Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp @ 2087:51c8b21b81e4

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 07 Nov 2023 18:11:13 +0100
parents 554bc96e7508
children 63d77859edee 7c3d65166c26
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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 class DicomStructuredReport::Structure : public boost::noncopyable
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122 {
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123 private:
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124 std::string sopInstanceUid_;
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125 bool hasFrameNumber_;
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126 unsigned int frameNumber_;
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127 bool hasProbabilityOfCancer_;
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128 float probabilityOfCancer_;
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129
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130 public:
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131 Structure(const std::string& sopInstanceUid) :
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132 sopInstanceUid_(sopInstanceUid),
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133 hasFrameNumber_(false),
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134 hasProbabilityOfCancer_(false)
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135 {
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136 }
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137
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138 virtual ~Structure()
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139 {
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140 }
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141
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142 void SetFrameNumber(unsigned int frame)
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143 {
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144 if (frame <= 0)
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145 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 hasFrameNumber_ = true;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 frameNumber_ = frame;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
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 SetProbabilityOfCancer(float probability)
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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:
diff changeset
157 if (probability < 0 ||
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 probability > 100)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 hasProbabilityOfCancer_ = true;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 probabilityOfCancer_ = probability;
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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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 bool HasFrameNumber() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 return hasFrameNumber_;
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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:
diff changeset
173
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 bool HasProbabilityOfCancer() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176 return hasProbabilityOfCancer_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179 unsigned int GetFrameNumber() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181 if (hasFrameNumber_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 return frameNumber_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 else
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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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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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:
diff changeset
189 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 float GetProbabilityOfCancer() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 if (hasProbabilityOfCancer_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 return probabilityOfCancer_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 class DicomStructuredReport::Point : public Structure
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 private:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 ScenePoint2D point_;
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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 public:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 Point(const std::string& sopInstanceUid,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 double x,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 double y) :
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 Structure(sopInstanceUid),
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215 point_(x, y)
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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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 const ScenePoint2D& GetPoint() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 return 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 };
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 class DicomStructuredReport::Polyline : public Structure
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 private:
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 std::vector<ScenePoint2D> points_;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 public:
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 Polyline(const std::string& sopInstanceUid,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 const float* points,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 unsigned long pointsCount) :
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 Structure(sopInstanceUid)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 if (pointsCount % 2 != 0)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 points_.reserve(pointsCount / 2);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 for (unsigned long i = 0; i < pointsCount; i += 2)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
245 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
246 points_.push_back(ScenePoint2D(points[i], points[i + 1]));
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
247 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
248 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250 size_t GetSize() const
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 return points_.size();
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
253 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255 const ScenePoint2D& GetPoint(size_t i) const
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 if (i >= points_.size())
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
260 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
261 else
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 return points_[i];
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
265 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 };
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
267
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
268
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
269 void DicomStructuredReport::AddStructure(const std::string& sopInstanceUid,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
270 DcmItem& group,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
271 bool hasFrameNumber,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
272 unsigned int frameNumber,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
273 bool hasProbabilityOfCancer,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
274 float probabilityOfCancer)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
275 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
276 const std::string graphicType = GetStringValue(group, DCM_GraphicType);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
277
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
278 const Float32* coords = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
279 unsigned long coordsCount = 0;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
280 if (!group.findAndGetFloat32Array(DCM_GraphicData, coords, &coordsCount).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
281 (coordsCount != 0 && coords == NULL))
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
284 "Cannot read coordinates for region in DICOM-SR");
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287 std::unique_ptr<Structure> structure;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
288
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289 if (graphicType == "POINT")
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
290 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 if (coordsCount != 2)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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 else
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 structure.reset(new Point(sopInstanceUid, coords[0], coords[1]));
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 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 else if (graphicType == "POLYLINE")
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 structure.reset(new Polyline(sopInstanceUid, coords, coordsCount));
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 else
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 return; // Unsupported graphic type
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309 assert(structure.get() != NULL);
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 if (hasFrameNumber)
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 structure->SetFrameNumber(frameNumber);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
316 if (hasProbabilityOfCancer)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
318 structure->SetProbabilityOfCancer(probabilityOfCancer);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
319 }
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 structures_.push_back(structure.release());
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
324
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
325 DicomStructuredReport::DicomStructuredReport(Orthanc::ParsedDicomFile& dicom)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
