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changeset 3600:4066998150ef

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/instances/{id}/preview route now takes the windowing into account
author Alain Mazy <alain@mazy.be>
date Thu, 09 Jan 2020 18:54:40 +0100
parents e01900f913e7
children a77e7839012a
files Core/Images/ImageProcessing.cpp Core/Images/ImageProcessing.h NEWS OrthancServer/OrthancRestApi/OrthancRestResources.cpp UnitTestsSources/ImageProcessingTests.cpp
diffstat 5 files changed, 310 insertions(+), 72 deletions(-) [+]
line wrap: on
line diff
--- a/Core/Images/ImageProcessing.cpp	Tue Jan 07 10:53:32 2020 +0100
+++ b/Core/Images/ImageProcessing.cpp	Thu Jan 09 18:54:40 2020 +0100
@@ -489,89 +489,120 @@
     }
   }
 
+  template <typename TargetType, typename SourceType>
+  static void ApplyWindowingInternal(ImageAccessor& target,
+                                     const ImageAccessor& source,
+                                     float windowCenter,
+                                     float windowWidth,
+                                     float rescaleSlope,
+                                     float rescaleIntercept,
+                                     bool invert)
+  {
+    // WARNING - "::min()" should be replaced by "::lowest()" if
+    // dealing with float or double (which is not the case so far)
+    assert(sizeof(TargetType) <= 2);  // Safeguard to remember about "float/double"
+    const TargetType minTargetValue = std::numeric_limits<TargetType>::min();
+    const TargetType maxTargetValue = std::numeric_limits<TargetType>::max();
+    const float minFloatValue = static_cast<float>(minTargetValue);
+    const float maxFloatValue = static_cast<float>(maxTargetValue);
+
+    const float windowIntercept = windowCenter - windowWidth / 2.0f;
+    const float windowSlope = (maxFloatValue + 1.0f) / windowWidth;
+
+    const unsigned int width = source.GetWidth();
+    const unsigned int height = source.GetHeight();
+
+    for (unsigned int y = 0; y < height; y++)
+    {
+      TargetType* t = reinterpret_cast<TargetType*>(target.GetRow(y));
+      const SourceType* s = reinterpret_cast<const SourceType*>(source.GetConstRow(y));
+
+      for (unsigned int x = 0; x < width; x++, t++, s++)
+      {
+        float rescaledValue = *s * rescaleSlope + rescaleIntercept;
+        float v = (rescaledValue - windowIntercept) * windowSlope;
+        if (v <= minFloatValue)
+        {
+          v = minFloatValue;
+        }
+        else if (v >= maxFloatValue)
+        {
+          v = maxFloatValue;
+        }
+
+        TargetType vv = static_cast<TargetType>(v);
+
+        if (invert)
+        {
+          vv = maxTargetValue - vv;
+        }
+
+        *t = static_cast<TargetType>(vv);
+      }
+    }
+  }
 
   void ImageProcessing::ApplyWindowing(ImageAccessor& target,
                                        const ImageAccessor& source,
                                        float windowCenter,
                                        float windowWidth,
-                                       Orthanc::PhotometricInterpretation sourcePhotometricInterpretation)
+                                       float rescaleSlope,
+                                       float rescaleIntercept,
+                                       bool invert)
   {
-    if (source.GetFormat() != Orthanc::PixelFormat_Float32)
-    {
-      throw OrthancException(ErrorCode_NotImplemented);
-    }
-
-    if (sourcePhotometricInterpretation != Orthanc::PhotometricInterpretation_Monochrome1
-        && sourcePhotometricInterpretation != Orthanc::PhotometricInterpretation_Monochrome2)
-    {
-      throw OrthancException(ErrorCode_ParameterOutOfRange);
-    }
-
     if (target.GetWidth() != source.GetWidth() ||
         target.GetHeight() != source.GetHeight())
     {
       throw OrthancException(ErrorCode_IncompatibleImageSize);
     }
 
