Mercurial > hg > orthanc
annotate OrthancServer/Internals/DicomFrameIndex.cpp @ 2271:fc260803b5df
Merged in Barnerd/orthanc-1/Barnerd/fix-build-with-libressl-libressl-comp-1488028354841 (pull request #5)
Fix build with LibreSSL
author | Sébastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 28 Feb 2017 08:28:37 +0000 |
parents | a3a65de1840f |
children | b8969010b534 |
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 Osimis, 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 General Public License as |
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9 * published by the Free Software Foundation, either version 3 of the |
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10 * License, or (at your option) any later version. |
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11 * |
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12 * In addition, as a special exception, the copyright holders of this |
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13 * program give permission to link the code of its release with the |
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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15 * that use the same license as the "OpenSSL" library), and distribute |
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16 * the linked executables. You must obey the GNU General Public License |
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17 * in all respects for all of the code used other than "OpenSSL". If you |
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18 * modify file(s) with this exception, you may extend this exception to |
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19 * your version of the file(s), but you are not obligated to do so. If |
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20 * you do not wish to do so, delete this exception statement from your |
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21 * version. If you delete this exception statement from all source files |
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22 * in the program, then also delete it here. |
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23 * |
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24 * This program is distributed in the hope that it will be useful, but |
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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27 * General Public License for more details. |
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28 * |
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29 * You should have received a copy of the GNU General Public License |
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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31 **/ |
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32 |
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33 |
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34 #include "../PrecompiledHeadersServer.h" |
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35 #include "DicomFrameIndex.h" |
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36 |
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37 #include "../../Core/OrthancException.h" |
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38 #include "../../Core/DicomFormat/DicomImageInformation.h" |
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39 #include "../FromDcmtkBridge.h" |
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40 #include "../OrthancInitialization.h" |
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41 #include "../../Core/Endianness.h" |
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42 #include "DicomImageDecoder.h" |
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43 |
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44 #include <boost/lexical_cast.hpp> |
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45 |
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46 #include <dcmtk/dcmdata/dcdeftag.h> |
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47 #include <dcmtk/dcmdata/dcpxitem.h> |
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48 #include <dcmtk/dcmdata/dcpixseq.h> |
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49 |
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50 namespace Orthanc |
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51 { |
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52 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex |
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53 { |
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54 private: |
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55 DcmPixelSequence* pixelSequence_; |
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56 std::vector<DcmPixelItem*> startFragment_; |
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57 std::vector<unsigned int> countFragments_; |
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58 std::vector<unsigned int> frameSize_; |
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59 |
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60 void GetOffsetTable(std::vector<uint32_t>& table) |
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61 { |
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62 DcmPixelItem* item = NULL; |
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63 if (!pixelSequence_->getItem(item, 0).good() || |
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64 item == NULL) |
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65 { |
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66 throw OrthancException(ErrorCode_BadFileFormat); |
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67 } |
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68 |
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69 uint32_t length = item->getLength(); |
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70 if (length == 0) |
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71 { |
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72 table.clear(); |
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73 return; |
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74 } |
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75 |
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76 if (length % 4 != 0) |
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77 { |
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78 // Error: Each fragment is index with 4 bytes (uint32_t) |
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79 throw OrthancException(ErrorCode_BadFileFormat); |
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80 } |
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81 |
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82 uint8_t* content = NULL; |
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83 if (!item->getUint8Array(content).good() || |
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84 content == NULL) |
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85 { |
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86 throw OrthancException(ErrorCode_InternalError); |
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87 } |
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88 |
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89 table.resize(length / 4); |
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90 |
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91 // The offset table is always in little endian in the DICOM |
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92 // file. Swap it to host endianness if needed. |
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93 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content); |
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94 for (size_t i = 0; i < table.size(); i++, offset++) |
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95 { |
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96 table[i] = le32toh(*offset); |
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97 } |
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98 } |
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99 |
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100 |
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101 public: |
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102 FragmentIndex(DcmPixelSequence* pixelSequence, |
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103 unsigned int countFrames) : |
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104 pixelSequence_(pixelSequence) |
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105 { |
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106 assert(pixelSequence != NULL); |
