectStructure(segments, structureIndex, plane))
+    {
+      for (size_t j = 0; j < segments.size(); j++)
+      {
+        std::vector<ScenePoint2D> chain(2);
+        chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y);
+        chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y);
+        layer.AddChain(chain, false, color.GetRed(), color.GetGreen(), color.GetBlue());
+      }
+    }
+#endif
+  }
+}