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annotate OrthancServer/FromDcmtkBridge.cpp @ 465:7a966b440f19

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 12 Jul 2013 11:15:27 +0200
parents 5987dd8e0776
children b22312081388 08eca5d86aad
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2013 Medical Physics Department, CHU of Liege,
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4 * Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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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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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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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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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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72 =========================================================================*/
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74
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75 #ifndef NOMINMAX
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76 #define NOMINMAX
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77 #endif
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79 #include "FromDcmtkBridge.h"
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81 #include "ToDcmtkBridge.h"
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82 #include "../Core/Toolbox.h"
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83 #include "../Core/OrthancException.h"
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84 #include "../Core/FileFormats/PngWriter.h"
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85 #include "../Core/Uuid.h"
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86 #include "../Core/DicomFormat/DicomString.h"
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87 #include "../Core/DicomFormat/DicomNullValue.h"
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88 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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90 #include <list>
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91 #include <limits>
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92
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93 #include <boost/lexical_cast.hpp>
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94
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95 #include <dcmtk/dcmdata/dcchrstr.h>
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96 #include <dcmtk/dcmdata/dcdicent.h>
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97 #include <dcmtk/dcmdata/dcdict.h>
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98 #include <dcmtk/dcmdata/dcfilefo.h>
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99 #include <dcmtk/dcmdata/dcistrmb.h>
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100 #include <dcmtk/dcmdata/dcuid.h>
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101
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102 #include <dcmtk/dcmdata/dcvrae.h>
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103 #include <dcmtk/dcmdata/dcvras.h>
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104 #include <dcmtk/dcmdata/dcvrcs.h>
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105 #include <dcmtk/dcmdata/dcvrda.h>
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106 #include <dcmtk/dcmdata/dcvrds.h>
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107 #include <dcmtk/dcmdata/dcvrdt.h>
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108 #include <dcmtk/dcmdata/dcvrfd.h>
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109 #include <dcmtk/dcmdata/dcvrfl.h>
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110 #include <dcmtk/dcmdata/dcvris.h>
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111 #include <dcmtk/dcmdata/dcvrlo.h>
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112 #include <dcmtk/dcmdata/dcvrlt.h>
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113 #include <dcmtk/dcmdata/dcvrpn.h>
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114 #include <dcmtk/dcmdata/dcvrsh.h>
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115 #include <dcmtk/dcmdata/dcvrsl.h>
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116 #include <dcmtk/dcmdata/dcvrss.h>
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117 #include <dcmtk/dcmdata/dcvrst.h>
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118 #include <dcmtk/dcmdata/dcvrtm.h>
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119 #include <dcmtk/dcmdata/dcvrui.h>
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120 #include <dcmtk/dcmdata/dcvrul.h>
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121 #include <dcmtk/dcmdata/dcvrus.h>
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122 #include <dcmtk/dcmdata/dcvrut.h>
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123
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124 #include <boost/math/special_functions/round.hpp>
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125 #include <glog/logging.h>
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126 #include <dcmtk/dcmdata/dcostrmb.h>
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127
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128 namespace Orthanc
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129 {
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130 void ParsedDicomFile::Setup(const char* buffer, size_t size)
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131 {
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132 DcmInputBufferStream is;
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133 if (size > 0)
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134 {
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135 is.setBuffer(buffer, size);
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136 }
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137 is.setEos();
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138
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139 file_.reset(new DcmFileFormat);
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140 file_->transferInit();
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141 if (!file_->read(is).good())
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142 {
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143 throw OrthancException(ErrorCode_BadFileFormat);
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144 }
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145 file_->loadAllDataIntoMemory();
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146 file_->transferEnd();
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147 }
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148
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149
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150 static void SendPathValueForDictionary(RestApiOutput& output,
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151 DcmItem& dicom)
285
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152 {
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153 Json::Value v = Json::arrayValue;
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154
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155 for (unsigned long i = 0; i < dicom.card(); i++)
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156 {
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157 DcmElement* element = dicom.getElement(i);
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158 if (element)
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159 {
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160 char buf[16];
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161 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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162 v.append(buf);
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163 }
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164 }
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165
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166 output.AnswerJson(v);
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167 }
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168
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169 static inline uint16_t GetCharValue(char c)
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170 {
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171 if (c >= '0' && c <= '9')
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172 return c - '0';
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173 else if (c >= 'a' && c <= 'f')
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174 return c - 'a' + 10;
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175 else if (c >= 'A' && c <= 'F')
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176 return c - 'A' + 10;
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177 else
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178 return 0;
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179 }
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180
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181 static inline uint16_t GetTagValue(const char* c)
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182 {
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183 return ((GetCharValue(c[0]) << 12) +
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184 (GetCharValue(c[1]) << 8) +
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185 (GetCharValue(c[2]) << 4) +
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186 GetCharValue(c[3]));
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187 }
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188
304
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189 static void ParseTagAndGroup(DcmTagKey& key,
285
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190 const std::string& tag)
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191 {
304
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192 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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193 key = DcmTagKey(t.GetGroup(), t.GetElement());
285
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194 }
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195
291
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196
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197 static void SendSequence(RestApiOutput& output,
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198 DcmSequenceOfItems& sequence)
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199 {
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200 // This element is a sequence
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201 Json::Value v = Json::arrayValue;
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202
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203 for (unsigned long i = 0; i < sequence.card(); i++)
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204 {
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205 v.append(boost::lexical_cast<std::string>(i));
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206 }
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207
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208 output.AnswerJson(v);
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209 }
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210
302
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211 static void AnswerDicomField(RestApiOutput& output,
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212 DcmElement& element)
291
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213 {
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214 // This element is not a sequence
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215 std::string buffer;
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216 buffer.resize(65536);
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217 Uint32 length = element.getLength();
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218 Uint32 offset = 0;
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219
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220 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL);
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221
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222 while (offset < length)
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223 {
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224 Uint32 nbytes;
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225 if (length - offset < buffer.size())
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226 {
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227 nbytes = length - offset;
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228 }
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229 else
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230 {
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231 nbytes = buffer.size();
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232 }
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233
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234 if (element.getPartialValue(&buffer[0], offset, nbytes).good())
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235 {
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236 output.GetLowLevelOutput().Send(&buffer[0], nbytes);
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237 offset += nbytes;
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238 }
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239 else
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240 {
302
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241 LOG(ERROR) << "Error while sending a DICOM field";
291
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242 return;
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243 }
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244 }
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245
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246 output.MarkLowLevelOutputDone();
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247 }
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248
285
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249 static void SendPathValueForLeaf(RestApiOutput& output,
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250 const std::string& tag,
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251 DcmItem& dicom)
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252 {
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253 DcmTagKey k;
304
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254 ParseTagAndGroup(k, tag);
285
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255
291
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256 DcmSequenceOfItems* sequence = NULL;
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257 if (dicom.findAndGetSequence(k, sequence).good() &&
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258 sequence != NULL &&
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259 sequence->getVR() == EVR_SQ)
285
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260 {
291
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261 SendSequence(output, *sequence);
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262 return;
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263 }
285
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264
291
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265 DcmElement* element = NULL;
