Mercurial > hg > orthanc
annotate OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.cpp @ 5834:79a497908b04 attach-custom-data tip
merged find-refactoring -> attach-custom-data
author | Alain Mazy <am@orthanc.team> |
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date | Wed, 09 Oct 2024 11:06:20 +0200 |
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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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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8 * |
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9 * This program is free software: you can redistribute it and/or |
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10 * modify it under the terms of the GNU Lesser General Public License |
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11 * as published by the Free Software Foundation, either version 3 of |
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12 * the License, or (at your option) any later version. |
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13 * |
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14 * This program is distributed in the hope that it will be useful, but |
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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17 * Lesser General Public License for more details. |
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18 * |
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19 * You should have received a copy of the GNU Lesser General Public |
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20 * License along with this program. If not, see |
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21 * <http://www.gnu.org/licenses/>. |
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22 **/ |
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23 |
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24 |
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25 #include "../../PrecompiledHeaders.h" |
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26 #include "DicomFrameIndex.h" |
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27 |
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28 #include "../../OrthancException.h" |
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29 #include "../../DicomFormat/DicomImageInformation.h" |
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30 #include "../FromDcmtkBridge.h" |
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31 #include "../../Endianness.h" |
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32 #include "DicomImageDecoder.h" |
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33 |
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34 #include <boost/lexical_cast.hpp> |
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35 |
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36 #include <dcmtk/dcmdata/dcdeftag.h> |
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37 #include <dcmtk/dcmdata/dcpxitem.h> |
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38 #include <dcmtk/dcmdata/dcpixseq.h> |
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39 |
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40 namespace Orthanc |
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41 { |
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42 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex |
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43 { |
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44 private: |
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45 DcmPixelSequence* pixelSequence_; |
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46 std::vector<DcmPixelItem*> startFragment_; |
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47 std::vector<unsigned int> countFragments_; |
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48 std::vector<unsigned int> frameSize_; |
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49 |
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50 void GetOffsetTable(std::vector<uint32_t>& table) |
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51 { |
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52 DcmPixelItem* item = NULL; |
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53 if (!pixelSequence_->getItem(item, 0).good() || |
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54 item == NULL) |
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55 { |
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56 throw OrthancException(ErrorCode_BadFileFormat); |
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57 } |
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58 |
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59 uint32_t length = item->getLength(); |
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60 if (length == 0) |
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61 { |
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62 // Degenerate case: Empty offset table means only one frame |
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63 // that overlaps all the fragments |
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64 table.resize(1); |
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65 table[0] = 0; |
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66 return; |
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67 } |
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68 |
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69 if (length % 4 != 0) |
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70 { |
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71 // Error: Each fragment is index with 4 bytes (uint32_t) |
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72 throw OrthancException(ErrorCode_BadFileFormat); |
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73 } |
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74 |
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75 uint8_t* content = NULL; |
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76 if (!item->getUint8Array(content).good() || |
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77 content == NULL) |
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78 { |
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79 throw OrthancException(ErrorCode_InternalError); |
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80 } |
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81 |
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82 table.resize(length / 4); |
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83 |
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84 // The offset table is always in little endian in the DICOM |
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85 // file. Swap it to host endianness if needed. |
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86 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content); |
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87 for (size_t i = 0; i < table.size(); i++, offset++) |
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88 { |
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89 table[i] = le32toh(*offset); |
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90 } |
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91 } |
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92 |
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93 |
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94 public: |
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95 FragmentIndex(DcmPixelSequence* pixelSequence, |
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96 unsigned int countFrames) : |
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97 pixelSequence_(pixelSequence) |
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98 { |
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99 assert(pixelSequence != NULL); |
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100 |
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101 startFragment_.resize(countFrames); |
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102 countFragments_.resize(countFrames); |
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103 frameSize_.resize(countFrames); |
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104 |
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105 // The first fragment corresponds to the offset table |
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106 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card()); |
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107 if (countFragments < countFrames + 1) |
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108 { |
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109 throw OrthancException(ErrorCode_BadFileFormat); |
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110 } |
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111 |
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112 if (countFragments == countFrames + 1) |
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113 { |
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114 // Simple case: There is one fragment per frame. |
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115 |
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116 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table |
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117 if (fragment == NULL) |
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118 { |
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119 throw OrthancException(ErrorCode_InternalError); |
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120 } |
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121 |
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122 for (unsigned int i = 0; i < countFrames; i++) |
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123 { |
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124 fragment = pixelSequence_->nextInContainer(fragment); |
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125 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment); |
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126 frameSize_[i] = fragment->getLength(); |
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127 countFragments_[i] = 1; |
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128 } |
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129 |
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130 return; |
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131 } |
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132 |
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133 // Parse the offset table |
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134 std::vector<uint32_t> offsetOfFrame; |
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135 GetOffsetTable(offsetOfFrame); |
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136 |
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137 if (offsetOfFrame.size() != countFrames || |
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138 offsetOfFrame[0] != 0) |
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139 { |
