Mercurial > hg > orthanc
view OrthancFramework/Sources/DicomFormat/DicomStreamReader.cpp @ 5931:7f0145ff63f3
fix documentation of /tools/find
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 16 Dec 2024 17:25:20 +0100 |
parents | ff0b54e8bc71 |
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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) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Lesser 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 * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/>. **/ #include "../PrecompiledHeaders.h" #include "DicomStreamReader.h" #include "../OrthancException.h" #include <cassert> #include <sstream> #include <boost/iostreams/device/array.hpp> #include <boost/iostreams/stream.hpp> #include <iostream> namespace Orthanc { static bool IsNormalizationNeeded(const std::string& source, ValueRepresentation vr) { return (!source.empty() && (source[source.size() - 1] == ' ' || source[source.size() - 1] == '\0') && // Normalization only applies to string-based VR (vr == ValueRepresentation_ApplicationEntity || vr == ValueRepresentation_AgeString || vr == ValueRepresentation_CodeString || vr == ValueRepresentation_DecimalString || vr == ValueRepresentation_IntegerString || vr == ValueRepresentation_LongString || vr == ValueRepresentation_LongText || vr == ValueRepresentation_PersonName || vr == ValueRepresentation_ShortString || vr == ValueRepresentation_ShortText || vr == ValueRepresentation_UniqueIdentifier || vr == ValueRepresentation_UnlimitedText)); } static void NormalizeValue(std::string& inplace, ValueRepresentation vr) { if (IsNormalizationNeeded(inplace, vr)) { assert(!inplace.empty()); inplace.resize(inplace.size() - 1); } } static uint16_t ReadUnsignedInteger16(const char* dicom, bool littleEndian) { const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); if (littleEndian) { return (static_cast<uint16_t>(p[0]) | (static_cast<uint16_t>(p[1]) << 8)); } else { return (static_cast<uint16_t>(p[1]) | (static_cast<uint16_t>(p[0]) << 8)); } } static uint32_t ReadUnsignedInteger32(const char* dicom, bool littleEndian) { const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); if (littleEndian) { return (static_cast<uint32_t>(p[0]) | (static_cast<uint32_t>(p[1]) << 8) | (static_cast<uint32_t>(p[2]) << 16) | (static_cast<uint32_t>(p[3]) << 24)); } else { return (static_cast<uint32_t>(p[3]) | (static_cast<uint32_t>(p[2]) << 8) | (static_cast<uint32_t>(p[1]) << 16) | (static_cast<uint32_t>(p[0]) << 24)); } } static DicomTag ReadTag(const char* dicom, bool littleEndian) { return DicomTag(ReadUnsignedInteger16(dicom, littleEndian), ReadUnsignedInteger16(dicom + 2, littleEndian)); } static bool IsShortExplicitTag(ValueRepresentation vr) { /** * Are we in the case of Table 7.1-2? "Data Element with * Explicit VR of AE, AS, AT, CS, DA, DS, DT, FL, FD, IS, LO, * LT, PN, SH, SL, SS, ST, TM, UI, UL and US" * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html#sect_7.1.2 **/ return (vr == ValueRepresentation_ApplicationEntity /* AE */ || vr == ValueRepresentation_AgeString /* AS */ || vr == ValueRepresentation_AttributeTag /* AT */ || vr == ValueRepresentation_CodeString /* CS */ || vr == ValueRepresentation_Date /* DA */ || vr == ValueRepresentation_DecimalString /* DS */ || vr == ValueRepresentation_DateTime /* DT */ || vr == ValueRepresentation_FloatingPointSingle /* FL */ || vr == ValueRepresentation_FloatingPointDouble /* FD */ || vr == ValueRepresentation_IntegerString /* IS */ || vr == ValueRepresentation_LongString /* LO */ || vr == ValueRepresentation_LongText /* LT */ || vr == ValueRepresentation_PersonName /* PN */ || vr == ValueRepresentation_ShortString /* SH */ || vr == ValueRepresentation_SignedLong /* SL */ || vr == ValueRepresentation_SignedShort /* SS */ || vr == ValueRepresentation_ShortText /* ST */ || vr == ValueRepresentation_Time /* TM */ || vr == ValueRepresentation_UniqueIdentifier /* UI */ || vr == ValueRepresentation_UnsignedLong /* UL */ || vr == ValueRepresentation_UnsignedShort /* US */); } bool DicomStreamReader::IsLittleEndian() const { return (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit); } void DicomStreamReader::HandlePreamble(IVisitor& visitor, const std::string& block) { assert(block.size() == 144u); assert(reader_.GetProcessedBytes() == 144u); /** * The "DICOM file meta information" is always encoded using * "Explicit VR Little Endian Transfer Syntax" * http://dicom.nema.org/medical/dicom/current/output/chtml/part10/chapter_7.html **/ if (block[128] != 'D' || block[129] != 'I' || block[130] != 'C' || block[131] != 'M' || ReadTag(block.c_str() + 132, true) != DicomTag(0x0002, 0x0000) || block[136] != 'U' || block[137] != 'L' || ReadUnsignedInteger16(block.c_str() + 138, true) != 4) { throw OrthancException(ErrorCode_BadFileFormat); } uint32_t length = ReadUnsignedInteger32(block.c_str() + 140, true); reader_.Schedule(length); state_ = State_MetaHeader; } void DicomStreamReader::HandleMetaHeader(IVisitor& visitor, const std::string& block) { size_t pos = 0; const char* p = block.c_str(); bool hasTransferSyntax = false; while (pos + 8 <= block.size()) { DicomTag tag = ReadTag(p + pos, true); ValueRepresentation vr = StringToValueRepresentation(std::string(p + pos + 4, 2), true); if (IsShortExplicitTag(vr)) { uint16_t length = ReadUnsignedInteger16(p + pos + 6, true); std::string value; value.assign(p + pos + 8, length); NormalizeValue(value, vr); if (tag.GetGroup() == 0x0002) { visitor.VisitMetaHeaderTag(tag, vr, value); } if (tag == DICOM_TAG_TRANSFER_SYNTAX_UID) { if (LookupTransferSyntax(transferSyntax_, value)) { hasTransferSyntax = true; } else { throw OrthancException(ErrorCode_NotImplemented, "Unsupported transfer syntax: " + value); } } pos += length + 8; } else if (pos + 12 <= block.size()) { uint16_t reserved = ReadUnsignedInteger16(p + pos + 6, true); if (reserved != 0) { break; } uint32_t length = ReadUnsignedInteger32(p + pos + 8, true); if (tag.GetGroup() == 0x0002) { std::string value; value.assign(p + pos + 12, length); NormalizeValue(value, vr); visitor.VisitMetaHeaderTag(tag, vr, value); } pos += length + 12; } else { throw OrthancException(ErrorCode_BadFileFormat, "Invalid DICOM File: Unable to parse Meta Header"); } } if (pos != block.size()) { throw OrthancException(ErrorCode_BadFileFormat); } if (!hasTransferSyntax) { throw OrthancException(ErrorCode_BadFileFormat, "DICOM file meta-header without transfer syntax UID"); } visitor.VisitTransferSyntax(transferSyntax_); reader_.Schedule(8); state_ = State_DatasetTag; } void DicomStreamReader::HandleDatasetTag(const std::string& block, const DicomTag& untilTag) { static const DicomTag DICOM_TAG_SEQUENCE_ITEM(0xfffe, 0xe000); static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_ITEM(0xfffe, 0xe00d); static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE(0xfffe, 0xe0dd); assert(block.size() == 8u); const bool littleEndian = IsLittleEndian(); DicomTag tag = ReadTag(block.c_str(), littleEndian); if (sequenceDepth_ == 0 && tag >= untilTag) { state_ = State_Done; return; } if (tag == DICOM_TAG_SEQUENCE_ITEM || tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM || tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) { // The special sequence items are encoded like "Implicit VR" uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, littleEndian); if (tag == DICOM_TAG_SEQUENCE_ITEM) { if (length == 0xffffffffu) { // Undefined length: Need to loop over the tags of the nested dataset reader_.Schedule(8); state_ = State_DatasetTag; } else { // Explicit length: Can skip the full sequence at once reader_.Schedule(length); state_ = State_DatasetValue; } } else if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM || tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) { if (length != 0 || sequenceDepth_ == 0) { throw OrthancException(ErrorCode_BadFileFormat); } if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) { sequenceDepth_ --; } reader_.Schedule(8); state_ = State_DatasetTag; } else { throw OrthancException(ErrorCode_InternalError); } } else { assert(reader_.GetProcessedBytes() >= block.size()); const uint64_t tagOffset = reader_.GetProcessedBytes() - block.size(); ValueRepresentation vr = ValueRepresentation_Unknown; if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit) { if (sequenceDepth_ == 0) { danglingTag_ = tag; danglingVR_ = vr; danglingOffset_ = tagOffset; } uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, true /* little endian */); HandleDatasetExplicitLength(length); } else { // This in an explicit transfer syntax vr = StringToValueRepresentation( std::string(block.c_str() + 4, 2), false /* ignore unknown VR */); if (vr == ValueRepresentation_Sequence) { sequenceDepth_ ++; reader_.Schedule(4); state_ = State_SequenceExplicitLength; } else if (IsShortExplicitTag(vr)) { uint16_t length = ReadUnsignedInteger16(block.c_str() + 6, littleEndian); reader_.Schedule(length); state_ = State_DatasetValue; } else { uint16_t reserved = ReadUnsignedInteger16(block.c_str() + 6, littleEndian); if (reserved != 0) { throw OrthancException(ErrorCode_BadFileFormat); } reader_.Schedule(4); state_ = State_DatasetExplicitLength; } if (sequenceDepth_ == 0) { danglingTag_ = tag; danglingVR_ = vr; danglingOffset_ = tagOffset; } } } } void DicomStreamReader::HandleDatasetExplicitLength(uint32_t length) { if (length == 0xffffffffu) { /** * This is the case of pixel data with compressed transfer * syntaxes. Schedule the reading of the first tag of the * nested dataset. * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html **/ state_ = State_DatasetTag; reader_.Schedule(8); sequenceDepth_ ++; } else { reader_.Schedule(length); state_ = State_DatasetValue; } } void DicomStreamReader::HandleDatasetExplicitLength(IVisitor& visitor, const std::string& block) { assert(block.size() == 4); uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); HandleDatasetExplicitLength(length); std::string empty; if (!visitor.VisitDatasetTag(danglingTag_, danglingVR_, empty, IsLittleEndian(), danglingOffset_)) { state_ = State_Done; } } void DicomStreamReader::HandleSequenceExplicitLength(const std::string& block) { assert(block.size() == 4); uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); if (length == 0xffffffffu) { state_ = State_DatasetTag; reader_.Schedule(8); } else { reader_.Schedule(length); state_ = State_SequenceExplicitValue; } } void DicomStreamReader::HandleSequenceExplicitValue() { if (sequenceDepth_ == 0) { throw OrthancException(ErrorCode_InternalError); } sequenceDepth_ --; state_ = State_DatasetTag; reader_.Schedule(8); } void DicomStreamReader::HandleDatasetValue(IVisitor& visitor, const std::string& block) { if (sequenceDepth_ == 0) { bool c; if (IsNormalizationNeeded(block, danglingVR_)) { std::string s(block.begin(), block.end() - 1); c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, s, IsLittleEndian(), danglingOffset_); } else { c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, block, IsLittleEndian(), danglingOffset_); } if (!c) { state_ = State_Done; return; } } reader_.Schedule(8); state_ = State_DatasetTag; } DicomStreamReader::DicomStreamReader(std::istream& stream) : reader_(stream), state_(State_Preamble), transferSyntax_(DicomTransferSyntax_LittleEndianImplicit), // Dummy danglingTag_(0x0000, 0x0000), // Dummy danglingVR_(ValueRepresentation_Unknown), // Dummy danglingOffset_(0), // Dummy sequenceDepth_(0) { reader_.Schedule(128 /* empty header */ + 4 /* "DICM" magic value */ + 4 /* (0x0002, 0x0000) tag */ + 2 /* value representation of (0x0002, 0x0000) == "UL" */ + 2 /* length of "UL" value == 4 */ + 4 /* actual length of the meta-header */); } void DicomStreamReader::Consume(IVisitor& visitor, const DicomTag& untilTag) { while (state_ != State_Done) { std::string block; if (reader_.Read(block)) { switch (state_) { case State_Preamble: HandlePreamble(visitor, block); break; case State_MetaHeader: HandleMetaHeader(visitor, block); break; case State_DatasetTag: HandleDatasetTag(block, untilTag); break; case State_DatasetExplicitLength: HandleDatasetExplicitLength(visitor, block); break; case State_SequenceExplicitLength: HandleSequenceExplicitLength(block); break; case State_SequenceExplicitValue: HandleSequenceExplicitValue(); break; case State_DatasetValue: HandleDatasetValue(visitor, block); break; default: throw OrthancException(ErrorCode_InternalError); } } else { return; // No more data in the stream } } } void DicomStreamReader::Consume(IVisitor& visitor) { DicomTag untilTag(0xffff, 0xffff); Consume(visitor, untilTag); } bool DicomStreamReader::IsDone() const { return (state_ == State_Done); } uint64_t DicomStreamReader::GetProcessedBytes() const { return reader_.GetProcessedBytes(); } class DicomStreamReader::PixelDataVisitor : public DicomStreamReader::IVisitor { private: bool hasPixelData_; uint64_t pixelDataOffset_; ValueRepresentation pixelDataVR_; DicomTransferSyntax transferSyntax_; public: PixelDataVisitor() : hasPixelData_(false), pixelDataOffset_(0), pixelDataVR_(ValueRepresentation_Unknown), transferSyntax_(DicomTransferSyntax_LittleEndianImplicit) // Default DICOM transfer syntax { } virtual void VisitMetaHeaderTag(const DicomTag& tag, const ValueRepresentation& vr, const std::string& value) ORTHANC_OVERRIDE { } virtual void VisitTransferSyntax(DicomTransferSyntax transferSyntax) ORTHANC_OVERRIDE { transferSyntax_ = transferSyntax; } virtual bool VisitDatasetTag(const DicomTag& tag, const ValueRepresentation& vr, const std::string& value, bool isLittleEndian, uint64_t fileOffset) ORTHANC_OVERRIDE { if (tag == DICOM_TAG_PIXEL_DATA) { hasPixelData_ = true; pixelDataOffset_ = fileOffset; if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit) { // Implicit Little Endian has always "OW" VR for pixel data // https://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_A.html pixelDataVR_ = ValueRepresentation_OtherWord; } else if (transferSyntax_ == DicomTransferSyntax_LittleEndianExplicit || transferSyntax_ == DicomTransferSyntax_BigEndianExplicit) { pixelDataVR_ = vr; } else { // Compressed transfer syntaxes must always be OB pixelDataVR_ = ValueRepresentation_OtherByte; } } // Stop processing once pixel data has been passed return (tag < DICOM_TAG_PIXEL_DATA); } bool HasPixelData() const { return hasPixelData_; } uint64_t GetPixelDataOffset() const { return pixelDataOffset_; } ValueRepresentation GetPixelDataVR() const { return pixelDataVR_; } static bool LookupPixelDataOffset(uint64_t& offset, ValueRepresentation& vr, std::istream& stream) { PixelDataVisitor visitor; bool isLittleEndian; { DicomStreamReader reader(stream); try { reader.Consume(visitor); isLittleEndian = reader.IsLittleEndian(); } catch (OrthancException& e) { // Invalid DICOM file return false; } } if (visitor.HasPixelData()) { // Sanity check if we face an unsupported DICOM file: Make // sure that we can read DICOM_TAG_PIXEL_DATA at the reported // position in the stream stream.seekg(visitor.GetPixelDataOffset(), stream.beg); std::string s; s.resize(4); stream.read(&s[0], s.size()); if (!isLittleEndian) { // Byte swapping if reading a file whose transfer syntax is // 1.2.840.10008.1.2.2 (big endian explicit) std::swap(s[0], s[1]); std::swap(s[2], s[3]); } if (stream.gcount() == static_cast<std::streamsize>(s.size()) && s[0] == char(0xe0) && s[1] == char(0x7f) && s[2] == char(0x10) && s[3] == char(0x00)) { offset = visitor.GetPixelDataOffset(); vr = visitor.GetPixelDataVR(); return true; } else { return false; } } else { return false; } } }; bool DicomStreamReader::LookupPixelDataOffset(uint64_t& offset, ValueRepresentation& vr, const std::string& dicom) { std::stringstream stream(dicom); return PixelDataVisitor::LookupPixelDataOffset(offset, vr, stream); } bool DicomStreamReader::LookupPixelDataOffset(uint64_t& offset, ValueRepresentation& vr, const void* buffer, size_t size) { boost::iostreams::array_source source(reinterpret_cast<const char*>(buffer), size); boost::iostreams::stream<boost::iostreams::array_source> stream(source); return PixelDataVisitor::LookupPixelDataOffset(offset, vr, stream); } }