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annotate OrthancServer/SliceOrdering.cpp @ 1703:b80e76dd1d56 db-changes

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 13 Oct 2015 16:10:35 +0200
parents 9980875edc7c
children ec66a16aa398
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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 {
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87 return false;
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88 }
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89 else
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90 {
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91 return TokenizeVector(result, value->AsString(), expectedSize);
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92 }
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93 }
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94
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95
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96 struct SliceOrdering::Instance : public boost::noncopyable
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97 {
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98 private:
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99 std::string instanceId_;
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100 bool hasPosition_;
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101 Vector position_;
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102 bool hasIndexInSeries_;
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103 size_t indexInSeries_;
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104 unsigned int framesCount_;
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105
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106 public:
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107 Instance(ServerIndex& index,
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108 const std::string& instanceId) :
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109 instanceId_(instanceId),
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110 framesCount_(1)
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111 {
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112 DicomMap instance;
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113 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance))
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114 {
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115 throw OrthancException(ErrorCode_UnknownResource);
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116 }
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117
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118 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES);
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119 if (frames != NULL &&
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120 !frames->IsNull())
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121 {
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122 try
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123 {
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124 framesCount_ = boost::lexical_cast<unsigned int>(frames->AsString());
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125 }
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126 catch (boost::bad_lexical_cast&)
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127 {
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128 }
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129 }
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130
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131 std::vector<float> tmp;
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132 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3);
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133
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134 if (hasPosition_)
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135 {
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136 position_[0] = tmp[0];
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137 position_[1] = tmp[1];
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138 position_[2] = tmp[2];
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139 }
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140
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141 std::string s;
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142 hasIndexInSeries_ = false;
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143
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144 try
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145 {
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146 if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries))
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147 {
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148 indexInSeries_ = boost::lexical_cast<size_t>(s);
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149 hasIndexInSeries_ = true;
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150 }
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151 }
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152 catch (boost::bad_lexical_cast&)
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153 {
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154 }
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155 }
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156
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157 const std::string& GetIdentifier() const
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158 {
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159 return instanceId_;
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160 }
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161
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162 bool HasPosition() const
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163 {
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164 return hasPosition_;
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165 }
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166
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167 float ComputeRelativePosition(const Vector& normal) const
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168 {
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169 assert(HasPosition());
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170 return (normal[0] * position_[0] +
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171 normal[1] * position_[1] +
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172 normal[2] * position_[2]);
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173 }
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174
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175 bool HasIndexInSeries() const
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176 {
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177 return hasIndexInSeries_;
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178 }
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179
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180 size_t GetIndexInSeries() const
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181 {
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182 assert(HasIndexInSeries());
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183 return indexInSeries_;
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184 }
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185
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186 unsigned int GetFramesCount() const
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187 {
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188 return framesCount_;
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189 }
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190 };
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191
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192
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193 class SliceOrdering::PositionComparator
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194 {
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195 private:
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196 const Vector& normal_;
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197
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198 public:
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199 PositionComparator(const Vector& normal) : normal_(normal)
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200 {
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201 }
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202
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203 int operator() (const Instance* a,
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204 const Instance* b) const
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205 {
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206 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_);
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207 }
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208 };
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209
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210
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211 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a,
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212 const SliceOrdering::Instance* b)
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213 {
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214 return a->GetIndexInSeries() < b->GetIndexInSeries();
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215 }
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216
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217
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218 void SliceOrdering::ComputeNormal()
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219 {
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220 DicomMap series;
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221 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series))
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222 {
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223 throw OrthancException(ErrorCode_UnknownResource);
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224 }
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225
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226 std::vector<float> cosines;
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227 hasNormal_ = TokenizeVector(cosines, series, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6);
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228
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229 if (hasNormal_)
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230 {
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231 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4];
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232 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5];
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233 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3];
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234 }
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235 }
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236
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237
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238 void SliceOrdering::CreateInstances()
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239 {
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240 std::list<std::string> instancesId;
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241 index_.GetChildren(instancesId, seriesId_);
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242
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243 instances_.reserve(instancesId.size());
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244 for (std::list<std::string>::const_iterator
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245 it = instancesId.begin(); it != instancesId.end(); ++it)
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246 {
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247 instances_.push_back(new Instance(index_, *it));
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248 }
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249 }
