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annotate Framework/Loaders/SeriesOrderedFrames.cpp @ 1228:c471a0aa137b broker

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adding the next generation of loaders
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 09 Dec 2019 13:58:37 +0100
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children 0ca50d275b9a
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1228
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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) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU 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::auto_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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diff changeset
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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diff changeset
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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diff changeset
223 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
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diff changeset
224 return true;
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225 }
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226 }
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diff changeset
227
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228
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diff changeset
229 void SeriesOrderedFrames::SortIndexInSeries()
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diff changeset
230 {
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diff changeset
231 std::vector<InstanceWithIndexInSeries> tmp;
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diff changeset
232 tmp.reserve(instances_.size());
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parents:
diff changeset
233
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diff changeset
234 for (size_t i = 0; i < instances_.size(); i++)
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diff changeset
235 {
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diff changeset
236 assert(instances_[i] != NULL);
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parents:
diff changeset
237 tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
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diff changeset
238 }
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parents:
diff changeset
239
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diff changeset
240 std::sort(tmp.begin(), tmp.end());
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diff changeset
241
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diff changeset
242 for (size_t i = 0; i < tmp.size(); i++)
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parents:
diff changeset
243 {
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diff changeset
244 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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diff changeset
245 {
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parents:
diff changeset
246 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), j));
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diff changeset
247 }
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diff changeset
248 }
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diff changeset
249 }
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parents:
diff changeset
250
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
251
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parents:
diff changeset
252 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
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diff changeset
253 {
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diff changeset
254 if (seriesIndex >= orderedFrames_.size())
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diff changeset
255 {
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diff changeset
256 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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diff changeset
257 }
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parents:
diff changeset
258 else
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parents:
diff changeset
259 {
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parents:
diff changeset
260 assert(orderedFrames_[seriesIndex] != NULL);
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parents:
diff changeset
261 return *(orderedFrames_[seriesIndex]);
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diff changeset
262 }
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diff changeset
263 }
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parents:
diff changeset
264
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parents:
diff changeset
265
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parents:
diff changeset
266 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
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diff changeset
267 isVolume_(false),
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diff changeset
268 isRegular_(false),
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parents:
diff changeset
269 spacingBetweenSlices_(0)
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diff changeset
270 {
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diff changeset
271 instances_.reserve(instances.GetSize());
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diff changeset
272
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diff changeset
273 size_t numberOfFrames = 0;
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parents:
diff changeset
274
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diff changeset
275 for (size_t i = 0; i < instances.GetSize(); i++)
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parents:
diff changeset
276 {
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parents:
diff changeset
277 try
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parents:
diff changeset
278 {
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diff changeset
279 std::auto_ptr<Instance> instance(new Instance(instances.GetResource(i)));
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diff changeset
280 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
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parents:
diff changeset
281 instances_.push_back(instance.release());
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parents:
diff changeset
282 }
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parents:
diff changeset
283 catch (Orthanc::OrthancException&)
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parents:
diff changeset
284 {
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diff changeset
285 // The instance has not all the required DICOM tags, skip it
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parents:
diff changeset
286 }
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parents:
diff changeset
287 }
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parents:
diff changeset
288
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parents:
diff changeset
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 }