Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 1658:54bafe0e7e7b
Optional argument "keepStrings" in "DumpJson()"
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 30 Sep 2015 09:44:38 +0200 |
| parents | 5360cdba70d8 |
| children | 14a32b2fa63e |
| rev | line source |
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| 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 | |
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160 namespace |
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161 { |
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162 class DictionaryLocker |
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163 { |
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164 private: |
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165 DcmDataDictionary& dictionary_; |
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166 |
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167 public: |
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168 DictionaryLocker() : dictionary_(dcmDataDict.wrlock()) |
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169 { |
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170 } |
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171 |
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172 ~DictionaryLocker() |
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173 { |
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174 dcmDataDict.unlock(); |
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175 } |
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176 |
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177 DcmDataDictionary& operator*() |
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178 { |
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179 return dictionary_; |
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180 } |
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181 |
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182 DcmDataDictionary* operator->() |
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183 { |
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184 return &dictionary_; |
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185 } |
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186 }; |
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187 } |
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188 |
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189 |
| 1656 | 190 void FromDcmtkBridge::InitializeDictionary() |
| 191 { | |
| 192 /* Disable "gethostbyaddr" (which results in memory leaks) and use raw IP addresses */ | |
| 193 dcmDisableGethostbyaddr.set(OFTrue); | |
| 194 | |
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195 { |
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196 DictionaryLocker locker; |
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197 |
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198 locker->clear(); |
| 1656 | 199 |
| 200 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
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201 LOG(WARNING) << "Loading the embedded dictionaries"; |
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202 /** |
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203 * Do not load DICONDE dictionary, it breaks the other tags. The |
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204 * command "strace storescu 2>&1 |grep dic" shows that DICONDE |
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205 * dictionary is not loaded by storescu. |
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206 **/ |
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207 //LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICONDE); |
| 1656 | 208 |
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209 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICOM); |
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210 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_PRIVATE); |
| 1656 | 211 |
| 212 #elif defined(__linux) || defined(__FreeBSD_kernel__) | |
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213 std::string path = DCMTK_DICTIONARY_DIR; |
| 1656 | 214 |
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215 const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE); |
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216 if (env != NULL) |
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217 { |
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218 path = std::string(env); |
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219 } |
| 1656 | 220 |
|
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221 LoadExternalDictionary(*locker, path, "dicom.dic"); |
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222 LoadExternalDictionary(*locker, path, "private.dic"); |
| 1656 | 223 |
| 224 #else | |
| 225 #error Support your platform here | |
| 226 #endif | |
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227 } |
| 1656 | 228 |
| 229 /* make sure data dictionary is loaded */ | |
| 230 if (!dcmDataDict.isDictionaryLoaded()) | |
| 231 { | |
| 232 LOG(ERROR) << "No DICOM dictionary loaded, check environment variable: " << DCM_DICT_ENVIRONMENT_VARIABLE; | |
| 233 throw OrthancException(ErrorCode_InternalError); | |
| 234 } | |
| 235 | |
| 236 { | |
| 237 // Test the dictionary with a simple DICOM tag | |
| 238 DcmTag key(0x0010, 0x1030); // This is PatientWeight | |
| 239 if (key.getEVR() != EVR_DS) | |
| 240 { | |
| 241 LOG(ERROR) << "The DICOM dictionary has not been correctly read"; | |
| 242 throw OrthancException(ErrorCode_InternalError); | |
| 243 } | |
| 244 } | |
| 245 } | |
| 246 | |
| 247 | |
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248 void FromDcmtkBridge::RegisterDictionaryTag(const DicomTag& tag, |
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249 const DcmEVR& vr, |
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250 const std::string& name, |
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251 unsigned int minMultiplicity, |
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252 unsigned int maxMultiplicity) |
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253 { |
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254 if (minMultiplicity < 1) |
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255 { |
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256 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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257 } |
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258 |
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259 if (maxMultiplicity == 0) |
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260 { |
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261 maxMultiplicity = DcmVariableVM; |
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262 } |
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263 else if (maxMultiplicity < minMultiplicity) |
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264 { |
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265 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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266 } |
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267 |
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268 std::auto_ptr<DcmDictEntry> entry(new DcmDictEntry(tag.GetGroup(), |
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269 tag.GetElement(), |
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270 vr, name.c_str(), |
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271 static_cast<int>(minMultiplicity), |
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272 static_cast<int>(maxMultiplicity), |
