Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 1739:df331354cea2
include binary in ToJson
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 22 Oct 2015 19:00:32 +0200 |
parents | 15a788a63846 |
children | 57b9e6890482 |
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" |
79 | 50 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
0 | 51 |
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52 #include <list> |
71 | 53 #include <limits> |
54 | |
0 | 55 #include <boost/lexical_cast.hpp> |
1656 | 56 #include <boost/filesystem.hpp> |
0 | 57 |
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58 #include <dcmtk/dcmdata/dcchrstr.h> |
0 | 59 #include <dcmtk/dcmdata/dcdicent.h> |
60 #include <dcmtk/dcmdata/dcdict.h> | |
61 #include <dcmtk/dcmdata/dcfilefo.h> | |
62 #include <dcmtk/dcmdata/dcistrmb.h> | |
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63 #include <dcmtk/dcmdata/dcuid.h> |
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64 #include <dcmtk/dcmdata/dcmetinf.h> |
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65 #include <dcmtk/dcmdata/dcdeftag.h> |
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66 |
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67 #include <dcmtk/dcmdata/dcvrae.h> |
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68 #include <dcmtk/dcmdata/dcvras.h> |
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69 #include <dcmtk/dcmdata/dcvrcs.h> |
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70 #include <dcmtk/dcmdata/dcvrda.h> |
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71 #include <dcmtk/dcmdata/dcvrds.h> |
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72 #include <dcmtk/dcmdata/dcvrdt.h> |
0 | 73 #include <dcmtk/dcmdata/dcvrfd.h> |
74 #include <dcmtk/dcmdata/dcvrfl.h> | |
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75 #include <dcmtk/dcmdata/dcvris.h> |
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76 #include <dcmtk/dcmdata/dcvrlo.h> |
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77 #include <dcmtk/dcmdata/dcvrlt.h> |
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78 #include <dcmtk/dcmdata/dcvrpn.h> |
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79 #include <dcmtk/dcmdata/dcvrsh.h> |
0 | 80 #include <dcmtk/dcmdata/dcvrsl.h> |
81 #include <dcmtk/dcmdata/dcvrss.h> | |
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82 #include <dcmtk/dcmdata/dcvrst.h> |
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83 #include <dcmtk/dcmdata/dcvrtm.h> |
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84 #include <dcmtk/dcmdata/dcvrui.h> |
0 | 85 #include <dcmtk/dcmdata/dcvrul.h> |
86 #include <dcmtk/dcmdata/dcvrus.h> | |
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87 #include <dcmtk/dcmdata/dcvrut.h> |
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88 #include <dcmtk/dcmdata/dcpixel.h> |
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89 #include <dcmtk/dcmdata/dcpixseq.h> |
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90 #include <dcmtk/dcmdata/dcpxitem.h> |
1131 | 91 #include <dcmtk/dcmdata/dcvrat.h> |
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92 |
1656 | 93 #include <dcmtk/dcmnet/dul.h> |
0 | 94 |
2 | 95 #include <boost/math/special_functions/round.hpp> |
1689 | 96 #include <boost/algorithm/string/predicate.hpp> |
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97 #include <dcmtk/dcmdata/dcostrmb.h> |
0 | 98 |
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99 |
62 | 100 namespace Orthanc |
0 | 101 { |
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102 static inline uint16_t GetCharValue(char c) |
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103 { |
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104 if (c >= '0' && c <= '9') |
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105 return c - '0'; |
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106 else if (c >= 'a' && c <= 'f') |
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107 return c - 'a' + 10; |
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108 else if (c >= 'A' && c <= 'F') |
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109 return c - 'A' + 10; |
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110 else |
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111 return 0; |
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112 } |
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113 |
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114 static inline uint16_t GetTagValue(const char* c) |
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115 { |
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116 return ((GetCharValue(c[0]) << 12) + |
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117 (GetCharValue(c[1]) << 8) + |
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118 (GetCharValue(c[2]) << 4) + |
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119 GetCharValue(c[3])); |
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120 } |
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121 |
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122 |
1656 | 123 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 |
124 static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary, | |
125 EmbeddedResources::FileResourceId resource) | |
126 { | |
127 Toolbox::TemporaryFile tmp; | |
128 | |
129 FILE* fp = fopen(tmp.GetPath().c_str(), "wb"); | |
130 fwrite(EmbeddedResources::GetFileResourceBuffer(resource), | |
131 EmbeddedResources::GetFileResourceSize(resource), 1, fp); | |
132 fclose(fp); | |
133 | |
134 if (!dictionary.loadDictionary(tmp.GetPath().c_str())) | |
135 { | |
136 throw OrthancException(ErrorCode_InternalError); | |
137 } | |
138 } | |
139 | |
140 #else | |
141 static void LoadExternalDictionary(DcmDataDictionary& dictionary, | |
142 const std::string& directory, | |
143 const std::string& filename) | |
144 { | |
145 boost::filesystem::path p = directory; | |
146 p = p / filename; | |
147 | |
148 LOG(WARNING) << "Loading the external DICOM dictionary " << p; | |
149 | |
150 if (!dictionary.loadDictionary(p.string().c_str())) | |
151 { | |
152 throw OrthancException(ErrorCode_InternalError); | |
153 } | |
154 } | |
155 | |
156 #endif | |
157 | |
158 | |
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159 namespace |
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160 { |
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161 class DictionaryLocker |
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162 { |
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163 private: |
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164 DcmDataDictionary& dictionary_; |
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165 |
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166 public: |
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167 DictionaryLocker() : dictionary_(dcmDataDict.wrlock()) |
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168 { |
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169 } |
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170 |
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171 ~DictionaryLocker() |
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172 { |
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173 dcmDataDict.unlock(); |
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174 } |
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175 |
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176 DcmDataDictionary& operator*() |
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177 { |
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178 return dictionary_; |
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179 } |
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180 |
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181 DcmDataDictionary* operator->() |
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182 { |
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183 return &dictionary_; |
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184 } |
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185 }; |
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186 } |
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187 |
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188 |
1656 | 189 void FromDcmtkBridge::InitializeDictionary() |
190 { | |
191 /* Disable "gethostbyaddr" (which results in memory leaks) and use raw IP addresses */ | |
192 dcmDisableGethostbyaddr.set(OFTrue); | |
193 | |
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194 { |
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195 DictionaryLocker locker; |
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196 |
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197 locker->clear(); |
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199 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
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200 LOG(WARNING) << "Loading the embedded dictionaries"; |
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201 /** |
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202 * Do not load DICONDE dictionary, it breaks the other tags. The |
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203 * command "strace storescu 2>&1 |grep dic" shows that DICONDE |
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204 * dictionary is not loaded by storescu. |
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205 **/ |
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206 //LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICONDE); |
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208 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICOM); |
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209 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_PRIVATE); |
1656 | 210 |
