Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 702:7592a48e97e4
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 11 Feb 2014 17:28:17 +0100 |
parents | 2d0a347e8cfc |
children | 8cfc6119a5bd efd0215736d9 |
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> | |
302
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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) |
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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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809 else |
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810 { |
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811 FillElementWithString(*element, tag, value); |
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812 } |
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813 |
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814 |
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815 /** |
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816 * dcmodify will automatically correct 'Media Storage SOP Class |
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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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819 * UID' and 'SOP Instance UID') via insert or modify mode |
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820 * options. You can disable this behaviour by using the -nmu |
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821 * option. |
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822 **/ |
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823 if (tag == DICOM_TAG_SOP_CLASS_UID) |
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824 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); |
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825 |
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826 if (tag == DICOM_TAG_SOP_INSTANCE_UID) |
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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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829 |
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830 |
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831 void ParsedDicomFile::Answer(RestApiOutput& output) |
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832 { |
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833 std::string serialized; |
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834 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset())) |
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835 { |
682
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836 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); |
302
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837 } |
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838 } |
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839 |
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840 |
308
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841 |
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842 bool ParsedDicomFile::GetTagValue(std::string& value, |
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843 const DicomTag& tag) |
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844 { |
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845 DcmTagKey k(tag.GetGroup(), tag.GetElement()); |
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846 DcmDataset& dataset = *file_->getDataset(); |
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847 DcmElement* element = NULL; |
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848 if (!dataset.findAndGetElement(k, element).good() || |
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849 element == NULL) |
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850 { |
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851 return false; |
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852 } |
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853 |
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854 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); |
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855 |
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856 if (v.get() == NULL) |
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857 { |
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858 value = ""; |
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859 } |
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860 else |
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861 { |
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862 value = v->AsString(); |
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863 } |
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864 |
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865 return true; |
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866 } |
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867 |
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868 |
315 | 869 |
870 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
871 { | |
872 std::string patientId, studyUid, seriesUid, instanceUid; | |
873 | |
874 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
875 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
876 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
877 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
878 { | |
879 throw OrthancException(ErrorCode_BadFileFormat); | |
880 } | |
881 | |
882 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
883 } | |
884 | |
885 | |
0 | 886 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
887 { | |
888 target.Clear(); | |
889 for (unsigned long i = 0; i < dataset.card(); i++) | |
890 { | |
891 DcmElement* element = dataset.getElement(i); | |
892 if (element && element->isLeaf()) | |
893 { | |
894 target.SetValue(element->getTag().getGTag(), | |
895 element->getTag().getETag(), | |
896 ConvertLeafElement(*element)); | |
897 } | |
898 } | |
899 } | |
900 | |
901 | |
902 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
903 { | |
904 return DicomTag(element.getGTag(), element.getETag()); | |
905 } | |
906 | |
907 | |
908 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
909 { | |
910 if (!element.isLeaf()) | |
911 { | |
62 | 912 throw OrthancException("Only applicable to leaf elements"); |
0 | 913 } |
914 | |
915 if (element.isaString()) | |
916 { | |
917 char *c; | |
918 if (element.getString(c).good() && | |
919 c != NULL) | |
920 { | |
921 std::string s(c); | |
107
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922 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 923 return new DicomString(utf8); |
924 } | |
925 else | |
926 { | |
927 return new DicomNullValue; | |
928 } | |
929 } | |
930 | |
931 try | |
932 { | |
933 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
934 switch (element.getVR()) | |
935 { | |
936 | |
937 /** | |
938 * TODO. | |
939 **/ | |
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940 |
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941 case EVR_OB: // other byte |
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942 case EVR_OF: // other float |
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943 case EVR_OW: // other word |
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944 case EVR_AT: // attribute tag |
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945 case EVR_UN: // unknown value representation |
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946 return new DicomNullValue(); |
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947 |
