Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 824:a811bdf8b8eb
precompiled headers
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 02 Jun 2014 11:36:07 +0200 |
| parents | 777b6b694da6 |
| children | 84513f2ee1f3 |
| rev | line source |
|---|---|
| 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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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 |
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75 #include "../Core/PrecompiledHeaders.h" |
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76 |
| 71 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 0 | 80 |
| 81 #include "FromDcmtkBridge.h" | |
| 82 | |
| 83 #include "ToDcmtkBridge.h" | |
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84 #include "../Core/Toolbox.h" |
| 62 | 85 #include "../Core/OrthancException.h" |
| 799 | 86 #include "../Core/ImageFormats/PngWriter.h" |
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87 #include "../Core/Uuid.h" |
| 0 | 88 #include "../Core/DicomFormat/DicomString.h" |
| 89 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 79 | 90 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
| 0 | 91 |
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92 #include <list> |
| 71 | 93 #include <limits> |
| 94 | |
| 0 | 95 #include <boost/lexical_cast.hpp> |
| 96 | |
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97 #include <dcmtk/dcmdata/dcchrstr.h> |
| 0 | 98 #include <dcmtk/dcmdata/dcdicent.h> |
| 99 #include <dcmtk/dcmdata/dcdict.h> | |
| 100 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 101 #include <dcmtk/dcmdata/dcistrmb.h> | |
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102 #include <dcmtk/dcmdata/dcuid.h> |
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103 #include <dcmtk/dcmdata/dcmetinf.h> |
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104 |
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105 #include <dcmtk/dcmdata/dcvrae.h> |
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106 #include <dcmtk/dcmdata/dcvras.h> |
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107 #include <dcmtk/dcmdata/dcvrcs.h> |
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108 #include <dcmtk/dcmdata/dcvrda.h> |
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109 #include <dcmtk/dcmdata/dcvrds.h> |
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110 #include <dcmtk/dcmdata/dcvrdt.h> |
| 0 | 111 #include <dcmtk/dcmdata/dcvrfd.h> |
| 112 #include <dcmtk/dcmdata/dcvrfl.h> | |
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113 #include <dcmtk/dcmdata/dcvris.h> |
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114 #include <dcmtk/dcmdata/dcvrlo.h> |
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115 #include <dcmtk/dcmdata/dcvrlt.h> |
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116 #include <dcmtk/dcmdata/dcvrpn.h> |
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117 #include <dcmtk/dcmdata/dcvrsh.h> |
| 0 | 118 #include <dcmtk/dcmdata/dcvrsl.h> |
| 119 #include <dcmtk/dcmdata/dcvrss.h> | |
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120 #include <dcmtk/dcmdata/dcvrst.h> |
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121 #include <dcmtk/dcmdata/dcvrtm.h> |
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122 #include <dcmtk/dcmdata/dcvrui.h> |
| 0 | 123 #include <dcmtk/dcmdata/dcvrul.h> |
| 124 #include <dcmtk/dcmdata/dcvrus.h> | |
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125 #include <dcmtk/dcmdata/dcvrut.h> |
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126 #include <dcmtk/dcmdata/dcpixel.h> |
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127 #include <dcmtk/dcmdata/dcpixseq.h> |
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128 #include <dcmtk/dcmdata/dcpxitem.h> |
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129 |
| 0 | 130 |
| 2 | 131 #include <boost/math/special_functions/round.hpp> |
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132 #include <glog/logging.h> |
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133 #include <dcmtk/dcmdata/dcostrmb.h> |
| 0 | 134 |
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135 |
| 62 | 136 namespace Orthanc |
| 0 | 137 { |
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138 static inline uint16_t GetCharValue(char c) |
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139 { |
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140 if (c >= '0' && c <= '9') |
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141 return c - '0'; |
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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 if (c >= 'A' && c <= 'F') |
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145 return c - 'A' + 10; |
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146 else |
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147 return 0; |
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148 } |
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149 |
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150 static inline uint16_t GetTagValue(const char* c) |
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151 { |
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152 return ((GetCharValue(c[0]) << 12) + |
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153 (GetCharValue(c[1]) << 8) + |
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154 (GetCharValue(c[2]) << 4) + |
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155 GetCharValue(c[3])); |
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156 } |
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157 |
| 0 | 158 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 159 { | |
| 160 target.Clear(); | |
| 161 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 162 { | |
| 163 DcmElement* element = dataset.getElement(i); | |
| 164 if (element && element->isLeaf()) | |
| 165 { | |
| 166 target.SetValue(element->getTag().getGTag(), | |
| 167 element->getTag().getETag(), | |
| 168 ConvertLeafElement(*element)); | |
| 169 } | |
| 170 } | |
| 171 } | |
| 172 | |
| 173 | |
| 174 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 175 { | |
| 176 return DicomTag(element.getGTag(), element.getETag()); | |
| 177 } | |
| 178 | |
| 179 | |
| 180 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 181 { | |
| 182 if (!element.isLeaf()) | |
| 183 { | |
| 62 | 184 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 185 } |