211 #elif defined(__linux) || defined(__FreeBSD_kernel__) | |
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212 std::string path = DCMTK_DICTIONARY_DIR; |
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214 const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE); |
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215 if (env != NULL) |
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216 { |
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217 path = std::string(env); |
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218 } |
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220 LoadExternalDictionary(*locker, path, "dicom.dic"); |
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221 LoadExternalDictionary(*locker, path, "private.dic"); |
1656 | 222 |
223 #else | |
224 #error Support your platform here | |
225 #endif | |
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226 } |
1656 | 227 |
228 /* make sure data dictionary is loaded */ | |
229 if (!dcmDataDict.isDictionaryLoaded()) | |
230 { | |
231 LOG(ERROR) << "No DICOM dictionary loaded, check environment variable: " << DCM_DICT_ENVIRONMENT_VARIABLE; | |
232 throw OrthancException(ErrorCode_InternalError); | |
233 } | |
234 | |
235 { | |
236 // Test the dictionary with a simple DICOM tag | |
237 DcmTag key(0x0010, 0x1030); // This is PatientWeight | |
238 if (key.getEVR() != EVR_DS) | |
239 { | |
240 LOG(ERROR) << "The DICOM dictionary has not been correctly read"; | |
241 throw OrthancException(ErrorCode_InternalError); | |
242 } | |
243 } | |
244 } | |
245 | |
246 | |
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247 void FromDcmtkBridge::RegisterDictionaryTag(const DicomTag& tag, |
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248 const DcmEVR& vr, |
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249 const std::string& name, |
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250 unsigned int minMultiplicity, |
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251 unsigned int maxMultiplicity) |
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252 { |
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253 if (minMultiplicity < 1) |
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254 { |
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255 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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256 } |
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257 |
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258 if (maxMultiplicity == 0) |
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259 { |
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260 maxMultiplicity = DcmVariableVM; |
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261 } |
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262 else if (maxMultiplicity < minMultiplicity) |
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263 { |
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264 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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265 } |
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266 |
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267 std::auto_ptr<DcmDictEntry> entry(new DcmDictEntry(tag.GetGroup(), |
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268 tag.GetElement(), |
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269 vr, name.c_str(), |
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270 static_cast<int>(minMultiplicity), |
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271 static_cast<int>(maxMultiplicity), |
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272 NULL /* version */, |
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273 OFTrue /* doCopyString */, |
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274 NULL /* private creator */)); |
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275 |
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276 entry->setGroupRangeRestriction(DcmDictRange_Unspecified); |
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277 entry->setElementRangeRestriction(DcmDictRange_Unspecified); |
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278 |
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279 { |
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280 DictionaryLocker locker; |
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281 locker->addEntry(entry.release()); |
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282 } |
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283 } |
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284 |
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285 |
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286 Encoding FromDcmtkBridge::DetectEncoding(DcmDataset& dataset) |
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287 { |
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288 // By default, Latin1 encoding is assumed |
1557 | 289 std::string s = Configuration::GetGlobalStringParameter("DefaultEncoding", "Latin1"); |
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290 Encoding encoding = s.empty() ? Encoding_Latin1 : StringToEncoding(s.c_str()); |
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291 |
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292 OFString tmp; |
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293 if (dataset.findAndGetOFString(DCM_SpecificCharacterSet, tmp).good()) |
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294 { |
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295 std::string characterSet = Toolbox::StripSpaces(std::string(tmp.c_str())); |
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296 |
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297 if (characterSet.empty()) |
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298 { |
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299 // Empty specific character set tag: Use the default encoding |
1087 | 300 } |
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301 else if (GetDicomEncoding(encoding, characterSet.c_str())) |
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303 // The specific character set is supported by the Orthanc core |
1087 | 304 } |
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305 else |
1087 | 306 { |
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307 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet |
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308 << ", fallback to ASCII (remove all special characters)"; |
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309 encoding = Encoding_Ascii; |
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310 } |
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311 } |
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312 else |
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313 { |
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314 // No specific character set tag: Use the default encoding |
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315 } |
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316 |
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317 return encoding; |
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318 } |
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319 |
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320 |
0 | 321 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
322 { | |
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323 Encoding encoding = DetectEncoding(dataset); |
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324 |
0 | 325 target.Clear(); |
326 for (unsigned long i = 0; i < dataset.card(); i++) | |
327 { | |
328 DcmElement* element = dataset.getElement(i); | |
329 if (element && element->isLeaf()) | |
330 { | |
331 target.SetValue(element->getTag().getGTag(), | |
332 element->getTag().getETag(), | |
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333 ConvertLeafElement(*element, DicomToJsonFlags_Default, encoding)); |
0 | 334 } |
335 } | |
336 } | |
337 | |
338 | |
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339 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag) |
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340 { |
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341 return DicomTag(tag.getGTag(), tag.getETag()); |
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342 } |
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343 |
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344 |
0 | 345 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) |
346 { | |
347 return DicomTag(element.getGTag(), element.getETag()); | |
348 } | |
349 | |
350 | |
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351 bool FromDcmtkBridge::IsPrivateTag(const DicomTag& tag) |
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352 { |
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353 #if 1 |
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354 DcmTagKey tmp(tag.GetGroup(), tag.GetElement()); |
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355 return tmp.isPrivate(); |
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356 #else |
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357 // Implementation for Orthanc versions <= 0.8.5 |
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358 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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359 return IsPrivateTag(tmp); |
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360 #endif |
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361 } |
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362 |
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363 |
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364 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element, |
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365 DicomToJsonFlags flags, |
