Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2089:63d77859edee dicom-sr

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 07 Nov 2023 19:30:44 +0100
parents 51c8b21b81e4
children 35de56fb6f89
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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 if (frame == 0)
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124 {
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125 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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126 }
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127 else
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128 {
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129 frames_.insert(frame);
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130 }
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131 }
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132
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133
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134 class DicomStructuredReport::Structure : public boost::noncopyable
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135 {
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136 private:
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137 std::string sopInstanceUid_;
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138 bool hasFrameNumber_;
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139 unsigned int frameNumber_;
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140 bool hasProbabilityOfCancer_;
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141 float probabilityOfCancer_;
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142
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143 public:
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144 Structure(const std::string& sopInstanceUid) :
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145 sopInstanceUid_(sopInstanceUid),
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146 hasFrameNumber_(false),
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147 hasProbabilityOfCancer_(false)
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148 {
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parents:
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149 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 virtual ~Structure()
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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152 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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153 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 void SetFrameNumber(unsigned int frame)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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157 if (frame <= 0)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
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160 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 hasFrameNumber_ = true;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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164 frameNumber_ = frame;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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165 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 void SetProbabilityOfCancer(float probability)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 if (probability < 0 ||
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 probability > 100)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
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174 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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175 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176 {
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Sebastien Jodogne <s.jodogne@gmail.com>
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177 hasProbabilityOfCancer_ = true;
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Sebastien Jodogne <s.jodogne@gmail.com>
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178 probabilityOfCancer_ = probability;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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179 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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180 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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181
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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182 bool HasFrameNumber() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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183 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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184 return hasFrameNumber_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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185 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 bool HasProbabilityOfCancer() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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189 return hasProbabilityOfCancer_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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190 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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191
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 unsigned int GetFrameNumber() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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194 if (hasFrameNumber_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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195 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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196 return frameNumber_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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197 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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198 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 {
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Sebastien Jodogne <s.jodogne@gmail.com>
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200 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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201 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 float GetProbabilityOfCancer() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 if (hasProbabilityOfCancer_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 return probabilityOfCancer_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215 };
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 class DicomStructuredReport::Point : public Structure
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 private:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 ScenePoint2D point_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 public:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 Point(const std::string& sopInstanceUid,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 double x,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 double y) :
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 Structure(sopInstanceUid),
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 point_(x, y)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 const ScenePoint2D& GetPoint() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 return point_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 };
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 class DicomStructuredReport::Polyline : public Structure
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 private:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 std::vector<ScenePoint2D> points_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 public:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
245 Polyline(const std::string& sopInstanceUid,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
246 const float* points,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
247 unsigned long pointsCount) :
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
248 Structure(sopInstanceUid)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250 if (pointsCount % 2 != 0)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
253 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255 points_.reserve(pointsCount / 2);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
257 for (unsigned long i = 0; i < pointsCount; i += 2)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
258 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
259 points_.push_back(ScenePoint2D(points[i], points[i + 1]));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
260 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
261 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263 size_t GetSize() const
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
265 return points_.size();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
267
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
268 const ScenePoint2D& GetPoint(size_t i) const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
269 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
270 if (i >= points_.size())
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
271 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
272 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
