Mercurial > hg > orthanc
view Core/DicomParsing/Internals/DicomFrameIndex.cpp @ 2953:210d5afd8f2b
GenerateErrorCodes.py
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 03 Dec 2018 11:49:39 +0100 |
parents | 878b59270859 |
children | 4e43e67f8ecf |
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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) 2017-2018 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. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * 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 "../../PrecompiledHeaders.h" #include "DicomFrameIndex.h" #include "../../OrthancException.h" #include "../../DicomFormat/DicomImageInformation.h" #include "../FromDcmtkBridge.h" #include "../../Endianness.h" #include "DicomImageDecoder.h" #include <boost/lexical_cast.hpp> #include <dcmtk/dcmdata/dcdeftag.h> #include <dcmtk/dcmdata/dcpxitem.h> #include <dcmtk/dcmdata/dcpixseq.h> namespace Orthanc { class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex { private: DcmPixelSequence* pixelSequence_; std::vector<DcmPixelItem*> startFragment_; std::vector<unsigned int> countFragments_; std::vector<unsigned int> frameSize_; void GetOffsetTable(std::vector<uint32_t>& table) { DcmPixelItem* item = NULL; if (!pixelSequence_->getItem(item, 0).good() || item == NULL) { throw OrthancException(ErrorCode_BadFileFormat); } uint32_t length = item->getLength(); if (length == 0) { table.clear(); return; } if (length % 4 != 0) { // Error: Each fragment is index with 4 bytes (uint32_t) throw OrthancException(ErrorCode_BadFileFormat); } uint8_t* content = NULL; if (!item->getUint8Array(content).good() || content == NULL) { throw OrthancException(ErrorCode_InternalError); } table.resize(length / 4); // The offset table is always in little endian in the DICOM // file. Swap it to host endianness if needed. const uint32_t* offset = reinterpret_cast<const uint32_t*>(content); for (size_t i = 0; i < table.size(); i++, offset++) { table[i] = le32toh(*offset); } } public: FragmentIndex(DcmPixelSequence* pixelSequence, unsigned int countFrames) : pixelSequence_(pixelSequence) { assert(pixelSequence != NULL); startFragment_.resize(countFrames); countFragments_.resize(countFrames); frameSize_.resize(countFrames); // The first fragment corresponds to the offset table unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card()); if (countFragments < countFrames + 1) { throw OrthancException(ErrorCode_BadFileFormat); } if (countFragments == countFrames + 1) { // Simple case: There is one fragment per frame. DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table if (fragment == NULL) { throw OrthancException(ErrorCode_InternalError); } for (unsigned int i = 0; i < countFrames; i++) { fragment = pixelSequence_->nextInContainer(fragment); startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment); frameSize_[i] = fragment->getLength(); countFragments_[i] = 1; } return; } // Parse the offset table std::vector<uint32_t> offsetOfFrame; GetOffsetTable(offsetOfFrame); if (offsetOfFrame.size() != countFrames || offsetOfFrame[0] != 0) { throw OrthancException(ErrorCode_BadFileFormat); } // Loop over the fragments (ignoring the offset table). This is // an alternative, faster implementation to DCMTK's // "DcmCodec::determineStartFragment()". DcmObject* fragment = pixelSequence_->nextInContainer(NULL); if (fragment == NULL) { throw OrthancException(ErrorCode_InternalError); } fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table if (fragment == NULL) { throw OrthancException(ErrorCode_InternalError); } uint32_t offset = 0; unsigned int currentFrame = 0; startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment); unsigned int currentFragment = 1; while (fragment != NULL) { if (currentFrame + 1 < countFrames && offset == offsetOfFrame[currentFrame + 1]) { currentFrame += 1; startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment); } frameSize_[currentFrame] += fragment->getLength(); countFragments_[currentFrame]++; // 8 bytes = overhead for the item tag and length field offset += fragment->getLength() + 8; currentFragment++; fragment = pixelSequence_->nextInContainer(fragment); } if (currentFragment != countFragments || currentFrame + 1 != countFrames || fragment != NULL) { throw OrthancException(ErrorCode_BadFileFormat); } assert(startFragment_.size() == countFragments_.size() && startFragment_.size() == frameSize_.size()); } virtual void GetRawFrame(std::string& frame, unsigned int index) const { if (index >= startFragment_.size()) { throw OrthancException(ErrorCode_ParameterOutOfRange); } frame.resize(frameSize_[index]); if (frame.size() == 0) { return; } uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]); size_t