Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 532:b22312081388 dicom-rt
extract roi geometry
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 30 Aug 2013 16:09:19 +0200 |
parents | 7a966b440f19 |
children | da8e064d0d49 |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
399 | 3 * Copyright (C) 2012-2013 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 | |
448
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32 |
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33 |
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34 /*========================================================================= |
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35 |
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36 This file is based on portions of the following project: |
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37 |
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38 Program: GDCM (Grassroots DICOM). A DICOM library |
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39 Module: http://gdcm.sourceforge.net/Copyright.html |
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40 |
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41 Copyright (c) 2006-2011 Mathieu Malaterre |
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42 Copyright (c) 1993-2005 CREATIS |
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43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) |
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44 All rights reserved. |
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45 |
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46 Redistribution and use in source and binary forms, with or without |
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47 modification, are permitted provided that the following conditions are met: |
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48 |
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49 * Redistributions of source code must retain the above copyright notice, |
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50 this list of conditions and the following disclaimer. |
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51 |
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52 * Redistributions in binary form must reproduce the above copyright notice, |
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53 this list of conditions and the following disclaimer in the documentation |
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54 and/or other materials provided with the distribution. |
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55 |
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56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any |
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57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to |
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58 endorse or promote products derived from this software without specific |
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59 prior written permission. |
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60 |
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61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' |
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62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE |
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63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE |
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64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR |
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65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL |
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66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR |
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67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER |
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68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, |
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69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE |
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70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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71 |
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72 =========================================================================*/ |
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73 |
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74 |
71 | 75 #ifndef NOMINMAX |
76 #define NOMINMAX | |
77 #endif | |
0 | 78 |
79 #include "FromDcmtkBridge.h" | |
80 | |
81 #include "ToDcmtkBridge.h" | |
107
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82 #include "../Core/Toolbox.h" |
62 | 83 #include "../Core/OrthancException.h" |
454 | 84 #include "../Core/FileFormats/PngWriter.h" |
306
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85 #include "../Core/Uuid.h" |
0 | 86 #include "../Core/DicomFormat/DicomString.h" |
87 #include "../Core/DicomFormat/DicomNullValue.h" | |
79 | 88 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
0 | 89 |
306
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90 #include <list> |
71 | 91 #include <limits> |
92 | |
0 | 93 #include <boost/lexical_cast.hpp> |
94 | |
302
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95 #include <dcmtk/dcmdata/dcchrstr.h> |
0 | 96 #include <dcmtk/dcmdata/dcdicent.h> |
97 #include <dcmtk/dcmdata/dcdict.h> | |
98 #include <dcmtk/dcmdata/dcfilefo.h> | |
99 #include <dcmtk/dcmdata/dcistrmb.h> | |
302
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100 #include <dcmtk/dcmdata/dcuid.h> |
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101 |
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102 #include <dcmtk/dcmdata/dcvrae.h> |
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103 #include <dcmtk/dcmdata/dcvras.h> |
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104 #include <dcmtk/dcmdata/dcvrcs.h> |
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105 #include <dcmtk/dcmdata/dcvrda.h> |
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106 #include <dcmtk/dcmdata/dcvrds.h> |
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107 #include <dcmtk/dcmdata/dcvrdt.h> |
0 | 108 #include <dcmtk/dcmdata/dcvrfd.h> |
109 #include <dcmtk/dcmdata/dcvrfl.h> | |
302
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110 #include <dcmtk/dcmdata/dcvris.h> |
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111 #include <dcmtk/dcmdata/dcvrlo.h> |
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112 #include <dcmtk/dcmdata/dcvrlt.h> |
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113 #include <dcmtk/dcmdata/dcvrpn.h> |
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114 #include <dcmtk/dcmdata/dcvrsh.h> |
0 | 115 #include <dcmtk/dcmdata/dcvrsl.h> |
116 #include <dcmtk/dcmdata/dcvrss.h> | |
302
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117 #include <dcmtk/dcmdata/dcvrst.h> |
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118 #include <dcmtk/dcmdata/dcvrtm.h> |
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119 #include <dcmtk/dcmdata/dcvrui.h> |
0 | 120 #include <dcmtk/dcmdata/dcvrul.h> |
121 #include <dcmtk/dcmdata/dcvrus.h> | |
302
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122 #include <dcmtk/dcmdata/dcvrut.h> |
0 | 123 |
2 | 124 #include <boost/math/special_functions/round.hpp> |
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125 #include <glog/logging.h> |
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126 #include <dcmtk/dcmdata/dcostrmb.h> |
0 | 127 |
62 | 128 namespace Orthanc |
0 | 129 { |
304 | 130 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
285
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131 { |
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132 DcmInputBufferStream is; |
304 | 133 if (size > 0) |
285
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134 { |
304 | 135 is.setBuffer(buffer, size); |
285
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136 } |
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137 is.setEos(); |
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138 |
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139 file_.reset(new DcmFileFormat); |
291
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140 file_->transferInit(); |
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141 if (!file_->read(is).good()) |
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142 { |
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143 throw OrthancException(ErrorCode_BadFileFormat); |
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144 } |
291
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145 file_->loadAllDataIntoMemory(); |
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146 file_->transferEnd(); |
285
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147 } |
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148 |
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149 |
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150 static void SendPathValueForDictionary(RestApiOutput& output, |
302
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151 DcmItem& dicom) |
285
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152 { |
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153 Json::Value v = Json::arrayValue; |
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154 |
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155 for (unsigned long i = 0; i < dicom.card(); i++) |
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156 { |
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157 DcmElement* element = dicom.getElement(i); |
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158 if (element) |
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159 { |
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160 char buf[16]; |
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161 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); |
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162 v.append(buf); |
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163 } |
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164 } |
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165 |
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166 output.AnswerJson(v); |
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167 } |
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168 |
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169 static inline uint16_t GetCharValue(char c) |
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170 { |
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171 if (c >= '0' && c <= '9') |
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172 return c - '0'; |
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173 else if (c >= 'a' && c <= 'f') |
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174 return c - 'a' + 10; |
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175 else if (c >= 'A' && c <= 'F') |
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176 return c - 'A' + 10; |
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177 else |
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178 return 0; |
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179 } |
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180 |
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181 static inline uint16_t GetTagValue(const char* c) |
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182 { |
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183 return ((GetCharValue(c[0]) << 12) + |
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184 (GetCharValue(c[1]) << 8) + |
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185 (GetCharValue(c[2]) << 4) + |
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186 GetCharValue(c[3])); |
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187 } |
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188 |
304 | 189 static void ParseTagAndGroup(DcmTagKey& key, |
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190 const std::string& tag) |
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191 { |
304 | 192 DicomTag t = FromDcmtkBridge::ParseTag(tag); |
193 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
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194 } |
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195 |
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196 |
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197 static void SendSequence(RestApiOutput& output, |
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198 DcmSequenceOfItems& sequence) |
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199 { |
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200 // This element is a sequence |
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201 Json::Value v = Json::arrayValue; |
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202 |
