Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 799:777b6b694da6
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 06 May 2014 12:55:41 +0200 |
| parents | 331eaf9d9d69 |
| children | a811bdf8b8eb |
| rev | line source |
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| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
| 689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
| 0 | 4 * Belgium |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 136 | 10 * |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 0 | 22 * |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
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32 |
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33 |
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34 /*========================================================================= |
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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" | |
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107
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82 #include "../Core/Toolbox.h" |
| 62 | 83 #include "../Core/OrthancException.h" |
| 799 | 84 #include "../Core/ImageFormats/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 |
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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> | |
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100 #include <dcmtk/dcmdata/dcuid.h> |
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101 #include <dcmtk/dcmdata/dcmetinf.h> |
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102 |
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103 #include <dcmtk/dcmdata/dcvrae.h> |
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104 #include <dcmtk/dcmdata/dcvras.h> |
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105 #include <dcmtk/dcmdata/dcvrcs.h> |
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106 #include <dcmtk/dcmdata/dcvrda.h> |
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107 #include <dcmtk/dcmdata/dcvrds.h> |
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108 #include <dcmtk/dcmdata/dcvrdt.h> |
| 0 | 109 #include <dcmtk/dcmdata/dcvrfd.h> |
| 110 #include <dcmtk/dcmdata/dcvrfl.h> | |
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111 #include <dcmtk/dcmdata/dcvris.h> |
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112 #include <dcmtk/dcmdata/dcvrlo.h> |
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113 #include <dcmtk/dcmdata/dcvrlt.h> |
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114 #include <dcmtk/dcmdata/dcvrpn.h> |
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115 #include <dcmtk/dcmdata/dcvrsh.h> |
| 0 | 116 #include <dcmtk/dcmdata/dcvrsl.h> |
| 117 #include <dcmtk/dcmdata/dcvrss.h> | |
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118 #include <dcmtk/dcmdata/dcvrst.h> |
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119 #include <dcmtk/dcmdata/dcvrtm.h> |
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120 #include <dcmtk/dcmdata/dcvrui.h> |
| 0 | 121 #include <dcmtk/dcmdata/dcvrul.h> |
| 122 #include <dcmtk/dcmdata/dcvrus.h> | |
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123 #include <dcmtk/dcmdata/dcvrut.h> |
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124 #include <dcmtk/dcmdata/dcpixel.h> |
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125 #include <dcmtk/dcmdata/dcpixseq.h> |
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126 #include <dcmtk/dcmdata/dcpxitem.h> |
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127 |
| 0 | 128 |
| 2 | 129 #include <boost/math/special_functions/round.hpp> |
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130 #include <glog/logging.h> |
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131 #include <dcmtk/dcmdata/dcostrmb.h> |
| 0 | 132 |
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133 |
| 62 | 134 namespace Orthanc |
| 0 | 135 { |
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136 static inline uint16_t GetCharValue(char c) |
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137 { |
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138 if (c >= '0' && c <= '9') |
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139 return c - '0'; |
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140 else if (c >= 'a' && c <= 'f') |
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141 return c - 'a' + 10; |
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142 else if (c >= 'A' && c <= 'F') |
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143 return c - 'A' + 10; |
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144 else |
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145 return 0; |
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146 } |
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147 |
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148 static inline uint16_t GetTagValue(const char* c) |
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149 { |
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150 return ((GetCharValue(c[0]) << 12) + |
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151 (GetCharValue(c[1]) << 8) + |
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152 (GetCharValue(c[2]) << 4) + |
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153 GetCharValue(c[3])); |
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154 } |
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155 |
| 0 | 156 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 157 { | |
| 158 target.Clear(); | |
| 159 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 160 { | |
| 161 DcmElement* element = dataset.getElement(i); | |
| 162 if (element && element->isLeaf()) | |
| 163 { | |
| 164 target.SetValue(element->getTag().getGTag(), | |
| 165 element->getTag().getETag(), | |
| 166 ConvertLeafElement(*element)); | |
| 167 } | |
| 168 } | |
| 169 } | |
| 170 | |
| 171 | |
| 172 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 173 { | |
| 174 return DicomTag(element.getGTag(), element.getETag()); | |
| 175 } | |
| 176 | |
| 177 | |
| 178 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 179 { | |
| 180 if (!element.isLeaf()) | |
| 181 { | |
| 62 | 182 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 183 } |
| 184 | |
| 185 if (element.isaString()) | |
| 186 { | |
| 187 char *c; | |
| 188 if (element.getString(c).good() && | |
| 189 c != NULL) | |
| 190 { | |
| 191 std::string s(c); | |
|
107
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192 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 193 return new DicomString(utf8); |
| 194 } | |
| 195 else | |
| 196 { | |
| 197 return new DicomNullValue; | |
| 198 } | |
| 199 } | |
| 200 | |
| 201 try | |
| 202 { | |
| 203 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 204 switch (element.getVR()) | |
| 205 { | |
| 206 | |
| 207 /** | |
| 208 * TODO. | |
| 209 **/ | |
|
306
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210 |
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211 case EVR_OB: // other byte |
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212 case EVR_OF: // other float |
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213 case EVR_OW: // other word |
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214 case EVR_AT: // attribute tag |
