# HG changeset patch # User Sebastien Jodogne # Date 1689083896 -7200 # Node ID 990f396484b1aecd74ddd9280047430753e5e91b # Parent d84bdcbd8bf185cc8ba135a6b25643ebcaf5bac7 fix rendering of RT-DOSE with negative GridFrameOffsetVector diff -r d84bdcbd8bf1 -r 990f396484b1 Applications/StoneWebViewer/WebAssembly/CMakeLists.txt --- a/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt Tue Jul 11 13:20:20 2023 +0200 +++ b/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt Tue Jul 11 15:58:16 2023 +0200 @@ -134,6 +134,8 @@ StoneWebViewer.cpp ) +DefineSourceBasenameForTarget(StoneWebViewer) + set_target_properties(StoneWebViewer PROPERTIES COMPILE_FLAGS "${WASM_FLAGS}" diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt --- a/OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt Tue Jul 11 15:58:16 2023 +0200 @@ -118,6 +118,8 @@ ${ORTHANC_STONE_SOURCES} ) +DefineSourceBasenameForTarget(UnitTests) + # Declare installation files for the module # --------------------------------------------------------------- diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Sources/Loaders/DicomVolumeLoader.cpp --- a/OrthancStone/Sources/Loaders/DicomVolumeLoader.cpp Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Sources/Loaders/DicomVolumeLoader.cpp Tue Jul 11 15:58:16 2023 +0200 @@ -57,7 +57,7 @@ double spacing; if (parameters.GetSopClassUid() == SopClassUid_RTDose) { - if (!parameters.ComputeRegularSpacing(spacing)) + if (!parameters.ComputeFrameOffsetsSpacing(spacing)) { LOG(WARNING) << "Unable to compute the spacing in a RT-DOSE instance"; spacing = frames.GetSpacingBetweenSlices(); diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp --- a/OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp Tue Jul 11 15:58:16 2023 +0200 @@ -215,7 +215,11 @@ switch (parameters.GetSopClassUid()) { case SopClassUid_RTDose: - spacingZ = parameters.GetSliceThickness(); + if (!parameters.ComputeFrameOffsetsSpacing(spacingZ)) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, + "Cannot load RT-DOSE with incorrect GridFrameOffsetVector (3004,000C)"); + } break; default: @@ -224,6 +228,8 @@ "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom)); } + isReversedFrameOffsets_ = parameters.IsReversedFrameOffsets(); + const unsigned int width = parameters.GetImageInformation().GetWidth(); const unsigned int height = parameters.GetImageInformation().GetHeight(); const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames(); @@ -231,7 +237,7 @@ { VolumeImageGeometry geometry; geometry.SetSizeInVoxels(width, height, depth); - geometry.SetAxialGeometry(parameters.GetGeometry()); + geometry.SetAxialGeometry(parameters.GetMultiFrameGeometry()); geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(), parameters.GetPixelSpacingY(), spacingZ); volume_->Initialize(geometry, format, true /* Do compute range */); @@ -241,8 +247,6 @@ ScheduleFrameDownloads(); - - BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_)); } @@ -322,7 +326,17 @@ for (unsigned int z = 0; z < depth; z++) { - ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z); + unsigned targetZ; + if (isReversedFrameOffsets_) + { + targetZ = depth - 1 - z; + } + else + { + targetZ = z; + } + + ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, targetZ); assert(writer.GetAccessor().GetWidth() == width && writer.GetAccessor().GetHeight() == height); @@ -554,6 +568,7 @@ float outliersHalfRejectionRate) : LoaderStateMachine(loadersContext) , volume_(volume) + , isReversedFrameOffsets_(false) , pixelDataLoaded_(false) , outliersHalfRejectionRate_(outliersHalfRejectionRate) , distributionRawMin_(0) diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.h --- a/OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.h Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.h Tue Jul 11 15:58:16 2023 +0200 @@ -49,6 +49,7 @@ }; boost::shared_ptr