Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 1656:d3ba98d6b6e9
refactoring
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 29 Sep 2015 15:13:34 +0200 |
| parents | e40fd0d925c5 |
| children | 5360cdba70d8 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
| 0 | 5 * |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 136 | 10 * |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 0 | 22 * |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
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32 |
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33 |
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34 #include "PrecompiledHeadersServer.h" |
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35 |
| 71 | 36 #ifndef NOMINMAX |
| 37 #define NOMINMAX | |
| 38 #endif | |
| 0 | 39 |
| 846 | 40 #include "Internals/DicomImageDecoder.h" |
| 41 | |
| 0 | 42 #include "FromDcmtkBridge.h" |
| 43 #include "ToDcmtkBridge.h" | |
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44 #include "OrthancInitialization.h" |
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45 #include "../Core/Logging.h" |
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46 #include "../Core/Toolbox.h" |
| 62 | 47 #include "../Core/OrthancException.h" |
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48 #include "../Core/Images/PngWriter.h" |
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49 #include "../Core/Uuid.h" |
| 0 | 50 #include "../Core/DicomFormat/DicomString.h" |
| 51 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 79 | 52 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
| 0 | 53 |
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54 #include <list> |
| 71 | 55 #include <limits> |
| 56 | |
| 0 | 57 #include <boost/lexical_cast.hpp> |
| 1656 | 58 #include <boost/filesystem.hpp> |
| 0 | 59 |
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60 #include <dcmtk/dcmdata/dcchrstr.h> |
| 0 | 61 #include <dcmtk/dcmdata/dcdicent.h> |
| 62 #include <dcmtk/dcmdata/dcdict.h> | |
| 63 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 64 #include <dcmtk/dcmdata/dcistrmb.h> | |
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65 #include <dcmtk/dcmdata/dcuid.h> |
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66 #include <dcmtk/dcmdata/dcmetinf.h> |
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67 #include <dcmtk/dcmdata/dcdeftag.h> |
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68 |
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69 #include <dcmtk/dcmdata/dcvrae.h> |
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70 #include <dcmtk/dcmdata/dcvras.h> |
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71 #include <dcmtk/dcmdata/dcvrcs.h> |
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72 #include <dcmtk/dcmdata/dcvrda.h> |
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73 #include <dcmtk/dcmdata/dcvrds.h> |
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74 #include <dcmtk/dcmdata/dcvrdt.h> |
| 0 | 75 #include <dcmtk/dcmdata/dcvrfd.h> |
| 76 #include <dcmtk/dcmdata/dcvrfl.h> | |
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77 #include <dcmtk/dcmdata/dcvris.h> |
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78 #include <dcmtk/dcmdata/dcvrlo.h> |
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79 #include <dcmtk/dcmdata/dcvrlt.h> |
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80 #include <dcmtk/dcmdata/dcvrpn.h> |
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81 #include <dcmtk/dcmdata/dcvrsh.h> |
| 0 | 82 #include <dcmtk/dcmdata/dcvrsl.h> |
| 83 #include <dcmtk/dcmdata/dcvrss.h> | |
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84 #include <dcmtk/dcmdata/dcvrst.h> |
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85 #include <dcmtk/dcmdata/dcvrtm.h> |
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86 #include <dcmtk/dcmdata/dcvrui.h> |
| 0 | 87 #include <dcmtk/dcmdata/dcvrul.h> |
| 88 #include <dcmtk/dcmdata/dcvrus.h> | |
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89 #include <dcmtk/dcmdata/dcvrut.h> |
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90 #include <dcmtk/dcmdata/dcpixel.h> |
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91 #include <dcmtk/dcmdata/dcpixseq.h> |
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92 #include <dcmtk/dcmdata/dcpxitem.h> |
| 1131 | 93 #include <dcmtk/dcmdata/dcvrat.h> |
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94 |
| 1656 | 95 #include <dcmtk/dcmnet/dul.h> |
| 0 | 96 |
| 2 | 97 #include <boost/math/special_functions/round.hpp> |
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98 #include <dcmtk/dcmdata/dcostrmb.h> |
| 0 | 99 |
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100 |
| 62 | 101 namespace Orthanc |
| 0 | 102 { |
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103 static inline uint16_t GetCharValue(char c) |
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104 { |
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105 if (c >= '0' && c <= '9') |
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106 return c - '0'; |
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107 else if (c >= 'a' && c <= 'f') |
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108 return c - 'a' + 10; |
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109 else if (c >= 'A' && c <= 'F') |
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110 return c - 'A' + 10; |
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111 else |
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112 return 0; |
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113 } |
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114 |
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115 static inline uint16_t GetTagValue(const char* c) |
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116 { |
