Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 759:8cfc6119a5bd dicom-rt
integration mainline -> dicom-rt
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 16 Apr 2014 16:04:55 +0200 |
parents | da8e064d0d49 2d0a347e8cfc |
children | e57e08ed510f |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
0 | 4 * Belgium |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
136 | 10 * |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
0 | 22 * |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
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" |
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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 | |
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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 #include <dcmtk/dcmdata/dcmetinf.h> |
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102 |
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103 #include <dcmtk/dcmdata/dcvrae.h> |
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104 #include <dcmtk/dcmdata/dcvras.h> |
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105 #include <dcmtk/dcmdata/dcvrcs.h> |
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106 #include <dcmtk/dcmdata/dcvrda.h> |
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107 #include <dcmtk/dcmdata/dcvrds.h> |
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108 #include <dcmtk/dcmdata/dcvrdt.h> |
0 | 109 #include <dcmtk/dcmdata/dcvrfd.h> |
110 #include <dcmtk/dcmdata/dcvrfl.h> | |
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111 #include <dcmtk/dcmdata/dcvris.h> |
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112 #include <dcmtk/dcmdata/dcvrlo.h> |
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113 #include <dcmtk/dcmdata/dcvrlt.h> |
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114 #include <dcmtk/dcmdata/dcvrpn.h> |
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115 #include <dcmtk/dcmdata/dcvrsh.h> |
0 | 116 #include <dcmtk/dcmdata/dcvrsl.h> |
117 #include <dcmtk/dcmdata/dcvrss.h> | |
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118 #include <dcmtk/dcmdata/dcvrst.h> |
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119 #include <dcmtk/dcmdata/dcvrtm.h> |
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120 #include <dcmtk/dcmdata/dcvrui.h> |
0 | 121 #include <dcmtk/dcmdata/dcvrul.h> |
122 #include <dcmtk/dcmdata/dcvrus.h> | |
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123 #include <dcmtk/dcmdata/dcvrut.h> |
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124 #include <dcmtk/dcmdata/dcpixel.h> |
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125 #include <dcmtk/dcmdata/dcpixseq.h> |
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126 #include <dcmtk/dcmdata/dcpxitem.h> |
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127 |
0 | 128 |
2 | 129 #include <boost/math/special_functions/round.hpp> |
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130 #include <glog/logging.h> |
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131 #include <dcmtk/dcmdata/dcostrmb.h> |
0 | 132 |
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133 |
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134 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; |
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135 |
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136 |
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137 |
62 | 138 namespace Orthanc |
0 | 139 { |
304 | 140 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
285
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141 { |
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142 DcmInputBufferStream is; |
304 | 143 if (size > 0) |
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144 { |
304 | 145 is.setBuffer(buffer, size); |
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146 } |
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147 is.setEos(); |
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148 |
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149 file_.reset(new DcmFileFormat); |
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150 file_->transferInit(); |
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151 if (!file_->read(is).good()) |
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152 { |
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153 throw OrthancException(ErrorCode_BadFileFormat); |
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154 } |
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155 file_->loadAllDataIntoMemory(); |
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156 file_->transferEnd(); |
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157 } |
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158 |
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159 |
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160 static void SendPathValueForDictionary(RestApiOutput& output, |
302
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161 DcmItem& dicom) |
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162 { |
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163 Json::Value v = Json::arrayValue; |
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164 |
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165 for (unsigned long i = 0; i < dicom.card(); i++) |
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166 { |
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167 DcmElement* element = dicom.getElement(i); |
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168 if (element) |
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169 { |
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170 char buf[16]; |
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171 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); |
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172 v.append(buf); |
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173 } |
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174 } |
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175 |
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176 output.AnswerJson(v); |
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177 } |
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178 |
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179 static inline uint16_t GetCharValue(char c) |
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180 { |
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181 if (c >= '0' && c <= '9') |
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182 return c - '0'; |
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183 else if (c >= 'a' && c <= 'f') |
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184 return c - 'a' + 10; |
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185 else if (c >= 'A' && c <= 'F') |
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186 return c - 'A' + 10; |
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187 else |
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188 return 0; |
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189 } |
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190 |
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191 static inline uint16_t GetTagValue(const char* c) |
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192 { |
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193 return ((GetCharValue(c[0]) << 12) + |
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194 (GetCharValue(c[1]) << 8) + |
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195 (GetCharValue(c[2]) << 4) + |
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196 GetCharValue(c[3])); |
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197 } |
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198 |
304 | 199 static void ParseTagAndGroup(DcmTagKey& key, |
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200 const std::string& tag) |
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201 { |
304 | 202 DicomTag t = FromDcmtkBridge::ParseTag(tag); |
203 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
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204 } |
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205 |
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206 |
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207 static void SendSequence(RestApiOutput& output, |
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208 DcmSequenceOfItems& sequence) |
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209 { |
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210 // This element is a sequence |
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211 Json::Value v = Json::arrayValue; |
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212 |
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213 for (unsigned long i = 0; i < sequence.card(); i++) |
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214 { |
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215 v.append(boost::lexical_cast<std::string>(i)); |
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216 } |
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217 |
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218 output.AnswerJson(v); |
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219 } |
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220 |
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221 |
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222 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, |
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223 E_TransferSyntax transferSyntax) |
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224 { |
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225 DcmPixelSequence* pixelSequence = NULL; |
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226 if (pixelData.getEncapsulatedRepresentation |
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227 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) |
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228 { |
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229 return pixelSequence->card(); |
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230 } |
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231 else |
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232 { |
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233 return 1; |
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234 } |
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235 } |
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236 |
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237 |
302
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238 static void AnswerDicomField(RestApiOutput& output, |
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239 DcmElement& element, |
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240 E_TransferSyntax transferSyntax) |
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241 { |
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242 // This element is nor a sequence, neither a pixel-data |
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243 std::string buffer; |
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244 buffer.resize(65536); |
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245 Uint32 length = element.getLength(transferSyntax); |
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246 Uint32 offset = 0; |
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247 |
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248 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); |
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249 |
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250 while (offset < length) |
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251 { |
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252 Uint32 nbytes; |
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253 if (length - offset < buffer.size()) |
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254 { |
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255 nbytes = length - offset; |
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256 } |
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257 else |
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258 { |
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259 nbytes = buffer.size(); |
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260 } |
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261 |
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262 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); |
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263 |
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264 if (cond.good()) |
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265 { |
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266 output.GetLowLevelOutput().Send(&buffer[0], nbytes); |
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267 offset += nbytes; |
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268 } |
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269 else |
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270 { |
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271 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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272 return; |
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273 } |
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274 } |
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275 |
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276 output.MarkLowLevelOutputDone(); |
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277 } |
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278 |
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279 |
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280 static bool AnswerPixelData(RestApiOutput& output, |
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281 DcmItem& dicom, |
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282 E_TransferSyntax transferSyntax, |