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215 case EVR_UN: // unknown value representation |
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216 return new DicomNullValue(); |
|
306
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217 |
|
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218 /** |
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219 * String types, should never happen at this point because of |
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220 * "element.isaString()". |
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221 **/ |
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222 |
|
306
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223 case EVR_DS: // decimal string |
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224 case EVR_IS: // integer string |
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225 case EVR_AS: // age string |
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226 case EVR_DA: // date string |
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227 case EVR_DT: // date time string |
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228 case EVR_TM: // time string |
|
302
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229 case EVR_AE: // application entity title |
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230 case EVR_CS: // code string |
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231 case EVR_SH: // short string |
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232 case EVR_LO: // long string |
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233 case EVR_ST: // short text |
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234 case EVR_LT: // long text |
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235 case EVR_UT: // unlimited text |
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236 case EVR_PN: // person name |
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237 case EVR_UI: // unique identifier |
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238 return new DicomNullValue(); |
| 0 | 239 |
| 240 | |
|
302
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241 /** |
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242 * Numerical types |
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243 **/ |
| 0 | 244 |
|
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245 case EVR_SL: // signed long |
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246 { |
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247 Sint32 f; |
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248 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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249 return new DicomString(boost::lexical_cast<std::string>(f)); |
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250 else |
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251 return new DicomNullValue(); |
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252 } |
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253 |
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254 case EVR_SS: // signed short |
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255 { |
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256 Sint16 f; |
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257 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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258 return new DicomString(boost::lexical_cast<std::string>(f)); |
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259 else |
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260 return new DicomNullValue(); |
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261 } |
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262 |
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263 case EVR_UL: // unsigned long |
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264 { |
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265 Uint32 f; |
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266 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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267 return new DicomString(boost::lexical_cast<std::string>(f)); |
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268 else |
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269 return new DicomNullValue(); |
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270 } |
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271 |
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272 case EVR_US: // unsigned short |
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273 { |
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274 Uint16 f; |
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275 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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276 return new DicomString(boost::lexical_cast<std::string>(f)); |
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277 else |
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278 return new DicomNullValue(); |
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279 } |
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280 |
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281 case EVR_FL: // float single-precision |
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282 { |
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283 Float32 f; |
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284 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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285 return new DicomString(boost::lexical_cast<std::string>(f)); |
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286 else |
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287 return new DicomNullValue(); |
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288 } |
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289 |
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290 case EVR_FD: // float double-precision |
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291 { |
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292 Float64 f; |
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293 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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294 return new DicomString(boost::lexical_cast<std::string>(f)); |
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295 else |
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296 return new DicomNullValue(); |
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297 } |
| 0 | 298 |
| 299 | |
| 300 /** | |
|
302
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301 * Sequence types, should never occur at this point because of |
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302 * "element.isLeaf()". |
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303 **/ |
| 0 | 304 |
|
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305 case EVR_SQ: // sequence of items |
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306 return new DicomNullValue; |
| 0 | 307 |
| 308 | |
|
302
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309 /** |
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310 * Internal to DCMTK. |
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311 **/ |
| 0 | 312 |
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313 case EVR_ox: // OB or OW depending on context |
