Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2091:35de56fb6f89 dicom-sr
support of referenced instances
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 08 Nov 2023 10:11:21 +0100 |
parents | 63d77859edee |
children | b7d4d288459a |
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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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7 * |
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8 * This program is free software: you can redistribute it and/or |
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9 * modify it under the terms of the GNU Lesser General Public License |
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10 * as published by the Free Software Foundation, either version 3 of |
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11 * the License, or (at your option) any later version. |
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12 * |
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13 * This program is distributed in the hope that it will be useful, but |
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
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21 **/ |
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22 |
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23 |
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24 #include "DicomStructuredReport.h" |
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25 |
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26 #include "../Scene2D/ScenePoint2D.h" |
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27 |
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28 #include <OrthancException.h> |
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29 #include <SerializationToolbox.h> |
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30 |
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31 #include <dcmtk/dcmdata/dcdeftag.h> |
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32 #include <dcmtk/dcmdata/dcsequen.h> |
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33 #include <dcmtk/dcmdata/dcfilefo.h> |
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34 |
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35 |
2087 | 36 static std::string FormatTag(const DcmTagKey& key) |
37 { | |
38 OFString s = key.toString(); | |
39 return std::string(s.c_str()); | |
40 } | |
41 | |
42 | |
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43 static std::string GetStringValue(DcmItem& dataset, |
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44 const DcmTagKey& key) |
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45 { |
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46 const char* value = NULL; |
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47 if (dataset.findAndGetString(key, value).good() && |
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48 value != NULL) |
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49 { |
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50 return value; |
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51 } |
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52 else |
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53 { |
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54 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
2087 | 55 "Missing tag in DICOM-SR: " + FormatTag(key)); |
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56 } |
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57 } |
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58 |
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59 |
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60 static DcmSequenceOfItems& GetSequenceValue(DcmItem& dataset, |
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61 const DcmTagKey& key) |
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62 { |
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63 DcmSequenceOfItems* sequence = NULL; |
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64 if (dataset.findAndGetSequence(key, sequence).good() && |
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65 sequence != NULL) |
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66 { |
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67 return *sequence; |
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68 } |
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69 else |
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70 { |
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71 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
2087 | 72 "Missing sequence in DICOM-SR: " + FormatTag(key)); |
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73 } |
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74 } |
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75 |
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76 |
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77 static void CheckStringValue(DcmItem& dataset, |
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78 const DcmTagKey& key, |
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79 const std::string& expected) |
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80 { |
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81 if (GetStringValue(dataset, key) != expected) |
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82 { |
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83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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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 static bool IsDicomTemplate(DcmItem& dataset, |
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89 const std::string& tid) |
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90 { |
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91 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_ContentTemplateSequence); |
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92 |
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93 return (sequence.card() == 1 && |
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94 GetStringValue(*sequence.getItem(0), DCM_MappingResource) == "DCMR" && |
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95 GetStringValue(*sequence.getItem(0), DCM_TemplateIdentifier) == tid); |
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96 } |
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97 |
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98 |
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99 static bool IsValidConcept(DcmItem& dataset, |
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100 const DcmTagKey& key, |
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101 const std::string& scheme, |
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102 const std::string& concept) |
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103 { |
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104 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, key); |
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105 |
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106 return (sequence.card() == 1 && |
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107 GetStringValue(*sequence.getItem(0), DCM_CodingSchemeDesignator) == scheme && |
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108 GetStringValue(*sequence.getItem(0), DCM_CodeValue) == concept); |
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109 } |
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110 |
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111 |
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112 static bool IsDicomConcept(DcmItem& dataset, |
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113 const std::string& concept) |
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114 { |
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115 return IsValidConcept(dataset, DCM_ConceptNameCodeSequence, "DCM", concept); |
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116 } |
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117 |
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118 |
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119 namespace OrthancStone |
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120 { |
2089 | 121 void DicomStructuredReport::ReferencedInstance::AddFrame(unsigned int frame) |
122 { | |
123 if (frame == 0) | |
124 { | |
125 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
126 } | |
127 else | |
128 { | |
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129 frames_.insert(frame - 1); |
2089 | 130 } |
131 } | |
132 | |
133 | |
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134 class DicomStructuredReport::Structure : public boost::noncopyable |
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135 { |
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136 private: |
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137 std::string sopInstanceUid_; |
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138 bool hasFrameNumber_; |
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139 unsigned int frameNumber_; |
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140 bool hasProbabilityOfCancer_; |
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141 float probabilityOfCancer_; |
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142 |
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143 public: |
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144 Structure(const std::string& sopInstanceUid) : |
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145 sopInstanceUid_(sopInstanceUid), |
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146 hasFrameNumber_(false), |
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147 hasProbabilityOfCancer_(false) |
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148 { |
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149 } |
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150 |
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151 virtual ~Structure() |
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152 { |
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153 } |
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154 |
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155 void SetFrameNumber(unsigned int frame) |
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156 { |
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157 if (frame <= 0) |
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158 { |
