Mercurial > hg > orthanc

annotate OrthancServer/SliceOrdering.cpp @ 3535:41365091a41e

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display a security warning in the logs at startup when ExecuteLuaEnabled is true
author Alain Mazy <alain@mazy.be>
date Sun, 06 Oct 2019 09:52:57 +0200
parents 4bced7d1ec20
children 23219b9da4d1
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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) 2017-2019 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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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 #include "ServerIndex.h"
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41
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42 #include <algorithm>
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43 #include <boost/lexical_cast.hpp>
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44 #include <boost/noncopyable.hpp>
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46
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47 namespace Orthanc
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48 {
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49 static bool TokenizeVector(std::vector<float>& result,
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50 const std::string& value,
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51 unsigned int expectedSize)
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52 {
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53 std::vector<std::string> tokens;
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54 Toolbox::TokenizeString(tokens, value, '\\');
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55
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56 if (tokens.size() != expectedSize)
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57 {
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58 return false;
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59 }
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60
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61 result.resize(tokens.size());
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62
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63 for (size_t i = 0; i < tokens.size(); i++)
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64 {
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65 try
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66 {
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67 result[i] = boost::lexical_cast<float>(tokens[i]);
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68 }
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69 catch (boost::bad_lexical_cast&)
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70 {
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71 return false;
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72 }
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73 }
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74
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75 return true;
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76 }
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78
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79 static bool TokenizeVector(std::vector<float>& result,
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80 const DicomMap& map,
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81 const DicomTag& tag,
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82 unsigned int expectedSize)
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83 {
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84 const DicomValue* value = map.TestAndGetValue(tag);
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85
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86 if (value == NULL ||
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87 value->IsNull() ||
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88 value->IsBinary())
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89 {
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90 return false;
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91 }
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92 else
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93 {
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94 return TokenizeVector(result, value->GetContent(), expectedSize);
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95 }
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96 }
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98
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99 static bool IsCloseToZero(double x)
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100 {
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101 return fabs(x) < 10.0 * std::numeric_limits<float>::epsilon();
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102 }
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103
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104
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105 bool SliceOrdering::ComputeNormal(Vector& normal,
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106 const DicomMap& dicom)
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107 {
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108 std::vector<float> cosines;
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109
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110 if (TokenizeVector(cosines, dicom, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6))
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111 {
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112 assert(cosines.size() == 6);
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113 normal[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4];
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114 normal[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5];
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115 normal[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3];
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116 return true;
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117 }
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118 else
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119 {
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120 return false;
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121 }
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122 }
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123
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124
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125 bool SliceOrdering::IsParallelOrOpposite(const Vector& u,
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126 const Vector& v)
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127 {
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128 // Check out "GeometryToolbox::IsParallelOrOpposite()" in Stone of
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129 // Orthanc for explanations
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130 const double u1 = u[0];
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131 const double u2 = u[1];
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132 const double u3 = u[2];
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133 const double normU = sqrt(u1 * u1 + u2 * u2 + u3 * u3);
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134
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135 const double v1 = v[0];
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136 const double v2 = v[1];
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137 const double v3 = v[2];
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138 const double normV = sqrt(v1 * v1 + v2 * v2 + v3 * v3);
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139
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140 if (IsCloseToZero(normU * normV))
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141 {
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142 return false;
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143 }
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144 else
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145 {
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146 const double cosAngle = (u1 * v1 + u2 * v2 + u3 * v3) / (normU * normV);
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147
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148 return (IsCloseToZero(cosAngle - 1.0) || // Close to +1: Parallel, non-opposite
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149 IsCloseToZero(fabs(cosAngle) - 1.0)); // Close to -1: Parallel, opposite
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150 }
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151 }
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152
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153
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154 struct SliceOrdering::Instance : public boost::noncopyable
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155 {
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156 private:
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157 std::string instanceId_;
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158 bool hasPosition_;
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159 Vector position_;
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160 bool hasNormal_;
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161 Vector normal_;
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162 bool hasIndexInSeries_;
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163 size_t indexInSeries_;
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164 unsigned int framesCount_;
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165
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166 public:
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167 Instance(ServerIndex& index,
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168 const std::string& instanceId) :
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169 instanceId_(instanceId),
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170 framesCount_(1)
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171 {
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172 DicomMap instance;
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173 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance))
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174 {
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175 throw OrthancException(ErrorCode_UnknownResource);
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176 }
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177
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178 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES);
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179 if (frames != NULL &&
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180 !frames->IsNull() &&
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181 !frames->IsBinary())
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182 {
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183 try
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184 {
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185 framesCount_ = boost::lexical_cast<unsigned int>(frames->GetContent());
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186 }
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187 catch (boost::bad_lexical_cast&)
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188 {
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189 }
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190 }
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191
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192 std::vector<float> tmp;
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193 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3);
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194
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195 if (hasPosition_)