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250
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251
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252 bool SliceOrdering::SortUsingPositions()
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253 {
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254 if (instances_.size() <= 1)
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255 {
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256 // One single instance: It is sorted by default
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257 return true;
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258 }
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259
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260 if (!hasNormal_)
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261 {
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262 return false;
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263 }
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264
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265 for (size_t i = 0; i < instances_.size(); i++)
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266 {
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267 assert(instances_[i] != NULL);
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268 if (!instances_[i]->HasPosition())
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269 {
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270 return false;
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271 }
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272 }
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273
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274 PositionComparator comparator(normal_);
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275 std::sort(instances_.begin(), instances_.end(), comparator);
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276
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277 float a = instances_.front()->ComputeRelativePosition(normal_);
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278 float b = instances_.back()->ComputeRelativePosition(normal_);
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279
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280 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon())
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281 {
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282 // Not enough difference between the minimum and maximum
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283 // positions along the normal of the volume
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284 return false;
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285 }
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286 else
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287 {
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288 // This is a 3D volume
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289 isVolume_ = true;
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290 return true;
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291 }
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292 }
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293
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294
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295 bool SliceOrdering::SortUsingIndexInSeries()
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296 {
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297 if (instances_.size() <= 1)
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298 {
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299 // One single instance: It is sorted by default
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300 return true;
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301 }
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302
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303 for (size_t i = 0; i < instances_.size(); i++)
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304 {
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305 assert(instances_[i] != NULL);
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306 if (!instances_[i]->HasIndexInSeries())
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307 {
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308 return false;
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309 }
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310 }
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311
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312 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator);
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313
1703
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314 for (size_t i = 1; i < instances_.size(); i++)
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315 {
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316 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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317 {
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318 // The current "IndexInSeries" occurs 2 times: Not a proper ordering
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319 return false;
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320 }
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321 }
1702
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322
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323 return true;
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324 }
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325
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326
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327 SliceOrdering::SliceOrdering(ServerIndex& index,
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328 const std::string& seriesId) :
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329 index_(index),
1703
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330 seriesId_(seriesId),
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331 isVolume_(false)
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332 {
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333 ComputeNormal();
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334 CreateInstances();
1703
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335
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336 if (!SortUsingPositions() &&
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337 !SortUsingIndexInSeries())
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338 {
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339 LOG(ERROR) << "Unable to order the slices of the series " << seriesId;
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340 throw OrthancException(ErrorCode_CannotOrderSlices);
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341 }
1702
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342 }
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343
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344
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345 SliceOrdering::~SliceOrdering()
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346 {
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347 for (std::vector<Instance*>::iterator
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348 it = instances_.begin(); it != instances_.end(); ++it)
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349 {
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350 if (*it != NULL)
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351 {
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352 delete *it;
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353 }
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354 }
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355 }
1703
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356
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357
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358 const std::string& SliceOrdering::GetInstanceId(size_t index) const
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359 {
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diff changeset
360 if (index >= instances_.size())
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361 {
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362 throw OrthancException(ErrorCode_ParameterOutOfRange);
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363 }
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364 else
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365 {
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366 return instances_[index]->GetIdentifier();
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367 }
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368 }
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diff changeset
369
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370
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diff changeset
371 unsigned int SliceOrdering::GetFramesCount(size_t index) const
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372 {
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diff changeset
373 if (index >= instances_.size())
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diff changeset
374 {
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diff changeset
375 throw OrthancException(ErrorCode_ParameterOutOfRange);
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376 }
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diff changeset
377 else
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diff changeset
378 {
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diff changeset
379 return instances_[index]->GetFramesCount();
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diff changeset
380 }
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diff changeset
381 }
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diff changeset
382
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diff changeset
383
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diff changeset
384 void SliceOrdering::Format(Json::Value& result) const
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385 {
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diff changeset
386 result = Json::objectValue;
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diff changeset
387 result["Type"] = (isVolume_ ? "Volume" : "Sequence");
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diff changeset
388
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diff changeset
389 Json::Value tmp = Json::arrayValue;
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diff changeset
390 for (size_t i = 0; i < GetInstancesCount(); i++)
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391 {
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diff changeset
392 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file");
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diff changeset
393 }
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diff changeset
394
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diff changeset
395 result["Dicom"] = tmp;
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diff changeset
396
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diff changeset
397 tmp.clear();
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diff changeset
398 for (size_t i = 0; i < GetInstancesCount(); i++)
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diff changeset
399 {
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diff changeset
400 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i));
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diff changeset
401 for (size_t j = 0; j < GetFramesCount(i); j++)
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diff changeset
402 {
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diff changeset
403 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j));
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diff changeset
404 }
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diff changeset
405 }
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parents: 1702
diff changeset
406
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diff changeset
407 result["Slices"] = tmp;
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diff changeset
408 }
1702
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diff changeset
409 }