# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1448645215 -3600
# Node ID a6ba21a083e588472de6f75849c6ed429f261a6a
# Parent  dbe7c97b6b4a7d35a914806b7951ff4cb390036c
major refactoring

diff -r dbe7c97b6b4a -r a6ba21a083e5 NEWS
--- a/NEWS	Fri Nov 27 16:19:09 2015 +0100
+++ b/NEWS	Fri Nov 27 18:26:55 2015 +0100
@@ -6,6 +6,13 @@
 * The GDCM decoder replaces the built-in Orthanc decoder
 
 
+TODO : Remove any dependency on GDCM in "Plugin"
+TODO : Use "/series/ordered-slices"
+TODO : Support cine and multi-frame images
+TODO : Remove class "ParsedDicomFile"
+TODO : Interpolation does not work at least with Firefox
+
+
 Version 1.3 (2015-11-27)
 ========================
 
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/Cache/CacheScheduler.cpp
--- a/Plugin/Cache/CacheScheduler.cpp	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/Cache/CacheScheduler.cpp	Fri Nov 27 18:26:55 2015 +0100
@@ -254,6 +254,11 @@
       content.clear();
       return factory_->Create(content, item);
     }
+
+    ICacheFactory& GetFactory()
+    {
+      return *factory_;
+    }
   };
 
 
@@ -401,4 +406,9 @@
     policy_.reset(policy);
   }
 
+
+  ICacheFactory& CacheScheduler::GetFactory(int bundle)
+  {
+    return GetBundleScheduler(bundle).GetFactory();
+  }
 }
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/Cache/CacheScheduler.h
--- a/Plugin/Cache/CacheScheduler.h	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/Cache/CacheScheduler.h	Fri Nov 27 18:26:55 2015 +0100
@@ -79,5 +79,7 @@
 
     void Prefetch(int bundle,
                   const std::string& item);
+
+    ICacheFactory& GetFactory(int bundle);
   };
 }
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/DecodedImageAdapter.cpp
--- a/Plugin/DecodedImageAdapter.cpp	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/DecodedImageAdapter.cpp	Fri Nov 27 18:26:55 2015 +0100
@@ -20,8 +20,13 @@
 
 #include "DecodedImageAdapter.h"
 
+#include "../Orthanc/Core/Images/ImageBuffer.h"
+#include "../Orthanc/Core/Images/ImageProcessing.h"
+#include "../Orthanc/Core/OrthancException.h"
+#include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h"
+#include "../Orthanc/Resources/ThirdParty/base64/base64.h"
+#include "ParsedDicomImage.h"
 #include "ViewerToolbox.h"
-#include "ParsedDicomImage.h"
 
 #include <boost/lexical_cast.hpp>
 #include <boost/algorithm/string/predicate.hpp>
@@ -84,10 +89,38 @@
       return false;
     }
 
+
+    bool ok = false;
+
+#if 1
+    Json::Value tags;
+    std::string dicom;
+    if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") ||
+        !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags"))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+    }
+
+    std::auto_ptr<OrthancImageWrapper> image(decoderCache_.Decode(context_, dicom.c_str(), dicom.size(), 0 /* TODO Frame */));
+
+    Json::Value json;
+    if (GetCornerstoneMetadata(json, tags, *image))
+    {
+      if (type == CompressionType_Deflate)
+      {
+        ok = EncodeUsingDeflate(json, *image, 9);
+      }
+      else if (type == CompressionType_Jpeg)
+      {
+        ok = EncodeUsingJpeg(json, *image, level);
+      }
+    }   
+
+#else
+
     ParsedDicomImage image(context_, instanceId);
 
     Json::Value json;
-    bool ok = false;
 
     if (type == CompressionType_Deflate)
     {
@@ -97,6 +130,7 @@
     {
       ok = image.EncodeUsingJpeg(json, level);
     }
+#endif
 