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117 return ((GetCharValue(c[0]) << 12) + |
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118 (GetCharValue(c[1]) << 8) + |
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119 (GetCharValue(c[2]) << 4) + |
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120 GetCharValue(c[3])); |
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121 } |
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122 |
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123 |
| 1656 | 124 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 |
| 125 static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary, | |
| 126 EmbeddedResources::FileResourceId resource) | |
| 127 { | |
| 128 Toolbox::TemporaryFile tmp; | |
| 129 | |
| 130 FILE* fp = fopen(tmp.GetPath().c_str(), "wb"); | |
| 131 fwrite(EmbeddedResources::GetFileResourceBuffer(resource), | |
| 132 EmbeddedResources::GetFileResourceSize(resource), 1, fp); | |
| 133 fclose(fp); | |
| 134 | |
| 135 if (!dictionary.loadDictionary(tmp.GetPath().c_str())) | |
| 136 { | |
| 137 throw OrthancException(ErrorCode_InternalError); | |
| 138 } | |
| 139 } | |
| 140 | |
| 141 #else | |
| 142 static void LoadExternalDictionary(DcmDataDictionary& dictionary, | |
| 143 const std::string& directory, | |
| 144 const std::string& filename) | |
| 145 { | |
| 146 boost::filesystem::path p = directory; | |
| 147 p = p / filename; | |
| 148 | |
| 149 LOG(WARNING) << "Loading the external DICOM dictionary " << p; | |
| 150 | |
| 151 if (!dictionary.loadDictionary(p.string().c_str())) | |
| 152 { | |
| 153 throw OrthancException(ErrorCode_InternalError); | |
| 154 } | |
| 155 } | |
| 156 | |
| 157 #endif | |
| 158 | |
| 159 | |
| 160 void FromDcmtkBridge::InitializeDictionary() | |
| 161 { | |
| 162 /* Disable "gethostbyaddr" (which results in memory leaks) and use raw IP addresses */ | |
| 163 dcmDisableGethostbyaddr.set(OFTrue); | |
| 164 | |
| 165 dcmDataDict.clear(); | |
| 166 DcmDataDictionary& d = dcmDataDict.wrlock(); | |
| 167 | |
| 168 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
| 169 LOG(WARNING) << "Loading the embedded dictionaries"; | |
| 170 /** | |
| 171 * Do not load DICONDE dictionary, it breaks the other tags. The | |
| 172 * command "strace storescu 2>&1 |grep dic" shows that DICONDE | |
| 173 * dictionary is not loaded by storescu. | |
| 174 **/ | |
| 175 //LoadEmbeddedDictionary(d, EmbeddedResources::DICTIONARY_DICONDE); | |
| 176 | |
| 177 LoadEmbeddedDictionary(d, EmbeddedResources::DICTIONARY_DICOM); | |
| 178 LoadEmbeddedDictionary(d, EmbeddedResources::DICTIONARY_PRIVATE); | |
| 179 | |
| 180 #elif defined(__linux) || defined(__FreeBSD_kernel__) | |
| 181 std::string path = DCMTK_DICTIONARY_DIR; | |
| 182 | |
| 183 const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE); | |
| 184 if (env != NULL) | |
| 185 { | |
| 186 path = std::string(env); | |
| 187 } | |
| 188 | |
| 189 LoadExternalDictionary(d, path, "dicom.dic"); | |
| 190 LoadExternalDictionary(d, path, "private.dic"); | |
| 191 | |
| 192 #else | |
| 193 #error Support your platform here | |
| 194 #endif | |
| 195 | |
| 196 dcmDataDict.unlock(); | |
| 197 | |
| 198 /* make sure data dictionary is loaded */ | |
| 199 if (!dcmDataDict.isDictionaryLoaded()) | |
| 200 { | |
| 201 LOG(ERROR) << "No DICOM dictionary loaded, check environment variable: " << DCM_DICT_ENVIRONMENT_VARIABLE; | |
| 202 throw OrthancException(ErrorCode_InternalError); | |
| 203 } | |
| 204 | |
| 205 { | |
| 206 // Test the dictionary with a simple DICOM tag | |
| 207 DcmTag key(0x0010, 0x1030); // This is PatientWeight | |
| 208 if (key.getEVR() != EVR_DS) | |
| 209 { | |
| 210 LOG(ERROR) << "The DICOM dictionary has not been correctly read"; | |
| 211 throw OrthancException(ErrorCode_InternalError); | |
| 212 } | |
| 213 } | |
| 214 } | |
| 215 | |
| 216 | |
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217 Encoding FromDcmtkBridge::DetectEncoding(DcmDataset& dataset) |
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218 { |
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219 // By default, Latin1 encoding is assumed |
| 1557 | 220 std::string s = Configuration::GetGlobalStringParameter("DefaultEncoding", "Latin1"); |
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221 Encoding encoding = s.empty() ? Encoding_Latin1 : StringToEncoding(s.c_str()); |
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222 |
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223 OFString tmp; |
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224 if (dataset.findAndGetOFString(DCM_SpecificCharacterSet, tmp).good()) |
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225 { |
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226 std::string characterSet = Toolbox::StripSpaces(std::string(tmp.c_str())); |
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227 |
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228 if (characterSet.empty()) |
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229 { |
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230 // Empty specific character set tag: Use the default encoding |
| 1087 | 231 } |
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232 else if (GetDicomEncoding(encoding, characterSet.c_str())) |
| 1087 | 233 { |
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234 // The specific character set is supported by the Orthanc core |
| 1087 | 235 } |
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236 else |
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238 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet |
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239 << ", fallback to ASCII (remove all special characters)"; |
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240 encoding = Encoding_Ascii; |
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241 } |
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242 } |
