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annotate UnitTestsSources/FromDcmtk.cpp @ 784:efd0215736d9

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start of anonymization refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 02 May 2014 15:06:31 +0200
parents a60040857ce6
children 7cbed653476f
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1 #include "gtest/gtest.h"
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2
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3 #include "../OrthancServer/FromDcmtkBridge.h"
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4 #include "../OrthancServer/OrthancInitialization.h"
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5 #include "../Core/OrthancException.h"
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6
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7 using namespace Orthanc;
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8
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9 TEST(DicomFormat, Tag)
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10 {
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11 ASSERT_EQ("PatientName", FromDcmtkBridge::GetName(DicomTag(0x0010, 0x0010)));
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12
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13 DicomTag t = FromDcmtkBridge::ParseTag("SeriesDescription");
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14 ASSERT_EQ(0x0008, t.GetGroup());
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15 ASSERT_EQ(0x103E, t.GetElement());
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16
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17 t = FromDcmtkBridge::ParseTag("0020-e040");
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18 ASSERT_EQ(0x0020, t.GetGroup());
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19 ASSERT_EQ(0xe040, t.GetElement());
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20
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21 // Test ==() and !=() operators
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22 ASSERT_TRUE(DICOM_TAG_PATIENT_ID == DicomTag(0x0010, 0x0020));
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23 ASSERT_FALSE(DICOM_TAG_PATIENT_ID != DicomTag(0x0010, 0x0020));
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24 }
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25
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26
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27 namespace Orthanc
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28 {
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29 class DicomModification
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30 {
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31 /**
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32 * Process:
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33 * (1) Remove private tags
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34 * (2) Remove tags specified by the user
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35 * (3) Replace tags
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36 **/
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37
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38 private:
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39 typedef std::set<DicomTag> Removals;
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40 typedef std::map<DicomTag, std::string> Replacements;
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41 typedef std::map< std::pair<DicomRootLevel, std::string>, std::string> UidMap;
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42
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43 Removals removals_;
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44 Replacements replacements_;
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45 bool removePrivateTags_;
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46 DicomRootLevel level_;
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47 UidMap uidMap_;
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48
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49 void MapDicomIdentifier(ParsedDicomFile& dicom,
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50 DicomRootLevel level)
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51 {
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52 std::auto_ptr<DicomTag> tag;
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53
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54 switch (level)
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55 {
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56 case DicomRootLevel_Study:
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57 tag.reset(new DicomTag(DICOM_TAG_STUDY_INSTANCE_UID));
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58 break;
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59
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60 case DicomRootLevel_Series:
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61 tag.reset(new DicomTag(DICOM_TAG_SERIES_INSTANCE_UID));
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62 break;
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63
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64 case DicomRootLevel_Instance:
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65 tag.reset(new DicomTag(DICOM_TAG_SOP_INSTANCE_UID));
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66 break;
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67
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68 default:
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69 throw OrthancException(ErrorCode_InternalError);
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70 }
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71
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72 std::string original;
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73 if (!dicom.GetTagValue(original, *tag))
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74 {
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75 original = "";
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76 }
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77
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78 std::string mapped;
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79 //bool isNew;
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80
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81 UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original));
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82 if (previous == uidMap_.end())
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83 {
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84 mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level);
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85 uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped));
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86 //isNew = true;
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87 }
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88 else
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89 {
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90 mapped = previous->second;
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91 //isNew = false;
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92 }
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93
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94 dicom.Replace(*tag, mapped);
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95
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96 //return isNew;
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97 }
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98
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99 public:
