Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 846:715ab7674993 jpeg
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 05 Jun 2014 16:23:03 +0200 |
parents | 84513f2ee1f3 |
children | 839be3022203 |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
0 | 4 * Belgium |
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 "../Core/Toolbox.h" |
62 | 45 #include "../Core/OrthancException.h" |
799 | 46 #include "../Core/ImageFormats/PngWriter.h" |
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47 #include "../Core/Uuid.h" |
0 | 48 #include "../Core/DicomFormat/DicomString.h" |
49 #include "../Core/DicomFormat/DicomNullValue.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> |
56 | |
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57 #include <dcmtk/dcmdata/dcchrstr.h> |
0 | 58 #include <dcmtk/dcmdata/dcdicent.h> |
59 #include <dcmtk/dcmdata/dcdict.h> | |
60 #include <dcmtk/dcmdata/dcfilefo.h> | |
61 #include <dcmtk/dcmdata/dcistrmb.h> | |
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62 #include <dcmtk/dcmdata/dcuid.h> |
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63 #include <dcmtk/dcmdata/dcmetinf.h> |
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64 |
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65 #include <dcmtk/dcmdata/dcvrae.h> |
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66 #include <dcmtk/dcmdata/dcvras.h> |
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67 #include <dcmtk/dcmdata/dcvrcs.h> |
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68 #include <dcmtk/dcmdata/dcvrda.h> |
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69 #include <dcmtk/dcmdata/dcvrds.h> |
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70 #include <dcmtk/dcmdata/dcvrdt.h> |
0 | 71 #include <dcmtk/dcmdata/dcvrfd.h> |
72 #include <dcmtk/dcmdata/dcvrfl.h> | |
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73 #include <dcmtk/dcmdata/dcvris.h> |
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74 #include <dcmtk/dcmdata/dcvrlo.h> |
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75 #include <dcmtk/dcmdata/dcvrlt.h> |
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76 #include <dcmtk/dcmdata/dcvrpn.h> |
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77 #include <dcmtk/dcmdata/dcvrsh.h> |
0 | 78 #include <dcmtk/dcmdata/dcvrsl.h> |
79 #include <dcmtk/dcmdata/dcvrss.h> | |
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80 #include <dcmtk/dcmdata/dcvrst.h> |
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81 #include <dcmtk/dcmdata/dcvrtm.h> |
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82 #include <dcmtk/dcmdata/dcvrui.h> |
0 | 83 #include <dcmtk/dcmdata/dcvrul.h> |
84 #include <dcmtk/dcmdata/dcvrus.h> | |
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85 #include <dcmtk/dcmdata/dcvrut.h> |
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86 #include <dcmtk/dcmdata/dcpixel.h> |
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87 #include <dcmtk/dcmdata/dcpixseq.h> |
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88 #include <dcmtk/dcmdata/dcpxitem.h> |
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89 |
0 | 90 |
2 | 91 #include <boost/math/special_functions/round.hpp> |
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92 #include <glog/logging.h> |
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93 #include <dcmtk/dcmdata/dcostrmb.h> |
0 | 94 |
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95 |
62 | 96 namespace Orthanc |
0 | 97 { |
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98 static inline uint16_t GetCharValue(char c) |
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99 { |
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100 if (c >= '0' && c <= '9') |
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101 return c - '0'; |
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102 else if (c >= 'a' && c <= 'f') |
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103 return c - 'a' + 10; |
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104 else if (c >= 'A' && c <= 'F') |
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105 return c - 'A' + 10; |
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106 else |
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107 return 0; |
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108 } |
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109 |
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110 static inline uint16_t GetTagValue(const char* c) |
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111 { |
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112 return ((GetCharValue(c[0]) << 12) + |
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113 (GetCharValue(c[1]) << 8) + |
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114 (GetCharValue(c[2]) << 4) + |
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115 GetCharValue(c[3])); |
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116 } |
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117 |
0 | 118 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
119 { | |
120 target.Clear(); | |
121 for (unsigned long i = 0; i < dataset.card(); i++) | |
122 { | |
123 DcmElement* element = dataset.getElement(i); | |
124 if (element && element->isLeaf()) | |
125 { | |
126 target.SetValue(element->getTag().getGTag(), | |
127 element->getTag().getETag(), | |
128 ConvertLeafElement(*element)); | |
129 } | |
130 } | |
131 } | |
132 | |
133 | |
134 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
135 { | |
136 return DicomTag(element.getGTag(), element.getETag()); | |
137 } | |
138 | |
139 | |
140 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
141 { | |
142 if (!element.isLeaf()) | |
143 { | |
62 | 144 throw OrthancException("Only applicable to leaf elements"); |
0 | 145 } |
146 | |
147 if (element.isaString()) | |
148 { | |
149 char *c; | |
150 if (element.getString(c).good() && | |
151 c != NULL) | |
152 { | |
153 std::string s(c); | |
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154 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 155 return new DicomString(utf8); |
156 } | |
157 else | |
158 { | |
159 return new DicomNullValue; | |
160 } | |
161 } | |
162 | |
163 try | |
164 { | |
165 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
166 switch (element.getVR()) | |
167 { | |
168 | |
169 /** | |
170 * TODO. | |
171 **/ | |
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172 |
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173 case EVR_OB: // other byte |
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174 case EVR_OF: // other float |
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175 case EVR_OW: // other word |
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176 case EVR_AT: // attribute tag |
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177 case EVR_UN: // unknown value representation |
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178 return new DicomNullValue(); |
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179 |
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180 /** |
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181 * String types, should never happen at this point because of |
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182 * "element.isaString()". |
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183 **/ |
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184 |
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185 case EVR_DS: // decimal string |
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186 case EVR_IS: // integer string |
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187 case EVR_AS: // age string |
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188 case EVR_DA: // date string |
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189 case EVR_DT: // date time string |
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190 case EVR_TM: // time string |
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191 case EVR_AE: // application entity title |
