Mercurial > hg > orthanc
annotate OrthancFramework/Sources/DicomFormat/DicomStreamReader.cpp @ 4320:08e3600dcb1b
fix logging
author | Alain Mazy <alain@mazy.be> |
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date | Mon, 23 Nov 2020 14:23:10 +0100 |
parents | 50b0c69b653a |
children | d9473bd5ed43 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
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6 * |
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7 * This program is free software: you can redistribute it and/or |
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8 * modify it under the terms of the GNU Lesser General Public License |
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9 * as published by the Free Software Foundation, either version 3 of |
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10 * the License, or (at your option) any later version. |
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11 * |
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12 * This program is distributed in the hope that it will be useful, but |
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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15 * Lesser General Public License for more details. |
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16 * |
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17 * You should have received a copy of the GNU Lesser General Public |
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18 * License along with this program. If not, see |
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19 * <http://www.gnu.org/licenses/>. |
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20 **/ |
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21 |
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22 |
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23 #include "../PrecompiledHeaders.h" |
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24 #include "DicomStreamReader.h" |
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25 |
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26 #include "../OrthancException.h" |
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27 |
4304 | 28 #include <cassert> |
29 | |
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30 namespace Orthanc |
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31 { |
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32 static bool IsNormalizationNeeded(const std::string& source, |
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33 ValueRepresentation vr) |
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34 { |
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35 return (!source.empty() && |
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36 (source[source.size() - 1] == ' ' || |
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37 source[source.size() - 1] == '\0') && |
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38 // Normalization only applies to string-based VR |
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39 (vr == ValueRepresentation_ApplicationEntity || |
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40 vr == ValueRepresentation_AgeString || |
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41 vr == ValueRepresentation_CodeString || |
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42 vr == ValueRepresentation_DecimalString || |
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43 vr == ValueRepresentation_IntegerString || |
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44 vr == ValueRepresentation_LongString || |
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45 vr == ValueRepresentation_LongText || |
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46 vr == ValueRepresentation_PersonName || |
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47 vr == ValueRepresentation_ShortString || |
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48 vr == ValueRepresentation_ShortText || |
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49 vr == ValueRepresentation_UniqueIdentifier || |
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50 vr == ValueRepresentation_UnlimitedText)); |
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51 } |
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52 |
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53 |
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54 static void NormalizeValue(std::string& inplace, |
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55 ValueRepresentation vr) |
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56 { |
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57 if (IsNormalizationNeeded(inplace, vr)) |
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58 { |
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59 assert(!inplace.empty()); |
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60 inplace.resize(inplace.size() - 1); |
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61 } |
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62 } |
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63 |
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64 |
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65 static uint16_t ReadUnsignedInteger16(const char* dicom, |
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66 bool littleEndian) |
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67 { |
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68 const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); |
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69 |
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70 if (littleEndian) |
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71 { |
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72 return (static_cast<uint16_t>(p[0]) | |
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73 (static_cast<uint16_t>(p[1]) << 8)); |
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74 } |
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75 else |
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76 { |
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77 return (static_cast<uint16_t>(p[1]) | |
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78 (static_cast<uint16_t>(p[0]) << 8)); |
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79 } |
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80 } |
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81 |
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82 |
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83 static uint32_t ReadUnsignedInteger32(const char* dicom, |
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84 bool littleEndian) |
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85 { |
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86 const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); |
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87 |
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88 if (littleEndian) |
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89 { |
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90 return (static_cast<uint32_t>(p[0]) | |
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91 (static_cast<uint32_t>(p[1]) << 8) | |
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92 (static_cast<uint32_t>(p[2]) << 16) | |
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93 (static_cast<uint32_t>(p[3]) << 24)); |
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94 } |
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95 else |
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96 { |
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97 return (static_cast<uint32_t>(p[3]) | |
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98 (static_cast<uint32_t>(p[2]) << 8) | |
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99 (static_cast<uint32_t>(p[1]) << 16) | |
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100 (static_cast<uint32_t>(p[0]) << 24)); |
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101 } |
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102 } |
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103 |
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104 |
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105 static DicomTag ReadTag(const char* dicom, |
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106 bool littleEndian) |
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107 { |
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108 return DicomTag(ReadUnsignedInteger16(dicom, littleEndian), |
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109 ReadUnsignedInteger16(dicom + 2, littleEndian)); |
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110 } |
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111 |
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112 |
