--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Deprecated/Toolbox/DicomFrameConverter.cpp	Tue May 21 14:27:35 2019 +0200
@@ -0,0 +1,282 @@
+/**
+ * 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 "DicomFrameConverter.h"
+
+#include "../../Toolbox/LinearAlgebra.h"
+
+#include <Core/Images/Image.h>
+#include <Core/Images/ImageProcessing.h>
+#include <Core/OrthancException.h>
+#include <Core/Toolbox.h>
+
+namespace Deprecated
+{
+  static const Orthanc::DicomTag IMAGE_TAGS[] =
+  {
+    Orthanc::DICOM_TAG_BITS_STORED,
+    Orthanc::DICOM_TAG_DOSE_GRID_SCALING,
+    Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION,
+    Orthanc::DICOM_TAG_PIXEL_REPRESENTATION,
+    Orthanc::DICOM_TAG_RESCALE_INTERCEPT,
+    Orthanc::DICOM_TAG_RESCALE_SLOPE,
+    Orthanc::DICOM_TAG_WINDOW_CENTER,
+    Orthanc::DICOM_TAG_WINDOW_WIDTH
+  };
+
+  
+  void DicomFrameConverter::SetDefaultParameters()
+  {
+    isSigned_ = true;
+    isColor_ = false;
+    hasRescale_ = false;
+    rescaleIntercept_ = 0;
+    rescaleSlope_ = 1;
+    hasDefaultWindow_ = false;
+    defaultWindowCenter_ = 128;
+    defaultWindowWidth_ = 256;
+    expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
+  }
+
+
+  void DicomFrameConverter::ReadParameters(const Orthanc::DicomMap& dicom)
+  {
+    SetDefaultParameters();
+
+    OrthancStone::Vector c, w;
+    if (OrthancStone::LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
+        OrthancStone::LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
+        c.size() > 0 && 
+        w.size() > 0)
+    {
+      hasDefaultWindow_ = true;
+      defaultWindowCenter_ = static_cast<float>(c[0]);
+      defaultWindowWidth_ = static_cast<float>(w[0]);
+    }
+
+    int32_t tmp;
+    if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))
+    {
+      // Type 1 tag, must be present
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+
+    isSigned_ = (tmp == 1);
+
+    double doseGridScaling;
+    bool isRTDose = false;
+    
+    if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
+        dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
+    {
+      hasRescale_ = true;
+    }
+    else if (dicom.ParseDouble(doseGridScaling, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
+    {
+      // This is for RT-DOSE
+      hasRescale_ = true;
+      isRTDose = true;
+      rescaleIntercept_ = 0;
+      rescaleSlope_ = doseGridScaling;
+
+      if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_BITS_STORED))
+      {
+        // Type 1 tag, must be present
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+      }
+
+      switch (tmp)
+      {
+        case 16:
+          expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
+          break;
+
+        case 32:
+          expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
+          break;
+
+        default:
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+      }
+    }
+
+    std::string photometric;
+    if (dicom.CopyToString(photometric, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false))
+    {
+      photometric = Orthanc::Toolbox::StripSpaces(photometric);
+    }
+    else
+    {
+      // Type 1 tag, must be present
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+
+    photometric_ = Orthanc::StringToPhotometricInterpretation(photometric.c_str());
+    
+    isColor_ = (photometric != "MONOCHROME1" &&
+                photometric != "MONOCHROME2");
+
+    // TODO Add more checks, e.g. on the number of bytes per value
+    // (cf. DicomImageInformation.h in Orthanc)
+
+    if (!isRTDose)
+    {
+      if (isColor_)
+      {
+        expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
+      }
+      else if (isSigned_)
+      {
+        expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
+      }
+      else
+      {
+        expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
+      }
+    }
+  }
+
+  
+  void DicomFrameConverter::ReadParameters(const OrthancPlugins::IDicomDataset& dicom)
+  {
+    Orthanc::DicomMap converted;
+
+    for (size_t i = 0; i < sizeof(IMAGE_TAGS) / sizeof(Orthanc::DicomTag); i++)
+    {
+      OrthancPlugins::DicomTag tag(IMAGE_TAGS[i].GetGroup(), IMAGE_TAGS[i].GetElement());
+    
+      std::string value;
+      if (dicom.GetStringValue(value, tag))
+      {
+        converted.SetValue(IMAGE_TAGS[i], value, false);
+      }
+    }
+
+    ReadParameters(converted);
+  }
+    
+
+  void DicomFrameConverter::ConvertFrameInplace(std::auto_ptr<Orthanc::ImageAccessor>& source) const
+  {
+    assert(sizeof(float) == 4);
+
+    if (source.get() == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    if (source->GetFormat() == GetExpectedPixelFormat() &&
+        source->GetFormat() == Orthanc::PixelFormat_RGB24)
+    {
+      // No conversion has to be done, check out (*)
+      return;
+    }
+    else
+    {
+      source.reset(ConvertFrame(*source));
+    }
+  }
+
+
+  Orthanc::ImageAccessor* DicomFrameConverter::ConvertFrame(const Orthanc::ImageAccessor& source) const
+  {
+    assert(sizeof(float) == 4);
+
+    Orthanc::PixelFormat sourceFormat = source.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 (*)
+      std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_RGB24, 
+                                                                 source.GetWidth(), 
+                                                                 source.GetHeight(),
+                                                                 false));
+      Orthanc::ImageProcessing::Copy(*converted, source);
+      return converted.release();
+    }
+    else
+    {
+      assert(sourceFormat == Orthanc::PixelFormat_Grayscale16 ||
+             sourceFormat == Orthanc::PixelFormat_Grayscale32 ||
+             sourceFormat == Orthanc::PixelFormat_SignedGrayscale16);
+
+      // This is the case of a grayscale frame. Convert it to Float32.
+      std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, 
+                                                                 source.GetWidth(), 
+                                                                 source.GetHeight(),
+                                                                 false));
+      Orthanc::ImageProcessing::Convert(*converted, source);
+
+      // Correct rescale slope/intercept if need be
+      ApplyRescale(*converted, sourceFormat != Orthanc::PixelFormat_Grayscale32);
+      
+      return converted.release();
+    }
+  }
+
+
+  void DicomFrameConverter::ApplyRescale(Orthanc::ImageAccessor& image,
+                                         bool useDouble) const
+  {
+    if (image.GetFormat() != Orthanc::PixelFormat_Float32)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
+    }
+    
+    if (hasRescale_)
+    {
+      for (unsigned int y = 0; y < image.GetHeight(); y++)
+      {
+        float* p = reinterpret_cast<float*>(image.GetRow(y));
+
+        if (useDouble)
+        {
+          // Slower, accurate implementation using double
+          for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
+          {
+            double value = static_cast<double>(*p);
+            *p = static_cast<float>(value * rescaleSlope_ + rescaleIntercept_);
+          }
+        }
+        else
+        {
+          // Fast, approximate implementation using float
+          for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
+          {
+            *p = (*p) * static_cast<float>(rescaleSlope_) + static_cast<float>(rescaleIntercept_);
+          }
+        }
+      }
+    }
+  }
+
+  
+  double DicomFrameConverter::Apply(double x) const
+  {
+    return x * rescaleSlope_ + rescaleIntercept_;
+  }
+
+}