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948 /** |
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949 * String types, should never happen at this point because of |
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950 * "element.isaString()". |
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951 **/ |
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952 |
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953 case EVR_DS: // decimal string |
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954 case EVR_IS: // integer string |
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955 case EVR_AS: // age string |
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956 case EVR_DA: // date string |
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957 case EVR_DT: // date time string |
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958 case EVR_TM: // time string |
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959 case EVR_AE: // application entity title |
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960 case EVR_CS: // code string |
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961 case EVR_SH: // short string |
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962 case EVR_LO: // long string |
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963 case EVR_ST: // short text |
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964 case EVR_LT: // long text |
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965 case EVR_UT: // unlimited text |
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966 case EVR_PN: // person name |
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967 case EVR_UI: // unique identifier |
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968 return new DicomNullValue(); |
0 | 969 |
970 | |
302
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971 /** |
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972 * Numerical types |
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973 **/ |
0 | 974 |
302
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975 case EVR_SL: // signed long |
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976 { |
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977 Sint32 f; |
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978 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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979 return new DicomString(boost::lexical_cast<std::string>(f)); |
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980 else |
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981 return new DicomNullValue(); |
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982 } |
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983 |
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984 case EVR_SS: // signed short |
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985 { |
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986 Sint16 f; |
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987 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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988 return new DicomString(boost::lexical_cast<std::string>(f)); |
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989 else |
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990 return new DicomNullValue(); |
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991 } |
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992 |
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993 case EVR_UL: // unsigned long |
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994 { |
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995 Uint32 f; |
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996 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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997 return new DicomString(boost::lexical_cast<std::string>(f)); |
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998 else |
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999 return new DicomNullValue(); |
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1000 } |
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1001 |
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1002 case EVR_US: // unsigned short |
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1003 { |
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1004 Uint16 f; |
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1005 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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1006 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1007 else |
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1008 return new DicomNullValue(); |
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1009 } |
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1010 |
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1011 case EVR_FL: // float single-precision |
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1012 { |
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1013 Float32 f; |
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1014 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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1015 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1016 else |
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1017 return new DicomNullValue(); |
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1018 } |
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1019 |
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1020 case EVR_FD: // float double-precision |
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1021 { |
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1022 Float64 f; |
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1023 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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1024 return new DicomString(boost::lexical_cast<std::string>(f)); |
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1025 else |
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1026 return new DicomNullValue(); |
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1027 } |
0 | 1028 |
1029 | |
1030 /** | |
302
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1031 * Sequence types, should never occur at this point because of |
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1032 * "element.isLeaf()". |
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1033 **/ |
0 | 1034 |
302
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1035 case EVR_SQ: // sequence of items |
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1036 return new DicomNullValue; |
0 | 1037 |
1038 | |
302
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1039 /** |
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1040 * Internal to DCMTK. |
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1041 **/ |
0 | 1042 |
302
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1043 case EVR_ox: // OB or OW depending on context |
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1044 case EVR_xs: // SS or US depending on context |
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1045 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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1046 case EVR_na: // na="not applicable", for data which has no VR |
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1047 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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1048 case EVR_item: // used internally for items |