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203 for (unsigned long i = 0; i < sequence.card(); i++) |
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204 { |
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205 v.append(boost::lexical_cast<std::string>(i)); |
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206 } |
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207 |
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208 output.AnswerJson(v); |
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209 } |
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210 |
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211 static void AnswerDicomField(RestApiOutput& output, |
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212 DcmElement& element) |
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213 { |
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214 // This element is not a sequence |
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215 std::string buffer; |
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216 buffer.resize(65536); |
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217 Uint32 length = element.getLength(); |
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218 Uint32 offset = 0; |
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219 |
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220 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL); |
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221 |
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222 while (offset < length) |
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223 { |
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224 Uint32 nbytes; |
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225 if (length - offset < buffer.size()) |
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226 { |
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227 nbytes = length - offset; |
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228 } |
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229 else |
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230 { |
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231 nbytes = buffer.size(); |
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232 } |
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233 |
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234 if (element.getPartialValue(&buffer[0], offset, nbytes).good()) |
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235 { |
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236 output.GetLowLevelOutput().Send(&buffer[0], nbytes); |
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237 offset += nbytes; |
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238 } |
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239 else |
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240 { |
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241 LOG(ERROR) << "Error while sending a DICOM field"; |
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242 return; |
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243 } |
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244 } |
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245 |
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246 output.MarkLowLevelOutputDone(); |
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247 } |
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248 |
285
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249 static void SendPathValueForLeaf(RestApiOutput& output, |
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250 const std::string& tag, |
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251 DcmItem& dicom) |
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252 { |
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253 DcmTagKey k; |
304 | 254 ParseTagAndGroup(k, tag); |
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255 |
291
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256 DcmSequenceOfItems* sequence = NULL; |
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257 if (dicom.findAndGetSequence(k, sequence).good() && |
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258 sequence != NULL && |
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259 sequence->getVR() == EVR_SQ) |
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260 { |
291
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261 SendSequence(output, *sequence); |
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262 return; |
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263 } |
285
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264 |
291
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265 DcmElement* element = NULL; |
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266 if (dicom.findAndGetElement(k, element).good() && |
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267 element != NULL && |
318
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268 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags |
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269 element->getVR() != EVR_SQ) |
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270 { |
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271 AnswerDicomField(output, *element); |
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272 } |
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273 } |
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274 |
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275 void ParsedDicomFile::SendPathValue(RestApiOutput& output, |
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276 const UriComponents& uri) |
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277 { |
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278 DcmItem* dicom = file_->getDataset(); |
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279 |
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280 // Go down in the tag hierarchy according to the URI |
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281 for (size_t pos = 0; pos < uri.size() / 2; pos++) |
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282 { |
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283 size_t index; |
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284 try |
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285 { |
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286 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); |
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287 } |
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288 catch (boost::bad_lexical_cast&) |
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289 { |
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290 return; |
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291 } |
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292 |
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293 DcmTagKey k; |
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294 DcmItem *child = NULL; |
304 | 295 ParseTagAndGroup(k, uri[2 * pos]); |
296 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
285
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297 child == NULL) |
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298 { |
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299 return; |
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300 } |
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301 |
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302 dicom = child; |
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303 } |
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304 |
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305 // We have reached the end of the URI |
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306 if (uri.size() % 2 == 0) |
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307 { |
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308 SendPathValueForDictionary(output, *dicom); |
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309 } |
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310 else |
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311 { |
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312 SendPathValueForLeaf(output, uri.back(), *dicom); |
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313 } |
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314 } |
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315 |
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316 |
302
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317 |
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318 |
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319 |
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320 static DcmElement* CreateElementForTag(const DicomTag& tag) |
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321 { |
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322 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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323 |
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324 switch (key.getEVR()) |
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325 { |
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326 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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327 |
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328 /** |
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329 * TODO. |
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330 **/ |
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331 |
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332 case EVR_OB: // other byte |
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333 case EVR_OF: // other float |
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334 case EVR_OW: // other word |
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335 case EVR_AT: // attribute tag |
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336 throw OrthancException(ErrorCode_NotImplemented); |
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337 |
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338 case EVR_UN: // unknown value representation |
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339 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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340 |
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341 |
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342 /** |
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343 * String types. |
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344 * http://support.dcmtk.org/docs/classDcmByteString.html |
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345 **/ |
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346 |
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347 case EVR_AS: // age string |
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348 return new DcmAgeString(key); |
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349 |
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350 case EVR_AE: // application entity title |
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351 return new DcmApplicationEntity(key); |
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352 |
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353 case EVR_CS: // code string |
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354 return new DcmCodeString(key); |
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355 |
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356 case EVR_DA: // date string |
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357 return new DcmDate(key); |
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358 |
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359 case EVR_DT: // date time string |
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360 return new DcmDateTime(key); |
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361 |
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362 case EVR_DS: // decimal string |
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363 return new DcmDecimalString(key); |
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364 |
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365 case EVR_IS: // integer string |
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366 return new DcmIntegerString(key); |
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367 |
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368 case EVR_TM: // time string |
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369 return new DcmTime(key); |
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370 |
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371 case EVR_UI: // unique identifier |
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372 return new DcmUniqueIdentifier(key); |
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373 |
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374 case EVR_ST: // short text |
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375 return new DcmShortText(key); |
