Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2117:48a7f05c3bd5 dicom-sr

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integration mainline->dicom-sr
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 09 Mar 2024 10:01:30 +0100
parents 129cb165ea8d c23eef785569
children 1a02e758eaf4
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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) 2017-2024 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2024 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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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::Structure::Copy(const Structure& other)
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122 {
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123 if (other.HasFrameNumber())
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124 {
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125 SetFrameNumber(other.GetFrameNumber());
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126 }
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127
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128 if (other.HasProbabilityOfCancer())
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129 {
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130 SetProbabilityOfCancer(other.GetProbabilityOfCancer());
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131 }
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132 }
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133
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134
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135 DicomStructuredReport::Structure::Structure(const std::string& sopInstanceUid) :
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136 sopInstanceUid_(sopInstanceUid),
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137 hasFrameNumber_(false),
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138 hasProbabilityOfCancer_(false)
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139 {
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140 }
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141
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142
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143 void DicomStructuredReport::Structure::SetFrameNumber(unsigned int frame)
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144 {
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145 hasFrameNumber_ = true;
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146 frameNumber_ = frame;
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147 }
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148
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149
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150 void DicomStructuredReport::Structure::SetProbabilityOfCancer(float probability)
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151 {
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152 if (probability < 0 ||
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153 probability > 100)
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154 {
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155 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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156 }
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157 else
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158 {
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159 hasProbabilityOfCancer_ = true;
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160 probabilityOfCancer_ = probability;
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161 }
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162 }
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163
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164
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165 unsigned int DicomStructuredReport::Structure::GetFrameNumber() const
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166 {
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167 if (hasFrameNumber_)
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168 {
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169 return frameNumber_;
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170 }
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171 else
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172 {
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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174 }
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175 }
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176
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177 float DicomStructuredReport::Structure::GetProbabilityOfCancer() const
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178 {
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179 if (hasProbabilityOfCancer_)
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180 {
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181 return probabilityOfCancer_;
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182 }
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183 else
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184 {
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185 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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186 }
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187 }
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188
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189
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190 DicomStructuredReport::Point::Point(const std::string& sopInstanceUid,
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191 double x,
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192 double y) :
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193 Structure(sopInstanceUid),
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194 point_(x, y)
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195 {
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196 }
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197
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198
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199 DicomStructuredReport::Structure* DicomStructuredReport::Point::Clone() const
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200 {
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201 std::unique_ptr<Point> cloned(new Point(GetSopInstanceUid(), point_.GetX(), point_.GetY()));
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202 cloned->Copy(*this);
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203 return cloned.release();
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204 }
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205
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206
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207 DicomStructuredReport::Polyline::Polyline(const std::string& sopInstanceUid,
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208 const float* points,
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209 unsigned long pointsCount) :
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210 Structure(sopInstanceUid)
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211 {
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212 if (pointsCount % 2 != 0)
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213 {
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214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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215 }
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216
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217 points_.reserve(pointsCount / 2);
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218
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219 for (unsigned long i = 0; i < pointsCount; i += 2)
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220 {
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221 points_.push_back(ScenePoint2D(points[i], points[i + 1]));
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222 }
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223 }
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224
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225
2099
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226 DicomStructuredReport::Polyline::Polyline(const std::string& sopInstanceUid,
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227 const std::vector<ScenePoint2D>& points) :
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228 Structure(sopInstanceUid),
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229 points_(points)
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230 {
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231 }
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232
554bc96e7508 added DicomStructuredReport
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parents:
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233
2099
67db5afb305d partial integration dicom-sr->mainline
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234 DicomStructuredReport::Structure* DicomStructuredReport::Polyline::Clone() const
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235 {
2099
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236 std::unique_ptr<Polyline> cloned(new Polyline(GetSopInstanceUid(), points_));
67db5afb305d partial integration dicom-sr->mainline
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237 cloned->Copy(*this);
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238 return cloned.release();
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239 }
2085
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240
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241
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242 const ScenePoint2D& DicomStructuredReport::Polyline::GetPoint(size_t i) const
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243 {
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244 if (i >= points_.size())
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245 {
2099
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246 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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247 }
2099
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248 else
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249 {
2099
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250 return points_[i];
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251 }
2099
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252 }
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253
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254
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255 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid,
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256 DcmItem& group,
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257 bool hasFrameNumber,
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258 unsigned int frameNumber,