| 186 | |
| 187 if (element.isaString()) | |
| 188 { | |
| 189 char *c; | |
| 190 if (element.getString(c).good() && | |
| 191 c != NULL) | |
| 192 { | |
| 193 std::string s(c); | |
|
107
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194 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 195 return new DicomString(utf8); |
| 196 } | |
| 197 else | |
| 198 { | |
| 199 return new DicomNullValue; | |
| 200 } | |
| 201 } | |
| 202 | |
| 203 try | |
| 204 { | |
| 205 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 206 switch (element.getVR()) | |
| 207 { | |
| 208 | |
| 209 /** | |
| 210 * TODO. | |
| 211 **/ | |
|
306
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212 |
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213 case EVR_OB: // other byte |
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214 case EVR_OF: // other float |
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215 case EVR_OW: // other word |
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216 case EVR_AT: // attribute tag |
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217 case EVR_UN: // unknown value representation |
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218 return new DicomNullValue(); |
|
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219 |
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220 /** |
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221 * String types, should never happen at this point because of |
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222 * "element.isaString()". |
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223 **/ |
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224 |
|
306
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225 case EVR_DS: // decimal string |
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226 case EVR_IS: // integer string |
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227 case EVR_AS: // age string |
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228 case EVR_DA: // date string |
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229 case EVR_DT: // date time string |
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230 case EVR_TM: // time string |
|
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231 case EVR_AE: // application entity title |
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232 case EVR_CS: // code string |
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233 case EVR_SH: // short string |
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234 case EVR_LO: // long string |
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235 case EVR_ST: // short text |
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236 case EVR_LT: // long text |
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237 case EVR_UT: // unlimited text |
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238 case EVR_PN: // person name |
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239 case EVR_UI: // unique identifier |
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240 return new DicomNullValue(); |
| 0 | 241 |
| 242 | |
|
302
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243 /** |
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244 * Numerical types |
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245 **/ |
| 0 | 246 |
|
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247 case EVR_SL: // signed long |
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248 { |
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249 Sint32 f; |
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250 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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251 return new DicomString(boost::lexical_cast<std::string>(f)); |
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252 else |
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253 return new DicomNullValue(); |
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254 } |
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255 |
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256 case EVR_SS: // signed short |
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257 { |
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258 Sint16 f; |
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259 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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260 return new DicomString(boost::lexical_cast<std::string>(f)); |
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261 else |
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262 return new DicomNullValue(); |
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263 } |
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264 |
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265 case EVR_UL: // unsigned long |
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266 { |
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267 Uint32 f; |
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268 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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269 return new DicomString(boost::lexical_cast<std::string>(f)); |
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270 else |
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271 return new DicomNullValue(); |
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272 } |
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273 |
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274 case EVR_US: // unsigned short |
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275 { |
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276 Uint16 f; |
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277 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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278 return new DicomString(boost::lexical_cast<std::string>(f)); |
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279 else |
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280 return new DicomNullValue(); |
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281 } |
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282 |
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283 case EVR_FL: // float single-precision |
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284 { |
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285 Float32 f; |