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159 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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160 } |
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161 else |
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162 { |
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163 hasFrameNumber_ = true; |
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164 frameNumber_ = frame - 1; |
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165 } |
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166 } |
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167 |
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168 void SetProbabilityOfCancer(float probability) |
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169 { |
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170 if (probability < 0 || |
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171 probability > 100) |
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172 { |
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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174 } |
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175 else |
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176 { |
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177 hasProbabilityOfCancer_ = true; |
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178 probabilityOfCancer_ = probability; |
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179 } |
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180 } |
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181 |
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182 bool HasFrameNumber() const |
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183 { |
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184 return hasFrameNumber_; |
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185 } |
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186 |
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187 bool HasProbabilityOfCancer() const |
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188 { |
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189 return hasProbabilityOfCancer_; |
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190 } |
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191 |
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192 unsigned int GetFrameNumber() const |
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193 { |
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194 if (hasFrameNumber_) |
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195 { |
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196 return frameNumber_; |
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197 } |
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198 else |
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199 { |
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200 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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201 } |
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202 } |
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203 |
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204 float GetProbabilityOfCancer() const |
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205 { |
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206 if (hasProbabilityOfCancer_) |
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207 { |
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208 return probabilityOfCancer_; |
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209 } |
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210 else |
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211 { |
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212 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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213 } |
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214 } |
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215 }; |
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216 |
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217 |
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218 class DicomStructuredReport::Point : public Structure |
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219 { |
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220 private: |
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221 ScenePoint2D point_; |
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222 |
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223 public: |
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224 Point(const std::string& sopInstanceUid, |
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225 double x, |
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226 double y) : |
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227 Structure(sopInstanceUid), |
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228 point_(x, y) |
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229 { |
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230 } |
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231 |
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232 const ScenePoint2D& GetPoint() const |
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233 { |
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234 return point_; |
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235 } |
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236 }; |
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237 |
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238 |
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239 class DicomStructuredReport::Polyline : public Structure |
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240 { |
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241 private: |
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242 std::vector<ScenePoint2D> points_; |
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243 |
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244 public: |
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245 Polyline(const std::string& sopInstanceUid, |
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246 const float* points, |
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247 unsigned long pointsCount) : |
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248 Structure(sopInstanceUid) |
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249 { |
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250 if (pointsCount % 2 != 0) |
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251 { |
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252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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253 } |
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254 |
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255 points_.reserve(pointsCount / 2); |
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256 |
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257 for (unsigned long i = 0; i < pointsCount; i += 2) |
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258 { |
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259 points_.push_back(ScenePoint2D(points[i], points[i + 1])); |
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260 } |
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261 } |
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262 |
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263 size_t GetSize() const |
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264 { |
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265 return points_.size(); |
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266 } |
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267 |
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268 const ScenePoint2D& GetPoint(size_t i) const |
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269 { |
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270 if (i >= points_.size()) |
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271 { |
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272 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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273 } |
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274 else |
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275 { |
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276 return points_[i]; |
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277 } |
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278 } |
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279 }; |
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280 |
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281 |
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282 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid, |
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283 DcmItem& group, |
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284 bool hasFrameNumber, |
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285 unsigned int frameNumber, |
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286 bool hasProbabilityOfCancer, |
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287 float probabilityOfCancer) |
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288 { |
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289 const std::string graphicType = GetStringValue(group, DCM_GraphicType); |
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290 |
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291 const Float32* coords = NULL; |
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292 unsigned long coordsCount = 0; |
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293 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() || |
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294 (coordsCount != 0 && coords == NULL)) |
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295 { |
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296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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297 "Cannot read coordinates for region in DICOM-SR"); |
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298 } |
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299 |
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300 std::unique_ptr<Structure> structure; |
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301 |