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376 |
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377 case EVR_LO: // long string |
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378 return new DcmLongString(key); |
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379 |
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380 case EVR_LT: // long text |
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381 return new DcmLongText(key); |
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382 |
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383 case EVR_UT: // unlimited text |
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384 return new DcmUnlimitedText(key); |
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385 |
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386 case EVR_SH: // short string |
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387 return new DcmShortString(key); |
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388 |
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389 case EVR_PN: // person name |
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390 return new DcmPersonName(key); |
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391 |
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392 |
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393 /** |
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394 * Numerical types |
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395 **/ |
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396 |
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397 case EVR_SL: // signed long |
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398 return new DcmSignedLong(key); |
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399 |
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400 case EVR_SS: // signed short |
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401 return new DcmSignedShort(key); |
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402 |
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403 case EVR_UL: // unsigned long |
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404 return new DcmUnsignedLong(key); |
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405 |
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406 case EVR_US: // unsigned short |
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407 return new DcmUnsignedShort(key); |
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408 |
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409 case EVR_FL: // float single-precision |
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410 return new DcmFloatingPointSingle(key); |
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411 |
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412 case EVR_FD: // float double-precision |
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413 return new DcmFloatingPointDouble(key); |
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414 |
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415 |
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416 /** |
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417 * Sequence types, should never occur at this point. |
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418 **/ |
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419 |
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420 case EVR_SQ: // sequence of items |
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421 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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422 |
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423 |
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424 /** |
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425 * Internal to DCMTK. |
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426 **/ |
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427 |
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428 case EVR_ox: // OB or OW depending on context |
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429 case EVR_xs: // SS or US depending on context |
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430 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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431 case EVR_na: // na="not applicable", for data which has no VR |
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432 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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433 case EVR_item: // used internally for items |
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434 case EVR_metainfo: // used internally for meta info datasets |
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435 case EVR_dataset: // used internally for datasets |
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436 case EVR_fileFormat: // used internally for DICOM files |
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437 case EVR_dicomDir: // used internally for DICOMDIR objects |
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438 case EVR_dirRecord: // used internally for DICOMDIR records |
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439 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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440 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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441 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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442 case EVR_PixelData: // used internally for uncompressed pixeld data |
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443 case EVR_OverlayData: // used internally for overlay data |
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444 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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445 default: |
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446 break; |
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447 } |
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448 |
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449 throw OrthancException(ErrorCode_InternalError); |
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450 } |
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451 |
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452 |
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453 |
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454 static void FillElementWithString(DcmElement& element, |
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455 const DicomTag& tag, |
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456 const std::string& value) |
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457 { |
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458 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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459 bool ok = false; |
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460 |
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461 try |
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462 { |
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463 switch (key.getEVR()) |
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464 { |
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465 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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466 |
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467 /** |
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468 * TODO. |
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469 **/ |
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470 |
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471 case EVR_OB: // other byte |
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472 case EVR_OF: // other float |
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473 case EVR_OW: // other word |
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474 case EVR_AT: // attribute tag |
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475 throw OrthancException(ErrorCode_NotImplemented); |
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476 |
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477 case EVR_UN: // unknown value representation |
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478 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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479 |
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480 |
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481 /** |
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482 * String types. |
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483 **/ |
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484 |
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485 case EVR_DS: // decimal string |
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486 case EVR_IS: // integer string |
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487 case EVR_AS: // age string |
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488 case EVR_DA: // date string |
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489 case EVR_DT: // date time string |
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490 case EVR_TM: // time string |
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491 case EVR_AE: // application entity title |
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492 case EVR_CS: // code string |
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493 case EVR_SH: // short string |
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494 case EVR_LO: // long string |
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495 case EVR_ST: // short text |
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496 case EVR_LT: // long text |
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497 case EVR_UT: // unlimited text |
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498 case EVR_PN: // person name |
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499 case EVR_UI: // unique identifier |
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500 { |
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501 ok = element.putString(value.c_str()).good(); |
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502 break; |
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503 } |
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504 |
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505 |
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506 /** |
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507 * Numerical types |
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508 **/ |
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509 |
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510 case EVR_SL: // signed long |
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511 { |
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512 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); |
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513 break; |
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514 } |
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515 |
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516 case EVR_SS: // signed short |
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517 { |
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518 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); |
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519 break; |
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520 } |
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521 |
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522 case EVR_UL: // unsigned long |
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523 { |
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524 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); |
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525 break; |
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526 } |
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527 |
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528 case EVR_US: // unsigned short |
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529 { |
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530 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); |
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531 break; |
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532 } |
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533 |
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534 case EVR_FL: // float single-precision |
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535 { |
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536 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); |
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537 break; |
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538 } |
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539 |
