Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/SortedFrames.cpp @ 1630:78509230f0d7
SortedFrames sharing code with CoordinateSystem3D
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 09 Nov 2020 18:01:32 +0100 |
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children | 960bb5fcc440 |
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1 /** |
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2 * Stone of Orthanc |
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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) 2017-2020 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 Lesser General Public License |
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9 * as published by the Free Software Foundation, either version 3 of |
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10 * the License, or (at your option) any later version. |
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11 * |
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12 * This program is distributed in the hope that it will be useful, but |
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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15 * Lesser General Public License for more details. |
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16 * |
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17 * You should have received a copy of the GNU Lesser General Public |
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18 * License along with this program. If not, see |
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19 * <http://www.gnu.org/licenses/>. |
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20 **/ |
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21 |
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22 |
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23 #include "SortedFrames.h" |
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24 |
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25 #include "GeometryToolbox.h" |
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26 |
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27 #include <OrthancException.h> |
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28 #include <Toolbox.h> |
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29 |
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30 namespace OrthancStone |
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31 { |
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32 SortedFrames::Instance::Instance(const Orthanc::DicomMap& tags) : |
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33 geometry_(tags) |
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34 { |
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35 tags_.Assign(tags); |
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36 |
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37 if (!tags.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
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38 { |
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39 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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40 } |
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41 |
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42 uint32_t tmp; |
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43 if (tags.ParseUnsignedInteger32(tmp, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
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44 { |
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45 numberOfFrames_ = tmp; |
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46 } |
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47 else |
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48 { |
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49 numberOfFrames_ = 1; |
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50 } |
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51 |
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52 std::string photometric; |
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53 if (tags.LookupStringValue(photometric, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false)) |
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54 { |
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55 Orthanc::Toolbox::StripSpaces(photometric); |
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56 monochrome1_ = (photometric == "MONOCHROME1"); |
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57 } |
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58 else |
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59 { |
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60 monochrome1_ = false; |
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61 } |
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62 } |
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63 |
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64 |
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65 SortedFrames::Frame::Frame(const Instance& instance, |
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66 unsigned int frameNumber) : |
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68 frameNumber_(frameNumber) |
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69 { |
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70 if (frameNumber >= instance.GetNumberOfFrames()) |
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71 { |
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72 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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73 } |
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74 } |
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75 |
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76 |
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77 const SortedFrames::Instance& SortedFrames::GetInstance(size_t instanceIndex) const |
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78 { |
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79 if (instanceIndex >= instances_.size()) |
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80 { |
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81 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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82 } |
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83 else |
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84 { |
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85 assert(instances_[instanceIndex] != NULL); |
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86 return *instances_[instanceIndex]; |
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87 } |
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88 } |
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89 |
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90 |
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91 const SortedFrames::Frame& SortedFrames::GetFrame(size_t frameIndex) const |
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92 { |
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93 if (!sorted_) |
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94 { |
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95 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls, |
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96 "Sort() has not been called"); |
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97 } |
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98 if (frameIndex >= frames_.size()) |
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99 { |
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100 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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101 } |
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102 else |
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103 { |
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104 return frames_[frameIndex]; |
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105 } |
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106 } |
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107 |
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108 |
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109 void SortedFrames::Clear() |
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110 { |
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111 for (size_t i = 0; i < instances_.size(); i++) |
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112 { |
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113 assert(instances_[i] != NULL); |
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114 delete instances_[i]; |
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115 } |
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116 |
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117 studyInstanceUid_.clear(); |
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118 seriesInstanceUid_.clear(); |