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140 throw OrthancException(ErrorCode_BadFileFormat); |
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141 } |
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142 |
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143 // Loop over the fragments (ignoring the offset table). This is |
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144 // an alternative, faster implementation to DCMTK's |
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145 // "DcmCodec::determineStartFragment()". |
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146 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); |
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147 if (fragment == NULL) |
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148 { |
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149 throw OrthancException(ErrorCode_InternalError); |
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150 } |
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151 |
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152 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table |
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153 if (fragment == NULL) |
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154 { |
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155 throw OrthancException(ErrorCode_InternalError); |
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156 } |
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157 |
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158 uint32_t offset = 0; |
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159 unsigned int currentFrame = 0; |
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160 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment); |
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161 |
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162 unsigned int currentFragment = 1; |
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163 while (fragment != NULL) |
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164 { |
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165 if (currentFrame + 1 < countFrames && |
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166 offset == offsetOfFrame[currentFrame + 1]) |
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167 { |
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168 currentFrame += 1; |
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169 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment); |
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170 } |
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171 |
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172 frameSize_[currentFrame] += fragment->getLength(); |
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173 countFragments_[currentFrame]++; |
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174 |
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175 // 8 bytes = overhead for the item tag and length field |
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176 offset += fragment->getLength() + 8; |
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177 |
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178 currentFragment++; |
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179 fragment = pixelSequence_->nextInContainer(fragment); |
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180 } |
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181 |
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182 if (currentFragment != countFragments || |
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183 currentFrame + 1 != countFrames || |
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184 fragment != NULL) |
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185 { |
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186 throw OrthancException(ErrorCode_BadFileFormat); |
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187 } |
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188 |
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189 assert(startFragment_.size() == countFragments_.size() && |
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190 startFragment_.size() == frameSize_.size()); |
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191 } |
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192 |
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193 |
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194 virtual void GetRawFrame(std::string& frame, |
4200 | 195 unsigned int index) const ORTHANC_OVERRIDE |
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196 { |
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197 if (index >= startFragment_.size()) |
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198 { |
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199 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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200 } |
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201 |
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202 frame.resize(frameSize_[index]); |
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203 if (frame.size() == 0) |
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204 { |
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205 return; |
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206 } |
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207 |
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208 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]); |
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209 |
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210 size_t offset = 0; |
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211 DcmPixelItem* fragment = startFragment_[index]; |
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212 for (unsigned int i = 0; i < countFragments_[index]; i++) |
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213 { |
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214 uint8_t* content = NULL; |
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215 if (!fragment->getUint8Array(content).good() || |
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216 content == NULL) |
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217 { |
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218 throw OrthancException(ErrorCode_InternalError); |
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219 } |
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220 |
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221 assert(offset + fragment->getLength() <= frame.size()); |
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222 |
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223 memcpy(target + offset, content, fragment->getLength()); |
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224 offset += fragment->getLength(); |
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225 |
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226 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment)); |
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227 } |
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228 } |
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229 }; |
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230 |
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231 |
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232 |
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233 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex |
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234 { |
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235 private: |
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236 uint8_t* pixelData_; |
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237 size_t frameSize_; |
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238 |
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239 public: |
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240 UncompressedIndex(DcmDataset& dataset, |
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241 unsigned int countFrames, |
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242 size_t frameSize) : |
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243 pixelData_(NULL), |
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244 frameSize_(frameSize) |
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245 { |
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246 size_t size = 0; |
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247 |
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248 DcmElement* e; |
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249 if (dataset.findAndGetElement(DCM_PixelData, e).good() && |
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250 e != NULL) |
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251 { |
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252 size = e->getLength(); |
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253 |
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254 if (size > 0) |
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255 { |
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256 pixelData_ = NULL; |
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257 if (!e->getUint8Array(pixelData_).good() || |
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258 pixelData_ == NULL) |
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259 { |
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260 throw OrthancException(ErrorCode_BadFileFormat); |
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261 } |
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262 } |
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263 } |
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264 |
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265 if (size < frameSize_ * countFrames) |
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266 { |
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267 throw OrthancException(ErrorCode_BadFileFormat); |
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268 } |
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269 } |
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270 |
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271 virtual void GetRawFrame(std::string& frame, |
4200 | 272 unsigned int index) const ORTHANC_OVERRIDE |
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273 { |
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274 frame.resize(frameSize_); |
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275 if (frameSize_ > 0) |
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276 { |
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277 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_); |
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278 } |
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279 } |
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280 }; |
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281 |
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282 |