volume_; + bool isReversedFrameOffsets_; std::string instanceId_; std::string transferSyntaxUid_; bool pixelDataLoaded_; diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp --- a/OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp Tue Jul 11 15:58:16 2023 +0200 @@ -114,16 +114,18 @@ } - bool sliceThicknessPresent = true; - if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) + if (dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) { + hasSliceThickness_ = true; + } + else + { + hasSliceThickness_ = false; + if (numberOfFrames_ > 1) { LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image"; } - - sliceThickness_ = 100.0 * std::numeric_limits::epsilon(); - sliceThicknessPresent = false; } hasPixelSpacing_ = GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); @@ -139,49 +141,6 @@ if (numberOfFrames_ > 1) { ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); - - // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets - // this only works if: - // - the first offset is 0.0 (case (a) of http://dicom.nema.org/medical/Dicom/2017c/output/chtml/part03/sect_C.8.8.3.2.html) - // - the offsets are all equal, to some small tolerance - // - the offsets is positive (increasing throughout the frames) - if (!sliceThicknessPresent) - { - if (frameOffsets_.size() >= 2) - { - double sliceThickness = std::abs(frameOffsets_[1] - frameOffsets_[0]); - - if (sliceThickness > 0) - { - bool sameSized = true; - - for (size_t i = 2; i < frameOffsets_.size(); ++i) - { - double currentThickness = std::abs(frameOffsets_[i] - frameOffsets_[i-1]); - if (!LinearAlgebra::IsNear(sliceThickness, currentThickness)) - { - LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)"; - sameSized = false; - break; - } - } - - if (sameSized) - { - sliceThickness_ = sliceThickness; - LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C)."; - } - } - } - else - { - LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)"; - } - } - } - else - { - frameOffsets_.resize(0); } if (sopClassUid_ == SopClassUid_RTDose) @@ -274,6 +233,19 @@ } + double DicomInstanceParameters::GetSliceThickness() const + { + if (data_.hasSliceThickness_) + { + return data_.sliceThickness_; + } + else + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); + } + } + + const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const { assert(tags_.get() != NULL); @@ -715,7 +687,7 @@ } - bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const + bool DicomInstanceParameters::ComputeFrameOffsetsSpacing(double& spacing) const { if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE { @@ -728,18 +700,32 @@ } else { - assert(data_.frameOffsets_.size() == GetNumberOfFrames()); + static double THRESHOLD = 0.001; - spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); + if (data_.frameOffsets_.size() != GetNumberOfFrames()) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); + } + + double a = data_.frameOffsets_[1] - data_.frameOffsets_[0]; for (size_t i = 1; i + 1 < data_.frameOffsets_.size(); i++) { - double s = std::abs(data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]); - if (!LinearAlgebra::IsNear(spacing, s, 0.001)) + double b = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; + if (!LinearAlgebra::IsNear(a, b, THRESHOLD)) { + LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)"; return false; } } + + spacing = std::abs(a); + + if (HasSliceThickness() && + !LinearAlgebra::IsNear(spacing, GetSliceThickness(), THRESHOLD)) + { + LOG(WARNING) << "SliceThickness and GridFrameOffsetVector (3004,000C) do not match"; + } return true; } @@ -816,4 +802,41 @@ } } } + + + CoordinateSystem3D DicomInstanceParameters::GetMultiFrameGeometry() const + { + if (data_.frameOffsets_.empty()) + { + return data_.geometry_; + } + else + { + assert(data_.frameOffsets_.size() == data_.numberOfFrames_); + + double lowest = data_.frameOffsets_[0]; + for (size_t i = 1; i < data_.frameOffsets_.size(); i++) + { + lowest = std::min(lowest, data_.frameOffsets_[i]); + } + + return CoordinateSystem3D( + data_.geometry_.GetOrigin() + lowest * data_.geometry_.GetNormal(), + data_.geometry_.GetAxisX(), + data_.geometry_.GetAxisY()); + } + } + + + bool DicomInstanceParameters::IsReversedFrameOffsets() const + { + if (data_.frameOffsets_.size() < 2) + { + return false; + } + else + { + return (data_.frameOffsets_[0] > data_.frameOffsets_[1]); + } + } } diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/Sources/Toolbox/DicomInstanceParameters.h --- a/OrthancStone/Sources/Toolbox/DicomInstanceParameters.h Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/Sources/Toolbox/DicomInstanceParameters.h Tue Jul 11 15:58:16 2023 +0200 @@ -48,6 +48,7 @@ unsigned int numberOfFrames_; unsigned int width_; unsigned int height_; + bool hasSliceThickness_; double sliceThickness_; double pixelSpacingX_; double pixelSpacingY_; @@ -143,11 +144,13 @@ return data_.height_; } - double GetSliceThickness() const + bool HasSliceThickness() const { - return data_.sliceThickness_; + return data_.hasSliceThickness_; } + double GetSliceThickness() const; + double GetPixelSpacingX() const { return data_.pixelSpacingX_; @@ -234,7 +237,7 @@ double ApplyRescale(double value) const; // Required for RT-DOSE - bool ComputeRegularSpacing(double& target) const; + bool ComputeFrameOffsetsSpacing(double& target) const; const std::string& GetFrameOfReferenceUid() const { @@ -260,5 +263,9 @@ { return data_.instanceNumber_; } + + CoordinateSystem3D GetMultiFrameGeometry() const; + + bool IsReversedFrameOffsets() const; }; } diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/UnitTestsSources/CMakeLists.txt --- a/OrthancStone/UnitTestsSources/CMakeLists.txt Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/UnitTestsSources/CMakeLists.txt Tue Jul 11 15:58:16 2023 +0200 @@ -59,6 +59,8 @@ ${ORTHANC_STONE_SOURCES} ) +DefineSourceBasenameForTarget(UnitTests) + add_custom_command( TARGET UnitTests POST_BUILD diff -r d84bdcbd8bf1 -r 990f396484b1 OrthancStone/UnitTestsSources/DicomTests.cpp --- a/OrthancStone/UnitTestsSources/DicomTests.cpp Tue Jul 11 13:20:20 2023 +0200 +++ b/OrthancStone/UnitTestsSources/DicomTests.cpp Tue Jul 11 15:58:16 2023 +0200 @@ -54,7 +54,8 @@ ASSERT_EQ(1u, p->GetNumberOfFrames()); ASSERT_EQ(0u, p->GetWidth()); ASSERT_EQ(0u, p->GetHeight()); - ASSERT_TRUE(OrthancStone::LinearAlgebra::IsCloseToZero(p->GetSliceThickness())); + ASSERT_FALSE(p->HasSliceThickness()); + ASSERT_THROW(p->GetSliceThickness(), Orthanc::OrthancException); ASSERT_FLOAT_EQ(1, p->GetPixelSpacingX()); ASSERT_FLOAT_EQ(1, p->GetPixelSpacingY()); ASSERT_FALSE(p->GetGeometry().IsValid()); @@ -81,7 +82,7 @@ ASSERT_DOUBLE_EQ(1.0, p->ApplyRescale(1.0)); double s; - ASSERT_FALSE(p->ComputeRegularSpacing(s)); + ASSERT_FALSE(p->ComputeFrameOffsetsSpacing(s)); ASSERT_TRUE(p->GetFrameOfReferenceUid().empty()); } @@ -223,3 +224,82 @@ } } } + + +TEST(DicomInstanceParameters, ReverseFrameOffsetsGrid) +{ + Orthanc::DicomMap m; + SetupUids(m); + + m.SetValue(Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, "-276.611\\-274.463\\100", false); + m.SetValue(Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, "1\\0\\0\\0\\1\\0", false); + m.SetValue(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES, "126", false); + m.SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, "0\\-2\\-4\\-6\\-8\\-10\\-12\\-14\\-16\\-18\\-20\\-22\\-24\\-26\\-28\\-30\\-32\\-34\\-36\\-38\\-40\\-42\\-44\\-46\\-48\\-50\\-52\\-54\\-56\\-58\\-60\\-62\\-64\\-66\\-68\\-70\\-72\\-74\\-76\\-78\\-80\\-82\\-84\\-86\\-88\\-90\\-92\\-94\\-96\\-98\\-100\\-102\\-104\\-106\\-108\\-110\\-112\\-114\\-116\\-118\\-120\\-122\\-124\\-126\\-128\\-130\\-132\\-134\\-136\\-138\\-140\\-142\\-144\\-146\\-148\\-150\\-152\\-154\\-156\\-158\\-160\\-162\\-164\\-166\\-168\\-170\\-172\\-174\\-176\\-178\\-180\\-182\\-184\\-186\\-188\\-190\\-192\\-194\\-196\\-198\\-200\\-202\\-204\\-206\\-208\\-210\\-212\\-214\\-216\\-218\\-220\\-222\\-224\\-226\\-228\\-230\\-232\\-234\\-236\\-238\\-240\\-242\\-244\\-246\\-248\\-250", false); + + std::unique_ptr