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266 if (dicom.findAndGetElement(k, element).good() &&
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diff changeset
267 element != NULL &&
318
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268 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags
291
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269 element->getVR() != EVR_SQ)
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diff changeset
270 {
302
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271 AnswerDicomField(output, *element);
285
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272 }
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273 }
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274
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275 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
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276 const UriComponents& uri)
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277 {
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278 DcmItem* dicom = file_->getDataset();
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279
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280 // Go down in the tag hierarchy according to the URI
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281 for (size_t pos = 0; pos < uri.size() / 2; pos++)
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282 {
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283 size_t index;
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284 try
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285 {
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286 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
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287 }
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288 catch (boost::bad_lexical_cast&)
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289 {
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290 return;
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291 }
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292
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293 DcmTagKey k;
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294 DcmItem *child = NULL;
304
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295 ParseTagAndGroup(k, uri[2 * pos]);
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296 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
285
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297 child == NULL)
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298 {
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299 return;
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300 }
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301
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302 dicom = child;
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303 }
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304
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305 // We have reached the end of the URI
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306 if (uri.size() % 2 == 0)
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307 {
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308 SendPathValueForDictionary(output, *dicom);
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309 }
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310 else
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311 {
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312 SendPathValueForLeaf(output, uri.back(), *dicom);
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313 }
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314 }
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315
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316
302
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317
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318
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319
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320 static DcmElement* CreateElementForTag(const DicomTag& tag)
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321 {
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322 DcmTag key(tag.GetGroup(), tag.GetElement());
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323
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324 switch (key.getEVR())
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325 {
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326 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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327
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328 /**
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329 * TODO.
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330 **/
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331
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332 case EVR_OB: // other byte
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333 case EVR_OF: // other float
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334 case EVR_OW: // other word
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335 case EVR_AT: // attribute tag
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336 throw OrthancException(ErrorCode_NotImplemented);
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337
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338 case EVR_UN: // unknown value representation
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339 throw OrthancException(ErrorCode_ParameterOutOfRange);
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340
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341
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342 /**
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343 * String types.
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344 * http://support.dcmtk.org/docs/classDcmByteString.html
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345 **/
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346
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347 case EVR_AS: // age string
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348 return new DcmAgeString(key);
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349
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350 case EVR_AE: // application entity title
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351 return new DcmApplicationEntity(key);
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352
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353 case EVR_CS: // code string
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354 return new DcmCodeString(key);
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355
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356 case EVR_DA: // date string
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357 return new DcmDate(key);
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358
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359 case EVR_DT: // date time string
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360 return new DcmDateTime(key);
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361
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362 case EVR_DS: // decimal string
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363 return new DcmDecimalString(key);
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364
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365 case EVR_IS: // integer string
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366 return new DcmIntegerString(key);
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367
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368 case EVR_TM: // time string
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369 return new DcmTime(key);
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370
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371 case EVR_UI: // unique identifier
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372 return new DcmUniqueIdentifier(key);
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373
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374 case EVR_ST: // short text
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375 return new DcmShortText(key);
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376
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377 case EVR_LO: // long string
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378 return new DcmLongString(key);
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379
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380 case EVR_LT: // long text
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381 return new DcmLongText(key);
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382
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383 case EVR_UT: // unlimited text
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384 return new DcmUnlimitedText(key);
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385
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386 case EVR_SH: // short string
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387 return new DcmShortString(key);
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388
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389 case EVR_PN: // person name
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390 return new DcmPersonName(key);
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391
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392
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393 /**
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394 * Numerical types
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395 **/
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396
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397 case EVR_SL: // signed long
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398 return new DcmSignedLong(key);
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399
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400 case EVR_SS: // signed short
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401 return new DcmSignedShort(key);
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402
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403 case EVR_UL: // unsigned long
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404 return new DcmUnsignedLong(key);
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405
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406 case EVR_US: // unsigned short
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407 return new DcmUnsignedShort(key);
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408
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409 case EVR_FL: // float single-precision
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410 return new DcmFloatingPointSingle(key);
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411
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412 case EVR_FD: // float double-precision
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413 return new DcmFloatingPointDouble(key);
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414
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415
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416 /**
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417 * Sequence types, should never occur at this point.
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418 **/
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419
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420 case EVR_SQ: // sequence of items
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421 throw OrthancException(ErrorCode_ParameterOutOfRange);
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422
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423
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424 /**
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425 * Internal to DCMTK.
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426 **/
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427
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428 case EVR_ox: // OB or OW depending on context
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429 case EVR_xs: // SS or US depending on context
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430 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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431 case EVR_na: // na="not applicable", for data which has no VR
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432 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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433 case EVR_item: // used internally for items
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434 case EVR_metainfo: // used internally for meta info datasets
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435 case EVR_dataset: // used internally for datasets
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436 case EVR_fileFormat: // used internally for DICOM files
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437 case EVR_dicomDir: // used internally for DICOMDIR objects
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438 case EVR_dirRecord: // used internally for DICOMDIR records
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439 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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440 case EVR_pixelItem: // used internally for pixel items in a compressed image
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441 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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442 case EVR_PixelData: // used internally for uncompressed pixeld data
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443 case EVR_OverlayData: // used internally for overlay data
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444 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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445 default:
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446 break;
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447 }
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448
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449 throw OrthancException(ErrorCode_InternalError);
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450 }
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451
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452
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453
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454 static void FillElementWithString(DcmElement& element,
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455 const DicomTag& tag,
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456 const std::string& value)
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457 {
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458 DcmTag key(tag.GetGroup(), tag.GetElement());
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459 bool ok = false;
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460
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461 try
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462 {
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463 switch (key.getEVR())
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464 {
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465 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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466
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467 /**
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468 * TODO.