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540 case EVR_FD: // float double-precision |
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541 { |
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542 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); |
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543 break; |
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544 } |
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545 |
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546 |
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547 /** |
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548 * Sequence types, should never occur at this point. |
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549 **/ |
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550 |
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551 case EVR_SQ: // sequence of items |
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552 { |
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553 ok = false; |
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554 break; |
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555 } |
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556 |
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557 |
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558 /** |
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559 * Internal to DCMTK. |
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560 **/ |
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561 |
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562 case EVR_ox: // OB or OW depending on context |
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563 case EVR_xs: // SS or US depending on context |
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564 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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565 case EVR_na: // na="not applicable", for data which has no VR |
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566 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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567 case EVR_item: // used internally for items |
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568 case EVR_metainfo: // used internally for meta info datasets |
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569 case EVR_dataset: // used internally for datasets |
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570 case EVR_fileFormat: // used internally for DICOM files |
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571 case EVR_dicomDir: // used internally for DICOMDIR objects |
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572 case EVR_dirRecord: // used internally for DICOMDIR records |
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573 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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574 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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575 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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576 case EVR_PixelData: // used internally for uncompressed pixeld data |
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577 case EVR_OverlayData: // used internally for overlay data |
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578 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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579 default: |
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580 break; |
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581 } |
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582 } |
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583 catch (boost::bad_lexical_cast&) |
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584 { |
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585 ok = false; |
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586 } |
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587 |
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588 if (!ok) |
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589 { |
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590 throw OrthancException(ErrorCode_InternalError); |
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591 } |
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592 } |
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593 |
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594 |
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595 void ParsedDicomFile::Remove(const DicomTag& tag) |
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596 { |
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597 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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598 DcmElement* element = file_->getDataset()->remove(key); |
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599 if (element != NULL) |
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600 { |
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601 delete element; |
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602 } |
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603 } |
302
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604 |
306
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605 |
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606 |
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607 void ParsedDicomFile::RemovePrivateTags() |
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608 { |
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609 typedef std::list<DcmElement*> Tags; |
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610 |
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611 Tags privateTags; |
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612 |
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613 DcmDataset& dataset = *file_->getDataset(); |
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614 for (unsigned long i = 0; i < dataset.card(); i++) |
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615 { |
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616 DcmElement* element = dataset.getElement(i); |
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617 DcmTag tag(element->getTag()); |
311 | 618 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK |
619 tag.getPrivateCreator() != NULL) | |
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620 { |
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621 privateTags.push_back(element); |
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622 } |
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623 } |
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624 |
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625 for (Tags::iterator it = privateTags.begin(); |
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626 it != privateTags.end(); it++) |
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627 { |
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628 DcmElement* tmp = dataset.remove(*it); |
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629 if (tmp != NULL) |
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630 { |
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631 delete tmp; |
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632 } |
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633 } |
302
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634 } |
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635 |
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636 |
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637 |
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638 void ParsedDicomFile::Insert(const DicomTag& tag, |
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639 const std::string& value) |
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640 { |
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641 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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642 FillElementWithString(*element, tag, value); |
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643 |
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644 if (!file_->getDataset()->insert(element.release(), false, false).good()) |
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645 { |
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646 // This field already exists |
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647 throw OrthancException(ErrorCode_InternalError); |
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648 } |
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649 } |
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650 |
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651 |
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652 void ParsedDicomFile::Replace(const DicomTag& tag, |
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653 const std::string& value, |
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654 DicomReplaceMode mode) |
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655 { |
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656 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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657 DcmElement* element = NULL; |
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658 |
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659 if (!file_->getDataset()->findAndGetElement(key, element).good() || |
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660 element == NULL) |
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661 { |
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662 // This field does not exist, act wrt. the specified "mode" |
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663 switch (mode) |
302
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664 { |
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665 case DicomReplaceMode_InsertIfAbsent: |
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666 Insert(tag, value); |
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667 break; |
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668 |
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669 case DicomReplaceMode_ThrowIfAbsent: |
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670 throw OrthancException(ErrorCode_InexistentItem); |
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671 |
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672 case DicomReplaceMode_IgnoreIfAbsent: |
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673 return; |
302
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674 } |
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675 } |
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676 else |
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677 { |
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678 FillElementWithString(*element, tag, value); |
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679 } |
303
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680 |
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681 |
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682 /** |
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683 * dcmodify will automatically correct 'Media Storage SOP Class |
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684 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if |
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685 * you make changes to the related tags in the dataset ('SOP Class |
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686 * UID' and 'SOP Instance UID') via insert or modify mode |
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687 * options. You can disable this behaviour by using the -nmu |
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688 * option. |
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689 **/ |
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690 if (tag == DICOM_TAG_SOP_CLASS_UID) |
305
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691 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); |
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692 |
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693 if (tag == DICOM_TAG_SOP_INSTANCE_UID) |
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694 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); |
302
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695 } |
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696 |
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697 |
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698 void ParsedDicomFile::Answer(RestApiOutput& output) |
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699 { |
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700 std::string serialized; |
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701 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset())) |
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702 { |