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1049 case EVR_metainfo: // used internally for meta info datasets |
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1050 case EVR_dataset: // used internally for datasets |
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1051 case EVR_fileFormat: // used internally for DICOM files |
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1052 case EVR_dicomDir: // used internally for DICOMDIR objects |
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1053 case EVR_dirRecord: // used internally for DICOMDIR records |
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1054 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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1055 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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1056 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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1057 case EVR_PixelData: // used internally for uncompressed pixeld data |
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1058 case EVR_OverlayData: // used internally for overlay data |
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1059 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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1060 return new DicomNullValue; |
0 | 1061 |
1062 | |
302
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|
1063 /** |
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1064 * Default case. |
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1065 **/ |
0 | 1066 |
302
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1067 default: |
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1068 return new DicomNullValue; |
0 | 1069 } |
1070 } | |
1071 catch (boost::bad_lexical_cast) | |
1072 { | |
1073 return new DicomNullValue; | |
1074 } | |
306
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1075 catch (std::bad_cast) |
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1076 { |
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1077 return new DicomNullValue; |
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1078 } |
0 | 1079 } |
1080 | |
1081 | |
1082 static void StoreElement(Json::Value& target, | |
1083 DcmElement& element, | |
1084 unsigned int maxStringLength); | |
1085 | |
1086 static void StoreItem(Json::Value& target, | |
1087 DcmItem& item, | |
1088 unsigned int maxStringLength) | |
1089 { | |
1090 target = Json::Value(Json::objectValue); | |
1091 | |
1092 for (unsigned long i = 0; i < item.card(); i++) | |
1093 { | |
1094 DcmElement* element = item.getElement(i); | |
1095 StoreElement(target, *element, maxStringLength); | |
1096 } | |
1097 } | |
1098 | |
1099 | |
1100 static void StoreElement(Json::Value& target, | |
1101 DcmElement& element, | |
1102 unsigned int maxStringLength) | |
1103 { | |
1104 assert(target.type() == Json::objectValue); | |
1105 | |
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1106 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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1107 const std::string formattedTag = tag.Format(); |
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1108 |
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1109 #if 0 |
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1110 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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1111 #else |
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1112 // This version of the code gives access to the name of the private tags |
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1113 DcmTag tagbis(element.getTag()); |
306
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1114 const std::string tagName(tagbis.getTagName()); |
305
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1115 #endif |
0 | 1116 |
1117 if (element.isLeaf()) | |
1118 { | |
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1119 Json::Value value(Json::objectValue); |
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1120 value["Name"] = tagName; |
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1121 |
306
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1122 if (tagbis.getPrivateCreator() != NULL) |
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1123 { |
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1124 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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1125 } |
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1126 |
0 | 1127 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
1128 if (v->IsNull()) | |
1129 { | |
35
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1130 value["Type"] = "Null"; |
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1131 value["Value"] = Json::nullValue; |
0 | 1132 } |
1133 else | |
1134 { | |
1135 std::string s = v->AsString(); | |
1136 if (maxStringLength == 0 || | |
1137 s.size() <= maxStringLength) | |
1138 { | |
35
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|
1139 value["Type"] = "String"; |
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1140 value["Value"] = s; |
0 | 1141 } |
1142 else | |
1143 { | |
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1144 value["Type"] = "TooLong"; |
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|
1145 value["Value"] = Json::nullValue; |
0 | 1146 } |
1147 } | |
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1148 |
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1149 target[formattedTag] = value; |
0 | 1150 } |
1151 else | |
1152 { | |
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1153 Json::Value children(Json::arrayValue); |
0 | 1154 |
1155 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
1156 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
1157 // etc. are not." The following cast is thus OK. | |
1158 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
1159 | |
1160 for (unsigned long i = 0; i < sequence.card(); i++) | |
1161 { | |
1162 DcmItem* child = sequence.getItem(i); | |
35
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1163 Json::Value& v = children.append(Json::objectValue); |
0 | 1164 StoreItem(v, *child, maxStringLength); |
1165 } | |
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1166 |
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1167 target[formattedTag]["Name"] = tagName; |
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|
1168 target[formattedTag]["Type"] = "Sequence"; |
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|
1169 target[formattedTag]["Value"] = children; |
0 | 1170 } |
1171 } | |
1172 | |
1173 | |
1174 void FromDcmtkBridge::ToJson(Json::Value& root, | |
1175 DcmDataset& dataset, | |
1176 unsigned int maxStringLength) | |
1177 { | |
1178 StoreItem(root, dataset, maxStringLength); | |
1179 } | |
1180 | |
1181 | |
1182 | |
1183 void FromDcmtkBridge::ToJson(Json::Value& target, | |
1184 const std::string& path, | |
1185 unsigned int maxStringLength) | |
1186 { | |
1187 DcmFileFormat dicom; | |
1188 if (!dicom.loadFile(path.c_str()).good()) | |
1189 { | |
62 | 1190 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1191 } |
1192 else | |
1193 { | |
1194 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
1195 } | |
1196 } | |
1197 | |
1198 | |
368
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1199 static void ExtractPngImageColorPreview(std::string& result, |
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1200 DicomIntegerPixelAccessor& accessor) |
42
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1201 { |