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469 **/
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470
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471 case EVR_OB: // other byte
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472 case EVR_OF: // other float
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473 case EVR_OW: // other word
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474 case EVR_AT: // attribute tag
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475 throw OrthancException(ErrorCode_NotImplemented);
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476
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477 case EVR_UN: // unknown value representation
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478 throw OrthancException(ErrorCode_ParameterOutOfRange);
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479
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480
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481 /**
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482 * String types.
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483 **/
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484
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485 case EVR_DS: // decimal string
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486 case EVR_IS: // integer string
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487 case EVR_AS: // age string
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488 case EVR_DA: // date string
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489 case EVR_DT: // date time string
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490 case EVR_TM: // time string
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491 case EVR_AE: // application entity title
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492 case EVR_CS: // code string
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493 case EVR_SH: // short string
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494 case EVR_LO: // long string
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495 case EVR_ST: // short text
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496 case EVR_LT: // long text
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497 case EVR_UT: // unlimited text
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498 case EVR_PN: // person name
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499 case EVR_UI: // unique identifier
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500 {
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501 ok = element.putString(value.c_str()).good();
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502 break;
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503 }
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504
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505
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506 /**
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507 * Numerical types
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508 **/
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509
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510 case EVR_SL: // signed long
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511 {
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512 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
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513 break;
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514 }
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515
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516 case EVR_SS: // signed short
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517 {
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518 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
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519 break;
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520 }
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521
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522 case EVR_UL: // unsigned long
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523 {
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524 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
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diff changeset
525 break;
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526 }
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527
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528 case EVR_US: // unsigned short
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529 {
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530 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
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531 break;
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532 }
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533
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534 case EVR_FL: // float single-precision
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535 {
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536 ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
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537 break;
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538 }
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539
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540 case EVR_FD: // float double-precision
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541 {
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542 ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
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543 break;
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544 }
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diff changeset
545
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546
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547 /**
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548 * Sequence types, should never occur at this point.
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549 **/
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550
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551 case EVR_SQ: // sequence of items
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552 {
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553 ok = false;
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554 break;
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555 }
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556
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diff changeset
557
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558 /**
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559 * Internal to DCMTK.
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560 **/
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561
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562 case EVR_ox: // OB or OW depending on context
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563 case EVR_xs: // SS or US depending on context
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564 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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565 case EVR_na: // na="not applicable", for data which has no VR
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566 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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567 case EVR_item: // used internally for items
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568 case EVR_metainfo: // used internally for meta info datasets
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569 case EVR_dataset: // used internally for datasets
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570 case EVR_fileFormat: // used internally for DICOM files
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571 case EVR_dicomDir: // used internally for DICOMDIR objects
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572 case EVR_dirRecord: // used internally for DICOMDIR records
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573 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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574 case EVR_pixelItem: // used internally for pixel items in a compressed image
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575 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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576 case EVR_PixelData: // used internally for uncompressed pixeld data
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577 case EVR_OverlayData: // used internally for overlay data
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578 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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diff changeset
579 default:
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580 break;
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diff changeset
581 }
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diff changeset
582 }
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parents: 291
diff changeset
583 catch (boost::bad_lexical_cast&)
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diff changeset
584 {
238134081136 modification of dicom files
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parents: 291
diff changeset
585 ok = false;
238134081136 modification of dicom files
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parents: 291
diff changeset
586 }
238134081136 modification of dicom files
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diff changeset
587
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
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588 if (!ok)
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
589 {
238134081136 modification of dicom files
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parents: 291
diff changeset
590 throw OrthancException(ErrorCode_InternalError);
238134081136 modification of dicom files
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parents: 291
diff changeset
591 }
238134081136 modification of dicom files
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parents: 291
diff changeset
592 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
593
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
594
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parents: 291
diff changeset
595 void ParsedDicomFile::Remove(const DicomTag& tag)
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596 {
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parents: 291
diff changeset
597 DcmTagKey key(tag.GetGroup(), tag.GetElement());
306
326d5a4a5af3 modification of instances
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diff changeset
598 DcmElement* element = file_->getDataset()->remove(key);
326d5a4a5af3 modification of instances
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diff changeset
599 if (element != NULL)
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
600 {
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
601 delete element;
326d5a4a5af3 modification of instances
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parents: 305
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602 }
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
603 }
302
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diff changeset
604
306
326d5a4a5af3 modification of instances
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diff changeset
605
326d5a4a5af3 modification of instances
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606
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
607 void ParsedDicomFile::RemovePrivateTags()
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
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608 {
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diff changeset
609 typedef std::list<DcmElement*> Tags;
326d5a4a5af3 modification of instances
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diff changeset
610
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diff changeset
611 Tags privateTags;
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
612
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
613 DcmDataset& dataset = *file_->getDataset();
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
614 for (unsigned long i = 0; i < dataset.card(); i++)
326d5a4a5af3 modification of instances
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diff changeset
615 {
326d5a4a5af3 modification of instances
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diff changeset
616 DcmElement* element = dataset.getElement(i);
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
617 DcmTag tag(element->getTag());
311
26efccdff583 anonymisation
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diff changeset
618 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK
26efccdff583 anonymisation
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parents: 308
diff changeset
619 tag.getPrivateCreator() != NULL)
306
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
620 {
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
621 privateTags.push_back(element);
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
622 }
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
623 }
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
624
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
625 for (Tags::iterator it = privateTags.begin();
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
626 it != privateTags.end(); it++)
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
627 {
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
628 DcmElement* tmp = dataset.remove(*it);
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
629 if (tmp != NULL)
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
630 {
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
631 delete tmp;
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
632 }
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
633 }
302
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diff changeset
634 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
635
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
636
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
637
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
638 void ParsedDicomFile::Insert(const DicomTag& tag,
238134081136 modification of dicom files
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parents: 291
diff changeset
639 const std::string& value)
238134081136 modification of dicom files
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parents: 291
diff changeset
640 {
238134081136 modification of dicom files
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diff changeset
641 std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
238134081136 modification of dicom files
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parents: 291
diff changeset
642 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
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parents: 291
diff changeset
643
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
644 if (!file_->getDataset()->insert(element.release(), false, false).good())
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
645 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
646 // This field already exists
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
647 throw OrthancException(ErrorCode_InternalError);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
648 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
649 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
650
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
651
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
