--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp	Tue Jul 07 16:21:02 2020 +0200
@@ -0,0 +1,530 @@
+/**
+ * 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 "DicomInstanceParameters.h"
+
+#include "../Scene2D/ColorTextureSceneLayer.h"
+#include "../Scene2D/FloatTextureSceneLayer.h"
+#include "../Toolbox/GeometryToolbox.h"
+#include "../Toolbox/ImageToolbox.h"
+
+#include <Images/Image.h>
+#include <Images/ImageProcessing.h>
+#include <Logging.h>
+#include <OrthancException.h>
+#include <Toolbox.h>
+
+
+namespace OrthancStone
+{
+  void DicomInstanceParameters::Data::ComputeDoseOffsets(const Orthanc::DicomMap& dicom)
+  {
+    // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
+
+    {
+      std::string increment;
+
+      if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
+      {
+        Orthanc::Toolbox::ToUpperCase(increment);
+        if (increment != "3004,000C")  // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR)
+        {
+          LOG(ERROR) << "RT-DOSE: Bad value for the \"FrameIncrementPointer\" tag";
+          return;
+        }
+      }
+    }
+
+    if (!LinearAlgebra::ParseVector(frameOffsets_, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) ||
+        frameOffsets_.size() < imageInformation_.GetNumberOfFrames())
+    {
+      LOG(ERROR) << "RT-DOSE: No information about the 3D location of some slice(s)";
+      frameOffsets_.clear();
+    }
+    else
+    {
+      if (frameOffsets_.size() >= 2)
+      {
+        thickness_ = std::abs(frameOffsets_[1] - frameOffsets_[0]);
+      }
+    }
+  }
+
+
+  DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) :
+    imageInformation_(dicom)
+  {
+    if (imageInformation_.GetNumberOfFrames() <= 0)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+
+    if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
+        !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) ||
+        !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+        
+    std::string s;
+    if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+    else
+    {
+      sopClassUid_ = StringToSopClassUid(s);
+    }
+
+    if (!dicom.ParseDouble(thickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS))
+    {
+      thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
+    }
+
+    GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
+
+    std::string position, orientation;
+    if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
+        dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
+    {
+      geometry_ = CoordinateSystem3D(position, orientation);
+    }
+
+    if (sopClassUid_ == SopClassUid_RTDose)
+    {
+      ComputeDoseOffsets(dicom);
+
+      static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
+
+      if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false))
+      {
+        LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
+        doseUnits_ = "";
+      }
+    }
+
+    isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 &&
+                imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2);
+
+    if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
+        dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
+    {
+      if (sopClassUid_ == SopClassUid_RTDose)
+      {
+        LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
+        // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
+        hasRescale_ = false;
+      }
+      else
+      {
+        hasRescale_ = true;
+      }
+      
+    }
+    else
+    {
+      hasRescale_ = false;
+    }
+
+    if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
+    {
+      if (sopClassUid_ == SopClassUid_RTDose)
+      {
+        LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_;
+      }
+    }
+    else
+    {
+      doseGridScaling_ = 1.0;
+      if (sopClassUid_ == SopClassUid_RTDose)
+      {
+        LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0";
+      }
+    }
+
+    Vector c, w;
+    if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
+        LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
+        c.size() > 0 && 
+        w.size() > 0)
+    {
+      hasDefaultWindowing_ = true;
+      defaultWindowingCenter_ = static_cast<float>(c[0]);
+      defaultWindowingWidth_ = static_cast<float>(w[0]);
+    }
+    else
+    {
+      hasDefaultWindowing_ = false;
+      defaultWindowingCenter_ = 0;
+      defaultWindowingWidth_  = 0;
+    }
+
+    if (sopClassUid_ == SopClassUid_RTDose)
+    {
+      switch (imageInformation_.GetBitsStored())
+      {
+        case 16:
+          expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
+          break;
+
+        case 32:
+          expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
+          break;
+
+        default:
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+      } 
+    }
+    else if (isColor_)
+    {
+      expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
+    }
+    else if (imageInformation_.IsSigned())
+    {
+      expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
+    }
+    else
+    {
+      expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
+    }
+
+    // This computes the "IndexInSeries" metadata from Orthanc (check
+    // out "Orthanc::ServerIndex::Store()")
+    hasIndexInSeries_ = (