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243 else |
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244 { |
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245 // No specific character set tag: Use the default encoding |
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246 } |
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247 |
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248 return encoding; |
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249 } |
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250 |
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251 |
| 0 | 252 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 253 { | |
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254 Encoding encoding = DetectEncoding(dataset); |
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255 |
| 0 | 256 target.Clear(); |
| 257 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 258 { | |
| 259 DcmElement* element = dataset.getElement(i); | |
| 260 if (element && element->isLeaf()) | |
| 261 { | |
| 262 target.SetValue(element->getTag().getGTag(), | |
| 263 element->getTag().getETag(), | |
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264 ConvertLeafElement(*element, encoding)); |
| 0 | 265 } |
| 266 } | |
| 267 } | |
| 268 | |
| 269 | |
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270 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag) |
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271 { |
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272 return DicomTag(tag.getGTag(), tag.getETag()); |
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273 } |
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274 |
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275 |
| 0 | 276 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) |
| 277 { | |
| 278 return DicomTag(element.getGTag(), element.getETag()); | |
| 279 } | |
| 280 | |
| 281 | |
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282 bool FromDcmtkBridge::IsPrivateTag(DcmTag& tag) |
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283 { |
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284 #if 1 |
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285 DcmTagKey tmp(tag.getGTag(), tag.getETag()); |
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286 return tmp.isPrivate(); |
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287 #else |
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288 // Implementation for Orthanc versions <= 0.8.5 |
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289 return (tag.getPrivateCreator() != NULL || |
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290 !strcmp("PrivateCreator", tag.getTagName())); // TODO - This may change with future versions of DCMTK |
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291 #endif |
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292 } |
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293 |
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294 |
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295 bool FromDcmtkBridge::IsPrivateTag(const DicomTag& tag) |
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296 { |
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297 #if 1 |
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298 DcmTagKey tmp(tag.GetGroup(), tag.GetElement()); |
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299 return tmp.isPrivate(); |
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300 #else |
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301 // Implementation for Orthanc versions <= 0.8.5 |
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302 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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303 return IsPrivateTag(tmp); |
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304 #endif |
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305 } |
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306 |
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307 |
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308 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element, |
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309 Encoding encoding) |
| 0 | 310 { |
| 311 if (!element.isLeaf()) | |
| 312 { | |
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313 // This function is only applicable to leaf elements |
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314 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 315 } |
| 316 | |
| 317 if (element.isaString()) | |
| 318 { | |
| 319 char *c; | |
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320 if (element.getString(c).good()) |
| 0 | 321 { |
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322 if (c == NULL) // This case corresponds to the empty string |
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323 { |
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324 return new DicomString(""); |
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325 } |
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326 else |
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327 { |
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328 std::string s(c); |
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329 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding); |
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330 return new DicomString(utf8); |
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331 } |
| 0 | 332 } |
| 333 else | |
| 334 { | |
| 335 return new DicomNullValue; | |
| 336 } | |
| 337 } | |
| 338 | |
| 339 try | |
| 340 { | |
| 341 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 342 switch (element.getVR()) | |
| 343 { | |
| 344 | |
| 345 /** | |
| 346 * TODO. | |
| 347 **/ | |
|
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348 |
|