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283 const std::string* blockUri) |
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284 { |
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285 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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286 DICOM_TAG_PIXEL_DATA.GetElement()); |
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287 |
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288 DcmElement *element = NULL; |
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289 if (!dicom.findAndGetElement(k, element).good() || |
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290 element == NULL) |
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291 { |
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292 return false; |
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293 } |
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294 |
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295 try |
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296 { |
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297 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); |
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298 if (blockUri == NULL) |
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299 { |
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300 // The user asks how many blocks are presents in this pixel data |
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301 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); |
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302 |
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303 Json::Value result(Json::arrayValue); |
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304 for (unsigned int i = 0; i < blocks; i++) |
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305 { |
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306 result.append(boost::lexical_cast<std::string>(i)); |
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307 } |
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308 |
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309 output.AnswerJson(result); |
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310 return true; |
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311 } |
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312 |
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313 |
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314 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); |
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315 |
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316 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) |
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317 { |
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318 DcmPixelSequence* pixelSequence = NULL; |
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319 if (pixelData.getEncapsulatedRepresentation |
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320 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) |
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321 { |
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322 // This is the case for JPEG transfer syntaxes |
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323 if (block < pixelSequence->card()) |
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324 { |
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325 DcmPixelItem* pixelItem = NULL; |
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326 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) |
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327 { |
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328 if (pixelItem->getLength() == 0) |
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329 { |
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330 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); |
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331 return true; |
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332 } |
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333 |
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334 Uint8* buffer = NULL; |
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335 if (pixelItem->getUint8Array(buffer).good() && buffer) |
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336 { |
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337 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); |
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338 return true; |
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339 } |
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340 } |
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341 } |
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342 } |
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343 else |
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344 { |
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345 // This is the case for raw, uncompressed image buffers |
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346 assert(*blockUri == "0"); |
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347 AnswerDicomField(output, *element, transferSyntax); |
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348 } |
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349 } |
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350 } |
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351 catch (boost::bad_lexical_cast&) |
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352 { |
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353 // The URI entered by the user is not a number |
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354 } |
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355 catch (std::bad_cast&) |
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356 { |
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357 // This should never happen |
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358 } |
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359 |
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360 return false; |
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361 } |
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362 |
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363 |
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364 |
285
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365 static void SendPathValueForLeaf(RestApiOutput& output, |
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366 const std::string& tag, |
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367 DcmItem& dicom, |
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368 E_TransferSyntax transferSyntax) |
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369 { |
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370 DcmTagKey k; |
304 | 371 ParseTagAndGroup(k, tag); |
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372 |
291
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373 DcmSequenceOfItems* sequence = NULL; |
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374 if (dicom.findAndGetSequence(k, sequence).good() && |
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375 sequence != NULL && |
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376 sequence->getVR() == EVR_SQ) |
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377 { |
291
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378 SendSequence(output, *sequence); |
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379 return; |
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380 } |
285
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381 |
291
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382 DcmElement* element = NULL; |
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383 if (dicom.findAndGetElement(k, element).good() && |
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384 element != NULL && |
318
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385 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags |
291
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386 element->getVR() != EVR_SQ) |
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387 { |
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388 AnswerDicomField(output, *element, transferSyntax); |
285
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389 } |
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390 } |
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391 |
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392 void ParsedDicomFile::SendPathValue(RestApiOutput& output, |
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393 const UriComponents& uri) |
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394 { |
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395 DcmItem* dicom = file_->getDataset(); |
682
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396 E_TransferSyntax transferSyntax = file_->getDataset()->getOriginalXfer(); |
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397 |
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398 // Special case: Accessing the pixel data |
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399 if (uri.size() == 1 || |
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400 uri.size() == 2) |
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401 { |
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402 DcmTagKey tag; |
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403 ParseTagAndGroup(tag, uri[0]); |
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404 |
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405 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && |
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406 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) |
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407 { |
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408 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); |
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409 return; |
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410 } |
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411 } |
285
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412 |
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413 // Go down in the tag hierarchy according to the URI |
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414 for (size_t pos = 0; pos < uri.size() / 2; pos++) |
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415 { |
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416 size_t index; |
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417 try |
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418 { |
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419 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); |
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420 } |
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421 catch (boost::bad_lexical_cast&) |
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422 { |
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423 return; |
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424 } |
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425 |
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426 DcmTagKey k; |
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427 DcmItem *child = NULL; |
304 | 428 ParseTagAndGroup(k, uri[2 * pos]); |
429 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
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430 child == NULL) |
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431 { |
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432 return; |
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433 } |
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434 |
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435 dicom = child; |
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436 } |
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437 |
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438 // We have reached the end of the URI |
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439 if (uri.size() % 2 == 0) |
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440 { |
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441 SendPathValueForDictionary(output, *dicom); |
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442 } |
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443 else |
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444 { |
682
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445 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); |
285
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446 } |
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447 } |
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448 |
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449 |
302
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450 |
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451 |
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452 |
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453 static DcmElement* CreateElementForTag(const DicomTag& tag) |
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454 { |
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455 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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456 |
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457 switch (key.getEVR()) |
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458 { |
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459 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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460 |
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461 /** |
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462 * TODO. |
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463 **/ |
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464 |
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465 case EVR_OB: // other byte |
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466 case EVR_OF: // other float |
