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0
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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "OrthancSeriesLoader.h"
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34
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35 #include "../Messaging/MessagingToolbox.h"
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16
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36 #include "../../Resources/Orthanc/Core/Images/Image.h"
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37 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h"
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38 #include "../../Resources/Orthanc/Core/Logging.h"
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39 #include "../../Resources/Orthanc/Core/OrthancException.h"
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0
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40 #include "DicomFrameConverter.h"
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41
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42 namespace OrthancStone
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43 {
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44 class OrthancSeriesLoader::Slice : public boost::noncopyable
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45 {
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46 private:
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47 std::string instanceId_;
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48 SliceGeometry geometry_;
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49 double projectionAlongNormal_;
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50
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51 public:
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52 Slice(const std::string& instanceId,
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53 const std::string& imagePositionPatient,
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54 const std::string& imageOrientationPatient) :
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55 instanceId_(instanceId),
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56 geometry_(imagePositionPatient, imageOrientationPatient)
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57 {
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58 }
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59
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60 const std::string GetInstanceId() const
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61 {
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62 return instanceId_;
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63 }
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64
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65 const SliceGeometry& GetGeometry() const
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66 {
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67 return geometry_;
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68 }
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69
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70 void SetNormal(const Vector& normal)
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71 {
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72 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal);
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73 }
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74
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75 double GetProjectionAlongNormal() const
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76 {
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77 return projectionAlongNormal_;
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78 }
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79 };
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80
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81
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82 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable
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83 {
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84 private:
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85 std::vector<Slice*> slices_;
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86
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87 struct Comparator
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88 {
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89 bool operator() (const Slice* const a,
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90 const Slice* const b) const
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91 {
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92 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal();
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93 }
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94 };
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95
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96 public:
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97 ~SetOfSlices()
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98 {
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99 for (size_t i = 0; i < slices_.size(); i++)
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100 {
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101 assert(slices_[i] != NULL);
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102 delete slices_[i];
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103 }
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104 }
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105
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106 void Reserve(size_t size)
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107 {
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108 slices_.reserve(size);
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109 }
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110
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111 void AddSlice(const std::string& instanceId,
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112 const std::string& imagePositionPatient,
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113 const std::string& imageOrientationPatient)
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114 {
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115 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient));
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116 }
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117
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118 size_t GetSliceCount() const
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119 {
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120 return slices_.size();
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121 }
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122
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123 const Slice& GetSlice(size_t index) const
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124 {
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125 assert(slices_[index] != NULL);
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126 return *slices_[index];
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127 }
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128
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129 void Sort(const Vector& normal)
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130 {
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131 for (size_t i = 0; i < slices_.size(); i++)
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132 {
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133 slices_[i]->SetNormal(normal);
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134 }
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135
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136 Comparator comparator;
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137 std::sort(slices_.begin(), slices_.end(), comparator);
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138 }
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139
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140 void LoadSeriesFast(IOrthancConnection& orthanc,
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141 const std::string& series)
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142 {
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143 // Retrieve the orientation of this series
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144 Json::Value info;
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145 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series);
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146
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147 if (info.type() != Json::objectValue ||
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148 !info.isMember("MainDicomTags") ||
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149 info["MainDicomTags"].type() != Json::objectValue ||
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150 !info["MainDicomTags"].isMember("ImageOrientationPatient") ||
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151 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue)
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152 {
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153 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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154 }
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155
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156 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString();
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157
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158
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159 // Retrieve the Orthanc ID of all the instances of this series
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160 Json::Value instances;
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161 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances");
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162
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163 if (instances.type() != Json::arrayValue)
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164 {
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165 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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166 }
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167
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168 if (instances.size() == 0)
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169 {
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170 LOG(ERROR) << "This series is empty";
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171 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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172 }
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173
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174
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175 // Retrieve the DICOM tags of all the instances
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176 std::vector<std::string> instancesId;
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177
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178 instancesId.resize(instances.size());
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179 Reserve(instances.size());
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180
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181 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++)
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182 {
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183 if (instances[i].type() != Json::objectValue ||
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184 !instances[i].isMember("ID") ||
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185 !instances[i].isMember("MainDicomTags") ||
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186 instances[i]["ID"].type() != Json::stringValue ||
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187 instances[i]["MainDicomTags"].type() != Json::objectValue ||
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188 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") ||
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189 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue)
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190 {
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191 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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192 }
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193 else
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194 {
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195 instancesId[i] = instances[i]["ID"].asString();
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196 AddSlice(instancesId[i],
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197 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(),
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198 imageOrientationPatient);
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199 }
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200 }
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201
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202 assert(GetSliceCount() == instances.size());
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203 }
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204
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205
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206 void LoadSeriesSafe(IOrthancConnection& orthanc,
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207 const std::string& seriesId)
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208 {
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209 Json::Value series;
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210 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify");
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211
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212 if (series.type() != Json::objectValue)
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213 {
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214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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215 }
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216
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217 if (series.size() == 0)
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218 {
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219 LOG(ERROR) << "This series is empty";
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220 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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221 }
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222
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223 Json::Value::Members instances = series.getMemberNames();
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224
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225 Reserve(instances.size());
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226
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227 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++)
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228 {
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229 const Json::Value& tags = series[instances[i]];
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230
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231 if (tags.type() != Json::objectValue ||
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232 !tags.isMember("ImagePositionPatient") ||
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233 !tags.isMember("ImageOrientationPatient") ||
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234 tags["ImagePositionPatient"].type() != Json::stringValue ||
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235 tags["ImageOrientationPatient"].type() != Json::stringValue)