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113 static bool IsShortExplicitTag(ValueRepresentation vr) |
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114 { |
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115 /** |
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116 * Are we in the case of Table 7.1-2? "Data Element with |
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117 * Explicit VR of AE, AS, AT, CS, DA, DS, DT, FL, FD, IS, LO, |
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118 * LT, PN, SH, SL, SS, ST, TM, UI, UL and US" |
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119 * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html#sect_7.1.2 |
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120 **/ |
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121 return (vr == ValueRepresentation_ApplicationEntity /* AE */ || |
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122 vr == ValueRepresentation_AgeString /* AS */ || |
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123 vr == ValueRepresentation_AttributeTag /* AT */ || |
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124 vr == ValueRepresentation_CodeString /* CS */ || |
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125 vr == ValueRepresentation_Date /* DA */ || |
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126 vr == ValueRepresentation_DecimalString /* DS */ || |
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127 vr == ValueRepresentation_DateTime /* DT */ || |
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128 vr == ValueRepresentation_FloatingPointSingle /* FL */ || |
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129 vr == ValueRepresentation_FloatingPointDouble /* FD */ || |
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130 vr == ValueRepresentation_IntegerString /* IS */ || |
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131 vr == ValueRepresentation_LongString /* LO */ || |
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132 vr == ValueRepresentation_LongText /* LT */ || |
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133 vr == ValueRepresentation_PersonName /* PN */ || |
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134 vr == ValueRepresentation_ShortString /* SH */ || |
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135 vr == ValueRepresentation_SignedLong /* SL */ || |
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136 vr == ValueRepresentation_SignedShort /* SS */ || |
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137 vr == ValueRepresentation_ShortText /* ST */ || |
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138 vr == ValueRepresentation_Time /* TM */ || |
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139 vr == ValueRepresentation_UniqueIdentifier /* UI */ || |
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140 vr == ValueRepresentation_UnsignedLong /* UL */ || |
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141 vr == ValueRepresentation_UnsignedShort /* US */); |
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142 } |
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143 |
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144 |
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145 bool DicomStreamReader::IsLittleEndian() const |
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146 { |
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147 return (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit); |
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148 } |
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149 |
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150 |
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151 void DicomStreamReader::HandlePreamble(IVisitor& visitor, |
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152 const std::string& block) |
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153 { |
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154 assert(block.size() == 144u); |
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155 assert(reader_.GetProcessedBytes() == 144u); |
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156 |
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157 /** |
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158 * The "DICOM file meta information" is always encoded using |
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159 * "Explicit VR Little Endian Transfer Syntax" |
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160 * http://dicom.nema.org/medical/dicom/current/output/chtml/part10/chapter_7.html |
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161 **/ |
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162 if (block[128] != 'D' || |
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163 block[129] != 'I' || |
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164 block[130] != 'C' || |
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165 block[131] != 'M' || |
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166 ReadTag(block.c_str() + 132, true) != DicomTag(0x0002, 0x0000) || |
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167 block[136] != 'U' || |
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168 block[137] != 'L' || |
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169 ReadUnsignedInteger16(block.c_str() + 138, true) != 4) |
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170 { |
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171 throw OrthancException(ErrorCode_BadFileFormat); |
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172 } |
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173 |
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174 uint32_t length = ReadUnsignedInteger32(block.c_str() + 140, true); |
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175 |
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176 reader_.Schedule(length); |
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177 state_ = State_MetaHeader; |
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178 } |
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179 |
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180 |
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181 void DicomStreamReader::HandleMetaHeader(IVisitor& visitor, |
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182 const std::string& block) |
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183 { |
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184 size_t pos = 0; |
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185 const char* p = block.c_str(); |
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186 |
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187 bool hasTransferSyntax = false; |
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188 |
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189 while (pos + 8 <= block.size()) |
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190 { |
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191 DicomTag tag = ReadTag(p + pos, true); |
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192 |
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193 ValueRepresentation vr = StringToValueRepresentation(std::string(p + pos + 4, 2), true); |
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194 |
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195 if (IsShortExplicitTag(vr)) |
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196 { |
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197 uint16_t length = ReadUnsignedInteger16(p + pos + 6, true); |
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198 |
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199 std::string value; |
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200 value.assign(p + pos + 8, length); |
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201 NormalizeValue(value, vr); |
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202 |
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203 if (tag.GetGroup() == 0x0002) |
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204 { |
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205 visitor.VisitMetaHeaderTag(tag, vr, value); |
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206 } |
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207 |
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208 if (tag == DICOM_TAG_TRANSFER_SYNTAX_UID) |
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209 { |
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210 if (LookupTransferSyntax(transferSyntax_, value)) |
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211 { |
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212 hasTransferSyntax = true; |
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213 } |