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467 case EVR_OW: // other word |
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468 case EVR_AT: // attribute tag |
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469 throw OrthancException(ErrorCode_NotImplemented); |
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470 |
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471 case EVR_UN: // unknown value representation |
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472 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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473 |
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474 |
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475 /** |
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476 * String types. |
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477 * http://support.dcmtk.org/docs/classDcmByteString.html |
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478 **/ |
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479 |
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480 case EVR_AS: // age string |
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481 return new DcmAgeString(key); |
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482 |
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483 case EVR_AE: // application entity title |
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484 return new DcmApplicationEntity(key); |
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485 |
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486 case EVR_CS: // code string |
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487 return new DcmCodeString(key); |
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488 |
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489 case EVR_DA: // date string |
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490 return new DcmDate(key); |
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491 |
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492 case EVR_DT: // date time string |
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493 return new DcmDateTime(key); |
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494 |
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495 case EVR_DS: // decimal string |
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496 return new DcmDecimalString(key); |
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497 |
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498 case EVR_IS: // integer string |
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499 return new DcmIntegerString(key); |
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500 |
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501 case EVR_TM: // time string |
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502 return new DcmTime(key); |
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503 |
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504 case EVR_UI: // unique identifier |
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505 return new DcmUniqueIdentifier(key); |
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506 |
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507 case EVR_ST: // short text |
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508 return new DcmShortText(key); |
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509 |
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510 case EVR_LO: // long string |
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511 return new DcmLongString(key); |
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512 |
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513 case EVR_LT: // long text |
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514 return new DcmLongText(key); |
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515 |
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516 case EVR_UT: // unlimited text |
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517 return new DcmUnlimitedText(key); |
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518 |
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519 case EVR_SH: // short string |
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520 return new DcmShortString(key); |
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521 |
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522 case EVR_PN: // person name |
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523 return new DcmPersonName(key); |
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524 |
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525 |
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526 /** |
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527 * Numerical types |
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528 **/ |
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529 |
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530 case EVR_SL: // signed long |
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531 return new DcmSignedLong(key); |
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532 |
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533 case EVR_SS: // signed short |
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534 return new DcmSignedShort(key); |
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535 |
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536 case EVR_UL: // unsigned long |
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537 return new DcmUnsignedLong(key); |
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538 |
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539 case EVR_US: // unsigned short |
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540 return new DcmUnsignedShort(key); |
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541 |
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542 case EVR_FL: // float single-precision |
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543 return new DcmFloatingPointSingle(key); |
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544 |
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545 case EVR_FD: // float double-precision |
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546 return new DcmFloatingPointDouble(key); |
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547 |
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548 |
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549 /** |
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550 * Sequence types, should never occur at this point. |
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551 **/ |
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552 |
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553 case EVR_SQ: // sequence of items |
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554 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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555 |
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556 |
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557 /** |
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558 * Internal to DCMTK. |
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559 **/ |
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560 |
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561 case EVR_ox: // OB or OW depending on context |
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562 case EVR_xs: // SS or US depending on context |
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563 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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564 case EVR_na: // na="not applicable", for data which has no VR |
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565 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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566 case EVR_item: // used internally for items |
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567 case EVR_metainfo: // used internally for meta info datasets |
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568 case EVR_dataset: // used internally for datasets |
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569 case EVR_fileFormat: // used internally for DICOM files |
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570 case EVR_dicomDir: // used internally for DICOMDIR objects |
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571 case EVR_dirRecord: // used internally for DICOMDIR records |
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572 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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573 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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574 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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575 case EVR_PixelData: // used internally for uncompressed pixeld data |
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576 case EVR_OverlayData: // used internally for overlay data |
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577 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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578 default: |
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579 break; |
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580 } |
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581 |
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582 throw OrthancException(ErrorCode_InternalError); |
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583 } |
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584 |
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585 |
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586 |
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587 static void FillElementWithString(DcmElement& element, |
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588 const DicomTag& tag, |
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589 const std::string& value) |
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590 { |
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591 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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592 bool ok = false; |
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593 |
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594 try |
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595 { |
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596 switch (key.getEVR()) |
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597 { |
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598 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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599 |
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600 /** |
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601 * TODO. |
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602 **/ |
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603 |
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604 case EVR_OB: // other byte |
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605 case EVR_OF: // other float |
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606 case EVR_OW: // other word |
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607 case EVR_AT: // attribute tag |
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608 throw OrthancException(ErrorCode_NotImplemented); |
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609 |
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610 case EVR_UN: // unknown value representation |
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611 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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612 |
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613 |
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614 /** |
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615 * String types. |
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616 **/ |
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617 |
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618 case EVR_DS: // decimal string |
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619 case EVR_IS: // integer string |
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620 case EVR_AS: // age string |
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621 case EVR_DA: // date string |
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622 case EVR_DT: // date time string |
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623 case EVR_TM: // time string |
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624 case EVR_AE: // application entity title |
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625 case EVR_CS: // code string |
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626 case EVR_SH: // short string |
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627 case EVR_LO: // long string |
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628 case EVR_ST: // short text |
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629 case EVR_LT: // long text |
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630 case EVR_UT: // unlimited text |
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631 case EVR_PN: // person name |
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632 case EVR_UI: // unique identifier |
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633 { |
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634 ok = element.putString(value.c_str()).good(); |
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635 break; |
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636 } |
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637 |
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638 |
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639 /** |
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640 * Numerical types |
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641 **/ |
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642 |
