Mercurial > hg > orthanc
changeset 4214:7b011cfda135
working on DicomStreamReader
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Mon, 28 Sep 2020 21:05:13 +0200 |
parents | be2eca8b02e1 |
children | 28e9457dc7ab |
files | OrthancFramework/Sources/DicomFormat/DicomMap.cpp OrthancFramework/UnitTestsSources/DicomMapTests.cpp |
diffstat | 2 files changed, 575 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/OrthancFramework/Sources/DicomFormat/DicomMap.cpp Mon Sep 28 15:23:04 2020 +0200 +++ b/OrthancFramework/Sources/DicomFormat/DicomMap.cpp Mon Sep 28 21:05:13 2020 +0200 @@ -506,10 +506,10 @@ { const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); - return (static_cast<uint16_t>(p[0]) | - (static_cast<uint16_t>(p[1]) << 8) | - (static_cast<uint16_t>(p[2]) << 16) | - (static_cast<uint16_t>(p[3]) << 24)); + 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)); }
--- a/OrthancFramework/UnitTestsSources/DicomMapTests.cpp Mon Sep 28 15:23:04 2020 +0200 +++ b/OrthancFramework/UnitTestsSources/DicomMapTests.cpp Mon Sep 28 21:05:13 2020 +0200 @@ -693,3 +693,574 @@ ASSERT_EQ(ts, it->second); } } + + +namespace +{ + class StreamBlockReader : public boost::noncopyable + { + private: + std::istream& stream_; + std::string block_; + size_t blockPos_; + uint64_t processedBytes_; + + public: + StreamBlockReader(std::istream& stream) : + stream_(stream), + blockPos_(0), + processedBytes_(0) + { + } + + void Schedule(size_t blockSize) + { + if (!block_.empty()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + block_.resize(blockSize); + blockPos_ = 0; + } + } + + bool Read(std::string& block) + { + if (block_.empty()) + { + if (blockPos_ != 0) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + + block.clear(); + return true; + } + else + { + while (blockPos_ < block_.size()) + { + char c; + stream_.get(c); + + if (stream_.good()) + { + block_[blockPos_] = c; + blockPos_++; + } + else + { + return false; + } + } + + processedBytes_ += block_.size(); + + block.swap(block_); + block_.clear(); + return true; + } + } + + uint64_t GetProcessedBytes() const + { + return processedBytes_; + } + }; + + + + + /** + * This class parses a stream containing a DICOM instance. It does + * *not* support the visit of sequences (it only works at the first + * level of the hierarchy), and it stops the processing once pixel + * data is reached in compressed transfer syntaxes. + **/ + class DicomStreamReader : public boost::noncopyable + { + public: + class IVisitor : public boost::noncopyable + { + public: + virtual ~IVisitor() + { + } + + virtual void VisitMetaHeaderTag(const DicomTag& tag, + const ValueRepresentation& vr, + const std::string& value) = 0; + + // Return "false" to stop processing + virtual bool VisitDatasetTag(const DicomTag& tag, + const ValueRepresentation& vr, + DicomTransferSyntax transferSyntax, + const std::string& value) = 0; + }; + + private: + enum State + { + State_Preamble, + State_MetaHeader, + State_DatasetTag, + State_DatasetExplicitLength, + State_DatasetValue, + State_Done + }; + + StreamBlockReader reader_; + State state_; + DicomTransferSyntax transferSyntax_; + DicomTag danglingTag_; + ValueRepresentation danglingVR_; + + 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 */); + } + + + void PrintBlock(const std::string& block) + { + for (size_t i = 0; i < block.size(); i++) + { + printf("%02x ", static_cast<uint8_t>(block[i])); + if (i % 16 == 15) + printf("\n"); + } + printf("\n"); + } + + void HandlePreamble(IVisitor& visitor, + const std::string& block) + { + printf("PREAMBLE:\n"); + PrintBlock(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 HandleMetaHeader(IVisitor& visitor, + const std::string& block) + { + printf("META-HEADER:\n"); + PrintBlock(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); + + if (tag.GetGroup() == 0x0002) + { + visitor.VisitMetaHeaderTag(tag, vr, value); + } + + if (tag == DICOM_TAG_TRANSFER_SYNTAX_UID) + { + // Remove possible padding byte + if (!value.empty() && + value[value.size() - 1] == '\0') + { + value.resize(value.size() - 1); + } + + 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); + + std::string value; + value.assign(p + pos + 12, length); + + if (tag.GetGroup() == 0x0002) + { + visitor.VisitMetaHeaderTag(tag, vr, value); + } + + pos += length + 12; + } + } + + if (pos != block.size()) + { + throw OrthancException(ErrorCode_BadFileFormat); + } + + if (!hasTransferSyntax) + { + throw OrthancException(ErrorCode_BadFileFormat, "DICOM file meta-header without transfer syntax UID"); + } + + reader_.Schedule(8); + state_ = State_DatasetTag; + } + + + void HandleDatasetTag(IVisitor& visitor, + const