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annotate OrthancServer/Search/HierarchicalMatcher.cpp @ 2409:e4045b3c9772

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ignore-length argument if retrieving DICOM tags
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 27 Sep 2017 17:36:13 +0200
parents 7284093111b0
children 878b59270859
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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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 Osimis, Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #include "../PrecompiledHeadersServer.h"
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35 #include "HierarchicalMatcher.h"
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36
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37 #include "../../Core/Logging.h"
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38 #include "../../Core/OrthancException.h"
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39 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
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40 #include "../../Core/DicomParsing/ToDcmtkBridge.h"
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41 #include "../OrthancInitialization.h"
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42
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43 #include <dcmtk/dcmdata/dcfilefo.h>
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44
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45 namespace Orthanc
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46 {
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47 HierarchicalMatcher::HierarchicalMatcher(ParsedDicomFile& query)
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48 {
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49 Setup(*query.GetDcmtkObject().getDataset(),
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50 Configuration::GetGlobalBoolParameter("CaseSensitivePN", false),
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51 query.GetEncoding());
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52 }
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53
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54
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55 HierarchicalMatcher::~HierarchicalMatcher()
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56 {
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57 for (Constraints::iterator it = constraints_.begin();
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58 it != constraints_.end(); ++it)
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59 {
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60 if (it->second != NULL)
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61 {
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62 delete it->second;
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63 }
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64 }
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65
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66 for (Sequences::iterator it = sequences_.begin();
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67 it != sequences_.end(); ++it)
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68 {
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69 if (it->second != NULL)
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70 {
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71 delete it->second;
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72 }
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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 void HierarchicalMatcher::Setup(DcmItem& dataset,
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78 bool caseSensitivePN,
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79 Encoding encoding)
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80 {
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81 for (unsigned long i = 0; i < dataset.card(); i++)
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82 {
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83 DcmElement* element = dataset.getElement(i);
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84 if (element == NULL)
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85 {
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86 throw OrthancException(ErrorCode_InternalError);
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87 }
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88
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89 DicomTag tag(FromDcmtkBridge::Convert(element->getTag()));
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90 if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET || // Ignore encoding
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91 tag.GetElement() == 0x0000) // Ignore all "Group Length" tags
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92 {
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93 continue;
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94 }
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95
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96 ValueRepresentation vr = FromDcmtkBridge::LookupValueRepresentation(tag);
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97
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98 if (constraints_.find(tag) != constraints_.end() ||
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99 sequences_.find(tag) != sequences_.end())
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100 {
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101 throw OrthancException(ErrorCode_BadRequest);
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102 }
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103
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104 if (vr == ValueRepresentation_Sequence)
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105 {
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106 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(*element);
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107
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108 if (sequence.card() == 0 ||
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109 (sequence.card() == 1 && sequence.getItem(0)->card() == 0))
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110 {
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111 // Universal matching of a sequence
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112 sequences_[tag] = NULL;
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113 }
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114 else if (sequence.card() == 1)
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115 {
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116 sequences_[tag] = new HierarchicalMatcher(*sequence.getItem(0), caseSensitivePN, encoding);
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117 }
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118 else
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119 {
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120 throw OrthancException(ErrorCode_BadRequest);
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121 }
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122 }
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123 else
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124 {
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125 std::set<DicomTag> ignoreTagLength;
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126 std::auto_ptr<DicomValue> value(FromDcmtkBridge::ConvertLeafElement
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127 (*element, DicomToJsonFlags_None,
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128 ORTHANC_MAXIMUM_TAG_LENGTH, encoding, ignoreTagLength));
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129
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130 if (value->IsBinary())
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131 {
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132 if (!value->GetContent().empty())
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133 {
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134 LOG(WARNING) << "This C-Find modality worklist query contains a non-empty tag ("
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135 << tag.Format() << ") with UN (unknown) value representation. "
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136 << "It will be ignored.";
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137 }
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138
