Mercurial > hg > orthanc
annotate OrthancServer/SliceOrdering.cpp @ 1858:483f26479743 dcmtk-3.6.1
update to latest dcmtk snapshot
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 02 Dec 2015 10:05:45 +0100 |
parents | 1ba224001fd0 |
children | c8877965d67d |
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) 2012-2015 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 "SliceOrdering.h" |
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35 |
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36 #include "../Core/Logging.h" |
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37 #include "../Core/Toolbox.h" |
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38 #include "ServerEnumerations.h" |
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39 |
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40 #include <algorithm> |
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41 #include <boost/lexical_cast.hpp> |
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42 #include <boost/noncopyable.hpp> |
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43 |
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44 |
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45 namespace Orthanc |
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46 { |
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47 static bool TokenizeVector(std::vector<float>& result, |
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48 const std::string& value, |
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49 unsigned int expectedSize) |
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50 { |
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51 std::vector<std::string> tokens; |
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52 Toolbox::TokenizeString(tokens, value, '\\'); |
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53 |
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54 if (tokens.size() != expectedSize) |
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55 { |
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56 return false; |
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57 } |
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58 |
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59 result.resize(tokens.size()); |
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60 |
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61 for (size_t i = 0; i < tokens.size(); i++) |
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62 { |
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63 try |
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64 { |
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65 result[i] = boost::lexical_cast<float>(tokens[i]); |
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66 } |
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67 catch (boost::bad_lexical_cast&) |
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68 { |
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69 return false; |
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70 } |
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71 } |
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72 |
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73 return true; |
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74 } |
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75 |
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76 |
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77 static bool TokenizeVector(std::vector<float>& result, |
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78 const DicomMap& map, |
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79 const DicomTag& tag, |
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80 unsigned int expectedSize) |
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81 { |
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82 const DicomValue* value = map.TestAndGetValue(tag); |
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83 |
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84 if (value == NULL || |
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85 value->IsNull() || |
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86 value->IsBinary()) |
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87 { |
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88 return false; |
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89 } |
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90 else |
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91 { |
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92 return TokenizeVector(result, value->GetContent(), expectedSize); |
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93 } |
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94 } |
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95 |
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96 |
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97 struct SliceOrdering::Instance : public boost::noncopyable |
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98 { |
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99 private: |
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100 std::string instanceId_; |
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101 bool hasPosition_; |
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102 Vector position_; |
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103 bool hasIndexInSeries_; |
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104 size_t indexInSeries_; |
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105 unsigned int framesCount_; |
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106 |
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107 public: |
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108 Instance(ServerIndex& index, |
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109 const std::string& instanceId) : |
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110 instanceId_(instanceId), |
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111 framesCount_(1) |
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112 { |
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113 DicomMap instance; |
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114 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance)) |
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115 { |
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116 throw OrthancException(ErrorCode_UnknownResource); |
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117 } |
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118 |
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119 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES); |
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120 if (frames != NULL && |
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121 !frames->IsNull() && |
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122 !frames->IsBinary()) |
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123 { |
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124 try |
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125 { |
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126 framesCount_ = boost::lexical_cast<unsigned int>(frames->GetContent()); |
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127 } |
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128 catch (boost::bad_lexical_cast&) |
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129 { |
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130 } |
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131 } |
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132 |
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133 std::vector<float> tmp; |
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134 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3); |
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135 |
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136 if (hasPosition_) |
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137 { |
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138 position_[0] = tmp[0]; |
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139 position_[1] = tmp[1]; |
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140 position_[2] = tmp[2]; |
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141 } |
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142 |
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143 std::string s; |
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144 hasIndexInSeries_ = false; |
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145 |
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146 try |
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147 { |
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148 if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries)) |
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149 { |
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150 indexInSeries_ = boost::lexical_cast<size_t>(s); |
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151 hasIndexInSeries_ = true; |
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152 } |
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153 } |
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154 catch (boost::bad_lexical_cast&) |
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155 { |
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156 } |
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157 } |
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158 |
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159 const std::string& GetIdentifier() const |
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160 { |
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161 return instanceId_; |
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162 } |
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163 |
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164 bool HasPosition() const |
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165 { |
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166 return hasPosition_; |
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167 } |
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168 |
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169 float ComputeRelativePosition(const Vector& normal) const |
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170 { |
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171 assert(HasPosition()); |
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172 return (normal[0] * position_[0] + |
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173 normal[1] * position_[1] + |
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174 normal[2] * position_[2]); |
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175 } |
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176 |
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177 bool HasIndexInSeries() const |
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178 { |
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179 return hasIndexInSeries_; |
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180 } |
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181 |
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182 size_t GetIndexInSeries() const |
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183 { |
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184 assert(HasIndexInSeries()); |
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185 return indexInSeries_; |
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186 } |
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187 |
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188 unsigned int GetFramesCount() const |
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189 { |
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190 return framesCount_; |
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191 } |
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192 }; |
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193 |
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194 |
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195 class SliceOrdering::PositionComparator |
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196 { |
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197 private: |
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198 const Vector& normal_; |
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199 |
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200 public: |
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201 PositionComparator(const Vector& normal) : normal_(normal) |
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202 { |
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203 } |
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204 |
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205 int operator() (const Instance* a, |
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206 const Instance* b) const |
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207 { |
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208 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_); |
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209 } |
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210 }; |
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211 |
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212 |
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213 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a, |
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214 const SliceOrdering::Instance* b) |
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215 { |
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216 return a->GetIndexInSeries() < b->GetIndexInSeries(); |
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217 } |
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218 |
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219 |
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220 void SliceOrdering::ComputeNormal() |
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221 { |
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222 DicomMap series; |
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223 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series)) |