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643 case EVR_SL: // signed long |
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644 { |
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645 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); |
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646 break; |
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647 } |
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648 |
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649 case EVR_SS: // signed short |
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650 { |
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651 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); |
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652 break; |
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653 } |
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654 |
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655 case EVR_UL: // unsigned long |
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656 { |
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657 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); |
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658 break; |
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659 } |
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660 |
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661 case EVR_US: // unsigned short |
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662 { |
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663 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); |
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664 break; |
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665 } |
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666 |
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667 case EVR_FL: // float single-precision |
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668 { |
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669 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); |
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670 break; |
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671 } |
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672 |
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673 case EVR_FD: // float double-precision |
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674 { |
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675 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); |
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676 break; |
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677 } |
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678 |
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679 |
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680 /** |
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681 * Sequence types, should never occur at this point. |
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682 **/ |
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683 |
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684 case EVR_SQ: // sequence of items |
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685 { |
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686 ok = false; |
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687 break; |
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688 } |
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689 |
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690 |
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691 /** |
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692 * Internal to DCMTK. |
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693 **/ |
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694 |
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695 case EVR_ox: // OB or OW depending on context |
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696 case EVR_xs: // SS or US depending on context |
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697 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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698 case EVR_na: // na="not applicable", for data which has no VR |
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699 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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700 case EVR_item: // used internally for items |
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701 case EVR_metainfo: // used internally for meta info datasets |
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702 case EVR_dataset: // used internally for datasets |
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703 case EVR_fileFormat: // used internally for DICOM files |
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704 case EVR_dicomDir: // used internally for DICOMDIR objects |
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705 case EVR_dirRecord: // used internally for DICOMDIR records |
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706 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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707 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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708 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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709 case EVR_PixelData: // used internally for uncompressed pixeld data |
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710 case EVR_OverlayData: // used internally for overlay data |
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711 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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712 default: |
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713 break; |
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714 } |
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715 } |
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716 catch (boost::bad_lexical_cast&) |
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717 { |
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718 ok = false; |
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719 } |
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720 |
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721 if (!ok) |
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722 { |
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723 throw OrthancException(ErrorCode_InternalError); |
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724 } |
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725 } |
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726 |
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727 |
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728 void ParsedDicomFile::Remove(const DicomTag& tag) |
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729 { |
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730 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
306
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731 DcmElement* element = file_->getDataset()->remove(key); |
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732 if (element != NULL) |
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733 { |
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734 delete element; |
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735 } |
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736 } |
302
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737 |
306
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738 |
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739 |
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740 void ParsedDicomFile::RemovePrivateTags() |
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741 { |
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742 typedef std::list<DcmElement*> Tags; |
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743 |
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744 Tags privateTags; |
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745 |
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746 DcmDataset& dataset = *file_->getDataset(); |
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747 for (unsigned long i = 0; i < dataset.card(); i++) |
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748 { |
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749 DcmElement* element = dataset.getElement(i); |
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750 DcmTag tag(element->getTag()); |
311 | 751 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK |
752 tag.getPrivateCreator() != NULL) | |
306
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753 { |
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754 privateTags.push_back(element); |
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755 } |
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756 } |
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757 |
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758 for (Tags::iterator it = privateTags.begin(); |
656 | 759 it != privateTags.end(); ++it) |
306
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760 { |
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761 DcmElement* tmp = dataset.remove(*it); |
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762 if (tmp != NULL) |
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763 { |
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764 delete tmp; |
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765 } |
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766 } |
302
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767 } |
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768 |
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769 |
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770 |
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771 void ParsedDicomFile::Insert(const DicomTag& tag, |
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772 const std::string& value) |
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773 { |
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774 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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775 FillElementWithString(*element, tag, value); |
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776 |
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777 if (!file_->getDataset()->insert(element.release(), false, false).good()) |
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778 { |
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779 // This field already exists |
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780 throw OrthancException(ErrorCode_InternalError); |
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781 } |
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782 } |
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783 |
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784 |
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785 void ParsedDicomFile::Replace(const DicomTag& tag, |
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786 const std::string& value, |
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787 DicomReplaceMode mode) |
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788 { |
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789 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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790 DcmElement* element = NULL; |
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791 |
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792 if (!file_->getDataset()->findAndGetElement(key, element).good() || |
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793 element == NULL) |
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794 { |
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795 // This field does not exist, act wrt. the specified "mode" |
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796 switch (mode) |
302
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797 { |
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798 case DicomReplaceMode_InsertIfAbsent: |
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799 Insert(tag, value); |
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800 break; |
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801 |
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802 case DicomReplaceMode_ThrowIfAbsent: |
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803 throw OrthancException(ErrorCode_InexistentItem); |
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804 |
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805 case DicomReplaceMode_IgnoreIfAbsent: |
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806 return; |
302
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|
807 } |
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|
808 } |
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diff
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|
809 else |
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|
810 { |
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|
811 FillElementWithString(*element, tag, value); |
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|
812 } |
303
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|
813 |
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diff
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|
814 |
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302
diff
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|
815 /** |
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|
816 * dcmodify will automatically correct 'Media Storage SOP Class |
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diff
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|
817 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if |
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818 * you make changes to the related tags in the dataset ('SOP Class |
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diff