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196 {
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197 position_[0] = tmp[0];
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198 position_[1] = tmp[1];
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199 position_[2] = tmp[2];
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200 }
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201
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202 hasNormal_ = ComputeNormal(normal_, instance);
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203
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204 std::string s;
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205 hasIndexInSeries_ = false;
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206
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207 try
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208 {
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209 if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries))
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210 {
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211 indexInSeries_ = boost::lexical_cast<size_t>(s);
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212 hasIndexInSeries_ = true;
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213 }
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214 }
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215 catch (boost::bad_lexical_cast&)
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216 {
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217 }
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218 }
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219
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220 const std::string& GetIdentifier() const
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221 {
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222 return instanceId_;
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223 }
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224
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225 bool HasPosition() const
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226 {
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227 return hasPosition_;
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228 }
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229
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230 float ComputeRelativePosition(const Vector& normal) const
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231 {
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232 assert(HasPosition());
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233 return (normal[0] * position_[0] +
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234 normal[1] * position_[1] +
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235 normal[2] * position_[2]);
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236 }
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237
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238 bool HasIndexInSeries() const
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239 {
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240 return hasIndexInSeries_;
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241 }
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242
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243 size_t GetIndexInSeries() const
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244 {
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245 assert(HasIndexInSeries());
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246 return indexInSeries_;
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247 }
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248
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249 unsigned int GetFramesCount() const
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250 {
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251 return framesCount_;
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252 }
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253
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254 bool HasNormal() const
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255 {
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256 return hasNormal_;
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257 }
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258
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259 const Vector& GetNormal() const
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260 {
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261 assert(hasNormal_);
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262 return normal_;
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263 }
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264 };
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265
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266
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267 class SliceOrdering::PositionComparator
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268 {
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269 private:
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270 const Vector& normal_;
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271
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272 public:
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273 PositionComparator(const Vector& normal) : normal_(normal)
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274 {
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275 }
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276
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277 int operator() (const Instance* a,
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278 const Instance* b) const
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279 {
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280 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_);
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281 }
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282 };
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283
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284
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285 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a,
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286 const SliceOrdering::Instance* b)
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287 {
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288 return a->GetIndexInSeries() < b->GetIndexInSeries();
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289 }
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290
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291
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292 void SliceOrdering::ComputeNormal()
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293 {
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294 DicomMap series;
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295 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series))
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296 {
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297 throw OrthancException(ErrorCode_UnknownResource);
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298 }
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299
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300 hasNormal_ = ComputeNormal(normal_, series);
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301 }
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302
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303
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304 void SliceOrdering::CreateInstances()
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305 {
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306 std::list<std::string> instancesId;
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307 index_.GetChildren(instancesId, seriesId_);
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308
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309 instances_.reserve(instancesId.size());
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310 for (std::list<std::string>::const_iterator
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311 it = instancesId.begin(); it != instancesId.end(); ++it)
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312 {
3512
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313 std::auto_ptr<Instance> instance(new Instance(index_, *it));
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314 if (instance->HasPosition() || instance->HasNormal() || instance->HasIndexInSeries())
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315 {
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316 instances_.push_back(instance.release());
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317 }
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318 }
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319 }
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320
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321
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322 bool SliceOrdering::SortUsingPositions()
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323 {
1703
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324 if (instances_.size() <= 1)
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325 {
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326 // One single instance: It is sorted by default
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327 return true;
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328 }
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329
1702
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330 if (!hasNormal_)
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331 {
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332 return false;
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333 }
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334
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335 for (size_t i = 0; i < instances_.size(); i++)
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336 {
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337 assert(instances_[i] != NULL);
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338
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339 if (!instances_[i]->HasPosition() ||
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340 (instances_[i]->HasNormal() &&
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341 !IsParallelOrOpposite(instances_[i]->GetNormal(), normal_)))
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342 {
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343 return false;
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344 }
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345 }
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346
1703
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347 PositionComparator comparator(normal_);
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348 std::sort(instances_.begin(), instances_.end(), comparator);
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349
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350 float a = instances_[0]->ComputeRelativePosition(normal_);
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351 for (size_t i = 1; i < instances_.size(); i++)
1703
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352 {
1842
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353 float b = instances_[i]->ComputeRelativePosition(normal_);
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354
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355 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon())
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356 {
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357 // Not enough space between two slices along the normal of the volume
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358 return false;