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107 |
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108 startFragment_.resize(countFrames); |
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109 countFragments_.resize(countFrames); |
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110 frameSize_.resize(countFrames); |
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111 |
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112 // The first fragment corresponds to the offset table |
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113 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card()); |
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114 if (countFragments < countFrames + 1) |
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115 { |
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116 throw OrthancException(ErrorCode_BadFileFormat); |
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117 } |
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118 |
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119 if (countFragments == countFrames + 1) |
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120 { |
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121 // Simple case: There is one fragment per frame. |
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122 |
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123 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table |
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124 if (fragment == NULL) |
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125 { |
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126 throw OrthancException(ErrorCode_InternalError); |
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127 } |
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128 |
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129 for (unsigned int i = 0; i < countFrames; i++) |
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130 { |
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131 fragment = pixelSequence_->nextInContainer(fragment); |
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132 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment); |
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133 frameSize_[i] = fragment->getLength(); |
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134 countFragments_[i] = 1; |
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135 } |
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136 |
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137 return; |
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138 } |
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139 |
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140 // Parse the offset table |
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141 std::vector<uint32_t> offsetOfFrame; |
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142 GetOffsetTable(offsetOfFrame); |
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143 |
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144 if (offsetOfFrame.size() != countFrames || |
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145 offsetOfFrame[0] != 0) |
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146 { |
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147 throw OrthancException(ErrorCode_BadFileFormat); |
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148 } |
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149 |
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150 |
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151 // Loop over the fragments (ignoring the offset table). This is |
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152 // an alternative, faster implementation to DCMTK's |
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153 // "DcmCodec::determineStartFragment()". |
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154 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); |
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155 if (fragment == NULL) |
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156 { |
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157 throw OrthancException(ErrorCode_InternalError); |
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158 } |
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159 |
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160 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table |
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161 if (fragment == NULL) |
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162 { |
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163 throw OrthancException(ErrorCode_InternalError); |
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164 } |
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165 |
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166 uint32_t offset = 0; |
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167 unsigned int currentFrame = 0; |
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168 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment); |
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169 |
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170 unsigned int currentFragment = 1; |
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171 while (fragment != NULL) |
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172 { |
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173 if (currentFrame + 1 < countFrames && |
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174 offset == offsetOfFrame[currentFrame + 1]) |
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175 { |
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176 currentFrame += 1; |
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177 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment); |
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178 } |
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179 |
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180 frameSize_[currentFrame] += fragment->getLength(); |
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181 countFragments_[currentFrame]++; |
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182 |
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183 // 8 bytes = overhead for the item tag and length field |
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184 offset += fragment->getLength() + 8; |
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185 |
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186 currentFragment++; |
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187 fragment = pixelSequence_->nextInContainer(fragment); |
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188 } |
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189 |
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190 if (currentFragment != countFragments || |
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191 currentFrame + 1 != countFrames || |
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192 fragment != NULL) |
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193 { |
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194 throw OrthancException(ErrorCode_BadFileFormat); |
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195 } |
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196 |
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197 assert(startFragment_.size() == countFragments_.size() && |
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198 startFragment_.size() == frameSize_.size()); |
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199 } |
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200 |
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201 |
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202 virtual void GetRawFrame(std::string& frame, |
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203 unsigned int index) const |
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204 { |
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205 if (index >= startFragment_.size()) |
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206 { |
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207 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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208 } |
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209 |
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210 frame.resize(frameSize_[index]); |
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211 if (frame.size() == 0) |
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212 { |
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213 return; |
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214 } |