p; + p.reset(OrthancStone::DicomInstanceParameters(m).Clone()); + + ASSERT_FALSE(p->HasSliceThickness()); + ASSERT_THROW(p->GetSliceThickness(), Orthanc::OrthancException); + + double s; + ASSERT_TRUE(p->ComputeFrameOffsetsSpacing(s)); + ASSERT_DOUBLE_EQ(s, 2.0); + ASSERT_TRUE(p->IsReversedFrameOffsets()); + + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetAxisX() [0]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisX() [1]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisX() [2]); + + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisY() [0]); + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetAxisY() [1]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisY() [2]); + + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetNormal() [0]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetNormal() [1]); + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetNormal() [2]); + + ASSERT_DOUBLE_EQ(-276.611, p->GetMultiFrameGeometry().GetOrigin() [0]); + ASSERT_DOUBLE_EQ(-274.463, p->GetMultiFrameGeometry().GetOrigin() [1]); + ASSERT_DOUBLE_EQ(100.0 - 250.0, p->GetMultiFrameGeometry().GetOrigin() [2]); +} + + +TEST(DicomInstanceParameters, StandardFrameOffsetsGrid) +{ + Orthanc::DicomMap m; + SetupUids(m); + + m.SetValue(Orthanc::DICOM_TAG_SLICE_THICKNESS, "2", false); + m.SetValue(Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, "-205.2157\\-388.4679\\-120", false); + m.SetValue(Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, "1\\0\\0\\0\\1\\0", false); + m.SetValue(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES, "155", false); + m.SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, "0\\2\\4\\6\\8\\10\\12\\14\\16\\18\\20\\22\\24\\26\\28\\30\\32\\34\\36\\38\\40\\42\\44\\46\\48\\50\\52\\54\\56\\58\\60\\62\\64\\66\\68\\70\\72\\74\\76\\78\\80\\82\\84\\86\\88\\90\\92\\94\\96\\98\\100\\102\\104\\106\\108\\110\\112\\114\\116\\118\\120\\122\\124\\126\\128\\130\\132\\134\\136\\138\\140\\142\\144\\146\\148\\150\\152\\154\\156\\158\\160\\162\\164\\166\\168\\170\\172\\174\\176\\178\\180\\182\\184\\186\\188\\190\\192\\194\\196\\198\\200\\202\\204\\206\\208\\210\\212\\214\\216\\218\\220\\222\\224\\226\\228\\230\\232\\234\\236\\238\\240\\242\\244\\246\\248\\250\\252\\254\\256\\258\\260\\262\\264\\266\\268\\270\\272\\274\\276\\278\\280\\282\\284\\286\\288\\290\\292\\294\\296\\298\\300\\302\\304\\306\\308", false); + + std::unique_ptr p; + p.reset(OrthancStone::DicomInstanceParameters(m).Clone()); + + ASSERT_TRUE(p->HasSliceThickness()); + ASSERT_DOUBLE_EQ(2.0, p->GetSliceThickness()); + + double s; + ASSERT_TRUE(p->ComputeFrameOffsetsSpacing(s)); + ASSERT_DOUBLE_EQ(s, 2.0); + ASSERT_FALSE(p->IsReversedFrameOffsets()); + + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetAxisX() [0]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisX() [1]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisX() [2]); + + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisY() [0]); + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetAxisY() [1]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetAxisY() [2]); + + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetNormal() [0]); + ASSERT_DOUBLE_EQ(0, p->GetMultiFrameGeometry().GetNormal() [1]); + ASSERT_DOUBLE_EQ(1, p->GetMultiFrameGeometry().GetNormal() [2]); + + ASSERT_DOUBLE_EQ(-205.2157, p->GetMultiFrameGeometry().GetOrigin() [0]); + ASSERT_DOUBLE_EQ(-388.4679, p->GetMultiFrameGeometry().GetOrigin() [1]); + ASSERT_DOUBLE_EQ(-120.0, p->GetMultiFrameGeometry().GetOrigin() [2]); +}