--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Deprecated/Radiography/RadiographyDicomLayer.cpp	Wed Apr 29 20:43:09 2020 +0200
@@ -0,0 +1,264 @@
+/**
+ * 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 "RadiographyDicomLayer.h"
+
+#include "RadiographyScene.h"
+#include "../Deprecated/Toolbox/DicomFrameConverter.h"
+
+#include <Core/OrthancException.h>
+#include <Core/Images/Image.h>
+#include <Core/Images/ImageProcessing.h>
+#include <Plugins/Samples/Common/DicomDatasetReader.h>
+#include "../Toolbox/ImageGeometry.h"
+
+static OrthancPlugins::DicomTag  ConvertTag(const Orthanc::DicomTag& tag)
+{
+  return OrthancPlugins::DicomTag(tag.GetGroup(), tag.GetElement());
+}
+
+namespace OrthancStone
+{
+
+  void RadiographyDicomLayer::ApplyConverter()
+  {
+    if (source_.get() != NULL &&
+        converter_.get() != NULL)
+    {
+      converted_.reset(converter_->ConvertFrame(*source_));
+    }
+  }
+
+
+  RadiographyDicomLayer::RadiographyDicomLayer(const RadiographyScene& scene) :
+    RadiographyLayer(scene)
+  {
+
+  }
+
+  void RadiographyDicomLayer::SetDicomTags(const OrthancPlugins::FullOrthancDataset& dataset)
+  {
+    converter_.reset(new Deprecated::DicomFrameConverter);
+    converter_->ReadParameters(dataset);
+    ApplyConverter();
+
+    std::string tmp;
+    Vector pixelSpacing;
+
+    if (dataset.GetStringValue(tmp, ConvertTag(Orthanc::DICOM_TAG_PIXEL_SPACING)) &&
+        LinearAlgebra::ParseVector(pixelSpacing, tmp) &&
+        pixelSpacing.size() == 2)
+    {
+      SetPixelSpacing(pixelSpacing[0], pixelSpacing[1]);
+    }
+
+    OrthancPlugins::DicomDatasetReader reader(dataset);
+
+    unsigned int width, height;
+    if (!reader.GetUnsignedIntegerValue(width, ConvertTag(Orthanc::DICOM_TAG_COLUMNS)) ||
+        !reader.GetUnsignedIntegerValue(height, ConvertTag(Orthanc::DICOM_TAG_ROWS)))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+    else
+    {
+      SetSize(width, height);
+    }
+
+    if (dataset.GetStringValue(tmp, ConvertTag(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION)))
+    {
+      if (tmp == "MONOCHROME1")
+      {
+        SetPreferredPhotomotricDisplayMode(RadiographyPhotometricDisplayMode_Monochrome1);
+      }
+      else if (tmp == "MONOCHROME2")
+      {
+        SetPreferredPhotomotricDisplayMode(RadiographyPhotometricDisplayMode_Monochrome2);
+      }
+    }
+  }
+
+  void RadiographyDicomLayer::SetSourceImage(Orthanc::ImageAccessor* image)   // Takes ownership
+  {
+    std::unique_ptr<Orthanc::ImageAccessor> raii(image);
+
+    if (image == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
+    }
+
+    SetSize(image->GetWidth(), image->GetHeight());
+
+#if __cplusplus < 201103L
+      source_.reset(raii.release());
+#else
+      source_ = std::move(raii);
+#endif
+
+    ApplyConverter();
+
+    BroadcastMessage(RadiographyLayer::LayerEditedMessage(*this));
+  }
+
+  void RadiographyDicomLayer::SetSourceImage(Orthanc::ImageAccessor* image, double newPixelSpacingX, double newPixelSpacingY, bool emitLayerEditedEvent)   // Takes ownership
+  {
+    std::unique_ptr<Orthanc::ImageAccessor> raii(image);
+
+    if (image == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
+    }
+
+    SetSize(image->GetWidth(), image->GetHeight(), false);
+
+#if __cplusplus < 201103L
+    source_.reset(raii.release());
+#else
+    source_ = std::move(raii);
+#endif
+
+    ApplyConverter();
+
+    SetPixelSpacing(newPixelSpacingX, newPixelSpacingY, false);
+
+    if (emitLayerEditedEvent)
+    {
+      BroadcastMessage(RadiographyLayer::LayerEditedMessage(*this));