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286 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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287 return new DicomString(boost::lexical_cast<std::string>(f)); |
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288 else |
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289 return new DicomNullValue(); |
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290 } |
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291 |
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292 case EVR_FD: // float double-precision |
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293 { |
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294 Float64 f; |
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295 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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296 return new DicomString(boost::lexical_cast<std::string>(f)); |
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297 else |
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298 return new DicomNullValue(); |
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299 } |
| 0 | 300 |
| 301 | |
| 302 /** | |
|
302
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303 * Sequence types, should never occur at this point because of |
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304 * "element.isLeaf()". |
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305 **/ |
| 0 | 306 |
|
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307 case EVR_SQ: // sequence of items |
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308 return new DicomNullValue; |
| 0 | 309 |
| 310 | |
|
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311 /** |
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312 * Internal to DCMTK. |
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313 **/ |
| 0 | 314 |
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315 case EVR_ox: // OB or OW depending on context |
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316 case EVR_xs: // SS or US depending on context |
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317 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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318 case EVR_na: // na="not applicable", for data which has no VR |
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319 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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320 case EVR_item: // used internally for items |
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321 case EVR_metainfo: // used internally for meta info datasets |
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322 case EVR_dataset: // used internally for datasets |
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323 case EVR_fileFormat: // used internally for DICOM files |
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324 case EVR_dicomDir: // used internally for DICOMDIR objects |
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325 case EVR_dirRecord: // used internally for DICOMDIR records |
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326 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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327 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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328 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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329 case EVR_PixelData: // used internally for uncompressed pixeld data |
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330 case EVR_OverlayData: // used internally for overlay data |
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331 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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332 return new DicomNullValue; |
| 0 | 333 |
| 334 | |
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335 /** |
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336 * Default case. |
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337 **/ |
| 0 | 338 |
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339 default: |
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340 return new DicomNullValue; |
| 0 | 341 } |
| 342 } | |
| 343 catch (boost::bad_lexical_cast) | |
| 344 { | |
| 345 return new DicomNullValue; | |
| 346 } | |
|
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347 catch (std::bad_cast) |
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348 { |
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349 return new DicomNullValue; |
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350 } |
| 0 | 351 } |
| 352 | |
| 353 | |
| 354 static void StoreElement(Json::Value& target, | |
| 355 DcmElement& element, | |
| 356 unsigned int maxStringLength); | |
| 357 | |
| 358 static void StoreItem(Json::Value& target, | |
| 359 DcmItem& item, | |
| 360 unsigned int maxStringLength) | |
| 361 { | |
| 362 target = Json::Value(Json::objectValue); | |
| 363 | |
| 364 for (unsigned long i = 0; i < item.card(); i++) | |
| 365 { | |
| 366 DcmElement* element = item.getElement(i); | |
| 367 StoreElement(target, *element, maxStringLength); | |
| 368 } | |
| 369 } | |
| 370 | |
| 371 | |
| 372 static void StoreElement(Json::Value& target, | |
| 373 DcmElement& element, | |
| 374 unsigned int maxStringLength) | |
| 375 { | |
| 376 assert(target.type() == Json::objectValue); | |
| 377 | |
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378 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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379 const std::string formattedTag = tag.Format(); |
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380 |
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381 #if 0 |
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382 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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383 #else |
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384 // This version of the code gives access to the name of the private tags |
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385 DcmTag tagbis(element.getTag()); |
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386 const std::string tagName(tagbis.getTagName()); |
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387 #endif |
| 0 | 388 |
| 389 if (element.isLeaf()) | |
| 390 { | |
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391 Json::Value value(Json::objectValue); |
