--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Deprecated/Toolbox/Slice.cpp	Tue May 21 14:27:35 2019 +0200
@@ -0,0 +1,367 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2019 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 "Slice.h"
+
+#include "../../StoneEnumerations.h"
+#include "../../Toolbox/GeometryToolbox.h"
+
+#include <Core/Logging.h>
+#include <Core/OrthancException.h>
+#include <Core/Toolbox.h>
+
+#include <boost/lexical_cast.hpp>
+
+namespace Deprecated
+{
+  static bool ParseDouble(double& target,
+                          const std::string& source)
+  {
+    try
+    {
+      target = boost::lexical_cast<double>(source);
+      return true;
+    }
+    catch (boost::bad_lexical_cast&)
+    {
+      return false;
+    }
+  }
+
+  Slice* Slice::Clone() const
+  {
+    std::auto_ptr<Slice> target(new Slice());
+
+    target->type_ = type_;
+    target->orthancInstanceId_ = orthancInstanceId_;
+    target->sopClassUid_ = sopClassUid_;
+    target->frame_ = frame_;
+    target->frameCount_ = frameCount_;
+    target->geometry_ = geometry_;
+    target->pixelSpacingX_ = pixelSpacingX_;
+    target->pixelSpacingY_ = pixelSpacingY_;
+    target->thickness_ = thickness_;
+    target->width_ = width_;
+    target->height_ = height_;
+    target->converter_ = converter_;
+    if (imageInformation_.get() != NULL)
+      target->imageInformation_.reset(imageInformation_->Clone());
+
+    return target.release();
+  }
+  
+  bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset,
+                                    unsigned int frame)
+  {
+    // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
+
+    {
+      std::string increment;
+
+      if (dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
+      {
+        Orthanc::Toolbox::ToUpperCase(increment);
+        if (increment != "3004,000C")  // This is the "Grid Frame Offset Vector" tag
+        {
+          LOG(ERROR) << "Bad value for the \"FrameIncrementPointer\" tag";
+          return false;
+        }
+      }
+    }
+
+    std::string offsetTag;
+
+    if (!dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false) ||
+        offsetTag.empty())
+    {
+      LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1";
+      return false;
+    }
+
+    std::vector<std::string> offsets;
+    Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\');
+
+    if (frameCount_ <= 1 ||
+        offsets.size() < frameCount_ ||
+        offsets.size() < 2 ||
+        frame >= frameCount_)
+    {
+      LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE";
+      return false;
+    }
+
+    double offset0, offset1, z;
+
+    if (!ParseDouble(offset0, offsets[0]) ||
+        !ParseDouble(offset1, offsets[1]) ||
+        !ParseDouble(z, offsets[frame]))
+    {
+      LOG(ERROR) << "Invalid syntax";
+      return false;
+    }
+
+    if (!OrthancStone::LinearAlgebra::IsCloseToZero(offset0))
+    {
+      LOG(ERROR) << "Invalid syntax";
+      return false;
+    }
+
+    geometry_ = OrthancStone::CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
+                                                 //+ 650 * geometry_.GetAxisX(),
+                                                 geometry_.GetAxisX(),
+                                                 geometry_.GetAxisY());
+
+    thickness_ = offset1 - offset0;
+    if (thickness_ < 0)
+    {
+      thickness_ = -thickness_;
+    }
+
+    return true;
+  }
+
+  
+  bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
+                                const std::string& instanceId,
+                                unsigned int frame)
+  {
+    orthancInstanceId_ = instanceId;
+    frame_ = frame;
+    type_ = Type_OrthancDecodableFrame;
+    imageInformation_.reset(new Orthanc::DicomImageInformation(dataset));
+
+    if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
+        sopClassUid_.empty())
+    {
+      LOG(ERROR) << "Instance without a SOP class UID";
+      return false; 
+    }
+
+    if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
+    {
+      frameCount_ = 1;   // Assume instance with one frame
+    }
+
+    if (frame >= frameCount_)
+    {
+      return false;
+    }
+
+    if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
+        !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
+    {
+      return false;
+    }
+
+    thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
+
+    std::string tmp;
+    if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
+    {
+      if (!tmp.empty() &&
+          !ParseDouble(thickness_, tmp))
+      {
+        return false;  // Syntax error
+      }
+    }
+    
+    converter_.ReadParameters(dataset);
+
+    OrthancStone::GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
+
+    std::string position, orientation;
+    if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
+        dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
+    {
+      geometry_ = OrthancStone::CoordinateSystem3D(position, orientation);
+
+      bool ok = true;
+
+      switch (OrthancStone::StringToSopClassUid(sopClassUid_))
+      {
+        case OrthancStone::SopClassUid_RTDose:
+          type_ = Type_OrthancRawFrame;
+          ok = ComputeRTDoseGeometry(dataset, frame);
+          break;
+            
+        default:
+          break;
+      }
+
+      if (!ok)
+      {
+        LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
+                   << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
+        return false;
+      }
+    }
+
+    return true;
+  }
+
+  
+  const std::string Slice::GetOrthancInstanceId() const
+  {
+    if (type_ == Type_OrthancDecodableFrame ||
+        type_ == Type_OrthancRawFrame)
+    {
+      return orthancInstanceId_;
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }   
+  }
+
+  
+  unsigned int Slice::GetFrame() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return frame_;
+  }
+
+  
+  const OrthancStone::CoordinateSystem3D& Slice::GetGeometry() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return geometry_;
+  }
+
+  
+  double Slice::GetThickness() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return thickness_;
+  }
+
+  
+  double Slice::GetPixelSpacingX() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return pixelSpacingX_;
+  }
+
+  
+  double Slice::GetPixelSpacingY() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return pixelSpacingY_;
+  }
+
+  
+  unsigned int Slice::GetWidth() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return width_;
+  }
+
+  
+  unsigned int Slice::GetHeight() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return height_;
+  }
+
+
+  const DicomFrameConverter& Slice::GetConverter() const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+        
+    return converter_;
+  }
+
+
+  bool Slice::ContainsPlane(const OrthancStone::CoordinateSystem3D& plane) const
+  {
+    if (type_ == Type_Invalid)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+
+    bool opposite;
+    return (OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite,
+                                                                GetGeometry().GetNormal(),
+                                                                plane.GetNormal()) &&
+            OrthancStone::LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
+                                                GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
+                                                thickness_ / 2.0));
+  }
+
+  
+  void Slice::GetExtent(std::vector<OrthancStone::Vector>& points) const
+  {
+    double sx = GetPixelSpacingX();
+    double sy = GetPixelSpacingY();
+    double w = static_cast<double>(GetWidth());
+    double h = static_cast<double>(GetHeight());
+
+    points.clear();
+    points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5      * sx, -0.5      * sy));
+    points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5      * sy));
+    points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5      * sx, (h - 0.5) * sy));
+    points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
+  }
+
+
+  const Orthanc::DicomImageInformation& Slice::GetImageInformation() const
+  {
+    if (imageInformation_.get() == NULL)
+    {
+      // Only available if constructing the "Slice" object with a DICOM map
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      return *imageInformation_;
+    }
+  }
+}