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283 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex |
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284 { |
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285 private: |
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286 std::string pixelData_; |
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287 size_t frameSize_; |
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288 |
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289 public: |
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290 PsmctRle1Index(DcmDataset& dataset, |
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291 unsigned int countFrames, |
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292 size_t frameSize) : |
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293 frameSize_(frameSize) |
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294 { |
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295 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) || |
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296 pixelData_.size() < frameSize * countFrames) |
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297 { |
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298 throw OrthancException(ErrorCode_BadFileFormat); |
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299 } |
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300 } |
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301 |
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302 virtual void GetRawFrame(std::string& frame, |
4200 | 303 unsigned int index) const ORTHANC_OVERRIDE |
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304 { |
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305 frame.resize(frameSize_); |
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306 if (frameSize_ > 0) |
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307 { |
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308 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_); |
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309 } |
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310 } |
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311 }; |
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312 |
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313 |
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314 unsigned int DicomFrameIndex::GetFramesCount(DcmDataset& dicom) |
1950
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315 { |
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316 DicomTransferSyntax transferSyntax; |
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317 if (FromDcmtkBridge::LookupOrthancTransferSyntax(transferSyntax, dicom) && |
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318 (transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtMainLevel || |
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319 transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtHighLevel || |
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320 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_1 || |
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321 transferSyntax == DicomTransferSyntax_MPEG4BDcompatibleHighProfileLevel4_1 || |
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322 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For2DVideo || |
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323 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For3DVideo || |
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324 transferSyntax == DicomTransferSyntax_MPEG4StereoHighProfileLevel4_2 || |
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325 transferSyntax == DicomTransferSyntax_HEVCMainProfileLevel5_1 || |
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326 transferSyntax == DicomTransferSyntax_HEVCMain10ProfileLevel5_1)) |
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327 { |
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328 /** |
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329 * Fixes an issue that was present from Orthanc 1.6.0 until |
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330 * 1.8.0 for the special case of the videos: In a video, the |
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331 * number of frames doesn't correspond to the number of |
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332 * fragments. We consider that there is one single frame (the |
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333 * video itself). |
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334 **/ |
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335 return 1; |
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336 } |
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337 |
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338 const char* tmp = NULL; |
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339 if (!dicom.findAndGetString(DCM_NumberOfFrames, tmp).good() || |
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340 tmp == NULL) |
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341 { |
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342 return 1; |
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343 } |
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344 |
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345 int count = -1; |
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346 try |
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347 { |
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348 count = boost::lexical_cast<int>(tmp); |
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349 } |
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350 catch (boost::bad_lexical_cast&) |
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351 { |
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352 } |
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353 |
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354 if (count < 0) |
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355 { |
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356 throw OrthancException(ErrorCode_BadFileFormat); |
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357 } |
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358 else |
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359 { |
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360 return static_cast<unsigned int>(count); |
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361 } |
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362 } |
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363 |
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364 |
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365 DicomFrameIndex::DicomFrameIndex(DcmDataset& dicom) |
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366 { |
1956 | 367 countFrames_ = GetFramesCount(dicom); |
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368 if (countFrames_ == 0) |
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369 { |
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370 // The image has no frame. No index is to be built. |
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371 return; |
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372 } |
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373 |
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374 // Extract information about the image structure |
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375 DicomMap tags; |
4137
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376 std::set<DicomTag> ignoreTagLength; |
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377 FromDcmtkBridge::ExtractDicomSummary(tags, dicom, DicomImageInformation::GetUsefulTagLength(), ignoreTagLength); |
1924
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378 |
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379 DicomImageInformation information(tags); |
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380 |
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381 // Test whether this image is composed of a sequence of fragments |
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382 if (dicom.tagExists(DCM_PixelData)) |
4184
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383 { |
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384 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dicom); |
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385 if (pixelSequence != NULL) |
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386 { |
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387 index_.reset(new FragmentIndex(pixelSequence, countFrames_)); |
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388 } |
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389 else |
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390 { |
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391 // Access to the raw pixel data |
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392 index_.reset(new UncompressedIndex(dicom, countFrames_, information.GetFrameSize())); |
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393 } |
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394 } |
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395 else if (DicomImageDecoder::IsPsmctRle1(dicom)) |
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396 { |
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397 index_.reset(new PsmctRle1Index(dicom, countFrames_, information.GetFrameSize())); |
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398 } |
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399 } |
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400 |
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401 |
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402 void DicomFrameIndex::GetRawFrame(std::string& frame, |
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403 unsigned int index) const |
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404 { |
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405 if (index >= countFrames_) |
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406 { |
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407 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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408 } |
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409 else if (index_.get() != NULL) |
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410 { |
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411 return index_->GetRawFrame(frame, index); |
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412 } |
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413 else |
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414 { |
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Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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415 throw OrthancException(ErrorCode_BadFileFormat, "Cannot access a raw frame"); |
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416 } |
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417 } |
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418 } |