326 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
327 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
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 CheckStringValue(dataset, DCM_Modality, "SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
330 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
331 CheckStringValue(dataset, DCM_ValueType, "CONTAINER");
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 if (!IsDicomConcept(dataset, "126000") /* Imaging measurement report */ ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 !IsDicomTemplate(dataset, "1500"))
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
339 DcmSequenceOfItems& sequence = GetSequenceValue(dataset, DCM_CurrentRequestedProcedureEvidenceSequence);
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 std::list<std::string> tmp;
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 for (unsigned long i = 0; i < sequence.card(); i++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345 std::string studyInstanceUid = GetStringValue(*sequence.getItem(i), DCM_StudyInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 DcmSequenceOfItems* referencedSeries = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
348 if (!sequence.getItem(i)->findAndGetSequence(DCM_ReferencedSeriesSequence, referencedSeries).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349 referencedSeries == NULL)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 }
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 for (unsigned long j = 0; j < referencedSeries->card(); j++)
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 std::string seriesInstanceUid = GetStringValue(*referencedSeries->getItem(j), DCM_SeriesInstanceUID);
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 DcmSequenceOfItems* referencedInstances = NULL;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359 if (!referencedSeries->getItem(j)->findAndGetSequence(DCM_ReferencedSOPSequence, referencedInstances).good() ||
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 referencedInstances == NULL)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
365 for (unsigned int k = 0; k < referencedInstances->card(); k++)
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 std::string sopClassUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPClassUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 std::string sopInstanceUid = GetStringValue(*referencedInstances->getItem(k), DCM_ReferencedSOPInstanceUID);
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 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
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 instancesInformation_[sopInstanceUid] = ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid);
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 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
377 "Multiple occurrences of the same instance in DICOM-SR: " + sopInstanceUid);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
380 tmp.push_back(sopInstanceUid);
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 }
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
385 orderedInstances_.reserve(tmp.size());
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 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
388 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 orderedInstances_.push_back(*it);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 }
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 sequence = GetSequenceValue(dataset, 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 i = 0; i < sequence.card(); i++)
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& item = *sequence.getItem(i);
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(item, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 GetStringValue(item, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400 IsDicomConcept(item, "126010" /* Imaging measurements */))
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 DcmSequenceOfItems& measurements = GetSequenceValue(item, DCM_ContentSequence);
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 for (unsigned long j = 0; j < measurements.card(); j++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 DcmItem& measurement = *measurements.getItem(j);
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 if (GetStringValue(measurement, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 GetStringValue(measurement, DCM_ValueType) == "CONTAINER" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 IsDicomConcept(measurement, "125007" /* Measurement group */) &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411 IsDicomTemplate(measurement, "1410"))
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 DcmSequenceOfItems& groups = GetSequenceValue(measurement, DCM_ContentSequence);
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 bool hasProbabilityOfCancer = false;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416 float probabilityOfCancer = 0;
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 for (unsigned int k = 0; k < groups.card(); k++)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
419 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
420 DcmItem& group = *groups.getItem(k);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
421
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422 if (GetStringValue(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
423 GetStringValue(group, DCM_ValueType) == "NUM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
424 IsDicomConcept(group, "111047" /* Probability of cancer */))
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& values = GetSequenceValue(group, DCM_MeasuredValueSequence);
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 if (values.card() == 1 &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429 IsValidConcept(*values.getItem(0), DCM_MeasurementUnitsCodeSequence, "UCUM", "%"))
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 std::string value = GetStringValue(*values.getItem(0), DCM_NumericValue);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
432 if (Orthanc::SerializationToolbox::ParseFloat(probabilityOfCancer, value))
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 hasProbabilityOfCancer = true;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
435 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
436 else
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
437 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
438 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 "Cannot parse float in DICOM-SR: " + value);
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 }
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 }
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 k = 0; k < groups.card(); k++)
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& group = *groups.getItem(k);
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(group, DCM_RelationshipType) == "CONTAINS" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 GetStringValue(group, DCM_ValueType) == "SCOORD" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451 IsDicomConcept(group, "111030" /* Image region */))
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& regions = GetSequenceValue(group, DCM_ContentSequence);
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 for (unsigned int l = 0; l < regions.card(); l++)
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 DcmItem& region = *regions.getItem(l);
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 if (GetStringValue(region, DCM_RelationshipType) == "SELECTED FROM" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
460 GetStringValue(region, DCM_ValueType) == "IMAGE" &&
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461 IsDicomConcept(region, "111040") /* Original source */)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 DcmSequenceOfItems& instances = GetSequenceValue(region, DCM_ReferencedSOPSequence);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 if (instances.card() != 1)
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
467 "Region cannot reference multiple instances in DICOM-SR");
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
468 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
469
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
470 std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471 if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
474 "Referencing unknown instance in DICOM-SR: " + sopInstanceUid);
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber))
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 std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
480 std::vector<std::string> tokens;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
481 Orthanc::Toolbox::SplitString(tokens, frames, '\\');
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 for (size_t m = 0; m < tokens.size(); m++)
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 uint32_t frame;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
486 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(frame, tokens[m]))
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 }
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
490 else
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 AddStructure(sopInstanceUid, group, true, frame, hasProbabilityOfCancer, probabilityOfCancer);
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 }
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 else
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 AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer);
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 }
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
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
510
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 DicomStructuredReport::~DicomStructuredReport()
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 for (std::list<Structure*>::iterator it = structures_.begin(); it != structures_.end(); ++it)
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
514 {
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
515 assert(*it != NULL);
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 delete *it;
554bc96e7508 added DicomStructuredReport
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
517 }
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 }