Mercurial > hg > orthanc
annotate OrthancServer/Sources/SliceOrdering.cpp @ 5834:79a497908b04 attach-custom-data tip
merged find-refactoring -> attach-custom-data
author | Alain Mazy <am@orthanc.team> |
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date | Wed, 09 Oct 2024 11:06:20 +0200 |
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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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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8 * |
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9 * This program is free software: you can redistribute it and/or |
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10 * modify it under the terms of the GNU General Public License as |
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11 * published by the Free Software Foundation, either version 3 of the |
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12 * License, or (at your option) any later version. |
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13 * |
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14 * This program is distributed in the hope that it will be useful, but |
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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17 * General Public License for more details. |
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18 * |
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19 * You should have received a copy of the GNU General Public License |
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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21 **/ |
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22 |
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23 |
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24 #include "PrecompiledHeadersServer.h" |
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25 #include "SliceOrdering.h" |
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26 |
4045 | 27 #include "../../OrthancFramework/Sources/Logging.h" |
28 #include "../../OrthancFramework/Sources/Toolbox.h" | |
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29 #include "ServerEnumerations.h" |
3097 | 30 #include "ServerIndex.h" |
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31 |
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32 #include <algorithm> |
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33 #include <boost/lexical_cast.hpp> |
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34 #include <boost/noncopyable.hpp> |
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35 |
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36 |
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37 namespace Orthanc |
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38 { |
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39 static bool TokenizeVector(std::vector<float>& result, |
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40 const std::string& value, |
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41 unsigned int expectedSize) |
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42 { |
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43 std::vector<std::string> tokens; |
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44 Toolbox::TokenizeString(tokens, value, '\\'); |
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45 |
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46 if (tokens.size() != expectedSize) |
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47 { |
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48 return false; |
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49 } |
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50 |
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51 result.resize(tokens.size()); |
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52 |
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53 for (size_t i = 0; i < tokens.size(); i++) |
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54 { |
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55 try |
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56 { |
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57 const std::string token = Toolbox::StripSpaces(tokens[i]); |
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58 result[i] = boost::lexical_cast<float>(token); |
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59 } |
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60 catch (boost::bad_lexical_cast&) |
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61 { |
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62 return false; |
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63 } |
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64 } |
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65 |
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66 return true; |
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67 } |
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68 |
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69 |
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70 static bool TokenizeVector(std::vector<float>& result, |
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71 const DicomMap& map, |
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72 const DicomTag& tag, |
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73 unsigned int expectedSize) |
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74 { |
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75 const DicomValue* value = map.TestAndGetValue(tag); |
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76 |
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77 if (value == NULL || |
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78 value->IsNull() || |
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79 value->IsBinary()) |
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80 { |
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81 return false; |
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82 } |
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83 else |
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84 { |
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85 return TokenizeVector(result, value->GetContent(), expectedSize); |
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86 } |
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87 } |
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88 |
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89 |
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90 static bool IsCloseToZero(double x) |
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91 { |
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92 return fabs(x) < 10.0 * std::numeric_limits<float>::epsilon(); |
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93 } |
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94 |
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95 |
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96 bool SliceOrdering::ComputeNormal(Vector& normal, |
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97 const DicomMap& dicom) |
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98 { |
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99 std::vector<float> cosines; |
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100 |
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101 if (TokenizeVector(cosines, dicom, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6)) |
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102 { |
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103 assert(cosines.size() == 6); |
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104 normal[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; |
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105 normal[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; |
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106 normal[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; |
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107 return true; |
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108 } |
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109 else |
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110 { |
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111 return false; |
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112 } |
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113 } |
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114 |
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115 |
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116 bool SliceOrdering::IsParallelOrOpposite(const Vector& u, |
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117 const Vector& v) |
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118 { |
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119 // Check out "GeometryToolbox::IsParallelOrOpposite()" in Stone of |
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120 // Orthanc for explanations |
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121 const double u1 = u[0]; |