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119 frames_.clear(); |
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120 |
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121 instancesIndex_.clear(); |
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122 framesIndex_.clear(); |
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123 |
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124 sorted_ = true; |
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125 } |
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126 |
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127 |
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128 void SortedFrames::AddInstance(const Orthanc::DicomMap& tags) |
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129 { |
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130 std::unique_ptr<Instance> instance(new Instance(tags)); |
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131 |
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132 std::string studyInstanceUid, seriesInstanceUid, sopInstanceUid; |
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133 if (!tags.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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134 !tags.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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135 !tags.LookupStringValue(sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
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136 { |
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137 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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138 } |
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139 |
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140 if (instances_.empty()) |
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141 { |
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142 studyInstanceUid_ = studyInstanceUid; |
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143 seriesInstanceUid_ = seriesInstanceUid; |
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144 } |
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145 else |
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146 { |
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147 if (studyInstanceUid_ != studyInstanceUid || |
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148 seriesInstanceUid_ != seriesInstanceUid) |
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149 { |
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150 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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151 "Mixing instances from different series"); |
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152 } |
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153 } |
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154 |
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155 if (instancesIndex_.find(sopInstanceUid) != instancesIndex_.end()) |
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156 { |
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157 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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158 "Cannot register twice the same SOP Instance UID"); |
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159 } |
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160 |
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161 instancesIndex_[sopInstanceUid] = instances_.size(); |
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162 |
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163 instances_.push_back(instance.release()); |
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164 sorted_ = false; |
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165 frames_.clear(); |
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166 } |
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167 |
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168 |
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169 bool SortedFrames::LookupSopInstanceUid(size_t& instanceIndex, |
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170 const std::string& sopInstanceUid) const |
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171 { |
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172 InstancesIndex::const_iterator found = instancesIndex_.find(sopInstanceUid); |
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173 |
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174 if (found == instancesIndex_.end()) |
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175 { |
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176 return false; |
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177 } |
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178 else |
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179 { |
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180 instanceIndex = found->second; |
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181 return true; |
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182 } |
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183 } |
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184 |
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185 |
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186 void SortedFrames::AddFramesOfInstance(std::set<size_t>& remainingInstances, |
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187 size_t instanceIndex) |
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188 { |
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189 assert(instances_[instanceIndex] != NULL); |
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190 const Instance& instance = *instances_[instanceIndex]; |
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191 |
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192 for (unsigned int i = 0; i < instance.GetNumberOfFrames(); i++) |
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193 { |
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194 framesIndex_[std::make_pair(instance.GetSopInstanceUid(), i)] = frames_.size(); |
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195 frames_.push_back(Frame(instance, i)); |
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196 } |
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197 |
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198 assert(remainingInstances.find(instanceIndex) != remainingInstances.end()); |
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199 remainingInstances.erase(instanceIndex); |
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200 } |
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201 |
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202 |
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203 namespace |
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204 { |
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205 template<typename T> |
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206 class SortableItem |
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207 { |
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208 private: |
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209 T value_; |
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210 size_t instanceIndex_; |
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211 std::string sopInstanceUid_; |
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212 |
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213 public: |
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214 SortableItem(const T& value, |
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215 size_t instanceIndex, |
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216 const std::string& sopInstanceUid) : |
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217 value_(value), |
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218 instanceIndex_(instanceIndex), |
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219 sopInstanceUid_(sopInstanceUid) |
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220 { |
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221 } |
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222 |
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223 size_t GetInstanceIndex() const |
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224 { |
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225 return instanceIndex_; |
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226 } |
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227 |
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228 bool operator< (const SortableItem& other) const |
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229 { |
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230 return (value_ < other.value_ || |