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819 * UID' and 'SOP Instance UID') via insert or modify mode |
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diff
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820 * options. You can disable this behaviour by using the -nmu |
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diff
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|
821 * option. |
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diff
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|
822 **/ |
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diff
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|
823 if (tag == DICOM_TAG_SOP_CLASS_UID) |
305
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304
diff
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|
824 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); |
303
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302
diff
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|
825 |
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diff
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|
826 if (tag == DICOM_TAG_SOP_INSTANCE_UID) |
305
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304
diff
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|
827 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); |
302
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|
828 } |
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diff
changeset
|
829 |
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291
diff
changeset
|
830 |
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diff
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|
831 void ParsedDicomFile::Answer(RestApiOutput& output) |
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291
diff
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|
832 { |
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291
diff
changeset
|
833 std::string serialized; |
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291
diff
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|
834 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset())) |
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291
diff
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|
835 { |
682
efc4928be6fb
Recover pixel data for more transfer syntaxes (notably JPEG)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
677
diff
changeset
|
836 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); |
302
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291
diff
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|
837 } |
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291
diff
changeset
|
838 } |
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parents:
291
diff
changeset
|
839 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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291
diff
changeset
|
840 |
308
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Sebastien Jodogne <s.jodogne@gmail.com>
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306
diff
changeset
|
841 |
532
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
465
diff
changeset
|
842 static bool GetTagValueInternal(std::string& value, |
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465
diff
changeset
|
843 DcmItem& item, |
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465
diff
changeset
|
844 const DicomTag& tag) |
308
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306
diff
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|
845 { |
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306
diff
changeset
|
846 DcmTagKey k(tag.GetGroup(), tag.GetElement()); |
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306
diff
changeset
|
847 DcmElement* element = NULL; |
532
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465
diff
changeset
|
848 if (!item.findAndGetElement(k, element).good() || |
308
fbf2b2282086
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306
diff
changeset
|
849 element == NULL) |
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306
diff
changeset
|
850 { |
fbf2b2282086
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306
diff
changeset
|
851 return false; |
fbf2b2282086
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306
diff
changeset
|
852 } |
fbf2b2282086
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306
diff
changeset
|
853 |
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306
diff
changeset
|
854 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); |
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diff
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|
855 |
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306
diff
changeset
|
856 if (v.get() == NULL) |
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306
diff
changeset
|
857 { |
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306
diff
changeset
|
858 value = ""; |
fbf2b2282086
inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
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306
diff
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|
859 } |
fbf2b2282086
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Sebastien Jodogne <s.jodogne@gmail.com>
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306
diff
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|
860 else |
fbf2b2282086
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Sebastien Jodogne <s.jodogne@gmail.com>
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306
diff
changeset
|
861 { |
fbf2b2282086
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306
diff
changeset
|
862 value = v->AsString(); |
fbf2b2282086
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306
diff
changeset
|
863 } |
fbf2b2282086
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parents:
306
diff
changeset
|
864 |
532
b22312081388
extract roi geometry
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465
diff
changeset
|
865 return true; |
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
866 } |
b22312081388
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Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
867 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
868 |
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465
diff
changeset
|
869 bool ParsedDicomFile::GetTagValue(std::string& value, |
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465
diff
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870 const DicomTag& tag) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
871 { |
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diff
changeset
|
872 DcmDataset& dataset = *file_->getDataset(); |
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extract roi geometry
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|
873 return GetTagValueInternal(value, dataset, tag); |
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diff
changeset
|
874 } |
b22312081388
extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
875 |
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
876 |
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
877 |
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
878 bool ParsedDicomFile::GetTagValue(std::string& value, |
b22312081388
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|
879 const SequencePath& path, |
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465
diff
changeset
|
880 const DicomTag& tag) |
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diff
changeset
|
881 { |
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465
diff
changeset
|
882 if (path.size() == 0) |
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465
diff
changeset
|
883 { |
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465
diff
changeset
|
884 return GetTagValue(value, tag); |
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465
diff
changeset
|
885 } |
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extract roi geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
886 |
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extract roi geometry
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465
diff
changeset
|
887 DcmItem* current = file_->getDataset(); |
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diff
changeset
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888 assert(current != NULL); |
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465
diff
changeset
|
889 |
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diff
changeset
|
890 for (SequencePath::const_iterator it = path.begin(); it != path.end(); it++) |
b22312081388
extract roi geometry
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|
891 { |
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diff
changeset
|
892 DcmTagKey k(it->first.GetGroup(), it->first.GetElement()); |
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diff
changeset
|
893 |
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diff
changeset
|
894 DcmSequenceOfItems* sequence = NULL; |
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465
diff
changeset
|
895 if (!current->findAndGetSequence(k, sequence).good() || |
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diff
changeset
|
896 sequence == NULL || |
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diff
changeset
|
897 sequence->getVR() != EVR_SQ) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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465
diff
changeset
|
898 { |
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diff
changeset
|
899 return false; |
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900 } |
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901 |
535 | 902 if (it->second < 0 || it->second > sequence->card()) |
532
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903 { |
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904 return false; |
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905 } |
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906 |
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907 current = sequence->getItem(it->second); |
535 | 908 |
909 if (current == NULL) | |
910 { | |
911 return false; | |
912 } | |
532
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913 } |
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914 |
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915 return GetTagValueInternal(value, *current, tag); |
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916 } |
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917 |
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918 |
315 | 919 |
920 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
921 { | |
922 std::string patientId, studyUid, seriesUid, instanceUid; | |
923 | |
924 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
925 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
926 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
927 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
928 { | |
929 throw OrthancException(ErrorCode_BadFileFormat); | |
930 } | |
931 | |
932 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
933 } | |
934 | |
935 | |
0 | 936 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
937 { | |
938 target.Clear(); | |
939 for (unsigned long i = 0; i < dataset.card(); i++) | |
940 { | |
941 DcmElement* element = dataset.getElement(i); | |
942 if (element && element->isLeaf()) | |
943 { | |
944 target.SetValue(element->getTag().getGTag(), | |
945 element->getTag().getETag(), | |
946 ConvertLeafElement(*element)); | |
947 } | |
948 } | |
949 } | |
950 | |
951 | |
952 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
953 { | |
954 return DicomTag(element.getGTag(), element.getETag()); | |
955 } | |
956 | |
957 | |
958 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
959 { | |
960 if (!element.isLeaf()) | |
961 { | |
62 | 962 throw OrthancException("Only applicable to leaf elements"); |
0 | 963 } |
964 | |
965 if (element.isaString()) | |
966 { | |
967 char *c; | |
968 if (element.getString(c).good() && | |
969 c != NULL) | |
970 { | |
971 std::string s(c); | |
107
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972 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 973 return new DicomString(utf8); |
974 } | |
975 else | |
976 { | |
977 return new DicomNullValue; | |
978 } | |
979 } | |
980 | |
981 try | |
982 { | |
983 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
984 switch (element.getVR()) | |
985 { | |
986 | |
987 /** | |
988 * TODO. | |
989 **/ | |
306
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990 |
302
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991 case EVR_OB: // other byte |
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992 case EVR_OF: // other float |
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993 case EVR_OW: // other word |
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994 case EVR_AT: // attribute tag |
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995 case EVR_UN: // unknown value representation |
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996 return new DicomNullValue(); |
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997 |
302
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998 /** |
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999 * String types, should never happen at this point because of |
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1000 * "element.isaString()". |
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1001 **/ |
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1002 |
306
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1003 case EVR_DS: // decimal string |
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1004 case EVR_IS: // integer string |
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1005 case EVR_AS: // age string |
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1006 case EVR_DA: // date string |
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1007 case EVR_DT: // date time string |
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1008 case EVR_TM: // time string |
302
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1009 case EVR_AE: // application entity title |