-    unsigned int targetBytesPerPixels = target.GetBytesPerPixel();
-    unsigned int targetChannelsPerPixels = 0;
-    switch (target.GetFormat())
-    {
-    case Orthanc::PixelFormat_Grayscale8:
-      targetChannelsPerPixels = 1;
-      break;
-    case Orthanc::PixelFormat_RGBA32:
-    case Orthanc::PixelFormat_BGRA32:
-    case Orthanc::PixelFormat_RGB24:
-      targetChannelsPerPixels = 3;
-      break;
-    default:
-      throw OrthancException(ErrorCode_NotImplemented);
-    }
-
-    const float a = windowCenter - windowWidth / 2.0f;
-    const float slope = 256.0f / windowWidth;
-    bool isInverted = sourcePhotometricInterpretation == Orthanc::PhotometricInterpretation_Monochrome1;
-
-    const unsigned int width = source.GetWidth();
-    const unsigned int height = source.GetHeight();
-
-    assert(sizeof(float) == 4);
-
-    for (unsigned int y = 0; y < height; y++)
+    switch (source.GetFormat())
     {
-      const float* p = reinterpret_cast<const float*>(source.GetConstRow(y));
-      uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y));
-
-      for (unsigned int x = 0; x < width; x++)
+      case Orthanc::PixelFormat_Float32:
       {
-        float v = (*p - a) * slope;
-        if (v <= 0)
+        switch (target.GetFormat())
         {
-          v = 0;
-        }
-        else if (v >= 255)
-        {
-          v = 255;
+        case Orthanc::PixelFormat_Grayscale8:
+          ApplyWindowingInternal<uint8_t, float>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        case Orthanc::PixelFormat_Grayscale16:
+          ApplyWindowingInternal<uint16_t, float>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        default:
+          throw OrthancException(ErrorCode_NotImplemented);
         }
-
-        uint8_t vv = static_cast<uint8_t>(v);
-
-        if (isInverted)
+      };break;
+      case Orthanc::PixelFormat_Grayscale8:
+      {
+        switch (target.GetFormat())
         {
-          vv = 255 - vv;
+        case Orthanc::PixelFormat_Grayscale8:
+          ApplyWindowingInternal<uint8_t, uint8_t>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        case Orthanc::PixelFormat_Grayscale16:
+          ApplyWindowingInternal<uint16_t, uint8_t>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        default:
+          throw OrthancException(ErrorCode_NotImplemented);
         }
-
-        for (unsigned int c = 0; c < targetChannelsPerPixels; c++)
+      };break;
+      case Orthanc::PixelFormat_Grayscale16:
+      {
+        switch (target.GetFormat())
         {
-          q[c] = vv;
+        case Orthanc::PixelFormat_Grayscale8:
+          ApplyWindowingInternal<uint8_t, uint16_t>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        case Orthanc::PixelFormat_Grayscale16:
+          ApplyWindowingInternal<uint16_t, uint16_t>(target, source, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+          break;
+        default:
+          throw OrthancException(ErrorCode_NotImplemented);
         }
-
-        p++;
-        q += targetBytesPerPixels;
-      }
+      };break;
+      default:
+        throw OrthancException(ErrorCode_NotImplemented);
     }
-
   }
 
 
--- a/Core/Images/ImageProcessing.h	Tue Jan 07 10:53:32 2020 +0100
+++ b/Core/Images/ImageProcessing.h	Thu Jan 09 18:54:40 2020 +0100
@@ -86,7 +86,9 @@
                         const ImageAccessor& source,
                         float windowCenter,
                         float windowWidth,
-                        Orthanc::PhotometricInterpretation sourcePhotometricInterpretation);
+                        float rescaleSlope,
+                        float rescaleIntercept,
+                        bool invert);
 
     void Set(ImageAccessor& image,
              int64_t value);
--- a/NEWS	Tue Jan 07 10:53:32 2020 +0100
+++ b/NEWS	Thu Jan 09 18:54:40 2020 +0100
@@ -15,6 +15,7 @@
 * C-Find SCU at Instance level now sets the 0008,0052 tag to IMAGE per default (was INSTANCE).
   Therefore, the "ClearCanvas" and "Dcm4Chee" modality manufacturer have now been deprecated.
 * Fix issue #156 (Chunked Dicom-web transfer uses 100% CPU)
+* /instances/{id}/preview route now takes the windowing into account
 