652 void ParsedDicomFile::Replace(const DicomTag& tag,
86bb79522f19 name of the private tags
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parents: 304
diff changeset
653 const std::string& value,
86bb79522f19 name of the private tags
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parents: 304
diff changeset
654 DicomReplaceMode mode)
302
238134081136 modification of dicom files
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parents: 291
diff changeset
655 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
656 DcmTagKey key(tag.GetGroup(), tag.GetElement());
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
657 DcmElement* element = NULL;
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
658
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
659 if (!file_->getDataset()->findAndGetElement(key, element).good() ||
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
660 element == NULL)
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
661 {
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
662 // This field does not exist, act wrt. the specified "mode"
86bb79522f19 name of the private tags
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parents: 304
diff changeset
663 switch (mode)
302
238134081136 modification of dicom files
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parents: 291
diff changeset
664 {
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
665 case DicomReplaceMode_InsertIfAbsent:
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
666 Insert(tag, value);
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
667 break;
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
668
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
669 case DicomReplaceMode_ThrowIfAbsent:
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
670 throw OrthancException(ErrorCode_InexistentItem);
86bb79522f19 name of the private tags
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parents: 304
diff changeset
671
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
672 case DicomReplaceMode_IgnoreIfAbsent:
86bb79522f19 name of the private tags
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diff changeset
673 return;
302
238134081136 modification of dicom files
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parents: 291
diff changeset
674 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
675 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
676 else
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
677 {
238134081136 modification of dicom files
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parents: 291
diff changeset
678 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
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parents: 291
diff changeset
679 }
303
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diff changeset
680
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
681
c76a35a85c69 ready for anonymization
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diff changeset
682 /**
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parents: 302
diff changeset
683 * dcmodify will automatically correct 'Media Storage SOP Class
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diff changeset
684 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
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parents: 302
diff changeset
685 * you make changes to the related tags in the dataset ('SOP Class
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diff changeset
686 * UID' and 'SOP Instance UID') via insert or modify mode
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parents: 302
diff changeset
687 * options. You can disable this behaviour by using the -nmu
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parents: 302
diff changeset
688 * option.
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diff changeset
689 **/
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
690 if (tag == DICOM_TAG_SOP_CLASS_UID)
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
691 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent);
303
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diff changeset
692
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parents: 302
diff changeset
693 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
694 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent);
302
238134081136 modification of dicom files
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parents: 291
diff changeset
695 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
696
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
697
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
698 void ParsedDicomFile::Answer(RestApiOutput& output)
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
699 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
700 std::string serialized;
238134081136 modification of dicom files
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parents: 291
diff changeset
701 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset()))
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
702 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
703 output.AnswerBuffer(serialized, "application/octet-stream");
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
704 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
705 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
706
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
707
308
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
708
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
709 bool ParsedDicomFile::GetTagValue(std::string& value,
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
710 const DicomTag& tag)
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
711 {
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
712 DcmTagKey k(tag.GetGroup(), tag.GetElement());
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
713 DcmDataset& dataset = *file_->getDataset();
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
714 DcmElement* element = NULL;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
715 if (!dataset.findAndGetElement(k, element).good() ||
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
716 element == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
717 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
718 return false;
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
719 }
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
720
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
721 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element));
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
722
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
723 if (v.get() == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
724 {
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
725 value = "";
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
726 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
727 else
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
728 {
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
729 value = v->AsString();
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
730 }
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parents: 306
diff changeset
731
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parents: 306
diff changeset
732 return true;
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
733 }
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parents: 306
diff changeset
734
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
735
315
fc856d175d18 modifications
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parents: 311
diff changeset
736
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parents: 311
diff changeset
737 DicomInstanceHasher ParsedDicomFile::GetHasher()
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parents: 311
diff changeset
738 {
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parents: 311
diff changeset
739 std::string patientId, studyUid, seriesUid, instanceUid;
fc856d175d18 modifications
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diff changeset
740
fc856d175d18 modifications
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parents: 311
diff changeset
741 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
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parents: 311
diff changeset
742 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
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parents: 311
diff changeset
743 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
fc856d175d18 modifications
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parents: 311
diff changeset
744 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
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parents: 311
diff changeset
745 {
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parents: 311
diff changeset
746 throw OrthancException(ErrorCode_BadFileFormat);
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parents: 311
diff changeset
747 }
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parents: 311
diff changeset
748
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parents: 311
diff changeset
749 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
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diff changeset
750 }
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parents: 311
diff changeset
751
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parents: 311
diff changeset
752
0
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parents:
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753 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset)
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parents:
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754 {
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parents:
diff changeset
755 target.Clear();
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parents:
diff changeset
756 for (unsigned long i = 0; i < dataset.card(); i++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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757 {
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parents:
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758 DcmElement* element = dataset.getElement(i);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
759 if (element && element->isLeaf())
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parents:
diff changeset
760 {
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761 target.SetValue(element->getTag().getGTag(),
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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762 element->getTag().getETag(),
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parents:
diff changeset
763 ConvertLeafElement(*element));
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parents:
diff changeset
764 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
765 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
766 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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767
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
768
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parents:
diff changeset
769 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element)
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parents:
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770 {
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771 return DicomTag(element.getGTag(), element.getETag());
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parents:
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772 }
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parents:
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773
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
774
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parents:
diff changeset
775 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
776 {
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parents:
diff changeset
777 if (!element.isLeaf())
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parents:
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778 {
62
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779 throw OrthancException("Only applicable to leaf elements");
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
780 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
781
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
782 if (element.isaString())
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
783 {
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parents:
diff changeset
784 char *c;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
785 if (element.getString(c).good() &&
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
786 c != NULL)
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parents:
diff changeset
787 {
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diff changeset
788 std::string s(c);
107
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789 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter?
0
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parents:
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790 return new DicomString(utf8);
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parents:
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791 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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792 else
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parents:
diff changeset
793 {
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parents:
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794 return new DicomNullValue;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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795 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
796 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
797
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
798 try
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
799 {
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800 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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801 switch (element.getVR())
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parents:
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802 {
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parents:
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803
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parents:
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804 /**
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parents:
diff changeset
805 * TODO.
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parents:
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806 **/
306
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diff changeset
807
302
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808 case EVR_OB: // other byte
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809 case EVR_OF: // other float
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810 case EVR_OW: // other word
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811 case EVR_AT: // attribute tag
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812 case EVR_UN: // unknown value representation
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813 return new DicomNullValue();
306
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814
302
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diff changeset
815 /**
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diff changeset
816 * String types, should never happen at this point because of
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817 * "element.isaString()".