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1010 case EVR_CS: // code string |
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1011 case EVR_SH: // short string |
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1012 case EVR_LO: // long string |
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1013 case EVR_ST: // short text |
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1014 case EVR_LT: // long text |
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1015 case EVR_UT: // unlimited text |
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1016 case EVR_PN: // person name |
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1017 case EVR_UI: // unique identifier |
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1018 return new DicomNullValue(); |
0 | 1019 |
1020 | |
302
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1021 /** |
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1022 * Numerical types |
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1023 **/ |
0 | 1024 |
302
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1025 case EVR_SL: // signed long |
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|
1026 { |
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|
1027 Sint32 f; |
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1028 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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1029 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1030 else |
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1031 return new DicomNullValue(); |
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|
1032 } |
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|
1033 |
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1034 case EVR_SS: // signed short |
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|
1035 { |
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|
1036 Sint16 f; |
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1037 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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1038 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1039 else |
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1040 return new DicomNullValue(); |
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1041 } |
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1042 |
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1043 case EVR_UL: // unsigned long |
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|
1044 { |
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|
1045 Uint32 f; |
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1046 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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1047 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1048 else |
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1049 return new DicomNullValue(); |
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|
1050 } |
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|
1051 |
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1052 case EVR_US: // unsigned short |
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|
1053 { |
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|
1054 Uint16 f; |
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1055 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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1056 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1057 else |
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1058 return new DicomNullValue(); |
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1059 } |
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1060 |
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1061 case EVR_FL: // float single-precision |
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1062 { |
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1063 Float32 f; |
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1064 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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1065 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1066 else |
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1067 return new DicomNullValue(); |
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1068 } |
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1069 |
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1070 case EVR_FD: // float double-precision |
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1071 { |
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1072 Float64 f; |
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1073 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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1074 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1075 else |
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1076 return new DicomNullValue(); |
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1077 } |
0 | 1078 |
1079 | |
1080 /** | |
302
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1081 * Sequence types, should never occur at this point because of |
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1082 * "element.isLeaf()". |
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1083 **/ |
0 | 1084 |
302
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1085 case EVR_SQ: // sequence of items |
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1086 return new DicomNullValue; |
0 | 1087 |
1088 | |
302
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1089 /** |
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1090 * Internal to DCMTK. |
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1091 **/ |
0 | 1092 |
302
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1093 case EVR_ox: // OB or OW depending on context |
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1094 case EVR_xs: // SS or US depending on context |
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1095 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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1096 case EVR_na: // na="not applicable", for data which has no VR |
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1097 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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1098 case EVR_item: // used internally for items |
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1099 case EVR_metainfo: // used internally for meta info datasets |
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1100 case EVR_dataset: // used internally for datasets |
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1101 case EVR_fileFormat: // used internally for DICOM files |
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1102 case EVR_dicomDir: // used internally for DICOMDIR objects |
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1103 case EVR_dirRecord: // used internally for DICOMDIR records |
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1104 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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1105 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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1106 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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1107 case EVR_PixelData: // used internally for uncompressed pixeld data |
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1108 case EVR_OverlayData: // used internally for overlay data |
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1109 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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1110 return new DicomNullValue; |
0 | 1111 |
1112 | |
302
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1113 /** |
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1114 * Default case. |
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1115 **/ |
0 | 1116 |
302
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1117 default: |
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1118 return new DicomNullValue; |
0 | 1119 } |
1120 } | |
1121 catch (boost::bad_lexical_cast) | |
1122 { | |
1123 return new DicomNullValue; | |
1124 } | |
306
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1125 catch (std::bad_cast) |
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1126 { |
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1127 return new DicomNullValue; |
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1128 } |
0 | 1129 } |
1130 | |
1131 | |
1132 static void StoreElement(Json::Value& target, | |
1133 DcmElement& element, | |
1134 unsigned int maxStringLength); | |
1135 | |
1136 static void StoreItem(Json::Value& target, | |
1137 DcmItem& item, | |
1138 unsigned int maxStringLength) | |
1139 { | |
1140 target = Json::Value(Json::objectValue); | |
1141 | |
1142 for (unsigned long i = 0; i < item.card(); i++) | |
1143 { | |
1144 DcmElement* element = item.getElement(i); | |
1145 StoreElement(target, *element, maxStringLength); | |
1146 } | |
1147 } | |
1148 | |
1149 | |
1150 static void StoreElement(Json::Value& target, | |
1151 DcmElement& element, | |
1152 unsigned int maxStringLength) | |
1153 { | |
1154 assert(target.type() == Json::objectValue); | |
1155 | |
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1156 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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1157 const std::string formattedTag = tag.Format(); |
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1158 |
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1159 #if 0 |
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1160 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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1161 #else |
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1162 // This version of the code gives access to the name of the private tags |
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1163 DcmTag tagbis(element.getTag()); |
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1164 const std::string tagName(tagbis.getTagName()); |
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1165 #endif |
0 | 1166 |
1167 if (element.isLeaf()) | |
1168 { | |
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1169 Json::Value value(Json::objectValue); |
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1170 value["Name"] = tagName; |
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1171 |
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1172 if (tagbis.getPrivateCreator() != NULL) |
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1173 { |
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1174 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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1175 } |
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1176 |
0 | 1177 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
1178 if (v->IsNull()) | |
1179 { | |
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1180 value["Type"] = "Null"; |
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1181 value["Value"] = Json::nullValue; |
0 | 1182 } |
1183 else | |
1184 { | |
1185 std::string s = v->AsString(); | |
1186 if (maxStringLength == 0 || | |
1187 s.size() <= maxStringLength) | |
1188 { | |
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1189 value["Type"] = "String"; |
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1190 value["Value"] = s; |
0 | 1191 } |
1192 else | |
1193 { | |
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1194 value["Type"] = "TooLong"; |
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1195 value["Value"] = Json::nullValue; |
0 | 1196 } |
1197 } | |
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1198 |
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1199 target[formattedTag] = value; |
0 | 1200 } |
1201 else | |
1202 { | |
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1203 Json::Value children(Json::arrayValue); |
0 | 1204 |
1205 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
1206 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
1207 // etc. are not." The following cast is thus OK. | |
1208 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
1209 | |
1210 for (unsigned long i = 0; i < sequence.card(); i++) | |
1211 { | |
1212 DcmItem* child = sequence.getItem(i); | |
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1213 Json::Value& v = children.append(Json::objectValue); |
0 | 1214 StoreItem(v, *child, maxStringLength); |
1215 } | |
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1216 |
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1217 target[formattedTag]["Name"] = tagName; |
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1218 target[formattedTag]["Type"] = "Sequence"; |
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1219 target[formattedTag]["Value"] = children; |
0 | 1220 } |
1221 } | |
1222 | |
1223 | |
1224 void FromDcmtkBridge::ToJson(Json::Value& root, | |
1225 DcmDataset& dataset, | |
1226 unsigned int maxStringLength) | |
1227 { | |
1228 StoreItem(root, dataset, maxStringLength); | |
1229 } | |
1230 | |
1231 | |
1232 | |
1233 void FromDcmtkBridge::ToJson(Json::Value& target, | |
1234 const std::string& path, | |
1235 unsigned int maxStringLength) | |
1236 { | |
1237 DcmFileFormat dicom; | |
1238 if (!dicom.loadFile(path.c_str()).good()) | |
1239 { | |
62 | 1240 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1241 } |
1242 else | |
1243 { | |
1244 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
1245 } | |
1246 } | |
1247 | |
1248 | |
368
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1249 static void ExtractPngImageColorPreview(std::string& result, |
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1250 DicomIntegerPixelAccessor& accessor) |
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1251 { |
368
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1252 assert(accessor.GetChannelCount() == 3); |
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1253 PngWriter w; |
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1254 |
