Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2097:a9e23ef9ee09 dicom-sr
preparing to extract dicom-sr annotations
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 08 Nov 2023 16:31:49 +0100 |
parents | 79e984a89a38 |
children | 4288d635d77e |
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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 { |
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121 void DicomStructuredReport::ReferencedInstance::AddFrame(unsigned int frame) |
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122 { |
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123 frames_.insert(frame); |
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124 } |
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125 |
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126 |
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127 class DicomStructuredReport::Structure : public boost::noncopyable |
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128 { |
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129 private: |
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130 std::string sopInstanceUid_; |
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131 bool hasFrameNumber_; |
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132 unsigned int frameNumber_; |
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133 bool hasProbabilityOfCancer_; |
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134 float probabilityOfCancer_; |
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135 |
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136 protected: |
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137 void Copy(const Structure& other) |
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138 { |
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139 if (other.HasFrameNumber()) |
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140 { |
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141 SetFrameNumber(other.GetFrameNumber()); |
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142 } |
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143 |
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144 if (other.HasProbabilityOfCancer()) |
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145 { |
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146 SetProbabilityOfCancer(other.GetProbabilityOfCancer()); |
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147 } |
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148 } |
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149 |
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150 public: |
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151 Structure(const std::string& sopInstanceUid) : |
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152 sopInstanceUid_(sopInstanceUid), |
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153 hasFrameNumber_(false), |
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154 hasProbabilityOfCancer_(false) |
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155 { |
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156 } |
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157 |
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158 virtual ~Structure() |
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159 { |
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160 } |
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161 |
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162 virtual Structure* Clone() const = 0; |
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163 |
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164 const std::string& GetSopInstanceUid() const |
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165 { |
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166 return sopInstanceUid_; |
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167 } |
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168 |
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169 void SetFrameNumber(unsigned int frame) |
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170 { |
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171 hasFrameNumber_ = true; |
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172 frameNumber_ = frame; |
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173 } |
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174 |
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175 void SetProbabilityOfCancer(float probability) |
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176 { |
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177 if (probability < 0 || |
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178 probability > 100) |
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179 { |
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180 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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181 } |
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182 else |
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183 { |
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184 hasProbabilityOfCancer_ = true; |
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185 probabilityOfCancer_ = probability; |
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186 } |
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187 } |
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188 |
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189 bool HasFrameNumber() const |
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190 { |
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191 return hasFrameNumber_; |
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192 } |
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193 |
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194 bool HasProbabilityOfCancer() const |
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195 { |
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196 return hasProbabilityOfCancer_; |
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197 } |
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198 |
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199 unsigned int GetFrameNumber() const |
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200 { |
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201 if (hasFrameNumber_) |
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202 { |
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203 return frameNumber_; |
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204 } |
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205 else |
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206 { |
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207 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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208 } |
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209 } |
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210 |
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211 float GetProbabilityOfCancer() const |
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212 { |
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213 if (hasProbabilityOfCancer_) |
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214 { |
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215 return probabilityOfCancer_; |
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216 } |
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217 else |
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218 { |
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219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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220 } |
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221 } |
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222 }; |
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223 |
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224 |
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225 class DicomStructuredReport::Point : public Structure |
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226 { |
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227 private: |
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228 ScenePoint2D point_; |
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229 |
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230 public: |
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231 Point(const std::string& sopInstanceUid, |
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232 double x, |
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233 double y) : |
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234 Structure(sopInstanceUid), |
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235 point_(x, y) |
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236 { |
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237 } |
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238 |