368
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1202 assert(accessor.GetChannelCount() == 3); |
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1203 PngWriter w; |
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1204 |
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1205 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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1206 uint8_t* pixel = &image[0]; |
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1207 |
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1208 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1209 { |
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|
1210 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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1211 { |
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1212 for (unsigned int c = 0; c < 3; c++, pixel++) |
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1213 { |
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|
1214 int32_t v = accessor.GetValue(x, y, c); |
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1215 if (v < 0) |
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1216 *pixel = 0; |
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1217 else if (v > 255) |
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1218 *pixel = 255; |
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1219 else |
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1220 *pixel = v; |
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1221 } |
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|
1222 } |
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|
1223 } |
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1224 |
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|
1225 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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|
1226 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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1227 } |
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|
1228 |
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|
1229 |
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|
1230 static void ExtractPngImageGrayscalePreview(std::string& result, |
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|
1231 DicomIntegerPixelAccessor& accessor) |
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|
1232 { |
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|
1233 assert(accessor.GetChannelCount() == 1); |
42
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|
1234 PngWriter w; |
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|
1235 |
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|
1236 int32_t min, max; |
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diff
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|
1237 accessor.GetExtremeValues(min, max); |
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41
diff
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|
1238 |
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41
diff
changeset
|
1239 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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diff
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|
1240 if (min != max) |
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41
diff
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|
1241 { |
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|
1242 uint8_t* pixel = &image[0]; |
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diff
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|
1243 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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diff
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|
1244 { |
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diff
changeset
|
1245 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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diff
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|
1246 { |
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diff
changeset
|
1247 int32_t v = accessor.GetValue(x, y); |
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diff
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|
1248 *pixel = static_cast<uint8_t>( |
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41
diff
changeset
|
1249 boost::math::lround(static_cast<float>(v - min) / |
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41
diff
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|
1250 static_cast<float>(max - min) * 255.0f)); |
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41
diff
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|
1251 } |
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41
diff
changeset
|
1252 } |
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41
diff
changeset
|
1253 } |
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41
diff
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|
1254 |
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41
diff
changeset
|
1255 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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diff
changeset
|
1256 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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diff
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|
1257 } |
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41
diff
changeset
|
1258 |
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diff
changeset
|
1259 |
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41
diff
changeset
|
1260 template <typename T> |
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diff
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|
1261 static void ExtractPngImageTruncate(std::string& result, |
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diff
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|
1262 DicomIntegerPixelAccessor& accessor, |
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diff
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|
1263 PixelFormat format) |
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|
1264 { |
368
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|
1265 assert(accessor.GetChannelCount() == 1); |
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|
1266 |
42
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diff
changeset
|
1267 PngWriter w; |
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diff
changeset
|
1268 |
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diff
changeset
|
1269 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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|
1270 T* pixel = &image[0]; |
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|
1271 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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|
1272 { |
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changeset
|
1273 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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diff
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|
1274 { |
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diff
changeset
|
1275 int32_t v = accessor.GetValue(x, y); |
464
5987dd8e0776
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diff
changeset
|
1276 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
42
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|
1277 *pixel = std::numeric_limits<T>::min(); |
464