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314 case EVR_xs: // SS or US depending on context |
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315 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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316 case EVR_na: // na="not applicable", for data which has no VR |
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317 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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318 case EVR_item: // used internally for items |
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319 case EVR_metainfo: // used internally for meta info datasets |
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320 case EVR_dataset: // used internally for datasets |
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321 case EVR_fileFormat: // used internally for DICOM files |
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322 case EVR_dicomDir: // used internally for DICOMDIR objects |
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323 case EVR_dirRecord: // used internally for DICOMDIR records |
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324 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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325 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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326 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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327 case EVR_PixelData: // used internally for uncompressed pixeld data |
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328 case EVR_OverlayData: // used internally for overlay data |
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329 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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330 return new DicomNullValue; |
| 0 | 331 |
| 332 | |
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333 /** |
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334 * Default case. |
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335 **/ |
| 0 | 336 |
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337 default: |
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338 return new DicomNullValue; |
| 0 | 339 } |
| 340 } | |
| 341 catch (boost::bad_lexical_cast) | |
| 342 { | |
| 343 return new DicomNullValue; | |
| 344 } | |
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345 catch (std::bad_cast) |
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346 { |
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347 return new DicomNullValue; |
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348 } |
| 0 | 349 } |
| 350 | |
| 351 | |
| 352 static void StoreElement(Json::Value& target, | |
| 353 DcmElement& element, | |
| 354 unsigned int maxStringLength); | |
| 355 | |
| 356 static void StoreItem(Json::Value& target, | |
| 357 DcmItem& item, | |
| 358 unsigned int maxStringLength) | |
| 359 { | |
| 360 target = Json::Value(Json::objectValue); | |
| 361 | |
| 362 for (unsigned long i = 0; i < item.card(); i++) | |
| 363 { | |
| 364 DcmElement* element = item.getElement(i); | |
| 365 StoreElement(target, *element, maxStringLength); | |
| 366 } | |
| 367 } | |
| 368 | |
| 369 | |
| 370 static void StoreElement(Json::Value& target, | |
| 371 DcmElement& element, | |
| 372 unsigned int maxStringLength) | |
| 373 { | |
| 374 assert(target.type() == Json::objectValue); | |
| 375 | |
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376 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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377 const std::string formattedTag = tag.Format(); |
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378 |
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379 #if 0 |
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380 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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381 #else |
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382 // This version of the code gives access to the name of the private tags |
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383 DcmTag tagbis(element.getTag()); |
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384 const std::string tagName(tagbis.getTagName()); |
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385 #endif |
| 0 | 386 |
| 387 if (element.isLeaf()) | |
| 388 { | |
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389 Json::Value value(Json::objectValue); |
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390 value["Name"] = tagName; |
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391 |
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392 if (tagbis.getPrivateCreator() != NULL) |
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393 { |
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394 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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395 } |
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396 |
| 0 | 397 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 398 if (v->IsNull()) | |
| 399 { | |
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400 value["Type"] = "Null"; |
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401 value["Value"] = Json::nullValue; |
| 0 | 402 } |
| 403 else | |
| 404 { | |
| 405 std::string s = v->AsString(); | |
| 406 if (maxStringLength == 0 || | |
| 407 s.size() <= maxStringLength) | |
| 408 { | |
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409 value["Type"] = "String"; |
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410 value["Value"] = s; |
| 0 | 411 } |
| 412 else | |
| 413 { | |
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414 value["Type"] = "TooLong"; |
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415 value["Value"] = Json::nullValue; |
| 0 | 416 } |
| 417 } | |
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418 |
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419 target[formattedTag] = value; |
| 0 | 420 } |
| 421 else | |
| 422 { | |
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423 Json::Value children(Json::arrayValue); |
| 0 | 424 |
| 425 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 426 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 427 // etc. are not." The following cast is thus OK. | |
| 428 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 429 | |
| 430 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 431 { | |
| 432 DcmItem* child = sequence.getItem(i); | |
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433 Json::Value& v = children.append(Json::objectValue); |
| 0 | 434 StoreItem(v, *child, maxStringLength); |
| 435 } | |
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436 |
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437 target[formattedTag]["Name"] = tagName; |
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438 target[formattedTag]["Type"] = "Sequence"; |
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439 target[formattedTag]["Value"] = children; |
| 0 | 440 } |
| 441 } | |
| 442 | |
| 443 | |
| 444 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 445 DcmDataset& dataset, | |
| 446 unsigned int maxStringLength) | |
| 447 { | |
| 448 StoreItem(root, dataset, maxStringLength); | |
| 449 } | |
| 450 | |
| 451 | |
| 452 | |