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392 value["Name"] = tagName; |
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393 |
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394 if (tagbis.getPrivateCreator() != NULL) |
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395 { |
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396 value["PrivateCreator"] = tagbis.getPrivateCreator(); |
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397 } |
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398 |
| 0 | 399 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 400 if (v->IsNull()) | |
| 401 { | |
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402 value["Type"] = "Null"; |
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403 value["Value"] = Json::nullValue; |
| 0 | 404 } |
| 405 else | |
| 406 { | |
| 407 std::string s = v->AsString(); | |
| 408 if (maxStringLength == 0 || | |
| 409 s.size() <= maxStringLength) | |
| 410 { | |
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411 value["Type"] = "String"; |
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412 value["Value"] = s; |
| 0 | 413 } |
| 414 else | |
| 415 { | |
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416 value["Type"] = "TooLong"; |
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417 value["Value"] = Json::nullValue; |
| 0 | 418 } |
| 419 } | |
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420 |
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421 target[formattedTag] = value; |
| 0 | 422 } |
| 423 else | |
| 424 { | |
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425 Json::Value children(Json::arrayValue); |
| 0 | 426 |
| 427 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 428 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 429 // etc. are not." The following cast is thus OK. | |
| 430 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 431 | |
| 432 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 433 { | |
| 434 DcmItem* child = sequence.getItem(i); | |
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435 Json::Value& v = children.append(Json::objectValue); |
| 0 | 436 StoreItem(v, *child, maxStringLength); |
| 437 } | |
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438 |
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439 target[formattedTag]["Name"] = tagName; |
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440 target[formattedTag]["Type"] = "Sequence"; |
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441 target[formattedTag]["Value"] = children; |
| 0 | 442 } |
| 443 } | |
| 444 | |
| 445 | |
| 446 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 447 DcmDataset& dataset, | |
| 448 unsigned int maxStringLength) | |
| 449 { | |
| 450 StoreItem(root, dataset, maxStringLength); | |
| 451 } | |
| 452 | |
| 453 | |
| 454 | |
| 455 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 456 const std::string& path, | |
| 457 unsigned int maxStringLength) | |
| 458 { | |
| 459 DcmFileFormat dicom; | |
| 460 if (!dicom.loadFile(path.c_str()).good()) | |
| 461 { | |
| 62 | 462 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 463 } |
| 464 else | |
| 465 { | |
| 466 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 467 } | |
| 468 } | |
| 469 | |
| 470 | |
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471 static void ExtractPngImageColorPreview(std::string& result, |
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472 DicomIntegerPixelAccessor& accessor) |
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473 { |
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474 assert(accessor.GetChannelCount() == 3); |
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475 PngWriter w; |
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476 |
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477 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0); |
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478 uint8_t* pixel = &image[0]; |
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479 |
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480 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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481 { |
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482 for (unsigned int x = 0; x < accessor.GetWidth(); x++) |
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483 { |
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484 for (unsigned int c = 0; c < 3; c++, pixel++) |
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485 { |
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486 int32_t v = accessor.GetValue(x, y, c); |
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487 if (v < 0) |
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488 *pixel = 0; |
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489 else if (v > 255) |
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490 *pixel = 255; |
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491 else |
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492 *pixel = v; |
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493 } |
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494 } |
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495 } |
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496 |
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497 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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498 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]); |
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499 } |
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500 |
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501 |
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502 static void ExtractPngImageGrayscalePreview(std::string& result, |
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503 DicomIntegerPixelAccessor& accessor) |
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504 { |
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505 assert(accessor.GetChannelCount() == 1); |
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506 PngWriter w; |
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507 |
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508 int32_t min, max; |
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509 accessor.GetExtremeValues(min, max); |
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510 |