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366 Encoding encoding) |
0 | 367 { |
368 if (!element.isLeaf()) | |
369 { | |
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370 // This function is only applicable to leaf elements |
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371 throw OrthancException(ErrorCode_BadParameterType); |
0 | 372 } |
373 | |
374 if (element.isaString()) | |
375 { | |
376 char *c; | |
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377 if (element.getString(c).good()) |
0 | 378 { |
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379 if (c == NULL) // This case corresponds to the empty string |
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380 { |
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381 return new DicomValue("", false); |
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382 } |
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383 else |
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384 { |
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385 std::string s(c); |
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386 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding); |
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387 return new DicomValue(utf8, false); |
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388 } |
0 | 389 } |
390 else | |
391 { | |
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392 return new DicomValue; |
0 | 393 } |
394 } | |
395 | |
396 try | |
397 { | |
398 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
399 switch (element.getVR()) | |
400 { | |
401 | |
402 /** | |
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403 * Deal with binary data (including PixelData). |
0 | 404 **/ |
306
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405 |
302
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406 case EVR_OB: // other byte |
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407 case EVR_OF: // other float |
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408 case EVR_OW: // other word |
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409 case EVR_UN: // unknown value representation |
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410 case EVR_ox: // OB or OW depending on context |
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411 { |
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412 if (!(flags & DicomToJsonFlags_ConvertBinaryToNull)) |
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413 { |
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414 Uint8* data = NULL; |
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415 if (element.getUint8Array(data) == EC_Normal) |
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416 { |
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417 return new DicomValue(reinterpret_cast<const char*>(data), element.getLength(), true); |
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418 } |
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419 } |
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420 |
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421 return new DicomValue; |
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422 } |
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423 |
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424 /** |
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425 * String types, should never happen at this point because of |
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426 * "element.isaString()". |
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427 **/ |
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428 |
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429 case EVR_DS: // decimal string |
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430 case EVR_IS: // integer string |
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431 case EVR_AS: // age string |
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432 case EVR_DA: // date string |
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433 case EVR_DT: // date time string |
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434 case EVR_TM: // time string |
302
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435 case EVR_AE: // application entity title |
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436 case EVR_CS: // code string |
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437 case EVR_SH: // short string |
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438 case EVR_LO: // long string |
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439 case EVR_ST: // short text |
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440 case EVR_LT: // long text |
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441 case EVR_UT: // unlimited text |
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442 case EVR_PN: // person name |
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443 case EVR_UI: // unique identifier |
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444 return new DicomValue; |
0 | 445 |
446 | |
302
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447 /** |
1131 | 448 * Numberic types |
302
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449 **/ |
0 | 450 |
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451 case EVR_SL: // signed long |
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452 { |
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453 Sint32 f; |
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454 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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455 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
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456 else |
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457 return new DicomValue; |
302
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458 } |
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459 |
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460 case EVR_SS: // signed short |
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461 { |
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462 Sint16 f; |
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463 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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464 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
302
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465 else |
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466 return new DicomValue; |
302
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467 } |
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468 |
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469 case EVR_UL: // unsigned long |
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470 { |
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471 Uint32 f; |
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472 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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473 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
302
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474 else |
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475 return new DicomValue; |
302
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476 } |
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477 |
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478 case EVR_US: // unsigned short |
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479 { |
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480 Uint16 f; |
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481 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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482 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
302
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483 else |
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484 return new DicomValue; |
302
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485 } |
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486 |
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487 case EVR_FL: // float single-precision |
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488 { |
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489 Float32 f; |
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490 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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491 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
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492 else |
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493 return new DicomValue; |
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494 } |
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495 |
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496 case EVR_FD: // float double-precision |
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497 { |
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498 Float64 f; |
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499 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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500 return new DicomValue(boost::lexical_cast<std::string>(f), false); |
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501 else |
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502 return new DicomValue; |
1131 | 503 } |
504 | |
505 | |
506 /** | |
507 * Attribute tag. | |
508 **/ | |
509 | |
510 case EVR_AT: | |
511 { | |
1147 | 512 DcmTagKey tag; |
513 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good()) | |
514 { | |
515 DicomTag t(tag.getGroup(), tag.getElement()); | |
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516 return new DicomValue(t.Format(), false); |
1147 | 517 } |
1131 | 518 else |
1147 | 519 { |
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520 return new DicomValue; |