| 453 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 454 const std::string& path, | |
| 455 unsigned int maxStringLength) | |
| 456 { | |
| 457 DcmFileFormat dicom; | |
| 458 if (!dicom.loadFile(path.c_str()).good()) | |
| 459 { | |
| 62 | 460 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 461 } |
| 462 else | |
| 463 { | |
| 464 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 465 } | |
| 466 } | |
| 467 | |
| 468 | |
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469 static void ExtractPngImageColorPreview(std::string& result, |
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470 DicomIntegerPixelAccessor& accessor) |
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471 { |
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472 assert(accessor.GetChannelCount() == 3); |
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473 PngWriter w; |
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474 |
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475 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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476 uint8_t* pixel = &image[0]; |
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477 |
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478 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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479 { |
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480 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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481 { |
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482 for (unsigned int c = 0; c < 3; c++, pixel++) |
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483 { |
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484 int32_t v = accessor.GetValue(x, y, c); |
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485 if (v < 0) |
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486 *pixel = 0; |
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487 else if (v > 255) |
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488 *pixel = 255; |
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489 else |
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490 *pixel = v; |
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491 } |
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492 } |
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493 } |
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494 |
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495 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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496 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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497 } |
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498 |
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499 |
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500 static void ExtractPngImageGrayscalePreview(std::string& result, |
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501 DicomIntegerPixelAccessor& accessor) |
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502 { |
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503 assert(accessor.GetChannelCount() == 1); |
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504 PngWriter w; |
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505 |
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506 int32_t min, max; |
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507 accessor.GetExtremeValues(min, max); |
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508 |
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509 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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510 if (min != max) |
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511 { |
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512 uint8_t* pixel = &image[0]; |
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513 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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514 { |
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515 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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516 { |
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517 int32_t v = accessor.GetValue(x, y); |
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518 *pixel = static_cast<uint8_t>( |
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519 boost::math::lround(static_cast<float>(v - min) / |
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520 static_cast<float>(max - min) * 255.0f)); |
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521 } |
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522 } |
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523 } |
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524 |
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525 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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526 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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527 } |
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528 |
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529 |
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530 template <typename T> |
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531 static void ExtractPngImageTruncate(std::string& result, |
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532 DicomIntegerPixelAccessor& accessor, |
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533 PixelFormat format) |
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534 { |
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535 assert(accessor.GetChannelCount() == 1); |
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536 |
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537 PngWriter w; |
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538 |
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539 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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540 T* pixel = &image[0]; |
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541 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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542 { |
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543 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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544 { |
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545 int32_t v = accessor.GetValue(x, y); |
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546 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
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547 *pixel = std::numeric_limits<T>::min(); |
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548 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
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549 *pixel = std::numeric_limits<T>::max(); |
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550 else |
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551 *pixel = static_cast<T>(v); |
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552 } |
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553 } |
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554 |