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139 constraints_[tag] = NULL;
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140 }
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141 else if (value->IsNull() ||
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142 value->GetContent().empty())
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143 {
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144 // This is an universal matcher
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145 constraints_[tag] = NULL;
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146 }
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147 else
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148 {
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149 // DICOM specifies that searches must be case sensitive, except
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150 // for tags with a PN value representation
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151 bool sensitive = true;
2007
655489d9165d DicomMap::ParseDicomMetaInformation()
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parents: 2006
diff changeset
152 if (vr == ValueRepresentation_PersonName)
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153 {
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154 sensitive = caseSensitivePN;
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155 }
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156
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157 constraints_[tag] = IFindConstraint::ParseDicomConstraint(tag, value->GetContent(), sensitive);
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158 }
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159 }
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parents:
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160 }
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161 }
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162
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163
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164 std::string HierarchicalMatcher::Format(const std::string& prefix) const
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165 {
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166 std::string s;
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167
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168 for (Constraints::const_iterator it = constraints_.begin();
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169 it != constraints_.end(); ++it)
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170 {
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171 s += prefix + it->first.Format() + " ";
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172
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173 if (it->second == NULL)
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174 {
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175 s += "*\n";
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176 }
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177 else
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178 {
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179 s += it->second->Format() + "\n";
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180 }
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181 }
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182
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183 for (Sequences::const_iterator it = sequences_.begin();
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184 it != sequences_.end(); ++it)
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185 {
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186 s += prefix + it->first.Format() + " ";
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187
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188 if (it->second == NULL)
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parents:
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189 {
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190 s += "*\n";
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parents:
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191 }
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192 else
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193 {
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194 s += "Sequence:\n" + it->second->Format(prefix + " ");
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195 }
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parents:
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196 }
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parents:
diff changeset
197
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198 return s;
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parents:
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199 }
1796
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diff changeset
200
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diff changeset
201
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diff changeset
202 bool HierarchicalMatcher::Match(ParsedDicomFile& dicom) const
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diff changeset
203 {
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diff changeset
204 return MatchInternal(*dicom.GetDcmtkObject().getDataset(),
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
205 dicom.GetEncoding());
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diff changeset
206 }
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diff changeset
207
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diff changeset
208
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diff changeset
209 bool HierarchicalMatcher::MatchInternal(DcmItem& item,
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diff changeset
210 Encoding encoding) const
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diff changeset
211 {
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diff changeset
212 for (Constraints::const_iterator it = constraints_.begin();
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diff changeset
213 it != constraints_.end(); ++it)
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diff changeset
214 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
215 if (it->second != NULL)
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
216 {
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diff changeset
217 DcmTagKey tag = ToDcmtkBridge::Convert(it->first);
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diff changeset
218
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diff changeset
219 DcmElement* element = NULL;
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parents: 1795
diff changeset
220 if (!item.findAndGetElement(tag, element).good() ||
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
221 element == NULL)
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parents: 1795
diff changeset
222 {
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diff changeset
223 return false;
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diff changeset
224 }
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parents: 1795
diff changeset
225
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2382
diff changeset
226 std::set<DicomTag> ignoreTagLength;
1796
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parents: 1795
diff changeset
227 std::auto_ptr<DicomValue> value(FromDcmtkBridge::ConvertLeafElement
1929
cda5b0ab4ce5 ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1900
diff changeset
228 (*element, DicomToJsonFlags_None,
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2382
diff changeset
229 ORTHANC_MAXIMUM_TAG_LENGTH, encoding, ignoreTagLength));
1796
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diff changeset
230
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
231 if (value->IsNull() ||
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
232 value->IsBinary() ||
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parents: 1795
diff changeset
233 !it->second->Match(value->GetContent()))
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diff changeset
234 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
235 return false;
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parents: 1795
diff changeset
236 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
237 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
238 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
239
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
240 for (Sequences::const_iterator it = sequences_.begin();