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231 (value_ == other.value_ && |
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232 sopInstanceUid_ < other.sopInstanceUid_)); |
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233 } |
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234 }; |
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235 } |
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236 |
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237 |
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238 void SortedFrames::SortUsingIntegerTag(std::set<size_t>& remainingInstances, |
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239 const Orthanc::DicomTag& tag) |
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240 { |
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241 std::vector< SortableItem<int32_t> > items; |
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242 items.reserve(remainingInstances.size()); |
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243 |
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244 for (std::set<size_t>::const_iterator it = remainingInstances.begin(); |
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245 it != remainingInstances.end(); ++it) |
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246 { |
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247 assert(instances_[*it] != NULL); |
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248 const Instance& instance = *instances_[*it]; |
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249 |
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250 int32_t value; |
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251 std::string sopInstanceUid; |
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252 if (instance.GetTags().ParseInteger32(value, tag) && |
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253 instance.GetTags().LookupStringValue( |
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254 sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
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255 { |
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256 items.push_back(SortableItem<int32_t>(value, *it, sopInstanceUid)); |
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257 } |
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258 } |
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259 |
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260 std::sort(items.begin(), items.end()); |
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261 |
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262 for (size_t i = 0; i < items.size(); i++) |
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263 { |
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264 AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex()); |
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265 } |
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266 } |
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267 |
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268 |
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269 void SortedFrames::SortUsingSopInstanceUid(std::set<size_t>& remainingInstances) |
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270 { |
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271 std::vector<SortableItem<int32_t> > items; |
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272 items.reserve(remainingInstances.size()); |
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273 |
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274 for (std::set<size_t>::const_iterator it = remainingInstances.begin(); |
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275 it != remainingInstances.end(); ++it) |
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276 { |
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277 assert(instances_[*it] != NULL); |
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278 const Instance& instance = *instances_[*it]; |
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279 |
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280 std::string sopInstanceUid; |
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281 if (instance.GetTags().LookupStringValue( |
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282 sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
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283 { |
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284 items.push_back(SortableItem<int32_t>(0 /* arbitrary value */, *it, sopInstanceUid)); |
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285 } |
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286 } |
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287 |
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288 std::sort(items.begin(), items.end()); |
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289 |
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290 for (size_t i = 0; i < items.size(); i++) |
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291 { |
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292 AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex()); |
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293 } |
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294 } |
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295 |
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296 |
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297 void SortedFrames::SortUsing3DLocation(std::set<size_t>& remainingInstances) |
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298 { |
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299 /** |
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300 * Compute the mean of the normal vectors, using the recursive |
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301 * formula for arithmetic means for numerical stability. |
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302 * https://diego.assencio.com/?index=c34d06f4f4de2375658ed41f70177d59 |
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303 **/ |
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304 |
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305 Vector meanNormal; |
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306 LinearAlgebra::AssignVector(meanNormal, 0, 0, 0); |
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307 |
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308 unsigned int n = 0; |
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309 |
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310 for (std::set<size_t>::const_iterator it = remainingInstances.begin(); |
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311 it != remainingInstances.end(); ++it) |
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312 { |
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313 assert(instances_[*it] != NULL); |
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314 const Instance& instance = *instances_[*it]; |
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315 |
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316 if (instance.GetGeometry().IsValid()) |
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317 { |
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318 n += 1; |
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319 meanNormal += (instance.GetGeometry().GetNormal() - meanNormal) / static_cast<float>(n); |
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320 } |
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321 } |
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322 |
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323 std::vector<SortableItem<float> > items; |
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324 items.reserve(n); |
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325 |
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326 for (std::set<size_t>::const_iterator it = remainingInstances.begin(); |
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327 it != remainingInstances.end(); ++it) |
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328 { |
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329 assert(instances_[*it] != NULL); |
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330 const Instance& instance = *instances_[*it]; |
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331 |
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332 std::string sopInstanceUid; |
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333 if (instance.GetGeometry().IsValid() && |
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334 instance.GetTags().LookupStringValue( |
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335 sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
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336 { |
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337 double p = LinearAlgebra::DotProduct(meanNormal, instance.GetGeometry().GetOrigin()); |