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349 case EVR_OB: // other byte |
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350 case EVR_OF: // other float |
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351 case EVR_OW: // other word |
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352 case EVR_UN: // unknown value representation |
| 1131 | 353 return new DicomNullValue; |
|
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354 |
|
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355 /** |
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356 * String types, should never happen at this point because of |
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357 * "element.isaString()". |
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358 **/ |
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359 |
|
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360 case EVR_DS: // decimal string |
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361 case EVR_IS: // integer string |
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362 case EVR_AS: // age string |
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363 case EVR_DA: // date string |
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364 case EVR_DT: // date time string |
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365 case EVR_TM: // time string |
|
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366 case EVR_AE: // application entity title |
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367 case EVR_CS: // code string |
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368 case EVR_SH: // short string |
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369 case EVR_LO: // long string |
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370 case EVR_ST: // short text |
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371 case EVR_LT: // long text |
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372 case EVR_UT: // unlimited text |
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373 case EVR_PN: // person name |
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374 case EVR_UI: // unique identifier |
| 1131 | 375 return new DicomNullValue; |
| 0 | 376 |
| 377 | |
|
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378 /** |
| 1131 | 379 * Numberic types |
|
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380 **/ |
| 0 | 381 |
|
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382 case EVR_SL: // signed long |
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383 { |
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384 Sint32 f; |
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385 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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386 return new DicomString(boost::lexical_cast<std::string>(f)); |
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387 else |
| 1131 | 388 return new DicomNullValue; |
|
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389 } |
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390 |
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391 case EVR_SS: // signed short |
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392 { |
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393 Sint16 f; |
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394 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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395 return new DicomString(boost::lexical_cast<std::string>(f)); |
|
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396 else |
| 1131 | 397 return new DicomNullValue; |
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398 } |
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399 |
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400 case EVR_UL: // unsigned long |
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401 { |
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402 Uint32 f; |
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403 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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404 return new DicomString(boost::lexical_cast<std::string>(f)); |
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405 else |
| 1131 | 406 return new DicomNullValue; |
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407 } |
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408 |
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409 case EVR_US: // unsigned short |
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410 { |
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411 Uint16 f; |
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412 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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413 return new DicomString(boost::lexical_cast<std::string>(f)); |
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414 else |
| 1131 | 415 return new DicomNullValue; |
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416 } |
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417 |
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418 case EVR_FL: // float single-precision |
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419 { |
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420 Float32 f; |
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421 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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422 return new DicomString(boost::lexical_cast<std::string>(f)); |
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423 else |
| 1131 | 424 return new DicomNullValue; |
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425 } |
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426 |
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427 case EVR_FD: // float double-precision |
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428 { |