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511 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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512 if (min != max) |
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513 { |
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514 uint8_t* pixel = &image[0]; |
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515 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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516 { |
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517 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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518 { |
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519 int32_t v = accessor.GetValue(x, y); |
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520 *pixel = static_cast<uint8_t>( |
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521 boost::math::lround(static_cast<float>(v - min) / |
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522 static_cast<float>(max - min) * 255.0f)); |
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523 } |
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524 } |
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525 } |
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526 |
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527 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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528 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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529 } |
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530 |
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531 |
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532 template <typename T> |
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533 static void ExtractPngImageTruncate(std::string& result, |
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534 DicomIntegerPixelAccessor& accessor, |
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535 PixelFormat format) |
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536 { |
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537 assert(accessor.GetChannelCount() == 1); |
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538 |
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539 PngWriter w; |
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540 |
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541 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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542 T* pixel = &image[0]; |
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543 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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544 { |
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545 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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546 { |
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547 int32_t v = accessor.GetValue(x, y); |
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548 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) |
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549 *pixel = std::numeric_limits<T>::min(); |
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550 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) |
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551 *pixel = std::numeric_limits<T>::max(); |
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552 else |
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553 *pixel = static_cast<T>(v); |
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554 } |
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555 } |
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556 |
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557 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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558 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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559 } |
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560 |
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561 |
| 319 | 562 static bool DecodePsmctRle1(std::string& output, |
| 563 DcmDataset& dataset) | |
| 564 { | |
| 565 static const DicomTag tagContent(0x07a1, 0x100a); | |
| 566 static const DicomTag tagCompressionType(0x07a1, 0x1011); | |
| 567 | |
| 568 DcmElement* e; | |
| 569 char* c; | |
| 570 | |
| 571 // Check whether the DICOM instance contains an image encoded with | |
| 572 // the PMSCT_RLE1 scheme. | |
| 573 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() || | |
| 574 e == NULL || | |
| 575 !e->isaString() || | |
| 576 !e->getString(c).good() || | |
| 577 c == NULL || | |
| 578 strcmp("PMSCT_RLE1", c)) | |
| 579 { | |
| 580 return false; | |
| 581 } | |
| 582 | |
| 583 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
| 584 // data from the appropriate private DICOM tag. | |
| 585 Uint8* pixData = NULL; | |
| 586 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() || | |
| 587 e == NULL || | |
| 588 e->getUint8Array(pixData) != EC_Normal) | |
| 589 { | |
| 590 return false; | |
| 591 } | |
| 592 | |
| 593 // The "unsigned" below IS VERY IMPORTANT | |
| 594 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
| 595 const size_t length = e->getLength(); | |
| 596 | |
| 597 /** | |
| 598 * The code below is an adaptation of a sample code for GDCM by | |
| 599 * Mathieu Malaterre (under a BSD license). | |
| 600 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
| 601 **/ | |
| 602 | |
| 603 // RLE pass | |
| 604 std::vector<uint8_t> temp; | |
| 605 temp.reserve(length); | |
| 606 for (size_t i = 0; i < length; i++) | |
| 607 { | |
| 608 if (inbuffer[i] == 0xa5) | |
| 609 { | |
| 610 temp.push_back(inbuffer[i+2]); | |
| 611 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
| 612 { | |
| 613 temp.push_back(inbuffer[i+2]); | |
| 614 } | |
| 615 i += 2; | |
| 616 } | |
| 617 else | |
| 618 { | |
| 619 temp.push_back(inbuffer[i]); | |
| 620 } | |
| 621 } | |
| 622 | |
| 623 // Delta encoding pass | |
| 624 uint16_t delta = 0; | |
| 625 output.clear(); | |
| 626 output.reserve(temp.size()); | |
| 627 for (size_t i = 0; i < temp.size(); i++) | |
| 628 { | |
| 629 uint16_t value; | |
| 630 | |
| 631 if (temp[i] == 0x5a) | |
| 632 { | |
| 633 uint16_t v1 = temp[i + 1]; | |
| 634 uint16_t v2 = temp[i + 2]; | |
| 635 value = (v2 << 8) + v1; | |
| 636 i += 2; | |
| 637 } | |
| 638 else | |
