Mercurial > hg > orthanc
annotate OrthancServer/Internals/DicomFrameIndex.cpp @ 1924:6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 07 Mar 2016 17:43:20 +0100 |
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children | 84c7eaeb5244 |
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 * |
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6 * This program is free software: you can redistribute it and/or |
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7 * modify it under the terms of the GNU General Public License as |
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8 * published by the Free Software Foundation, either version 3 of the |
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9 * License, or (at your option) any later version. |
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10 * |
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11 * In addition, as a special exception, the copyright holders of this |
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12 * program give permission to link the code of its release with the |
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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14 * that use the same license as the "OpenSSL" library), and distribute |
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15 * the linked executables. You must obey the GNU General Public License |
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16 * in all respects for all of the code used other than "OpenSSL". If you |
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17 * modify file(s) with this exception, you may extend this exception to |
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18 * your version of the file(s), but you are not obligated to do so. If |
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19 * you do not wish to do so, delete this exception statement from your |
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20 * version. If you delete this exception statement from all source files |
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21 * in the program, then also delete it here. |
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22 * |
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23 * This program is distributed in the hope that it will be useful, but |
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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26 * General Public License for more details. |
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27 * |
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28 * You should have received a copy of the GNU General Public License |
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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30 **/ |
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31 |
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32 |
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33 #include "../PrecompiledHeadersServer.h" |
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34 #include "DicomFrameIndex.h" |
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35 |
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36 #include "../../Core/OrthancException.h" |
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37 #include "../../Core/DicomFormat/DicomImageInformation.h" |
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38 #include "../FromDcmtkBridge.h" |
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39 #include "DicomImageDecoder.h" |
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40 |
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41 #include <boost/lexical_cast.hpp> |
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42 |
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43 #include <dcmtk/dcmdata/dcdeftag.h> |
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44 #include <dcmtk/dcmdata/dcpxitem.h> |
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45 #include <dcmtk/dcmdata/dcpixseq.h> |
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46 |
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47 #if defined(_WIN32) // Windows machines are always little-endian |
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48 # define le32toh(x) x |
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49 #elif defined(__APPLE__) |
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50 # include <libkern/OSByteOrder.h> |
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51 # define le32toh(x) OSSwapLittleToHostInt32(x) |
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52 #else |
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53 # include <endian.h> |
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54 #endif |
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55 |
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56 |
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57 namespace Orthanc |
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58 { |
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59 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex |
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60 { |
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61 private: |
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62 DcmPixelSequence* pixelSequence_; |
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63 std::vector<DcmPixelItem*> startFragment_; |
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64 std::vector<unsigned int> countFragments_; |
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65 std::vector<unsigned int> frameSize_; |
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66 |
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67 void GetOffsetTable(std::vector<uint32_t>& table) |
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68 { |
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69 DcmPixelItem* item = NULL; |
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70 if (!pixelSequence_->getItem(item, 0).good() || |
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71 item == NULL) |
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72 { |
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73 throw OrthancException(ErrorCode_BadFileFormat); |
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74 } |
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75 |
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76 uint32_t length = item->getLength(); |
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77 if (length == 0) |
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78 { |
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79 table.clear(); |
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80 return; |
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81 } |
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82 |
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83 if (length % 4 != 0) |
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84 { |
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85 // Error: Each fragment is index with 4 bytes (uint32_t) |
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86 throw OrthancException(ErrorCode_BadFileFormat); |
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87 } |
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88 |
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89 uint8_t* content = NULL; |
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90 if (!item->getUint8Array(content).good() || |
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91 content == NULL) |
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92 { |
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93 throw OrthancException(ErrorCode_InternalError); |
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94 } |
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95 |
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96 table.resize(length / 4); |
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97 |
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98 // The offset table is always in little endian in the DICOM |
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99 // file. Swap it to host endianness if needed. |
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100 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content); |
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101 for (size_t i = 0; i < table.size(); i++, offset++) |
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102 { |
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103 table[i] = le32toh(*offset); |
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104 } |
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105 } |
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106 |
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107 |
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108 public: |
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109 FragmentIndex(DcmPixelSequence* pixelSequence, |
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110 unsigned int countFrames) : |
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111 pixelSequence_(pixelSequence) |
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112 { |
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113 assert(pixelSequence != NULL); |
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114 |
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115 startFragment_.resize(countFrames); |
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116 countFragments_.resize(countFrames); |
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117 frameSize_.resize(countFrames); |
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118 |
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119 // The first fragment corresponds to the offset table |
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120 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card()); |
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121 if (countFragments < countFrames + 1) |
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122 { |
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123 throw OrthancException(ErrorCode_BadFileFormat); |
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124 } |
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125 |
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126 if (countFragments == countFrames + 1) |
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127 { |
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128 // Simple case: There is one fragment per frame. |
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129 |
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130 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table |