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214 else |
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215 { |
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216 throw OrthancException(ErrorCode_NotImplemented, "Unsupported transfer syntax: " + value); |
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217 } |
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218 } |
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219 |
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220 pos += length + 8; |
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221 } |
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222 else if (pos + 12 <= block.size()) |
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223 { |
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224 uint16_t reserved = ReadUnsignedInteger16(p + pos + 6, true); |
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225 if (reserved != 0) |
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226 { |
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227 break; |
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228 } |
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229 |
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230 uint32_t length = ReadUnsignedInteger32(p + pos + 8, true); |
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231 |
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232 if (tag.GetGroup() == 0x0002) |
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233 { |
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234 std::string value; |
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235 value.assign(p + pos + 12, length); |
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236 NormalizeValue(value, vr); |
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237 visitor.VisitMetaHeaderTag(tag, vr, value); |
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238 } |
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239 |
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240 pos += length + 12; |
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241 } |
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242 } |
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243 |
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244 if (pos != block.size()) |
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245 { |
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246 throw OrthancException(ErrorCode_BadFileFormat); |
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247 } |
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248 |
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249 if (!hasTransferSyntax) |
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250 { |
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251 throw OrthancException(ErrorCode_BadFileFormat, "DICOM file meta-header without transfer syntax UID"); |
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252 } |
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253 |
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254 visitor.VisitTransferSyntax(transferSyntax_); |
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255 |
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256 reader_.Schedule(8); |
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257 state_ = State_DatasetTag; |
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258 } |
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259 |
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260 |
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261 void DicomStreamReader::HandleDatasetTag(const std::string& block, |
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262 const DicomTag& untilTag) |
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263 { |
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264 static const DicomTag DICOM_TAG_SEQUENCE_ITEM(0xfffe, 0xe000); |
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265 static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_ITEM(0xfffe, 0xe00d); |
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266 static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE(0xfffe, 0xe0dd); |
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267 |
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268 assert(block.size() == 8u); |
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269 |
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270 const bool littleEndian = IsLittleEndian(); |
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271 DicomTag tag = ReadTag(block.c_str(), littleEndian); |
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272 |
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273 if (sequenceDepth_ == 0 && |
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274 tag >= untilTag) |
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275 { |
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276 state_ = State_Done; |
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277 return; |
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278 } |
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279 |
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280 if (tag == DICOM_TAG_SEQUENCE_ITEM || |
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281 tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM || |
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282 tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) |
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283 { |
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284 // The special sequence items are encoded like "Implicit VR" |
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285 uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, littleEndian); |
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286 |
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287 if (tag == DICOM_TAG_SEQUENCE_ITEM) |
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288 { |
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289 if (length == 0xffffffffu) |
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290 { |
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291 // Undefined length: Need to loop over the tags of the nested dataset |
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292 reader_.Schedule(8); |
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293 state_ = State_DatasetTag; |
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294 } |
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295 else |
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296 { |
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297 // Explicit length: Can skip the full sequence at once |
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298 reader_.Schedule(length); |
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299 state_ = State_DatasetValue; |
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300 } |
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301 } |
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302 else if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM || |
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303 tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) |
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304 { |
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305 if (length != 0 || |
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306 sequenceDepth_ == 0) |
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307 { |
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308 throw OrthancException(ErrorCode_BadFileFormat); |
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309 } |
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310 |
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311 if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE) |
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312 { |
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313 sequenceDepth_ --; |
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314 } |
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315 |
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316 reader_.Schedule(8); |
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317 state_ = State_DatasetTag; |
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318 } |
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319 else |
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320 { |
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321 throw OrthancException(ErrorCode_InternalError); |
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322 } |
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323 } |
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324 else |
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325 { |