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215 |
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216 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]); |
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217 |
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218 size_t offset = 0; |
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219 DcmPixelItem* fragment = startFragment_[index]; |
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220 for (unsigned int i = 0; i < countFragments_[index]; i++) |
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221 { |
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222 uint8_t* content = NULL; |
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223 if (!fragment->getUint8Array(content).good() || |
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224 content == NULL) |
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225 { |
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226 throw OrthancException(ErrorCode_InternalError); |
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227 } |
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228 |
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229 assert(offset + fragment->getLength() <= frame.size()); |
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230 |
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231 memcpy(target + offset, content, fragment->getLength()); |
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232 offset += fragment->getLength(); |
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233 |
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234 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment)); |
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235 } |
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236 } |
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237 }; |
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238 |
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239 |
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240 |
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241 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex |
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242 { |
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243 private: |
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244 uint8_t* pixelData_; |
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245 size_t frameSize_; |
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246 |
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247 public: |
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248 UncompressedIndex(DcmDataset& dataset, |
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249 unsigned int countFrames, |
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250 size_t frameSize) : |
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251 pixelData_(NULL), |
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252 frameSize_(frameSize) |
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253 { |
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254 size_t size = 0; |
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255 |
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256 DcmElement* e; |
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257 if (dataset.findAndGetElement(DCM_PixelData, e).good() && |
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258 e != NULL) |
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259 { |
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260 size = e->getLength(); |
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261 |
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262 if (size > 0) |
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263 { |
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264 pixelData_ = NULL; |
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265 if (!e->getUint8Array(pixelData_).good() || |
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266 pixelData_ == NULL) |
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267 { |
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268 throw OrthancException(ErrorCode_BadFileFormat); |
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269 } |
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270 } |
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271 } |
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272 |
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273 if (size < frameSize_ * countFrames) |
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274 { |
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275 throw OrthancException(ErrorCode_BadFileFormat); |
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276 } |
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277 } |
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278 |
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279 virtual void GetRawFrame(std::string& frame, |
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280 unsigned int index) const |
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281 { |
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282 frame.resize(frameSize_); |
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283 if (frameSize_ > 0) |
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284 { |
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285 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_); |
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286 } |
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287 } |
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288 }; |
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289 |
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290 |
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291 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex |
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292 { |
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293 private: |
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294 std::string pixelData_; |
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295 size_t frameSize_; |
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296 |
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297 public: |
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298 PsmctRle1Index(DcmDataset& dataset, |
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299 unsigned int countFrames, |
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300 size_t frameSize) : |
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301 frameSize_(frameSize) |
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302 { |
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303 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) || |
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304 pixelData_.size() < frameSize * countFrames) |
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305 { |
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306 throw OrthancException(ErrorCode_BadFileFormat); |
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307 } |
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308 } |
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309 |
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310 virtual void GetRawFrame(std::string& frame, |
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311 unsigned int index) const |
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312 { |
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313 frame.resize(frameSize_); |
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314 if (frameSize_ > 0) |
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315 { |
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316 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_); |
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317 } |
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318 } |
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319 }; |
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320 |
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321 |
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322 |
1956 | 323 bool DicomFrameIndex::IsVideo(DcmFileFormat& dicom) |
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324 { |
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325 // Retrieve the transfer syntax from the DICOM header |
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326 const char* value = NULL; |
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327 if (!dicom.getMetaInfo()->findAndGetString(DCM_TransferSyntaxUID, value).good() || |
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328 value == NULL) |
