--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancStone/Sources/Volumes/ImageBuffer3D.cpp	Tue Jul 07 16:21:02 2020 +0200
@@ -0,0 +1,311 @@
+/**
+ * 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 "ImageBuffer3D.h"
+
+#include <Images/ImageProcessing.h>
+#include <Logging.h>
+#include <OrthancException.h>
+
+#include <string.h>
+
+namespace OrthancStone
+{
+  void ImageBuffer3D::GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
+                                            unsigned int slice,
+                                            bool readOnly) const
+  {
+    if (slice >= depth_)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    if (readOnly)
+    {
+      target.AssignReadOnly(format_, width_, height_, image_.GetPitch(),
+                            image_.GetConstRow(height_ * (depth_ - 1 - slice)));
+    }
+    else
+    {
+      target.AssignWritable(format_, width_, height_, image_.GetPitch(),
+                            image_.GetRow(height_ * (depth_ - 1 - slice)));
+    }
+  }
+
+
+  void ImageBuffer3D::GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
+                                              unsigned int slice,
+                                              bool readOnly) const
+  {
+    if (slice >= height_)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    if (readOnly)
+    {
+      target.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_,
+                            image_.GetConstRow(slice));
+    }
+    else
+    {
+      target.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_,
+                            image_.GetRow(slice));
+    }
+  }
+
+
+  Orthanc::Image*  ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const
+  {
+    //LOG(TRACE) << "ImageBuffer3D::ExtractSagittalSlice this= " << std::hex << this << std::dec << " width_ = " << width_ << " height_ = " << height_ << " depth_ = " << depth_ << " slice = " << slice;
+    if (slice >= width_)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    std::unique_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false));
+    //LOG(TRACE) << "ImageBuffer3D::ExtractSagittalSlice result will be an image of WIDTH = " << height_ << " and HEIGHT = " << depth_;
+
+    unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_);
+
+    for (unsigned int z = 0; z < depth_; z++)
+    {
+      //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z));
+      uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z));
+
+      for (unsigned int y = 0; y < height_; y++)
+      {
+        const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) + bytesPerPixel * slice);
+        const uint8_t* byteSrc = reinterpret_cast<const uint8_t*>(source);
+        for (size_t byte = 0; byte < bytesPerPixel; ++byte)
+          target[byte] = byteSrc[byte];
+        target += bytesPerPixel;
+      }
+    }
+
+    return result.release();
+  }
+
+
+  ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format,
+                               unsigned int width,
+                               unsigned int height,
+                               unsigned int depth,
+                               bool computeRange) :
+    image_(format, width, height * depth, false),
+    format_(format),
+    width_(width),
+    height_(height),
+    depth_(depth),
+    computeRange_(computeRange),
+    hasRange_(false)
+  {
+    LOG(TRACE) << "Created a 3D image of size " << width << "x" << height
+              << "x" << depth << " in " << Orthanc::EnumerationToString(format)
+              << " (" << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB)";
+  }
+
+
+  void ImageBuffer3D::Clear()
+  {
+    memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch());
+  }
+
+
+  uint64_t ImageBuffer3D::GetEstimatedMemorySize() const
+  {
+    return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_);
+  }
+
+
+  void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice)
+  {
+    if (!computeRange_ ||
+        slice.GetWidth() == 0 ||
+        slice.GetHeight() == 0)
+    {
+      return;
+    }
+
+    float sliceMin, sliceMax;
+
+    switch (slice.GetFormat())
+    {
+      case Orthanc::PixelFormat_Grayscale8:
+      case Orthanc::PixelFormat_Grayscale16:
+      case Orthanc::PixelFormat_Grayscale32:
+      case Orthanc::PixelFormat_SignedGrayscale16:
+      {
+        int64_t a, b;
+        Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice);
+        sliceMin = static_cast<float>(a);
+        sliceMax = static_cast<float>(b);
+        break;
+      }
+
+      case Orthanc::PixelFormat_Float32:
+        Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice);
+        break;
+
+      default:
+        return;
+    }
+
+    if (hasRange_)
+    {
+      minValue_ = std::min(minValue_, sliceMin);
+      maxValue_ = std::max(maxValue_, sliceMax);
+    }
+    else
+    {
+      hasRange_ = true;
+      minValue_ = sliceMin;
+      maxValue_ = sliceMax;
+    }
+  }
+
+
+  bool ImageBuffer3D::GetRange(float& minValue,
+                               float& maxValue) const
+  {
+    if (hasRange_)
+    {
+      minValue = minValue_;
+      maxValue = maxValue_;
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
+  ImageBuffer3D::SliceReader::SliceReader(const ImageBuffer3D& that,
+                                          VolumeProjection projection,
+                                          unsigned int slice)
+  {
+    switch (projection)
+    {
+      case VolumeProjection_Axial:
+        that.GetAxialSliceAccessor(accessor_, slice, true);
+        break;
+
+      case VolumeProjection_Coronal:
+        that.GetCoronalSliceAccessor(accessor_, slice, true);
+        break;
+
+      case VolumeProjection_Sagittal:
+        sagittal_.reset(that.ExtractSagittalSlice(slice));
+        sagittal_->GetReadOnlyAccessor(accessor_);
+        break;
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+  }
+
+
+  void ImageBuffer3D::SliceWriter::Flush()
+  {
+    if (modified_)
+    {
+      if (sagittal_.get() != NULL)
+      {
+        // TODO
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+      }
+
+      // Update the dynamic range of the underlying image, if
+      // "computeRange_" is set to true
+      that_.ExtendImageRange(accessor_);
+    }
+  }
+
+
+  ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that,
+                                          VolumeProjection projection,
+                                          unsigned int slice) :
+    that_(that),
+    modified_(false)
+  {
+    switch (projection)
+    {
+      case VolumeProjection_Axial:
+        that.GetAxialSliceAccessor(accessor_, slice, false);
+        break;
+
+      case VolumeProjection_Coronal:
+        that.GetCoronalSliceAccessor(accessor_, slice, false);
+        break;
+
+      case VolumeProjection_Sagittal:
+        sagittal_.reset(that.ExtractSagittalSlice(slice));
+        sagittal_->GetWriteableAccessor(accessor_);
+        break;
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+  }
+
+
+  uint8_t ImageBuffer3D::GetVoxelGrayscale8(unsigned int x,
+                                            unsigned int y,
+                                            unsigned int z) const
+  {
+    if (format_ != Orthanc::PixelFormat_Grayscale8)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
+    }
+
+    if (x >= width_ ||
+        y >= height_ ||
+        z >= depth_)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
+    return reinterpret_cast<const uint8_t*>(p) [x];
+  }
+
+
+  uint16_t ImageBuffer3D::GetVoxelGrayscale16(unsigned int x,
+                                              unsigned int y,
+                                              unsigned int z) const
+  {
+    if (format_ != Orthanc::PixelFormat_Grayscale16)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
+    }
+
+    if (x >= width_ ||
+        y >= height_ ||
+        z >= depth_)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
+    return reinterpret_cast<const uint16_t*>(p) [x];
+  }
+}