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annotate OrthancServer/SliceOrdering.cpp @ 3007:c9f93628215a

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author am@osimis.io
date Thu, 13 Dec 2018 14:48:23 +0100
parents bbfd95a0c429
children 4e43e67f8ecf
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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) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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33
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34 #include "PrecompiledHeadersServer.h"
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35 #include "SliceOrdering.h"
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36
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37 #include "../Core/Logging.h"
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38 #include "../Core/Toolbox.h"
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39 #include "ServerEnumerations.h"
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40
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41 #include <algorithm>
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42 #include <boost/lexical_cast.hpp>
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43 #include <boost/noncopyable.hpp>
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45
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46 namespace Orthanc
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47 {
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48 static bool TokenizeVector(std::vector<float>& result,
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49 const std::string& value,
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50 unsigned int expectedSize)
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51 {
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52 std::vector<std::string> tokens;
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53 Toolbox::TokenizeString(tokens, value, '\\');
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54
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55 if (tokens.size() != expectedSize)
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56 {
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57 return false;
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58 }
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59
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60 result.resize(tokens.size());
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61
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62 for (size_t i = 0; i < tokens.size(); i++)
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63 {
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64 try
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65 {
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66 result[i] = boost::lexical_cast<float>(tokens[i]);
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67 }
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68 catch (boost::bad_lexical_cast&)
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69 {
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70 return false;
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71 }
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72 }
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73
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74 return true;
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75 }
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78 static bool TokenizeVector(std::vector<float>& result,
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79 const DicomMap& map,
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80 const DicomTag& tag,
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81 unsigned int expectedSize)
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82 {
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83 const DicomValue* value = map.TestAndGetValue(tag);
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84
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85 if (value == NULL ||
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86 value->IsNull() ||
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87 value->IsBinary())
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88 {
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89 return false;
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90 }
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91 else
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92 {
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93 return TokenizeVector(result, value->GetContent(), expectedSize);
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94 }
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95 }
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97
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98 static bool IsCloseToZero(double x)
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99 {
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100 return fabs(x) < 10.0 * std::numeric_limits<float>::epsilon();
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101 }
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102
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103
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104 bool SliceOrdering::ComputeNormal(Vector& normal,
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105 const DicomMap& dicom)
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106 {
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107 std::vector<float> cosines;
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108
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109 if (TokenizeVector(cosines, dicom, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6))
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110 {
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111 assert(cosines.size() == 6);
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112 normal[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4];
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113 normal[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5];
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114 normal[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3];
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115 return true;
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116 }
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117 else
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118 {
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119 return false;
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120 }
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121 }
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122
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123
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124 bool SliceOrdering::IsParallelOrOpposite(const Vector& u,
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125 const Vector& v)
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126 {
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127 // Check out "GeometryToolbox::IsParallelOrOpposite()" in Stone of
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128 // Orthanc for explanations
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129 const double u1 = u[0];
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130 const double u2 = u[1];
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131 const double u3 = u[2];
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132 const double normU = sqrt(u1 * u1 + u2 * u2 + u3 * u3);
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133
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134 const double v1 = v[0];
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135 const double v2 = v[1];
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136 const double v3 = v[2];
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137 const double normV = sqrt(v1 * v1 + v2 * v2 + v3 * v3);
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138
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139 if (IsCloseToZero(normU * normV))
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140 {
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141 return false;
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142 }
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143 else
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144 {
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145 const double cosAngle = (u1 * v1 + u2 * v2 + u3 * v3) / (normU * normV);
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146
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147 return (IsCloseToZero(cosAngle - 1.0) || // Close to +1: Parallel, non-opposite
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148 IsCloseToZero(fabs(cosAngle) - 1.0)); // Close to -1: Parallel, opposite
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149 }
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150 }
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151
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152
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153 struct SliceOrdering::Instance : public boost::noncopyable
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154 {
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155 private:
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156 std::string instanceId_;
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157 bool hasPosition_;
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158 Vector position_;
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159 bool hasNormal_;
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160 Vector normal_;
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161 bool hasIndexInSeries_;
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162 size_t indexInSeries_;
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163 unsigned int framesCount_;
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164
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165 public:
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166 Instance(ServerIndex& index,
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167 const std::string& instanceId) :
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168 instanceId_(instanceId),
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169 framesCount_(1)
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170 {
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171 DicomMap instance;
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172 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance))
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173 {
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174 throw OrthancException(ErrorCode_UnknownResource);
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175 }
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176
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177 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES);
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178 if (frames != NULL &&
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179 !frames->IsNull() &&
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180 !frames->IsBinary())
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181 {
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182 try
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183 {
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184 framesCount_ = boost::lexical_cast<unsigned int>(frames->GetContent());
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185 }
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186 catch (boost::bad_lexical_cast&)