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224 { |
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225 throw OrthancException(ErrorCode_UnknownResource); |
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226 } |
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227 |
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228 std::vector<float> cosines; |
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229 hasNormal_ = TokenizeVector(cosines, series, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6); |
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230 |
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231 if (hasNormal_) |
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232 { |
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233 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; |
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234 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; |
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235 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; |
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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 void SliceOrdering::CreateInstances() |
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241 { |
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242 std::list<std::string> instancesId; |
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243 index_.GetChildren(instancesId, seriesId_); |
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244 |
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245 instances_.reserve(instancesId.size()); |
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246 for (std::list<std::string>::const_iterator |
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247 it = instancesId.begin(); it != instancesId.end(); ++it) |
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248 { |
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249 instances_.push_back(new Instance(index_, *it)); |
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250 } |
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251 } |
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252 |
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253 |
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254 bool SliceOrdering::SortUsingPositions() |
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255 { |
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256 if (instances_.size() <= 1) |
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257 { |
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258 // One single instance: It is sorted by default |
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259 return true; |
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260 } |
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261 |
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262 if (!hasNormal_) |
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263 { |
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264 return false; |
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265 } |
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266 |
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267 for (size_t i = 0; i < instances_.size(); i++) |
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268 { |
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269 assert(instances_[i] != NULL); |
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270 if (!instances_[i]->HasPosition()) |
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271 { |
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272 return false; |
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273 } |
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274 } |
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275 |
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276 PositionComparator comparator(normal_); |
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277 std::sort(instances_.begin(), instances_.end(), comparator); |
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278 |
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279 float a = instances_[0]->ComputeRelativePosition(normal_); |
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280 for (size_t i = 1; i < instances_.size(); i++) |
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281 { |
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282 float b = instances_[i]->ComputeRelativePosition(normal_); |
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283 |
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284 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon()) |
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285 { |
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286 // Not enough space between two slices along the normal of the volume |
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287 return false; |
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288 } |
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289 |
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290 a = b; |
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291 } |
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292 |
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293 // This is a 3D volume |
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294 isVolume_ = true; |
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295 return true; |
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296 } |
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297 |
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298 |
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299 bool SliceOrdering::SortUsingIndexInSeries() |
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300 { |
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301 if (instances_.size() <= 1) |
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302 { |
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303 // One single instance: It is sorted by default |
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304 return true; |
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305 } |
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306 |
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307 for (size_t i = 0; i < instances_.size(); i++) |
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308 { |
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309 assert(instances_[i] != NULL); |
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310 if (!instances_[i]->HasIndexInSeries()) |
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311 { |
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312 return false; |
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313 } |
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314 } |
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315 |
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316 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator); |
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317 |
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318 for (size_t i = 1; i < instances_.size(); i++) |
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319 { |
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320 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries()) |
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321 { |
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322 // The current "IndexInSeries" occurs 2 times: Not a proper ordering |
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323 return false; |
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324 } |
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325 } |
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326 |
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327 return true; |
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328 } |
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329 |
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330 |
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331 SliceOrdering::SliceOrdering(ServerIndex& index, |
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332 const std::string& seriesId) : |
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333 index_(index), |
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334 seriesId_(seriesId), |
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335 isVolume_(false) |
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336 { |
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337 ComputeNormal(); |
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338 CreateInstances(); |
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339 |
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340 if (!SortUsingPositions() && |
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341 !SortUsingIndexInSeries()) |
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342 { |
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343 LOG(ERROR) << "Unable to order the slices of the series " << seriesId; |
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344 throw OrthancException(ErrorCode_CannotOrderSlices); |
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345 } |
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346 } |
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347 |
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348 |
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349 SliceOrdering::~SliceOrdering() |
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350 { |
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351 for (std::vector<Instance*>::iterator |
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352 it = instances_.begin(); it != instances_.end(); ++it) |
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353 { |
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354 if (*it != NULL) |
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355 { |
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356 delete *it; |
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357 } |
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358 } |
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359 } |
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360 |
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361 |
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362 const std::string& SliceOrdering::GetInstanceId(size_t index) const |
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363 { |
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364 if (index >= instances_.size()) |
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365 { |
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366 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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367 } |
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368 else |
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369 { |
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370 return instances_[index]->GetIdentifier(); |
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371 } |
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372 } |
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373 |
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374 |
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375 unsigned int SliceOrdering::GetFramesCount(size_t index) const |
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376 { |
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377 if (index >= instances_.size()) |
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378 { |
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379 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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380 } |
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381 else |
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382 { |
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383 return instances_[index]->GetFramesCount(); |
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384 } |
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385 } |
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386 |
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387 |
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388 void SliceOrdering::Format(Json::Value& result) const |
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389 { |
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390 result = Json::objectValue; |
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391 result["Type"] = (isVolume_ ? "Volume" : "Sequence"); |
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392 |
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393 Json::Value tmp = Json::arrayValue; |
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394 for (size_t i = 0; i < GetInstancesCount(); i++) |
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395 { |
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396 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file"); |
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397 } |
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398 |
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399 result["Dicom"] = tmp; |
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400 |
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401 tmp.clear(); |
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402 for (size_t i = 0; i < GetInstancesCount(); i++) |
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403 { |
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404 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i)); |
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405 for (size_t j = 0; j < GetFramesCount(i); j++) |
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406 { |
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407 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j)); |
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408 } |
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409 } |
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410 |
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411 result["Slices"] = tmp; |
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412 } |
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413 } |