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273 NULL /* version */, |
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274 OFTrue /* doCopyString */, |
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275 NULL /* private creator */)); |
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276 |
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277 entry->setGroupRangeRestriction(DcmDictRange_Unspecified); |
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278 entry->setElementRangeRestriction(DcmDictRange_Unspecified); |
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279 |
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280 { |
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281 DictionaryLocker locker; |
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282 locker->addEntry(entry.release()); |
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283 } |
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284 } |
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285 |
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286 |
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287 Encoding FromDcmtkBridge::DetectEncoding(DcmDataset& dataset) |
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288 { |
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289 // By default, Latin1 encoding is assumed |
| 1557 | 290 std::string s = Configuration::GetGlobalStringParameter("DefaultEncoding", "Latin1"); |
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291 Encoding encoding = s.empty() ? Encoding_Latin1 : StringToEncoding(s.c_str()); |
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292 |
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293 OFString tmp; |
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294 if (dataset.findAndGetOFString(DCM_SpecificCharacterSet, tmp).good()) |
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295 { |
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296 std::string characterSet = Toolbox::StripSpaces(std::string(tmp.c_str())); |
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297 |
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298 if (characterSet.empty()) |
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299 { |
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300 // Empty specific character set tag: Use the default encoding |
| 1087 | 301 } |
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302 else if (GetDicomEncoding(encoding, characterSet.c_str())) |
| 1087 | 303 { |
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304 // The specific character set is supported by the Orthanc core |
| 1087 | 305 } |
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306 else |
| 1087 | 307 { |
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308 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet |
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309 << ", fallback to ASCII (remove all special characters)"; |
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310 encoding = Encoding_Ascii; |
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311 } |
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312 } |
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313 else |
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314 { |
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315 // No specific character set tag: Use the default encoding |
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316 } |
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317 |
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318 return encoding; |
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319 } |
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320 |
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321 |
| 0 | 322 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 323 { | |
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324 Encoding encoding = DetectEncoding(dataset); |
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325 |
| 0 | 326 target.Clear(); |
| 327 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 328 { | |
| 329 DcmElement* element = dataset.getElement(i); | |
| 330 if (element && element->isLeaf()) | |
| 331 { | |
| 332 target.SetValue(element->getTag().getGTag(), | |
| 333 element->getTag().getETag(), | |
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334 ConvertLeafElement(*element, encoding)); |
| 0 | 335 } |
| 336 } | |
| 337 } | |
| 338 | |
| 339 | |
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340 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag) |
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341 { |
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342 return DicomTag(tag.getGTag(), tag.getETag()); |
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343 } |
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344 |
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345 |
| 0 | 346 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) |
| 347 { | |
| 348 return DicomTag(element.getGTag(), element.getETag()); | |
| 349 } | |
| 350 | |
| 351 | |
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352 bool FromDcmtkBridge::IsPrivateTag(DcmTag& tag) |
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353 { |
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354 #if 1 |
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355 DcmTagKey tmp(tag.getGTag(), tag.getETag()); |
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356 return tmp.isPrivate(); |
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357 #else |
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358 // Implementation for Orthanc versions <= 0.8.5 |
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359 return (tag.getPrivateCreator() != NULL || |
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360 !strcmp("PrivateCreator", tag.getTagName())); // TODO - This may change with future versions of DCMTK |
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361 #endif |
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362 } |
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363 |
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364 |
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365 bool FromDcmtkBridge::IsPrivateTag(const DicomTag& tag) |
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366 { |
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367 #if 1 |
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368 DcmTagKey tmp(tag.GetGroup(), tag.GetElement()); |
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369 return tmp.isPrivate(); |
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370 #else |
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371 // Implementation for Orthanc versions <= 0.8.5 |
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372 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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373 return IsPrivateTag(tmp); |
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374 #endif |
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375 } |
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376 |
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377 |
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378 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element, |
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379 Encoding encoding) |
| 0 | 380 { |
| 381 if (!element.isLeaf()) | |
| 382 { | |
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383 // This function is only applicable to leaf elements |
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384 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 385 } |
