Mercurial > hg > orthanc-stone
annotate Framework/Loaders/SeriesOrderedFrames.cpp @ 1311:3d26447ddd28 broker
warning fixes + doc + indentation + header files in cmake for VC++ sln browsing
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Mon, 09 Mar 2020 14:55:22 +0100 |
parents | c38c89684d83 |
children | c0af7657d398 |
rev | line source |
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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 Affero 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 * Affero 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 Affero General Public License |
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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19 **/ |
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20 |
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21 |
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22 #include "../Toolbox/SlicesSorter.h" |
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23 #include "SeriesOrderedFrames.h" |
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24 |
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25 #include <Core/OrthancException.h> |
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26 |
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27 namespace OrthancStone |
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28 { |
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29 class SeriesOrderedFrames::Instance : public boost::noncopyable |
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30 { |
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31 private: |
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32 std::unique_ptr<Orthanc::DicomMap> dicom_; |
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33 DicomInstanceParameters parameters_; |
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34 |
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35 public: |
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36 Instance(const Orthanc::DicomMap& dicom) : |
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37 dicom_(dicom.Clone()), |
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38 parameters_(dicom) |
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39 { |
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40 } |
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41 |
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42 const Orthanc::DicomMap& GetInstance() const |
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43 { |
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44 return *dicom_; |
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45 } |
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46 |
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47 const DicomInstanceParameters& GetInstanceParameters() const |
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48 { |
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49 return parameters_; |
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50 } |
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51 |
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52 bool Lookup3DGeometry(CoordinateSystem3D& target) const |
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53 { |
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54 try |
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55 { |
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56 std::string imagePositionPatient, imageOrientationPatient; |
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57 if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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58 dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
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59 { |
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60 target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient); |
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61 return true; |
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62 } |
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63 } |
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64 catch (Orthanc::OrthancException&) |
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65 { |
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66 } |
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67 |
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68 return false; |
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69 } |
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70 |
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71 bool LookupIndexInSeries(int& target) const |
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72 { |
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73 std::string value; |
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74 |
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75 if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) || |
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76 dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false)) |
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77 { |
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78 try |
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79 { |
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80 target = boost::lexical_cast<int>(value); |
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81 return true; |
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82 } |
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83 catch (boost::bad_lexical_cast&) |
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84 { |
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85 } |
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86 } |
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87 |
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88 return false; |
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89 } |
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90 }; |
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91 |
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92 |
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93 class SeriesOrderedFrames::Frame : public boost::noncopyable |
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94 { |
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95 private: |
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96 const Instance* instance_; |
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97 unsigned int frameIndex_; |
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98 |
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99 public: |
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100 Frame(const Instance& instance, |
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101 unsigned int frameIndex) : |
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102 instance_(&instance), |
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103 frameIndex_(frameIndex) |
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104 { |
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105 if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames()) |
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106 { |
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107 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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108 } |
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109 } |
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110 |
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111 const Orthanc::DicomMap& GetInstance() const |
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112 { |
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113 assert(instance_ != NULL); |
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114 return instance_->GetInstance(); |
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115 } |
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116 |
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117 const DicomInstanceParameters& GetInstanceParameters() const |
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118 { |
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119 assert(instance_ != NULL); |
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120 return instance_->GetInstanceParameters(); |
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121 } |
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122 |
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123 unsigned int GetFrameIndex() const |
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124 { |
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125 return frameIndex_; |
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126 } |
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127 }; |
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128 |
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129 |
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130 class SeriesOrderedFrames::InstanceWithIndexInSeries |
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131 { |
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132 private: |
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133 const Instance* instance_; // Don't use a reference to make "std::sort()" happy |
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134 int index_; |
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135 |
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136 public: |
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137 InstanceWithIndexInSeries(const Instance& instance) : |
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138 instance_(&instance) |
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139 { |
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140 if (!instance_->LookupIndexInSeries(index_)) |
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141 { |
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142 index_ = std::numeric_limits<int>::max(); |
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143 } |
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144 } |
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145 |
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146 const Instance& GetInstance() const |
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147 { |
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148 return *instance_; |
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149 } |
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150 |
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151 int GetIndexInSeries() const |
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152 { |
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153 return index_; |
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154 } |
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155 |
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156 bool operator< (const InstanceWithIndexInSeries& other) const |
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157 { |
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158 return (index_ < other.index_); |
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159 } |
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160 }; |
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161 |
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162 |
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163 void SeriesOrderedFrames::Clear() |
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164 { |
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165 for (size_t i = 0; i < instances_.size(); i++) |
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166 { |
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167 assert(instances_[i] != NULL); |
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168 delete instances_[i]; |
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169 } |
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170 |
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171 for (size_t i = 0; i < orderedFrames_.size(); i++) |
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172 { |
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173 assert(orderedFrames_[i] != NULL); |
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174 delete orderedFrames_[i]; |
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175 } |
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176 |
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177 instances_.clear(); |
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178 orderedFrames_.clear(); |