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122 const double u2 = u[1]; |
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123 const double u3 = u[2]; |
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124 const double normU = sqrt(u1 * u1 + u2 * u2 + u3 * u3); |
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125 |
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126 const double v1 = v[0]; |
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127 const double v2 = v[1]; |
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128 const double v3 = v[2]; |
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129 const double normV = sqrt(v1 * v1 + v2 * v2 + v3 * v3); |
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130 |
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131 if (IsCloseToZero(normU * normV)) |
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132 { |
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133 return false; |
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134 } |
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135 else |
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136 { |
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137 const double cosAngle = (u1 * v1 + u2 * v2 + u3 * v3) / (normU * normV); |
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138 |
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139 return (IsCloseToZero(cosAngle - 1.0) || // Close to +1: Parallel, non-opposite |
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140 IsCloseToZero(fabs(cosAngle) - 1.0)); // Close to -1: Parallel, opposite |
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141 } |
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142 } |
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143 |
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144 |
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145 struct SliceOrdering::Instance : public boost::noncopyable |
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146 { |
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147 private: |
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148 std::string instanceId_; |
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149 bool hasPosition_; |
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150 Vector position_; |
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151 bool hasNormal_; |
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152 Vector normal_; |
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153 bool hasIndexInSeries_; |
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154 size_t indexInSeries_; |
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155 unsigned int framesCount_; |
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156 |
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157 public: |
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158 Instance(ServerIndex& index, |
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159 const std::string& instanceId) : |
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160 instanceId_(instanceId), |
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161 framesCount_(1) |
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162 { |
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163 DicomMap instance; |
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164 if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance)) |
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165 { |
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166 throw OrthancException(ErrorCode_UnknownResource); |
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167 } |
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168 |
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169 const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES); |
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170 if (frames != NULL && |
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171 !frames->IsNull() && |
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172 !frames->IsBinary()) |
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173 { |
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174 try |
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175 { |
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176 const std::string token = Toolbox::StripSpaces(frames->GetContent()); |
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177 framesCount_ = boost::lexical_cast<unsigned int>(token); |
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178 } |
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179 catch (boost::bad_lexical_cast&) |
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180 { |
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181 } |
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182 } |
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183 |
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184 std::vector<float> tmp; |
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185 hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3); |
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186 |
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187 if (hasPosition_) |
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188 { |
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189 position_[0] = tmp[0]; |
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190 position_[1] = tmp[1]; |
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191 position_[2] = tmp[2]; |
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192 } |
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193 |
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194 hasNormal_ = ComputeNormal(normal_, instance); |
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195 |
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196 std::string s; |
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197 hasIndexInSeries_ = false; |
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198 |
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199 try |
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200 { |
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201 int64_t revision; // Ignored |
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202 if (index.LookupMetadata(s, revision, instanceId, ResourceType_Instance, MetadataType_Instance_IndexInSeries)) |
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203 { |
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204 indexInSeries_ = boost::lexical_cast<size_t>(Toolbox::StripSpaces(s)); |
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205 hasIndexInSeries_ = true; |
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206 } |
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207 } |
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208 catch (boost::bad_lexical_cast&) |
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209 { |
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210 } |
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211 } |
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212 |
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213 const std::string& GetIdentifier() const |
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214 { |
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215 return instanceId_; |
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216 } |
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217 |
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218 bool HasPosition() const |
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219 { |
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220 return hasPosition_; |
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221 } |
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222 |
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223 float ComputeRelativePosition(const Vector& normal) const |
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224 { |
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225 assert(HasPosition()); |
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226 return (normal[0] * position_[0] + |
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227 normal[1] * position_[1] + |
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228 normal[2] * position_[2]); |
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229 } |
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230 |
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231 bool HasIndexInSeries() const |
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232 { |
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233 return hasIndexInSeries_; |
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234 } |
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235 |
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236 size_t GetIndexInSeries() const |
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237 { |
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238 assert(HasIndexInSeries()); |
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239 return indexInSeries_; |
