Mercurial > hg > orthanc
view Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 3837:963ea9fab402
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 15 Apr 2020 17:28:27 +0200 |
parents | 6110a4995ace |
children | 7e33516965f8 |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * 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 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 * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "GdcmImageDecoder.h" #include "../../../Core/Compatibility.h" #include "OrthancImageWrapper.h" #include <gdcmImageReader.h> #include <gdcmImageApplyLookupTable.h> #include <gdcmImageChangePlanarConfiguration.h> #include <gdcmImageChangePhotometricInterpretation.h> #include <stdexcept> #include <boost/iostreams/stream.hpp> #include <boost/iostreams/device/array.hpp> namespace OrthancPlugins { struct GdcmImageDecoder::PImpl { const void* dicom_; size_t size_; gdcm::ImageReader reader_; std::unique_ptr<gdcm::ImageApplyLookupTable> lut_; std::unique_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; std::unique_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; std::string decoded_; PImpl(const void* dicom, size_t size) : dicom_(dicom), size_(size) { } const gdcm::DataSet& GetDataSet() const { return reader_.GetFile().GetDataSet(); } const gdcm::Image& GetImage() const { if (interleaved_.get() != NULL) { return interleaved_->GetOutput(); } if (lut_.get() != NULL) { return lut_->GetOutput(); } if (photometric_.get() != NULL) { return photometric_->GetOutput(); } return reader_.GetImage(); } void Decode() { // Change photometric interpretation or apply LUT, if required { const gdcm::Image& image = GetImage(); if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) { lut_.reset(new gdcm::ImageApplyLookupTable()); lut_->SetInput(image); if (!lut_->Apply()) { throw std::runtime_error( "GDCM cannot apply the lookup table"); } } else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) { if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) { photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); photometric_->SetInput(image); photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); if (!photometric_->Change() || GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) { throw std::runtime_error("GDCM cannot change the photometric interpretation"); } } } else { if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_FULL && (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) { photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); photometric_->SetInput(image); photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); if (!photometric_->Change() || GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) { throw std::runtime_error("GDCM cannot change the photometric interpretation"); } } } } // Possibly convert planar configuration to interleaved { const gdcm::Image& image = GetImage(); if (image.GetPlanarConfiguration() != 0 && image.GetPixelFormat().GetSamplesPerPixel() != 1) { interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); interleaved_->SetInput(image); if (!interleaved_->Change() || GetImage().GetPlanarConfiguration() != 0) { throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); } } } } }; GdcmImageDecoder::GdcmImageDecoder(const void* dicom, size_t size) : pimpl_(new PImpl(dicom, size)) { // Setup a stream to the memory buffer using namespace boost::iostreams; basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); stream<basic_array_source<char> > stream(source); // Parse the DICOM instance using GDCM pimpl_->reader_.SetStream(stream); if (!pimpl_->reader_.Read()) { throw std::runtime_error("Bad file format"); } pimpl_->Decode(); } OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const { const gdcm::Image& image = pimpl_->GetImage(); if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) { switch (image.GetPixelFormat()) { case gdcm::PixelFormat::UINT16: return OrthancPluginPixelFormat_Grayscale16; case gdcm::PixelFormat::INT16: return OrthancPluginPixelFormat_SignedGrayscale16; case gdcm::PixelFormat::UINT8: return OrthancPluginPixelFormat_Grayscale8; default: throw std::runtime_error("Unsupported pixel format"); } } else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_FULL || image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) { switch (image.GetPixelFormat()) { case gdcm::PixelFormat::UINT8: return OrthancPluginPixelFormat_RGB24; case gdcm::PixelFormat::UINT16: #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) return OrthancPluginPixelFormat_RGB48; #else throw std::runtime_error("RGB48 pixel format is only supported if compiled against Orthanc SDK >= 1.3.1"); #endif default: break; } } throw std::runtime_error("Unsupported pixel format"); } unsigned int GdcmImageDecoder::GetWidth() const { return pimpl_->GetImage().GetColumns(); } unsigned int GdcmImageDecoder::GetHeight() const { return pimpl_->GetImage().GetRows(); } unsigned int GdcmImageDecoder::GetFramesCount() const { return pimpl_->GetImage().GetDimension(2); } size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) { switch (format) { case OrthancPluginPixelFormat_Grayscale8: return 1; case OrthancPluginPixelFormat_Grayscale16: case OrthancPluginPixelFormat_SignedGrayscale16: return 2; case OrthancPluginPixelFormat_RGB24: return 3; #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) case OrthancPluginPixelFormat_RGB48: return 6; #endif default: throw std::runtime_error("Unsupport pixel format"); } } static void ConvertYbrToRgb(uint8_t rgb[3], const uint8_t ybr[3]) { // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2 // https://en.wikipedia.org/wiki/YCbCr#JPEG_conversion // TODO - Check out the outcome of Mathieu's discussion about // truncation of YCbCr-to-RGB conversion: // https://groups.google.com/forum/#!msg/comp.protocols.dicom/JHuGeyWbTz8/ARoTWrJzAQAJ const float Y = ybr[0]; const float Cb = ybr[1]; const float Cr = ybr[2]; const float result[3] = { Y + 1.402f * (Cr - 128.0f), Y - 0.344136f * (Cb - 128.0f) - 0.714136f * (Cr - 128.0f), Y + 1.772f * (Cb - 128.0f) }; for (uint8_t i = 0; i < 3 ; i++) { if (result[i] < 0) { rgb[i] = 0; } else if (result[i] > 255) { rgb[i] = 255; } else { rgb[i] = static_cast<uint8_t>(result[i]); } } } static void FixPhotometricInterpretation(OrthancImageWrapper& image, gdcm::PhotometricInterpretation interpretation) { switch (interpretation) { case gdcm::PhotometricInterpretation::MONOCHROME1: case gdcm::PhotometricInterpretation::MONOCHROME2: case gdcm::PhotometricInterpretation::RGB: return; case gdcm::PhotometricInterpretation::YBR_FULL: { // Fix for Osimis issue WVB-319: Some images are not loading in US_MF uint32_t width = image.GetWidth(); uint32_t height = image.GetHeight(); uint32_t pitch = image.GetPitch(); uint8_t* buffer = reinterpret_cast<uint8_t*>(image.GetBuffer()); if (image.GetFormat() != OrthancPluginPixelFormat_RGB24 || pitch < 3 * width) { throw std::runtime_error("Internal error"); } for (uint32_t y = 0; y < height; y++) { uint8_t* p = buffer + y * pitch; for (uint32_t x = 0; x < width; x++, p += 3) { const uint8_t ybr[3] = { p[0], p[1], p[2] }; uint8_t rgb[3]; ConvertYbrToRgb(rgb, ybr); p[0] = rgb[0]; p[1] = rgb[1]; p[2] = rgb[2]; } } return; } default: throw std::runtime_error("Unsupported output photometric interpretation"); } } OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, unsigned int frameIndex) const { unsigned int frames = GetFramesCount(); unsigned int width = GetWidth(); unsigned int height = GetHeight(); OrthancPluginPixelFormat format = GetFormat(); size_t bpp = GetBytesPerPixel(format); if (frameIndex >= frames) { throw std::runtime_error("Inexistent frame index"); } std::string& decoded = pimpl_->decoded_; OrthancImageWrapper target(context, format, width, height); if (width == 0 || height == 0) { return target.Release(); } if (decoded.empty()) { decoded.resize(pimpl_->GetImage().GetBufferLength()); if (!pimpl_->GetImage().GetBuffer(&decoded[0])) { throw std::runtime_error("Image not properly decoded to a memory buffer"); } } const void* sourceBuffer = &decoded[0]; if (target.GetPitch() == bpp * width && frames == 1) { assert(decoded.size() == target.GetPitch() * target.GetHeight()); memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); } else { size_t targetPitch = target.GetPitch(); size_t sourcePitch = width * bpp; const char* a = &decoded[sourcePitch * height * frameIndex]; char* b = target.GetBuffer(); for (uint32_t y = 0; y < height; y++) { memcpy(b, a, sourcePitch); a += sourcePitch; b += targetPitch; } } FixPhotometricInterpretation(target, pimpl_->GetImage().GetPhotometricInterpretation()); return target.Release(); } }