offset = 0; DcmPixelItem* fragment = startFragment_[index]; for (unsigned int i = 0; i < countFragments_[index]; i++) { uint8_t* content = NULL; if (!fragment->getUint8Array(content).good() || content == NULL) { throw OrthancException(ErrorCode_InternalError); } assert(offset + fragment->getLength() <= frame.size()); memcpy(target + offset, content, fragment->getLength()); offset += fragment->getLength(); fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment)); } } }; class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex { private: uint8_t* pixelData_; size_t frameSize_; public: UncompressedIndex(DcmDataset& dataset, unsigned int countFrames, size_t frameSize) : pixelData_(NULL), frameSize_(frameSize) { size_t size = 0; DcmElement* e; if (dataset.findAndGetElement(DCM_PixelData, e).good() && e != NULL) { size = e->getLength(); if (size > 0) { pixelData_ = NULL; if (!e->getUint8Array(pixelData_).good() || pixelData_ == NULL) { throw OrthancException(ErrorCode_BadFileFormat); } } } if (size < frameSize_ * countFrames) { throw OrthancException(ErrorCode_BadFileFormat); } } virtual void GetRawFrame(std::string& frame, unsigned int index) const { frame.resize(frameSize_); if (frameSize_ > 0) { memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_); } } }; class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex { private: std::string pixelData_; size_t frameSize_; public: PsmctRle1Index(DcmDataset& dataset, unsigned int countFrames, size_t frameSize) : frameSize_(frameSize) { if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) || pixelData_.size() < frameSize * countFrames) { throw OrthancException(ErrorCode_BadFileFormat); } } virtual void GetRawFrame(std::string& frame, unsigned int index) const { frame.resize(frameSize_); if (frameSize_ > 0) { memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_); } } }; bool DicomFrameIndex::IsVideo(DcmFileFormat& dicom) { // Retrieve the transfer syntax from the DICOM header const char* value = NULL; if (!dicom.getMetaInfo()->findAndGetString(DCM_TransferSyntaxUID, value).good() || value == NULL) { return false; } const std::string transferSyntax(value); // Video standards supported in DICOM 2016a // http://dicom.nema.org/medical/dicom/2016a/output/html/part05.html if (transferSyntax == "1.2.840.10008.1.2.4.100" || // MPEG2 MP@ML option of ISO/IEC MPEG2 transferSyntax == "1.2.840.10008.1.2.4.101" || // MPEG2 MP@HL option of ISO/IEC MPEG2 transferSyntax == "1.2.840.10008.1.2.4.102" || // MPEG-4 AVC/H.264 High Profile / Level 4.1 of ITU-T H.264 transferSyntax == "1.2.840.10008.1.2.4.103" || // MPEG-4 AVC/H.264 BD-compat High Profile / Level 4.1 of ITU-T H.264 transferSyntax == "1.2.840.10008.1.2.4.104" || // MPEG-4 AVC/H.264 High Profile / Level 4.2 of ITU-T H.264 transferSyntax == "1.2.840.10008.1.2.4.105" || // MPEG-4 AVC/H.264 High Profile / Level 4.2 of ITU-T H.264 transferSyntax == "1.2.840.10008.1.2.4.106") // MPEG-4 AVC/H.264 Stereo High Profile / Level 4.2 of the ITU-T H.264 { return true; } return false; } unsigned int DicomFrameIndex::GetFramesCount(DcmFileFormat& dicom) { // Assume 1 frame for video transfer syntaxes if (IsVideo(dicom)) { return 1; } const char* tmp = NULL; if (!dicom.getDataset()->findAndGetString(DCM_NumberOfFrames, tmp).good() || tmp == NULL) { return 1; } int count = -1; try { count = boost::lexical_cast<int>(tmp); } catch (boost::bad_lexical_cast&) { } if (count < 0) { throw OrthancException(ErrorCode_BadFileFormat); } else { return count; } } DicomFrameIndex::DicomFrameIndex(DcmFileFormat& dicom) { countFrames_ = GetFramesCount(dicom); if (countFrames_ == 0) { // The image has no frame. No index is to be built. return; } DcmDataset& dataset = *dicom.getDataset(); // Test whether this image is composed of a sequence of fragments DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dataset); if (pixelSequence != NULL) { index_.reset(new FragmentIndex(pixelSequence, countFrames_)); return; } // Extract information about the image structure DicomMap tags; FromDcmtkBridge::ExtractDicomSummary(tags, dataset); DicomImageInformation information(tags); // Access to the raw pixel data if (DicomImageDecoder::IsPsmctRle1(dataset)) { index_.reset(new PsmctRle1Index(dataset, countFrames_, information.GetFrameSize())); } else { index_.reset(new UncompressedIndex(dataset, countFrames_, information.GetFrameSize())); } } void DicomFrameIndex::GetRawFrame(std::string& frame, unsigned int index) const { if (index >= countFrames_) { throw OrthancException(ErrorCode_ParameterOutOfRange); } else if (index_.get() != NULL) { return index_->GetRawFrame(frame, index); } else { frame.clear(); } } }