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302 if (graphicType == "POINT") |
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303 { |
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304 if (coordsCount != 2) |
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305 { |
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306 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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307 } |
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308 else |
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309 { |
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310 structure.reset(new Point(sopInstanceUid, coords[0], coords[1])); |
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311 } |
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312 } |
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313 else if (graphicType == "POLYLINE") |
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314 { |
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315 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount)); |
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316 } |
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317 else |
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318 { |
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319 return; // Unsupported graphic type |
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320 } |
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321 |
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322 assert(structure.get() != NULL); |
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323 |
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324 if (hasFrameNumber) |
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325 { |
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326 structure->SetFrameNumber(frameNumber); |
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327 } |
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328 |
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329 if (hasProbabilityOfCancer) |
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330 { |
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331 structure->SetProbabilityOfCancer(probabilityOfCancer); |
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332 } |
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333 |
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334 structures_.push_back(structure.release()); |
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335 } |
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336 |
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337 |
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338 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom) |
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339 { |
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340 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
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341 |
2091
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342 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID); |
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343 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID); |
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344 |
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345 CheckStringValue(dataset, DCM_Modality, "SR"); |
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346 CheckStringValue(dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.88.33"); // Comprehensive SR IOD |
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347 CheckStringValue(dataset, DCM_ValueType, "CONTAINER"); |
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348 |
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349 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ || |
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350 !IsDicomTemplate(dataset, "1500")) |
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351 { |
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352 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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353 } |
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354 |
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355 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence); |
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356 |
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357 std::list<std::string> tmp; |
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358 |
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359 for (unsigned long i = 0; i < sequence.card(); i++) |
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360 { |
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361 std::string studyInstanceUid = GetStringValue(*sequence.getItem(i), DCM_StudyInstanceUID); |
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362 |
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363 DcmSequenceOfItems* referencedSeries = NULL; |
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364 if (!sequence.getItem(i)->findAndGetSequence(DCM_ReferencedSeriesSequence, referencedSeries).good() || |
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365 referencedSeries == NULL) |
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366 { |
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367 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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368 } |
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369 |
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370 for (unsigned long j = 0; j < referencedSeries->card(); j++) |
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371 { |
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372 std::string seriesInstanceUid = GetStringValue(*referencedSeries->getItem(j), DCM_SeriesInstanceUID); |
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373 |
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374 DcmSequenceOfItems* referencedInstances = NULL; |
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375 if (!referencedSeries->getItem(j)->findAndGetSequence(DCM_ReferencedSOPSequence, referencedInstances).good() || |
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376 referencedInstances == NULL) |
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377 { |
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378 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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379 } |
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380 |
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381 for (unsigned int k = 0; k < referencedInstances->card(); k++) |
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382 { |
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383 std::string sopClassUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPClassUID); |
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384 std::string sopInstanceUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPInstanceUID); |
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385 |
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386 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end()) |
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387 { |
2089 | 388 instancesInformation_[sopInstanceUid] = new ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid); |
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389 } |
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390 else |
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391 { |
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392 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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393 "Multiple occurrences of the same instance in DICOM-SR: " + sopInstanceUid); |
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394 } |
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395 |
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396 tmp.push_back(sopInstanceUid); |
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397 } |
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398 } |
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399 } |
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|
400 |
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changeset
|
401 orderedInstances_.reserve(tmp.size()); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
402 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
403 for (std::list<std::string>::const_iterator it = tmp.begin(); it != tmp.end(); ++it) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
404 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
405 orderedInstances_.push_back(*it); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
406 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
407 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
408 sequence = GetSequenceValue(dataset, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
409 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
410 for (unsigned long i = 0; i < sequence.card(); i++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
411 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
412 DcmItem& item = *sequence.getItem(i); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
413 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
414 if (GetStringValue(item, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
415 GetStringValue(item, DCM_ValueType) == "CONTAINER" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
416 IsDicomConcept(item, "126010" /* Imaging measurements */)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
417 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
418 DcmSequenceOfItems& measurements = GetSequenceValue(item, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
419 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
420 for (unsigned long j = 0; j < measurements.card(); j++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
421 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
422 DcmItem& measurement = *measurements.getItem(j); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
423 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
424 if (GetStringValue(measurement, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
425 GetStringValue(measurement, DCM_ValueType) == "CONTAINER" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
426 IsDicomConcept(measurement, "125007" /* Measurement group */) && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