+    }
+  }
+
+
+  void RadiographyDicomLayer::SetDicomFrameConverter(Deprecated::DicomFrameConverter* converter)
+  {
+    converter_.reset(converter);
+  }
+
+  void RadiographyDicomLayer::Render(Orthanc::ImageAccessor& buffer,
+                                     const AffineTransform2D& viewTransform,
+                                     ImageInterpolation interpolation,
+                                     float windowCenter,
+                                     float windowWidth,
+                                     bool applyWindowing) const
+  {
+    if (converted_.get() != NULL)
+    {
+      if (converted_->GetFormat() != Orthanc::PixelFormat_Float32)
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      unsigned int cropX, cropY, cropWidth, cropHeight;
+      GetCrop(cropX, cropY, cropWidth, cropHeight);
+
+      AffineTransform2D t = AffineTransform2D::Combine(
+            viewTransform, GetTransform(),
+            AffineTransform2D::CreateOffset(cropX, cropY));
+
+      Orthanc::ImageAccessor cropped;
+      converted_->GetRegion(cropped, cropX, cropY, cropWidth, cropHeight);
+
+      unsigned int x1, y1, x2, y2;
+      if (!OrthancStone::GetProjectiveTransformExtent(x1, y1, x2, y2,
+                                                      t.GetHomogeneousMatrix(),
+                                                      cropped.GetWidth(),
+                                                      cropped.GetHeight(),
+                                                      buffer.GetWidth(),
+                                                      buffer.GetHeight()))
+      {
+        return;  // layer is outside the buffer
+      }
+
+      t.Apply(buffer, cropped, interpolation, false);
+
+      if (applyWindowing)
+      {
+        // apply windowing but stay in the range [0.0, 65535.0]
+        float w0 = windowCenter - windowWidth / 2.0f;
+        float w1 = windowCenter + windowWidth / 2.0f;
+
+        if (windowWidth >= 0.001f)  // Avoid division by zero at (*)
+        {
+          float scaling = 1.0f / (w1 - w0) * 65535.0f;
+          for (unsigned int y = y1; y <= y2; y++)
+          {
+            float* p = reinterpret_cast<float*>(buffer.GetRow(y)) + x1;
+
+            for (unsigned int x = x1; x <= x2; x++, p++)
+            {
+              if (*p >= w1)
+              {
+                *p = 65535.0;
+              }
+              else if (*p <= w0)
+              {
+                *p = 0;
+              }
+              else
+              {
+                // https://en.wikipedia.org/wiki/Linear_interpolation
+                *p = scaling * (*p - w0);  // (*)
+              }
+            }
+          }
+        }
+      }
+
+    }
+  }
+
+
+  bool RadiographyDicomLayer::GetDefaultWindowing(float& center,
+                                                  float& width) const
+  {
+    if (converter_.get() != NULL &&
+        converter_->HasDefaultWindow())
+    {
+      center = static_cast<float>(converter_->GetDefaultWindowCenter());
+      width = static_cast<float>(converter_->GetDefaultWindowWidth());
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
+  bool RadiographyDicomLayer::GetRange(float& minValue,
+                                       float& maxValue) const
+  {
+    if (converted_.get() != NULL)
+    {
+      if (converted_->GetFormat() != Orthanc::PixelFormat_Float32)
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      Orthanc::ImageProcessing::GetMinMaxFloatValue(minValue, maxValue, *converted_);
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+}