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818 **/
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parents: 291
diff changeset
819
306
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820 case EVR_DS: // decimal string
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diff changeset
821 case EVR_IS: // integer string
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822 case EVR_AS: // age string
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parents: 305
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823 case EVR_DA: // date string
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diff changeset
824 case EVR_DT: // date time string
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parents: 305
diff changeset
825 case EVR_TM: // time string
302
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diff changeset
826 case EVR_AE: // application entity title
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diff changeset
827 case EVR_CS: // code string
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diff changeset
828 case EVR_SH: // short string
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parents: 291
diff changeset
829 case EVR_LO: // long string
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parents: 291
diff changeset
830 case EVR_ST: // short text
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parents: 291
diff changeset
831 case EVR_LT: // long text
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parents: 291
diff changeset
832 case EVR_UT: // unlimited text
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parents: 291
diff changeset
833 case EVR_PN: // person name
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parents: 291
diff changeset
834 case EVR_UI: // unique identifier
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parents: 291
diff changeset
835 return new DicomNullValue();
0
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parents:
diff changeset
836
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parents:
diff changeset
837
302
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diff changeset
838 /**
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parents: 291
diff changeset
839 * Numerical types
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parents: 291
diff changeset
840 **/
0
3959d33612cc initial commit
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parents:
diff changeset
841
302
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parents: 291
diff changeset
842 case EVR_SL: // signed long
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parents: 291
diff changeset
843 {
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diff changeset
844 Sint32 f;
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diff changeset
845 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
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parents: 291
diff changeset
846 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
847 else
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parents: 291
diff changeset
848 return new DicomNullValue();
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parents: 291
diff changeset
849 }
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parents: 291
diff changeset
850
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parents: 291
diff changeset
851 case EVR_SS: // signed short
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parents: 291
diff changeset
852 {
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diff changeset
853 Sint16 f;
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diff changeset
854 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
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parents: 291
diff changeset
855 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
856 else
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parents: 291
diff changeset
857 return new DicomNullValue();
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parents: 291
diff changeset
858 }
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parents: 291
diff changeset
859
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parents: 291
diff changeset
860 case EVR_UL: // unsigned long
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parents: 291
diff changeset
861 {
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parents: 291
diff changeset
862 Uint32 f;
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parents: 291
diff changeset
863 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
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parents: 291
diff changeset
864 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
865 else
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parents: 291
diff changeset
866 return new DicomNullValue();
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parents: 291
diff changeset
867 }
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parents: 291
diff changeset
868
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parents: 291
diff changeset
869 case EVR_US: // unsigned short
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parents: 291
diff changeset
870 {
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parents: 291
diff changeset
871 Uint16 f;
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parents: 291
diff changeset
872 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
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parents: 291
diff changeset
873 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
874 else
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parents: 291
diff changeset
875 return new DicomNullValue();
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parents: 291
diff changeset
876 }
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parents: 291
diff changeset
877
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parents: 291
diff changeset
878 case EVR_FL: // float single-precision
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parents: 291
diff changeset
879 {
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parents: 291
diff changeset
880 Float32 f;
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parents: 291
diff changeset
881 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
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diff changeset
882 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
883 else
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parents: 291
diff changeset
884 return new DicomNullValue();
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parents: 291
diff changeset
885 }
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parents: 291
diff changeset
886
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parents: 291
diff changeset
887 case EVR_FD: // float double-precision
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diff changeset
888 {
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diff changeset
889 Float64 f;
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diff changeset
890 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
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parents: 291
diff changeset
891 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
892 else
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parents: 291
diff changeset
893 return new DicomNullValue();
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parents: 291
diff changeset
894 }
0
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parents:
diff changeset
895
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
896
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parents:
diff changeset
897 /**
302
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parents: 291
diff changeset
898 * Sequence types, should never occur at this point because of
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parents: 291
diff changeset
899 * "element.isLeaf()".
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parents: 291
diff changeset
900 **/
0
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parents:
diff changeset
901
302
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diff changeset
902 case EVR_SQ: // sequence of items
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diff changeset
903 return new DicomNullValue;
0
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parents:
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904
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parents:
diff changeset
905
302
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diff changeset
906 /**
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diff changeset
907 * Internal to DCMTK.
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diff changeset
908 **/
0
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parents:
diff changeset
909
302
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diff changeset
910 case EVR_ox: // OB or OW depending on context
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diff changeset
911 case EVR_xs: // SS or US depending on context
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diff changeset
912 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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diff changeset
913 case EVR_na: // na="not applicable", for data which has no VR
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diff changeset
914 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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parents: 291
diff changeset
915 case EVR_item: // used internally for items
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diff changeset
916 case EVR_metainfo: // used internally for meta info datasets
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diff changeset
917 case EVR_dataset: // used internally for datasets
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parents: 291
diff changeset
918 case EVR_fileFormat: // used internally for DICOM files
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diff changeset
919 case EVR_dicomDir: // used internally for DICOMDIR objects
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parents: 291
diff changeset
920 case EVR_dirRecord: // used internally for DICOMDIR records
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parents: 291
diff changeset
921 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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diff changeset
922 case EVR_pixelItem: // used internally for pixel items in a compressed image
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parents: 291
diff changeset
923 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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parents: 291
diff changeset
924 case EVR_PixelData: // used internally for uncompressed pixeld data
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parents: 291
diff changeset
925 case EVR_OverlayData: // used internally for overlay data
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parents: 291
diff changeset
926 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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parents: 291
diff changeset
927 return new DicomNullValue;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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928
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
929
302
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diff changeset
930 /**
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parents: 291
diff changeset
931 * Default case.