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192 case EVR_CS: // code string |
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193 case EVR_SH: // short string |
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194 case EVR_LO: // long string |
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195 case EVR_ST: // short text |
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196 case EVR_LT: // long text |
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197 case EVR_UT: // unlimited text |
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198 case EVR_PN: // person name |
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199 case EVR_UI: // unique identifier |
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200 return new DicomNullValue(); |
0 | 201 |
202 | |
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203 /** |
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204 * Numerical types |
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205 **/ |
0 | 206 |
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207 case EVR_SL: // signed long |
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208 { |
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209 Sint32 f; |
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210 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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211 return new DicomString(boost::lexical_cast<std::string>(f)); |
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212 else |
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213 return new DicomNullValue(); |
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214 } |
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215 |
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216 case EVR_SS: // signed short |
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217 { |
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218 Sint16 f; |
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219 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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220 return new DicomString(boost::lexical_cast<std::string>(f)); |
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221 else |
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222 return new DicomNullValue(); |
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223 } |
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224 |
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225 case EVR_UL: // unsigned long |
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226 { |
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227 Uint32 f; |
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228 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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229 return new DicomString(boost::lexical_cast<std::string>(f)); |
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230 else |
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231 return new DicomNullValue(); |
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232 } |
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233 |
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234 case EVR_US: // unsigned short |
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235 { |
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236 Uint16 f; |
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237 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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238 return new DicomString(boost::lexical_cast<std::string>(f)); |
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239 else |
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240 return new DicomNullValue(); |
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241 } |
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242 |
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243 case EVR_FL: // float single-precision |
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244 { |
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245 Float32 f; |
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246 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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247 return new DicomString(boost::lexical_cast<std::string>(f)); |
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248 else |
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249 return new DicomNullValue(); |
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250 } |
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251 |
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252 case EVR_FD: // float double-precision |
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253 { |
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254 Float64 f; |
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255 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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256 return new DicomString(boost::lexical_cast<std::string>(f)); |
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257 else |
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258 return new DicomNullValue(); |
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259 } |
0 | 260 |
261 | |
262 /** | |
302
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263 * Sequence types, should never occur at this point because of |
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264 * "element.isLeaf()". |
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265 **/ |
0 | 266 |
302
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267 case EVR_SQ: // sequence of items |
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268 return new DicomNullValue; |
0 | 269 |
270 | |
302
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271 /** |
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272 * Internal to DCMTK. |
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273 **/ |
0 | 274 |
302
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275 case EVR_ox: // OB or OW depending on context |
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276 case EVR_xs: // SS or US depending on context |
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277 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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278 case EVR_na: // na="not applicable", for data which has no VR |
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279 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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280 case EVR_item: // used internally for items |
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281 case EVR_metainfo: // used internally for meta info datasets |
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282 case EVR_dataset: // used internally for datasets |
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283 case EVR_fileFormat: // used internally for DICOM files |
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284 case EVR_dicomDir: // used internally for DICOMDIR objects |
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285 case EVR_dirRecord: // used internally for DICOMDIR records |
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286 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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287 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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288 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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289 case EVR_PixelData: // used internally for uncompressed pixeld data |
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290 case EVR_OverlayData: // used internally for overlay data |
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291 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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292 return new DicomNullValue; |
0 | 293 |
294 | |
302
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295 /** |