1147 | 521 } |
302
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522 } |
0 | 523 |
524 | |
525 /** | |
302
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526 * Sequence types, should never occur at this point because of |
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527 * "element.isLeaf()". |
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528 **/ |
0 | 529 |
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530 case EVR_SQ: // sequence of items |
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531 return new DicomValue; |
0 | 532 |
533 | |
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534 /** |
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535 * Internal to DCMTK. |
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536 **/ |
0 | 537 |
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538 case EVR_xs: // SS or US depending on context |
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539 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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540 case EVR_na: // na="not applicable", for data which has no VR |
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541 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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542 case EVR_item: // used internally for items |
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543 case EVR_metainfo: // used internally for meta info datasets |
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544 case EVR_dataset: // used internally for datasets |
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545 case EVR_fileFormat: // used internally for DICOM files |
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546 case EVR_dicomDir: // used internally for DICOMDIR objects |
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547 case EVR_dirRecord: // used internally for DICOMDIR records |
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548 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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549 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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550 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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551 case EVR_PixelData: // used internally for uncompressed pixeld data |
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552 case EVR_OverlayData: // used internally for overlay data |
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553 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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554 return new DicomValue; |
0 | 555 |
556 | |
302
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557 /** |
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558 * Default case. |
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559 **/ |
0 | 560 |
302
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561 default: |
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562 return new DicomValue; |
0 | 563 } |
564 } | |
565 catch (boost::bad_lexical_cast) | |
566 { | |
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567 return new DicomValue; |
0 | 568 } |
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569 catch (std::bad_cast) |
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570 { |
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571 return new DicomValue; |
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572 } |
0 | 573 } |
574 | |
575 | |
1687 | 576 static Json::Value& PrepareNode(Json::Value& parent, |
577 DcmElement& element, | |
578 DicomToJsonFormat format) | |
0 | 579 { |
1687 | 580 assert(parent.type() == Json::objectValue); |
0 | 581 |
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582 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
305
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583 const std::string formattedTag = tag.Format(); |
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584 |
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585 if (format == DicomToJsonFormat_Short) |
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586 { |
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587 parent[formattedTag] = Json::nullValue; |
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588 return parent[formattedTag]; |
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589 } |
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590 |
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591 // This code gives access to the name of the private tags |
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592 DcmTag tagbis(element.getTag()); |
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593 const std::string tagName(tagbis.getTagName()); |
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594 |
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595 switch (format) |
0 | 596 { |
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597 case DicomToJsonFormat_Simple: |
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598 parent[tagName] = Json::nullValue; |
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599 return parent[tagName]; |
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600 |
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601 case DicomToJsonFormat_Full: |
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602 { |
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603 parent[formattedTag] = Json::objectValue; |
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604 Json::Value& node = parent[formattedTag]; |
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605 |
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606 if (element.isLeaf()) |
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607 { |
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608 node["Name"] = tagName; |
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609 |
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610 if (tagbis.getPrivateCreator() != NULL) |
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611 { |
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612 node["PrivateCreator"] = tagbis.getPrivateCreator(); |
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613 } |
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614 |
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615 return node; |
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616 } |
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617 else |
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618 { |
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619 node["Name"] = tagName; |
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620 node["Type"] = "Sequence"; |
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621 node["Value"] = Json::nullValue; |
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622 return node["Value"]; |
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623 } |
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624 } |
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625 |
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626 default: |
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627 throw OrthancException(ErrorCode_ParameterOutOfRange); |
1687 | 628 } |
629 } | |
630 | |
631 | |
632 static void LeafValueToJson(Json::Value& target, | |
633 const DicomValue& value, | |
634 DicomToJsonFormat format, | |
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635 DicomToJsonFlags flags, |
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636 unsigned int maxStringLength) |
1687 | 637 { |
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638 Json::Value* targetValue = NULL; |
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639 Json::Value* targetType = NULL; |
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640 |
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641 switch (format) |
1687 | 642 { |
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643 case DicomToJsonFormat_Short: |
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644 case DicomToJsonFormat_Simple: |
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645 { |
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646 assert(target.type() == Json::nullValue); |
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647 targetValue = ⌖ |
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648 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
649 } |
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DicomToJsonFormat enumeration
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diff
changeset
|
650 |
27d70e9ee2e4
DicomToJsonFormat enumeration
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parents:
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diff
changeset
|
651 case DicomToJsonFormat_Full: |
0 | 652 { |
1688
27d70e9ee2e4
DicomToJsonFormat enumeration
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diff
changeset
|
653 assert(target.type() == Json::objectValue); |
1738
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DicomToJsonFlags_IncludeBinary
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diff
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|
654 target["Value"] = Json::nullValue; |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
655 target["Type"] = Json::nullValue; |
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DicomToJsonFlags_IncludeBinary
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diff
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|
656 targetType = &target["Type"]; |
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DicomToJsonFlags_IncludeBinary
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diff
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|
657 targetValue = &target["Value"]; |
1688
27d70e9ee2e4