| 639 { | |
| 640 value = delta + (int8_t) temp[i]; | |
| 641 } | |
| 642 | |
| 643 output.push_back(value & 0xff); | |
| 644 output.push_back(value >> 8); | |
| 645 delta = value; | |
| 646 } | |
| 647 | |
| 648 if (output.size() % 2) | |
| 649 { | |
| 650 output.resize(output.size() - 1); | |
| 651 } | |
| 652 | |
| 653 return true; | |
| 654 } | |
| 655 | |
| 656 | |
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657 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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658 DcmDataset& dataset, |
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659 unsigned int frame, |
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660 ImageExtractionMode mode) |
| 0 | 661 { |
| 662 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 663 | |
| 664 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 665 | |
| 666 DicomMap m; | |
| 667 FromDcmtkBridge::Convert(m, dataset); | |
| 668 | |
| 319 | 669 std::string privateContent; |
| 670 | |
| 0 | 671 DcmElement* e; |
| 80 | 672 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 673 e != NULL) |
| 674 { | |
| 675 Uint8* pixData = NULL; | |
| 676 if (e->getUint8Array(pixData) == EC_Normal) | |
| 677 { | |
| 678 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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679 accessor->SetCurrentFrame(frame); |
| 0 | 680 } |
| 681 } | |
| 319 | 682 else if (DecodePsmctRle1(privateContent, dataset)) |
| 683 { | |
| 684 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
| 685 Uint8* pixData = NULL; | |
| 686 if (privateContent.size() > 0) | |
| 687 pixData = reinterpret_cast<Uint8*>(&privateContent[0]); | |
| 688 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size())); | |
| 689 accessor->SetCurrentFrame(frame); | |
| 690 } | |
| 419 | 691 |
| 692 if (accessor.get() == NULL) | |
| 693 { | |
| 694 throw OrthancException(ErrorCode_BadFileFormat); | |
| 695 } | |
| 0 | 696 |
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697 PixelFormat format; |
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698 bool supported = false; |
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699 |
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700 if (accessor->GetChannelCount() == 1) |
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701 { |
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702 switch (mode) |
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703 { |
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704 case ImageExtractionMode_Preview: |
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705 supported = true; |
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706 format = PixelFormat_Grayscale8; |
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707 break; |
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708 |
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709 case ImageExtractionMode_UInt8: |
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710 supported = true; |
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711 format = PixelFormat_Grayscale8; |
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712 break; |
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713 |
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714 case ImageExtractionMode_UInt16: |
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715 supported = true; |
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716 format = PixelFormat_Grayscale16; |
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717 break; |
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718 |
|
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719 case ImageExtractionMode_Int16: |
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720 supported = true; |
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721 format = PixelFormat_SignedGrayscale16; |
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722 break; |
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723 |
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724 default: |
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725 supported = false; |
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726 break; |
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727 } |
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728 } |
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729 else if (accessor->GetChannelCount() == 3) |
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730 { |
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|
731 switch (mode) |
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732 { |
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733 case ImageExtractionMode_Preview: |
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734 supported = true; |
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735 format = PixelFormat_RGB24; |
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736 break; |
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737 |
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738 default: |
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739 supported = false; |
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740 break; |
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|
741 } |
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742 } |
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743 |
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744 if (!supported) |
|
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745 { |
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746 throw OrthancException(ErrorCode_NotImplemented); |
|
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747 } |
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748 |
| 0 | 749 if (accessor.get() == NULL || |
| 750 accessor->GetWidth() == 0 || | |
| 751 accessor->GetHeight() == 0) | |
| 752 { | |
|
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753 PngWriter w; |
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754 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 755 } |
| 756 else | |
| 757 { | |
|
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758 switch (mode) |
| 0 | 759 { |
|
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760 case ImageExtractionMode_Preview: |
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761 if (format == PixelFormat_Grayscale8) |
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762 ExtractPngImageGrayscalePreview(result, *accessor); |