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296 * Default case. |
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297 **/ |
0 | 298 |
302
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299 default: |
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300 return new DicomNullValue; |
0 | 301 } |
302 } | |
303 catch (boost::bad_lexical_cast) | |
304 { | |
305 return new DicomNullValue; | |
306 } | |
306
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307 catch (std::bad_cast) |
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308 { |
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309 return new DicomNullValue; |
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310 } |
0 | 311 } |
312 | |
313 | |
314 static void StoreElement(Json::Value& target, | |
315 DcmElement& element, | |
316 unsigned int maxStringLength); | |
317 | |
318 static void StoreItem(Json::Value& target, | |
319 DcmItem& item, | |
320 unsigned int maxStringLength) | |
321 { | |
322 target = Json::Value(Json::objectValue); | |
323 | |
324 for (unsigned long i = 0; i < item.card(); i++) | |
325 { | |
326 DcmElement* element = item.getElement(i); | |
327 StoreElement(target, *element, maxStringLength); | |
328 } | |
329 } | |
330 | |
331 | |
332 static void StoreElement(Json::Value& target, | |
333 DcmElement& element, | |
334 unsigned int maxStringLength) | |
335 { | |
336 assert(target.type() == Json::objectValue); | |
337 | |
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338 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
305
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339 const std::string formattedTag = tag.Format(); |
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340 |
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341 #if 0 |
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342 const std::string tagName = FromDcmtkBridge::GetName(tag); |
305
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343 #else |
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344 // This version of the code gives access to the name of the private tags |
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345 DcmTag tagbis(element.getTag()); |
306
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346 const std::string tagName(tagbis.getTagName()); |
305
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347 #endif |
0 | 348 |
349 if (element.isLeaf()) | |
350 { | |
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351 Json::Value value(Json::objectValue); |
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352 value["Name"] = tagName; |
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353 |
306
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354 if (tagbis.getPrivateCreator() != NULL) |
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355 { |
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356 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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357 } |
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358 |
0 | 359 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
360 if (v->IsNull()) | |
361 { | |
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362 value["Type"] = "Null"; |
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363 value["Value"] = Json::nullValue; |
0 | 364 } |
365 else | |
366 { | |
367 std::string s = v->AsString(); | |
368 if (maxStringLength == 0 || | |
369 s.size() <= maxStringLength) | |
370 { | |
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371 value["Type"] = "String"; |
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372 value["Value"] = s; |
0 | 373 } |
374 else | |
375 { | |
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376 value["Type"] = "TooLong"; |
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377 value["Value"] = Json::nullValue; |
0 | 378 } |
379 } | |
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380 |
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381 target[formattedTag] = value; |
0 | 382 } |
383 else | |
384 { | |
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385 Json::Value children(Json::arrayValue); |
0 | 386 |
387 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
388 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
389 // etc. are not." The following cast is thus OK. | |
390 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
391 | |
392 for (unsigned long i = 0; i < sequence.card(); i++) | |
393 { | |
394 DcmItem* child = sequence.getItem(i); | |
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395 Json::Value& v = children.append(Json::objectValue); |
0 | 396 StoreItem(v, *child, maxStringLength); |
397 } | |
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398 |
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399 target[formattedTag]["Name"] = tagName; |
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400 target[formattedTag]["Type"] = "Sequence"; |
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401 target[formattedTag]["Value"] = children; |
0 | 402 } |
403 } | |
404 | |
405 | |
406 void FromDcmtkBridge::ToJson(Json::Value& root, | |
407 DcmDataset& dataset, | |
408 unsigned int maxStringLength) | |
409 { | |
410 StoreItem(root, dataset, maxStringLength); | |
411 } | |
412 | |
413 | |
414 | |
415 void FromDcmtkBridge::ToJson(Json::Value& target, | |
416 const std::string& path, | |
417 unsigned int maxStringLength) | |
418 { | |
419 DcmFileFormat dicom; | |
420 if (!dicom.loadFile(path.c_str()).good()) | |
421 { | |
62 | 422 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 423 } |
424 else | |
425 { | |
426 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
427 } | |
428 } | |
429 | |
430 | |
368
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431 static void ExtractPngImageColorPreview(std::string& result, |
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432 DicomIntegerPixelAccessor& accessor) |
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433 { |
368
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434 assert(accessor.GetChannelCount() == 3); |
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435 PngWriter w; |
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436 |
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437 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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438 uint8_t* pixel = &image[0]; |
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439 |
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440 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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441 { |
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442 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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443 { |
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444 for (unsigned int c = 0; c < 3; c++, pixel++) |
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445 { |
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446 int32_t v = accessor.GetValue(x, y, c); |
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447 if (v < 0) |
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448 *pixel = 0; |
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449 else if (v > 255) |
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450 *pixel = 255; |
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451 else |
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452 *pixel = v; |
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453 } |
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454 } |
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455 } |
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456 |
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457 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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458 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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459 } |
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460 |