DicomToJsonFormat enumeration
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diff
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|
658 break; |
0 | 659 } |
1688
27d70e9ee2e4
DicomToJsonFormat enumeration
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1687
diff
changeset
|
660 |
27d70e9ee2e4
DicomToJsonFormat enumeration
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diff
changeset
|
661 default: |
27d70e9ee2e4
DicomToJsonFormat enumeration
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parents:
1687
diff
changeset
|
662 throw OrthancException(ErrorCode_ParameterOutOfRange); |
1687 | 663 } |
1738
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
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|
664 |
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
changeset
|
665 assert(targetValue != NULL); |
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
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|
666 assert(targetValue->type() == Json::nullValue); |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
667 assert(targetType == NULL || targetType->type() == Json::nullValue); |
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
changeset
|
668 |
15a788a63846
DicomToJsonFlags_IncludeBinary
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parents:
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diff
changeset
|
669 if (value.IsNull()) |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
670 { |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
671 if (targetType != NULL) |
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DicomToJsonFlags_IncludeBinary
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diff
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|
672 { |
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DicomToJsonFlags_IncludeBinary
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|
673 *targetType = "Null"; |
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DicomToJsonFlags_IncludeBinary
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|
674 } |
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DicomToJsonFlags_IncludeBinary
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parents:
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diff
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|
675 } |
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DicomToJsonFlags_IncludeBinary
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|
676 else if (value.IsBinary()) |
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DicomToJsonFlags_IncludeBinary
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diff
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|
677 { |
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DicomToJsonFlags_IncludeBinary
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|
678 if (flags & DicomToJsonFlags_ConvertBinaryToAscii) |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
679 { |
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DicomToJsonFlags_IncludeBinary
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parents:
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|
680 *targetValue = Toolbox::ConvertToAscii(value.GetContent()); |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
681 } |
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DicomToJsonFlags_IncludeBinary
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parents:
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diff
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|
682 else |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
683 { |
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DicomToJsonFlags_IncludeBinary
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diff
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|
684 std::string s; |
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DicomToJsonFlags_IncludeBinary
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diff
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|
685 value.FormatDataUriScheme(s); |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
686 *targetValue = s; |
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DicomToJsonFlags_IncludeBinary
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diff
changeset
|
687 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
688 |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
689 if (targetType != NULL) |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
690 { |
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DicomToJsonFlags_IncludeBinary
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parents:
1737
diff
changeset
|
691 *targetType = "Binary"; |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
692 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
693 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
changeset
|
694 else if (maxStringLength == 0 || |
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DicomToJsonFlags_IncludeBinary
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parents:
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diff
changeset
|
695 value.GetContent().size() <= maxStringLength) |
15a788a63846
DicomToJsonFlags_IncludeBinary
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diff
changeset
|
696 { |
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DicomToJsonFlags_IncludeBinary
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parents:
1737
diff
changeset
|
697 *targetValue = value.GetContent(); |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
698 |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
699 if (targetType != NULL) |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
700 { |
15a788a63846
DicomToJsonFlags_IncludeBinary
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parents:
1737
diff
changeset
|
701 *targetType = "String"; |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
702 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
703 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
704 else |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
705 { |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
706 if (targetType != NULL) |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
707 { |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
708 *targetType = "TooLong"; |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
709 } |
15a788a63846
DicomToJsonFlags_IncludeBinary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
710 } |
1687 | 711 } |
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
712 |
1687 | 713 |
714 static void DatasetToJson(Json::Value& parent, | |
715 DcmItem& item, | |
716 DicomToJsonFormat format, | |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
717 DicomToJsonFlags flags, |
1687 | 718 unsigned int maxStringLength, |
719 Encoding encoding); | |
720 | |
721 | |
1690 | 722 void FromDcmtkBridge::ToJson(Json::Value& parent, |
723 DcmElement& element, | |
724 DicomToJsonFormat format, | |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
725 DicomToJsonFlags flags, |
1690 | 726 unsigned int maxStringLength, |
727 Encoding encoding) | |
1687 | 728 { |
1691 | 729 if (parent.type() == Json::nullValue) |
730 { | |
731 parent = Json::objectValue; | |
732 } | |
733 | |
734 assert(parent.type() == Json::objectValue); | |
1687 | 735 Json::Value& target = PrepareNode(parent, element, format); |
736 | |
737 if (element.isLeaf()) | |
738 { | |
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
739 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element, flags, encoding)); |
1738
15a788a63846
DicomToJsonFlags_IncludeBinary
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parents:
1737
diff
changeset
|
740 LeafValueToJson(target, *v, format, flags, maxStringLength); |
0 | 741 } |
742 else | |
743 { | |
1688
27d70e9ee2e4
DicomToJsonFormat enumeration
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1687
diff
changeset
|
744 assert(target.type() == Json::nullValue); |
27d70e9ee2e4
DicomToJsonFormat enumeration
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1687
diff
changeset
|
745 target = Json::arrayValue; |
0 | 746 |
747 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
748 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
1687 | 749 // etc. are not." The following dynamic_cast is thus OK. |
0 | 750 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); |
751 | |
752 for (unsigned long i = 0; i < sequence.card(); i++) | |
753 { | |
754 DcmItem* child = sequence.getItem(i); | |
1687 | 755 Json::Value& v = target.append(Json::objectValue); |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
756 DatasetToJson(v, *child, format, flags, maxStringLength, encoding); |
1687 | 757 } |
0 | 758 } |
759 } | |
760 | |
761 | |
1687 | 762 static void DatasetToJson(Json::Value& parent, |
1686 | 763 DcmItem& item, |
764 DicomToJsonFormat format, | |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
765 DicomToJsonFlags flags, |
1686 | 766 unsigned int maxStringLength, |
767 Encoding encoding) | |
768 { | |
1688
27d70e9ee2e4
DicomToJsonFormat enumeration
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1687
diff
changeset
|
769 assert(parent.type() == Json::objectValue); |
1686 | 770 |
771 for (unsigned long i = 0; i < item.card(); i++) | |
772 { | |
773 DcmElement* element = item.getElement(i); | |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
774 if (element == NULL) |
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
775 { |
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
776 throw OrthancException(ErrorCode_InternalError); |
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
777 } |
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
778 |
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
779 if (!(flags & DicomToJsonFlags_IncludePrivateTags) && |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