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240 } |
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241 |
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242 unsigned int GetFramesCount() const |
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243 { |
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244 return framesCount_; |
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245 } |
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246 |
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247 bool HasNormal() const |
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248 { |
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249 return hasNormal_; |
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250 } |
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251 |
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252 const Vector& GetNormal() const |
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253 { |
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254 assert(hasNormal_); |
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255 return normal_; |
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256 } |
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257 }; |
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258 |
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259 |
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260 class SliceOrdering::PositionComparator |
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261 { |
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262 private: |
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263 const Vector& normal_; |
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264 |
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265 public: |
4205 | 266 explicit PositionComparator(const Vector& normal) : normal_(normal) |
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267 { |
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268 } |
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269 |
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270 int operator() (const Instance* a, |
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271 const Instance* b) const |
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272 { |
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273 return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_); |
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274 } |
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275 }; |
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276 |
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277 |
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278 bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a, |
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279 const SliceOrdering::Instance* b) |
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280 { |
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281 return a->GetIndexInSeries() < b->GetIndexInSeries(); |
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282 } |
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283 |
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284 |
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285 void SliceOrdering::ComputeNormal() |
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286 { |
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287 DicomMap series; |
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288 if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series)) |
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289 { |
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290 throw OrthancException(ErrorCode_UnknownResource); |
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291 } |
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292 |
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293 hasNormal_ = ComputeNormal(normal_, series); |
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294 } |
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295 |
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296 |
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297 void SliceOrdering::CreateInstances() |
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298 { |
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299 std::list<std::string> instancesId; |
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300 index_.GetChildren(instancesId, seriesId_); |
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301 |
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302 instances_.reserve(instancesId.size()); |
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303 for (std::list<std::string>::const_iterator |
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304 it = instancesId.begin(); it != instancesId.end(); ++it) |
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305 { |
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306 instances_.push_back(new Instance(index_, *it)); |
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307 } |
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308 } |
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309 |
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310 |
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311 bool SliceOrdering::SortUsingPositions() |
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312 { |
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313 if (instances_.size() <= 1) |
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314 { |
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315 // One single instance: It is sorted by default |
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316 return true; |
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317 } |
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318 |
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319 if (!hasNormal_) |
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320 { |
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321 return false; |
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322 } |
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323 |
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324 for (size_t i = 0; i < instances_.size(); i++) |
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325 { |
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326 assert(instances_[i] != NULL); |
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327 |
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328 if (!instances_[i]->HasPosition() || |
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329 (instances_[i]->HasNormal() && |
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330 !IsParallelOrOpposite(instances_[i]->GetNormal(), normal_))) |
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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 |
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336 PositionComparator comparator(normal_); |
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337 std::sort(instances_.begin(), instances_.end(), comparator); |
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338 |
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339 float a = instances_[0]->ComputeRelativePosition(normal_); |
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340 for (size_t i = 1; i < instances_.size(); i++) |
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341 { |
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342 float b = instances_[i]->ComputeRelativePosition(normal_); |
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343 |
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344 if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon()) |
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345 { |
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346 // Not enough space between two slices along the normal of the volume |
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347 return false; |
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348 } |
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349 |
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350 a = b; |
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351 } |
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352 |
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353 // This is a 3D volume |
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354 isVolume_ = true; |
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355 return true; |
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356 } |
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357 |
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358 |
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359 bool SliceOrdering::SortUsingIndexInSeries() |
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360 { |
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361 if (instances_.size() <= 1) |
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362 { |
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363 // One single instance: It is sorted by default |
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364 return true; |