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461 |
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462 static void ExtractPngImageGrayscalePreview(std::string& result, |
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463 DicomIntegerPixelAccessor& accessor) |
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464 { |
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465 assert(accessor.GetChannelCount() == 1); |
42
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466 PngWriter w; |
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467 |
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468 int32_t min, max; |
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469 accessor.GetExtremeValues(min, max); |
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470 |
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471 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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472 if (min != max) |
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473 { |
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474 uint8_t* pixel = &image[0]; |
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475 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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476 { |
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477 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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478 { |
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479 int32_t v = accessor.GetValue(x, y); |
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480 *pixel = static_cast<uint8_t>( |
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481 boost::math::lround(static_cast<float>(v - min) / |
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482 static_cast<float>(max - min) * 255.0f)); |
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483 } |
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484 } |
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485 } |
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486 |
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487 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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488 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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489 } |
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490 |
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491 |
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492 template <typename T> |
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493 static void ExtractPngImageTruncate(std::string& result, |
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494 DicomIntegerPixelAccessor& accessor, |
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495 PixelFormat format) |
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496 { |
368
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497 assert(accessor.GetChannelCount() == 1); |
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498 |
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499 PngWriter w; |
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500 |
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501 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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502 T* pixel = &image[0]; |
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503 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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504 { |
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505 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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506 { |
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507 int32_t v = accessor.GetValue(x, y); |
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508 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
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509 *pixel = std::numeric_limits<T>::min(); |
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510 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
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511 *pixel = std::numeric_limits<T>::max(); |
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512 else |
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513 *pixel = static_cast<T>(v); |
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514 } |
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515 } |
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516 |
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517 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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518 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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519 } |
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520 |
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521 |
319 | 522 |
523 | |
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524 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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525 DcmDataset& dataset, |
53
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526 unsigned int frame, |
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527 ImageExtractionMode mode) |
0 | 528 { |
529 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
530 | |
531 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
532 | |
533 DicomMap m; | |
534 FromDcmtkBridge::Convert(m, dataset); | |
535 | |
319 | 536 std::string privateContent; |
537 | |
0 | 538 DcmElement* e; |
80 | 539 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 540 e != NULL) |
541 { | |
542 Uint8* pixData = NULL; | |
543 if (e->getUint8Array(pixData) == EC_Normal) | |
544 { | |
545 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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546 accessor->SetCurrentFrame(frame); |
0 | 547 } |
548 } | |
846 | 549 else if (DicomImageDecoder::DecodePsmctRle1(privateContent, dataset)) |
319 | 550 { |
551 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
552 Uint8* pixData = NULL; | |
553 if (privateContent.size() > 0) | |
554 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
555 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
556 accessor->SetCurrentFrame(frame); | |
557 } | |
419 | 558 |
559 if (accessor.get() == NULL) | |
560 { | |
561 throw OrthancException(ErrorCode_BadFileFormat); | |
562 } | |
0 | 563 |
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564 PixelFormat format; |
369
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565 bool supported = false; |
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566 |
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567 if (accessor->GetChannelCount() == 1) |
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568 { |
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569 switch (mode) |
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570 { |
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571 case ImageExtractionMode_Preview: |
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572 supported = true; |
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573 format = PixelFormat_Grayscale8; |
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574 break; |
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575 |
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576 case ImageExtractionMode_UInt8: |
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577 supported = true; |
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578 format = PixelFormat_Grayscale8; |
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579 break; |
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580 |
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581 case ImageExtractionMode_UInt16: |
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582 supported = true; |
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583 format = PixelFormat_Grayscale16; |