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429 Float64 f; |
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430 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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431 return new DicomString(boost::lexical_cast<std::string>(f)); |
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432 else |
| 1131 | 433 return new DicomNullValue; |
| 434 } | |
| 435 | |
| 436 | |
| 437 /** | |
| 438 * Attribute tag. | |
| 439 **/ | |
| 440 | |
| 441 case EVR_AT: | |
| 442 { | |
| 1147 | 443 DcmTagKey tag; |
| 444 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good()) | |
| 445 { | |
| 446 DicomTag t(tag.getGroup(), tag.getElement()); | |
| 447 return new DicomString(t.Format()); | |
| 448 } | |
| 1131 | 449 else |
| 1147 | 450 { |
| 1131 | 451 return new DicomNullValue; |
| 1147 | 452 } |
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453 } |
| 0 | 454 |
| 455 | |
| 456 /** | |
|
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457 * Sequence types, should never occur at this point because of |
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458 * "element.isLeaf()". |
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459 **/ |
| 0 | 460 |
|
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461 case EVR_SQ: // sequence of items |
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462 return new DicomNullValue; |
| 0 | 463 |
| 464 | |
|
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465 /** |
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466 * Internal to DCMTK. |
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467 **/ |
| 0 | 468 |
|
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469 case EVR_ox: // OB or OW depending on context |
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470 case EVR_xs: // SS or US depending on context |
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471 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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472 case EVR_na: // na="not applicable", for data which has no VR |
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473 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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474 case EVR_item: // used internally for items |
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475 case EVR_metainfo: // used internally for meta info datasets |
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476 case EVR_dataset: // used internally for datasets |
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477 case EVR_fileFormat: // used internally for DICOM files |
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478 case EVR_dicomDir: // used internally for DICOMDIR objects |
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479 case EVR_dirRecord: // used internally for DICOMDIR records |
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480 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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481 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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482 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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483 case EVR_PixelData: // used internally for uncompressed pixeld data |
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484 case EVR_OverlayData: // used internally for overlay data |
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485 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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486 return new DicomNullValue; |
| 0 | 487 |
| 488 | |
|
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489 /** |
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490 * Default case. |
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491 **/ |
| 0 | 492 |
|
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493 default: |
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494 return new DicomNullValue; |
| 0 | 495 } |
| 496 } | |
| 497 catch (boost::bad_lexical_cast) | |
| 498 { | |
| 499 return new DicomNullValue; | |
| 500 } | |
|
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501 catch (std::bad_cast) |
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502 { |
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503 return new DicomNullValue; |
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504 } |
| 0 | 505 } |
| 506 | |
| 507 | |
| 508 static void StoreElement(Json::Value& target, | |
| 509 DcmElement& element, | |
|
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510 unsigned int maxStringLength, |
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511 Encoding encoding); |
| 0 | 512 |
| 513 static void StoreItem(Json::Value& target, | |
| 514 DcmItem& item, | |
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515 unsigned int maxStringLength, |
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516 Encoding encoding) |
| 0 | 517 { |
| 518 target = Json::Value(Json::objectValue); | |
| 519 | |
| 520 for (unsigned long i = 0; i < item.card(); i++) | |
| 521 { | |
| 522 DcmElement* element = item.getElement(i); | |
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523 StoreElement(target, *element, maxStringLength, encoding); |
| 0 | 524 } |
| 525 } | |
| 526 | |
| 527 | |
| 528 static void StoreElement(Json::Value& target, | |
| 529 DcmElement& element, | |
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530 unsigned int maxStringLength, |
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531 Encoding encoding) |
| 0 | 532 { |
| 533 assert(target.type() == Json::objectValue); | |
| 534 | |
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535 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
|
305
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536 const std::string formattedTag = tag.Format(); |
