Mercurial > hg > orthanc-stone
changeset 683:dbc1d8bfc68a
reorganizing ImageBuffer3D
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Thu, 16 May 2019 16:01:36 +0200 |
parents | 9723fceccb9f |
children | 7719eb852dd5 |
files | Framework/Toolbox/SlicesSorter.h Framework/Volumes/ImageBuffer3D.cpp Framework/Volumes/ImageBuffer3D.h Samples/Sdl/Loader.cpp |
diffstat | 4 files changed, 118 insertions(+), 27 deletions(-) [+] |
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--- a/Framework/Toolbox/SlicesSorter.h Thu May 16 14:26:11 2019 +0200 +++ b/Framework/Toolbox/SlicesSorter.h Thu May 16 16:01:36 2019 +0200 @@ -84,7 +84,8 @@ // slices. This is notably the case if all the slices are not // parallel to the reference normal that will be selected. bool Sort(); - + + // TODO - Remove this bool LookupClosestSlice(size_t& index, double& distance, const CoordinateSystem3D& slice) const;
--- a/Framework/Volumes/ImageBuffer3D.cpp Thu May 16 14:26:11 2019 +0200 +++ b/Framework/Volumes/ImageBuffer3D.cpp Thu May 16 16:01:36 2019 +0200 @@ -21,6 +21,8 @@ #include "ImageBuffer3D.h" +#include "../Toolbox/GeometryToolbox.h" + #include <Core/Images/ImageProcessing.h> #include <Core/Logging.h> #include <Core/OrthancException.h> @@ -121,6 +123,8 @@ LOG(INFO) << "Created a 3D image of size " << width << "x" << height << "x" << depth << " in " << Orthanc::EnumerationToString(format) << " (" << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB)"; + + UpdateGeometry(); } @@ -133,6 +137,7 @@ void ImageBuffer3D::SetAxialGeometry(const CoordinateSystem3D& geometry) { axialGeometry_ = geometry; + UpdateGeometry(); } @@ -146,35 +151,30 @@ { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } - + else { LinearAlgebra::AssignVector(voxelDimensions_, x, y, z); + UpdateGeometry(); } } Vector ImageBuffer3D::GetVoxelDimensions(VolumeProjection projection) const { - Vector result; switch (projection) { case VolumeProjection_Axial: - result = voxelDimensions_; - break; + return voxelDimensions_; case VolumeProjection_Coronal: - LinearAlgebra::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]); - break; + return LinearAlgebra::CreateVector(voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]); case VolumeProjection_Sagittal: - LinearAlgebra::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]); - break; + return LinearAlgebra::CreateVector(voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]); default: throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } - - return result; } @@ -459,20 +459,78 @@ } + void ImageBuffer3D::UpdateGeometry() + { + Vector p = (axialGeometry_.GetOrigin() + + static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal()); + + coronalGeometry_ = CoordinateSystem3D(p, + axialGeometry_.GetAxisX(), + -axialGeometry_.GetNormal()); + + sagittalGeometry_ = CoordinateSystem3D(p, + axialGeometry_.GetAxisY(), + -axialGeometry_.GetNormal()); + + Vector origin = ( + axialGeometry_.MapSliceToWorldCoordinates(-0.5 * voxelDimensions_[0], + -0.5 * voxelDimensions_[1]) - + 0.5 * voxelDimensions_[2] * axialGeometry_.GetNormal()); + + Vector scaling = ( + axialGeometry_.GetAxisX() * voxelDimensions_[0] * static_cast<double>(width_) + + axialGeometry_.GetAxisY() * voxelDimensions_[1] * static_cast<double>(height_) + + axialGeometry_.GetNormal() * voxelDimensions_[2] * static_cast<double>(depth_)); + + transform_ = LinearAlgebra::Product( + GeometryToolbox::CreateTranslationMatrix(origin[0], origin[1], origin[2]), + GeometryToolbox::CreateScalingMatrix(scaling[0], scaling[1], scaling[2])); + + LinearAlgebra::InvertMatrix(transformInverse_, transform_); + } + + Vector ImageBuffer3D::GetCoordinates(float x, float y, float z) const { - Vector ps = GetVoxelDimensions(OrthancStone::VolumeProjection_Axial); + Vector p = LinearAlgebra::Product(transform_, LinearAlgebra::CreateVector(x, y, z, 1)); + + assert(LinearAlgebra::IsNear(p[3], 1)); // Affine transform, no perspective effect + + // Back to non-homogeneous coordinates + return LinearAlgebra::CreateVector(p[0], p[1], p[2]); + } + + + bool ImageBuffer3D::DetectProjection(VolumeProjection& projection, + const CoordinateSystem3D& plane) const + { + if (GeometryToolbox::IsParallel(plane.GetNormal(), + axialGeometry_.GetNormal())) + { + projection = VolumeProjection_Axial; + return true; + } - const CoordinateSystem3D& axial = GetAxialGeometry(); - - Vector origin = (axial.MapSliceToWorldCoordinates(-0.5 * ps[0], -0.5 * ps[1]) - - 0.5 * ps[2] * axial.GetNormal()); + { + if (GeometryToolbox::IsParallel(plane.GetNormal(), + coronalGeometry_.GetNormal())) + { + projection = VolumeProjection_Coronal; + return true; + } + } - return (origin + - axial.GetAxisX() * ps[0] * x * static_cast<double>(GetWidth()) + - axial.GetAxisY() * ps[1] * y * static_cast<double>(GetHeight()) + - axial.GetNormal() * ps[2] * z * static_cast<double>(GetDepth())); + { + if (GeometryToolbox::IsParallel(plane.GetNormal(), + sagittalGeometry_.GetNormal())) + { + projection = VolumeProjection_Sagittal; + return true; + } + } + + return false; } }
--- a/Framework/Volumes/ImageBuffer3D.h Thu May 16 14:26:11 2019 +0200 +++ b/Framework/Volumes/ImageBuffer3D.h Thu May 16 16:01:36 2019 +0200 @@ -35,6 +35,8 @@ { private: CoordinateSystem3D axialGeometry_; + CoordinateSystem3D coronalGeometry_; + CoordinateSystem3D sagittalGeometry_; Vector voxelDimensions_; Orthanc::Image image_; Orthanc::PixelFormat format_; @@ -45,6 +47,10 @@ bool hasRange_; float minValue_; float maxValue_; + Matrix transform_; + Matrix transformInverse_; + + void UpdateGeometry(); void ExtendImageRange(const Orthanc::ImageAccessor& slice); @@ -86,6 +92,16 @@ return axialGeometry_; } + const CoordinateSystem3D& GetCoronalGeometry() const + { + return coronalGeometry_; + } + + const CoordinateSystem3D& GetSagittalGeometry() const + { + return sagittalGeometry_; + } + void SetVoxelDimensions(double x, double y, double z); @@ -121,6 +137,7 @@ return format_; } + // TODO - Remove ParallelSlices* GetGeometry(VolumeProjection projection) const; uint64_t GetEstimatedMemorySize() const; @@ -166,6 +183,9 @@ float y, float z) const; + bool DetectProjection(VolumeProjection& projection, + const CoordinateSystem3D& plane) const; + class SliceReader : public boost::noncopyable {
--- a/Samples/Sdl/Loader.cpp Thu May 16 14:26:11 2019 +0200 +++ b/Samples/Sdl/Loader.cpp Thu May 16 16:01:36 2019 +0200 @@ -25,8 +25,9 @@ #include "../../Framework/Messages/MessageBroker.h" #include "../../Framework/StoneInitialization.h" #include "../../Framework/Toolbox/GeometryToolbox.h" +#include "../../Framework/Toolbox/SlicesSorter.h" #include "../../Framework/Volumes/ImageBuffer3D.h" -#include "../../Framework/Toolbox/SlicesSorter.h" +#include "../../Framework/Scene2D/ScenePoint2D.h" // From Orthanc framework #include <Core/Compression/GzipCompressor.h> @@ -44,8 +45,8 @@ #include <Core/Logging.h> #include <Core/MultiThreading/SharedMessageQueue.h> #include <Core/OrthancException.h> +#include <Core/SystemToolbox.h> #include <Core/Toolbox.h> -#include <Core/SystemToolbox.h> #include <json/reader.h> #include <json/value.h> @@ -101,6 +102,17 @@ + class IVolumeSlicer : public boost::noncopyable + { + public: + virtual ~IVolumeSlicer() + { + } + + virtual void SetViewportPlane(const OrthancStone::CoordinateSystem3D& plane) = 0; + }; + + class OracleCommandWithPayload : public IOracleCommand { @@ -1444,11 +1456,11 @@ slices.AddSlice(geometry, instance.release()); } - that_.image_.SetGeometry(slices); + that_.volume_.SetGeometry(slices); - for (size_t i = 0; i < that_.image_.GetSlicesCount(); i++) + for (size_t i = 0; i < that_.volume_.GetSlicesCount(); i++) { - const DicomInstanceParameters& slice = that_.image_.GetSliceParameters(i); + const DicomInstanceParameters& slice = that_.volume_.GetSliceParameters(i); const std::string& instance = slice.GetOrthancInstanceIdentifier(); if (instance.empty()) @@ -1490,7 +1502,7 @@ #endif command->SetExpectedPixelFormat(slice.GetExpectedPixelFormat()); - command->SetPayload(new LoadSliceImage(that_.image_, i)); + command->SetPayload(new LoadSliceImage(that_.volume_, i)); that_.oracle_.Schedule(that_, command.release()); } @@ -1521,7 +1533,7 @@ IOracle& oracle_; bool active_; - DicomVolumeImage image_; + DicomVolumeImage volume_; public: VolumeSeriesOrthancLoader(IOracle& oracle,