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changeset
|
1278 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
42
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changeset
|
1279 *pixel = std::numeric_limits<T>::max(); |
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|
1280 else |
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|
1281 *pixel = static_cast<T>(v); |
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|
1282 } |
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changeset
|
1283 } |
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changeset
|
1284 |
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1285 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1286 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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1287 } |
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1288 |
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1289 |
319 | 1290 static bool DecodePsmctRle1(std::string& output, |
1291 DcmDataset& dataset) | |
1292 { | |
1293 static const DicomTag tagContent(0x07a1, 0x100a); | |
1294 static const DicomTag tagCompressionType(0x07a1, 0x1011); | |
1295 | |
1296 DcmElement* e; | |
1297 char* c; | |
1298 | |
1299 // Check whether the DICOM instance contains an image encoded with | |
1300 // the PMSCT_RLE1 scheme. | |
1301 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() || | |
1302 e == NULL || | |
1303 !e->isaString() || | |
1304 !e->getString(c).good() || | |
1305 c == NULL || | |
1306 strcmp("PMSCT_RLE1", c)) | |
1307 { | |
1308 return false; | |
1309 } | |
1310 | |
1311 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
1312 // data from the appropriate private DICOM tag. | |
1313 Uint8* pixData = NULL; | |
1314 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() || | |
1315 e == NULL || | |
1316 e->getUint8Array(pixData) != EC_Normal) | |
1317 { | |
1318 return false; | |
1319 } | |
1320 | |
1321 // The "unsigned" below IS VERY IMPORTANT | |
1322 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
1323 const size_t length = e->getLength(); | |
1324 | |
1325 /** | |
1326 * The code below is an adaptation of a sample code for GDCM by | |
1327 * Mathieu Malaterre (under a BSD license). | |
1328 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
1329 **/ | |
1330 | |
1331 // RLE pass | |
1332 std::vector<uint8_t> temp; | |
1333 temp.reserve(length); | |
1334 for (size_t i = 0; i < length; i++) | |
1335 { | |
1336 if (inbuffer[i] == 0xa5) | |
1337 { | |
1338 temp.push_back(inbuffer[i+2]); | |
1339 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
1340 { | |
1341 temp.push_back(inbuffer[i+2]); | |
1342 } | |
1343 i += 2; | |
1344 } | |
1345 else | |
1346 { | |
1347 temp.push_back(inbuffer[i]); | |
1348 } | |
1349 } | |
1350 | |
1351 // Delta encoding pass | |
1352 uint16_t delta = 0; | |
1353 output.clear(); | |
1354 output.reserve(temp.size()); | |
1355 for (size_t i = 0; i < temp.size(); i++) | |
1356 { | |
1357 uint16_t value; | |
1358 | |
1359 if (temp[i] == 0x5a) | |
1360 { | |
1361 uint16_t v1 = temp[i + 1]; | |
1362 uint16_t v2 = temp[i + 2]; | |
1363 value = (v2 << 8) + v1; | |
1364 i += 2; | |
1365 } | |
1366 else | |
1367 { | |
1368 value = delta + (int8_t) temp[i]; | |
1369 } | |
1370 | |
1371 output.push_back(value & 0xff); | |
1372 output.push_back(value >> 8); | |
1373 delta = value; | |
1374 } | |
1375 | |
1376 if (output.size() % 2) | |
1377 { | |
1378 output.resize(output.size() - 1); | |
1379 } | |
1380 | |
1381 return true; | |
1382 } | |
1383 | |
1384 | |
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1385 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1386 DcmDataset& dataset, |
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1387 unsigned int frame, |
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1388 ImageExtractionMode mode) |
0 | 1389 { |
1390 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
1391 | |
1392 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
1393 | |
1394 DicomMap m; | |
1395 FromDcmtkBridge::Convert(m, dataset); | |
1396 | |
319 | 1397 std::string privateContent; |
1398 | |
0 | 1399 DcmElement* e; |
80 | 1400 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 1401 e != NULL) |
1402 { | |
1403 Uint8* pixData = NULL; | |
1404 if (e->getUint8Array(pixData) == EC_Normal) | |
1405 { | |
1406 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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1407 accessor->SetCurrentFrame(frame); |
0 | 1408 } |
1409 } | |
319 | 1410 else if (DecodePsmctRle1(privateContent, dataset)) |
1411 { | |
1412 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
1413 Uint8* pixData = NULL; | |
1414 if (privateContent.size() > 0) | |
1415 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
1416 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
1417 accessor->SetCurrentFrame(frame); | |
1418 } | |
419 | 1419 |
1420 if (accessor.get() == NULL) | |
1421 { | |
1422 throw OrthancException(ErrorCode_BadFileFormat); | |
1423 } | |
0 | 1424 |
42
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1425 PixelFormat format; |
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1426 bool supported = false; |
368
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1427 |
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1428 if (accessor->GetChannelCount() == 1) |
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1429 { |
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1430 switch (mode) |
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1431 { |
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1432 case ImageExtractionMode_Preview: |
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1433 supported = true; |
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1434 format = PixelFormat_Grayscale8; |
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1435 break; |
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1436 |
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1437 case ImageExtractionMode_UInt8: |
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1438 supported = true; |
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1439 format = PixelFormat_Grayscale8; |
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1440 break; |
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1441 |
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1442 case ImageExtractionMode_UInt16: |
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1443 supported = true; |
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1444 format = PixelFormat_Grayscale16; |
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1445 break; |
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1446 |
465
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1447 case ImageExtractionMode_Int16: |
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1448 supported = true; |
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1449 format = PixelFormat_SignedGrayscale16; |
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1450 break; |
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1451 |
369
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1452 default: |
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1453 supported = false; |
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1454 break; |
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1455 } |
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1456 } |
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1457 else if (accessor->GetChannelCount() == 3) |
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1458 { |