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1255 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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1256 uint8_t* pixel = &image[0]; |
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1257 |
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1258 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1259 { |
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1260 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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1261 { |
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1262 for (unsigned int c = 0; c < 3; c++, pixel++) |
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1263 { |
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1264 int32_t v = accessor.GetValue(x, y, c); |
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1265 if (v < 0) |
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1266 *pixel = 0; |
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1267 else if (v > 255) |
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1268 *pixel = 255; |
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1269 else |
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1270 *pixel = v; |
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1271 } |
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1272 } |
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1273 } |
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1274 |
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1275 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1276 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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1277 } |
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1278 |
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1279 |
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1280 static void ExtractPngImageGrayscalePreview(std::string& result, |
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1281 DicomIntegerPixelAccessor& accessor) |
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1282 { |
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1283 assert(accessor.GetChannelCount() == 1); |
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1284 PngWriter w; |
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1285 |
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1286 int32_t min, max; |
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1287 accessor.GetExtremeValues(min, max); |
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1288 |
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1289 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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1290 if (min != max) |
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1291 { |
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1292 uint8_t* pixel = &image[0]; |
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1293 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1294 { |
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1295 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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1296 { |
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1297 int32_t v = accessor.GetValue(x, y); |
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1298 *pixel = static_cast<uint8_t>( |
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1299 boost::math::lround(static_cast<float>(v - min) / |
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1300 static_cast<float>(max - min) * 255.0f)); |
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1301 } |
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1302 } |
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1303 } |
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1304 |
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1305 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1306 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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1307 } |
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1308 |
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1309 |
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1310 template <typename T> |
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1311 static void ExtractPngImageTruncate(std::string& result, |
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1312 DicomIntegerPixelAccessor& accessor, |
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1313 PixelFormat format) |
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1314 { |
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1315 assert(accessor.GetChannelCount() == 1); |
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1316 |
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1317 PngWriter w; |
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1318 |
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1319 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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1320 T* pixel = &image[0]; |
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1321 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1322 { |
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1323 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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1324 { |
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1325 int32_t v = accessor.GetValue(x, y); |
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1326 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
42
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1327 *pixel = std::numeric_limits<T>::min(); |
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1328 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
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1329 *pixel = std::numeric_limits<T>::max(); |
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1330 else |
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1331 *pixel = static_cast<T>(v); |
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1332 } |
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1333 } |
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1334 |
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1335 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1336 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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1337 } |
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1338 |
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1339 |
319 | 1340 static bool DecodePsmctRle1(std::string& output, |
1341 DcmDataset& dataset) | |
1342 { | |
1343 static const DicomTag tagContent(0x07a1, 0x100a); | |
1344 static const DicomTag tagCompressionType(0x07a1, 0x1011); | |
1345 | |
1346 DcmElement* e; | |
1347 char* c; | |
1348 | |
1349 // Check whether the DICOM instance contains an image encoded with | |
1350 // the PMSCT_RLE1 scheme. | |
1351 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() || | |
1352 e == NULL || | |
1353 !e->isaString() || | |
1354 !e->getString(c).good() || | |
1355 c == NULL || | |
1356 strcmp("PMSCT_RLE1", c)) | |
1357 { | |
1358 return false; | |
1359 } | |
1360 | |
1361 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
1362 // data from the appropriate private DICOM tag. | |
1363 Uint8* pixData = NULL; | |
1364 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() || | |
1365 e == NULL || | |
1366 e->getUint8Array(pixData) != EC_Normal) | |
1367 { | |
1368 return false; | |
1369 } | |
1370 | |
1371 // The "unsigned" below IS VERY IMPORTANT | |
1372 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
1373 const size_t length = e->getLength(); | |
1374 | |
1375 /** | |
1376 * The code below is an adaptation of a sample code for GDCM by | |
1377 * Mathieu Malaterre (under a BSD license). | |
1378 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
1379 **/ | |
1380 | |
1381 // RLE pass | |
1382 std::vector<uint8_t> temp; | |
1383 temp.reserve(length); | |
1384 for (size_t i = 0; i < length; i++) | |
1385 { | |
1386 if (inbuffer[i] == 0xa5) | |
1387 { | |
1388 temp.push_back(inbuffer[i+2]); | |
1389 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
1390 { | |
1391 temp.push_back(inbuffer[i+2]); | |
1392 } | |
1393 i += 2; | |
1394 } | |
1395 else | |
1396 { | |
1397 temp.push_back(inbuffer[i]); | |
1398 } | |
1399 } | |
1400 | |
1401 // Delta encoding pass | |
1402 uint16_t delta = 0; | |
1403 output.clear(); | |
1404 output.reserve(temp.size()); | |
1405 for (size_t i = 0; i < temp.size(); i++) | |
1406 { | |
1407 uint16_t value; | |
1408 | |
1409 if (temp[i] == 0x5a) | |
1410 { | |
1411 uint16_t v1 = temp[i + 1]; | |
1412 uint16_t v2 = temp[i + 2]; | |
1413 value = (v2 << 8) + v1; | |
1414 i += 2; | |
1415 } | |
1416 else | |
1417 { | |
1418 value = delta + (int8_t) temp[i]; | |
1419 } | |
1420 | |
1421 output.push_back(value & 0xff); | |
1422 output.push_back(value >> 8); | |
1423 delta = value; | |
1424 } | |
1425 | |
1426 if (output.size() % 2) | |
1427 { | |
1428 output.resize(output.size() - 1); | |
1429 } | |
1430 | |
1431 return true; | |
1432 } | |
1433 | |
1434 | |
42
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1435 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1436 DcmDataset& dataset, |
53
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1437 unsigned int frame, |
42
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1438 ImageExtractionMode mode) |
0 | 1439 { |
1440 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
1441 | |
1442 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
1443 | |
1444 DicomMap m; | |
1445 FromDcmtkBridge::Convert(m, dataset); | |
1446 | |
319 | 1447 std::string privateContent; |
1448 | |
0 | 1449 DcmElement* e; |
80 | 1450 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 1451 e != NULL) |
1452 { | |
1453 Uint8* pixData = NULL; | |
1454 if (e->getUint8Array(pixData) == EC_Normal) | |
1455 { | |
1456 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
53
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1457 accessor->SetCurrentFrame(frame); |
0 | 1458 } |
1459 } | |
319 | 1460 else if (DecodePsmctRle1(privateContent, dataset)) |
1461 { | |
1462 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
1463 Uint8* pixData = NULL; | |
1464 if (privateContent.size() > 0) | |
1465 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
1466 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
1467 accessor->SetCurrentFrame(frame); | |
1468 } | |
419 | 1469 |
1470 if (accessor.get() == NULL) | |
1471 { | |
1472 throw OrthancException(ErrorCode_BadFileFormat); | |
1473 } | |
0 | 1474 |
42
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1475 PixelFormat format; |
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1476 bool supported = false; |
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1477 |
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1478 if (accessor->GetChannelCount() == 1) |
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1479 { |
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1480 switch (mode) |
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1481 { |
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1482 case ImageExtractionMode_Preview: |
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1483 supported = true; |
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1484 format = PixelFormat_Grayscale8; |
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1485 break; |
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1486 |
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1487 case ImageExtractionMode_UInt8: |
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1488 supported = true; |
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1489 format = PixelFormat_Grayscale8; |
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1490 break; |
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1491 |
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1492 case ImageExtractionMode_UInt16: |
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1493 supported = true; |
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1494 format = PixelFormat_Grayscale16; |
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1495 break; |
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1496 |
465
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1497 case ImageExtractionMode_Int16: |
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1498 supported = true; |
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1499 format = PixelFormat_SignedGrayscale16; |
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1500 break; |
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1501 |
369
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1502 default: |
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1503 supported = false; |
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1504 break; |
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1505 } |
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1506 } |
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1507 else if (accessor->GetChannelCount() == 3) |
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1508 { |
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1509 switch (mode) |
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1510 { |
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1511 case ImageExtractionMode_Preview: |
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1512 supported = true; |
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1513 format = PixelFormat_RGB24; |
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1514 break; |
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1515 |
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1516 default: |
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1517 supported = false; |
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1518 break; |
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1519 } |
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1520 } |
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1521 |