 Version 1.5.8 (2019-10-16)
 ==========================
--- a/OrthancServer/OrthancRestApi/OrthancRestResources.cpp	Tue Jan 07 10:53:32 2020 +0100
+++ b/OrthancServer/OrthancRestApi/OrthancRestResources.cpp	Thu Jan 09 18:54:40 2020 +0100
@@ -39,6 +39,7 @@
 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
 #include "../../Core/DicomParsing/Internals/DicomImageDecoder.h"
 #include "../../Core/HttpServer/HttpContentNegociation.h"
+#include "../../Core/Images/ImageProcessing.h"
 #include "../../Core/Logging.h"
 #include "../DefaultDicomImageDecoder.h"
 #include "../OrthancConfiguration.h"
@@ -502,6 +503,38 @@
   }
 
 
+  void LookupWindowingTags(const ParsedDicomFile& dicom, float& windowCenter, float& windowWidth, float& rescaleSlope, float& rescaleIntercept, bool& invert)
+  {
+    DicomMap dicomTags;
+    dicom.ExtractDicomSummary(dicomTags);
+
+
+    unsigned int bitsStored = boost::lexical_cast<unsigned int>(dicomTags.GetStringValue(Orthanc::DICOM_TAG_BITS_STORED, "8", false));
+    windowWidth = static_cast<float>(2 << (bitsStored - 1));
+    windowCenter = windowWidth / 2;
+    rescaleSlope = 1.0f;
+    rescaleIntercept = 0.0f;
+    invert = false;
+
+    if (dicomTags.HasTag(Orthanc::DICOM_TAG_WINDOW_CENTER) && dicomTags.HasTag(Orthanc::DICOM_TAG_WINDOW_WIDTH))
+    {
+      windowCenter = boost::lexical_cast<float>(dicomTags.GetStringValue(Orthanc::DICOM_TAG_WINDOW_CENTER, "", false));
+      windowWidth = boost::lexical_cast<float>(dicomTags.GetStringValue(Orthanc::DICOM_TAG_WINDOW_WIDTH, "", false));
+    }
+
+    if (dicomTags.HasTag(Orthanc::DICOM_TAG_RESCALE_SLOPE) && dicomTags.HasTag(Orthanc::DICOM_TAG_RESCALE_INTERCEPT))
+    {
+      rescaleSlope = boost::lexical_cast<float>(dicomTags.GetStringValue(Orthanc::DICOM_TAG_RESCALE_SLOPE, "", false));
+      rescaleIntercept = boost::lexical_cast<float>(dicomTags.GetStringValue(Orthanc::DICOM_TAG_RESCALE_INTERCEPT, "", false));
+    }
+
+    PhotometricInterpretation photometric;
+    if (dicom.LookupPhotometricInterpretation(photometric))
+    {
+      invert = (photometric == PhotometricInterpretation_Monochrome1);
+    }
+  }
+
   template <enum ImageExtractionMode mode>
   static void GetImage(RestApiGetCall& call)
   {
@@ -520,6 +553,11 @@
     }
 
     bool invert = false;
+    float windowCenter = 128.0f;
+    float windowWidth = 256.0f;
+    float rescaleSlope = 1.0f;
+    float rescaleIntercept = 0.0f;
+
     std::auto_ptr<ImageAccessor> decoded;
 
     try
@@ -549,11 +587,7 @@
           // twice the DICOM file
           ParsedDicomFile parsed(dicomContent);
           