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
241 it != sequences_.end(); ++it)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
242 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
243 if (it->second != NULL)
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
244 {
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parents: 1795
diff changeset
245 DcmTagKey tag = ToDcmtkBridge::Convert(it->first);
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
246
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
247 DcmSequenceOfItems* sequence = NULL;
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
248 if (!item.findAndGetSequence(tag, sequence).good() ||
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
249 sequence == NULL)
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
250 {
1891
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1890
diff changeset
251 continue;
1796
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diff changeset
252 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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diff changeset
253
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diff changeset
254 bool match = false;
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diff changeset
255
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
256 for (unsigned long i = 0; i < sequence->card(); i++)
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
257 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
258 if (it->second->MatchInternal(*sequence->getItem(i), encoding))
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
259 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
260 match = true;
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
261 break;
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
262 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
263 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
264
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
265 if (!match)
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
266 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
267 return false;
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
268 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
269 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
270 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
271
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
272 return true;
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
273 }
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
274
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
275
1797
23722a191e4e worklists are working
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1796
diff changeset
276 DcmDataset* HierarchicalMatcher::ExtractInternal(DcmItem& source,
1796
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
277 Encoding encoding) const
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
278 {
1797
23722a191e4e worklists are working
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diff changeset
279 std::auto_ptr<DcmDataset> target(new DcmDataset);
1796
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parents: 1795
diff changeset
280
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
281 for (Constraints::const_iterator it = constraints_.begin();
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
282 it != constraints_.end(); ++it)
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
283 {
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
284 DcmTagKey tag = ToDcmtkBridge::Convert(it->first);
5e08a5fe6b27 HierarchicalMatcher - extracting tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1795
diff changeset
285
5e08a5fe6b27 HierarchicalMatcher - extracting tags
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parents: 1795
diff changeset
286 DcmElement* element = NULL;
1797
23722a191e4e worklists are working
Sebastien Jodogne <s.jodogne@gmail.com>
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287 if (source.findAndGetElement(tag, element).good() &&
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288 element != NULL)
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289 {
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290 std::auto_ptr<DcmElement> cloned(FromDcmtkBridge::CreateElementForTag(it->first));
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291 cloned->copyFrom(*element);
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292 target->insert(cloned.release());
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293 }
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294 }
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295
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296 for (Sequences::const_iterator it = sequences_.begin();
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297 it != sequences_.end(); ++it)
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298 {
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299 DcmTagKey tag = ToDcmtkBridge::Convert(it->first);
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300
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301 DcmSequenceOfItems* sequence = NULL;
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302 if (source.findAndGetSequence(tag, sequence).good() &&
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303 sequence != NULL)
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304 {
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305 std::auto_ptr<DcmSequenceOfItems> cloned(new DcmSequenceOfItems(tag));
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306
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307 for (unsigned long i = 0; i < sequence->card(); i++)
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308 {
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309 if (it->second == NULL)
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310 {
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311 cloned->append(new DcmItem(*sequence->getItem(i)));
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312 }
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313 else if (it->second->MatchInternal(*sequence->getItem(i), encoding)) // TODO Might be optimized
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314 {
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315 // It is necessary to encapsulate the child dataset into a
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316 // "DcmItem" object before it can be included in a
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317 // sequence. Otherwise, "dciodvfy" reports an error "Bad
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318 // tag in sequence - Expecting Item or Sequence Delimiter."
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319 std::auto_ptr<DcmDataset> child(it->second->ExtractInternal(*sequence->getItem(i), encoding));
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320 cloned->append(new DcmItem(*child));
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321 }
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322 }
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323
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324 target->insert(cloned.release());
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325 }
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326 }
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327
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328 return target.release();
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329 }
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330
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331
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332 ParsedDicomFile* HierarchicalMatcher::Extract(ParsedDicomFile& dicom) const
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333 {
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334 std::auto_ptr<DcmDataset> dataset(ExtractInternal(*dicom.GetDcmtkObject().getDataset(),
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335 dicom.GetEncoding()));
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336
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337 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(*dataset));
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338 result->SetEncoding(dicom.GetEncoding());
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339
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340 return result.release();
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341 }
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342 }