Mercurial > hg > orthanc
annotate OrthancServer/SliceOrdering.cpp @ 2436:e2f167ce9149
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 29 Nov 2017 17:32:31 +0100 |
parents | a3a65de1840f |
children | 878b59270859 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 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 "SliceOrdering.h" |
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36 |
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37 #include "../Core/Logging.h" |
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38 #include "../Core/Toolbox.h" |
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39 #include "ServerEnumerations.h" |
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40 |
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41 #include <algorithm> |
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42 #include <boost/lexical_cast.hpp> |
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43 #include <boost/noncopyable.hpp> |
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44 |
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45 |
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46 namespace Orthanc |
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47 { |
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48 static bool TokenizeVector(std::vector<float>& result, |
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49 const std::string& value, |
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50 unsigned int expectedSize) |
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51 { |
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52 std::vector<std::string> tokens; |
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53 Toolbox::TokenizeString(tokens, value, '\\'); |
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54 |
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55 if (tokens.size() != expectedSize) |
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56 { |
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57 return false; |
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58 } |
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59 |
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60 result.resize(tokens.size()); |
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61 |
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62 for (size_t i = 0; i < tokens.size(); i++) |
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63 { |
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64 try |
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65 { |
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66 result[i] = boost::lexical_cast<float>(tokens[i]); |
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67 } |
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68 catch (boost::bad_lexical_cast&) |
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69 { |
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70 return false; |
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71 } |
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72 } |
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73 |
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74 return true; |
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75 } |
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76 |
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77 |
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78 static bool TokenizeVector(std::vector<float>& result, |
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79 const DicomMap& map, |
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80 const DicomTag& tag, |
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81 unsigned int expectedSize) |
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82 { |
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83 const DicomValue* value = map.TestAndGetValue(tag); |
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84 |
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85 if (value == NULL || |
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86 value->IsNull() || |
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87 value->IsBinary()) |
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88 { |
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89 return false; |
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90 } |
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91 else |
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92 { |
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93 return TokenizeVector(result, value->GetContent(), expectedSize); |
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94 } |
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95 } |
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96 |
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97 |
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98 struct SliceOrdering::Instance : public boost::noncopyable |
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99 { |
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100 private: |
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101 std::string instanceId_; |
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102 bool hasPosition_; |
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103 Vector position_; |
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104 bool hasIndexInSeries_; |
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105 size_t indexInSeries_; |
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106 unsigned int framesCount_; |
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107 |
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108 public: |
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109 Instance(ServerIndex& index, |
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110 const std::string& instanceId) : |
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111 instanceId_(instanceId), |
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112 framesCount_(1) |
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113 { |
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114 DicomMap instance; |
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115 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance)) |
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116 { |
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117 throw OrthancException(ErrorCode_UnknownResource); |
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118 } |
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119 |
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120 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES); |
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121 if (frames != NULL && |
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122 !frames->IsNull() && |
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123 !frames->IsBinary()) |
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124 { |
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125 try |
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126 { |
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127 framesCount_ = boost::lexical_cast<unsigned int>(frames->GetContent()); |
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128 } |
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129 catch (boost::bad_lexical_cast&) |
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130 { |
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131 } |
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132 } |
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133 |
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134 std::vector<float> tmp; |
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135 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3); |
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136 |
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137 if (hasPosition_) |
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138 { |
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139 position_[0] = tmp[0]; |
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140 position_[1] = tmp[1]; |
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141 position_[2] = tmp[2]; |
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142 } |
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143 |
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144 std::string s; |
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145 hasIndexInSeries_ = false; |
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146 |
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147 try |
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148 { |
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149 if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries)) |
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150 { |
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151 indexInSeries_ = boost::lexical_cast<size_t>(s); |
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152 hasIndexInSeries_ = true; |
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153 } |
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154 } |
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155 catch (boost::bad_lexical_cast&) |
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156 { |
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157 } |
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158 } |
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159 |
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160 const std::string& GetIdentifier() const |
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161 { |