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187 {
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188 }
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189 }
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190
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191 std::vector<float> tmp;
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192 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3);
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193
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194 if (hasPosition_)
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195 {
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196 position_[0] = tmp[0];
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197 position_[1] = tmp[1];
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198 position_[2] = tmp[2];
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199 }
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200
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201 hasNormal_ = ComputeNormal(normal_, instance);
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202
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203 std::string s;
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204 hasIndexInSeries_ = false;
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205
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206 try
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207 {
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208 if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries))
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209 {
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210 indexInSeries_ = boost::lexical_cast<size_t>(s);
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211 hasIndexInSeries_ = true;
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212 }
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213 }
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214 catch (boost::bad_lexical_cast&)
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215 {
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216 }
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217 }
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218
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219 const std::string& GetIdentifier() const
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220 {
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221 return instanceId_;
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222 }
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223
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224 bool HasPosition() const
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225 {
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226 return hasPosition_;
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227 }
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228
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229 float ComputeRelativePosition(const Vector& normal) const
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230 {
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231 assert(HasPosition());
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232 return (normal[0] * position_[0] +
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233 normal[1] * position_[1] +
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234 normal[2] * position_[2]);
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235 }
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236
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237 bool HasIndexInSeries() const
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238 {
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239 return hasIndexInSeries_;
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240 }
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241
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242 size_t GetIndexInSeries() const
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243 {
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244 assert(HasIndexInSeries());
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245 return indexInSeries_;
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246 }
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247
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248 unsigned int GetFramesCount() const
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249 {
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250 return framesCount_;
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251 }
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252
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253 bool HasNormal() const
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254 {
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255 return hasNormal_;
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256 }
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257
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258 const Vector& GetNormal() const
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259 {
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260 assert(hasNormal_);
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261 return normal_;
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262 }
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263 };
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264
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265
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266 class SliceOrdering::PositionComparator
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267 {
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268 private:
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269 const Vector& normal_;
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270
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271 public:
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272 PositionComparator(const Vector& normal) : normal_(normal)
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273 {
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274 }
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275
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276 int operator() (const Instance* a,
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277 const Instance* b) const
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278 {
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279 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_);
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280 }
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281 };
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282
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283
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284 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a,
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285 const SliceOrdering::Instance* b)
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286 {
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287 return a->GetIndexInSeries() < b->GetIndexInSeries();
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288 }
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289
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290
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291 void SliceOrdering::ComputeNormal()
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292 {
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293 DicomMap series;
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294 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series))
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295 {
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296 throw OrthancException(ErrorCode_UnknownResource);
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297 }
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298
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299 hasNormal_ = ComputeNormal(normal_, series);
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300 }
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301
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302
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303 void SliceOrdering::CreateInstances()
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304 {
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305 std::list<std::string> instancesId;
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306 index_.GetChildren(instancesId, seriesId_);
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307
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308 instances_.reserve(instancesId.size());
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309 for (std::list<std::string>::const_iterator
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310 it = instancesId.begin(); it != instancesId.end(); ++it)
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311 {
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312 instances_.push_back(new Instance(index_, *it));
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313 }
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314 }
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315
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316
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317 bool SliceOrdering::SortUsingPositions()
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318 {
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319 if (instances_.size() <= 1)
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320 {
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321 // One single instance: It is sorted by default
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322 return true;
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323 }
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324
1702
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325 if (!hasNormal_)
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326 {
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327 return false;
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328 }
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329
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330 for (size_t i = 0; i < instances_.size(); i++)
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331 {
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332 assert(instances_[i] != NULL);
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333
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334 if (!instances_[i]->HasPosition() ||
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335 (instances_[i]->HasNormal() &&
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336 !IsParallelOrOpposite(instances_[i]->GetNormal(), normal_)))
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337 {
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338 return false;
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339 }
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340 }
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341
1703
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342 PositionComparator comparator(normal_);
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343 std::sort(instances_.begin(), instances_.end(), comparator);
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344
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345 float a = instances_[0]->ComputeRelativePosition(normal_);
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346 for (size_t i = 1; i < instances_.size(); i++)
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347 {
1842