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763 else |
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764 ExtractPngImageColorPreview(result, *accessor); |
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765 break; |
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766 |
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767 case ImageExtractionMode_UInt8: |
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768 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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769 break; |
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770 |
|
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771 case ImageExtractionMode_UInt16: |
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772 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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773 break; |
|
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774 |
|
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775 case ImageExtractionMode_Int16: |
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776 ExtractPngImageTruncate<int16_t>(result, *accessor, format); |
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777 break; |
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778 |
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779 default: |
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780 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 781 } |
| 782 } | |
| 783 } | |
| 784 | |
| 785 | |
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786 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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787 const std::string& dicomContent, |
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788 unsigned int frame, |
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789 ImageExtractionMode mode) |
| 0 | 790 { |
| 791 DcmInputBufferStream is; | |
| 792 if (dicomContent.size() > 0) | |
| 793 { | |
| 794 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 795 } | |
| 796 is.setEos(); | |
| 797 | |
| 798 DcmFileFormat dicom; | |
| 799 if (dicom.read(is).good()) | |
| 800 { | |
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801 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 802 } |
| 803 else | |
| 804 { | |
| 62 | 805 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 806 } |
| 807 } | |
| 808 | |
| 809 | |
| 810 | |
| 811 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 812 { | |
| 106 | 813 // Some patches for important tags because of different DICOM |
| 814 // dictionaries between DCMTK versions | |
|
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815 std::string n = t.GetMainTagsName(); |
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816 if (n.size() != 0) |
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817 { |
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818 return n; |
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819 } |
| 106 | 820 // End of patches |
| 821 | |
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822 #if 0 |
| 0 | 823 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 824 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 825 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 826 | |
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827 std::string s(DcmTag_ERROR_TagName); |
| 0 | 828 if (entry != NULL) |
| 829 { | |
| 830 s = std::string(entry->getTagName()); | |
| 831 } | |
| 832 | |
| 833 dcmDataDict.unlock(); | |
| 834 return s; | |
|
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835 #else |
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836 DcmTag tag(t.GetGroup(), t.GetElement()); |
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837 const char* name = tag.getTagName(); |
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838 if (name == NULL) |
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839 { |
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840 return DcmTag_ERROR_TagName; |
|
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841 } |
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842 else |
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843 { |
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844 return std::string(name); |
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845 } |
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846 #endif |
| 0 | 847 } |
| 848 | |
| 849 | |
| 304 | 850 DicomTag FromDcmtkBridge::ParseTag(const char* name) |
| 0 | 851 { |
| 304 | 852 if (strlen(name) == 9 && |
| 853 isxdigit(name[0]) && | |
| 854 isxdigit(name[1]) && | |
| 855 isxdigit(name[2]) && | |
| 856 isxdigit(name[3]) && | |
| 857 name[4] == '-' && | |
| 858 isxdigit(name[5]) && | |
| 859 isxdigit(name[6]) && | |
| 860 isxdigit(name[7]) && | |
| 861 isxdigit(name[8])) | |
| 862 { | |
| 863 uint16_t group = GetTagValue(name); | |
| 864 uint16_t element = GetTagValue(name + 5); | |
| 865 return DicomTag(group, element); | |
| 866 } | |
| 867 | |
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868 #if 0 |
| 0 | 869 const DcmDataDictionary& dict = dcmDataDict.rdlock(); |
| 870 const DcmDictEntry* entry = dict.findEntry(name); | |
| 871 | |
| 872 if (entry == NULL) | |
| 873 { | |
| 874 dcmDataDict.unlock(); | |
| 62 | 875 throw OrthancException("Unknown DICOM tag"); |
| 0 | 876 } |
| 877 else | |
| 878 { | |
| 879 DcmTagKey key = entry->getKey(); | |
| 880 DicomTag tag(key.getGroup(), key.getElement()); | |
| 881 dcmDataDict.unlock(); | |
| 882 return tag; | |
| 883 } | |
|
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884 #else |
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885 DcmTag tag; |
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886 if (DcmTag::findTagFromName(name, tag).good()) |
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887 { |
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888 return DicomTag(tag.getGTag(), tag.getETag()); |
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889 } |
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890 else |
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891 { |
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892 throw OrthancException("Unknown DICOM tag"); |
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893 } |
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894 #endif |
| 0 | 895 } |
| 896 | |
| 897 | |
| 898 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 899 { | |