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162 return instanceId_; |
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163 } |
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164 |
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165 bool HasPosition() const |
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166 { |
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167 return hasPosition_; |
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168 } |
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169 |
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170 float ComputeRelativePosition(const Vector& normal) const |
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171 { |
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172 assert(HasPosition()); |
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173 return (normal[0] * position_[0] + |
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174 normal[1] * position_[1] + |
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175 normal[2] * position_[2]); |
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176 } |
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177 |
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178 bool HasIndexInSeries() const |
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179 { |
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180 return hasIndexInSeries_; |
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181 } |
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182 |
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183 size_t GetIndexInSeries() const |
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184 { |
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185 assert(HasIndexInSeries()); |
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186 return indexInSeries_; |
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187 } |
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188 |
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189 unsigned int GetFramesCount() const |
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190 { |
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191 return framesCount_; |
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192 } |
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193 }; |
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194 |
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195 |
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196 class SliceOrdering::PositionComparator |
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197 { |
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198 private: |
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199 const Vector& normal_; |
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200 |
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201 public: |
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202 PositionComparator(const Vector& normal) : normal_(normal) |
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203 { |
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204 } |
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205 |
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206 int operator() (const Instance* a, |
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207 const Instance* b) const |
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208 { |
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209 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_); |
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210 } |
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211 }; |
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212 |
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213 |
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214 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a, |
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215 const SliceOrdering::Instance* b) |
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216 { |
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217 return a->GetIndexInSeries() < b->GetIndexInSeries(); |
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218 } |
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219 |
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220 |
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221 void SliceOrdering::ComputeNormal() |
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222 { |
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223 DicomMap series; |
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224 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series)) |
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225 { |
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226 throw OrthancException(ErrorCode_UnknownResource); |
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227 } |
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228 |
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229 std::vector<float> cosines; |
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230 hasNormal_ = TokenizeVector(cosines, series, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6); |
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231 |
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232 if (hasNormal_) |
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233 { |
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234 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; |
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235 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; |
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236 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; |
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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 void SliceOrdering::CreateInstances() |
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242 { |
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243 std::list<std::string> instancesId; |
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244 index_.GetChildren(instancesId, seriesId_); |
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245 |
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246 instances_.reserve(instancesId.size()); |
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247 for (std::list<std::string>::const_iterator |
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248 it = instancesId.begin(); it != instancesId.end(); ++it) |
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249 { |
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250 instances_.push_back(new Instance(index_, *it)); |
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251 } |
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252 } |
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253 |
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254 |
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255 bool SliceOrdering::SortUsingPositions() |
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256 { |
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257 if (instances_.size() <= 1) |
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258 { |
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259 // One single instance: It is sorted by default |
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260 return true; |
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261 } |
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262 |
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263 if (!hasNormal_) |
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264 { |
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265 return false; |
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266 } |
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267 |
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268 for (size_t i = 0; i < instances_.size(); i++) |
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269 { |
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270 assert(instances_[i] != NULL); |
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271 if (!instances_[i]->HasPosition()) |
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272 { |
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273 return false; |
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274 } |
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275 } |
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276 |
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277 PositionComparator comparator(normal_); |
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278 std::sort(instances_.begin(), instances_.end(), comparator); |
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279 |
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280 float a = instances_[0]->ComputeRelativePosition(normal_); |
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281 for (size_t i = 1; i < instances_.size(); i++) |
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282 { |
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283 float b = instances_[i]->ComputeRelativePosition(normal_); |
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284 |
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285 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon()) |
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286 { |
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287 // Not enough space between two slices along the normal of the volume |
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288 return false; |
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289 } |
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290 |
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291 a = b; |
