Mercurial > hg > orthanc
annotate OrthancServer/SliceOrdering.cpp @ 3535:41365091a41e
display a security warning in the logs at startup when ExecuteLuaEnabled is true
author | Alain Mazy <alain@mazy.be> |
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date | Sun, 06 Oct 2019 09:52:57 +0200 |
parents | 4bced7d1ec20 |
children | 23219b9da4d1 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 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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32 |
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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" |
3097 | 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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45 |
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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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77 |
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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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97 |
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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 { |
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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 { |
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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 |
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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 |
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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++) |
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352 { |
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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; |
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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; |
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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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387 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator); |
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388 |
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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 |
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394 LOG(WARNING) << "This series contains 2 slices with the same index, trying to display it anyway"; |
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395 break; |
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396 } |
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397 } |
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398 |
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399 return true; |
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400 } |
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401 |
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402 |
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403 SliceOrdering::SliceOrdering(ServerIndex& index, |
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404 const std::string& seriesId) : |
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405 index_(index), |
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406 seriesId_(seriesId), |
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407 isVolume_(false) |
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408 { |
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409 ComputeNormal(); |
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410 CreateInstances(); |
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411 |
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412 if (!SortUsingPositions() && |
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413 !SortUsingIndexInSeries()) |
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414 { |
2955 | 415 throw OrthancException(ErrorCode_CannotOrderSlices, |
416 "Unable to order the slices of series " + seriesId); | |
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417 } |
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418 } |
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419 |
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420 |
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421 SliceOrdering::~SliceOrdering() |
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422 { |
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423 for (std::vector<Instance*>::iterator |
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424 it = instances_.begin(); it != instances_.end(); ++it) |
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425 { |
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426 if (*it != NULL) |
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427 { |
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428 delete *it; |
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429 } |
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430 } |
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431 } |
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432 |
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433 |
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434 const std::string& SliceOrdering::GetInstanceId(size_t index) const |
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435 { |
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436 if (index >= instances_.size()) |
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437 { |
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438 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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439 } |
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440 else |
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441 { |
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442 return instances_[index]->GetIdentifier(); |
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443 } |
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444 } |
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445 |
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446 |
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447 unsigned int SliceOrdering::GetFramesCount(size_t index) const |
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448 { |
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449 if (index >= instances_.size()) |
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450 { |
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451 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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452 } |
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453 else |
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454 { |
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455 return instances_[index]->GetFramesCount(); |
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456 } |
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457 } |
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458 |
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459 |
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460 void SliceOrdering::Format(Json::Value& result) const |
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461 { |
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462 result = Json::objectValue; |
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463 result["Type"] = (isVolume_ ? "Volume" : "Sequence"); |
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464 |
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465 Json::Value tmp = Json::arrayValue; |
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466 for (size_t i = 0; i < GetInstancesCount(); i++) |
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467 { |
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468 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file"); |
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469 } |
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470 |
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471 result["Dicom"] = tmp; |
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472 |
1873 | 473 Json::Value slicesShort = Json::arrayValue; |
474 | |
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475 tmp.clear(); |
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476 for (size_t i = 0; i < GetInstancesCount(); i++) |
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477 { |
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478 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i)); |
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479 for (size_t j = 0; j < GetFramesCount(i); j++) |
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480 { |
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481 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j)); |
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482 } |
1873 | 483 |
484 Json::Value tmp2 = Json::arrayValue; | |
485 tmp2.append(GetInstanceId(i)); | |
486 tmp2.append(0); | |
487 tmp2.append(GetFramesCount(i)); | |
488 | |
489 slicesShort.append(tmp2); | |
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490 } |
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ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
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491 |
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492 result["Slices"] = tmp; |
1873 | 493 result["SlicesShort"] = slicesShort; |
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494 } |
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495 } |