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1459 switch (mode) |
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1460 { |
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1461 case ImageExtractionMode_Preview: |
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1462 supported = true; |
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1463 format = PixelFormat_RGB24; |
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1464 break; |
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1465 |
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1466 default: |
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1467 supported = false; |
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1468 break; |
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1469 } |
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1470 } |
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1471 |
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1472 if (!supported) |
368
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1473 { |
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1474 throw OrthancException(ErrorCode_NotImplemented); |
369
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1475 } |
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1476 |
0 | 1477 if (accessor.get() == NULL || |
1478 accessor->GetWidth() == 0 || | |
1479 accessor->GetHeight() == 0) | |
1480 { | |
42
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1481 PngWriter w; |
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1482 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 1483 } |
1484 else | |
1485 { | |
42
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1486 switch (mode) |
0 | 1487 { |
302
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1488 case ImageExtractionMode_Preview: |
368
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1489 if (format == PixelFormat_Grayscale8) |
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1490 ExtractPngImageGrayscalePreview(result, *accessor); |
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1491 else |
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1492 ExtractPngImageColorPreview(result, *accessor); |
302
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1493 break; |
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1494 |
302
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1495 case ImageExtractionMode_UInt8: |
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1496 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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1497 break; |
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1498 |
302
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1499 case ImageExtractionMode_UInt16: |
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1500 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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1501 break; |
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1502 |
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1503 case ImageExtractionMode_Int16: |
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1504 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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1505 break; |
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1506 |
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1507 default: |
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1508 throw OrthancException(ErrorCode_NotImplemented); |
0 | 1509 } |
1510 } | |
1511 } | |
1512 | |
1513 | |
42
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1514 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1515 const std::string& dicomContent, |
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1516 unsigned int frame, |
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1517 ImageExtractionMode mode) |
0 | 1518 { |
1519 DcmInputBufferStream is; | |
1520 if (dicomContent.size() > 0) | |
1521 { | |
1522 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
1523 } | |
1524 is.setEos(); | |
1525 | |
1526 DcmFileFormat dicom; | |
1527 if (dicom.read(is).good()) | |
1528 { | |
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1529 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 1530 } |
1531 else | |
1532 { | |
62 | 1533 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1534 } |
1535 } | |
1536 | |
1537 | |
1538 | |
1539 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
1540 { | |
106 | 1541 // Some patches for important tags because of different DICOM |
1542 // dictionaries between DCMTK versions | |
291
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1543 std::string n = t.GetMainTagsName(); |
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1544 if (n.size() != 0) |
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1545 { |
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1546 return n; |
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1547 } |
106 | 1548 // End of patches |
1549 | |
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1550 #if 0 |
0 | 1551 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
1552 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1553 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
1554 | |
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1555 std::string s(DcmTag_ERROR_TagName); |
0 | 1556 if (entry != NULL) |
1557 { | |
1558 s = std::string(entry->getTagName()); | |
1559 } | |
1560 | |
1561 dcmDataDict.unlock(); | |
1562 return s; | |
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1563 #else |
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1564 DcmTag tag(t.GetGroup(), t.GetElement()); |
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1565 const char* name = tag.getTagName(); |
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1566 if (name == NULL) |
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1567 { |
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1568 return DcmTag_ERROR_TagName; |
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1569 } |
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1570 else |
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1571 { |
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1572 return std::string(name); |
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1573 } |
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1574 #endif |
0 | 1575 } |
1576 | |
1577 | |
304 | 1578 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
0 | 1579 { |
304 | 1580 if (strlen(name) == 9 && |
1581 isxdigit(name[0]) && | |
1582 isxdigit(name[1]) && | |
1583 isxdigit(name[2]) && | |
1584 isxdigit(name[3]) && | |
1585 name[4] == '-' && | |
1586 isxdigit(name[5]) && | |
1587 isxdigit(name[6]) && | |
1588 isxdigit(name[7]) && | |
1589 isxdigit(name[8])) | |
1590 { | |
1591 uint16_t group = GetTagValue(name); | |
1592 uint16_t element = GetTagValue(name + 5); | |
1593 return DicomTag(group, element); | |
1594 } | |
1595 | |
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1596 #if 0 |
0 | 1597 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
1598 const DcmDictEntry* entry = dict.findEntry(name); | |
1599 | |
1600 if (entry == NULL) | |
1601 { | |
1602 dcmDataDict.unlock(); | |
62 | 1603 throw OrthancException("Unknown DICOM tag"); |
0 | 1604 } |
1605 else | |
1606 { | |
1607 DcmTagKey key = entry->getKey(); | |
1608 DicomTag tag(key.getGroup(), key.getElement()); | |
1609 dcmDataDict.unlock(); | |
1610 return tag; | |
1611 } | |
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1612 #else |