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703 output.AnswerBuffer(serialized, "application/octet-stream"); |
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704 } |
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705 } |
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706 |
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707 |
308
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708 |
532
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709 static bool GetTagValueInternal(std::string& value, |
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710 DcmItem& item, |
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711 const DicomTag& tag) |
308
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712 { |
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713 DcmTagKey k(tag.GetGroup(), tag.GetElement()); |
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714 DcmElement* element = NULL; |
532
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715 if (!item.findAndGetElement(k, element).good() || |
308
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716 element == NULL) |
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717 { |
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718 return false; |
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719 } |
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720 |
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721 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); |
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722 |
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723 if (v.get() == NULL) |
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724 { |
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725 value = ""; |
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726 } |
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727 else |
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728 { |
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729 value = v->AsString(); |
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730 } |
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731 |
532
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732 return true; |
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733 } |
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734 |
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735 |
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736 bool ParsedDicomFile::GetTagValue(std::string& value, |
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737 const DicomTag& tag) |
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738 { |
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739 DcmDataset& dataset = *file_->getDataset(); |
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740 return GetTagValueInternal(value, dataset, tag); |
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741 } |
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742 |
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743 |
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744 |
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745 bool ParsedDicomFile::GetTagValue(std::string& value, |
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746 const SequencePath& path, |
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747 const DicomTag& tag) |
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748 { |
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749 if (path.size() == 0) |
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750 { |
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751 return GetTagValue(value, tag); |
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752 } |
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753 |
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754 DcmItem* current = file_->getDataset(); |
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755 assert(current != NULL); |
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756 |
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757 for (SequencePath::const_iterator it = path.begin(); it != path.end(); it++) |
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758 { |
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759 DcmTagKey k(it->first.GetGroup(), it->first.GetElement()); |
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760 |
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761 DcmSequenceOfItems* sequence = NULL; |
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762 if (!current->findAndGetSequence(k, sequence).good() || |
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763 sequence == NULL || |
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764 sequence->getVR() != EVR_SQ) |
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765 { |
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766 return false; |
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767 } |
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768 |
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769 if (it->second > sequence->card()) |
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770 { |
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771 return false; |
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772 } |
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|
773 |
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774 current = sequence->getItem(it->second); |
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775 assert(current != NULL); |
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776 } |
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777 |
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778 return GetTagValueInternal(value, *current, tag); |
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779 } |
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780 |
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781 |
315 | 782 |
783 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
784 { | |
785 std::string patientId, studyUid, seriesUid, instanceUid; | |
786 | |
787 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
788 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
789 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
790 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
791 { | |
792 throw OrthancException(ErrorCode_BadFileFormat); | |
793 } | |
794 | |
795 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
796 } | |
797 | |
798 | |
0 | 799 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
800 { | |
801 target.Clear(); | |
802 for (unsigned long i = 0; i < dataset.card(); i++) | |
803 { | |
804 DcmElement* element = dataset.getElement(i); | |
805 if (element && element->isLeaf()) | |
806 { | |
807 target.SetValue(element->getTag().getGTag(), | |
808 element->getTag().getETag(), | |
809 ConvertLeafElement(*element)); | |
810 } | |
811 } | |
812 } | |
813 | |
814 | |
815 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
816 { | |
817 return DicomTag(element.getGTag(), element.getETag()); | |
818 } | |
819 | |
820 | |
821 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
822 { | |
823 if (!element.isLeaf()) | |
824 { | |
62 | 825 throw OrthancException("Only applicable to leaf elements"); |
0 | 826 } |
827 | |
828 if (element.isaString()) | |
829 { | |
830 char *c; | |
831 if (element.getString(c).good() && | |
832 c != NULL) | |
833 { | |
834 std::string s(c); | |
107
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835 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 836 return new DicomString(utf8); |
837 } | |
838 else | |
839 { | |
840 return new DicomNullValue; | |
841 } | |
842 } | |
843 | |
844 try | |
845 { | |
846 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
847 switch (element.getVR()) | |
848 { | |
849 | |
850 /** | |
851 * TODO. | |
852 **/ | |
306
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853 |
302
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854 case EVR_OB: // other byte |
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855 case EVR_OF: // other float |
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856 case EVR_OW: // other word |
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857 case EVR_AT: // attribute tag |
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858 case EVR_UN: // unknown value representation |
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859 return new DicomNullValue(); |
306
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860 |
302
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861 /** |
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862 * String types, should never happen at this point because of |
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|
863 * "element.isaString()". |
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864 **/ |
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865 |
306
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866 case EVR_DS: // decimal string |
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867 case EVR_IS: // integer string |
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868 case EVR_AS: // age string |
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869 case EVR_DA: // date string |
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870 case EVR_DT: // date time string |
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871 case EVR_TM: // time string |
302
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872 case EVR_AE: // application entity title |
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873 case EVR_CS: // code string |
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874 case EVR_SH: // short string |
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875 case EVR_LO: // long string |
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876 case EVR_ST: // short text |
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877 case EVR_LT: // long text |
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|
878 case EVR_UT: // unlimited text |
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879 case EVR_PN: // person name |
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880 case EVR_UI: // unique identifier |
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|
881 return new DicomNullValue(); |
0 | 882 |
883 | |
302
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|
884 /** |
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|
885 * Numerical types |
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886 **/ |
0 | 887 |
302
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888 case EVR_SL: // signed long |
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|
889 { |
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|
890 Sint32 f; |
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891 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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892 return new DicomString(boost::lexical_cast<std::string>(f)); |
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893 else |
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894 return new DicomNullValue(); |
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|
895 } |
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|
896 |
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897 case EVR_SS: // signed short |
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|
898 { |
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|
899 Sint16 f; |
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900 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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901 return new DicomString(boost::lexical_cast<std::string>(f)); |
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902 else |
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903 return new DicomNullValue(); |
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|
904 } |
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|
905 |
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906 case EVR_UL: // unsigned long |
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|
907 { |
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|
908 Uint32 f; |
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909 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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910 return new DicomString(boost::lexical_cast<std::string>(f)); |
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911 else |
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912 return new DicomNullValue(); |
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|
913 } |
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|
914 |
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|
915 case EVR_US: // unsigned short |
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|
916 { |
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|
917 Uint16 f; |