| 386 | |
| 387 if (element.isaString()) | |
| 388 { | |
| 389 char *c; | |
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390 if (element.getString(c).good()) |
| 0 | 391 { |
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392 if (c == NULL) // This case corresponds to the empty string |
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393 { |
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394 return new DicomString(""); |
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395 } |
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396 else |
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397 { |
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398 std::string s(c); |
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399 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding); |
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400 return new DicomString(utf8); |
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401 } |
| 0 | 402 } |
| 403 else | |
| 404 { | |
| 405 return new DicomNullValue; | |
| 406 } | |
| 407 } | |
| 408 | |
| 409 try | |
| 410 { | |
| 411 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 412 switch (element.getVR()) | |
| 413 { | |
| 414 | |
| 415 /** | |
| 416 * TODO. | |
| 417 **/ | |
|
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418 |
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419 case EVR_OB: // other byte |
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420 case EVR_OF: // other float |
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421 case EVR_OW: // other word |
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422 case EVR_UN: // unknown value representation |
| 1131 | 423 return new DicomNullValue; |
|
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424 |
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425 /** |
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426 * String types, should never happen at this point because of |
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427 * "element.isaString()". |
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428 **/ |
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429 |
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430 case EVR_DS: // decimal string |
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431 case EVR_IS: // integer string |
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432 case EVR_AS: // age string |
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433 case EVR_DA: // date string |
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434 case EVR_DT: // date time string |
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435 case EVR_TM: // time string |
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436 case EVR_AE: // application entity title |
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437 case EVR_CS: // code string |
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438 case EVR_SH: // short string |
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439 case EVR_LO: // long string |
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440 case EVR_ST: // short text |
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441 case EVR_LT: // long text |
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442 case EVR_UT: // unlimited text |
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443 case EVR_PN: // person name |
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444 case EVR_UI: // unique identifier |
| 1131 | 445 return new DicomNullValue; |
| 0 | 446 |
| 447 | |
|
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448 /** |
| 1131 | 449 * Numberic types |
|
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450 **/ |
| 0 | 451 |
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452 case EVR_SL: // signed long |
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453 { |
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454 Sint32 f; |
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455 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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456 return new DicomString(boost::lexical_cast<std::string>(f)); |
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457 else |
| 1131 | 458 return new DicomNullValue; |
|
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459 } |
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460 |
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461 case EVR_SS: // signed short |
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462 { |
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463 Sint16 f; |
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464 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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465 return new DicomString(boost::lexical_cast<std::string>(f)); |
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466 else |
| 1131 | 467 return new DicomNullValue; |
|
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468 } |
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469 |
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470 case EVR_UL: // unsigned long |
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471 { |
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472 Uint32 f; |
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473 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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474 return new DicomString(boost::lexical_cast<std::string>(f)); |
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475 else |
| 1131 | 476 return new DicomNullValue; |
|
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477 } |
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478 |
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479 case EVR_US: // unsigned short |
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480 { |
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481 Uint16 f; |
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482 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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483 return new DicomString(boost::lexical_cast<std::string>(f)); |
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484 else |
| 1131 | 485 return new DicomNullValue; |
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486 } |
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487 |
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488 case EVR_FL: // float single-precision |
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489 { |
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490 Float32 f; |
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491 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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492 return new DicomString(boost::lexical_cast<std::string>(f)); |
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493 else |
| 1131 | 494 return new DicomNullValue; |
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495 } |
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496 |
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497 case EVR_FD: // float double-precision |
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498 { |
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499 Float64 f; |
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500 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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501 return new DicomString(boost::lexical_cast<std::string>(f)); |
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502 else |
| 1131 | 503 return new DicomNullValue; |
| 504 } | |
| 505 | |
| 506 | |