-          PhotometricInterpretation photometric;
-          if (parsed.LookupPhotometricInterpretation(photometric))
-          {
-            invert = (photometric == PhotometricInterpretation_Monochrome1);
-          }
+          LookupWindowingTags(dicomContent, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
         }
       }
 #endif
@@ -564,12 +598,11 @@
         // things on multi-frame images
         ServerContext::DicomCacheLocker locker(context, publicId);        
         decoded.reset(DicomImageDecoder::Decode(locker.GetDicom(), frame));
+        LookupWindowingTags(locker.GetDicom(), windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
 
-        PhotometricInterpretation photometric;
-        if (mode == ImageExtractionMode_Preview &&
-            locker.GetDicom().LookupPhotometricInterpretation(photometric))
+        if (mode != ImageExtractionMode_Preview)
         {
-          invert = (photometric == PhotometricInterpretation_Monochrome1);
+          invert = false;
         }
       }
     }
@@ -593,6 +626,13 @@
       return;
     }
 
+    if (mode == ImageExtractionMode_Preview
+        && (decoded->GetFormat() == Orthanc::PixelFormat_Grayscale8 || decoded->GetFormat() == Orthanc::PixelFormat_Grayscale16))
+    {
+      ImageProcessing::ApplyWindowing(*decoded, *decoded, windowCenter, windowWidth, rescaleSlope, rescaleIntercept, invert);
+      invert = false; // don't invert it later on when encoding it, it has been inverted in the ApplyWindowing function
+    }
+
     ImageToEncode image(decoded, mode, invert);
 
     HttpContentNegociation negociation;
--- a/UnitTestsSources/ImageProcessingTests.cpp	Tue Jan 07 10:53:32 2020 +0100
+++ b/UnitTestsSources/ImageProcessingTests.cpp	Thu Jan 09 18:54:40 2020 +0100
@@ -282,6 +282,25 @@
   return p == value;
 }
 
