Mercurial > hg > orthanc
diff OrthancFramework/Sources/DicomFormat/DicomStreamReader.cpp @ 4220:92a21efa5c96
reorganization of DicomStreamReader
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 30 Sep 2020 15:33:47 +0200 |
parents | |
children | e4c0218b6b23 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancFramework/Sources/DicomFormat/DicomStreamReader.cpp Wed Sep 30 15:33:47 2020 +0200 @@ -0,0 +1,599 @@ +/** + * 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 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" + +namespace Orthanc +{ + 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 */); + } + + + static 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"); + } + + + + bool DicomStreamReader::IsLittleEndian() const + { + return (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit); + } + + + void DicomStreamReader::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 DicomStreamReader::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"); + } + + 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) + { + //printf("SEQUENCE TAG:\n"); + //PrintBlock(block); + + // The special sequence items are encoded like "Implicit VR" + uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, littleEndian); + + if (tag == DICOM_TAG_SEQUENCE_ITEM) + { + for (unsigned int i = 0; i <= sequenceDepth_; i++) + printf(" "); + if (length == 0xffffffffu) + { + // Undefined length: Need to loop over the tags of the nested dataset + printf("...next dataset in sequence...\n"); + reader_.Schedule(8); + state_ = State_DatasetTag; + } + else + { + // Explicit length: Can skip the full sequence at once + printf("...next dataset in sequence... %u bytes\n", length); + 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) + { + for (unsigned int i = 0; i < sequenceDepth_; i++) + printf(" "); + printf("...leaving sequence...\n"); + + sequenceDepth_ --; + } + else + { + if (sequenceDepth_ == 0) + { + throw OrthancException(ErrorCode_BadFileFormat); + } + } + + reader_.Schedule(8); + state_ = State_DatasetTag; + } + else + { + throw OrthancException(ErrorCode_InternalError); + } + } + else + { + //printf("DATASET TAG:\n"); + //PrintBlock(block); + + previousTag_ = tag; + + ValueRepresentation vr = ValueRepresentation_Unknown; + + if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit) + { + if (sequenceDepth_ == 0) + { + danglingTag_ = tag; + danglingVR_ = vr; + } + + 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_ > 0) + { + for (unsigned int i = 0; i <= sequenceDepth_; i++) + printf(" "); + printf("%s\n", tag.Format().c_str()); + } + + if (vr == ValueRepresentation_Sequence) + { + for (unsigned int i = 0; i <= sequenceDepth_; i++) + printf(" "); + printf("...entering sequence... %s\n", tag.Format().c_str()); + 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; + } + } + } + } + + + 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 + **/ + + for (unsigned int i = 0; i <= sequenceDepth_; i++) + printf(" "); + printf("...entering sequence... %s\n", previousTag_.Format().c_str()); + + state_ = State_DatasetTag; + reader_.Schedule(8); + sequenceDepth_ ++; + } + else + { + reader_.Schedule(length); + state_ = State_DatasetValue; + } + } + + + void DicomStreamReader::HandleDatasetExplicitLength(const std::string& block) + { + //printf("DATASET TAG LENGTH:\n"); + //PrintBlock(block); + + assert(block.size() == 4); + + uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); + HandleDatasetExplicitLength(length); + } + + + void DicomStreamReader::HandleSequenceExplicitLength(const std::string& block) + { + //printf("DATASET TAG LENGTH:\n"); + //PrintBlock(block); + + assert(block.size() == 4); + + uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); + if (length == 0xffffffffu) + { + state_ = State_DatasetTag; + reader_.Schedule(8); + } + else + { + for (unsigned int i = 0; i <= sequenceDepth_; i++) + printf(" "); + printf("...skipping sequence thanks to explicit length... %d\n", length); + + 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 (!block.empty() && + (block[block.size() - 1] == ' ' || + block[block.size() - 1] == '\0') && + (danglingVR_ == ValueRepresentation_ApplicationEntity || + danglingVR_ == ValueRepresentation_AgeString || + danglingVR_ == ValueRepresentation_CodeString || + danglingVR_ == ValueRepresentation_DecimalString || + danglingVR_ == ValueRepresentation_IntegerString || + danglingVR_ == ValueRepresentation_LongString || + danglingVR_ == ValueRepresentation_LongText || + danglingVR_ == ValueRepresentation_PersonName || + danglingVR_ == ValueRepresentation_ShortString || + danglingVR_ == ValueRepresentation_ShortText || + danglingVR_ == ValueRepresentation_UniqueIdentifier || + danglingVR_ == ValueRepresentation_UnlimitedText)) + { + std::string s(block.begin(), block.end() - 1); + c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, s, IsLittleEndian()); + } + else + { + c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, block, IsLittleEndian()); + } + + 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 + previousTag_(0x0000, 0x0000), // Dummy + danglingTag_(0x0000, 0x0000), // Dummy + danglingVR_(ValueRepresentation_Unknown), // 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(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); + } +}