427 IsDicomTemplate(measurement, "1410")) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
428 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
429 DcmSequenceOfItems& groups = GetSequenceValue(measurement, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
430 |
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added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
431 bool hasProbabilityOfCancer = false; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
432 float probabilityOfCancer = 0; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
433 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
434 for (unsigned int k = 0; k < groups.card(); k++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
435 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
436 DcmItem& group = *groups.getItem(k); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
437 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
438 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
439 GetStringValue(group, DCM_ValueType) == "NUM" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
440 IsDicomConcept(group, "111047" /* Probability of cancer */)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
441 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
442 DcmSequenceOfItems& values = GetSequenceValue(group, DCM_MeasuredValueSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
443 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
444 if (values.card() == 1 && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
445 IsValidConcept(*values.getItem(0), DCM_MeasurementUnitsCodeSequence, "UCUM", "%")) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
446 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
447 std::string value = GetStringValue(*values.getItem(0), DCM_NumericValue); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
448 if (Orthanc::SerializationToolbox::ParseFloat(probabilityOfCancer, value)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
449 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
450 hasProbabilityOfCancer = true; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
451 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
452 else |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
453 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
454 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
455 "Cannot parse float in DICOM-SR: " + value); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
456 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
457 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
458 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
459 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
460 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
461 for (unsigned int k = 0; k < groups.card(); k++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
462 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
463 DcmItem& group = *groups.getItem(k); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
464 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
465 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
466 GetStringValue(group, DCM_ValueType) == "SCOORD" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
467 IsDicomConcept(group, "111030" /* Image region */)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
468 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
469 DcmSequenceOfItems& regions = GetSequenceValue(group, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
470 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
471 for (unsigned int l = 0; l < regions.card(); l++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
472 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
473 DcmItem& region = *regions.getItem(l); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
474 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
475 if (GetStringValue(region, DCM_RelationshipType) == "SELECTED FROM" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
476 GetStringValue(region, DCM_ValueType) == "IMAGE" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
477 IsDicomConcept(region, "111040") /* Original source */) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
478 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
479 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
480 if (instances.card() != 1) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
481 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
482 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
483 "Region cannot reference multiple instances in DICOM-SR"); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
484 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
485 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
486 std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID); |
2089 | 487 std::map<std::string, ReferencedInstance*>::iterator instanceInformation = instancesInformation_.find(sopInstanceUid); |
488 | |
489 if (instanceInformation == instancesInformation_.end()) | |
2085
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
490 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
491 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
492 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
493 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
494 |
2089 | 495 assert(instanceInformation->second != NULL); |
496 | |
2085
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
497 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
498 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
499 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
500 std::vector<std::string> tokens; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
501 Orthanc::Toolbox::SplitString(tokens, frames, '\\'); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
502 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
503 for (size_t m = 0; m < tokens.size(); m++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
504 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
505 uint32_t frame; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
506 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m])) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
507 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
508 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
509 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
510 else |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
511 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
512 AddStructure(sopInstanceUid, group, true, frame, hasProbabilityOfCancer, probabilityOfCancer); |
2089 | 513 instanceInformation->second->AddFrame(frame); |
2085
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
514 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
515 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
516 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
517 else |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
518 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
519 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer); |
2089 | 520 instanceInformation->second->AddFrame(1); |
2085
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
521 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
522 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
523 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
524 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
525 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
526 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
527 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
528 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
529 } |
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530 } |
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531 |
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532 |
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533 DicomStructuredReport::~DicomStructuredReport() |
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534 { |
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535 for (std::list<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it) |
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536 { |
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537 assert(*it != NULL); |
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538 delete *it; |
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539 } |
2089 | 540 |
541 for (std::map<std::string, ReferencedInstance*>::iterator | |
542 it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it) | |
543 { | |
544 assert(it->second != NULL); | |
545 delete it->second; | |
546 } | |
547 } | |
548 | |
549 | |
550 void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid, | |
551 std::string& seriesInstanceUid, | |
552 std::string& sopInstanceUid, | |
553 std::string& sopClassUid, | |
554 size_t i) const | |
555 { | |
556 if (i >= orderedInstances_.size()) | |
557 { | |
558 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
559 } | |
560 | |
561 sopInstanceUid = orderedInstances_[i]; | |
562 | |
563 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(sopInstanceUid); | |
564 if (found == instancesInformation_.end()) | |
565 { | |
566 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
567 } | |
568 | |
569 assert(found->second != NULL); | |
570 studyInstanceUid = found->second->GetStudyInstanceUid(); | |
571 seriesInstanceUid = found->second->GetSeriesInstanceUid(); | |
572 sopClassUid = found->second->GetSopClassUid(); | |
573 } | |
574 | |
575 | |
576 void DicomStructuredReport::ExportOrderedFrames(std::list<Frame>& frames) const | |
577 { | |
578 frames.clear(); | |
579 | |
580 for (size_t i = 0; i < orderedInstances_.size(); i++) | |
581 { | |
582 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(orderedInstances_[i]); | |
583 if (found == instancesInformation_.end()) | |
584 { | |
585 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
586 } | |
587 | |
588 assert(found->second != NULL); | |
589 | |
590 for (std::set<unsigned int>::const_iterator frame = found->second->GetFrames().begin(); | |
591 frame != found->second->GetFrames().end(); ++frame) | |
592 { | |
593 frames.push_back(Frame(found->second->GetStudyInstanceUid(), | |
594 found->second->GetSeriesInstanceUid(), | |
595 orderedInstances_[i], | |
596 found->second->GetSopClassUid(), *frame)); | |
597 } | |
598 } | |
2085
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599 } |
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600 } |