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259 bool hasProbabilityOfCancer,
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260 float probabilityOfCancer)
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261 {
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262 const std::string graphicType = GetStringValue(group, DCM_GraphicType);
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263
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264 const Float32* coords = NULL;
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265 unsigned long coordsCount = 0;
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266 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() ||
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267 (coordsCount != 0 && coords == NULL))
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268 {
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269 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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270 "Cannot read coordinates for region in DICOM-SR");
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271 }
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272
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273 std::unique_ptr<Structure> structure;
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274
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275 if (graphicType == "POINT")
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276 {
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277 if (coordsCount != 2)
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278 {
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279 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
280 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
281 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
282 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
283 structure.reset(new Point(sopInstanceUid, coords[0], coords[1]));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
284 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
285 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
286 else if (graphicType == "POLYLINE")
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
288 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
290 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 return; // Unsupported graphic type
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293 }
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 assert(structure.get() != NULL);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
296
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
297 if (hasFrameNumber)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
298 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299 structure->SetFrameNumber(frameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 }
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 if (hasProbabilityOfCancer)
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 structure->SetProbabilityOfCancer(probabilityOfCancer);
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 structures_.push_back(structure.release());
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
311 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
312 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
313 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
314
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
315 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
316 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
317 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
318
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
319 CheckStringValue(dataset, DCM_Modality, "SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
320 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
321 CheckStringValue(dataset, DCM_ValueType, "CONTAINER");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
323 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
324 !IsDicomTemplate(dataset, "1500"))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
325 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
326 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
329 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
330
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
331 std::list<std::string> tmp;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
332
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
333 for (unsigned long i = 0; i < sequence.card(); i++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
335 std::string studyInstanceUid = GetStringValue(*sequence.getItem(i), DCM_StudyInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
336
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
337 DcmSequenceOfItems* referencedSeries = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
338 if (!sequence.getItem(i)->findAndGetSequence(DCM_ReferencedSeriesSequence, referencedSeries).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
339 referencedSeries == NULL)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344 for (unsigned long j = 0; j < referencedSeries->card(); j++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 std::string seriesInstanceUid = GetStringValue(*referencedSeries->getItem(j), DCM_SeriesInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
348 DcmSequenceOfItems* referencedInstances = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349 if (!referencedSeries->getItem(j)->findAndGetSequence(DCM_ReferencedSOPSequence, referencedInstances).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 referencedInstances == 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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 for (unsigned int k = 0; k < referencedInstances->card(); k++)
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 std::string sopClassUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPClassUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 std::string sopInstanceUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 {
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
362 instancesInformation_[sopInstanceUid] = new ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid);
2085
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 else
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 "Multiple occurrences of the same instance in DICOM-SR: " + sopInstanceUid);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370 tmp.push_back(sopInstanceUid);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
371 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
372 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
373 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
374
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375 orderedInstances_.reserve(tmp.size());
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
377 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
378 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379 orderedInstances_.push_back(*it);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 sequence = GetSequenceValue(dataset, DCM_ContentSequence);
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 for (unsigned long i = 0; i < sequence.card(); i++)
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 DcmItem& item = *sequence.getItem(i);
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 if (GetStringValue(item, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 GetStringValue(item, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 IsDicomConcept(item, "126010" /* Imaging measurements */))
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& measurements = GetSequenceValue(item, DCM_ContentSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
393
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 for (unsigned long j = 0; j < measurements.card(); j++)
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 DcmItem& measurement = *measurements.getItem(j);
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 if (GetStringValue(measurement, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 GetStringValue(measurement, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400 IsDicomConcept(measurement, "125007" /* Measurement group */) &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401 IsDicomTemplate(measurement, "1410"))
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& groups = GetSequenceValue(measurement, DCM_ContentSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 bool hasProbabilityOfCancer = false;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 float probabilityOfCancer = 0;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408 for (unsigned int k = 0; k < groups.card(); k++)
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 DcmItem& group = *groups.getItem(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 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 GetStringValue(group, DCM_ValueType) == "NUM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
414 IsDicomConcept(group, "111047" /* Probability of cancer */))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
415 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416 DcmSequenceOfItems& values = GetSequenceValue(group, DCM_MeasuredValueSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
417
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
418 if (values.card() == 1 &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
419 IsValidConcept(*values.getItem(0), DCM_MeasurementUnitsCodeSequence, "UCUM", "%"))
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 std::string value = GetStringValue(*values.getItem(0), DCM_NumericValue);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422 if (Orthanc::SerializationToolbox::ParseFloat(probabilityOfCancer, value))
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 hasProbabilityOfCancer = true;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
426 else
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429 "Cannot parse float in DICOM-SR: " + value);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
430 }
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 }
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
435 for (unsigned int k = 0; k < groups.card(); k++)
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 DcmItem& group = *groups.getItem(k);
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 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440 GetStringValue(group, DCM_ValueType) == "SCOORD" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 IsDicomConcept(group, "111030" /* Image region */))
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 DcmSequenceOfItems& regions = GetSequenceValue(group, DCM_ContentSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 for (unsigned int l = 0; l < regions.card(); l++)
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 DcmItem& region = *regions.getItem(l);