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239 virtual Structure* Clone() const |
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240 { |
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241 std::unique_ptr<Point> cloned(new Point(GetSopInstanceUid(), point_.GetX(), point_.GetY())); |
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242 cloned->Copy(*this); |
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243 return cloned.release(); |
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244 } |
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245 |
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246 const ScenePoint2D& GetPoint() const |
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247 { |
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248 return point_; |
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249 } |
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250 }; |
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251 |
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252 |
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253 class DicomStructuredReport::Polyline : public Structure |
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254 { |
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255 private: |
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256 std::vector<ScenePoint2D> points_; |
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257 |
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258 public: |
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259 Polyline(const std::string& sopInstanceUid, |
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260 const float* points, |
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261 unsigned long pointsCount) : |
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262 Structure(sopInstanceUid) |
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263 { |
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264 if (pointsCount % 2 != 0) |
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265 { |
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266 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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267 } |
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268 |
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269 points_.reserve(pointsCount / 2); |
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270 |
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271 for (unsigned long i = 0; i < pointsCount; i += 2) |
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272 { |
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273 points_.push_back(ScenePoint2D(points[i], points[i + 1])); |
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274 } |
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275 } |
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276 |
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277 Polyline(const std::string& sopInstanceUid, |
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278 const std::vector<ScenePoint2D>& points) : |
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279 Structure(sopInstanceUid), |
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280 points_(points) |
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281 { |
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282 } |
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283 |
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284 virtual Structure* Clone() const |
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285 { |
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286 std::unique_ptr<Polyline> cloned(new Polyline(GetSopInstanceUid(), points_)); |
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287 cloned->Copy(*this); |
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288 return cloned.release(); |
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289 } |
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290 |
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291 size_t GetSize() const |
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292 { |
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293 return points_.size(); |
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294 } |
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295 |
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296 const ScenePoint2D& GetPoint(size_t i) const |
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297 { |
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298 if (i >= points_.size()) |
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299 { |
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300 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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301 } |
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302 else |
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303 { |
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304 return points_[i]; |
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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 |
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310 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid, |
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311 DcmItem& group, |
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312 bool hasFrameNumber, |
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313 unsigned int frameNumber, |
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314 bool hasProbabilityOfCancer, |
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315 float probabilityOfCancer) |
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316 { |
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317 const std::string graphicType = GetStringValue(group, DCM_GraphicType); |
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318 |
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319 const Float32* coords = NULL; |
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320 unsigned long coordsCount = 0; |
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321 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() || |
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322 (coordsCount != 0 && coords == NULL)) |
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323 { |
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324 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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325 "Cannot read coordinates for region in DICOM-SR"); |
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326 } |
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327 |
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328 std::unique_ptr<Structure> structure; |
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329 |
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330 if (graphicType == "POINT") |
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331 { |
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332 if (coordsCount != 2) |
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333 { |
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334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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335 } |
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336 else |
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337 { |
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338 structure.reset(new Point(sopInstanceUid, coords[0], coords[1])); |
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339 } |
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340 } |
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341 else if (graphicType == "POLYLINE") |
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342 { |
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343 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount)); |
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344 } |
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345 else |
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346 { |
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347 return; // Unsupported graphic type |
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348 } |
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349 |
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350 assert(structure.get() != NULL); |
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351 |
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352 if (hasFrameNumber) |
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353 { |
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354 structure->SetFrameNumber(frameNumber); |
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355 } |
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356 |
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357 if (hasProbabilityOfCancer) |
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358 { |
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359 structure->SetProbabilityOfCancer(probabilityOfCancer); |