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339 } |
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340 } |
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341 |
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342 assert(items.size() <= n); |
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343 |
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344 std::sort(items.begin(), items.end()); |
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345 |
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346 for (size_t i = 0; i < items.size(); i++) |
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347 { |
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348 AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex()); |
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349 } |
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350 } |
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351 |
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352 |
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353 size_t SortedFrames::GetFramesCount() const |
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354 { |
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355 if (sorted_) |
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356 { |
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357 return frames_.size(); |
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358 } |
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359 else |
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360 { |
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361 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls, |
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362 "Sort() has not been called"); |
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363 } |
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364 } |
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365 |
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366 |
1602
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367 bool SortedFrames::LookupFrame(size_t& frameIndex, |
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368 const std::string& sopInstanceUid, |
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369 unsigned int frameNumber) const |
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370 { |
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371 if (sorted_) |
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372 { |
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373 FramesIndex::const_iterator found = framesIndex_.find( |
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374 std::make_pair(sopInstanceUid, frameNumber)); |
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375 |
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376 if (found == framesIndex_.end()) |
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377 { |
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378 return false; |
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379 } |
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380 else |
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381 { |
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382 frameIndex = found->second; |
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383 return true; |
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384 } |
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385 } |
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SortedFrames::LookupFrame()
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386 else |
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387 { |
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls, |
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389 "Sort() has not been called"); |
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390 } |
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SortedFrames::LookupFrame()
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391 } |
b2941196cabf
SortedFrames::LookupFrame()
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392 |
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|
393 |
1478
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394 void SortedFrames::Sort() |
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395 { |
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396 if (!sorted_) |
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|
397 { |
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398 size_t totalFrames = 0; |
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399 std::set<size_t> remainingInstances; |
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|
400 |
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|
401 for (size_t i = 0; i < instances_.size(); i++) |
fab6c6e795a3
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402 { |
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403 assert(instances_[i] != NULL); |
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404 totalFrames += instances_[i]->GetNumberOfFrames(); |
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405 |
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parents:
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406 remainingInstances.insert(i); |
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|
407 } |
fab6c6e795a3
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parents:
diff
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|
408 |
fab6c6e795a3
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409 frames_.clear(); |
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410 frames_.reserve(totalFrames); |
1602
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411 framesIndex_.clear(); |
1478
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412 |
fab6c6e795a3
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diff
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413 SortUsingIntegerTag(remainingInstances, Orthanc::DICOM_TAG_INSTANCE_NUMBER); // VR is "IS" |
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|
414 SortUsingIntegerTag(remainingInstances, Orthanc::DICOM_TAG_IMAGE_INDEX); // VR is "US" |
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415 SortUsing3DLocation(remainingInstances); |
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diff
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|
416 SortUsingSopInstanceUid(remainingInstances); |
fab6c6e795a3
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parents:
diff
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|
417 |
fab6c6e795a3
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parents:
diff
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|
418 // The following could in theory happen if several instances |
fab6c6e795a3
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419 // have the same SOPInstanceUID, no ordering is available |
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420 for (std::set<size_t>::const_iterator it = remainingInstances.begin(); |
1571 | 421 it != remainingInstances.end(); ++it) |
1478
fab6c6e795a3
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parents:
diff
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|
422 { |
fab6c6e795a3
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parents:
diff
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|
423 AddFramesOfInstance(remainingInstances, *it); |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
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parents:
diff
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|
424 } |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
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parents:
diff
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|
425 |
fab6c6e795a3
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parents:
diff
changeset
|
426 if (frames_.size() != totalFrames || |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
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parents:
diff
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|
427 !remainingInstances.empty()) |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
428 { |
fab6c6e795a3
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parents:
diff
changeset
|
429 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
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parents:
diff
changeset
|
430 } |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
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parents:
diff
changeset
|
431 |
fab6c6e795a3
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parents:
diff
changeset
|
432 sorted_ = true; |
fab6c6e795a3
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parents:
diff
changeset
|
433 } |
fab6c6e795a3
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
434 } |
fab6c6e795a3
Framework/Toolbox/SortedFrames.cpp
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
435 } |