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131 if (fragment == NULL) |
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132 { |
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133 throw OrthancException(ErrorCode_InternalError); |
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134 } |
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135 |
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136 for (unsigned int i = 0; i < countFrames; i++) |
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137 { |
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138 fragment = pixelSequence_->nextInContainer(fragment); |
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139 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment); |
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140 frameSize_[i] = fragment->getLength(); |
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141 countFragments_[i] = 1; |
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142 } |
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143 |
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144 return; |
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145 } |
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146 |
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147 // Parse the offset table |
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148 std::vector<uint32_t> offsetOfFrame; |
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149 GetOffsetTable(offsetOfFrame); |
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150 |
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151 if (offsetOfFrame.size() != countFrames || |
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152 offsetOfFrame[0] != 0) |
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153 { |
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154 throw OrthancException(ErrorCode_BadFileFormat); |
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155 } |
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156 |
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157 |
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158 // Loop over the fragments (ignoring the offset table). This is |
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159 // an alternative, faster implementation to DCMTK's |
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160 // "DcmCodec::determineStartFragment()". |
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161 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); |
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162 if (fragment == NULL) |
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163 { |
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164 throw OrthancException(ErrorCode_InternalError); |
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165 } |
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166 |
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167 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table |
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168 if (fragment == NULL) |
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169 { |
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170 throw OrthancException(ErrorCode_InternalError); |
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171 } |
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172 |
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173 uint32_t offset = 0; |
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174 unsigned int currentFrame = 0; |
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175 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment); |
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176 |
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177 unsigned int currentFragment = 1; |
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178 while (fragment != NULL) |
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179 { |
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180 if (currentFrame + 1 < countFrames && |
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181 offset == offsetOfFrame[currentFrame + 1]) |
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182 { |
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183 currentFrame += 1; |
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184 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment); |
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185 } |
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186 |
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187 frameSize_[currentFrame] += fragment->getLength(); |
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188 countFragments_[currentFrame]++; |
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189 |
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190 // 8 bytes = overhead for the item tag and length field |
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191 offset += fragment->getLength() + 8; |
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192 |
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193 currentFragment++; |
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194 fragment = pixelSequence_->nextInContainer(fragment); |
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195 } |
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196 |
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197 if (currentFragment != countFragments || |
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198 currentFrame + 1 != countFrames || |
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199 fragment != NULL) |
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200 { |
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201 throw OrthancException(ErrorCode_BadFileFormat); |
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202 } |
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203 |
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204 assert(startFragment_.size() == countFragments_.size() && |
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205 startFragment_.size() == frameSize_.size()); |
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206 } |
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207 |
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208 |
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209 virtual void GetRawFrame(std::string& frame, |
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210 unsigned int index) const |
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211 { |
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212 if (index >= startFragment_.size()) |
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213 { |
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214 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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215 } |
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216 |
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217 frame.resize(frameSize_[index]); |
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218 if (frame.size() == 0) |
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219 { |
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220 return; |
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221 } |
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222 |
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223 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]); |
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224 |
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225 size_t offset = 0; |
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226 DcmPixelItem* fragment = startFragment_[index]; |
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227 for (unsigned int i = 0; i < countFragments_[index]; i++) |
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228 { |
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229 uint8_t* content = NULL; |
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230 if (!fragment->getUint8Array(content).good() || |
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231 content == NULL) |
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232 { |
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233 throw OrthancException(ErrorCode_InternalError); |
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234 } |
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235 |
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236 assert(offset + fragment->getLength() <= frame.size()); |
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237 |
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238 memcpy(target + offset, content, fragment->getLength()); |
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239 offset += fragment->getLength(); |
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240 |
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241 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment)); |
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242 } |
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243 } |
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244 }; |
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245 |
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246 |
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247 |
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248 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex |
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249 { |
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250 private: |
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251 uint8_t* pixelData_; |
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252 size_t frameSize_; |
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253 |
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254 public: |
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255 UncompressedIndex(DcmDataset& dataset, |
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256 unsigned int countFrames, |
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257 size_t frameSize) : |
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258 pixelData_(NULL), |
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259 frameSize_(frameSize) |
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260 { |
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261 size_t size = 0; |
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262 |
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263 DcmElement* e; |
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264 if (dataset.findAndGetElement(DCM_PixelData, e).good() && |