| 507 /** | |
| 508 * Attribute tag. | |
| 509 **/ | |
| 510 | |
| 511 case EVR_AT: | |
| 512 { | |
| 1147 | 513 DcmTagKey tag; |
| 514 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good()) | |
| 515 { | |
| 516 DicomTag t(tag.getGroup(), tag.getElement()); | |
| 517 return new DicomString(t.Format()); | |
| 518 } | |
| 1131 | 519 else |
| 1147 | 520 { |
| 1131 | 521 return new DicomNullValue; |
| 1147 | 522 } |
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523 } |
| 0 | 524 |
| 525 | |
| 526 /** | |
|
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527 * Sequence types, should never occur at this point because of |
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528 * "element.isLeaf()". |
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529 **/ |
| 0 | 530 |
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531 case EVR_SQ: // sequence of items |
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532 return new DicomNullValue; |
| 0 | 533 |
| 534 | |
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535 /** |
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536 * Internal to DCMTK. |
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537 **/ |
| 0 | 538 |
|
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539 case EVR_ox: // OB or OW depending on context |
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540 case EVR_xs: // SS or US depending on context |
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541 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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542 case EVR_na: // na="not applicable", for data which has no VR |
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543 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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544 case EVR_item: // used internally for items |
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545 case EVR_metainfo: // used internally for meta info datasets |
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546 case EVR_dataset: // used internally for datasets |
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547 case EVR_fileFormat: // used internally for DICOM files |
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548 case EVR_dicomDir: // used internally for DICOMDIR objects |
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549 case EVR_dirRecord: // used internally for DICOMDIR records |
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550 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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551 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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552 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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553 case EVR_PixelData: // used internally for uncompressed pixeld data |
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554 case EVR_OverlayData: // used internally for overlay data |
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555 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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556 return new DicomNullValue; |
| 0 | 557 |
| 558 | |
|
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559 /** |
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560 * Default case. |
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561 **/ |
| 0 | 562 |
|
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563 default: |
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564 return new DicomNullValue; |
| 0 | 565 } |
| 566 } | |
| 567 catch (boost::bad_lexical_cast) | |
| 568 { | |
| 569 return new DicomNullValue; | |
| 570 } | |
|
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571 catch (std::bad_cast) |
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572 { |
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573 return new DicomNullValue; |
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574 } |
| 0 | 575 } |
| 576 | |
| 577 | |
| 578 static void StoreElement(Json::Value& target, | |
| 579 DcmElement& element, | |
|
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580 unsigned int maxStringLength, |
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581 Encoding encoding); |
| 0 | 582 |
| 583 static void StoreItem(Json::Value& target, | |
| 584 DcmItem& item, | |
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585 unsigned int maxStringLength, |
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586 Encoding encoding) |
| 0 | 587 { |
| 588 target = Json::Value(Json::objectValue); | |
| 589 | |
| 590 for (unsigned long i = 0; i < item.card(); i++) | |
| 591 { | |
| 592 DcmElement* element = item.getElement(i); | |
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593 StoreElement(target, *element, maxStringLength, encoding); |
| 0 | 594 } |
| 595 } | |
| 596 | |
| 597 | |
| 598 static void StoreElement(Json::Value& target, | |
| 599 DcmElement& element, | |
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600 unsigned int maxStringLength, |
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601 Encoding encoding) |
| 0 | 602 { |
| 603 assert(target.type() == Json::objectValue); | |
| 604 | |
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605 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
|
305
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606 const std::string formattedTag = tag.Format(); |
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607 |
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608 #if 0 |
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609 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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610 #else |
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611 // This version of the code gives access to the name of the private tags |
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612 DcmTag tagbis(element.getTag()); |
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613 const std::string tagName(tagbis.getTagName()); |
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614 #endif |
| 0 | 615 |
| 616 if (element.isLeaf()) | |
| 617 { | |
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618 Json::Value value(Json::objectValue); |
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619 value["Name"] = tagName; |
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620 |
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621 if (tagbis.getPrivateCreator() != NULL) |
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622 { |
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623 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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624 } |
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625 |
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626 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element, encoding)); |
| 0 | 627 if (v->IsNull()) |
| 628 { | |
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629 value["Type"] = "Null"; |
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630 value["Value"] = Json::nullValue; |
| 0 | 631 } |
| 632 else | |
| 633 { | |
| 634 std::string s = v->AsString(); | |
| 635 if (maxStringLength == 0 || | |
| 636 s.size() <= maxStringLength) | |
| 637 { | |
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638 value["Type"] = "String"; |
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639 value["Value"] = s; |
| 0 | 640 } |
| 641 else | |
| 642 { | |
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643 value["Type"] = "TooLong"; |
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644 value["Value"] = Json::nullValue; |