+      dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
+      dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
+  }
+
+
+  CoordinateSystem3D  DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const
+  {
+    if (frame == 0)
+    {
+      return geometry_;
+    }
+    else if (frame >= imageInformation_.GetNumberOfFrames())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+    else if (sopClassUid_ == SopClassUid_RTDose)
+    {
+      if (frame >= frameOffsets_.size())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      return CoordinateSystem3D(
+        geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(),
+        geometry_.GetAxisX(),
+        geometry_.GetAxisY());
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+    }
+  }
+
+
+  bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame,
+                                                         const CoordinateSystem3D& plane) const
+  {
+    if (frame >= imageInformation_.GetNumberOfFrames())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    CoordinateSystem3D tmp = geometry_;
+
+    if (frame != 0)
+    {
+      tmp = GetFrameGeometry(frame);
+    }
+
+    double distance;
+
+    return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
+            distance <= thickness_ / 2.0);
+  }
+
+  void DicomInstanceParameters::Data::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
+                                                                 bool useDouble) const
+  {
+    if (image.GetFormat() != Orthanc::PixelFormat_Float32)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
+    }
+
+    double factor = doseGridScaling_;
+    double offset = 0.0;
+
+    if (hasRescale_)
+    {
+      factor *= rescaleSlope_;
+      offset = rescaleIntercept_;
+    }
+
+    if ( (factor != 1.0) || (offset != 0.0) )
+    {
+      const unsigned int width = image.GetWidth();
+      const unsigned int height = image.GetHeight();
+        
+      for (unsigned int y = 0; y < height; y++)
+      {
+        float* p = reinterpret_cast<float*>(image.GetRow(y));
+
+        if (useDouble)
+        {
+          // Slower, accurate implementation using double
+          for (unsigned int x = 0; x < width; x++, p++)
+          {
+            double value = static_cast<double>(*p);
+            *p = static_cast<float>(value * factor + offset);
+          }
+        }
+        else
+        {
+          // Fast, approximate implementation using float
+          for (unsigned int x = 0; x < width; x++, p++)
+          {
+            *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset);
+          }
+        }
+      }
+    }
+  }
+
+  double DicomInstanceParameters::GetRescaleIntercept() const
+  {
+    if (data_.hasRescale_)
+    {
+      return data_.rescaleIntercept_;
+    }
+    else
+    {
+      LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  double DicomInstanceParameters::GetRescaleSlope() const
+  {
+    if (data_.hasRescale_)
+    {
+      return data_.rescaleSlope_;
+    }
+    else
+    {
+      LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  float DicomInstanceParameters::GetDefaultWindowingCenter() const
+  {
+    if (data_.hasDefaultWindowing_)
+    {
+      return data_.defaultWindowingCenter_;
+    }
+    else
+    {
+      LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  float DicomInstanceParameters::GetDefaultWindowingWidth() const
+  {
+    if (data_.hasDefaultWindowing_)
+    {
+      return data_.defaultWindowingWidth_;
+    }
+    else
+    {
+      LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
+  {
+    std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, 
+                                                               pixelData.GetWidth(), 
+                                                               pixelData.GetHeight(),
+                                                               false));
+    Orthanc::ImageProcessing::Convert(*converted, pixelData);
+
+                                                   
+    // Correct rescale slope/intercept if need be
+    //data_.ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
+    data_.ApplyRescaleAndDoseScaling(*converted, false);
+
+    return converted.release();
+  }
+
+
+  TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
+  (const Orthanc::ImageAccessor& pixelData) const
+  {
+    // {
+    //   const Orthanc::ImageAccessor& source = pixelData;
+    //   const void* sourceBuffer = source.GetConstBuffer();
+    //   intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
+    //   int sourceWidth = source.GetWidth();
+    //   int sourceHeight = source.GetHeight();
+    //   int sourcePitch = source.GetPitch();
+
+    //   // TODO: turn error into trace below
+    //   LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
+    //     << " W = " << sourceWidth << " H = " << sourceHeight
+    //     << " P = " << sourcePitch << " B = " << sourceBufferInt
+    //     << " B % 4 == " << sourceBufferInt % 4;
+    // }
+
+    assert(sizeof(float) == 4);
+
+    Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
+
+    if (sourceFormat != GetExpectedPixelFormat())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
+    }
+
+    if (sourceFormat == Orthanc::PixelFormat_RGB24)
+    {
+      // This is the case of a color image. No conversion has to be done.