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parents: 291
diff changeset
932 **/
0
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parents:
diff changeset
933
302
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diff changeset
934 default:
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diff changeset
935 return new DicomNullValue;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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936 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
937 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
938 catch (boost::bad_lexical_cast)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
939 {
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parents:
diff changeset
940 return new DicomNullValue;
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parents:
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941 }
306
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diff changeset
942 catch (std::bad_cast)
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943 {
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944 return new DicomNullValue;
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parents: 305
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945 }
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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946 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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947
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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948
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Sebastien Jodogne <s.jodogne@gmail.com>
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949 static void StoreElement(Json::Value& target,
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950 DcmElement& element,
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parents:
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951 unsigned int maxStringLength);
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parents:
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952
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953 static void StoreItem(Json::Value& target,
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954 DcmItem& item,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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955 unsigned int maxStringLength)
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parents:
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956 {
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957 target = Json::Value(Json::objectValue);
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parents:
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958
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parents:
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959 for (unsigned long i = 0; i < item.card(); i++)
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parents:
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960 {
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961 DcmElement* element = item.getElement(i);
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962 StoreElement(target, *element, maxStringLength);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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963 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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964 }
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parents:
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965
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
966
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parents:
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967 static void StoreElement(Json::Value& target,
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968 DcmElement& element,
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parents:
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969 unsigned int maxStringLength)
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parents:
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970 {
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971 assert(target.type() == Json::objectValue);
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972
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973 DicomTag tag(FromDcmtkBridge::GetTag(element));
305
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974 const std::string formattedTag = tag.Format();
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975
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parents: 304
diff changeset
976 #if 0
35
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977 const std::string tagName = FromDcmtkBridge::GetName(tag);
305
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diff changeset
978 #else
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diff changeset
979 // This version of the code gives access to the name of the private tags
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980 DcmTag tagbis(element.getTag());
306
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diff changeset
981 const std::string tagName(tagbis.getTagName());
305
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diff changeset
982 #endif
0
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parents:
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983
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parents:
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984 if (element.isLeaf())
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parents:
diff changeset
985 {
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diff changeset
986 Json::Value value(Json::objectValue);
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987 value["Name"] = tagName;
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parents: 2
diff changeset
988
306
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989 if (tagbis.getPrivateCreator() != NULL)
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990 {
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991 value["PrivateCreator"] = tagbis.getPrivateCreator();
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parents: 305
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992 }
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diff changeset
993
0
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994 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
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parents:
diff changeset
995 if (v->IsNull())
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parents:
diff changeset
996 {
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diff changeset
997 value["Type"] = "Null";
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
998 value["Value"] = Json::nullValue;
0
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parents:
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999 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1000 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1001 {
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1002 std::string s = v->AsString();
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1003 if (maxStringLength == 0 ||
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1004 s.size() <= maxStringLength)
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1005 {
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diff changeset
1006 value["Type"] = "String";
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1007 value["Value"] = s;
0
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1008 }
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parents:
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1009 else
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1010 {
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diff changeset
1011 value["Type"] = "TooLong";
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diff changeset
1012 value["Value"] = Json::nullValue;
0
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parents:
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1013 }
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parents:
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1014 }
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parents: 2
diff changeset
1015
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diff changeset
1016 target[formattedTag] = value;
0
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parents:
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1017 }
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parents:
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1018 else
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1019 {
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diff changeset
1020 Json::Value children(Json::arrayValue);
0
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parents:
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1021
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1022 // "All subclasses of DcmElement except for DcmSequenceOfItems
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1023 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
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1024 // etc. are not." The following cast is thus OK.
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1025 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
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parents:
diff changeset
1026
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1027 for (unsigned long i = 0; i < sequence.card(); i++)
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diff changeset
1028 {
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1029 DcmItem* child = sequence.getItem(i);
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diff changeset
1030 Json::Value& v = children.append(Json::objectValue);
0
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parents:
diff changeset
1031 StoreItem(v, *child, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1032 }
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1033
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1034 target[formattedTag]["Name"] = tagName;
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1035 target[formattedTag]["Type"] = "Sequence";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1036 target[formattedTag]["Value"] = children;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1037 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1038 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1039
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1040
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1041 void FromDcmtkBridge::ToJson(Json::Value& root,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1042 DcmDataset& dataset,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1043 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1044 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1045 StoreItem(root, dataset, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1046 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1047
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1048
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1049
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1050 void FromDcmtkBridge::ToJson(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1051 const std::string& path,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1052 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1053 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1054 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1055 if (!dicom.loadFile(path.c_str()).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1056 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1057 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1058 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1059 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1060 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1061 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1062 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1063 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1064
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1065
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1066 static void ExtractPngImageColorPreview(std::string& result,
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1067 DicomIntegerPixelAccessor& accessor)
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1068 {
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1069 assert(accessor.GetChannelCount() == 3);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1070 PngWriter w;
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1071
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1072 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1073 uint8_t* pixel = &image[0];
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1074
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1075 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1076 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1077 for (unsigned int x = 0; x < accessor.GetWidth(); x++)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1078 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1079 for (unsigned int c = 0; c < 3; c++, pixel++)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1080 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1081 int32_t v = accessor.GetValue(x, y, c);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1082 if (v < 0)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1083 *pixel = 0;
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1084 else if (v > 255)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1085 *pixel = 255;
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1086 else
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1087 *pixel = v;
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1088 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1089 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1090 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1091
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1092 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1093 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1094 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1095
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1096
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1097 static void ExtractPngImageGrayscalePreview(std::string& result,
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1098 DicomIntegerPixelAccessor& accessor)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1099 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1100 assert(accessor.GetChannelCount() == 1);
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1101 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1102
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1103 int32_t min, max;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1104 accessor.GetExtremeValues(min, max);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1105
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1106 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1107 if (min != max)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1108 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1109 uint8_t* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1110 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1111 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1112 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1113 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1114 int32_t v = accessor.GetValue(x, y);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1115 *pixel = static_cast<uint8_t>(
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1116 boost::math::lround(static_cast<float>(v - min) /
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1117 static_cast<float>(max - min) * 255.0f));
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1118 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1119 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1120 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1121
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1122 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1123 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1124 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1125
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1126
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1127 template <typename T>
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1128 static void ExtractPngImageTruncate(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1129 DicomIntegerPixelAccessor& accessor,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1130 PixelFormat format)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1131 {
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1132 assert(accessor.GetChannelCount() == 1);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1133
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1134 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1135
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1136 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1137 T* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1138 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1139 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1140 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1141 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1142 int32_t v = accessor.GetValue(x, y);
464
5987dd8e0776 fix reading signed values in dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 454
diff changeset
1143 if (v < static_cast<int32_t>(std::numeric_limits<T>::min()))
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1144 *pixel = std::numeric_limits<T>::min();
464
5987dd8e0776 fix reading signed values in dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 454
diff changeset
1145 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max()))
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1146 *pixel = std::numeric_limits<T>::max();
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1147 else
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1148 *pixel = static_cast<T>(v);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1149 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1150 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1151
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1152 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1153 accessor.GetWidth() * sizeof(T), format, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1154 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1155
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1156
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1157 static bool DecodePsmctRle1(std::string& output,
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1158 DcmDataset& dataset)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1159 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1160 static const DicomTag tagContent(0x07a1, 0x100a);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1161 static const DicomTag tagCompressionType(0x07a1, 0x1011);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1162
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1163 DcmElement* e;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1164 char* c;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1165
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1166 // Check whether the DICOM instance contains an image encoded with
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1167 // the PMSCT_RLE1 scheme.
