Mercurial > hg > orthanc-stone
changeset 1746:4bedae500652
Automatically compute SliceThickness from
GridFrameOffsetVector when SliceThickness
is not present in the DICOM tags
author | Benjamin Golinvaux <bgo@osimis.io> |
---|---|
date | Fri, 12 Feb 2021 10:41:17 +0100 |
parents | 04019fd631aa |
children | 730604db88b8 |
files | OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp |
diffstat | 1 files changed, 43 insertions(+), 2 deletions(-) [+] |
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line diff
--- a/OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp Fri Feb 12 10:40:18 2021 +0100 +++ b/OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp Fri Feb 12 10:41:17 2021 +0100 @@ -48,7 +48,8 @@ { Orthanc::Toolbox::ToUpperCase(increment); - // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) + // We only support volumes where the FrameIncrementPointer (0028,0009) (required) contains + // the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) if (increment != "3004,000C") { LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image"; @@ -60,7 +61,7 @@ if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || target.size() != numberOfFrames) { - LOG(INFO) << "The frame offset information is missing in a multiframe image"; + LOG(ERROR) << "The frame offset information (GridFrameOffsetVector (3004,000C)) is missing in a multiframe image"; // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector! target.resize(0); @@ -109,9 +110,13 @@ height_ = 0; } + + bool sliceThicknessPresent = true; if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) { + LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image"; sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); + sliceThicknessPresent = false; } GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); @@ -127,6 +132,42 @@ 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 = frameOffsets_[1] - frameOffsets_[0]; + bool sameSized = true; + if (sliceThickness > 0) + { + for (size_t i = 2; i < frameOffsets_.size(); ++i) + { + double currentThickness = 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 {