273 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
274 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
275 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
276 return points_[i];
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
277 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
278 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
279 };
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
280
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
281
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
282 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
283 DcmItem& group,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
284 bool hasFrameNumber,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
285 unsigned int frameNumber,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
286 bool hasProbabilityOfCancer,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287 float probabilityOfCancer)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
288 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289 const std::string graphicType = GetStringValue(group, DCM_GraphicType);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
290
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 const Float32* coords = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 unsigned long coordsCount = 0;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
294 (coordsCount != 0 && coords == NULL))
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
295 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
297 "Cannot read coordinates for region in DICOM-SR");
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
298 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 std::unique_ptr<Structure> structure;
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 (graphicType == "POINT")
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 if (coordsCount != 2)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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 else
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 structure.reset(new Point(sopInstanceUid, coords[0], coords[1]));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
311 }
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 else if (graphicType == "POLYLINE")
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
314 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
315 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount));
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 else
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 return; // Unsupported graphic type
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
320 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
321
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322 assert(structure.get() != 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 if (hasFrameNumber)
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 structure->SetFrameNumber(frameNumber);
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 if (hasProbabilityOfCancer)
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 structure->SetProbabilityOfCancer(probabilityOfCancer);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 structures_.push_back(structure.release());
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
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 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom)
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 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
341
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342 CheckStringValue(dataset, DCM_Modality, "SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
343 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
344 CheckStringValue(dataset, DCM_ValueType, "CONTAINER");
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 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 !IsDicomTemplate(dataset, "1500"))
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 }
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 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence);
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 std::list<std::string> tmp;
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 for (unsigned long i = 0; i < sequence.card(); i++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 std::string studyInstanceUid = GetStringValue(*sequence.getItem(i), DCM_StudyInstanceUID);
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 DcmSequenceOfItems* referencedSeries = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 if (!sequence.getItem(i)->findAndGetSequence(DCM_ReferencedSeriesSequence, referencedSeries).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 referencedSeries == NULL)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 for (unsigned long j = 0; j < referencedSeries->card(); j++)
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 std::string seriesInstanceUid = GetStringValue(*referencedSeries->getItem(j), DCM_SeriesInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
371 DcmSequenceOfItems* referencedInstances = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
372 if (!referencedSeries->getItem(j)->findAndGetSequence(DCM_ReferencedSOPSequence, referencedInstances).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
373 referencedInstances == NULL)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
378 for (unsigned int k = 0; k < referencedInstances->card(); k++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
380 std::string sopClassUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPClassUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381 std::string sopInstanceUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPInstanceUID);
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 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 {
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
385 instancesInformation_[sopInstanceUid] = new ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
386 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
387 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
388 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 "Multiple occurrences of the same instance in DICOM-SR: " + sopInstanceUid);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
393 tmp.push_back(sopInstanceUid);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 }
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 }
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 orderedInstances_.reserve(tmp.size());
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400 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
401 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402 orderedInstances_.push_back(*it);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 }
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 sequence = GetSequenceValue(dataset, DCM_ContentSequence);
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 for (unsigned long i = 0; i < sequence.card(); i++)
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 DcmItem& item = *sequence.getItem(i);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411 if (GetStringValue(item, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412 GetStringValue(item, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 IsDicomConcept(item, "126010" /* Imaging measurements */))
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 DcmSequenceOfItems& measurements = GetSequenceValue(item, DCM_ContentSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
417 for (unsigned long j = 0; j < measurements.card(); j++)
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 DcmItem& measurement = *measurements.getItem(j);
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 if (GetStringValue(measurement, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422 GetStringValue(measurement, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
423 IsDicomConcept(measurement, "125007" /* Measurement group */) &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
424 IsDicomTemplate(measurement, "1410"))
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 DcmSequenceOfItems& groups = GetSequenceValue(measurement, DCM_ContentSequence);
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 bool hasProbabilityOfCancer = false;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429 float probabilityOfCancer = 0;
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 for (unsigned int k = 0; k < groups.card(); k++)
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 DcmItem& group = *groups.getItem(k);
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 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
436 GetStringValue(group, DCM_ValueType) == "NUM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
437 IsDicomConcept(group, "111047" /* Probability of cancer */))
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 DcmSequenceOfItems& values = GetSequenceValue(group, DCM_MeasuredValueSequence);
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 if (values.card() == 1 &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442 IsValidConcept(*values.getItem(0), DCM_MeasurementUnitsCodeSequence, "UCUM", "%"))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 std::string value = GetStringValue(*values.getItem(0), DCM_NumericValue);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 if (Orthanc::SerializationToolbox::ParseFloat(probabilityOfCancer, value))