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100 DicomModification()
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101 {
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102 removePrivateTags_ = false;
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103 level_ = DicomRootLevel_Instance;
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104 }
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105
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106 void Keep(const DicomTag& tag)
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107 {
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108 removals_.erase(tag);
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109 }
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110
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111 void Remove(const DicomTag& tag)
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112 {
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113 removals_.insert(tag);
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114 replacements_.erase(tag);
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115 }
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116
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117 bool IsRemoved(const DicomTag& tag) const
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118 {
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119 return removals_.find(tag) != removals_.end();
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120 }
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121
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122 void Replace(const DicomTag& tag,
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123 const std::string& value)
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124 {
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125 removals_.erase(tag);
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126 replacements_[tag] = value;
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127 }
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128
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129 bool IsReplaced(const DicomTag& tag) const
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130 {
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131 return replacements_.find(tag) != replacements_.end();
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132 }
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133
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134 const std::string& GetReplacement(const DicomTag& tag) const
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135 {
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136 Replacements::const_iterator it = replacements_.find(tag);
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137
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138 if (it == replacements_.end())
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139 {
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140 throw OrthancException(ErrorCode_InexistentItem);
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141 }
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142 else
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143 {
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diff changeset
144 return it->second;
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145 }
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parents: 782
diff changeset
146 }
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parents: 782
diff changeset
147
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148 void SetRemovePrivateTags(bool removed)
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149 {
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150 removePrivateTags_ = removed;
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151 }
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diff changeset
152
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153 bool ArePrivateTagsRemoved() const
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154 {
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155 return removePrivateTags_;
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156 }
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diff changeset
157
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158 void SetLevel(DicomRootLevel level)
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159 {
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160 uidMap_.clear();
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161 level_ = level;
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162 }
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diff changeset
163
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164 DicomRootLevel GetLevel() const
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165 {
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166 return level_;
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167 }
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168
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169 void SetupAnonymization()
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170 {
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171 removals_.clear();
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172 replacements_.clear();
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173 removePrivateTags_ = true;
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174 level_ = DicomRootLevel_Patient;
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175 uidMap_.clear();
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176
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177 // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles
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178 removals_.insert(DicomTag(0x0008, 0x0014)); // Instance Creator UID
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179 //removals_.insert(DicomTag(0x0008, 0x0018)); // SOP Instance UID => set in Apply()
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180 removals_.insert(DicomTag(0x0008, 0x0050)); // Accession Number
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parents: 782
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181 removals_.insert(DicomTag(0x0008, 0x0080)); // Institution Name
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parents: 782
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182 removals_.insert(DicomTag(0x0008, 0x0081)); // Institution Address
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183 removals_.insert(DicomTag(0x0008, 0x0090)); // Referring Physician's Name
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diff changeset
184 removals_.insert(DicomTag(0x0008, 0x0092)); // Referring Physician's Address
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parents: 782
diff changeset
185 removals_.insert(DicomTag(0x0008, 0x0094)); // Referring Physician's Telephone Numbers
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186 removals_.insert(DicomTag(0x0008, 0x1010)); // Station Name
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parents: 782
diff changeset
187 removals_.insert(DicomTag(0x0008, 0x1030)); // Study Description
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parents: 782
diff changeset
188 removals_.insert(DicomTag(0x0008, 0x103e)); // Series Description
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parents: 782
diff changeset
189 removals_.insert(DicomTag(0x0008, 0x1040)); // Institutional Department Name
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parents: 782
diff changeset
190 removals_.insert(DicomTag(0x0008, 0x1048)); // Physician(s) of Record
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parents: 782
diff changeset