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179 } |
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180 |
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181 |
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182 bool SeriesOrderedFrames::Sort3DVolume() |
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183 { |
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184 SlicesSorter sorter; |
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185 sorter.Reserve(instances_.size()); |
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186 |
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187 for (size_t i = 0; i < instances_.size(); i++) |
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188 { |
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189 CoordinateSystem3D geometry; |
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190 if (instances_[i]->Lookup3DGeometry(geometry)) |
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191 { |
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192 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i])); |
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193 } |
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194 else |
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195 { |
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196 return false; // Not a 3D volume |
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197 } |
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198 } |
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199 |
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200 if (!sorter.Sort() || |
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201 sorter.GetSlicesCount() != instances_.size() || |
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202 !sorter.AreAllSlicesDistinct()) |
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203 { |
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204 return false; |
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205 } |
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206 else |
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207 { |
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208 for (size_t i = 0; i < sorter.GetSlicesCount(); i++) |
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209 { |
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210 assert(sorter.HasSlicePayload(i)); |
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211 |
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212 const Orthanc::SingleValueObject<Instance*>& payload = |
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213 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i)); |
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214 |
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215 assert(payload.GetValue() != NULL); |
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216 |
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217 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) |
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218 { |
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219 orderedFrames_.push_back(new Frame(*payload.GetValue(), j)); |
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220 } |
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221 } |
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222 |
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223 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_); |
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224 return true; |
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225 } |
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226 } |
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227 |
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228 |
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229 void SeriesOrderedFrames::SortIndexInSeries() |
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230 { |
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231 std::vector<InstanceWithIndexInSeries> tmp; |
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232 tmp.reserve(instances_.size()); |
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233 |
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234 for (size_t i = 0; i < instances_.size(); i++) |
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235 { |
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236 assert(instances_[i] != NULL); |
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237 tmp.push_back(InstanceWithIndexInSeries(*instances_[i])); |
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238 } |
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239 |
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240 std::sort(tmp.begin(), tmp.end()); |
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241 |
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242 for (size_t i = 0; i < tmp.size(); i++) |
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243 { |
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244 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) |
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245 { |
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246 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), j)); |
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247 } |
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248 } |
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249 } |
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250 |
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251 |
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252 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const |
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253 { |
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254 if (seriesIndex >= orderedFrames_.size()) |
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255 { |
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256 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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257 } |
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258 else |
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259 { |
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260 assert(orderedFrames_[seriesIndex] != NULL); |
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261 return *(orderedFrames_[seriesIndex]); |
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262 } |
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263 } |
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264 |
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265 |
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266 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) : |
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267 isVolume_(false), |
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268 isRegular_(false), |
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269 spacingBetweenSlices_(0) |
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270 { |
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271 instances_.reserve(instances.GetSize()); |
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272 |
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273 size_t numberOfFrames = 0; |
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274 |
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275 for (size_t i = 0; i < instances.GetSize(); i++) |
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276 { |
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277 try |
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278 { |
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279 std::unique_ptr<Instance> instance(new Instance(instances.GetResource(i))); |
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280 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); |
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281 instances_.push_back(instance.release()); |
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282 } |
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283 catch (Orthanc::OrthancException&) |
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284 { |
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285 // The instance has not all the required DICOM tags, skip it |
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286 } |
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287 } |
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288 |
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289 orderedFrames_.reserve(numberOfFrames); |
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290 |
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291 if (Sort3DVolume()) |
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292 { |
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293 isVolume_ = true; |
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294 |
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295 if (isRegular_) |
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296 { |
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297 LOG(INFO) << "Regular 3D volume detected"; |
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298 } |
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299 else |
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300 { |
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301 LOG(INFO) << "Non-regular 3D volume detected"; |
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302 } |
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303 } |
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304 else |
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305 { |
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306 LOG(INFO) << "Series is not a 3D volume, sorting by index"; |
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307 SortIndexInSeries(); |
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308 } |
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309 |
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310 LOG(INFO) << "Number of frames: " << orderedFrames_.size(); |
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311 } |
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312 |
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313 |
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314 unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const |
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315 { |
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316 return GetFrame(seriesIndex).GetFrameIndex(); |
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317 } |
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318 |
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319 |
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320 const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const |
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321 { |
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322 return GetFrame(seriesIndex).GetInstance(); |
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323 } |
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324 |
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325 |
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326 const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const |
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327 { |
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328 return GetFrame(seriesIndex).GetInstanceParameters(); |
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329 } |
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330 |
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331 |
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332 double SeriesOrderedFrames::GetSpacingBetweenSlices() const |
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333 { |
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334 if (IsRegular3DVolume()) |
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335 { |
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336 return spacingBetweenSlices_; |
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337 } |
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338 else |
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339 { |
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340 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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341 } |
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342 } |
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343 } |