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359 }
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360
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361 a = b;
1703
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362 }
1842
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363
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364 // This is a 3D volume
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365 isVolume_ = true;
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366 return true;
1703
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367 }
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368
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369
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370 bool SliceOrdering::SortUsingIndexInSeries()
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371 {
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372 if (instances_.size() <= 1)
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373 {
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374 // One single instance: It is sorted by default
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375 return true;
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376 }
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377
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378 for (size_t i = 0; i < instances_.size(); i++)
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379 {
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380 assert(instances_[i] != NULL);
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381 if (!instances_[i]->HasIndexInSeries())
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382 {
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383 return false;
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384 }
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385 }
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386
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diff changeset
387 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator);
1702
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388
1703
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389 for (size_t i = 1; i < instances_.size(); i++)
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390 {
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391 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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392 {
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393 // The current "IndexInSeries" occurs 2 times: Not a proper ordering
1868
c8877965d67d More tolerant "/series/.../ordered-slices" with broken series
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parents: 1844
diff changeset
394 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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diff changeset
395 break;
1703
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396 }
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397 }
1702
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parents:
diff changeset
398
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diff changeset
399 return true;
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parents:
diff changeset
400 }
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parents:
diff changeset
401
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parents:
diff changeset
402
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diff changeset
403 SliceOrdering::SliceOrdering(ServerIndex& index,
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diff changeset
404 const std::string& seriesId) :
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diff changeset
405 index_(index),
1703
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diff changeset
406 seriesId_(seriesId),
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diff changeset
407 isVolume_(false)
1702
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parents:
diff changeset
408 {
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diff changeset
409 ComputeNormal();
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parents:
diff changeset
410 CreateInstances();
1703
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diff changeset
411
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diff changeset
412 if (!SortUsingPositions() &&
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
413 !SortUsingIndexInSeries())
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
414 {
2955
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2804
diff changeset
415 throw OrthancException(ErrorCode_CannotOrderSlices,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2804
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416 "Unable to order the slices of series " + seriesId);
1703
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parents: 1702
diff changeset
417 }
1702
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parents:
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418 }
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parents:
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419
9980875edc7c started work on SliceOrdering
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parents:
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420
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parents:
diff changeset
421 SliceOrdering::~SliceOrdering()
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parents:
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422 {
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parents:
diff changeset
423 for (std::vector<Instance*>::iterator
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parents:
diff changeset
424 it = instances_.begin(); it != instances_.end(); ++it)
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parents:
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425 {
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parents:
diff changeset
426 if (*it != NULL)
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parents:
diff changeset
427 {
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parents:
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428 delete *it;
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parents:
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429 }
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parents:
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430 }
9980875edc7c started work on SliceOrdering
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parents:
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431 }
1703
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parents: 1702
diff changeset
432
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parents: 1702
diff changeset
433
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parents: 1702
diff changeset
434 const std::string& SliceOrdering::GetInstanceId(size_t index) const
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parents: 1702
diff changeset
435 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
436 if (index >= instances_.size())
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parents: 1702
diff changeset
437 {
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parents: 1702
diff changeset
438 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 1702
diff changeset
439 }
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parents: 1702
diff changeset
440 else
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parents: 1702
diff changeset
441 {
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parents: 1702
diff changeset
442 return instances_[index]->GetIdentifier();
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parents: 1702
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443 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
444 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
445
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parents: 1702
diff changeset
446
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parents: 1702
diff changeset
447 unsigned int SliceOrdering::GetFramesCount(size_t index) const
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parents: 1702
diff changeset
448 {
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parents: 1702
diff changeset
449 if (index >= instances_.size())
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parents: 1702
diff changeset
450 {
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parents: 1702
diff changeset
451 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 1702
diff changeset
452 }
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
453 else
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
454 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
455 return instances_[index]->GetFramesCount();
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
456 }
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
457 }
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
458
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
459
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
460 void SliceOrdering::Format(Json::Value& result) const
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
461 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
462 result = Json::objectValue;
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
463 result["Type"] = (isVolume_ ? "Volume" : "Sequence");
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
464
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
465 Json::Value tmp = Json::arrayValue;
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
466 for (size_t i = 0; i < GetInstancesCount(); i++)
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
467 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
468 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file");
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
469 }
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
470
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parents: 1702
diff changeset
471 result["Dicom"] = tmp;
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
472
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
473 Json::Value slicesShort = Json::arrayValue;
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
474
1703
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parents: 1702
diff changeset
475 tmp.clear();
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
476 for (size_t i = 0; i < GetInstancesCount(); i++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
477 {
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
478 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i));
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
479 for (size_t j = 0; j < GetFramesCount(i); j++)
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
480 {
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
481 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j));
b80e76dd1d56 ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1702
diff changeset
482 }
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
483
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
484 Json::Value tmp2 = Json::arrayValue;
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
485 tmp2.append(GetInstanceId(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
486 tmp2.append(0);
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
487 tmp2.append(GetFramesCount(i));
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
488
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
489 slicesShort.append(tmp2);
1703
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
490 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
491
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
492 result["Slices"] = tmp;
1873
5e7feeb63d1f SlicesShort
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1868
diff changeset
493 result["SlicesShort"] = slicesShort;
1703
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
494 }
1702
9980875edc7c started work on SliceOrdering
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 }