     if (ok)
     {
@@ -112,4 +146,266 @@
       return false;
     }
   }
+
+
+  static bool GetTagValue(std::string& value,
+                          const Json::Value& tags,
+                          const std::string& tag)
+  {
+    if (tags.type() == Json::objectValue &&
+        tags.isMember(tag) &&
+        tags[tag].type() == Json::objectValue &&
+        tags[tag].isMember("Type") &&
+        tags[tag].isMember("Value") &&
+        tags[tag]["Type"].type() == Json::stringValue &&
+        tags[tag]["Value"].type() == Json::stringValue &&
+        tags[tag]["Type"].asString() == "String")
+    {
+      value = tags[tag]["Value"].asString();
+      return true;
+    }        
+    else
+    {
+      return false;
+    }
+  }
+                                 
+
+
+  bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result,
+                                                   const Json::Value& tags,
+                                                   OrthancImageWrapper& image)
+  {
+    using namespace Orthanc;
+
+    float windowCenter, windowWidth;
+
+    Orthanc::ImageAccessor accessor;
+    accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(),
+                            image.GetHeight(), image.GetPitch(), image.GetBuffer());
+
+    switch (accessor.GetFormat())
+    {
+      case PixelFormat_Grayscale8:
+      case PixelFormat_Grayscale16:
+      case PixelFormat_SignedGrayscale16:
+      {
+        int64_t a, b;
+        Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor);
+        result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0);
+        result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1);
+        result["color"] = false;
+        
+        windowCenter = static_cast<float>(a + b) / 2.0f;
+        
+        if (a == b)
+        {
+          windowWidth = 256.0f;  // Arbitrary value
+        }
+        else
+        {
+          windowWidth = static_cast<float>(b - a) / 2.0f;
+        }
+
+        break;
+      }
+
+      case PixelFormat_RGB24:
+        result["minPixelValue"] = 0;
+        result["maxPixelValue"] = 255;
+        result["color"] = true;
+        windowCenter = 127.5f;
+        windowWidth = 256.0f;
+        break;
+
+      default:
+        return false;
+    }
+
+    result["slope"] = image.GetSlope();
+    result["intercept"] = image.GetIntercept();
+    result["rows"] = image.GetHeight();
+    result["columns"] = image.GetWidth();
+    result["height"] = image.GetHeight();
+    result["width"] = image.GetWidth();
+    result["columnPixelSpacing"] = image.GetColumnPixelSpacing();
+    result["rowPixelSpacing"] = image.GetRowPixelSpacing();
+
+    result["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept();
+    result["windowWidth"] = windowWidth * image.GetSlope();
+
+    try
+    {
+      std::string width, center;
+      if (GetTagValue(center, tags, "0028,1050" /*DICOM_TAG_WINDOW_CENTER*/) &&
+          GetTagValue(width, tags, "0028,1051" /*DICOM_TAG_WINDOW_WIDTH*/))
+      {
+        float a = boost::lexical_cast<float>(width);
+        float b = boost::lexical_cast<float>(center);
+        result["windowWidth"] = a;
+        result["windowCenter"] = b;
+      }
+    }
+    catch (boost::bad_lexical_cast&)
+    {
+    }
+
+    return true;
+  }
+
+
+
+  bool  DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result,
+                                                OrthancImageWrapper& image,
+                                                uint8_t compressionLevel  /* between 0 and 9 */)
+  {
+    Orthanc::ImageAccessor accessor;
+    accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(),
+                            image.GetHeight(), image.GetPitch(), image.GetBuffer());
+
+    Orthanc::ImageBuffer buffer;
+    buffer.SetMinimalPitchForced(true);
+
+    Orthanc::ImageAccessor converted;
+
+    switch (accessor.GetFormat())
+    {
+      case Orthanc::PixelFormat_RGB24:
+        converted = accessor;
+        break;
+
+      case Orthanc::PixelFormat_Grayscale8:
+      case Orthanc::PixelFormat_Grayscale16:
+        buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
+        buffer.SetWidth(accessor.GetWidth());
+        buffer.SetHeight(accessor.GetHeight());
+        converted = buffer.GetAccessor();
+        Orthanc::ImageProcessing::Convert(converted, accessor);
+        break;
+
+      case Orthanc::PixelFormat_SignedGrayscale16:
+        converted = accessor;
+        break;
+
+      default:
+        // Unsupported pixel format
+        return false;
+    }
+
+    // Sanity check: The pitch must be minimal
+    assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * 
+           GetBytesPerPixel(converted.GetFormat()));
+    result["Orthanc"]["Compression"] = "Deflate";
+    result["sizeInBytes"] = converted.GetSize();
+
+    std::string z;
+    CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize());
+
+    result["Orthanc"]["PixelData"] = base64_encode(z);  
+
+    return true;
+  }
+
+
+
+  template <typename TargetType, typename SourceType>
+  static void ChangeDynamics(Orthanc::ImageAccessor& target,
+                             const Orthanc::ImageAccessor& source,
+                             SourceType source1, TargetType target1,
+                             SourceType source2, TargetType target2)
+  {
+    if (source.GetWidth() != target.GetWidth() ||
+        source.GetHeight() != target.GetHeight())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
+    }
+
+    float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1);
+    float offset = static_cast<float>(target1) - scale * static_cast<float>(source1);
+
+    const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min());
+    const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max());
+
+    for (unsigned int y = 0; y < source.GetHeight(); y++)
+    {
+      const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y));
+      TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y));
+
+      for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++)
+      {
+        float v = (scale * static_cast<float>(*p)) + offset;
+
+        if (v > maxValue)
+        {
+          *q = std::numeric_limits<TargetType>::max();
+        }
+        else if (v < minValue)
+        {
+          *q = std::numeric_limits<TargetType>::min();
+        }
+        else
+        {
+          *q = static_cast<TargetType>(boost::math::iround(v));
+        }
+      }
+    }
+  }
+
+
+  bool  DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result,
+                                             OrthancImageWrapper& image,
+                                             uint8_t quality /* between 0 and 100 */)
+  {
+    Orthanc::ImageAccessor accessor;
+    accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(),
+                            image.GetHeight(), image.GetPitch(), image.GetBuffer());
+
+    Orthanc::ImageBuffer buffer;
+    buffer.SetMinimalPitchForced(true);
+
+    Orthanc::ImageAccessor converted;
+
+    if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 ||
+        accessor.GetFormat() == Orthanc::PixelFormat_RGB24)
+    {
+      result["Orthanc"]["Stretched"] = false;
+      converted = accessor;
+    }
+    else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 ||
+             accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16)
+    {
+      result["Orthanc"]["Stretched"] = true;
+      buffer.SetFormat(Orthanc::PixelFormat_Grayscale8);
+      buffer.SetWidth(accessor.GetWidth());
+      buffer.SetHeight(accessor.GetHeight());
+      converted = buffer.GetAccessor();
+
+      int64_t a, b;
+      Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor);
+      result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a);
+      result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b);
+
+      if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16)
+      {
+        ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255);
+      }
+      else
+      {
+        ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255);
+      }
+    }
+    else
+    {
+      return false;
+    }
+    
+    result["Orthanc"]["Compression"] = "Jpeg";
+    result["sizeInBytes"] = converted.GetSize();
+
+    std::string jpeg;
+    WriteJpegToMemory(jpeg, image.GetContext(), converted, quality);
+
+    result["Orthanc"]["PixelData"] = base64_encode(jpeg);  
+    return true;
+  }
 }
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/DecodedImageAdapter.h
--- a/Plugin/DecodedImageAdapter.h	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/DecodedImageAdapter.h	Fri Nov 27 18:26:55 2015 +0100
@@ -24,6 +24,11 @@
 