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1613 DcmTag tag; |
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1614 if (DcmTag::findTagFromName(name, tag).good()) |
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1615 { |
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1616 return DicomTag(tag.getGTag(), tag.getETag()); |
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1617 } |
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1618 else |
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1619 { |
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1620 throw OrthancException("Unknown DICOM tag"); |
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1621 } |
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1622 #endif |
0 | 1623 } |
1624 | |
1625 | |
1626 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
1627 { | |
1628 for (DicomMap::Map::const_iterator | |
656 | 1629 it = m.map_.begin(); it != m.map_.end(); ++it) |
0 | 1630 { |
1631 DicomTag t = it->first; | |
1632 std::string s = it->second->AsString(); | |
319 | 1633 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
0 | 1634 } |
1635 } | |
1636 | |
1637 | |
1638 void FromDcmtkBridge::ToJson(Json::Value& result, | |
1639 const DicomMap& values) | |
1640 { | |
1641 if (result.type() != Json::objectValue) | |
1642 { | |
62 | 1643 throw OrthancException(ErrorCode_BadParameterType); |
0 | 1644 } |
1645 | |
1646 result.clear(); | |
1647 | |
1648 for (DicomMap::Map::const_iterator | |
656 | 1649 it = values.map_.begin(); it != values.map_.end(); ++it) |
0 | 1650 { |
1651 result[GetName(it->first)] = it->second->AsString(); | |
1652 } | |
1653 } | |
176 | 1654 |
1655 | |
1656 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
1657 { | |
1658 char uid[100]; | |
1659 | |
1660 switch (level) | |
1661 { | |
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1662 case DicomRootLevel_Patient: |
311 | 1663 // The "PatientID" field is of type LO (Long String), 64 |
1664 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
1665 // as a random PatientID. | |
1666 return Toolbox::GenerateUuid(); | |
306
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1667 |
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1668 case DicomRootLevel_Instance: |
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1669 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 1670 |
302
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1671 case DicomRootLevel_Series: |
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1672 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 1673 |
302
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1674 case DicomRootLevel_Study: |
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1675 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 1676 |
302
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1677 default: |
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1678 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 1679 } |
1680 } | |
1681 | |
291
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1682 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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1683 DcmDataset* dataSet) |
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1684 { |
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1685 // Determine the transfer syntax which shall be used to write the |
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1686 // information to the file. We always switch to the Little Endian |
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1687 // syntax, with explicit length. |
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1688 |
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1689 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
661
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1690 |
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1691 |
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1692 /** |
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1693 * Note that up to Orthanc 0.7.1 (inclusive), the |
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1694 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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1695 * dataset into memory. We now keep the original transfer syntax |
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1696 * (if available). |
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1697 **/ |
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1698 E_TransferSyntax xfer = dataSet->getOriginalXfer(); |
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1699 if (xfer == EXS_Unknown) |
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1700 { |
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1701 // No information about the original transfer syntax: This is |
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1702 // most probably a DICOM dataset that was read from memory. |
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1703 xfer = EXS_LittleEndianExplicit; |
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1704 } |
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1705 |
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1706 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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1707 |
661
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1708 // Create the meta-header information |
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1709 DcmFileFormat ff(dataSet); |
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1710 ff.validateMetaInfo(xfer); |
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1711 |
661
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1712 // Create a memory buffer with the proper size |
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1713 uint32_t s = ff.calcElementLength(xfer, encodingType); |
291
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1714 buffer.resize(s); |
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1715 DcmOutputBufferStream ob(&buffer[0], s); |
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1716 |
661
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1717 // Fill the memory buffer with the meta-header and the dataset |
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1718 ff.transferInit(); |
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1719 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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1720 /*opt_groupLength*/ EGL_recalcGL, |
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1721 /*opt_paddingType*/ EPD_withoutPadding); |
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1722 ff.transferEnd(); |
291
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1723 |
661
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1724 // Handle errors |
291
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1725 if (c.good()) |
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1726 { |
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1727 return true; |
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1728 } |
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1729 else |
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1730 { |
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1731 buffer.clear(); |
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1732 return false; |
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1733 } |
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1734 } |
0 | 1735 } |