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265 e != NULL) |
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266 { |
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267 size = e->getLength(); |
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268 |
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269 if (size > 0) |
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270 { |
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271 pixelData_ = NULL; |
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272 if (!e->getUint8Array(pixelData_).good() || |
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273 pixelData_ == NULL) |
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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 |
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280 if (size < frameSize_ * countFrames) |
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281 { |
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282 throw OrthancException(ErrorCode_BadFileFormat); |
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283 } |
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284 } |
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285 |
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286 virtual void GetRawFrame(std::string& frame, |
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287 unsigned int index) const |
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288 { |
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289 frame.resize(frameSize_); |
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290 if (frameSize_ > 0) |
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291 { |
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292 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_); |
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293 } |
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294 } |
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295 }; |
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296 |
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297 |
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298 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex |
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299 { |
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300 private: |
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301 std::string pixelData_; |
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302 size_t frameSize_; |
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303 |
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304 public: |
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305 PsmctRle1Index(DcmDataset& dataset, |
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306 unsigned int countFrames, |
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307 size_t frameSize) : |
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308 frameSize_(frameSize) |
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309 { |
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310 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) || |
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311 pixelData_.size() < frameSize * countFrames) |
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312 { |
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313 throw OrthancException(ErrorCode_BadFileFormat); |
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314 } |
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315 } |
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316 |
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317 virtual void GetRawFrame(std::string& frame, |
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318 unsigned int index) const |
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319 { |
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320 frame.resize(frameSize_); |
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321 if (frameSize_ > 0) |
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322 { |
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323 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_); |
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324 } |
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325 } |
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326 }; |
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327 |
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328 |
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329 |
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330 |
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331 unsigned int DicomFrameIndex::GetFramesCount(DcmDataset& dataset) |
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332 { |
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333 const char* tmp = NULL; |
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334 if (!dataset.findAndGetString(DCM_NumberOfFrames, tmp).good() || |
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335 tmp == NULL) |
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336 { |
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337 return 1; |
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338 } |
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339 |
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340 int count = -1; |
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341 try |
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342 { |
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343 count = boost::lexical_cast<int>(tmp); |
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344 } |
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345 catch (boost::bad_lexical_cast&) |
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346 { |
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347 } |
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348 |
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349 if (count < 0) |
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350 { |
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351 throw OrthancException(ErrorCode_BadFileFormat); |
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352 } |
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353 else |
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354 { |
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355 return count; |
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356 } |
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357 } |
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358 |
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359 |
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360 DicomFrameIndex::DicomFrameIndex(DcmDataset& dataset) |
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361 { |
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362 countFrames_ = GetFramesCount(dataset); |
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363 if (countFrames_ == 0) |
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364 { |
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365 // The image has no frame. No index is to be built. |
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366 return; |
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367 } |
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368 |
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369 // Test whether this image is composed of a sequence of fragments |
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370 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dataset); |
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371 if (pixelSequence != NULL) |
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372 { |
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373 index_.reset(new FragmentIndex(pixelSequence, countFrames_)); |
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374 return; |
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375 } |
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376 |
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377 // Extract information about the image structure |
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378 DicomMap tags; |
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379 FromDcmtkBridge::Convert(tags, dataset); |
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380 |
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381 DicomImageInformation information(tags); |
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382 |
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383 // Access to the raw pixel data |
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384 if (DicomImageDecoder::IsPsmctRle1(dataset)) |
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385 { |
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386 index_.reset(new PsmctRle1Index(dataset, countFrames_, information.GetFrameSize())); |
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387 } |
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388 else |
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389 { |
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390 index_.reset(new UncompressedIndex(dataset, countFrames_, information.GetFrameSize())); |
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391 } |
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392 } |
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393 |
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394 |
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395 void DicomFrameIndex::GetRawFrame(std::string& frame, |
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396 unsigned int index) const |
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397 { |
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398 if (index >= countFrames_) |
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399 { |
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400 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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401 } |
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402 else if (index_.get() != NULL) |
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403 { |
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404 return index_->GetRawFrame(frame, index); |
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405 } |
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406 else |
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407 { |
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408 frame.clear(); |
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409 } |
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410 } |
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411 } |