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326 ValueRepresentation vr = ValueRepresentation_Unknown; |
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327 |
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328 if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit) |
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329 { |
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330 if (sequenceDepth_ == 0) |
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331 { |
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332 danglingTag_ = tag; |
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333 danglingVR_ = vr; |
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334 } |
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335 |
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336 uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, true /* little endian */); |
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337 HandleDatasetExplicitLength(length); |
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338 } |
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339 else |
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340 { |
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341 // This in an explicit transfer syntax |
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342 |
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343 vr = StringToValueRepresentation( |
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344 std::string(block.c_str() + 4, 2), false /* ignore unknown VR */); |
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345 |
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346 if (vr == ValueRepresentation_Sequence) |
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347 { |
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348 sequenceDepth_ ++; |
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349 reader_.Schedule(4); |
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350 state_ = State_SequenceExplicitLength; |
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351 } |
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352 else if (IsShortExplicitTag(vr)) |
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353 { |
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354 uint16_t length = ReadUnsignedInteger16(block.c_str() + 6, littleEndian); |
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355 |
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356 reader_.Schedule(length); |
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357 state_ = State_DatasetValue; |
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358 } |
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359 else |
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360 { |
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361 uint16_t reserved = ReadUnsignedInteger16(block.c_str() + 6, littleEndian); |
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362 if (reserved != 0) |
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363 { |
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364 throw OrthancException(ErrorCode_BadFileFormat); |
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365 } |
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366 |
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367 reader_.Schedule(4); |
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368 state_ = State_DatasetExplicitLength; |
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369 } |
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370 |
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371 if (sequenceDepth_ == 0) |
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372 { |
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373 danglingTag_ = tag; |
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374 danglingVR_ = vr; |
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375 } |
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376 } |
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377 } |
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378 } |
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379 |
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380 |
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381 void DicomStreamReader::HandleDatasetExplicitLength(uint32_t length) |
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382 { |
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383 if (length == 0xffffffffu) |
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384 { |
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385 /** |
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386 * This is the case of pixel data with compressed transfer |
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387 * syntaxes. Schedule the reading of the first tag of the |
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388 * nested dataset. |
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389 * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html |
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390 **/ |
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391 state_ = State_DatasetTag; |
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392 reader_.Schedule(8); |
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393 sequenceDepth_ ++; |
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394 } |
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395 else |
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396 { |
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397 reader_.Schedule(length); |
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398 state_ = State_DatasetValue; |
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399 } |
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400 } |
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401 |
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402 |
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403 void DicomStreamReader::HandleDatasetExplicitLength(const std::string& block) |
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404 { |
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405 assert(block.size() == 4); |
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406 |
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407 uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); |
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408 HandleDatasetExplicitLength(length); |
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409 } |
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410 |
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411 |
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412 void DicomStreamReader::HandleSequenceExplicitLength(const std::string& block) |
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413 { |
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414 assert(block.size() == 4); |
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415 |
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416 uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian()); |
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417 if (length == 0xffffffffu) |
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418 { |
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419 state_ = State_DatasetTag; |
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420 reader_.Schedule(8); |
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421 } |
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422 else |
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423 { |
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424 reader_.Schedule(length); |
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425 state_ = State_SequenceExplicitValue; |
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426 } |
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427 } |
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428 |
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429 |
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430 void DicomStreamReader::HandleSequenceExplicitValue() |
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431 { |
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432 if (sequenceDepth_ == 0) |
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433 { |
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434 throw OrthancException(ErrorCode_InternalError); |
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435 } |
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436 |
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437 sequenceDepth_ --; |
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438 |
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439 state_ = State_DatasetTag; |
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440 reader_.Schedule(8); |
