Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2097:a9e23ef9ee09 dicom-sr

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preparing to extract dicom-sr annotations
author Sebastien Jodogne <s.jodogne@gmail.com>
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
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36 static std::string FormatTag(const DcmTagKey& key)
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37 {
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38 OFString s = key.toString();
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39 return std::string(s.c_str());
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40 }
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41
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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,
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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,
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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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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293 return points_.size();
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
294 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
295
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
296 const ScenePoint2D& GetPoint(size_t i) const
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
297 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
298 if (i >= points_.size())
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
301 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
302 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
303 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
304 return points_[i];
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
305 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307 };
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
310 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
311 DcmItem& group,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
312 bool hasFrameNumber,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
313 unsigned int frameNumber,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
314 bool hasProbabilityOfCancer,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
315 float probabilityOfCancer)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
316 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317 const std::string graphicType = GetStringValue(group, DCM_GraphicType);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
318
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
319 const Float32* coords = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
320 unsigned long coordsCount = 0;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
321 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322 (coordsCount != 0 && coords == NULL))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
323 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
324 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
325 "Cannot read coordinates for region in DICOM-SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
326 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
327
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
328 std::unique_ptr<Structure> structure;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
329
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
330 if (graphicType == "POINT")
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
331 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
332 if (coordsCount != 2)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
333 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
335 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
336 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
337 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
338 structure.reset(new Point(sopInstanceUid, coords[0], coords[1]));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
339 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
340 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
341 else if (graphicType == "POLYLINE")
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
343 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 return; // Unsupported graphic type
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
348 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 assert(structure.get() != NULL);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
351
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 if (hasFrameNumber)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
353 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 structure->SetFrameNumber(frameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 if (hasProbabilityOfCancer)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359 structure->SetProbabilityOfCancer(probabilityOfCancer);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 structures_.push_back(structure.release());
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
365
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
370 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
371 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
372 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
373
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
374 CheckStringValue(dataset, DCM_Modality, "SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375 CheckStringValue(dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.88.33"); // Comprehensive SR IOD
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376 CheckStringValue(dataset, DCM_ValueType, "CONTAINER");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
377
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
378 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379 !IsDicomTemplate(dataset, "1500"))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
380 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
385
554bc96e7508 added DicomStructuredReport
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 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
508 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
509 if (instances.card() != 1)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
510 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512 "Region cannot reference multiple instances in DICOM-SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
513 }
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 std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID);
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
516 std::map<std::string, ReferencedInstance*>::iterator instanceInformation = instancesInformation_.find(sopInstanceUid);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
517
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
518 if (instanceInformation == instancesInformation_.end())
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid);
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
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
524 assert(instanceInformation->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
525
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber))
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 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529 std::vector<std::string> tokens;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 Orthanc::Toolbox::SplitString(tokens, frames, '\\');
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
531
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532 for (size_t m = 0; m < tokens.size(); m++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
533 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 uint32_t frame;
2097
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
535 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m]) ||
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
536 frame <= 0)
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
537 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
538 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
540 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
541 {
2097
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
542 AddStructure(sopInstanceUid, group, true, frame - 1, hasProbabilityOfCancer, probabilityOfCancer);
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
543 instanceInformation->second->AddFrame(frame - 1);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
544 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
545 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
546 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
547 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
548 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
549 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer);
2097
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
550 instanceInformation->second->AddFrame(0);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
551 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
552 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
553 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
554 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
555 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
556 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
557 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
558 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
559 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
560 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
561
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
562
2097
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
563 DicomStructuredReport::DicomStructuredReport(const DicomStructuredReport& other) :
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
564 studyInstanceUid_(other.studyInstanceUid_),
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
565 seriesInstanceUid_(other.seriesInstanceUid_),
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
566 sopInstanceUid_(other.sopInstanceUid_),
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
567 orderedInstances_(other.orderedInstances_)
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
568 {
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
569 for (std::map<std::string, ReferencedInstance*>::const_iterator
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
570 it = other.instancesInformation_.begin(); it != other.instancesInformation_.end(); ++it)
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
571 {
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
572 assert(it->second != NULL);
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
573 instancesInformation_[it->first] = new ReferencedInstance(*it->second);
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
574 }
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
575
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
576 for (std::list<Structure*>::const_iterator it = other.structures_.begin(); it != other.structures_.end(); ++it)
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
577 {
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
578 assert(*it != NULL);
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
579 structures_.push_back((*it)->Clone());
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
580 }
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
581 }
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
582
a9e23ef9ee09 preparing to extract dicom-sr annotations
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2096
diff changeset
583
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
584 DicomStructuredReport::~DicomStructuredReport()
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
585 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
586 for (std::list<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
587 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
591
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
592 for (std::map<std::string, ReferencedInstance*>::iterator
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
593 it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it)
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
594 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
595 assert(it->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
596 delete it->second;
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
597 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
598 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
599
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
600
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
601 void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
602 std::string& seriesInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
603 std::string& sopInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
604 std::string& sopClassUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
605 size_t i) const
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
606 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
607 if (i >= orderedInstances_.size())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
608 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
609 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
610 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
611
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
612 sopInstanceUid = orderedInstances_[i];
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
613
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
614 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(sopInstanceUid);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
615 if (found == instancesInformation_.end())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
616 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
617 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
618 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
619
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
620 assert(found->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
621 studyInstanceUid = found->second->GetStudyInstanceUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
622 seriesInstanceUid = found->second->GetSeriesInstanceUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
623 sopClassUid = found->second->GetSopClassUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
624 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
625
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
626
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
627 void DicomStructuredReport::ExportReferencedFrames(std::list<ReferencedFrame>& frames) const
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
628 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
629 frames.clear();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
630
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
631 for (size_t i = 0; i < orderedInstances_.size(); i++)
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
632 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
633 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(orderedInstances_[i]);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
634 if (found == instancesInformation_.end())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
635 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
636 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
637 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
638
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
639 assert(found->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
640
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
641 for (std::set<unsigned int>::const_iterator frame = found->second->GetFrames().begin();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
642 frame != found->second->GetFrames().end(); ++frame)
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
643 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
644 frames.push_back(ReferencedFrame(found->second->GetStudyInstanceUid(),
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
645 found->second->GetSeriesInstanceUid(),
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
646 orderedInstances_[i],
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
647 found->second->GetSopClassUid(), *frame));
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
648 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
649 }
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
650 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
651 }