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360 } |
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361 |
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362 structures_.push_back(structure.release()); |
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363 } |
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364 |
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365 |
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366 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom) |
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367 { |
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368 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
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369 |
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370 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID); |
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371 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID); |
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372 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID); |
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373 |
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374 CheckStringValue(dataset, DCM_Modality, "SR"); |
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375 CheckStringValue(dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.88.33"); // Comprehensive SR IOD |
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376 CheckStringValue(dataset, DCM_ValueType, "CONTAINER"); |
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377 |
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378 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ || |
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379 !IsDicomTemplate(dataset, "1500")) |
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380 { |
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381 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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382 } |
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383 |
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384 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence); |
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385 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
386 std::list<std::string> tmp; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
387 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
388 for (unsigned long i = 0; i < sequence.card(); i++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
389 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
390 std::string studyInstanceUid = GetStringValue(*sequence.getItem(i), DCM_StudyInstanceUID); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
391 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
392 DcmSequenceOfItems* referencedSeries = NULL; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
393 if (!sequence.getItem(i)->findAndGetSequence(DCM_ReferencedSeriesSequence, referencedSeries).good() || |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
394 referencedSeries == NULL) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
395 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
396 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
397 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
398 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
399 for (unsigned long j = 0; j < referencedSeries->card(); j++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
400 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
401 std::string seriesInstanceUid = GetStringValue(*referencedSeries->getItem(j), DCM_SeriesInstanceUID); |
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 DcmSequenceOfItems* referencedInstances = NULL; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
404 if (!referencedSeries->getItem(j)->findAndGetSequence(DCM_ReferencedSOPSequence, referencedInstances).good() || |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
405 referencedInstances == NULL) |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
408 } |
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 int k = 0; k < referencedInstances->card(); k++) |
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 std::string sopClassUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPClassUID); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
413 std::string sopInstanceUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPInstanceUID); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
414 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
415 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end()) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
416 { |
2094
7c3d65166c26
partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2087
diff
changeset
|
417 instancesInformation_[sopInstanceUid] = new ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid); |
2085
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
418 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
419 else |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
420 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
421 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
422 "Multiple occurrences of the same instance in DICOM-SR: " + sopInstanceUid); |
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 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
425 tmp.push_back(sopInstanceUid); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
426 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
427 } |
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 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
430 orderedInstances_.reserve(tmp.size()); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
431 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
432 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
|
433 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
434 orderedInstances_.push_back(*it); |
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 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
437 sequence = GetSequenceValue(dataset, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
438 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
439 for (unsigned long i = 0; i < sequence.card(); i++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
440 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
441 DcmItem& item = *sequence.getItem(i); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
442 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
443 if (GetStringValue(item, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
444 GetStringValue(item, DCM_ValueType) == "CONTAINER" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
445 IsDicomConcept(item, "126010" /* Imaging measurements */)) |
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 DcmSequenceOfItems& measurements = GetSequenceValue(item, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
448 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
449 for (unsigned long j = 0; j < measurements.card(); j++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
450 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
451 DcmItem& measurement = *measurements.getItem(j); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
452 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
453 if (GetStringValue(measurement, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
454 GetStringValue(measurement, DCM_ValueType) == "CONTAINER" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
455 IsDicomConcept(measurement, "125007" /* Measurement group */) && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
456 IsDicomTemplate(measurement, "1410")) |
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 DcmSequenceOfItems& groups = GetSequenceValue(measurement, DCM_ContentSequence); |
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 bool hasProbabilityOfCancer = false; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
461 float probabilityOfCancer = 0; |
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 for (unsigned int k = 0; k < groups.card(); 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 DcmItem& group = *groups.getItem(k); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
466 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
467 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
468 GetStringValue(group, DCM_ValueType) == "NUM" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
469 IsDicomConcept(group, "111047" /* Probability of cancer */)) |
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 DcmSequenceOfItems& values = GetSequenceValue(group, DCM_MeasuredValueSequence); |
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 if (values.card() == 1 && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
474 IsValidConcept(*values.getItem(0), DCM_MeasurementUnitsCodeSequence, "UCUM", "%")) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
475 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