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1168 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1169 e == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1170 !e->isaString() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1171 !e->getString(c).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1172 c == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1173 strcmp("PMSCT_RLE1", c))
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1174 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1175 return false;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1176 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1177
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1178 // OK, this is a custom RLE encoding from Philips. Get the pixel
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1179 // data from the appropriate private DICOM tag.
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1180 Uint8* pixData = NULL;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1181 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1182 e == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1183 e->getUint8Array(pixData) != EC_Normal)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1184 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1185 return false;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1186 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1187
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1188 // The "unsigned" below IS VERY IMPORTANT
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1189 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1190 const size_t length = e->getLength();
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1191
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1192 /**
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1193 * The code below is an adaptation of a sample code for GDCM by
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1194 * Mathieu Malaterre (under a BSD license).
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1195 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1196 **/
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1197
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1198 // RLE pass
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1199 std::vector<uint8_t> temp;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1200 temp.reserve(length);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1201 for (size_t i = 0; i < length; i++)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1202 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1203 if (inbuffer[i] == 0xa5)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1204 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1205 temp.push_back(inbuffer[i+2]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1206 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1207 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1208 temp.push_back(inbuffer[i+2]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1209 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1210 i += 2;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1211 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1212 else
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1213 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1214 temp.push_back(inbuffer[i]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1215 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1216 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1217
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1218 // Delta encoding pass
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1219 uint16_t delta = 0;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1220 output.clear();
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1221 output.reserve(temp.size());
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1222 for (size_t i = 0; i < temp.size(); i++)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1223 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1224 uint16_t value;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1225
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1226 if (temp[i] == 0x5a)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1227 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1228 uint16_t v1 = temp[i + 1];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1229 uint16_t v2 = temp[i + 2];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1230 value = (v2 << 8) + v1;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1231 i += 2;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1232 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1233 else
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1234 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1235 value = delta + (int8_t) temp[i];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1236 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1237
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1238 output.push_back(value & 0xff);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1239 output.push_back(value >> 8);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1240 delta = value;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1241 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1242
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1243 if (output.size() % 2)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1244 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1245 output.resize(output.size() - 1);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1246 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1247
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1248 return true;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1249 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1250
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1251
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1252 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1253 DcmDataset& dataset,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1254 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1255 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1256 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1257 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1258
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1259 std::auto_ptr<DicomIntegerPixelAccessor> accessor;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1260
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1261 DicomMap m;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1262 FromDcmtkBridge::Convert(m, dataset);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1263
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1264 std::string privateContent;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1265
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1266 DcmElement* e;
80
6212bf978584 status of series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 79
diff changeset
1267 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() &&
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1268 e != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1269 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1270 Uint8* pixData = NULL;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1271 if (e->getUint8Array(pixData) == EC_Normal)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1272 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1273 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength()));
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1274 accessor->SetCurrentFrame(frame);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1275 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1276 }
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1277 else if (DecodePsmctRle1(privateContent, dataset))
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1278 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1279 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded";
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1280 Uint8* pixData = NULL;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1281 if (privateContent.size() > 0)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1282 pixData = reinterpret_cast<Uint8*>(&privateContent[0]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1283 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size()));
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1284 accessor->SetCurrentFrame(frame);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1285 }
419
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1286
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1287 if (accessor.get() == NULL)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1288 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1289 throw OrthancException(ErrorCode_BadFileFormat);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1290 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1291
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1292 PixelFormat format;
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1293 bool supported = false;
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1294
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1295 if (accessor->GetChannelCount() == 1)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1296 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1297 switch (mode)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1298 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1299 case ImageExtractionMode_Preview:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1300 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1301 format = PixelFormat_Grayscale8;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1302 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1303
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1304 case ImageExtractionMode_UInt8:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1305 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1306 format = PixelFormat_Grayscale8;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1307 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1308
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1309 case ImageExtractionMode_UInt16:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1310 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1311 format = PixelFormat_Grayscale16;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1312 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1313
465
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1314 case ImageExtractionMode_Int16:
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1315 supported = true;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1316 format = PixelFormat_SignedGrayscale16;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1317 break;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1318
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1319 default:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1320 supported = false;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1321 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1322 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1323 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1324 else if (accessor->GetChannelCount() == 3)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1325 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1326 switch (mode)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1327 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1328 case ImageExtractionMode_Preview:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1329 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1330 format = PixelFormat_RGB24;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1331 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1332
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1333 default:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1334 supported = false;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1335 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1336 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1337 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1338
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1339 if (!supported)
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1340 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1341 throw OrthancException(ErrorCode_NotImplemented);
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1342 }
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1343
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1344 if (accessor.get() == NULL ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1345 accessor->GetWidth() == 0 ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1346 accessor->GetHeight() == 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1347 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1348 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1349 w.WriteToMemory(result, 0, 0, 0, format, NULL);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1350 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1351 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1352 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1353 switch (mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1354 {
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1355 case ImageExtractionMode_Preview:
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1356 if (format == PixelFormat_Grayscale8)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1357 ExtractPngImageGrayscalePreview(result, *accessor);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1358 else
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1359 ExtractPngImageColorPreview(result, *accessor);
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1360 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1361
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1362 case ImageExtractionMode_UInt8:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1363 ExtractPngImageTruncate<uint8_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1364 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1365
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1366 case ImageExtractionMode_UInt16:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1367 ExtractPngImageTruncate<uint16_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1368 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1369
465
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1370 case ImageExtractionMode_Int16:
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1371 ExtractPngImageTruncate<int16_t>(result, *accessor, format);
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1372 break;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1373
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1374 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1375 throw OrthancException(ErrorCode_NotImplemented);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1376 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1377 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1378 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1379
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1380