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555 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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556 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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557 } |
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558 |
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559 |
| 319 | 560 static bool DecodePsmctRle1(std::string& output, |
| 561 DcmDataset& dataset) | |
| 562 { | |
| 563 static const DicomTag tagContent(0x07a1, 0x100a); | |
| 564 static const DicomTag tagCompressionType(0x07a1, 0x1011); | |
| 565 | |
| 566 DcmElement* e; | |
| 567 char* c; | |
| 568 | |
| 569 // Check whether the DICOM instance contains an image encoded with | |
| 570 // the PMSCT_RLE1 scheme. | |
| 571 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() || | |
| 572 e == NULL || | |
| 573 !e->isaString() || | |
| 574 !e->getString(c).good() || | |
| 575 c == NULL || | |
| 576 strcmp("PMSCT_RLE1", c)) | |
| 577 { | |
| 578 return false; | |
| 579 } | |
| 580 | |
| 581 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
| 582 // data from the appropriate private DICOM tag. | |
| 583 Uint8* pixData = NULL; | |
| 584 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() || | |
| 585 e == NULL || | |
| 586 e->getUint8Array(pixData) != EC_Normal) | |
| 587 { | |
| 588 return false; | |
| 589 } | |
| 590 | |
| 591 // The "unsigned" below IS VERY IMPORTANT | |
| 592 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
| 593 const size_t length = e->getLength(); | |
| 594 | |
| 595 /** | |
| 596 * The code below is an adaptation of a sample code for GDCM by | |
| 597 * Mathieu Malaterre (under a BSD license). | |
| 598 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
| 599 **/ | |
| 600 | |
| 601 // RLE pass | |
| 602 std::vector<uint8_t> temp; | |
| 603 temp.reserve(length); | |
| 604 for (size_t i = 0; i < length; i++) | |
| 605 { | |
| 606 if (inbuffer[i] == 0xa5) | |
| 607 { | |
| 608 temp.push_back(inbuffer[i+2]); | |
| 609 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
| 610 { | |
| 611 temp.push_back(inbuffer[i+2]); | |
| 612 } | |
| 613 i += 2; | |
| 614 } | |
| 615 else | |
| 616 { | |
| 617 temp.push_back(inbuffer[i]); | |
| 618 } | |
| 619 } | |
| 620 | |
| 621 // Delta encoding pass | |
| 622 uint16_t delta = 0; | |
| 623 output.clear(); | |
| 624 output.reserve(temp.size()); | |
| 625 for (size_t i = 0; i < temp.size(); i++) | |
| 626 { | |
| 627 uint16_t value; | |
| 628 | |
| 629 if (temp[i] == 0x5a) | |
| 630 { | |
| 631 uint16_t v1 = temp[i + 1]; | |
| 632 uint16_t v2 = temp[i + 2]; | |
| 633 value = (v2 << 8) + v1; | |
| 634 i += 2; | |
| 635 } | |
| 636 else | |
| 637 { | |
| 638 value = delta + (int8_t) temp[i]; | |
| 639 } | |
| 640 | |
| 641 output.push_back(value & 0xff); | |
| 642 output.push_back(value >> 8); | |
| 643 delta = value; | |
| 644 } | |
| 645 | |
| 646 if (output.size() % 2) | |
| 647 { | |
| 648 output.resize(output.size() - 1); | |
| 649 } | |
| 650 | |
| 651 return true; | |
| 652 } | |
| 653 | |
| 654 | |
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655 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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656 DcmDataset& dataset, |
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657 unsigned int frame, |
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658 ImageExtractionMode mode) |
| 0 | 659 { |
| 660 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 661 | |
| 662 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 663 | |
| 664 DicomMap m; | |
| 665 FromDcmtkBridge::Convert(m, dataset); | |
| 666 | |
| 319 | 667 std::string privateContent; |
| 668 | |
| 0 | 669 DcmElement* e; |
| 80 | 670 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 671 e != NULL) |
| 672 { | |
| 673 Uint8* pixData = NULL; | |
| 674 if (e->getUint8Array(pixData) == EC_Normal) | |
| 675 { | |
| 676 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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677 accessor->SetCurrentFrame(frame); |
| 0 | 678 } |
| 679 } | |
| 319 | 680 else if (DecodePsmctRle1(privateContent, dataset)) |
| 681 { | |
| 682 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
| 683 Uint8* pixData = NULL; | |
| 684 if (privateContent.size() > 0) | |
| 685 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
| 686 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
| 687 accessor->SetCurrentFrame(frame); | |
| 688 } | |
| 419 | 689 |
| 690 if (accessor.get() == NULL) | |
| 691 { | |
| 692 throw OrthancException(ErrorCode_BadFileFormat); | |
| 693 } | |
| 0 | 694 |
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695 PixelFormat format; |
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696 bool supported = false; |
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697 |
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698 if (accessor->GetChannelCount() == 1) |
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699 { |
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700 switch (mode) |
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701 { |
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702 case ImageExtractionMode_Preview: |
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703 supported = true; |
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704 format = PixelFormat_Grayscale8; |
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705 break; |
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706 |
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707 case ImageExtractionMode_UInt8: |
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708 supported = true; |
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709 format = PixelFormat_Grayscale8; |
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710 break; |
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711 |
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712 case ImageExtractionMode_UInt16: |
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713 supported = true; |
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714 format = PixelFormat_Grayscale16; |
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715 break; |
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716 |
|
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717 case ImageExtractionMode_Int16: |
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718 supported = true; |
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719 format = PixelFormat_SignedGrayscale16; |
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720 break; |
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721 |
|
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722 default: |
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723 supported = false; |
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724 break; |
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725 } |
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726 } |
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727 else if (accessor->GetChannelCount() == 3) |
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728 { |
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729 switch (mode) |
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730 { |
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731 case ImageExtractionMode_Preview: |