476 std::string value = GetStringValue(*values.getItem(0), DCM_NumericValue); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
477 if (Orthanc::SerializationToolbox::ParseFloat(probabilityOfCancer, value)) |
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 hasProbabilityOfCancer = true; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
480 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
481 else |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
482 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
483 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
484 "Cannot parse float in DICOM-SR: " + value); |
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 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
487 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
488 } |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
489 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
490 for (unsigned int k = 0; k < groups.card(); k++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
491 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
492 DcmItem& group = *groups.getItem(k); |
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 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
495 GetStringValue(group, DCM_ValueType) == "SCOORD" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
496 IsDicomConcept(group, "111030" /* Image region */)) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
497 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
498 DcmSequenceOfItems& regions = GetSequenceValue(group, DCM_ContentSequence); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
499 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
500 for (unsigned int l = 0; l < regions.card(); l++) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
501 { |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
502 DcmItem& region = *regions.getItem(l); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
503 |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
504 if (GetStringValue(region, DCM_RelationshipType) == "SELECTED FROM" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
505 GetStringValue(region, DCM_ValueType) == "IMAGE" && |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
506 IsDicomConcept(region, "111040") /* Original source */) |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
507 { |
554bc96e7508
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508 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence); |
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509 if (instances.card() != 1) |
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510 { |
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511 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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512 "Region cannot reference multiple instances in DICOM-SR"); |
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513 } |
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514 |
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515 std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID); |
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516 std::map<std::string, ReferencedInstance*>::iterator instanceInformation = instancesInformation_.find(sopInstanceUid); |
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517 |
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518 if (instanceInformation == instancesInformation_.end()) |
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519 { |
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520 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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521 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid); |
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522 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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523 |
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524 assert(instanceInformation->second != NULL); |
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|
525 |
2085
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526 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber)) |
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diff
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|
527 { |
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528 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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529 std::vector<std::string> tokens; |
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530 Orthanc::Toolbox::SplitString(tokens, frames, '\\'); |
554bc96e7508
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|
531 |
554bc96e7508
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532 for (size_t m = 0; m < tokens.size(); m++) |
554bc96e7508
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533 { |
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|
534 uint32_t frame; |
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535 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m]) || |
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536 frame <= 0) |
2085
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|
537 { |
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538 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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539 } |
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540 else |
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|
541 { |
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542 AddStructure(sopInstanceUid, group, true, frame - 1, hasProbabilityOfCancer, probabilityOfCancer); |
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543 instanceInformation->second->AddFrame(frame - 1); |
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544 } |
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parents:
diff
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|
545 } |
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|
546 } |
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parents:
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|
547 else |
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parents:
diff
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|
548 { |
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diff
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|
549 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer); |
2097
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|
550 instanceInformation->second->AddFrame(0); |
2085
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|
551 } |
554bc96e7508
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|
552 } |
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diff
changeset
|
553 } |
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changeset
|
554 } |
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parents:
diff
changeset
|
555 } |
554bc96e7508
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parents:
diff
changeset
|
556 } |
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parents:
diff
changeset
|
557 } |
554bc96e7508
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parents:
diff
changeset
|
558 } |
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parents:
diff
changeset
|
559 } |
554bc96e7508
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parents:
diff
changeset
|
560 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
561 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
562 |
2097
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diff
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|
563 DicomStructuredReport::DicomStructuredReport(const DicomStructuredReport& other) : |
a9e23ef9ee09
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parents:
2096
diff
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564 studyInstanceUid_(other.studyInstanceUid_), |
a9e23ef9ee09
preparing to extract dicom-sr annotations
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parents:
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diff
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|
565 seriesInstanceUid_(other.seriesInstanceUid_), |
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parents:
2096
diff
changeset
|
566 sopInstanceUid_(other.sopInstanceUid_), |
a9e23ef9ee09
preparing to extract dicom-sr annotations
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parents:
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diff
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|
567 orderedInstances_(other.orderedInstances_) |
a9e23ef9ee09
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parents:
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diff
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|
568 { |
a9e23ef9ee09
preparing to extract dicom-sr annotations
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diff
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|
569 for (std::map<std::string, ReferencedInstance*>::const_iterator |
a9e23ef9ee09