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348 float b = instances_[i]->ComputeRelativePosition(normal_);
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349
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350 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon())
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351 {
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352 // Not enough space between two slices along the normal of the volume
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353 return false;
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354 }
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355
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356 a = b;
1703
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357 }
1842
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358
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359 // This is a 3D volume
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360 isVolume_ = true;
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361 return true;
1703
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362 }
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363
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364
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365 bool SliceOrdering::SortUsingIndexInSeries()
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366 {
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367 if (instances_.size() <= 1)
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368 {
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369 // One single instance: It is sorted by default
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370 return true;
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371 }
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372
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373 for (size_t i = 0; i < instances_.size(); i++)
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374 {
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375 assert(instances_[i] != NULL);
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376 if (!instances_[i]->HasIndexInSeries())
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377 {
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378 return false;
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379 }
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380 }
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381
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diff changeset
382 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator);
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383
1703
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diff changeset
384 for (size_t i = 1; i < instances_.size(); i++)
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diff changeset
385 {
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diff changeset
386 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries())
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diff changeset
387 {
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diff changeset
388 // The current "IndexInSeries" occurs 2 times: Not a proper ordering
1868
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parents: 1844
diff changeset
389 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
390 break;
1703
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diff changeset
391 }
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392 }
1702
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diff changeset
393
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diff changeset
394 return true;
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parents:
diff changeset
395 }
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diff changeset
396
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diff changeset
397
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diff changeset
398 SliceOrdering::SliceOrdering(ServerIndex& index,
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diff changeset
399 const std::string& seriesId) :
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diff changeset
400 index_(index),
1703
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diff changeset
401 seriesId_(seriesId),
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diff changeset
402 isVolume_(false)
1702
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diff changeset
403 {
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diff changeset
404 ComputeNormal();
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diff changeset
405 CreateInstances();
1703
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diff changeset
406
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diff changeset
407 if (!SortUsingPositions() &&
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parents: 1702
diff changeset
408 !SortUsingIndexInSeries())
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diff changeset
409 {
2955
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parents: 2804
diff changeset
410 throw OrthancException(ErrorCode_CannotOrderSlices,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2804
diff changeset
411 "Unable to order the slices of series " + seriesId);
1703
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diff changeset
412 }
1702
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parents:
diff changeset
413 }
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parents:
diff changeset
414
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415
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416 SliceOrdering::~SliceOrdering()
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417 {
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418 for (std::vector<Instance*>::iterator
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419 it = instances_.begin(); it != instances_.end(); ++it)
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420 {
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421 if (*it != NULL)
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422 {
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423 delete *it;
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424 }
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425 }
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426 }
1703
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427
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428
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429 const std::string& SliceOrdering::GetInstanceId(size_t index) const
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430 {
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431 if (index >= instances_.size())
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432 {
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433 throw OrthancException(ErrorCode_ParameterOutOfRange);
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434 }
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435 else
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436 {
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437 return instances_[index]->GetIdentifier();
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438 }
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439 }
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440
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441
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442 unsigned int SliceOrdering::GetFramesCount(size_t index) const
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443 {
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444 if (index >= instances_.size())
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445 {
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446 throw OrthancException(ErrorCode_ParameterOutOfRange);
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447 }
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448 else
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449 {
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450 return instances_[index]->GetFramesCount();
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451 }
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452 }
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diff changeset
453
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parents: 1702
diff changeset
454
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455 void SliceOrdering::Format(Json::Value& result) const
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parents: 1702
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456 {
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457 result = Json::objectValue;
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458 result["Type"] = (isVolume_ ? "Volume" : "Sequence");
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parents: 1702
diff changeset
459
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diff changeset
460 Json::Value tmp = Json::arrayValue;
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diff changeset
461 for (size_t i = 0; i < GetInstancesCount(); i++)
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462 {
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463 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file");
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diff changeset
464 }
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parents: 1702
diff changeset
465
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466 result["Dicom"] = tmp;
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diff changeset
467
1873
5e7feeb63d1f SlicesShort
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diff changeset
468 Json::Value slicesShort = Json::arrayValue;
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
469
1703
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diff changeset
470 tmp.clear();
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diff changeset
471 for (size_t i = 0; i < GetInstancesCount(); i++)
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diff changeset
472 {
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diff changeset
473 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i));
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diff changeset
474 for (size_t j = 0; j < GetFramesCount(i); j++)
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diff changeset
475 {
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diff changeset
476 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j));
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parents: 1702
diff changeset
477 }
1873
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
478
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
479 Json::Value tmp2 = Json::arrayValue;
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diff changeset
480 tmp2.append(GetInstanceId(i));
5e7feeb63d1f SlicesShort
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diff changeset
481 tmp2.append(0);
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
482 tmp2.append(GetFramesCount(i));
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
483
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
484 slicesShort.append(tmp2);
1703
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diff changeset
485 }
b80e76dd1d56 ordered-slices continued
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parents: 1702
diff changeset
486
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diff changeset
487 result["Slices"] = tmp;
1873
5e7feeb63d1f SlicesShort
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parents: 1868
diff changeset
488 result["SlicesShort"] = slicesShort;
1703
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diff changeset
489 }
1702
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diff changeset
490 }