| 900 for (DicomMap::Map::const_iterator | |
| 656 | 901 it = m.map_.begin(); it != m.map_.end(); ++it) |
| 0 | 902 { |
| 903 DicomTag t = it->first; | |
| 904 std::string s = it->second->AsString(); | |
| 319 | 905 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); |
| 0 | 906 } |
| 907 } | |
| 908 | |
| 909 | |
| 910 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 911 const DicomMap& values) | |
| 912 { | |
| 913 if (result.type() != Json::objectValue) | |
| 914 { | |
| 62 | 915 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 916 } |
| 917 | |
| 918 result.clear(); | |
| 919 | |
| 920 for (DicomMap::Map::const_iterator | |
| 656 | 921 it = values.map_.begin(); it != values.map_.end(); ++it) |
| 0 | 922 { |
| 923 result[GetName(it->first)] = it->second->AsString(); | |
| 924 } | |
| 925 } | |
| 176 | 926 |
| 927 | |
| 788 | 928 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) |
| 176 | 929 { |
| 930 char uid[100]; | |
| 931 | |
| 932 switch (level) | |
| 933 { | |
| 788 | 934 case ResourceType_Patient: |
| 311 | 935 // The "PatientID" field is of type LO (Long String), 64 |
| 936 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
| 937 // as a random PatientID. | |
| 938 return Toolbox::GenerateUuid(); | |
|
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939 |
| 788 | 940 case ResourceType_Instance: |
|
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941 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
| 176 | 942 |
| 788 | 943 case ResourceType_Series: |
|
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944 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
| 176 | 945 |
| 788 | 946 case ResourceType_Study: |
|
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947 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
| 176 | 948 |
|
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949 default: |
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950 throw OrthancException(ErrorCode_ParameterOutOfRange); |
| 176 | 951 } |
| 952 } | |
| 953 | |
|
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954 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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955 DcmDataset* dataSet) |
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956 { |
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957 // Determine the transfer syntax which shall be used to write the |
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958 // information to the file. We always switch to the Little Endian |
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959 // syntax, with explicit length. |
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960 |
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961 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
|
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962 |
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963 |
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964 /** |
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965 * Note that up to Orthanc 0.7.1 (inclusive), the |
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966 * "EXS_LittleEndianExplicit" was always used to save the DICOM |
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967 * dataset into memory. We now keep the original transfer syntax |
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968 * (if available). |
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969 **/ |
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970 E_TransferSyntax xfer = dataSet->getOriginalXfer(); |
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971 if (xfer == EXS_Unknown) |
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972 { |
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973 // No information about the original transfer syntax: This is |
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974 // most probably a DICOM dataset that was read from memory. |
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975 xfer = EXS_LittleEndianExplicit; |
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976 } |
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977 |
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978 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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979 |
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980 // Create the meta-header information |
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981 DcmFileFormat ff(dataSet); |
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982 ff.validateMetaInfo(xfer); |
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983 |
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984 // Create a memory buffer with the proper size |
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985 uint32_t s = ff.calcElementLength(xfer, encodingType); |
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986 buffer.resize(s); |
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987 DcmOutputBufferStream ob(&buffer[0], s); |
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988 |
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989 // Fill the memory buffer with the meta-header and the dataset |
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990 ff.transferInit(); |
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991 OFCondition c = ff.write(ob, xfer, encodingType, NULL, |
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992 /*opt_groupLength*/ EGL_recalcGL, |
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993 /*opt_paddingType*/ EPD_withoutPadding); |
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994 ff.transferEnd(); |
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995 |
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996 // Handle errors |
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997 if (c.good()) |
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998 { |
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999 return true; |
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1000 } |
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1001 else |
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1002 { |
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1003 buffer.clear(); |
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1004 return false; |
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1005 } |
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1006 } |
| 0 | 1007 } |