+static void SetGrayscale16Pixel(ImageAccessor& image,
+                                unsigned int x,
+                                unsigned int y,
+                                uint8_t value)
+{
+  ImageTraits<PixelFormat_Grayscale16>::SetPixel(image, value, x, y);
+}
+
+static bool TestGrayscale16Pixel(const ImageAccessor& image,
+                                 unsigned int x,
+                                 unsigned int y,
+                                 uint16_t value)
+{
+  PixelTraits<PixelFormat_Grayscale16>::PixelType p;
+  ImageTraits<PixelFormat_Grayscale16>::GetPixel(p, image, x, y);
+  if (p != value) printf("%d %d\n", p, value);
+  return p == value;
+}
+
 static void SetRGB24Pixel(ImageAccessor& image,
                           unsigned int x,
                           unsigned int y,
@@ -774,3 +793,148 @@
     ASSERT_TRUE(TestRGB24Pixel(image, 4, 4, 0, 0, 0));
   }
 }
+
+TEST(ImageProcessing, ApplyWindowingFloatToGrayScale8)
+{
+  {
+    Image image(PixelFormat_Float32, 6, 1, false);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, -5.0f, 0, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 0.0f, 1, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 5.0f, 2, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 10.0f, 3, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 1000.0f, 4, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 2.0f, 5, 0);
+
+    {
+      Image target(PixelFormat_Grayscale8, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5.0f, 10.0f, 1.0f, 0.0f, false);
+
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 0, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 1, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 2, 0, 128));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 3, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 4, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 5, 0, 255*2/10));
+    }
+
+    {
+      Image target(PixelFormat_Grayscale8, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5.0f, 10.0f, 1.0f, 0.0f, true);
+
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 0, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 1, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 2, 0, 127));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 3, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 4, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 5, 0, 255 - 255*2/10));
+    }
+
+    {
+      Image target(PixelFormat_Grayscale8, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5000.0f, 10000.0f, 1000.0f, 0.0f, false);
+
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 0, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 1, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 2, 0, 128));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 3, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 4, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 5, 0, 255*2/10));
+    }
+
+    {
+      Image target(PixelFormat_Grayscale8, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5000.0f, 10000.0f, 1000.0f, 0.0f, true);
+
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 0, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 1, 0, 255));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 2, 0, 127));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 3, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 4, 0, 0));
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 5, 0, 255 - 256*2/10));
+    }
+
+    {
+      Image target(PixelFormat_Grayscale8, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 50.0f, 100.0f, 10.0f, 30.0f, false);
+
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 0, 0, 0));  // (-5 * 10) + 30 => pixel value = -20 => 0
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 1, 0, 256*30/100));  // ((0 * 10) + 30 => pixel value = 30 => 30%
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 2, 0, 256*80/100)); // ((5 * 10) + 30 => pixel value = 80 => 80%
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 3, 0, 255)); // ((10 * 10) + 30 => pixel value = 130 => 100%
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 4, 0, 255)); // ((1000 * 10) + 30 => pixel value = 10030 => 100%
+      ASSERT_TRUE(TestGrayscale8Pixel(target, 5, 0, 128)); // ((2 * 10) + 30 => pixel value = 50 => 50%
+    }
+
+  }
+}
+
+TEST(ImageProcessing, ApplyWindowingFloatToGrayScale16)
+{
+  {
+    Image image(PixelFormat_Float32, 6, 1, false);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, -5.0f, 0, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 0.0f, 1, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 5.0f, 2, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 10.0f, 3, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 1000.0f, 4, 0);
+    ImageTraits<PixelFormat_Float32>::SetFloatPixel(image, 2.0f, 5, 0);
+
+    {
+      Image target(PixelFormat_Grayscale16, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5.0f, 10.0f, 1.0f, 0.0f, false);
+
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 0, 0, 0));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 1, 0, 0));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 2, 0, 32768));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 3, 0, 65535));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 4, 0, 65535));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 5, 0, 65536*2/10));
+    }
+  }
+}
+
+TEST(ImageProcessing, ApplyWindowingGrayScale8ToGrayScale16)
+{
+  {
+    Image image(PixelFormat_Grayscale8, 6, 1, false);
+    SetGrayscale8Pixel(image, 0, 0, 0);
+    SetGrayscale8Pixel(image, 1, 0, 2);
+    SetGrayscale8Pixel(image, 2, 0, 5);
+    SetGrayscale8Pixel(image, 3, 0, 10);
+    SetGrayscale8Pixel(image, 4, 0, 255);
+
+    {
+      Image target(PixelFormat_Grayscale16, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5.0f, 10.0f, 1.0f, 0.0f, false);
+
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 0, 0, 0));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 1, 0, 65536*2/10));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 2, 0, 65536*5/10));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 3, 0, 65535));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 4, 0, 65535));
+    }
+  }
+}
+
+TEST(ImageProcessing, ApplyWindowingGrayScale16ToGrayScale16)
+{
+  {
+    Image image(PixelFormat_Grayscale16, 6, 1, false);
+    SetGrayscale16Pixel(image, 0, 0, 0);
+    SetGrayscale16Pixel(image, 1, 0, 2);
+    SetGrayscale16Pixel(image, 2, 0, 5);
+    SetGrayscale16Pixel(image, 3, 0, 10);
+    SetGrayscale16Pixel(image, 4, 0, 255);
+
+    {
+      Image target(PixelFormat_Grayscale16, 6, 1, false);
+      ImageProcessing::ApplyWindowing(target, image, 5.0f, 10.0f, 1.0f, 0.0f, false);
+
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 0, 0, 0));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 1, 0, 65536*2/10));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 2, 0, 65536*5/10));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 3, 0, 65535));
+      ASSERT_TRUE(TestGrayscale16Pixel(target, 4, 0, 65535));
+    }
+  }
+}