| 0 | 645 } |
| 646 } | |
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647 |
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648 target[formattedTag] = value; |
| 0 | 649 } |
| 650 else | |
| 651 { | |
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652 Json::Value children(Json::arrayValue); |
| 0 | 653 |
| 654 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 655 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 656 // etc. are not." The following cast is thus OK. | |
| 657 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 658 | |
| 659 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 660 { | |
| 661 DcmItem* child = sequence.getItem(i); | |
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662 Json::Value& v = children.append(Json::objectValue); |
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663 StoreItem(v, *child, maxStringLength, encoding); |
| 0 | 664 } |
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665 |
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666 target[formattedTag]["Name"] = tagName; |
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667 target[formattedTag]["Type"] = "Sequence"; |
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668 target[formattedTag]["Value"] = children; |
| 0 | 669 } |
| 670 } | |
| 671 | |
| 672 | |
| 673 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 674 DcmDataset& dataset, | |
| 675 unsigned int maxStringLength) | |
| 676 { | |
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677 StoreItem(root, dataset, maxStringLength, DetectEncoding(dataset)); |
| 0 | 678 } |
| 679 | |
| 680 | |
| 681 | |
| 682 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 683 const std::string& path, | |
| 684 unsigned int maxStringLength) | |
| 685 { | |
| 686 DcmFileFormat dicom; | |
| 687 if (!dicom.loadFile(path.c_str()).good()) | |
| 688 { | |
| 62 | 689 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 690 } |
| 691 else | |
| 692 { | |
| 693 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 694 } | |
| 695 } | |
| 696 | |
| 697 | |
| 698 | |
| 699 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 700 { | |
| 106 | 701 // Some patches for important tags because of different DICOM |
| 702 // dictionaries between DCMTK versions | |
|
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703 std::string n = t.GetMainTagsName(); |
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704 if (n.size() != 0) |
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705 { |
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706 return n; |
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707 } |
| 106 | 708 // End of patches |
| 709 | |
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710 #if 0 |
| 0 | 711 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 712 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 713 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 714 | |
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715 std::string s(DcmTag_ERROR_TagName); |
| 0 | 716 if (entry != NULL) |
| 717 { | |
| 718 s = std::string(entry->getTagName()); | |
| 719 } | |
| 720 | |
| 721 dcmDataDict.unlock(); | |
| 722 return s; | |
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723 #else |
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724 DcmTag tag(t.GetGroup(), t.GetElement()); |
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725 const char* name = tag.getTagName(); |
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726 if (name == NULL) |
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727 { |
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728 return DcmTag_ERROR_TagName; |
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729 } |
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730 else |
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731 { |
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732 return std::string(name); |
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733 } |
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734 #endif |
| 0 | 735 } |
| 736 | |
| 737 | |
| 304 | 738 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
| 0 | 739 { |
| 304 | 740 if (strlen(name) == 9 && |
| 741 isxdigit(name[0]) && | |
| 742 isxdigit(name[1]) && | |
| 743 isxdigit(name[2]) && | |
| 744 isxdigit(name[3]) && | |
|
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745 (name[4] == '-' || name[4] == ',') && |
| 304 | 746 isxdigit(name[5]) && |
| 747 isxdigit(name[6]) && | |
| 748 isxdigit(name[7]) && | |
| 749 isxdigit(name[8])) | |
| 750 { | |
| 751 uint16_t group = GetTagValue(name); | |
| 752 uint16_t element = GetTagValue(name + 5); | |
| 753 return DicomTag(group, element); | |
| 754 } | |
| 755 | |
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756 #if 0 |
| 0 | 757 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
| 758 const DcmDictEntry* entry = dict.findEntry(name); | |
| 759 | |
| 760 if (entry == NULL) | |
| 761 { | |
| 762 dcmDataDict.unlock(); | |
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763 throw OrthancException(ErrorCode_UnknownDicomTag); |
| 0 | 764 } |
| 765 else | |
| 766 { | |
| 767 DcmTagKey key = entry->getKey(); | |
| 768 DicomTag tag(key.getGroup(), key.getElement()); | |
| 769 dcmDataDict.unlock(); | |
| 770 return tag; | |
| 771 } | |
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772 #else |
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773 DcmTag tag; |
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774 if (DcmTag::findTagFromName(name, tag).good()) |
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775 { |
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776 return DicomTag(tag.getGTag(), tag.getETag()); |
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777 } |
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778 else |
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779 { |
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780 throw OrthancException(ErrorCode_UnknownDicomTag); |
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781 } |
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782 #endif |
| 0 | 783 } |
| 784 | |
| 785 | |
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786 bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag) |
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787 { |
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788 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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789 return tmp.isUnknownVR(); |
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790 } |
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791 |
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792 |
| 0 | 793 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) |
| 794 { | |
| 795 for (DicomMap::Map::const_iterator | |
| 656 | 796 it = m.map_.begin(); it != m.map_.end(); ++it) |
| 0 | 797 { |
| 798 DicomTag t = it->first; | |
| 799 std::string s = it->second->AsString(); | |
| 319 | 800 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
| 0 | 801 } |
| 802 } | |
| 803 | |
| 804 | |
| 805 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 1368 | 806 const DicomMap& values, |
| 807 bool simplify) | |
| 0 | 808 { |
| 809 if (result.type() != Json::objectValue) | |
| 810 { | |
| 62 | 811 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 812 } |
| 813 | |
| 814 result.clear(); | |
| 815 | |
| 816 for (DicomMap::Map::const_iterator | |
| 656 | 817 it = values.map_.begin(); it != values.map_.end(); ++it) |
| 0 | 818 { |
| 1368 | 819 if (simplify) |
| 820 { | |
| 821 result[GetName(it->first)] = it->second->AsString(); | |
| 822 } | |
| 823 else | |