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918 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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919 return new DicomString(boost::lexical_cast<std::string>(f)); |
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|
920 else |
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|
921 return new DicomNullValue(); |
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|
922 } |
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|
923 |
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|
924 case EVR_FL: // float single-precision |
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|
925 { |
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|
926 Float32 f; |
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|
927 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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928 return new DicomString(boost::lexical_cast<std::string>(f)); |
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|
929 else |
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|
930 return new DicomNullValue(); |
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|
931 } |
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|
932 |
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|
933 case EVR_FD: // float double-precision |
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|
934 { |
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|
935 Float64 f; |
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|
936 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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|
937 return new DicomString(boost::lexical_cast<std::string>(f)); |
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|
938 else |
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|
939 return new DicomNullValue(); |
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diff
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|
940 } |
0 | 941 |
942 | |
943 /** | |
302
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|
944 * Sequence types, should never occur at this point because of |
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diff
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|
945 * "element.isLeaf()". |
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|
946 **/ |
0 | 947 |
302
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|
948 case EVR_SQ: // sequence of items |
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|
949 return new DicomNullValue; |
0 | 950 |
951 | |
302
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|
952 /** |
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|
953 * Internal to DCMTK. |
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|
954 **/ |
0 | 955 |
302
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956 case EVR_ox: // OB or OW depending on context |
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957 case EVR_xs: // SS or US depending on context |
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958 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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959 case EVR_na: // na="not applicable", for data which has no VR |
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960 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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961 case EVR_item: // used internally for items |
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962 case EVR_metainfo: // used internally for meta info datasets |
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963 case EVR_dataset: // used internally for datasets |
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964 case EVR_fileFormat: // used internally for DICOM files |
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965 case EVR_dicomDir: // used internally for DICOMDIR objects |
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966 case EVR_dirRecord: // used internally for DICOMDIR records |
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967 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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diff
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|
968 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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diff
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|
969 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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|
970 case EVR_PixelData: // used internally for uncompressed pixeld data |
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diff
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|
971 case EVR_OverlayData: // used internally for overlay data |
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|
972 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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|
973 return new DicomNullValue; |
0 | 974 |
975 | |
302
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diff
changeset
|
976 /** |
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diff
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|
977 * Default case. |
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|
978 **/ |
0 | 979 |
302
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diff
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|
980 default: |
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diff
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|
981 return new DicomNullValue; |
0 | 982 } |
983 } | |
984 catch (boost::bad_lexical_cast) | |
985 { | |
986 return new DicomNullValue; | |
987 } | |
306
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|
988 catch (std::bad_cast) |
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|
989 { |
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990 return new DicomNullValue; |
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991 } |
0 | 992 } |
993 | |
994 | |
995 static void StoreElement(Json::Value& target, | |
996 DcmElement& element, | |
997 unsigned int maxStringLength); | |
998 | |
999 static void StoreItem(Json::Value& target, | |
1000 DcmItem& item, | |
1001 unsigned int maxStringLength) | |
1002 { | |
1003 target = Json::Value(Json::objectValue); | |
1004 | |
1005 for (unsigned long i = 0; i < item.card(); i++) | |
1006 { | |
1007 DcmElement* element = item.getElement(i); | |
1008 StoreElement(target, *element, maxStringLength); | |
1009 } | |
1010 } | |
1011 | |
1012 | |
1013 static void StoreElement(Json::Value& target, | |
1014 DcmElement& element, | |
1015 unsigned int maxStringLength) | |
1016 { | |
1017 assert(target.type() == Json::objectValue); | |
1018 | |
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1019 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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1020 const std::string formattedTag = tag.Format(); |
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1021 |
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1022 #if 0 |
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1023 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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1024 #else |
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1025 // This version of the code gives access to the name of the private tags |
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1026 DcmTag tagbis(element.getTag()); |
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1027 const std::string tagName(tagbis.getTagName()); |
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1028 #endif |
0 | 1029 |
1030 if (element.isLeaf()) | |
1031 { | |
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1032 Json::Value value(Json::objectValue); |
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1033 value["Name"] = tagName; |
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1034 |
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1035 if (tagbis.getPrivateCreator() != NULL) |
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1036 { |
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1037 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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1038 } |
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1039 |
0 | 1040 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
1041 if (v->IsNull()) | |
1042 { | |
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1043 value["Type"] = "Null"; |
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1044 value["Value"] = Json::nullValue; |
0 | 1045 } |
1046 else | |
1047 { | |
1048 std::string s = v->AsString(); | |
1049 if (maxStringLength == 0 || | |
1050 s.size() <= maxStringLength) | |
1051 { | |
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1052 value["Type"] = "String"; |
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1053 value["Value"] = s; |
0 | 1054 } |
1055 else | |
1056 { | |
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1057 value["Type"] = "TooLong"; |
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1058 value["Value"] = Json::nullValue; |
0 | 1059 } |
1060 } | |
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1061 |
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1062 target[formattedTag] = value; |
0 | 1063 } |
1064 else | |
1065 { | |
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1066 Json::Value children(Json::arrayValue); |
0 | 1067 |
1068 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
1069 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
1070 // etc. are not." The following cast is thus OK. | |
1071 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
1072 | |
1073 for (unsigned long i = 0; i < sequence.card(); i++) | |
1074 { | |
1075 DcmItem* child = sequence.getItem(i); | |
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1076 Json::Value& v = children.append(Json::objectValue); |
0 | 1077 StoreItem(v, *child, maxStringLength); |
1078 } | |
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1079 |
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1080 target[formattedTag]["Name"] = tagName; |
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1081 target[formattedTag]["Type"] = "Sequence"; |
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1082 target[formattedTag]["Value"] = children; |
0 | 1083 } |
1084 } | |
1085 | |
1086 | |
1087 void FromDcmtkBridge::ToJson(Json::Value& root, | |
1088 DcmDataset& dataset, | |
1089 unsigned int maxStringLength) | |
1090 { | |
1091 StoreItem(root, dataset, maxStringLength); | |
1092 } | |
1093 | |
1094 | |
1095 | |
1096 void FromDcmtkBridge::ToJson(Json::Value& target, | |
1097 const std::string& path, | |
1098 unsigned int maxStringLength) | |
1099 { | |
1100 DcmFileFormat dicom; | |
1101 if (!dicom.loadFile(path.c_str()).good()) | |
1102 { | |
62 | 1103 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1104 } |
1105 else | |
1106 { | |
1107 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
1108 } | |
1109 } | |
1110 | |
1111 | |
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1112 static void ExtractPngImageColorPreview(std::string& result, |
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1113 DicomIntegerPixelAccessor& accessor) |
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1114 { |
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1115 assert(accessor.GetChannelCount() == 3); |
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1116 PngWriter w; |
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1117 |
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1118 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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1119 uint8_t* pixel = &image[0]; |
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1120 |
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1121 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1122 { |
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1123 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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1124 { |
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1125 for (unsigned int c = 0; c < 3; c++, pixel++) |
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1126 { |
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1127 int32_t v = accessor.GetValue(x, y, c); |
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1128 if (v < 0) |
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1129 *pixel = 0; |
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1130 else if (v > 255) |
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1131 *pixel = 255; |
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1132 else |
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1133 *pixel = v; |
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1134 } |
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1135 } |
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1136 } |
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1137 |
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1138 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1139 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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1140 } |