191 removals_.insert(DicomTag(0x0008, 0x1050)); // Performing Physicians' Name
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parents: 782
diff changeset
192 removals_.insert(DicomTag(0x0008, 0x1060)); // Name of Physician(s) Reading Study
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parents: 782
diff changeset
193 removals_.insert(DicomTag(0x0008, 0x1070)); // Operators' Name
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parents: 782
diff changeset
194 removals_.insert(DicomTag(0x0008, 0x1080)); // Admitting Diagnoses Description
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parents: 782
diff changeset
195 removals_.insert(DicomTag(0x0008, 0x1155)); // Referenced SOP Instance UID
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parents: 782
diff changeset
196 removals_.insert(DicomTag(0x0008, 0x2111)); // Derivation Description
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parents: 782
diff changeset
197 //removals_.insert(DicomTag(0x0010, 0x0010)); // Patient's Name => cf. below (*)
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parents: 782
diff changeset
198 //removals_.insert(DicomTag(0x0010, 0x0020)); // Patient ID => cf. below (*)
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parents: 782
diff changeset
199 removals_.insert(DicomTag(0x0010, 0x0030)); // Patient's Birth Date
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parents: 782
diff changeset
200 removals_.insert(DicomTag(0x0010, 0x0032)); // Patient's Birth Time
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parents: 782
diff changeset
201 removals_.insert(DicomTag(0x0010, 0x0040)); // Patient's Sex
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parents: 782
diff changeset
202 removals_.insert(DicomTag(0x0010, 0x1000)); // Other Patient Ids
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
203 removals_.insert(DicomTag(0x0010, 0x1001)); // Other Patient Names
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parents: 782
diff changeset
204 removals_.insert(DicomTag(0x0010, 0x1010)); // Patient's Age
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parents: 782
diff changeset
205 removals_.insert(DicomTag(0x0010, 0x1020)); // Patient's Size
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parents: 782
diff changeset
206 removals_.insert(DicomTag(0x0010, 0x1030)); // Patient's Weight
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parents: 782
diff changeset
207 removals_.insert(DicomTag(0x0010, 0x1090)); // Medical Record Locator
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parents: 782
diff changeset
208 removals_.insert(DicomTag(0x0010, 0x2160)); // Ethnic Group
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parents: 782
diff changeset
209 removals_.insert(DicomTag(0x0010, 0x2180)); // Occupation
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parents: 782
diff changeset
210 removals_.insert(DicomTag(0x0010, 0x21b0)); // Additional Patient's History
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
211 removals_.insert(DicomTag(0x0010, 0x4000)); // Patient Comments
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
212 removals_.insert(DicomTag(0x0018, 0x1000)); // Device Serial Number
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
213 removals_.insert(DicomTag(0x0018, 0x1030)); // Protocol Name
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parents: 782
diff changeset
214 //removals_.insert(DicomTag(0x0020, 0x000d)); // Study Instance UID => set in Apply()
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parents: 782
diff changeset
215 //removals_.insert(DicomTag(0x0020, 0x000e)); // Series Instance UID => set in Apply()
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parents: 782
diff changeset
216 removals_.insert(DicomTag(0x0020, 0x0010)); // Study ID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
217 removals_.insert(DicomTag(0x0020, 0x0052)); // Frame of Reference UID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
218 removals_.insert(DicomTag(0x0020, 0x0200)); // Synchronization Frame of Reference UID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
219 removals_.insert(DicomTag(0x0020, 0x4000)); // Image Comments
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
220 removals_.insert(DicomTag(0x0040, 0x0275)); // Request Attributes Sequence
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
221 removals_.insert(DicomTag(0x0040, 0xa124)); // UID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
222 removals_.insert(DicomTag(0x0040, 0xa730)); // Content Sequence
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parents: 782
diff changeset
223 removals_.insert(DicomTag(0x0088, 0x0140)); // Storage Media File-set UID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
224 removals_.insert(DicomTag(0x3006, 0x0024)); // Referenced Frame of Reference UID
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parents: 782
diff changeset
225 removals_.insert(DicomTag(0x3006, 0x00c2)); // Related Frame of Reference UID
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
226
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parents: 782
diff changeset
227 // Some more removals (from the experience of DICOM files at the CHU of Liege)
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parents: 782
diff changeset
228 removals_.insert(DicomTag(0x0010, 0x1040)); // Patient's Address
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parents: 782
diff changeset
229 removals_.insert(DicomTag(0x0032, 0x1032)); // Requesting Physician
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parents: 782
diff changeset
230 removals_.insert(DicomTag(0x0010, 0x2154)); // PatientTelephoneNumbers
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parents: 782
diff changeset
231 removals_.insert(DicomTag(0x0010, 0x2000)); // Medical Alerts
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parents: 782
diff changeset
232
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parents: 782
diff changeset
233 // Set the DeidentificationMethod tag
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parents: 782
diff changeset
234 replacements_.insert(std::make_pair(DicomTag(0x0012, 0x0063), "Orthanc " ORTHANC_VERSION " - PS 3.15-2008 Table E.1-1"));
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parents: 782
diff changeset
235
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parents: 782
diff changeset
236 // Set the PatientIdentityRemoved tag
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parents: 782
diff changeset
237 replacements_.insert(std::make_pair(DicomTag(0x0012, 0x0062), "YES"));
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parents: 782
diff changeset
238
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parents: 782
diff changeset
239 // (*) Choose a random patient name and ID
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diff changeset
240 std::string patientId = FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Patient);
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parents: 782
diff changeset
241 replacements_[DICOM_TAG_PATIENT_ID] = patientId;
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parents: 782
diff changeset
242 replacements_[DICOM_TAG_PATIENT_NAME] = patientId;
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parents: 782
diff changeset
243 }
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parents: 782
diff changeset
244
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parents: 782
diff changeset
245 void Apply(ParsedDicomFile& toModify)
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diff changeset
246 {
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diff changeset
247 // Check the request
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diff changeset
248 assert(DicomRootLevel_Patient + 1 == DicomRootLevel_Study &&
