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annotate OrthancServer/SliceOrdering.cpp @ 2617:912a767911b0 jobs

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 22 May 2018 12:45:34 +0200
parents 878b59270859
children d88970f1ffbf
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2018 Osimis S.A., 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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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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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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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 {
1842
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parents: 1737
diff changeset
283 float b = instances_[i]->ComputeRelativePosition(normal_);
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diff changeset
284
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diff changeset
285 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon())
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diff changeset
286 {
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diff changeset
287 // Not enough space between two slices along the normal of the volume
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diff changeset
288 return false;
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289 }
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290
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diff changeset
291 a = b;
1703
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292 }
1842
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diff changeset
293
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diff changeset
294 // This is a 3D volume
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diff changeset
295 isVolume_ = true;
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diff changeset
296 return true;
1703
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297 }
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298
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299
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diff changeset
300 bool SliceOrdering::SortUsingIndexInSeries()
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diff changeset
301 {
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diff changeset
302 if (instances_.size() <= 1)
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diff changeset
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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diff changeset
306 }
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diff changeset
307
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diff changeset
308 for (size_t i = 0; i < instances_.size(); i++)
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diff changeset
309 {
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diff changeset
310 assert(instances_[i] != NULL);
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parents: 1702
diff changeset
311 if (!instances_[i]->HasIndexInSeries())
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diff changeset
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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diff changeset
317 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator);
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parents:
diff changeset
318
1703
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diff changeset
319 for (size_t i = 1; i < instances_.size(); i++)
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diff changeset
320 {
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parents: 1702
diff changeset
321 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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parents: 1702
diff changeset
322 {
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323 // The current "IndexInSeries" occurs 2 times: Not a proper ordering
1868
c8877965d67d More tolerant "/series/.../ordered-slices" with broken series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1844
diff changeset
324 LOG(WARNING) << "This series contains 2 slices with the same index, trying to display it anyway";
c8877965d67d More tolerant "/series/.../ordered-slices" with broken series
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parents: 1844
diff changeset
325 break;
1703
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diff changeset
326 }
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diff changeset
327 }
1702
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parents:
diff changeset
328
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diff changeset
329 return true;
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parents:
diff changeset
330 }
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parents:
diff changeset
331
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parents:
diff changeset
332
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parents:
diff changeset
333 SliceOrdering::SliceOrdering(ServerIndex& index,
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parents:
diff changeset
334 const std::string& seriesId) :
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parents:
diff changeset
335 index_(index),
1703
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diff changeset
336 seriesId_(seriesId),
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diff changeset
337 isVolume_(false)
1702
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parents:
diff changeset
338 {
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parents:
diff changeset
339 ComputeNormal();
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parents:
diff changeset
340 CreateInstances();
1703
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diff changeset
341
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diff changeset
342 if (!SortUsingPositions() &&
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parents: 1702
diff changeset
343 !SortUsingIndexInSeries())
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diff changeset
344 {
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345 LOG(ERROR) << "Unable to order the slices of the series " << seriesId;
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parents: 1702
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346 throw OrthancException(ErrorCode_CannotOrderSlices);
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347 }
1702
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348 }
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349
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diff changeset
350
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parents:
diff changeset
351 SliceOrdering::~SliceOrdering()
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parents:
diff changeset
352 {
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parents:
diff changeset
353 for (std::vector<Instance*>::iterator
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parents:
diff changeset
354 it = instances_.begin(); it != instances_.end(); ++it)
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parents:
diff changeset
355 {
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parents:
diff changeset
356 if (*it != NULL)
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parents:
diff changeset
357 {
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parents:
diff changeset
358 delete *it;
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parents:
diff changeset
359 }
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parents:
diff changeset
360 }
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parents:
diff changeset
361 }
1703
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diff changeset
362
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diff changeset
363
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diff changeset
364 const std::string& SliceOrdering::GetInstanceId(size_t index) const
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parents: 1702
diff changeset
365 {
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parents: 1702
diff changeset
366 if (index >= instances_.size())
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parents: 1702
diff changeset
367 {
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parents: 1702
diff changeset
368 throw OrthancException(ErrorCode_ParameterOutOfRange);
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diff changeset
369 }
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parents: 1702
diff changeset
370 else
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parents: 1702
diff changeset
371 {
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parents: 1702
diff changeset
372 return instances_[index]->GetIdentifier();
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parents: 1702
diff changeset
373 }
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parents: 1702
diff changeset
374 }
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parents: 1702
diff changeset
375
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diff changeset
376
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diff changeset
377 unsigned int SliceOrdering::GetFramesCount(size_t index) const
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parents: 1702
diff changeset
378 {
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parents: 1702
diff changeset
379 if (index >= instances_.size())
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parents: 1702
diff changeset
380 {
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parents: 1702
diff changeset
381 throw OrthancException(ErrorCode_ParameterOutOfRange);
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diff changeset
382 }
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parents: 1702
diff changeset
383 else
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
384 {
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parents: 1702
diff changeset
385 return instances_[index]->GetFramesCount();
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
386 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
387 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
388
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
389
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
390 void SliceOrdering::Format(Json::Value& result) const
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parents: 1702
diff changeset
391 {
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parents: 1702
diff changeset
392 result = Json::objectValue;
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parents: 1702
diff changeset
393 result["Type"] = (isVolume_ ? "Volume" : "Sequence");
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parents: 1702
diff changeset
394
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parents: 1702
diff changeset
395 Json::Value tmp = Json::arrayValue;
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
396 for (size_t i = 0; i < GetInstancesCount(); i++)
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parents: 1702
diff changeset
397 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
398 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file");
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
399 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
400
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parents: 1702
diff changeset
401 result["Dicom"] = tmp;
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parents: 1702
diff changeset
402
1873
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
403 Json::Value slicesShort = Json::arrayValue;
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
404
1703
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diff changeset
405 tmp.clear();
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
406 for (size_t i = 0; i < GetInstancesCount(); i++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
407 {
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
408 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i));
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parents: 1702
diff changeset
409 for (size_t j = 0; j < GetFramesCount(i); j++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
410 {
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parents: 1702
diff changeset
411 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j));
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
412 }
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
413
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
414 Json::Value tmp2 = Json::arrayValue;
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
415 tmp2.append(GetInstanceId(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
416 tmp2.append(0);
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
417 tmp2.append(GetFramesCount(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
418
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
419 slicesShort.append(tmp2);
1703
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diff changeset
420 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
421
b80e76dd1d56 ordered-slices continued
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diff changeset
422 result["Slices"] = tmp;
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
423 result["SlicesShort"] = slicesShort;
1703
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
424 }
1702
9980875edc7c started work on SliceOrdering
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425 }