Mercurial > hg > orthanc

annotate OrthancServer/SliceOrdering.cpp @ 2294:e371519d4ac9

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added -U option to gdcmconv to prevent gdcmconv to mess up the files. Without that option, we have seen the SpecificCharSet tag becoming invalid !!! (seen on the VIX samples)
author Alain Mazy <am@osimis.io>
date Tue, 04 Jul 2017 15:36:19 +0000
parents a3a65de1840f
children 878b59270859
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 * Copyright (C) 2017 Osimis, Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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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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76
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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
1842
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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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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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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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diff changeset
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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295 isVolume_ = true;
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diff changeset
296 return true;
1703
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diff changeset
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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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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parents: 1702
diff changeset
310 assert(instances_[i] != NULL);
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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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321 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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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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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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341
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diff changeset
342 if (!SortUsingPositions() &&
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parents: 1702
diff changeset
343 !SortUsingIndexInSeries())
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344 {
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345 LOG(ERROR) << "Unable to order the slices of the series " << seriesId;
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346 throw OrthancException(ErrorCode_CannotOrderSlices);
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347 }
1702
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348 }
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349
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parents:
diff changeset
350
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parents:
diff changeset
351 SliceOrdering::~SliceOrdering()
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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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parents: 1702
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())
b80e76dd1d56 ordered-slices continued
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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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parents: 1702
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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parents: 1702
diff changeset
382 }
b80e76dd1d56 ordered-slices continued
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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 {
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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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parents: 1702
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
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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
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parents: 1702
diff changeset
412 }
1873
5e7feeb63d1f SlicesShort
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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
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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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parents: 1702
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 }