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236 {
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237 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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238 }
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239 else
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240 {
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241 AddSlice(instances[i],
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242 tags["ImagePositionPatient"].asString(),
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243 tags["ImageOrientationPatient"].asString());
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244 }
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245 }
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246
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247 assert(GetSliceCount() == instances.size());
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248 }
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249
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250
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251 void SelectNormal(Vector& normal) const
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252 {
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253 std::vector<Vector> normalCandidates;
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254 std::vector<unsigned int> normalCount;
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255
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256 bool found = false;
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257
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258 for (size_t i = 0; !found && i < GetSliceCount(); i++)
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259 {
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260 const Vector& normal = GetSlice(i).GetGeometry().GetNormal();
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261
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262 bool add = true;
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263 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*)
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264 {
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265 if (GeometryToolbox::IsParallel(normal, normalCandidates[j]))
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266 {
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267 normalCount[j] += 1;
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268 add = false;
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269 }
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270 }
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271
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272 if (add)
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273 {
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274 if (normalCount.size() > 2)
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275 {
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276 // To get linear-time complexity in (*). This heuristics
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277 // allows the series to have one single frame that is
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278 // not parallel to the others (such a frame could be a
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279 // generated preview)
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280 found = false;
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281 }
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282 else
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283 {
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284 normalCandidates.push_back(normal);
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285 normalCount.push_back(1);
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286 }
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287 }
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288 }
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289
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290 for (size_t i = 0; !found && i < normalCandidates.size(); i++)
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291 {
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292 unsigned int count = normalCount[i];
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293 if (count == GetSliceCount() ||
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294 count + 1 == GetSliceCount())
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295 {
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296 normal = normalCandidates[i];
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297 found = true;
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298 }
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299 }
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300
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301 if (!found)
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302 {
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303 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series";
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304 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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305 }
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306 }
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307
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308
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309 void FilterNormal(const Vector& normal)
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310 {
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311 size_t pos = 0;
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312
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313 for (size_t i = 0; i < slices_.size(); i++)
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314 {
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315 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal()))
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316 {
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317 // This slice is compatible with the selected normal
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318 slices_[pos] = slices_[i];
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319 pos += 1;
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320 }
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321 else
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322 {
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323 delete slices_[i];
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324 slices_[i] = NULL;
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325 }
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326 }
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327
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328 slices_.resize(pos);
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329 }
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330 };
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331
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332
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333
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334 OrthancSeriesLoader::OrthancSeriesLoader(IOrthancConnection& orthanc,
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335 const std::string& series) :
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336 orthanc_(orthanc),
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337 slices_(new SetOfSlices)
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338 {
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339 /**
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340 * The function "LoadSeriesFast()" might now behave properly if
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341 * some slice has some outsider value for its normal, which
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342 * happens sometimes on reprojected series (e.g. coronal and
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343 * sagittal of Delphine). Don't use it.
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344 **/
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345
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346 slices_->LoadSeriesSafe(orthanc, series);
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347
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348 Vector normal;
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349 slices_->SelectNormal(normal);
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350 slices_->FilterNormal(normal);
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351 slices_->Sort(normal);
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352
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353 if (slices_->GetSliceCount() == 0) // Sanity check
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354 {
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355 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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356 }
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357
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358 for (size_t i = 0; i < slices_->GetSliceCount(); i++)
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359 {
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360 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal()));
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361 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry());
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362 }
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363
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364 std::auto_ptr<DicomDataset> dataset(new DicomDataset(orthanc_, slices_->GetSlice(0).GetInstanceId()));
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365 if (!dataset->HasTag(DICOM_TAG_ROWS) ||
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366 !dataset->HasTag(DICOM_TAG_COLUMNS))
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367 {
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368 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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369 }
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370
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371 DicomFrameConverter converter;
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372 converter.ReadParameters(*dataset);
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373
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374 format_ = converter.GetExpectedPixelFormat();
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375 width_ = dataset->GetUnsignedIntegerValue(DICOM_TAG_COLUMNS);
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376 height_ = dataset->GetUnsignedIntegerValue(DICOM_TAG_ROWS);
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377 }
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378
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379
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380 DicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index)
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381 {
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382 std::auto_ptr<DicomDataset> dataset(new DicomDataset(orthanc_, slices_->GetSlice(index).GetInstanceId()));
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383
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384 if (dataset->HasTag(DICOM_TAG_NUMBER_OF_FRAMES) &&
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385 dataset->GetUnsignedIntegerValue(DICOM_TAG_NUMBER_OF_FRAMES) != 1)
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386 {
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387 LOG(ERROR) << "One instance in this series has more than 1 frame";
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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389 }
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390
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391 return dataset.release();
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392 }
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393
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394
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395 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const
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396 {
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397 if (frame.GetFormat() != format_ ||
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398 frame.GetWidth() != width_ ||
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399 frame.GetHeight() != height_)
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400 {
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401 LOG(ERROR) << "The parameters of this series vary accross its slices";
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402 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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403 }
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404 }
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405
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406
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407 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index)
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408 {
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409 const Slice& slice = slices_->GetSlice(index);
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410
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411 std::auto_ptr<Orthanc::ImageAccessor> frame
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412 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_));
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413
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414 if (frame.get() != NULL)
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415 {
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416 CheckFrame(*frame);
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417 }
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418
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419 return frame.release();
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420 }
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421
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422
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423 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index,
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424 unsigned int quality)
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425 {
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426 const Slice& slice = slices_->GetSlice(index);
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427
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428 std::auto_ptr<Orthanc::ImageAccessor> frame
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429 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_));
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430
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431 if (frame.get() != NULL)
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432 {
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433 CheckFrame(*frame);
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434 }
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435
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436 return frame.release();
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437 }
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438
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439
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440 bool OrthancSeriesLoader::IsJpegAvailable()
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441 {
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442 return MessagingToolbox::HasWebViewerInstalled(orthanc_);
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443 }
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444 }
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