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annotate OrthancServer/SliceOrdering.cpp @ 2075:bec08e9236f5

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more robust AutoClassify.py sample
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 16 Aug 2016 12:49:38 +0200
parents b1291df2f780
children a3a65de1840f
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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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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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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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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diff changeset
283
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diff changeset
284 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon())
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diff changeset
285 {
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286 // Not enough space between two slices along the normal of the volume
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diff changeset
287 return false;
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diff changeset
288 }
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diff changeset
289
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diff changeset
290 a = b;
1703
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291 }
1842
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diff changeset
292
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diff changeset
293 // This is a 3D volume
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diff changeset
294 isVolume_ = true;
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diff changeset
295 return true;
1703
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diff changeset
296 }
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diff changeset
297
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diff changeset
298
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diff changeset
299 bool SliceOrdering::SortUsingIndexInSeries()
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diff changeset
300 {
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diff changeset
301 if (instances_.size() <= 1)
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diff changeset
302 {
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303 // One single instance: It is sorted by default
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diff changeset
304 return true;
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diff changeset
305 }
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diff changeset
306
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diff changeset
307 for (size_t i = 0; i < instances_.size(); i++)
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diff changeset
308 {
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parents: 1702
diff changeset
309 assert(instances_[i] != NULL);
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parents: 1702
diff changeset
310 if (!instances_[i]->HasIndexInSeries())
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diff changeset
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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diff changeset
316 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator);
1702
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parents:
diff changeset
317
1703
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diff changeset
318 for (size_t i = 1; i < instances_.size(); i++)
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parents: 1702
diff changeset
319 {
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diff changeset
320 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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parents: 1702
diff changeset
321 {
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diff changeset
322 // 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
323 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
324 break;
1703
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diff changeset
325 }
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diff changeset
326 }
1702
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parents:
diff changeset
327
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parents:
diff changeset
328 return true;
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parents:
diff changeset
329 }
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parents:
diff changeset
330
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parents:
diff changeset
331
9980875edc7c started work on SliceOrdering
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parents:
diff changeset
332 SliceOrdering::SliceOrdering(ServerIndex& index,
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parents:
diff changeset
333 const std::string& seriesId) :
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parents:
diff changeset
334 index_(index),
1703
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parents: 1702
diff changeset
335 seriesId_(seriesId),
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parents: 1702
diff changeset
336 isVolume_(false)
1702
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parents:
diff changeset
337 {
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parents:
diff changeset
338 ComputeNormal();
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parents:
diff changeset
339 CreateInstances();
1703
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diff changeset
340
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diff changeset
341 if (!SortUsingPositions() &&
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
342 !SortUsingIndexInSeries())
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diff changeset
343 {
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diff changeset
344 LOG(ERROR) << "Unable to order the slices of the series " << seriesId;
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parents: 1702
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345 throw OrthancException(ErrorCode_CannotOrderSlices);
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346 }
1702
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diff changeset
347 }
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parents:
diff changeset
348
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diff changeset
349
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parents:
diff changeset
350 SliceOrdering::~SliceOrdering()
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parents:
diff changeset
351 {
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parents:
diff changeset
352 for (std::vector<Instance*>::iterator
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parents:
diff changeset
353 it = instances_.begin(); it != instances_.end(); ++it)
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parents:
diff changeset
354 {
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parents:
diff changeset
355 if (*it != NULL)
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parents:
diff changeset
356 {
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parents:
diff changeset
357 delete *it;
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parents:
diff changeset
358 }
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parents:
diff changeset
359 }
9980875edc7c started work on SliceOrdering
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parents:
diff changeset
360 }
1703
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parents: 1702
diff changeset
361
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parents: 1702
diff changeset
362
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parents: 1702
diff changeset
363 const std::string& SliceOrdering::GetInstanceId(size_t index) const
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parents: 1702
diff changeset
364 {
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parents: 1702
diff changeset
365 if (index >= instances_.size())
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
366 {
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parents: 1702
diff changeset
367 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 1702
diff changeset
368 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
369 else
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parents: 1702
diff changeset
370 {
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parents: 1702
diff changeset
371 return instances_[index]->GetIdentifier();
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
372 }
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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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parents: 1702
diff changeset
376 unsigned int SliceOrdering::GetFramesCount(size_t index) const
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parents: 1702
diff changeset
377 {
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parents: 1702
diff changeset
378 if (index >= instances_.size())
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
379 {
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parents: 1702
diff changeset
380 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 1702
diff changeset
381 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
382 else
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
383 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
384 return instances_[index]->GetFramesCount();
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
385 }
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 void SliceOrdering::Format(Json::Value& result) const
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parents: 1702
diff changeset
390 {
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parents: 1702
diff changeset
391 result = Json::objectValue;
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parents: 1702
diff changeset
392 result["Type"] = (isVolume_ ? "Volume" : "Sequence");
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
393
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
394 Json::Value tmp = Json::arrayValue;
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
395 for (size_t i = 0; i < GetInstancesCount(); i++)
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parents: 1702
diff changeset
396 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
397 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file");
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
398 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
399
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parents: 1702
diff changeset
400 result["Dicom"] = tmp;
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parents: 1702
diff changeset
401
1873
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
402 Json::Value slicesShort = Json::arrayValue;
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
403
1703
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parents: 1702
diff changeset
404 tmp.clear();
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
405 for (size_t i = 0; i < GetInstancesCount(); i++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
406 {
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
407 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i));
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
408 for (size_t j = 0; j < GetFramesCount(i); j++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
409 {
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
410 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j));
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
411 }
1873
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
412
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
413 Json::Value tmp2 = Json::arrayValue;
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
414 tmp2.append(GetInstanceId(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
415 tmp2.append(0);
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
416 tmp2.append(GetFramesCount(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
417
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
418 slicesShort.append(tmp2);
1703
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
419 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
420
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
421 result["Slices"] = tmp;
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
422 result["SlicesShort"] = slicesShort;
1703
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
423 }
1702
9980875edc7c started work on SliceOrdering
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
424 }