780 element->getTag().isPrivate()) |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
781 { |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
782 continue; |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
783 } |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
784 |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
785 if (!(flags & DicomToJsonFlags_IncludeUnknownTags)) |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
786 { |
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
787 DictionaryLocker locker; |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
788 if (locker->findEntry(element->getTag(), NULL) == NULL) |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
789 { |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
790 continue; |
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
791 } |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1695
diff
changeset
|
792 } |
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
793 |
1739
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
794 DcmEVR evr = element->getTag().getEVR(); |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
795 if (evr == EVR_OB || |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
796 evr == EVR_OF || |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
797 evr == EVR_OW || |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
798 evr == EVR_UN || |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
799 evr == EVR_ox) |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
800 { |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
801 // This is a binary tag |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
802 DicomTag tag(FromDcmtkBridge::Convert(element->getTag())); |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
803 |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
804 if ((tag == DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludePixelData)) || |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
805 (tag != DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludeBinary))) |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
806 { |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
807 continue; |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
808 } |
df331354cea2
include binary in ToJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1738
diff
changeset
|
809 } |
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810 |
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811 FromDcmtkBridge::ToJson(parent, *element, format, flags, maxStringLength, encoding); |
1686 | 812 } |
813 } | |
814 | |
815 | |
1687 | 816 void FromDcmtkBridge::ToJson(Json::Value& target, |
0 | 817 DcmDataset& dataset, |
1686 | 818 DicomToJsonFormat format, |
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819 DicomToJsonFlags flags, |
0 | 820 unsigned int maxStringLength) |
821 { | |
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822 target = Json::objectValue; |
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823 DatasetToJson(target, dataset, format, flags, maxStringLength, DetectEncoding(dataset)); |
0 | 824 } |
825 | |
826 | |
827 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
828 { | |
106 | 829 // Some patches for important tags because of different DICOM |
830 // dictionaries between DCMTK versions | |
291
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831 std::string n = t.GetMainTagsName(); |
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832 if (n.size() != 0) |
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833 { |
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834 return n; |
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835 } |
106 | 836 // End of patches |
837 | |
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838 #if 0 |
0 | 839 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
840 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
841 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
842 | |
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843 std::string s(DcmTag_ERROR_TagName); |
0 | 844 if (entry != NULL) |
845 { | |
846 s = std::string(entry->getTagName()); | |
847 } | |
848 | |
849 dcmDataDict.unlock(); | |
850 return s; | |
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851 #else |
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852 DcmTag tag(t.GetGroup(), t.GetElement()); |
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853 const char* name = tag.getTagName(); |
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854 if (name == NULL) |
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855 { |
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856 return DcmTag_ERROR_TagName; |
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857 } |
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858 else |
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859 { |
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860 return std::string(name); |
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861 } |
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862 #endif |
0 | 863 } |
864 | |
865 | |
304 | 866 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
0 | 867 { |
304 | 868 if (strlen(name) == 9 && |
869 isxdigit(name[0]) && | |
870 isxdigit(name[1]) && | |
871 isxdigit(name[2]) && | |
872 isxdigit(name[3]) && | |
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873 (name[4] == '-' || name[4] == ',') && |
304 | 874 isxdigit(name[5]) && |
875 isxdigit(name[6]) && | |
876 isxdigit(name[7]) && | |
877 isxdigit(name[8])) | |
878 { | |
879 uint16_t group = GetTagValue(name); | |
880 uint16_t element = GetTagValue(name + 5); | |
881 return DicomTag(group, element); | |
882 } | |
883 | |
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884 #if 0 |
0 | 885 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
886 const DcmDictEntry* entry = dict.findEntry(name); | |
887 | |
888 if (entry == NULL) | |
889 { | |
890 dcmDataDict.unlock(); | |
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891 throw OrthancException(ErrorCode_UnknownDicomTag); |
0 | 892 } |
893 else | |
894 { | |
895 DcmTagKey key = entry->getKey(); | |
896 DicomTag tag(key.getGroup(), key.getElement()); | |
897 dcmDataDict.unlock(); | |
898 return tag; | |
899 } | |
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900 #else |
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901 DcmTag tag; |
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902 if (DcmTag::findTagFromName(name, tag).good()) |
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903 { |
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904 return DicomTag(tag.getGTag(), tag.getETag()); |
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905 } |
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906 else |
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907 { |
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908 throw OrthancException(ErrorCode_UnknownDicomTag); |
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909 } |
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910 #endif |
0 | 911 } |
912 | |
913 | |
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914 bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag) |
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915 { |
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916 DcmTag tmp(tag.GetGroup(), tag.GetElement()); |
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917 return tmp.isUnknownVR(); |
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918 } |
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919 |
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920 |
0 | 921 void FromDcmtkBridge::ToJson(Json::Value& result, |
1368 | 922 const DicomMap& values, |
923 bool simplify) | |
0 | 924 { |
925 if (result.type() != Json::objectValue) | |
926 { | |
62 | 927 throw OrthancException(ErrorCode_BadParameterType); |
0 | 928 } |
929 | |
930 result.clear(); | |
931 | |
932 for (DicomMap::Map::const_iterator | |
656 | 933 it = values.map_.begin(); it != values.map_.end(); ++it) |
0 | 934 { |
1368 | 935 if (simplify) |
936 { | |
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937 if (it->second->IsNull()) |
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938 { |
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939 result[GetName(it->first)] = Json::nullValue; |
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940 } |
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941 else |
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942 { |
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943 // TODO IsBinary |
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944 result[GetName(it->first)] = it->second->GetContent(); |
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945 } |
1368 | 946 } |
947 else | |
948 { | |
949 Json::Value value = Json::objectValue; | |
950 | |
951 value["Name"] = GetName(it->first); | |
952 | |
953 if (it->second->IsNull()) | |
954 { | |
955 value["Type"] = "Null"; | |
956 value["Value"] = Json::nullValue; | |
957 } | |
958 else | |
959 { | |
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960 // TODO IsBinary |
1368 | 961 value["Type"] = "String"; |
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962 value["Value"] = it->second->GetContent(); |
1368 | 963 } |
964 | |
965 result[it->first.Format()] = value; | |
966 } | |
0 | 967 } |
968 } | |
176 | 969 |
970 | |
788 | 971 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
176 | 972 { |
973 char uid[100]; | |
974 | |
975 switch (level) | |
976 { | |
788 | 977 case ResourceType_Patient: |
311 | 978 // The "PatientID" field is of type LO (Long String), 64 |
979 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
980 // as a random PatientID. | |
981 return Toolbox::GenerateUuid(); | |
306
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982 |
788 | 983 case ResourceType_Instance: |