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 hasProbabilityOfCancer = true;
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 else
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
452 "Cannot parse float in DICOM-SR: " + value);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
453 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
454 }
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 }
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 for (unsigned int k = 0; k < groups.card(); k++)
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 DcmItem& group = *groups.getItem(k);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 GetStringValue(group, DCM_ValueType) == "SCOORD" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 IsDicomConcept(group, "111030" /* Image region */))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
466 DcmSequenceOfItems& regions = GetSequenceValue(group, DCM_ContentSequence);
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 for (unsigned int l = 0; l < regions.card(); l++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
469 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
470 DcmItem& region = *regions.getItem(l);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
472 if (GetStringValue(region, DCM_RelationshipType) == "SELECTED FROM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
473 GetStringValue(region, DCM_ValueType) == "IMAGE" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
474 IsDicomConcept(region, "111040") /* Original source */)
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 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 if (instances.card() != 1)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
480 "Region cannot reference multiple instances in DICOM-SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
481 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
482
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
483 std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID);
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
484 std::map<std::string, ReferencedInstance*>::iterator instanceInformation = instancesInformation_.find(sopInstanceUid);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
485
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
486 if (instanceInformation == instancesInformation_.end())
2085
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
489 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid);
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
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
492 assert(instanceInformation->second != NULL);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
493
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
494 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
496 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
497 std::vector<std::string> tokens;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
498 Orthanc::Toolbox::SplitString(tokens, frames, '\\');
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 (size_t m = 0; m < tokens.size(); m++)
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 uint32_t frame;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
503 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m]))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
504 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
505 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
508 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
509 AddStructure(sopInstanceUid, group, true, frame, hasProbabilityOfCancer, probabilityOfCancer);
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
510 instanceInformation->second->AddFrame(frame);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512 }
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 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
515 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer);
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
517 instanceInformation->second->AddFrame(1);
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
518 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
524 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
525 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
527 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
528
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 DicomStructuredReport::~DicomStructuredReport()
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 (std::list<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it)
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 assert(*it != NULL);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
535 delete *it;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
536 }
2089
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
537
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
538 for (std::map<std::string, ReferencedInstance*>::iterator
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
539 it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
540 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
541 assert(it->second != NULL);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
542 delete it->second;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
543 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
544 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
545
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
546
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
547 void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
548 std::string& seriesInstanceUid,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
549 std::string& sopInstanceUid,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
550 std::string& sopClassUid,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
551 size_t i) const
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
552 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
553 if (i >= orderedInstances_.size())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
554 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
555 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
556 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
557
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
558 sopInstanceUid = orderedInstances_[i];
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
559
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
560 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(sopInstanceUid);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
561 if (found == instancesInformation_.end())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
562 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
563 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
564 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
565
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
566 assert(found->second != NULL);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
567 studyInstanceUid = found->second->GetStudyInstanceUid();
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
568 seriesInstanceUid = found->second->GetSeriesInstanceUid();
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
569 sopClassUid = found->second->GetSopClassUid();
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
570 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
571
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
572
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
573 void DicomStructuredReport::ExportOrderedFrames(std::list<Frame>& frames) const
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
574 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
575 frames.clear();
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
576
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
577 for (size_t i = 0; i < orderedInstances_.size(); i++)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
578 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
579 std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(orderedInstances_[i]);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
580 if (found == instancesInformation_.end())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
581 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
582 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
583 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
584
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
585 assert(found->second != NULL);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
586
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
587 for (std::set<unsigned int>::const_iterator frame = found->second->GetFrames().begin();
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
588 frame != found->second->GetFrames().end(); ++frame)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
589 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
590 frames.push_back(Frame(found->second->GetStudyInstanceUid(),
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
591 found->second->GetSeriesInstanceUid(),
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
592 orderedInstances_[i],
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
593 found->second->GetSopClassUid(), *frame));
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
594 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2087
diff changeset
595 }
2085
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
596 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
597 }