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732 supported = true; |
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733 format = PixelFormat_RGB24; |
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734 break; |
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735 |
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736 default: |
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737 supported = false; |
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738 break; |
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739 } |
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740 } |
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741 |
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742 if (!supported) |
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743 { |
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744 throw OrthancException(ErrorCode_NotImplemented); |
|
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745 } |
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746 |
| 0 | 747 if (accessor.get() == NULL || |
| 748 accessor->GetWidth() == 0 || | |
| 749 accessor->GetHeight() == 0) | |
| 750 { | |
|
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751 PngWriter w; |
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|
752 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 753 } |
| 754 else | |
| 755 { | |
|
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756 switch (mode) |
| 0 | 757 { |
|
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758 case ImageExtractionMode_Preview: |
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759 if (format == PixelFormat_Grayscale8) |
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760 ExtractPngImageGrayscalePreview(result, *accessor); |
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761 else |
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762 ExtractPngImageColorPreview(result, *accessor); |
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763 break; |
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764 |
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765 case ImageExtractionMode_UInt8: |
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766 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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767 break; |
|
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768 |
|
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769 case ImageExtractionMode_UInt16: |
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770 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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771 break; |
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772 |
|
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773 case ImageExtractionMode_Int16: |
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774 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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775 break; |
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776 |
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777 default: |
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778 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 779 } |
| 780 } | |
| 781 } | |
| 782 | |
| 783 | |
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784 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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785 const std::string& dicomContent, |
|
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786 unsigned int frame, |
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787 ImageExtractionMode mode) |
| 0 | 788 { |
| 789 DcmInputBufferStream is; | |
| 790 if (dicomContent.size() > 0) | |
| 791 { | |
| 792 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 793 } | |
| 794 is.setEos(); | |
| 795 | |
| 796 DcmFileFormat dicom; | |
| 797 if (dicom.read(is).good()) | |
| 798 { | |
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799 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 800 } |
| 801 else | |
| 802 { | |
| 62 | 803 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 804 } |
| 805 } | |
| 806 | |
| 807 | |
| 808 | |
| 809 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 810 { | |
| 106 | 811 // Some patches for important tags because of different DICOM |
| 812 // dictionaries between DCMTK versions | |
|
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813 std::string n = t.GetMainTagsName(); |
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814 if (n.size() != 0) |
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815 { |
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816 return n; |
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817 } |
| 106 | 818 // End of patches |
| 819 | |
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820 #if 0 |
| 0 | 821 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 822 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 823 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 824 | |
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825 std::string s(DcmTag_ERROR_TagName); |
| 0 | 826 if (entry != NULL) |
| 827 { | |
| 828 s = std::string(entry->getTagName()); | |
| 829 } | |
| 830 | |
| 831 dcmDataDict.unlock(); | |
| 832 return s; | |
|
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833 #else |
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834 DcmTag tag(t.GetGroup(), t.GetElement()); |
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835 const char* name = tag.getTagName(); |
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836 if (name == NULL) |
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837 { |
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838 return DcmTag_ERROR_TagName; |
|
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839 } |
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840 else |
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841 { |
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842 return std::string(name); |
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843 } |
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844 #endif |
| 0 | 845 } |
| 846 | |
| 847 | |
| 304 | 848 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
| 0 | 849 { |
| 304 | 850 if (strlen(name) == 9 && |
| 851 isxdigit(name[0]) && | |
| 852 isxdigit(name[1]) && | |
| 853 isxdigit(name[2]) && | |
| 854 isxdigit(name[3]) && | |
| 855 name[4] == '-' && | |
| 856 isxdigit(name[5]) && | |
| 857 isxdigit(name[6]) && | |
| 858 isxdigit(name[7]) && | |
| 859 isxdigit(name[8])) | |
| 860 { | |
| 861 uint16_t group = GetTagValue(name); | |
| 862 uint16_t element = GetTagValue(name + 5); | |
| 863 return DicomTag(group, element); | |
| 864 } | |
| 865 | |
|
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866 #if 0 |
| 0 | 867 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
| 868 const DcmDictEntry* entry = dict.findEntry(name); | |
| 869 | |
| 870 if (entry == NULL) | |
| 871 { | |
| 872 dcmDataDict.unlock(); | |
| 62 | 873 throw OrthancException("Unknown DICOM tag"); |
| 0 | 874 } |
| 875 else | |
| 876 { | |
| 877 DcmTagKey key = entry->getKey(); | |
| 878 DicomTag tag(key.getGroup(), key.getElement()); | |
| 879 dcmDataDict.unlock(); | |
| 880 return tag; | |
| 881 } | |
|
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882 #else |
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883 DcmTag tag; |