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584 break; |
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585 |
465
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signed images to PNG
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586 case ImageExtractionMode_Int16: |
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587 supported = true; |
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588 format = PixelFormat_SignedGrayscale16; |
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|
589 break; |
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590 |
369
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591 default: |
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592 supported = false; |
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593 break; |
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594 } |
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595 } |
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596 else if (accessor->GetChannelCount() == 3) |
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597 { |
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598 switch (mode) |
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599 { |
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600 case ImageExtractionMode_Preview: |
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601 supported = true; |
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602 format = PixelFormat_RGB24; |
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603 break; |
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604 |
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605 default: |
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606 supported = false; |
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607 break; |
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|
608 } |
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609 } |
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610 |
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611 if (!supported) |
368
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612 { |
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613 throw OrthancException(ErrorCode_NotImplemented); |
369
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614 } |
42
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615 |
0 | 616 if (accessor.get() == NULL || |
617 accessor->GetWidth() == 0 || | |
618 accessor->GetHeight() == 0) | |
619 { | |
42
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620 PngWriter w; |
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621 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 622 } |
623 else | |
624 { | |
42
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625 switch (mode) |
0 | 626 { |
302
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627 case ImageExtractionMode_Preview: |
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628 if (format == PixelFormat_Grayscale8) |
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629 ExtractPngImageGrayscalePreview(result, *accessor); |
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630 else |
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631 ExtractPngImageColorPreview(result, *accessor); |
302
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632 break; |
42
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633 |
302
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634 case ImageExtractionMode_UInt8: |
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635 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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636 break; |
42
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637 |
302
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638 case ImageExtractionMode_UInt16: |
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639 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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640 break; |
42
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641 |
465
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642 case ImageExtractionMode_Int16: |
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643 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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644 break; |
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645 |
302
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646 default: |
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647 throw OrthancException(ErrorCode_NotImplemented); |
0 | 648 } |
649 } | |
650 } | |
651 | |
652 | |
42
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653 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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654 const std::string& dicomContent, |
53
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diff
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655 unsigned int frame, |
42
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656 ImageExtractionMode mode) |
0 | 657 { |
658 DcmInputBufferStream is; | |
659 if (dicomContent.size() > 0) | |
660 { | |
661 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
662 } | |
663 is.setEos(); | |
664 | |
665 DcmFileFormat dicom; | |
666 if (dicom.read(is).good()) | |
667 { | |
53
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668 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 669 } |
670 else | |
671 { | |
62 | 672 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 673 } |
674 } | |
675 | |
676 | |
677 | |
678 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
679 { | |
106 | 680 // Some patches for important tags because of different DICOM |
681 // dictionaries between DCMTK versions | |
291
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682 std::string n = t.GetMainTagsName(); |
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683 if (n.size() != 0) |
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684 { |
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685 return n; |
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686 } |
106 | 687 // End of patches |
688 | |
305
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689 #if 0 |
0 | 690 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
691 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
692 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
693 | |
306
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694 std::string s(DcmTag_ERROR_TagName); |
0 | 695 if (entry != NULL) |
696 { | |
697 s = std::string(entry->getTagName()); | |
698 } | |
699 | |
700 dcmDataDict.unlock(); | |
701 return s; | |
305
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parents:
304
diff
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|
702 #else |
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|
703 DcmTag tag(t.GetGroup(), t.GetElement()); |
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diff
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|
704 const char* name = tag.getTagName(); |
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705 if (name == NULL) |
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diff
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|
706 { |
306
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305
diff
changeset
|
707 return DcmTag_ERROR_TagName; |
305
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|
708 } |
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diff
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|
709 else |
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|
710 { |
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711 return std::string(name); |
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712 } |
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|
713 #endif |
0 | 714 } |
715 | |
716 | |
304 | 717 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
0 | 718 { |
304 | 719 if (strlen(name) == 9 && |
720 isxdigit(name[0]) && | |
721 isxdigit(name[1]) && | |
722 isxdigit(name[2]) && | |
723 isxdigit(name[3]) && | |