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537 |
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538 #if 0 |
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539 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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540 #else |
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541 // This version of the code gives access to the name of the private tags |
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542 DcmTag tagbis(element.getTag()); |
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543 const std::string tagName(tagbis.getTagName()); |
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544 #endif |
| 0 | 545 |
| 546 if (element.isLeaf()) | |
| 547 { | |
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548 Json::Value value(Json::objectValue); |
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549 value["Name"] = tagName; |
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550 |
|
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551 if (tagbis.getPrivateCreator() != NULL) |
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552 { |
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553 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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554 } |
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555 |
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556 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element, encoding)); |
| 0 | 557 if (v->IsNull()) |
| 558 { | |
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559 value["Type"] = "Null"; |
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560 value["Value"] = Json::nullValue; |
| 0 | 561 } |
| 562 else | |
| 563 { | |
| 564 std::string s = v->AsString(); | |
| 565 if (maxStringLength == 0 || | |
| 566 s.size() <= maxStringLength) | |
| 567 { | |
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568 value["Type"] = "String"; |
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569 value["Value"] = s; |
| 0 | 570 } |
| 571 else | |
| 572 { | |
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573 value["Type"] = "TooLong"; |
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574 value["Value"] = Json::nullValue; |
| 0 | 575 } |
| 576 } | |
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577 |
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578 target[formattedTag] = value; |
| 0 | 579 } |
| 580 else | |
| 581 { | |
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582 Json::Value children(Json::arrayValue); |
| 0 | 583 |
| 584 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 585 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 586 // etc. are not." The following cast is thus OK. | |
| 587 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 588 | |
| 589 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 590 { | |
| 591 DcmItem* child = sequence.getItem(i); | |
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592 Json::Value& v = children.append(Json::objectValue); |
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593 StoreItem(v, *child, maxStringLength, encoding); |
| 0 | 594 } |
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595 |
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596 target[formattedTag]["Name"] = tagName; |
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597 target[formattedTag]["Type"] = "Sequence"; |
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598 target[formattedTag]["Value"] = children; |
| 0 | 599 } |
| 600 } | |
| 601 | |
| 602 | |
| 603 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 604 DcmDataset& dataset, | |
| 605 unsigned int maxStringLength) | |
| 606 { | |
|
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607 StoreItem(root, dataset, maxStringLength, DetectEncoding(dataset)); |
| 0 | 608 } |
| 609 | |
| 610 | |
| 611 | |
| 612 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 613 const std::string& path, | |
| 614 unsigned int maxStringLength) | |
| 615 { | |
| 616 DcmFileFormat dicom; | |
| 617 if (!dicom.loadFile(path.c_str()).good()) | |
| 618 { | |
| 62 | 619 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 620 } |
| 621 else | |
| 622 { | |
| 623 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 624 } | |
| 625 } | |
| 626 | |
| 627 | |
| 628 | |
| 629 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 630 { | |
| 106 | 631 // Some patches for important tags because of different DICOM |
| 632 // dictionaries between DCMTK versions | |
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633 std::string n = t.GetMainTagsName(); |
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634 if (n.size() != 0) |
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635 { |
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636 return n; |
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637 } |
| 106 | 638 // End of patches |
| 639 | |
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640 #if 0 |
| 0 | 641 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 642 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 643 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 644 | |
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645 std::string s(DcmTag_ERROR_TagName); |
| 0 | 646 if (entry != NULL) |
| 647 { | |
| 648 s = std::string(entry->getTagName()); | |
| 649 } | |
| 650 | |
| 651 dcmDataDict.unlock(); | |
| 652 return s; | |
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653 #else |
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654 DcmTag tag(t.GetGroup(), t.GetElement()); |
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655 const char* name = tag.getTagName(); |
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656 if (name == NULL) |
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657 { |