302
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984 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 985 |
788 | 986 case ResourceType_Series: |
302
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987 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 988 |
788 | 989 case ResourceType_Study: |
302
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990 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 991 |
302
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992 default: |
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993 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 994 } |
995 } | |
996 | |
291
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997 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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998 DcmDataset& dataSet) |
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999 { |
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1000 // Determine the transfer syntax which shall be used to write the |
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1001 // information to the file. We always switch to the Little Endian |
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1002 // syntax, with explicit length. |
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1003 |
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1004 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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1005 |
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1006 |
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1007 /** |
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1008 * Note that up to Orthanc 0.7.1 (inclusive), the |
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1009 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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1010 * dataset into memory. We now keep the original transfer syntax |
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1011 * (if available). |
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1012 **/ |
1004
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1013 E_TransferSyntax xfer = dataSet.getOriginalXfer(); |
661
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1014 if (xfer == EXS_Unknown) |
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1015 { |
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1016 // No information about the original transfer syntax: This is |
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1017 // most probably a DICOM dataset that was read from memory. |
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1018 xfer = EXS_LittleEndianExplicit; |
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1019 } |
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1020 |
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1021 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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1022 |
661
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1023 // Create the meta-header information |
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1024 DcmFileFormat ff(&dataSet); |
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1025 ff.validateMetaInfo(xfer); |
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1026 ff.removeInvalidGroups(); |
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1027 |
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1028 // Create a memory buffer with the proper size |
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1029 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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1030 buffer.resize(s); |
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1031 DcmOutputBufferStream ob(&buffer[0], s); |
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1032 |
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1033 // Fill the memory buffer with the meta-header and the dataset |
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1034 ff.transferInit(); |
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1035 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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1036 /*opt_groupLength*/ EGL_recalcGL, |
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1037 /*opt_paddingType*/ EPD_withoutPadding); |
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1038 ff.transferEnd(); |
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1039 |
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1040 // Handle errors |
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1041 if (c.good()) |
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1042 { |
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1043 return true; |
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1044 } |
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1045 else |
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1046 { |
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1047 buffer.clear(); |
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1048 return false; |
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1049 } |
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1050 } |
1360 | 1051 |
1052 | |
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1053 ValueRepresentation FromDcmtkBridge::GetValueRepresentation(const DicomTag& tag) |
1360 | 1054 { |
1055 DcmTag t(tag.GetGroup(), tag.GetElement()); | |
1417
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1056 switch (t.getEVR()) |
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1057 { |
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1058 case EVR_PN: |
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1059 return ValueRepresentation_PatientName; |
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1060 |
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1061 case EVR_DA: |
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1062 return ValueRepresentation_Date; |
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1063 |
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1064 case EVR_DT: |
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1065 return ValueRepresentation_DateTime; |
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1066 |
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1067 case EVR_TM: |
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1068 return ValueRepresentation_Time; |
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1069 |
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1070 default: |
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1071 return ValueRepresentation_Other; |
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1072 } |
1360 | 1073 } |
1074 | |
1689 | 1075 |
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1076 static bool IsBinaryTag(const DcmTag& key) |
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1077 { |
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1078 return (key.isPrivate() || |
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1079 key.isUnknownVR() || |
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1080 key.getEVR() == EVR_OB || |
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1081 key.getEVR() == EVR_OF || |
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1082 key.getEVR() == EVR_OW || |
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1083 key.getEVR() == EVR_UN || |
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1084 key.getEVR() == EVR_ox); |
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1085 } |
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1086 |
1689 | 1087 |
1088 DcmElement* FromDcmtkBridge::CreateElementForTag(const DicomTag& tag) | |
1089 { | |
1090 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
1091 | |
1693
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1092 if (IsBinaryTag(key)) |
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1093 { |
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1094 return new DcmOtherByteOtherWord(key); |
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1095 } |
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1096 |
1689 | 1097 switch (key.getEVR()) |
1098 { | |
1099 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
1100 | |
1101 /** | |
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1102 * Binary types, handled above |
1689 | 1103 **/ |
1104 | |
1105 case EVR_OB: // other byte | |
1106 case EVR_OF: // other float | |
1107 case EVR_OW: // other word | |
1108 case EVR_UN: // unknown value representation | |
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1109 case EVR_ox: // OB or OW depending on context |
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1110 throw OrthancException(ErrorCode_InternalError); |
1689 | 1111 |
1112 | |
1113 /** | |
1114 * String types. | |
1115 * http://support.dcmtk.org/docs/classDcmByteString.html | |
1116 **/ | |
1117 | |
1118 case EVR_AS: // age string | |
1119 return new DcmAgeString(key); | |
1120 | |
1121 case EVR_AE: // application entity title | |
1122 return new DcmApplicationEntity(key); | |
1123 | |
1124 case EVR_CS: // code string | |
1125 return new DcmCodeString(key); | |
1126 | |
1127 case EVR_DA: // date string | |
1128 return new DcmDate(key); | |
1129 | |
1130 case EVR_DT: // date time string | |
1131 return new DcmDateTime(key); | |
1132 | |
1133 case EVR_DS: // decimal string | |
1134 return new DcmDecimalString(key); | |
1135 | |
1136 case EVR_IS: // integer string | |
1137 return new DcmIntegerString(key); | |
1138 | |
1139 case EVR_TM: // time string | |
1140 return new DcmTime(key); | |
1141 | |
1142 case EVR_UI: // unique identifier | |
1143 return new DcmUniqueIdentifier(key); | |
1144 | |
1145 case EVR_ST: // short text | |
1146 return new DcmShortText(key); | |
1147 | |
1148 case EVR_LO: // long string | |
1149 return new DcmLongString(key); | |