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1381 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1382 const std::string& dicomContent,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1383 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1384 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1385 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1386 DcmInputBufferStream is;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1387 if (dicomContent.size() > 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1388 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1389 is.setBuffer(&dicomContent[0], dicomContent.size());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1390 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1391 is.setEos();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1392
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1393 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1394 if (dicom.read(is).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1395 {
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1396 ExtractPngImage(result, *dicom.getDataset(), frame, mode);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1397 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1398 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1399 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1400 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1401 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1402 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1403
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1404
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1405
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1406 std::string FromDcmtkBridge::GetName(const DicomTag& t)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1407 {
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1408 // Some patches for important tags because of different DICOM
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1409 // dictionaries between DCMTK versions
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1410 std::string n = t.GetMainTagsName();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1411 if (n.size() != 0)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1412 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1413 return n;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1414 }
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1415 // End of patches
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1416
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1417 #if 0
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1418 DcmTagKey tag(t.GetGroup(), t.GetElement());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1419 const DcmDataDictionary& dict = dcmDataDict.rdlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1420 const DcmDictEntry* entry = dict.findEntry(tag, NULL);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1421
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1422 std::string s(DcmTag_ERROR_TagName);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1423 if (entry != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1424 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1425 s = std::string(entry->getTagName());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1426 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1427
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1428 dcmDataDict.unlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1429 return s;
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1430 #else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1431 DcmTag tag(t.GetGroup(), t.GetElement());
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1432 const char* name = tag.getTagName();
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1433 if (name == NULL)
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1434 {
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1435 return DcmTag_ERROR_TagName;
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1436 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1437 else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1438 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1439 return std::string(name);
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1440 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1441 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1442 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1443
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1444
304
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1445 DicomTag FromDcmtkBridge::ParseTag(const char* name)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1446 {
304
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1447 if (strlen(name) == 9 &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1448 isxdigit(name[0]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1449 isxdigit(name[1]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1450 isxdigit(name[2]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1451 isxdigit(name[3]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1452 name[4] == '-' &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1453 isxdigit(name[5]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1454 isxdigit(name[6]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1455 isxdigit(name[7]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1456 isxdigit(name[8]))
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1457 {
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1458 uint16_t group = GetTagValue(name);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1459 uint16_t element = GetTagValue(name + 5);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1460 return DicomTag(group, element);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1461 }
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1462
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1463 #if 0
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1464 const DcmDataDictionary& dict = dcmDataDict.rdlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1465 const DcmDictEntry* entry = dict.findEntry(name);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1466
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1467 if (entry == NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1468 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1469 dcmDataDict.unlock();
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1470 throw OrthancException("Unknown DICOM tag");
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1471 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1472 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1473 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1474 DcmTagKey key = entry->getKey();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1475 DicomTag tag(key.getGroup(), key.getElement());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1476 dcmDataDict.unlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1477 return tag;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1478 }
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
1479 #else
86bb79522f19 name of the private tags
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parents: 304
diff changeset
1480 DcmTag tag;
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1481 if (DcmTag::findTagFromName(name, tag).good())
86bb79522f19 name of the private tags
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parents: 304
diff changeset
1482 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1483 return DicomTag(tag.getGTag(), tag.getETag());
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1484 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1485 else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1486 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1487 throw OrthancException("Unknown DICOM tag");
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1488 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1489 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1490 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1491
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1492
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1493 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1494 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1495 for (DicomMap::Map::const_iterator
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1496 it = m.map_.begin(); it != m.map_.end(); it++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1497 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1498 DicomTag t = it->first;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1499 std::string s = it->second->AsString();
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1500 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str());
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1501 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1502 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1503
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1504
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1505 void FromDcmtkBridge::ToJson(Json::Value& result,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1506 const DicomMap& values)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1507 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1508 if (result.type() != Json::objectValue)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1509 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1510 throw OrthancException(ErrorCode_BadParameterType);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1511 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1512
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1513 result.clear();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1514
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1515 for (DicomMap::Map::const_iterator
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1516 it = values.map_.begin(); it != values.map_.end(); it++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1517 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1518 result[GetName(it->first)] = it->second->AsString();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1519 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1520 }
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1521
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1522
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1523 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1524 {
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1525 char uid[100];
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1526
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1527 switch (level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1528 {
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1529 case DicomRootLevel_Patient:
311
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1530 // The "PatientID" field is of type LO (Long String), 64
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1531 // Bytes Maximum. An UUID is of length 36, thus it can be used
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1532 // as a random PatientID.
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1533 return Toolbox::GenerateUuid();
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1534
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1535 case DicomRootLevel_Instance:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1536 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1537
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1538 case DicomRootLevel_Series:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1539 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1540
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1541 case DicomRootLevel_Study:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1542 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1543
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1544 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1545 throw OrthancException(ErrorCode_ParameterOutOfRange);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1546 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1547 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1548
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1549 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1550 DcmDataset* dataSet)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1551 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1552 // Determine the transfer syntax which shall be used to write the
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1553 // information to the file. We always switch to the Little Endian
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1554 // syntax, with explicit length.
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1555
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1556 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1557 E_TransferSyntax xfer = EXS_LittleEndianExplicit;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1558 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1559
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1560 uint32_t s = dataSet->getLength(xfer, encodingType);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1561
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1562 buffer.resize(s);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1563 DcmOutputBufferStream ob(&buffer[0], s);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1564
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1565 dataSet->transferInit();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1566
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1567 #if DCMTK_VERSION_NUMBER >= 360
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1568 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1569 /*opt_groupLength*/ EGL_recalcGL,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1570 /*opt_paddingType*/ EPD_withoutPadding);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1571 #else
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1572 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1573 #endif
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1574
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1575 dataSet->transferEnd();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1576 if (c.good())
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1577 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1578 return true;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1579 }
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1580 else
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1581 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1582 buffer.clear();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1583 return false;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1584 }
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1585
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1586 #if 0
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1587 OFCondition cond = cbdata->dcmff->saveFile(fileName.c_str(), xfer,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1588 encodingType,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1589 /*opt_groupLength*/ EGL_recalcGL,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1590 /*opt_paddingType*/ EPD_withoutPadding,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1591 OFstatic_cast(Uint32, /*opt_filepad*/ 0),
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1592 OFstatic_cast(Uint32, /*opt_itempad*/ 0),
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1593 (opt_useMetaheader) ? EWM_fileformat : EWM_dataset);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1594 #endif
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1595 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1596 }