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441 } |
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442 |
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443 |
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444 void DicomStreamReader::HandleDatasetValue(IVisitor& visitor, |
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445 const std::string& block) |
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446 { |
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447 if (sequenceDepth_ == 0) |
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448 { |
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449 bool c; |
4221
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450 |
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451 if (IsNormalizationNeeded(block, danglingVR_)) |
4220
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452 { |
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453 std::string s(block.begin(), block.end() - 1); |
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454 c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, s, IsLittleEndian()); |
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455 } |
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456 else |
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457 { |
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458 c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, block, IsLittleEndian()); |
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459 } |
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460 |
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461 if (!c) |
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462 { |
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463 state_ = State_Done; |
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464 return; |
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465 } |
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466 } |
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467 |
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468 reader_.Schedule(8); |
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469 state_ = State_DatasetTag; |
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470 } |
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471 |
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472 |
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473 DicomStreamReader::DicomStreamReader(std::istream& stream) : |
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474 reader_(stream), |
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475 state_(State_Preamble), |
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476 transferSyntax_(DicomTransferSyntax_LittleEndianImplicit), // Dummy |
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477 danglingTag_(0x0000, 0x0000), // Dummy |
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478 danglingVR_(ValueRepresentation_Unknown), // Dummy |
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479 sequenceDepth_(0) |
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480 { |
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481 reader_.Schedule(128 /* empty header */ + |
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482 4 /* "DICM" magic value */ + |
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483 4 /* (0x0002, 0x0000) tag */ + |
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484 2 /* value representation of (0x0002, 0x0000) == "UL" */ + |
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485 2 /* length of "UL" value == 4 */ + |
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486 4 /* actual length of the meta-header */); |
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487 } |
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488 |
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489 |
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490 void DicomStreamReader::Consume(IVisitor& visitor, |
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491 const DicomTag& untilTag) |
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492 { |
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493 while (state_ != State_Done) |
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494 { |
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495 std::string block; |
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496 if (reader_.Read(block)) |
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497 { |
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498 switch (state_) |
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499 { |
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500 case State_Preamble: |
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501 HandlePreamble(visitor, block); |
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502 break; |
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503 |
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504 case State_MetaHeader: |
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505 HandleMetaHeader(visitor, block); |
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506 break; |
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507 |
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508 case State_DatasetTag: |
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509 HandleDatasetTag(block, untilTag); |
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510 break; |
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511 |
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512 case State_DatasetExplicitLength: |
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513 HandleDatasetExplicitLength(block); |
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514 break; |
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515 |
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516 case State_SequenceExplicitLength: |
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517 HandleSequenceExplicitLength(block); |
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518 break; |
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519 |
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520 case State_SequenceExplicitValue: |
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521 HandleSequenceExplicitValue(); |
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522 break; |
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523 |
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524 case State_DatasetValue: |
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525 HandleDatasetValue(visitor, block); |
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526 break; |
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527 |
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528 default: |
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529 throw OrthancException(ErrorCode_InternalError); |
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530 } |
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531 } |
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532 else |
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533 { |
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534 return; // No more data in the stream |
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535 } |
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536 } |
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537 } |
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538 |
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539 |
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540 void DicomStreamReader::Consume(IVisitor& visitor) |
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541 { |
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542 DicomTag untilTag(0xffff, 0xffff); |
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543 Consume(visitor, untilTag); |
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544 } |
4277
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545 |
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546 |
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547 bool DicomStreamReader::IsDone() const |
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548 { |
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549 return (state_ == State_Done); |
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550 } |
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551 |
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552 |
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553 uint64_t DicomStreamReader::GetProcessedBytes() const |
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554 { |
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555 return reader_.GetProcessedBytes(); |
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556 } |
4220
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557 } |