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diff changeset
249 DicomRootLevel_Study + 1 == DicomRootLevel_Series &&
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parents: 782
diff changeset
250 DicomRootLevel_Series + 1 == DicomRootLevel_Instance);
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parents: 782
diff changeset
251
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parents: 782
diff changeset
252 if (IsRemoved(DICOM_TAG_PATIENT_ID) ||
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parents: 782
diff changeset
253 IsRemoved(DICOM_TAG_STUDY_INSTANCE_UID) ||
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parents: 782
diff changeset
254 IsRemoved(DICOM_TAG_SERIES_INSTANCE_UID) ||
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parents: 782
diff changeset
255 IsRemoved(DICOM_TAG_SOP_INSTANCE_UID))
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parents: 782
diff changeset
256 {
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parents: 782
diff changeset
257 throw OrthancException(ErrorCode_BadRequest);
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parents: 782
diff changeset
258 }
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parents: 782
diff changeset
259
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parents: 782
diff changeset
260 if (level_ == DicomRootLevel_Patient && !IsReplaced(DICOM_TAG_PATIENT_ID))
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parents: 782
diff changeset
261 {
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parents: 782
diff changeset
262 throw OrthancException(ErrorCode_BadRequest);
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parents: 782
diff changeset
263 }
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264
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265 if (level_ > DicomRootLevel_Patient && IsReplaced(DICOM_TAG_PATIENT_ID))
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266 {
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267 throw OrthancException(ErrorCode_BadRequest);
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268 }
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269
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270 if (level_ > DicomRootLevel_Study && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
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271 {
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272 throw OrthancException(ErrorCode_BadRequest);
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273 }
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274
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275 if (level_ > DicomRootLevel_Series && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
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276 {
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277 throw OrthancException(ErrorCode_BadRequest);
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278 }
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279
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280 // (1) Remove the private tags, if need be
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281 if (removePrivateTags_)
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282 {
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283 toModify.RemovePrivateTags();
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284 }
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285
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286 // (2) Remove the tags specified by the user
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287 for (Removals::const_iterator it = removals_.begin();
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288 it != removals_.end(); ++it)
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289 {
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290 toModify.Remove(*it);
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291 }
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292
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293 // (3) Replace the tags
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294 for (Replacements::const_iterator it = replacements_.begin();
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295 it != replacements_.end(); ++it)
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296 {
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297 toModify.Replace(it->first, it->second, DicomReplaceMode_InsertIfAbsent);
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298 }
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299
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300 // Update the DICOM identifiers
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301 if (level_ <= DicomRootLevel_Study)
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302 {
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303 MapDicomIdentifier(toModify, DicomRootLevel_Study);
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304 }
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305
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306 if (level_ <= DicomRootLevel_Series)
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307 {
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308 MapDicomIdentifier(toModify, DicomRootLevel_Series);
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309 }
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310
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311 if (level_ <= DicomRootLevel_Instance) // Always true
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312 {
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313 MapDicomIdentifier(toModify, DicomRootLevel_Instance);
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314 }
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315 }
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316 };
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317 }
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318
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319
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320
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321 TEST(DicomModification, Basic)
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322 {
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323 DicomModification m;
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324 m.SetupAnonymization();
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325 //m.SetLevel(DicomRootLevel_Study);
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326 //m.Replace(DICOM_TAG_PATIENT_ID, "coucou");
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327 //m.Replace(DICOM_TAG_PATIENT_NAME, "coucou");
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328
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329 ParsedDicomFile o;
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330 o.SaveToFile("/tmp/tutu.dcm");
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331
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332 for (int i = 0; i < 10; i++)
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333 {
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334 char b[1024];
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335 sprintf(b, "/tmp/tutu%06d.dcm", i);
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336 std::auto_ptr<ParsedDicomFile> f(o.Clone());
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337 if (i > 4)
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338 o.Replace(DICOM_TAG_SERIES_INSTANCE_UID, "coucou");
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339 m.Apply(*f);
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340 f->SaveToFile(b);
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341 }
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342 }