1150 | |
1151 case EVR_LT: // long text | |
1152 return new DcmLongText(key); | |
1153 | |
1154 case EVR_UT: // unlimited text | |
1155 return new DcmUnlimitedText(key); | |
1156 | |
1157 case EVR_SH: // short string | |
1158 return new DcmShortString(key); | |
1159 | |
1160 case EVR_PN: // person name | |
1161 return new DcmPersonName(key); | |
1162 | |
1163 | |
1164 /** | |
1165 * Numerical types | |
1166 **/ | |
1167 | |
1168 case EVR_SL: // signed long | |
1169 return new DcmSignedLong(key); | |
1170 | |
1171 case EVR_SS: // signed short | |
1172 return new DcmSignedShort(key); | |
1173 | |
1174 case EVR_UL: // unsigned long | |
1175 return new DcmUnsignedLong(key); | |
1176 | |
1177 case EVR_US: // unsigned short | |
1178 return new DcmUnsignedShort(key); | |
1179 | |
1180 case EVR_FL: // float single-precision | |
1181 return new DcmFloatingPointSingle(key); | |
1182 | |
1183 case EVR_FD: // float double-precision | |
1184 return new DcmFloatingPointDouble(key); | |
1185 | |
1186 | |
1187 /** | |
1188 * Sequence types, should never occur at this point. | |
1189 **/ | |
1190 | |
1191 case EVR_SQ: // sequence of items | |
1192 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
1193 | |
1194 | |
1195 /** | |
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1196 * TODO |
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1197 **/ |
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1198 |
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1199 case EVR_AT: // attribute tag |
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1200 throw OrthancException(ErrorCode_NotImplemented); |
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1201 |
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1202 |
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1203 /** |
1689 | 1204 * Internal to DCMTK. |
1205 **/ | |
1206 | |
1207 case EVR_xs: // SS or US depending on context | |
1208 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
1209 case EVR_na: // na="not applicable", for data which has no VR | |
1210 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
1211 case EVR_item: // used internally for items | |
1212 case EVR_metainfo: // used internally for meta info datasets | |
1213 case EVR_dataset: // used internally for datasets | |
1214 case EVR_fileFormat: // used internally for DICOM files | |
1215 case EVR_dicomDir: // used internally for DICOMDIR objects | |
1216 case EVR_dirRecord: // used internally for DICOMDIR records | |
1217 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
1218 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
1219 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
1220 case EVR_PixelData: // used internally for uncompressed pixeld data | |
1221 case EVR_OverlayData: // used internally for overlay data | |
1222 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
1223 default: | |
1224 break; | |
1225 } | |
1226 | |
1227 throw OrthancException(ErrorCode_InternalError); | |
1228 } | |
1229 | |
1230 | |
1231 | |
1232 void FromDcmtkBridge::FillElementWithString(DcmElement& element, | |
1233 const DicomTag& tag, | |
1695 | 1234 const std::string& utf8Value, |
1235 bool decodeBinaryTags, | |
1236 Encoding dicomEncoding) | |
1689 | 1237 { |
1238 std::string binary; | |
1695 | 1239 const std::string* decoded = &utf8Value; |
1689 | 1240 |
1241 if (decodeBinaryTags && | |
1695 | 1242 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
1689 | 1243 { |
1244 std::string mime; | |
1695 | 1245 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
1246 decoded = &binary; | |
1247 } | |
1248 else if (dicomEncoding != Encoding_Utf8) | |
1249 { | |
1250 binary = Toolbox::ConvertFromUtf8(utf8Value, dicomEncoding); | |
1689 | 1251 decoded = &binary; |
1252 } | |
1253 | |
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1254 DcmTag key(tag.GetGroup(), tag.GetElement()); |
1689 | 1255 |
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1256 if (IsBinaryTag(key)) |
1689 | 1257 { |
1258 if (element.putUint8Array((const Uint8*) decoded->c_str(), decoded->size()).good()) | |
1259 { | |
1260 return; | |
1261 } | |
1262 else | |
1263 { | |
1264 throw OrthancException(ErrorCode_InternalError); | |
1265 } | |
1266 } | |
1267 | |
1268 bool ok = false; | |
1269 | |
1270 try | |
1271 { | |
1272 switch (key.getEVR()) | |
1273 { | |
1274 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
1275 | |
1276 /** | |
1277 * TODO. | |
1278 **/ | |
1279 | |
1280 case EVR_OB: // other byte | |
1281 case EVR_OF: // other float | |
1282 case EVR_OW: // other word | |
1283 case EVR_AT: // attribute tag | |
1284 throw OrthancException(ErrorCode_NotImplemented); | |
1285 | |
1286 case EVR_UN: // unknown value representation | |
1287 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
1288 | |
1289 | |
1290 /** | |
1291 * String types. | |
1292 **/ | |
1293 | |
1294 case EVR_DS: // decimal string | |
1295 case EVR_IS: // integer string | |
1296 case EVR_AS: // age string | |
1297 case EVR_DA: // date string | |
1298 case EVR_DT: // date time string | |
1299 case EVR_TM: // time string | |
1300 case EVR_AE: // application entity title | |
1301 case EVR_CS: // code string | |
1302 case EVR_SH: // short string | |
1303 case EVR_LO: // long string | |
1304 case EVR_ST: // short text | |
1305 case EVR_LT: // long text | |
1306 case EVR_UT: // unlimited text | |
1307 case EVR_PN: // person name | |
1308 case EVR_UI: // unique identifier | |
1309 { | |
1310 ok = element.putString(decoded->c_str()).good(); | |
1311 break; | |
1312 } | |
1313 | |
1314 | |
1315 /** | |
1316 * Numerical types | |
1317 **/ | |
1318 | |
1319 case EVR_SL: // signed long | |
1320 { | |
1321 ok = element.putSint32(boost::lexical_cast<Sint32>(*decoded)).good(); | |
1322 break; | |
1323 } | |
1324 | |
1325 case EVR_SS: // signed short | |
1326 { | |
1327 ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good(); | |
1328 break; | |
1329 } | |
1330 | |
1331 case EVR_UL: // unsigned long | |
1332 { | |
1333 ok = element.putUint32(boost::lexical_cast<Uint32>(*decoded)).good(); | |
1334 break; | |
1335 } | |
1336 | |
1337 case EVR_US: // unsigned short | |
1338 { | |
1339 ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good(); | |
1340 break; | |
1341 } | |
1342 | |
1343 case EVR_FL: // float single-precision | |
1344 { | |
1345 ok = element.putFloat32(boost::lexical_cast<float>(*decoded)).good(); | |
1346 break; | |
1347 } | |
1348 | |
1349 case EVR_FD: // float double-precision | |
1350 { | |
1351 ok = element.putFloat64(boost::lexical_cast<double>(*decoded)).good(); | |
1352 break; | |
1353 } | |
1354 | |
1355 | |
1356 /** | |
1357 * Sequence types, should never occur at this point. | |
1358 **/ | |
1359 | |
1360 case EVR_SQ: // sequence of items | |
1361 { | |
1362 ok = false; | |
1363 break; | |
1364 } | |
1365 | |
1366 | |
1367 /** | |
1368 * Internal to DCMTK. | |
1369 **/ | |
1370 | |
1371 case EVR_ox: // OB or OW depending on context | |
1372 case EVR_xs: // SS or US depending on context | |
1373 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
1374 case EVR_na: // na="not applicable", for data which has no VR | |
1375 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
1376 case EVR_item: // used internally for items | |
1377 case EVR_metainfo: // used internally for meta info datasets | |
1378 case EVR_dataset: // used internally for datasets | |
1379 case EVR_fileFormat: // used internally for DICOM files | |
1380 case EVR_dicomDir: // used internally for DICOMDIR objects | |
1381 case EVR_dirRecord: // used internally for DICOMDIR records | |
1382 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
1383 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
1384 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
1385 case EVR_PixelData: // used internally for uncompressed pixeld data | |
1386 case EVR_OverlayData: // used internally for overlay data | |
1387 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
1388 default: | |
1389 break; | |
1390 } | |
1391 } | |
1392 catch (boost::bad_lexical_cast&) | |
1393 { | |
1394 ok = false; | |
1395 } | |
1396 | |
1397 if (!ok) | |
1398 { | |
1399 throw OrthancException(ErrorCode_InternalError); | |
1400 } | |
1401 } | |
1402 | |
1403 | |
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1691
diff
changeset
|
1404 DcmElement* FromDcmtkBridge::FromJson(const DicomTag& tag, |
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1691
diff
changeset
|
1405 const Json::Value& value, |
1695 | 1406 bool decodeBinaryTags, |
1407 Encoding dicomEncoding) | |
1689 | 1408 { |
1409 std::auto_ptr<DcmElement> element; | |
1410 | |
1690 | 1411 switch (value.type()) |
1689 | 1412 { |
1690 | 1413 case Json::stringValue: |
1414 element.reset(CreateElementForTag(tag)); | |
1695 | 1415 FillElementWithString(*element, tag, value.asString(), decodeBinaryTags, dicomEncoding); |
1690 | 1416 break; |
1417 | |
1418 case Json::arrayValue: | |
1419 { | |
1420 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
1421 if (key.getEVR() != EVR_SQ) | |
1422 { | |
1423 throw OrthancException(ErrorCode_BadParameterType); | |
1424 } | |
1425 | |
1426 DcmSequenceOfItems* sequence = new DcmSequenceOfItems(key, value.size()); | |
1427 element.reset(sequence); | |
1428 | |
1429 for (Json::Value::ArrayIndex i = 0; i < value.size(); i++) | |
1430 { | |
1431 std::auto_ptr<DcmItem> item(new DcmItem); | |
1432 | |
1433 Json::Value::Members members = value[i].getMemberNames(); | |
1434 for (Json::Value::ArrayIndex j = 0; j < members.size(); j++) | |
1435 { | |
1695 | 1436 item->insert(FromJson(ParseTag(members[j]), value[i][members[j]], decodeBinaryTags, dicomEncoding)); |
1690 | 1437 } |
1438 | |
1439 sequence->append(item.release()); | |
1440 } | |
1441 | |
1442 break; | |
1443 } | |
1444 | |
1445 default: | |
1446 throw OrthancException(ErrorCode_BadParameterType); | |
1689 | 1447 } |
1448 | |
1449 return element.release(); | |
1450 } | |
0 | 1451 } |