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884 if (DcmTag::findTagFromName(name, tag).good()) |
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885 { |
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886 return DicomTag(tag.getGTag(), tag.getETag()); |
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887 } |
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888 else |
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889 { |
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890 throw OrthancException("Unknown DICOM tag"); |
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891 } |
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892 #endif |
| 0 | 893 } |
| 894 | |
| 895 | |
| 896 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 897 { | |
| 898 for (DicomMap::Map::const_iterator | |
| 656 | 899 it = m.map_.begin(); it != m.map_.end(); ++it) |
| 0 | 900 { |
| 901 DicomTag t = it->first; | |
| 902 std::string s = it->second->AsString(); | |
| 319 | 903 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
| 0 | 904 } |
| 905 } | |
| 906 | |
| 907 | |
| 908 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 909 const DicomMap& values) | |
| 910 { | |
| 911 if (result.type() != Json::objectValue) | |
| 912 { | |
| 62 | 913 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 914 } |
| 915 | |
| 916 result.clear(); | |
| 917 | |
| 918 for (DicomMap::Map::const_iterator | |
| 656 | 919 it = values.map_.begin(); it != values.map_.end(); ++it) |
| 0 | 920 { |
| 921 result[GetName(it->first)] = it->second->AsString(); | |
| 922 } | |
| 923 } | |
| 176 | 924 |
| 925 | |
| 788 | 926 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
| 176 | 927 { |
| 928 char uid[100]; | |
| 929 | |
| 930 switch (level) | |
| 931 { | |
| 788 | 932 case ResourceType_Patient: |
| 311 | 933 // The "PatientID" field is of type LO (Long String), 64 |
| 934 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
| 935 // as a random PatientID. | |
| 936 return Toolbox::GenerateUuid(); | |
|
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937 |
| 788 | 938 case ResourceType_Instance: |
|
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939 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
| 176 | 940 |
| 788 | 941 case ResourceType_Series: |
|
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942 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
| 176 | 943 |
| 788 | 944 case ResourceType_Study: |
|
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945 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
| 176 | 946 |
|
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947 default: |
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948 throw OrthancException(ErrorCode_ParameterOutOfRange); |
| 176 | 949 } |
| 950 } | |
| 951 | |
|
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952 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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953 DcmDataset* dataSet) |
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954 { |
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955 // Determine the transfer syntax which shall be used to write the |
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956 // information to the file. We always switch to the Little Endian |
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957 // syntax, with explicit length. |
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958 |
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959 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
|
661
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960 |
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961 |
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962 /** |
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963 * Note that up to Orthanc 0.7.1 (inclusive), the |
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964 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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965 * dataset into memory. We now keep the original transfer syntax |
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966 * (if available). |
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967 **/ |
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968 E_TransferSyntax xfer = dataSet->getOriginalXfer(); |
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969 if (xfer == EXS_Unknown) |
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970 { |
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971 // No information about the original transfer syntax: This is |
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972 // most probably a DICOM dataset that was read from memory. |
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973 xfer = EXS_LittleEndianExplicit; |
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974 } |
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975 |
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976 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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977 |
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661
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978 // Create the meta-header information |
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979 DcmFileFormat ff(dataSet); |
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980 ff.validateMetaInfo(xfer); |
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981 |
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661
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982 // Create a memory buffer with the proper size |
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983 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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984 buffer.resize(s); |
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985 DcmOutputBufferStream ob(&buffer[0], s); |
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986 |
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987 // Fill the memory buffer with the meta-header and the dataset |
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988 ff.transferInit(); |
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989 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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990 /*opt_groupLength*/ EGL_recalcGL, |
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991 /*opt_paddingType*/ EPD_withoutPadding); |
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992 ff.transferEnd(); |
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993 |
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994 // Handle errors |
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995 if (c.good()) |
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996 { |
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997 return true; |
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998 } |
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999 else |
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1000 { |
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1001 buffer.clear(); |
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1002 return false; |
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1003 } |
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1004 } |
| 0 | 1005 } |