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329 { |
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330 return false; |
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331 } |
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332 |
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333 const std::string transferSyntax(value); |
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334 |
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335 // Video standards supported in DICOM 2016a |
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336 // http://dicom.nema.org/medical/dicom/2016a/output/html/part05.html |
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337 if (transferSyntax == "1.2.840.10008.1.2.4.100" || // MPEG2 MP@ML option of ISO/IEC MPEG2 |
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338 transferSyntax == "1.2.840.10008.1.2.4.101" || // MPEG2 MP@HL option of ISO/IEC MPEG2 |
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339 transferSyntax == "1.2.840.10008.1.2.4.102" || // MPEG-4 AVC/H.264 High Profile / Level 4.1 of ITU-T H.264 |
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340 transferSyntax == "1.2.840.10008.1.2.4.103" || // MPEG-4 AVC/H.264 BD-compat High Profile / Level 4.1 of ITU-T H.264 |
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341 transferSyntax == "1.2.840.10008.1.2.4.104" || // MPEG-4 AVC/H.264 High Profile / Level 4.2 of ITU-T H.264 |
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342 transferSyntax == "1.2.840.10008.1.2.4.105" || // MPEG-4 AVC/H.264 High Profile / Level 4.2 of ITU-T H.264 |
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343 transferSyntax == "1.2.840.10008.1.2.4.106") // MPEG-4 AVC/H.264 Stereo High Profile / Level 4.2 of the ITU-T H.264 |
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344 { |
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345 return true; |
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346 } |
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347 |
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348 return false; |
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349 } |
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350 |
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351 |
1956 | 352 unsigned int DicomFrameIndex::GetFramesCount(DcmFileFormat& dicom) |
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353 { |
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354 // Assume 1 frame for video transfer syntaxes |
1956 | 355 if (IsVideo(dicom)) |
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356 { |
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357 return 1; |
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358 } |
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359 |
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360 const char* tmp = NULL; |
1956 | 361 if (!dicom.getDataset()->findAndGetString(DCM_NumberOfFrames, tmp).good() || |
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362 tmp == NULL) |
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363 { |
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364 return 1; |
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365 } |
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366 |
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367 int count = -1; |
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368 try |
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369 { |
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370 count = boost::lexical_cast<int>(tmp); |
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371 } |
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372 catch (boost::bad_lexical_cast&) |
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373 { |
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374 } |
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375 |
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376 if (count < 0) |
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377 { |
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378 throw OrthancException(ErrorCode_BadFileFormat); |
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379 } |
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380 else |
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381 { |
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382 return count; |
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383 } |
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384 } |
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385 |
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386 |
1956 | 387 DicomFrameIndex::DicomFrameIndex(DcmFileFormat& dicom) |
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388 { |
1956 | 389 countFrames_ = GetFramesCount(dicom); |
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390 if (countFrames_ == 0) |
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391 { |
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392 // The image has no frame. No index is to be built. |
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393 return; |
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394 } |
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395 |
1956 | 396 DcmDataset& dataset = *dicom.getDataset(); |
397 | |
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398 // Test whether this image is composed of a sequence of fragments |
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399 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dataset); |
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400 if (pixelSequence != NULL) |
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401 { |
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402 index_.reset(new FragmentIndex(pixelSequence, countFrames_)); |
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403 return; |
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404 } |
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405 |
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406 // Extract information about the image structure |
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407 DicomMap tags; |
2131 | 408 Configuration::ExtractDicomSummary(tags, dataset); |
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409 |
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410 DicomImageInformation information(tags); |
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411 |
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412 // Access to the raw pixel data |
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413 if (DicomImageDecoder::IsPsmctRle1(dataset)) |
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414 { |
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415 index_.reset(new PsmctRle1Index(dataset, countFrames_, information.GetFrameSize())); |
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416 } |
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417 else |
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418 { |
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419 index_.reset(new UncompressedIndex(dataset, countFrames_, information.GetFrameSize())); |
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420 } |
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421 } |
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422 |
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423 |
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424 void DicomFrameIndex::GetRawFrame(std::string& frame, |
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425 unsigned int index) const |
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426 { |
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427 if (index >= countFrames_) |
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428 { |
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429 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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430 } |
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431 else if (index_.get() != NULL) |
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432 { |
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433 return index_->GetRawFrame(frame, index); |
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434 } |
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435 else |
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436 { |
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437 frame.clear(); |
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438 } |
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439 } |
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440 } |