std::string& block) + { + printf("DATASET TAG:\n"); + PrintBlock(block); + + assert(block.size() == 8u); + + const bool littleEndian = (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit); + + danglingTag_ = ReadTag(block.c_str(), littleEndian); + danglingVR_ = ValueRepresentation_Unknown; + + /*if (danglingTag_ == DICOM_TAG_PIXEL_DATA) + { + state_ = State_Done; + return; + }*/ + + if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit) + { + uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, true /* little endian */); + + reader_.Schedule(length); + state_ = State_DatasetValue; + } + else + { + // This in an explicit transfer syntax + + danglingVR_ = StringToValueRepresentation( + std::string(block.c_str() + 4, 2), false /* ignore unknown VR */); + + if (IsShortExplicitTag(danglingVR_)) + { + 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; + } + }; + } + + + void HandleDatasetExplicitLength(IVisitor& visitor, + const std::string& block) + { + //printf("DATASET TAG LENGTH:\n"); + //PrintBlock(block); + + assert(block.size() == 4); + + const bool littleEndian = (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit); + + uint32_t length = ReadUnsignedInteger32(block.c_str(), littleEndian); + if (length == 0xffffffffu) + { + // http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html + printf("AIE\n"); + + /** + * This is the case for compressed transfer syntaxes. We stop + * the processing here, as this would cause StreamBlockReader + * to allocate a huge memory buffer of 2GB. + **/ + state_ = State_Done; + } + else + { + reader_.Schedule(length); + state_ = State_DatasetValue; + } + } + + + public: + DicomStreamReader(std::istream& stream) : + reader_(stream), + state_(State_Preamble), + transferSyntax_(DicomTransferSyntax_LittleEndianImplicit), // Dummy + danglingTag_(0x0000, 0x0000), // Dummy + danglingVR_(ValueRepresentation_Unknown) // Dummy + { + 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 Consume(IVisitor& visitor) + { + 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(visitor, block); + break; + + case State_DatasetExplicitLength: + HandleDatasetExplicitLength(visitor, block); + break; + + case State_DatasetValue: + if (visitor.VisitDatasetTag(danglingTag_, danglingVR_, transferSyntax_, block)) + { + reader_.Schedule(8); + state_ = State_DatasetTag; + } + else + { + state_ = State_Done; + } + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + } + else + { + return; // No more data in the stream + } + } + } + + bool IsDone() const + { + return (state_ == State_Done); + } + + uint64_t GetProcessedBytes() const + { + return reader_.GetProcessedBytes(); + } + }; + + + + class V : public DicomStreamReader::IVisitor + { + public: + virtual void VisitMetaHeaderTag(const DicomTag& tag, + const ValueRepresentation& vr, + const std::string& value) + { + std::cout << "Header: " << tag.Format() << " [" << value.c_str() << "] (" << value.size() << ")" << std::endl; + } + + virtual bool VisitDatasetTag(const DicomTag& tag, + const ValueRepresentation& vr, + DicomTransferSyntax transferSyntax, + const std::string& value) + { + if (tag.GetGroup() < 0x7f00) + std::cout << "Dataset: " << tag.Format() << " [" << value.c_str() << "] (" << value.size() << ")" << std::endl; + else + std::cout << "Dataset: " << tag.Format() << " [PIXEL] (" << value.size() << ")" << std::endl; + + return true; + } + }; +} + + + +TEST(DicomStreamReader, DISABLED_Tutu) +{ + static const std::string PATH = "/home/jodogne/Subversion/orthanc-tests/Database/TransferSyntaxes/"; + + std::string dicom; + //SystemToolbox::ReadFile(dicom, PATH + "../ColorTestMalaterre.dcm", false); + //SystemToolbox::ReadFile(dicom, PATH + "1.2.840.10008.1.2.2.dcm", false); // Big Endian + //SystemToolbox::ReadFile(dicom, PATH + "1.2.840.10008.1.2.1.dcm", false); + //SystemToolbox::ReadFile(dicom, PATH + "1.2.840.10008.1.2.4.50.dcm", false); + SystemToolbox::ReadFile(dicom, PATH + "1.2.840.10008.1.2.4.51.dcm", false); + + std::stringstream stream; + size_t pos = 0; + + DicomStreamReader r(stream); + V visitor; + + while (pos < dicom.size() && + !r.IsDone()) + { + //printf("."); + //printf("%d\n", pos); + r.Consume(visitor); + stream.clear(); + stream.put(dicom[pos++]); + } + + r.Consume(visitor); + + printf(">> %d\n", r.GetProcessedBytes()); +} + +TEST(DicomStreamReader, DISABLED_Tutu2) +{ + static const std::string PATH = "/home/jodogne/Subversion/orthanc-tests/Database/TransferSyntaxes/"; + + //std::ifstream stream(PATH + "1.2.840.10008.1.2.4.50.dcm"); + std::ifstream stream(PATH + "1.2.840.10008.1.2.2.dcm"); + + DicomStreamReader r(stream); + V visitor; + + r.Consume(visitor); + + printf(">> %d\n", r.GetProcessedBytes()); +}