+      return new ColorTextureSceneLayer(pixelData);
+    }
+    else
+    {
+      // This is the case of a grayscale frame. Convert it to Float32.
+      std::unique_ptr<FloatTextureSceneLayer> texture;
+
+      if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
+      {
+        texture.reset(new FloatTextureSceneLayer(pixelData));
+      }
+      else
+      {
+        std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
+        texture.reset(new FloatTextureSceneLayer(*converted));
+      }
+
+      if (data_.hasDefaultWindowing_)
+      {
+        texture->SetCustomWindowing(data_.defaultWindowingCenter_,
+                                    data_.defaultWindowingWidth_);
+      }
+      
+
+      if (data_.imageInformation_.GetPhotometricInterpretation()
+        == Orthanc::PhotometricInterpretation_Monochrome1)
+      {
+        texture->SetInverted(true);
+      }
+      else if (data_.imageInformation_.GetPhotometricInterpretation()
+        == Orthanc::PhotometricInterpretation_Monochrome2)
+      {
+        texture->SetInverted(false);
+      }
+
+      return texture.release();
+    }
+  }
+
+
+  LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
+  (const Orthanc::ImageAccessor& pixelData) const
+  {
+    std::unique_ptr<FloatTextureSceneLayer> texture;
+
+    if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
+    {
+      return new LookupTableTextureSceneLayer(pixelData);
+    }
+    else
+    {
+      std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
+      return new LookupTableTextureSceneLayer(*converted);
+    }
+  }
+
+  
+  unsigned int DicomInstanceParameters::GetIndexInSeries() const
+  {
+    if (data_.hasIndexInSeries_)
+    {
+      return data_.indexInSeries_;
+    }
+    else
+    {
+      LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  double DicomInstanceParameters::Data::ApplyRescale(double value) const
+  {
+    double factor = doseGridScaling_;
+    double offset = 0.0;
+
+    if (hasRescale_)
+    {
+      factor *= rescaleSlope_;
+      offset = rescaleIntercept_;
+    }
+
+    return (value * factor + offset);
+  }
+
+
+  bool DicomInstanceParameters::Data::ComputeRegularSpacing(double& spacing) const
+  {
+    if (frameOffsets_.size() == 0)  // Not a RT-DOSE
+    {
+      return false;
+    }
+    else if (frameOffsets_.size() == 1)
+    {
+      spacing = 1;   // Edge case: RT-DOSE with one single frame
+      return true;
+    }
+    else
+    {
+      spacing = std::abs(frameOffsets_[1] - frameOffsets_[0]);
+
+      for (size_t i = 1; i + 1 < frameOffsets_.size(); i++)
+      {
+        double s = frameOffsets_[i + 1] - frameOffsets_[i];
+        if (!LinearAlgebra::IsNear(spacing, s, 0.001))
+        {
+          return false;
+        }
+      }
+      
+      return true;
+    }
+  }
+}