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1522 if (!supported) |
368
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1523 { |
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1524 throw OrthancException(ErrorCode_NotImplemented); |
369
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1525 } |
42
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1526 |
0 | 1527 if (accessor.get() == NULL || |
1528 accessor->GetWidth() == 0 || | |
1529 accessor->GetHeight() == 0) | |
1530 { | |
42
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1531 PngWriter w; |
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1532 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 1533 } |
1534 else | |
1535 { | |
42
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1536 switch (mode) |
0 | 1537 { |
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1538 case ImageExtractionMode_Preview: |
368
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1539 if (format == PixelFormat_Grayscale8) |
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1540 ExtractPngImageGrayscalePreview(result, *accessor); |
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1541 else |
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1542 ExtractPngImageColorPreview(result, *accessor); |
302
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1543 break; |
42
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1544 |
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1545 case ImageExtractionMode_UInt8: |
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1546 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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1547 break; |
42
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1548 |
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1549 case ImageExtractionMode_UInt16: |
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1550 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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1551 break; |
42
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1552 |
465
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1553 case ImageExtractionMode_Int16: |
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1554 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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1555 break; |
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1556 |
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1557 default: |
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1558 throw OrthancException(ErrorCode_NotImplemented); |
0 | 1559 } |
1560 } | |
1561 } | |
1562 | |
1563 | |
42
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1564 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1565 const std::string& dicomContent, |
53
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1566 unsigned int frame, |
42
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1567 ImageExtractionMode mode) |
0 | 1568 { |
1569 DcmInputBufferStream is; | |
1570 if (dicomContent.size() > 0) | |
1571 { | |
1572 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
1573 } | |
1574 is.setEos(); | |
1575 | |
1576 DcmFileFormat dicom; | |
1577 if (dicom.read(is).good()) | |
1578 { | |
53
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1579 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 1580 } |
1581 else | |
1582 { | |
62 | 1583 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1584 } |
1585 } | |
1586 | |
1587 | |
1588 | |
1589 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
1590 { | |
106 | 1591 // Some patches for important tags because of different DICOM |
1592 // dictionaries between DCMTK versions | |
291
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1593 std::string n = t.GetMainTagsName(); |
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1594 if (n.size() != 0) |
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1595 { |
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1596 return n; |
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1597 } |
106 | 1598 // End of patches |
1599 | |
305
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1600 #if 0 |
0 | 1601 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
1602 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1603 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
1604 | |
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1605 std::string s(DcmTag_ERROR_TagName); |
0 | 1606 if (entry != NULL) |
1607 { | |
1608 s = std::string(entry->getTagName()); | |
1609 } | |
1610 | |
1611 dcmDataDict.unlock(); | |
1612 return s; | |
305
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1613 #else |
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1614 DcmTag tag(t.GetGroup(), t.GetElement()); |
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1615 const char* name = tag.getTagName(); |
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1616 if (name == NULL) |
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1617 { |
306
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1618 return DcmTag_ERROR_TagName; |
305
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1619 } |
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1620 else |
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1621 { |
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1622 return std::string(name); |
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1623 } |
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1624 #endif |
0 | 1625 } |
1626 | |
1627 | |
304 | 1628 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
0 | 1629 { |
304 | 1630 if (strlen(name) == 9 && |
1631 isxdigit(name[0]) && | |
1632 isxdigit(name[1]) && | |
1633 isxdigit(name[2]) && | |
1634 isxdigit(name[3]) && | |
1635 name[4] == '-' && | |
1636 isxdigit(name[5]) && | |
1637 isxdigit(name[6]) && | |
1638 isxdigit(name[7]) && | |
1639 isxdigit(name[8])) | |
1640 { | |
1641 uint16_t group = GetTagValue(name); | |
1642 uint16_t element = GetTagValue(name + 5); | |
1643 return DicomTag(group, element); | |
1644 } | |
1645 | |
305
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1646 #if 0 |
0 | 1647 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
1648 const DcmDictEntry* entry = dict.findEntry(name); | |
1649 | |
1650 if (entry == NULL) | |
1651 { | |
1652 dcmDataDict.unlock(); | |
62 | 1653 throw OrthancException("Unknown DICOM tag"); |
0 | 1654 } |
1655 else | |
1656 { | |
1657 DcmTagKey key = entry->getKey(); | |
1658 DicomTag tag(key.getGroup(), key.getElement()); | |
1659 dcmDataDict.unlock(); | |
1660 return tag; | |
1661 } | |
305
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1662 #else |
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1663 DcmTag tag; |
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1664 if (DcmTag::findTagFromName(name, tag).good()) |
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1665 { |
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1666 return DicomTag(tag.getGTag(), tag.getETag()); |
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1667 } |
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1668 else |
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1669 { |
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1670 throw OrthancException("Unknown DICOM tag"); |
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1671 } |
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1672 #endif |
0 | 1673 } |
1674 | |
1675 | |
1676 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
1677 { | |
1678 for (DicomMap::Map::const_iterator | |
656 | 1679 it = m.map_.begin(); it != m.map_.end(); ++it) |
0 | 1680 { |
1681 DicomTag t = it->first; | |
1682 std::string s = it->second->AsString(); | |
319 | 1683 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
0 | 1684 } |
1685 } | |
1686 | |
1687 | |
1688 void FromDcmtkBridge::ToJson(Json::Value& result, | |
1689 const DicomMap& values) | |
1690 { | |
1691 if (result.type() != Json::objectValue) | |
1692 { | |
62 | 1693 throw OrthancException(ErrorCode_BadParameterType); |
0 | 1694 } |
1695 | |
1696 result.clear(); | |
1697 | |
1698 for (DicomMap::Map::const_iterator | |
656 | 1699 it = values.map_.begin(); it != values.map_.end(); ++it) |
0 | 1700 { |
1701 result[GetName(it->first)] = it->second->AsString(); | |
1702 } | |
1703 } | |
176 | 1704 |
1705 | |
1706 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
1707 { | |
1708 char uid[100]; | |
1709 | |
1710 switch (level) | |
1711 { | |
306
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1712 case DicomRootLevel_Patient: |
311 | 1713 // The "PatientID" field is of type LO (Long String), 64 |
1714 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
1715 // as a random PatientID. | |
1716 return Toolbox::GenerateUuid(); | |
306
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1717 |
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1718 case DicomRootLevel_Instance: |
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1719 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 1720 |
302
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1721 case DicomRootLevel_Series: |
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1722 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 1723 |
302
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1724 case DicomRootLevel_Study: |
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1725 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 1726 |
302
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1727 default: |
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1728 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 1729 } |
1730 } | |
1731 | |
291
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1732 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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1733 DcmDataset* dataSet) |
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1734 { |
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1735 // Determine the transfer syntax which shall be used to write the |
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1736 // information to the file. We always switch to the Little Endian |
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1737 // syntax, with explicit length. |
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1738 |
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1739 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
661
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1740 |
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1741 |
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1742 /** |
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1743 * Note that up to Orthanc 0.7.1 (inclusive), the |
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1744 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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1745 * dataset into memory. We now keep the original transfer syntax |
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1746 * (if available). |
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1747 **/ |
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1748 E_TransferSyntax xfer = dataSet->getOriginalXfer(); |
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1749 if (xfer == EXS_Unknown) |
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1750 { |
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1751 // No information about the original transfer syntax: This is |
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1752 // most probably a DICOM dataset that was read from memory. |
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1753 xfer = EXS_LittleEndianExplicit; |
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1754 } |
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1755 |
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1756 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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1757 |
661
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1758 // Create the meta-header information |
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1759 DcmFileFormat ff(dataSet); |
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1760 ff.validateMetaInfo(xfer); |
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1761 |
661
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1762 // Create a memory buffer with the proper size |
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1763 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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1764 buffer.resize(s); |
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1765 DcmOutputBufferStream ob(&buffer[0], s); |
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1766 |
661
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1767 // Fill the memory buffer with the meta-header and the dataset |
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1768 ff.transferInit(); |
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1769 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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1770 /*opt_groupLength*/ EGL_recalcGL, |
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1771 /*opt_paddingType*/ EPD_withoutPadding); |
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1772 ff.transferEnd(); |
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1773 |
661
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1774 // Handle errors |
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1775 if (c.good()) |
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1776 { |
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1777 return true; |
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1778 } |
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1779 else |
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1780 { |
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1781 buffer.clear(); |
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1782 return false; |
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1783 } |
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1784 } |
0 | 1785 } |