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658 return DcmTag_ERROR_TagName; |
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659 } |
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660 else |
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661 { |
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662 return std::string(name); |
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663 } |
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664 #endif |
| 0 | 665 } |
| 666 | |
| 667 | |
| 304 | 668 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
| 0 | 669 { |
| 304 | 670 if (strlen(name) == 9 && |
| 671 isxdigit(name[0]) && | |
| 672 isxdigit(name[1]) && | |
| 673 isxdigit(name[2]) && | |
| 674 isxdigit(name[3]) && | |
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675 (name[4] == '-' || name[4] == ',') && |
| 304 | 676 isxdigit(name[5]) && |
| 677 isxdigit(name[6]) && | |
| 678 isxdigit(name[7]) && | |
| 679 isxdigit(name[8])) | |
| 680 { | |
| 681 uint16_t group = GetTagValue(name); | |
| 682 uint16_t element = GetTagValue(name + 5); | |
| 683 return DicomTag(group, element); | |
| 684 } | |
| 685 | |
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686 #if 0 |
| 0 | 687 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
| 688 const DcmDictEntry* entry = dict.findEntry(name); | |
| 689 | |
| 690 if (entry == NULL) | |
| 691 { | |
| 692 dcmDataDict.unlock(); | |
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693 throw OrthancException(ErrorCode_UnknownDicomTag); |
| 0 | 694 } |
| 695 else | |
| 696 { | |
| 697 DcmTagKey key = entry->getKey(); | |
| 698 DicomTag tag(key.getGroup(), key.getElement()); | |
| 699 dcmDataDict.unlock(); | |
| 700 return tag; | |
| 701 } | |
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702 #else |
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703 DcmTag tag; |
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704 if (DcmTag::findTagFromName(name, tag).good()) |
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705 { |
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706 return DicomTag(tag.getGTag(), tag.getETag()); |
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707 } |
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708 else |
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709 { |
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710 throw OrthancException(ErrorCode_UnknownDicomTag); |
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711 } |
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712 #endif |
| 0 | 713 } |
| 714 | |
| 715 | |
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716 bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag) |
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717 { |
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718 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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719 return tmp.isUnknownVR(); |
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720 } |
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721 |
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722 |
| 0 | 723 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) |
| 724 { | |
| 725 for (DicomMap::Map::const_iterator | |
| 656 | 726 it = m.map_.begin(); it != m.map_.end(); ++it) |
| 0 | 727 { |
| 728 DicomTag t = it->first; | |
| 729 std::string s = it->second->AsString(); | |
| 319 | 730 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
| 0 | 731 } |
| 732 } | |
| 733 | |
| 734 | |
| 735 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 1368 | 736 const DicomMap& values, |
| 737 bool simplify) | |
| 0 | 738 { |
| 739 if (result.type() != Json::objectValue) | |
| 740 { | |
| 62 | 741 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 742 } |
| 743 | |
| 744 result.clear(); | |
| 745 | |
| 746 for (DicomMap::Map::const_iterator | |
| 656 | 747 it = values.map_.begin(); it != values.map_.end(); ++it) |
| 0 | 748 { |
| 1368 | 749 if (simplify) |
| 750 { | |
| 751 result[GetName(it->first)] = it->second->AsString(); | |
| 752 } | |
| 753 else | |
| 754 { | |
| 755 Json::Value value = Json::objectValue; | |
| 756 | |
| 757 value["Name"] = GetName(it->first); | |
| 758 | |
| 759 if (it->second->IsNull()) | |
| 760 { | |
| 761 value["Type"] = "Null"; | |
| 762 value["Value"] = Json::nullValue; | |
| 763 } | |
| 764 else | |
| 765 { | |
| 766 value["Type"] = "String"; | |
| 767 value["Value"] = it->second->AsString(); | |
| 768 } | |
| 769 | |
| 770 result[it->first.Format()] = value; | |
| 771 } | |
| 0 | 772 } |
| 773 } | |
| 176 | 774 |
| 775 | |
| 788 | 776 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
| 176 | 777 { |
| 778 char uid[100]; | |
| 779 | |
| 780 switch (level) | |
| 781 { | |
| 788 | 782 case ResourceType_Patient: |
| 311 | 783 // The "PatientID" field is of type LO (Long String), 64 |
| 784 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
| 785 // as a random PatientID. | |
| 786 return Toolbox::GenerateUuid(); | |
|
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787 |
| 788 | 788 case ResourceType_Instance: |
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789 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
| 176 | 790 |
| 788 | 791 case ResourceType_Series: |
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792 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
| 176 | 793 |
| 788 | 794 case ResourceType_Study: |
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795 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
| 176 | 796 |
|
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797 default: |
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798 throw OrthancException(ErrorCode_ParameterOutOfRange); |
| 176 | 799 } |
| 800 } | |
| 801 | |
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802 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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803 DcmDataset& dataSet) |