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 if (GetStringValue(region, DCM_RelationshipType) == "SELECTED FROM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 GetStringValue(region, DCM_ValueType) == "IMAGE" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451 IsDicomConcept(region, "111040") /* Original source */)
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 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
454 if (instances.card() != 1)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
455 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
456 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
457 "Region cannot reference multiple instances in DICOM-SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
458 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
459
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
460 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
461 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
462
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
463 if (instanceInformation == instancesInformation_.end())
2085
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
466 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
467 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
468
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
469 assert(instanceInformation->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
470
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber))
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 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
474 std::vector<std::string> tokens;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
475 Orthanc::Toolbox::SplitString(tokens, frames, '\\');
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
476
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 for (size_t m = 0; m < tokens.size(); m++)
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 uint32_t frame;
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
480 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m]) ||
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
481 frame <= 0)
2085
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 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
485 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
486 {
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
487 AddStructure(sopInstanceUid, group, true, frame - 1, hasProbabilityOfCancer, probabilityOfCancer);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
488 instanceInformation->second->AddFrame(frame - 1);
2085
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 }
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 else
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 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer);
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
495 instanceInformation->second->AddFrame(0);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
496 }
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 }
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 }
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 }
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 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
505 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
506
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
507
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
508 DicomStructuredReport::DicomStructuredReport(const DicomStructuredReport& other) :
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
509 studyInstanceUid_(other.studyInstanceUid_),
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
510 seriesInstanceUid_(other.seriesInstanceUid_),
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
511 sopInstanceUid_(other.sopInstanceUid_),
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
512 orderedInstances_(other.orderedInstances_)
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
513 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
514 for (std::map<std::string, ReferencedInstance*>::const_iterator
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
515 it = other.instancesInformation_.begin(); it != other.instancesInformation_.end(); ++it)
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
516 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
517 assert(it->second != NULL);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
518 instancesInformation_[it->first] = new ReferencedInstance(*it->second);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
519 }
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
520
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
521 for (std::deque<Structure*>::const_iterator it = other.structures_.begin(); it != other.structures_.end(); ++it)
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
522 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
523 assert(*it != NULL);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
524 structures_.push_back((*it)->Clone());
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
525 }
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
526 }
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
527
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
528
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529 DicomStructuredReport::~DicomStructuredReport()
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 {
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
531 for (std::deque<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it)
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
533 assert(*it != NULL);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 delete *it;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
535 }
2094
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
536
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
537 for (std::map<std::string, ReferencedInstance*>::iterator
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
538 it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it)
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
539 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
540 assert(it->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
541 delete it->second;
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
542 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
543 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
544
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
545
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
546 void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
547 std::string& seriesInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
548 std::string& sopInstanceUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
549 std::string& sopClassUid,
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
550 size_t i) const
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
551 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
552 if (i >= orderedInstances_.size())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
553 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
554 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
555 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
556
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
557 sopInstanceUid = orderedInstances_[i];
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
558
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
559 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
560 if (found == instancesInformation_.end())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
561 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
562 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
563 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
564
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
565 assert(found->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
566 studyInstanceUid = found->second->GetStudyInstanceUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
567 seriesInstanceUid = found->second->GetSeriesInstanceUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
568 sopClassUid = found->second->GetSopClassUid();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
569 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
570
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
571
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
572 void DicomStructuredReport::ExportReferencedFrames(std::list<ReferencedFrame>& frames) const
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
573 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
574 frames.clear();
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
575
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
576 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
577 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
578 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
579 if (found == instancesInformation_.end())
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
580 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
581 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
582 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
583
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
584 assert(found->second != NULL);
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
585
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
586 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
587 frame != found->second->GetFrames().end(); ++frame)
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
588 {
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
589 frames.push_back(ReferencedFrame(found->second->GetStudyInstanceUid(),
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
590 found->second->GetSeriesInstanceUid(),
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
591 orderedInstances_[i],
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
592 found->second->GetSopClassUid(), *frame));
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
593 }
7c3d65166c26 partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
594 }
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
595 }
2099
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
596
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
597
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
598 const DicomStructuredReport::Structure& DicomStructuredReport::GetStructure(size_t index) const
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
599 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
600 if (index >= structures_.size())
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
601 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
602 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
603 }
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
604 else
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
605 {
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
606 assert(structures_[index] != NULL);
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
607 return *structures_[index];
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
608 }
67db5afb305d partial integration dicom-sr->mainline
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2094
diff changeset
609 }
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
610 }