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365 } |
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366 |
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367 for (size_t i = 0; i < instances_.size(); i++) |
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368 { |
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369 assert(instances_[i] != NULL); |
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370 if (!instances_[i]->HasIndexInSeries()) |
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371 { |
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372 return false; |
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373 } |
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374 } |
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375 |
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376 std::sort(instances_.begin(), instances_.end(), IndexInSeriesComparator); |
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377 |
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378 for (size_t i = 1; i < instances_.size(); i++) |
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379 { |
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380 if (instances_[i - 1]->GetIndexInSeries() == instances_[i]->GetIndexInSeries()) |
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381 { |
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382 // The current "IndexInSeries" occurs 2 times: Not a proper ordering |
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383 LOG(WARNING) << "This series contains 2 slices with the same index, trying to display it anyway"; |
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384 break; |
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385 } |
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386 } |
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387 |
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388 return true; |
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389 } |
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390 |
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391 |
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392 SliceOrdering::SliceOrdering(ServerIndex& index, |
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393 const std::string& seriesId) : |
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394 index_(index), |
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395 seriesId_(seriesId), |
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396 isVolume_(false) |
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397 { |
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398 ComputeNormal(); |
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399 CreateInstances(); |
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400 |
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401 if (!SortUsingPositions() && |
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402 !SortUsingIndexInSeries()) |
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403 { |
2955 | 404 throw OrthancException(ErrorCode_CannotOrderSlices, |
405 "Unable to order the slices of series " + seriesId); | |
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406 } |
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407 } |
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408 |
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409 |
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410 SliceOrdering::~SliceOrdering() |
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411 { |
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412 for (std::vector<Instance*>::iterator |
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413 it = instances_.begin(); it != instances_.end(); ++it) |
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414 { |
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415 if (*it != NULL) |
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416 { |
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417 delete *it; |
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418 } |
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419 } |
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420 } |
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421 |
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422 |
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423 const std::string& SliceOrdering::GetInstanceId(size_t index) const |
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424 { |
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425 if (index >= instances_.size()) |
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426 { |
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427 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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428 } |
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429 else |
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430 { |
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431 return instances_[index]->GetIdentifier(); |
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432 } |
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433 } |
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434 |
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435 |
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436 unsigned int SliceOrdering::GetFramesCount(size_t index) const |
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437 { |
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438 if (index >= instances_.size()) |
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439 { |
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440 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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441 } |
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442 else |
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443 { |
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444 return instances_[index]->GetFramesCount(); |
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445 } |
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446 } |
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447 |
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448 |
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449 void SliceOrdering::Format(Json::Value& result) const |
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450 { |
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451 result = Json::objectValue; |
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452 result["Type"] = (isVolume_ ? "Volume" : "Sequence"); |
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453 |
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454 Json::Value tmp = Json::arrayValue; |
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455 for (size_t i = 0; i < GetInstancesCount(); i++) |
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456 { |
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457 tmp.append(GetBasePath(ResourceType_Instance, GetInstanceId(i)) + "/file"); |
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458 } |
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459 |
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460 result["Dicom"] = tmp; |
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461 |
1873 | 462 Json::Value slicesShort = Json::arrayValue; |
463 | |
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464 tmp.clear(); |
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465 for (size_t i = 0; i < GetInstancesCount(); i++) |
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466 { |
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467 std::string base = GetBasePath(ResourceType_Instance, GetInstanceId(i)); |
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468 for (size_t j = 0; j < GetFramesCount(i); j++) |
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469 { |
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470 tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j)); |
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471 } |
1873 | 472 |
473 Json::Value tmp2 = Json::arrayValue; | |
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474 tmp2.append(GetInstanceId(i)); |
1873 | 475 tmp2.append(0); |
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476 tmp2.append(GetFramesCount(i)); |
1873 | 477 |
478 slicesShort.append(tmp2); | |
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479 } |
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480 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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481 result["Slices"] = tmp; |
1873 | 482 result["SlicesShort"] = slicesShort; |
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ordered-slices continued
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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483 } |
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9980875edc7c
started work on SliceOrdering
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
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484 } |