 #include <orthanc/OrthancCPlugin.h>
 #include <stdint.h>
+#include <json/value.h>
+
+#include "../Orthanc/Plugins/Samples/GdcmDecoder/GdcmDecoderCache.h"
+#include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h"
+
 
 namespace OrthancPlugins
 {
@@ -41,7 +46,20 @@
                          std::string& instanceId,
                          const std::string& uri);
 
+    static bool GetCornerstoneMetadata(Json::Value& result,
+                                       const Json::Value& tags,
+                                       OrthancImageWrapper& image);
+
+    static bool EncodeUsingDeflate(Json::Value& result,
+                                   OrthancImageWrapper& image,
+                                   uint8_t compressionLevel  /* between 0 and 9 */);
+
+    static bool EncodeUsingJpeg(Json::Value& result,
+                                OrthancImageWrapper& image,
+                                uint8_t quality /* between 0 and 100 */);
+
     OrthancPluginContext* context_;
+    GdcmDecoderCache  decoderCache_;
 
   public:
     DecodedImageAdapter(OrthancPluginContext* context) : context_(context)
@@ -50,5 +68,10 @@
 
     virtual bool Create(std::string& content,
                         const std::string& uri);  
+
+    GdcmDecoderCache& GetDecoderCache()
+    {
+      return decoderCache_;
+    }
   };
 }
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/ParsedDicomImage.cpp
--- a/Plugin/ParsedDicomImage.cpp	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/ParsedDicomImage.cpp	Fri Nov 27 18:26:55 2015 +0100
@@ -36,6 +36,8 @@
 #include "../Orthanc/Resources/ThirdParty/base64/base64.h"
 
 
+
+
 namespace OrthancPlugins
 {
   class ParsedDicomImage::PImpl
diff -r dbe7c97b6b4a -r a6ba21a083e5 Plugin/Plugin.cpp
--- a/Plugin/Plugin.cpp	Fri Nov 27 16:19:09 2015 +0100
+++ b/Plugin/Plugin.cpp	Fri Nov 27 18:26:55 2015 +0100
@@ -327,14 +327,20 @@
 {
   try
   {
-#if 1
+    std::auto_ptr<OrthancPlugins::OrthancImageWrapper> image;
+
+#if 0
     // Do not use the cache
     OrthancPlugins::GdcmImageDecoder decoder(dicom, size);
-    *target = decoder.Decode(context_, frameIndex);
+    image.reset(new OrthancPlugins::OrthancImageWrapper(context_, decoder, frameIndex));
 #else
-    *target = cache_.Decode(context_, dicom, size, frameIndex);
+    using namespace OrthancPlugins;
+    ICacheFactory& factory = cache_->GetScheduler().GetFactory(CacheBundle_DecodedImage);
+    image.reset(dynamic_cast<DecodedImageAdapter&>(factory).GetDecoderCache().Decode(context_, dicom, size, frameIndex));
 #endif
 
+    *target = image->Release();
+
     return OrthancPluginErrorCode_Success;
   }
   catch (std::runtime_error& e)