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804 { |
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805 // Determine the transfer syntax which shall be used to write the |
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806 // information to the file. We always switch to the Little Endian |
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807 // syntax, with explicit length. |
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808 |
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809 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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810 |
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811 |
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812 /** |
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813 * Note that up to Orthanc 0.7.1 (inclusive), the |
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814 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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815 * dataset into memory. We now keep the original transfer syntax |
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816 * (if available). |
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817 **/ |
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818 E_TransferSyntax xfer = dataSet.getOriginalXfer(); |
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819 if (xfer == EXS_Unknown) |
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820 { |
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821 // No information about the original transfer syntax: This is |
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822 // most probably a DICOM dataset that was read from memory. |
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823 xfer = EXS_LittleEndianExplicit; |
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824 } |
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825 |
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826 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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827 |
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828 // Create the meta-header information |
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829 DcmFileFormat ff(&dataSet); |
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830 ff.validateMetaInfo(xfer); |
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831 ff.removeInvalidGroups(); |
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832 |
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833 // Create a memory buffer with the proper size |
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834 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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835 buffer.resize(s); |
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836 DcmOutputBufferStream ob(&buffer[0], s); |
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837 |
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838 // Fill the memory buffer with the meta-header and the dataset |
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839 ff.transferInit(); |
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840 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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841 /*opt_groupLength*/ EGL_recalcGL, |
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842 /*opt_paddingType*/ EPD_withoutPadding); |
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843 ff.transferEnd(); |
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844 |
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845 // Handle errors |
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846 if (c.good()) |
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847 { |
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848 return true; |
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849 } |
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850 else |
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851 { |
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852 buffer.clear(); |
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853 return false; |
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854 } |
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855 } |
| 1360 | 856 |
| 857 | |
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858 ValueRepresentation FromDcmtkBridge::GetValueRepresentation(const DicomTag& tag) |
| 1360 | 859 { |
| 860 DcmTag t(tag.GetGroup(), tag.GetElement()); | |
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861 switch (t.getEVR()) |
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862 { |
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863 case EVR_PN: |
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864 return ValueRepresentation_PatientName; |
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865 |
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866 case EVR_DA: |
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867 return ValueRepresentation_Date; |
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868 |
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869 case EVR_DT: |
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870 return ValueRepresentation_DateTime; |
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871 |
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872 case EVR_TM: |
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873 return ValueRepresentation_Time; |
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874 |
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875 default: |
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876 return ValueRepresentation_Other; |
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877 } |
| 1360 | 878 } |
| 879 | |
| 0 | 880 } |