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292 } |
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293 |
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294 // This is a 3D volume |
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295 isVolume_ = true; |
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296 return true; |
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297 } |
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298 |
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299 |
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300 bool SliceOrdering::SortUsingIndexInSeries() |
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301 { |
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302 if (instances_.size() <= 1) |
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303 { |
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304 // One single instance: It is sorted by default |
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305 return true; |
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306 } |
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307 |
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308 for (size_t i = 0; i < instances_.size(); i++) |
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309 { |
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310 assert(instances_[i] != NULL); |
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311 if (!instances_[i]->HasIndexInSeries()) |
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312 { |
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313 return false; |
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314 } |
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315 } |
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316 |
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317 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator); |
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318 |
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319 for (size_t i = 1; i < instances_.size(); i++) |
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320 { |
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321 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries()) |
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322 { |
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323 // The current "IndexInSeries" occurs 2 times: Not a proper ordering |
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324 LOG(WARNING) << "This series contains 2 slices with the same index, trying to display it anyway"; |
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325 break; |
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326 } |
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327 } |
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328 |
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329 return true; |
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330 } |
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331 |
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332 |
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333 SliceOrdering::SliceOrdering(ServerIndex& index, |
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334 const std::string& seriesId) : |
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335 index_(index), |
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336 seriesId_(seriesId), |
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337 isVolume_(false) |
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338 { |
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339 ComputeNormal(); |
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340 CreateInstances(); |
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341 |
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342 if (!SortUsingPositions() && |
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343 !SortUsingIndexInSeries()) |
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344 { |
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345 LOG(ERROR) << "Unable to order the slices of the series " << seriesId; |
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346 throw OrthancException(ErrorCode_CannotOrderSlices); |
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347 } |
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348 } |
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349 |
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350 |
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351 SliceOrdering::~SliceOrdering() |
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352 { |
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353 for (std::vector<Instance*>::iterator |
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354 it = instances_.begin(); it != instances_.end(); ++it) |
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355 { |
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356 if (*it != NULL) |
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357 { |
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358 delete *it; |
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359 } |
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360 } |
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361 } |
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362 |
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363 |
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364 const std::string& SliceOrdering::GetInstanceId(size_t index) const |
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365 { |
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366 if (index >= instances_.size()) |
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367 { |
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368 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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369 } |
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370 else |
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371 { |
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372 return instances_[index]->GetIdentifier(); |
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373 } |
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374 } |
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375 |
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376 |
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377 unsigned int SliceOrdering::GetFramesCount(size_t index) const |
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378 { |
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379 if (index >= instances_.size()) |
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380 { |
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381 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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382 } |
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383 else |
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384 { |
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385 return instances_[index]->GetFramesCount(); |
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386 } |
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387 } |
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388 |
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389 |
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390 void SliceOrdering::Format(Json::Value& result) const |
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391 { |
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392 result = Json::objectValue; |
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393 result["Type"] = (isVolume_ ? "Volume" : "Sequence"); |
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394 |
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395 Json::Value tmp = Json::arrayValue; |
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396 for (size_t i = 0; i < GetInstancesCount(); i++) |
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397 { |
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398 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file"); |
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399 } |
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400 |
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401 result["Dicom"] = tmp; |
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402 |
1873 | 403 Json::Value slicesShort = Json::arrayValue; |
404 | |
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405 tmp.clear(); |
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406 for (size_t i = 0; i < GetInstancesCount(); i++) |
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407 { |
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408 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i)); |
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409 for (size_t j = 0; j < GetFramesCount(i); j++) |
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410 { |
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411 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j)); |
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412 } |
1873 | 413 |
414 Json::Value tmp2 = Json::arrayValue; | |
415 tmp2.append(GetInstanceId(i)); | |
416 tmp2.append(0); | |
417 tmp2.append(GetFramesCount(i)); | |
418 | |
419 slicesShort.append(tmp2); | |
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420 } |
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421 |
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422 result["Slices"] = tmp; |
1873 | 423 result["SlicesShort"] = slicesShort; |
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424 } |
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425 } |