| 824 { | |
| 825 Json::Value value = Json::objectValue; | |
| 826 | |
| 827 value["Name"] = GetName(it->first); | |
| 828 | |
| 829 if (it->second->IsNull()) | |
| 830 { | |
| 831 value["Type"] = "Null"; | |
| 832 value["Value"] = Json::nullValue; | |
| 833 } | |
| 834 else | |
| 835 { | |
| 836 value["Type"] = "String"; | |
| 837 value["Value"] = it->second->AsString(); | |
| 838 } | |
| 839 | |
| 840 result[it->first.Format()] = value; | |
| 841 } | |
| 0 | 842 } |
| 843 } | |
| 176 | 844 |
| 845 | |
| 788 | 846 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
| 176 | 847 { |
| 848 char uid[100]; | |
| 849 | |
| 850 switch (level) | |
| 851 { | |
| 788 | 852 case ResourceType_Patient: |
| 311 | 853 // The "PatientID" field is of type LO (Long String), 64 |
| 854 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
| 855 // as a random PatientID. | |
| 856 return Toolbox::GenerateUuid(); | |
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857 |
| 788 | 858 case ResourceType_Instance: |
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859 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
| 176 | 860 |
| 788 | 861 case ResourceType_Series: |
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862 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
| 176 | 863 |
| 788 | 864 case ResourceType_Study: |
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865 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
| 176 | 866 |
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867 default: |
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868 throw OrthancException(ErrorCode_ParameterOutOfRange); |
| 176 | 869 } |
| 870 } | |
| 871 | |
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872 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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873 DcmDataset& dataSet) |
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874 { |
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875 // Determine the transfer syntax which shall be used to write the |
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876 // information to the file. We always switch to the Little Endian |
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877 // syntax, with explicit length. |
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878 |
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879 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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880 |
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881 |
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882 /** |
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883 * Note that up to Orthanc 0.7.1 (inclusive), the |
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884 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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885 * dataset into memory. We now keep the original transfer syntax |
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886 * (if available). |
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887 **/ |
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888 E_TransferSyntax xfer = dataSet.getOriginalXfer(); |
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889 if (xfer == EXS_Unknown) |
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890 { |
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891 // No information about the original transfer syntax: This is |
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892 // most probably a DICOM dataset that was read from memory. |
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893 xfer = EXS_LittleEndianExplicit; |
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894 } |
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895 |
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896 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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897 |
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898 // Create the meta-header information |
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899 DcmFileFormat ff(&dataSet); |
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900 ff.validateMetaInfo(xfer); |
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901 ff.removeInvalidGroups(); |
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902 |
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903 // Create a memory buffer with the proper size |
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904 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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905 buffer.resize(s); |
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906 DcmOutputBufferStream ob(&buffer[0], s); |
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907 |
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908 // Fill the memory buffer with the meta-header and the dataset |
|
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909 ff.transferInit(); |
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910 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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911 /*opt_groupLength*/ EGL_recalcGL, |
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912 /*opt_paddingType*/ EPD_withoutPadding); |
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913 ff.transferEnd(); |
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914 |
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915 // Handle errors |
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916 if (c.good()) |
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917 { |
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918 return true; |
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919 } |
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920 else |
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921 { |
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922 buffer.clear(); |
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923 return false; |
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924 } |
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925 } |
| 1360 | 926 |
| 927 | |
|
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928 ValueRepresentation FromDcmtkBridge::GetValueRepresentation(const DicomTag& tag) |
| 1360 | 929 { |
| 930 DcmTag t(tag.GetGroup(), tag.GetElement()); | |
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931 switch (t.getEVR()) |
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932 { |
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933 case EVR_PN: |
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934 return ValueRepresentation_PatientName; |
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935 |
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936 case EVR_DA: |
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937 return ValueRepresentation_Date; |
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938 |
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939 case EVR_DT: |
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940 return ValueRepresentation_DateTime; |
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941 |
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942 case EVR_TM: |
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943 return ValueRepresentation_Time; |
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944 |
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945 default: |
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946 return ValueRepresentation_Other; |
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947 } |
| 1360 | 948 } |
| 949 | |
| 0 | 950 } |