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1141 |
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1142 |
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1143 static void ExtractPngImageGrayscalePreview(std::string& result, |
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1144 DicomIntegerPixelAccessor& accessor) |
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1145 { |
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1146 assert(accessor.GetChannelCount() == 1); |
42
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1147 PngWriter w; |
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1148 |
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1149 int32_t min, max; |
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1150 accessor.GetExtremeValues(min, max); |
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1151 |
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1152 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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1153 if (min != max) |
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1154 { |
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1155 uint8_t* pixel = &image[0]; |
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1156 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1157 { |
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1158 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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1159 { |
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1160 int32_t v = accessor.GetValue(x, y); |
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1161 *pixel = static_cast<uint8_t>( |
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1162 boost::math::lround(static_cast<float>(v - min) / |
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1163 static_cast<float>(max - min) * 255.0f)); |
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1164 } |
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1165 } |
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1166 } |
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1167 |
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1168 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1169 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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1170 } |
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1171 |
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1172 |
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1173 template <typename T> |
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1174 static void ExtractPngImageTruncate(std::string& result, |
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1175 DicomIntegerPixelAccessor& accessor, |
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1176 PixelFormat format) |
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1177 { |
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1178 assert(accessor.GetChannelCount() == 1); |
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1179 |
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1180 PngWriter w; |
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1181 |
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1182 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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1183 T* pixel = &image[0]; |
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1184 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1185 { |
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1186 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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1187 { |
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1188 int32_t v = accessor.GetValue(x, y); |
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1189 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
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1190 *pixel = std::numeric_limits<T>::min(); |
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1191 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
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1192 *pixel = std::numeric_limits<T>::max(); |
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1193 else |
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1194 *pixel = static_cast<T>(v); |
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1195 } |
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1196 } |
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1197 |
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1198 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1199 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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1200 } |
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1201 |
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1202 |
319 | 1203 static bool DecodePsmctRle1(std::string& output, |
1204 DcmDataset& dataset) | |
1205 { | |
1206 static const DicomTag tagContent(0x07a1, 0x100a); | |
1207 static const DicomTag tagCompressionType(0x07a1, 0x1011); | |
1208 | |
1209 DcmElement* e; | |
1210 char* c; | |
1211 | |
1212 // Check whether the DICOM instance contains an image encoded with | |
1213 // the PMSCT_RLE1 scheme. | |
1214 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() || | |
1215 e == NULL || | |
1216 !e->isaString() || | |
1217 !e->getString(c).good() || | |
1218 c == NULL || | |
1219 strcmp("PMSCT_RLE1", c)) | |
1220 { | |
1221 return false; | |
1222 } | |
1223 | |
1224 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
1225 // data from the appropriate private DICOM tag. | |
1226 Uint8* pixData = NULL; | |
1227 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() || | |
1228 e == NULL || | |
1229 e->getUint8Array(pixData) != EC_Normal) | |
1230 { | |
1231 return false; | |
1232 } | |
1233 | |
1234 // The "unsigned" below IS VERY IMPORTANT | |
1235 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
1236 const size_t length = e->getLength(); | |
1237 | |
1238 /** | |
1239 * The code below is an adaptation of a sample code for GDCM by | |
1240 * Mathieu Malaterre (under a BSD license). | |
1241 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
1242 **/ | |
1243 | |
1244 // RLE pass | |
1245 std::vector<uint8_t> temp; | |
1246 temp.reserve(length); | |
1247 for (size_t i = 0; i < length; i++) | |
1248 { | |
1249 if (inbuffer[i] == 0xa5) | |
1250 { | |
1251 temp.push_back(inbuffer[i+2]); | |
1252 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
1253 { | |
1254 temp.push_back(inbuffer[i+2]); | |
1255 } | |
1256 i += 2; | |
1257 } | |
1258 else | |
1259 { | |
1260 temp.push_back(inbuffer[i]); | |
1261 } | |
1262 } | |
1263 | |
1264 // Delta encoding pass | |
1265 uint16_t delta = 0; | |
1266 output.clear(); | |
1267 output.reserve(temp.size()); | |
1268 for (size_t i = 0; i < temp.size(); i++) | |
1269 { | |
1270 uint16_t value; | |
1271 | |
1272 if (temp[i] == 0x5a) | |
1273 { | |
1274 uint16_t v1 = temp[i + 1]; | |
1275 uint16_t v2 = temp[i + 2]; | |
1276 value = (v2 << 8) + v1; | |
1277 i += 2; | |
1278 } | |
1279 else | |
1280 { | |
1281 value = delta + (int8_t) temp[i]; | |
1282 } | |
1283 | |
1284 output.push_back(value & 0xff); | |
1285 output.push_back(value >> 8); | |
1286 delta = value; | |
1287 } | |
1288 | |
1289 if (output.size() % 2) | |
1290 { | |
1291 output.resize(output.size() - 1); | |
1292 } | |
1293 | |
1294 return true; | |
1295 } | |
1296 | |
1297 | |
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1298 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1299 DcmDataset& dataset, |
53
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1300 unsigned int frame, |
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1301 ImageExtractionMode mode) |
0 | 1302 { |
1303 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
1304 | |
1305 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
1306 | |
1307 DicomMap m; | |
1308 FromDcmtkBridge::Convert(m, dataset); | |
1309 | |
319 | 1310 std::string privateContent; |
1311 | |
0 | 1312 DcmElement* e; |
80 | 1313 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 1314 e != NULL) |
1315 { | |
1316 Uint8* pixData = NULL; | |
1317 if (e->getUint8Array(pixData) == EC_Normal) | |
1318 { | |
1319 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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1320 accessor->SetCurrentFrame(frame); |
0 | 1321 } |
1322 } | |
319 | 1323 else if (DecodePsmctRle1(privateContent, dataset)) |
1324 { | |
1325 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
1326 Uint8* pixData = NULL; | |
1327 if (privateContent.size() > 0) | |
1328 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
1329 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
1330 accessor->SetCurrentFrame(frame); | |
1331 } | |
419 | 1332 |
1333 if (accessor.get() == NULL) | |
1334 { | |
1335 throw OrthancException(ErrorCode_BadFileFormat); | |
1336 } | |
0 | 1337 |
42
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1338 PixelFormat format; |
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1339 bool supported = false; |
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1340 |
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1341 if (accessor->GetChannelCount() == 1) |
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1342 { |
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1343 switch (mode) |
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1344 { |
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1345 case ImageExtractionMode_Preview: |
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1346 supported = true; |
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1347 format = PixelFormat_Grayscale8; |
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1348 break; |
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1349 |
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1350 case ImageExtractionMode_UInt8: |
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1351 supported = true; |
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1352 format = PixelFormat_Grayscale8; |
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1353 break; |
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1354 |
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1355 case ImageExtractionMode_UInt16: |
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1356 supported = true; |
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1357 format = PixelFormat_Grayscale16; |
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1358 break; |
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1359 |
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1360 case ImageExtractionMode_Int16: |
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1361 supported = true; |
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1362 format = PixelFormat_SignedGrayscale16; |
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1363 break; |
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1364 |
369
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1365 default: |
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1366 supported = false; |
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1367 break; |
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1368 } |
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1369 } |
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1370 else if (accessor->GetChannelCount() == 3) |
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1371 { |
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1372 switch (mode) |
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1373 { |
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1374 case ImageExtractionMode_Preview: |
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1375 supported = true; |
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1376 format = PixelFormat_RGB24; |
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1377 break; |
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1378 |
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1379 default: |
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1380 supported = false; |
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1381 break; |
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1382 } |
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1383 } |
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1384 |
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1385 if (!supported) |
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1386 { |
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1387 throw OrthancException(ErrorCode_NotImplemented); |
369
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1388 } |
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1389 |
0 | 1390 if (accessor.get() == NULL || |
1391 accessor->GetWidth() == 0 || | |
1392 accessor->GetHeight() == 0) | |
1393 { | |