724 name[4] == '-' && | |
725 isxdigit(name[5]) && | |
726 isxdigit(name[6]) && | |
727 isxdigit(name[7]) && | |
728 isxdigit(name[8])) | |
729 { | |
730 uint16_t group = GetTagValue(name); | |
731 uint16_t element = GetTagValue(name + 5); | |
732 return DicomTag(group, element); | |
733 } | |
734 | |
305
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735 #if 0 |
0 | 736 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
737 const DcmDictEntry* entry = dict.findEntry(name); | |
738 | |
739 if (entry == NULL) | |
740 { | |
741 dcmDataDict.unlock(); | |
62 | 742 throw OrthancException("Unknown DICOM tag"); |
0 | 743 } |
744 else | |
745 { | |
746 DcmTagKey key = entry->getKey(); | |
747 DicomTag tag(key.getGroup(), key.getElement()); | |
748 dcmDataDict.unlock(); | |
749 return tag; | |
750 } | |
305
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751 #else |
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|
752 DcmTag tag; |
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|
753 if (DcmTag::findTagFromName(name, tag).good()) |
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|
754 { |
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|
755 return DicomTag(tag.getGTag(), tag.getETag()); |
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|
756 } |
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|
757 else |
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|
758 { |
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|
759 throw OrthancException("Unknown DICOM tag"); |
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760 } |
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|
761 #endif |
0 | 762 } |
763 | |
764 | |
765 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
766 { | |
767 for (DicomMap::Map::const_iterator | |
656 | 768 it = m.map_.begin(); it != m.map_.end(); ++it) |
0 | 769 { |
770 DicomTag t = it->first; | |
771 std::string s = it->second->AsString(); | |
319 | 772 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
0 | 773 } |
774 } | |
775 | |
776 | |
777 void FromDcmtkBridge::ToJson(Json::Value& result, | |
778 const DicomMap& values) | |
779 { | |
780 if (result.type() != Json::objectValue) | |
781 { | |
62 | 782 throw OrthancException(ErrorCode_BadParameterType); |
0 | 783 } |
784 | |
785 result.clear(); | |
786 | |
787 for (DicomMap::Map::const_iterator | |
656 | 788 it = values.map_.begin(); it != values.map_.end(); ++it) |
0 | 789 { |
790 result[GetName(it->first)] = it->second->AsString(); | |
791 } | |
792 } | |
176 | 793 |
794 | |
788 | 795 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
176 | 796 { |
797 char uid[100]; | |
798 | |
799 switch (level) | |
800 { | |
788 | 801 case ResourceType_Patient: |
311 | 802 // The "PatientID" field is of type LO (Long String), 64 |
803 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
804 // as a random PatientID. | |
805 return Toolbox::GenerateUuid(); | |
306
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806 |
788 | 807 case ResourceType_Instance: |
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808 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 809 |
788 | 810 case ResourceType_Series: |
302
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811 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 812 |
788 | 813 case ResourceType_Study: |
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814 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 815 |
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816 default: |
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817 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 818 } |
819 } | |
820 | |
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821 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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822 DcmDataset* dataSet) |
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823 { |
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824 // Determine the transfer syntax which shall be used to write the |
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825 // information to the file. We always switch to the Little Endian |
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826 // syntax, with explicit length. |
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827 |
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828 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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829 |
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830 |
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831 /** |
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832 * Note that up to Orthanc 0.7.1 (inclusive), the |
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833 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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834 * dataset into memory. We now keep the original transfer syntax |
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835 * (if available). |
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836 **/ |
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837 E_TransferSyntax xfer = dataSet->getOriginalXfer(); |
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838 if (xfer == EXS_Unknown) |
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839 { |
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840 // No information about the original transfer syntax: This is |
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841 // most probably a DICOM dataset that was read from memory. |
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842 xfer = EXS_LittleEndianExplicit; |
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843 } |
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844 |
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845 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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846 |
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847 // Create the meta-header information |
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848 DcmFileFormat ff(dataSet); |
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849 ff.validateMetaInfo(xfer); |
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850 |
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851 // Create a memory buffer with the proper size |
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852 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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853 buffer.resize(s); |
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854 DcmOutputBufferStream ob(&buffer[0], s); |
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855 |
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856 // Fill the memory buffer with the meta-header and the dataset |
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857 ff.transferInit(); |
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858 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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859 /*opt_groupLength*/ EGL_recalcGL, |
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860 /*opt_paddingType*/ EPD_withoutPadding); |
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861 ff.transferEnd(); |
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862 |
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863 // Handle errors |
291
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864 if (c.good()) |
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865 { |
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866 return true; |
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867 } |
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868 else |
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869 { |
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870 buffer.clear(); |
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871 return false; |
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872 } |
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873 } |
0 | 874 } |