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parents:
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diff
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|
570 it = other.instancesInformation_.begin(); it != other.instancesInformation_.end(); ++it) |
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preparing to extract dicom-sr annotations
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diff
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|
571 { |
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preparing to extract dicom-sr annotations
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diff
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|
572 assert(it->second != NULL); |
a9e23ef9ee09
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diff
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|
573 instancesInformation_[it->first] = new ReferencedInstance(*it->second); |
a9e23ef9ee09
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diff
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|
574 } |
a9e23ef9ee09
preparing to extract dicom-sr annotations
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diff
changeset
|
575 |
a9e23ef9ee09
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diff
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|
576 for (std::list<Structure*>::const_iterator it = other.structures_.begin(); it != other.structures_.end(); ++it) |
a9e23ef9ee09
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diff
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|
577 { |
a9e23ef9ee09
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diff
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|
578 assert(*it != NULL); |
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diff
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|
579 structures_.push_back((*it)->Clone()); |
a9e23ef9ee09
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diff
changeset
|
580 } |
a9e23ef9ee09
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diff
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|
581 } |
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diff
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|
582 |
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diff
changeset
|
583 |
2085
554bc96e7508
added DicomStructuredReport
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diff
changeset
|
584 DicomStructuredReport::~DicomStructuredReport() |
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added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
585 { |
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added DicomStructuredReport
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diff
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|
586 for (std::list<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it) |
554bc96e7508
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
587 { |
554bc96e7508
added DicomStructuredReport
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diff
changeset
|
588 assert(*it != NULL); |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
589 delete *it; |
554bc96e7508
added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
590 } |
2094
7c3d65166c26
partial integration dicom-sr->mainline
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diff
changeset
|
591 |
7c3d65166c26
partial integration dicom-sr->mainline
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diff
changeset
|
592 for (std::map<std::string, ReferencedInstance*>::iterator |
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partial integration dicom-sr->mainline
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593 it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it) |
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|
594 { |
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partial integration dicom-sr->mainline
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diff
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|
595 assert(it->second != NULL); |
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diff
changeset
|
596 delete it->second; |
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diff
changeset
|
597 } |
7c3d65166c26
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parents:
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diff
changeset
|
598 } |
7c3d65166c26
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diff
changeset
|
599 |
7c3d65166c26
partial integration dicom-sr->mainline
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diff
changeset
|
600 |
7c3d65166c26
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changeset
|
601 void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid, |
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diff
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|
602 std::string& seriesInstanceUid, |
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diff
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|
603 std::string& sopInstanceUid, |
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604 std::string& sopClassUid, |
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605 size_t i) const |
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606 { |
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607 if (i >= orderedInstances_.size()) |
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|
608 { |
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|
609 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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|
610 } |
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|
611 |
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612 sopInstanceUid = orderedInstances_[i]; |
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|
613 |
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614 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(sopInstanceUid); |
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615 if (found == instancesInformation_.end()) |
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|
616 { |
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|
617 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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|
618 } |
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|
619 |
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|
620 assert(found->second != NULL); |
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621 studyInstanceUid = found->second->GetStudyInstanceUid(); |
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622 seriesInstanceUid = found->second->GetSeriesInstanceUid(); |
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623 sopClassUid = found->second->GetSopClassUid(); |
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624 } |
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625 |
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626 |
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627 void DicomStructuredReport::ExportReferencedFrames(std::list<ReferencedFrame>& frames) const |
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628 { |
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629 frames.clear(); |
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630 |
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631 for (size_t i = 0; i < orderedInstances_.size(); i++) |
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632 { |
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633 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(orderedInstances_[i]); |
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634 if (found == instancesInformation_.end()) |
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635 { |
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636 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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637 } |
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638 |
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639 assert(found->second != NULL); |
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640 |
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641 for (std::set<unsigned int>::const_iterator frame = found->second->GetFrames().begin(); |
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642 frame != found->second->GetFrames().end(); ++frame) |
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643 { |
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644 frames.push_back(ReferencedFrame(found->second->GetStudyInstanceUid(), |
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645 found->second->GetSeriesInstanceUid(), |
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646 orderedInstances_[i], |
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647 found->second->GetSopClassUid(), *frame)); |
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648 } |
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649 } |
2085
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650 } |
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651 } |