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1394 PngWriter w; |
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1395 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 1396 } |
1397 else | |
1398 { | |
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1399 switch (mode) |
0 | 1400 { |
302
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1401 case ImageExtractionMode_Preview: |
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1402 if (format == PixelFormat_Grayscale8) |
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1403 ExtractPngImageGrayscalePreview(result, *accessor); |
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1404 else |
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1405 ExtractPngImageColorPreview(result, *accessor); |
302
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1406 break; |
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1407 |
302
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1408 case ImageExtractionMode_UInt8: |
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1409 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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1410 break; |
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1411 |
302
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1412 case ImageExtractionMode_UInt16: |
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1413 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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1414 break; |
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1415 |
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1416 case ImageExtractionMode_Int16: |
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1417 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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1418 break; |
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1419 |
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1420 default: |
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1421 throw OrthancException(ErrorCode_NotImplemented); |
0 | 1422 } |
1423 } | |
1424 } | |
1425 | |
1426 | |
42
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1427 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1428 const std::string& dicomContent, |
53
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1429 unsigned int frame, |
42
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1430 ImageExtractionMode mode) |
0 | 1431 { |
1432 DcmInputBufferStream is; | |
1433 if (dicomContent.size() > 0) | |
1434 { | |
1435 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
1436 } | |
1437 is.setEos(); | |
1438 | |
1439 DcmFileFormat dicom; | |
1440 if (dicom.read(is).good()) | |
1441 { | |
53
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1442 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 1443 } |
1444 else | |
1445 { | |
62 | 1446 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1447 } |
1448 } | |
1449 | |
1450 | |
1451 | |
1452 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
1453 { | |
106 | 1454 // Some patches for important tags because of different DICOM |
1455 // dictionaries between DCMTK versions | |
291
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1456 std::string n = t.GetMainTagsName(); |
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1457 if (n.size() != 0) |
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1458 { |
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1459 return n; |
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1460 } |
106 | 1461 // End of patches |
1462 | |
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1463 #if 0 |
0 | 1464 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
1465 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1466 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
1467 | |
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1468 std::string s(DcmTag_ERROR_TagName); |
0 | 1469 if (entry != NULL) |
1470 { | |
1471 s = std::string(entry->getTagName()); | |
1472 } | |
1473 | |
1474 dcmDataDict.unlock(); | |
1475 return s; | |
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1476 #else |
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1477 DcmTag tag(t.GetGroup(), t.GetElement()); |
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1478 const char* name = tag.getTagName(); |
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1479 if (name == NULL) |
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1480 { |
306
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1481 return DcmTag_ERROR_TagName; |
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1482 } |
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1483 else |
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1484 { |
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1485 return std::string(name); |
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1486 } |
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1487 #endif |
0 | 1488 } |
1489 | |
1490 | |
304 | 1491 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
0 | 1492 { |
304 | 1493 if (strlen(name) == 9 && |
1494 isxdigit(name[0]) && | |
1495 isxdigit(name[1]) && | |
1496 isxdigit(name[2]) && | |
1497 isxdigit(name[3]) && | |
1498 name[4] == '-' && | |
1499 isxdigit(name[5]) && | |
1500 isxdigit(name[6]) && | |
1501 isxdigit(name[7]) && | |
1502 isxdigit(name[8])) | |
1503 { | |
1504 uint16_t group = GetTagValue(name); | |
1505 uint16_t element = GetTagValue(name + 5); | |
1506 return DicomTag(group, element); | |
1507 } | |
1508 | |
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1509 #if 0 |
0 | 1510 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
1511 const DcmDictEntry* entry = dict.findEntry(name); | |
1512 | |
1513 if (entry == NULL) | |
1514 { | |
1515 dcmDataDict.unlock(); | |
62 | 1516 throw OrthancException("Unknown DICOM tag"); |
0 | 1517 } |
1518 else | |
1519 { | |
1520 DcmTagKey key = entry->getKey(); | |
1521 DicomTag tag(key.getGroup(), key.getElement()); | |
1522 dcmDataDict.unlock(); | |
1523 return tag; | |
1524 } | |
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1525 #else |
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1526 DcmTag tag; |
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1527 if (DcmTag::findTagFromName(name, tag).good()) |
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1528 { |
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1529 return DicomTag(tag.getGTag(), tag.getETag()); |
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1530 } |
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1531 else |
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1532 { |
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1533 throw OrthancException("Unknown DICOM tag"); |
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1534 } |
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1535 #endif |
0 | 1536 } |
1537 | |
1538 | |
1539 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
1540 { | |
1541 for (DicomMap::Map::const_iterator | |
1542 it = m.map_.begin(); it != m.map_.end(); it++) | |
1543 { | |
1544 DicomTag t = it->first; | |
1545 std::string s = it->second->AsString(); | |
319 | 1546 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
0 | 1547 } |
1548 } | |
1549 | |
1550 | |
1551 void FromDcmtkBridge::ToJson(Json::Value& result, | |
1552 const DicomMap& values) | |
1553 { | |
1554 if (result.type() != Json::objectValue) | |
1555 { | |
62 | 1556 throw OrthancException(ErrorCode_BadParameterType); |
0 | 1557 } |
1558 | |
1559 result.clear(); | |
1560 | |
1561 for (DicomMap::Map::const_iterator | |
1562 it = values.map_.begin(); it != values.map_.end(); it++) | |
1563 { | |
1564 result[GetName(it->first)] = it->second->AsString(); | |
1565 } | |
1566 } | |
176 | 1567 |
1568 | |
1569 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
1570 { | |
1571 char uid[100]; | |
1572 | |
1573 switch (level) | |
1574 { | |
306
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1575 case DicomRootLevel_Patient: |
311 | 1576 // The "PatientID" field is of type LO (Long String), 64 |
1577 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
1578 // as a random PatientID. | |
1579 return Toolbox::GenerateUuid(); | |
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1580 |
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1581 case DicomRootLevel_Instance: |
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1582 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 1583 |
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1584 case DicomRootLevel_Series: |
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1585 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 1586 |
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1587 case DicomRootLevel_Study: |
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1588 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 1589 |
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1590 default: |
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1591 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 1592 } |
1593 } | |
1594 | |
291
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1595 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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1596 DcmDataset* dataSet) |
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1597 { |
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1598 // Determine the transfer syntax which shall be used to write the |
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1599 // information to the file. We always switch to the Little Endian |
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1600 // syntax, with explicit length. |
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1601 |
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1602 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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1603 E_TransferSyntax xfer = EXS_LittleEndianExplicit; |
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1604 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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1605 |
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1606 uint32_t s = dataSet->getLength(xfer, encodingType); |
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1607 |
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1608 buffer.resize(s); |
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1609 DcmOutputBufferStream ob(&buffer[0], s); |
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1610 |
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1611 dataSet->transferInit(); |
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1612 |
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1613 #if DCMTK_VERSION_NUMBER >= 360 |
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1614 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL, |
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1615 /*opt_groupLength*/ EGL_recalcGL, |
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1616 /*opt_paddingType*/ EPD_withoutPadding); |
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1617 #else |
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1618 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL); |
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1619 #endif |
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1620 |
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1621 dataSet->transferEnd(); |
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1622 if (c.good()) |
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1623 { |
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1624 return true; |
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1625 } |
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1626 else |
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1627 { |
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1628 buffer.clear(); |
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1629 return false; |
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1630 } |
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1631 |
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1632 #if 0 |
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1633 OFCondition cond = cbdata->dcmff->saveFile(fileName.c_str(), xfer, |
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1634 encodingType, |
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1635 /*opt_groupLength*/ EGL_recalcGL, |
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1636 /*opt_paddingType*/ EPD_withoutPadding, |
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1637 OFstatic_cast(Uint32, /*opt_filepad*/ 0), |
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1638 OFstatic_cast(Uint32, /*opt_itempad*/ 0), |
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1639 (opt_useMetaheader) ? EWM_fileformat : EWM_dataset); |
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1640 #endif |
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1641 } |
0 | 1642 } |