annotate OrthancServer/FromDcmtkBridge.cpp @ 681:3bdb5db8e839 query-retrieve

generalization of query/retrieve
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 24 Jan 2014 17:40:45 +0100
parents 27acbc5985f5
children efc4928be6fb
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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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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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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 #include <dcmtk/dcmdata/dcmetinf.h>
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102
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103 #include <dcmtk/dcmdata/dcvrae.h>
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104 #include <dcmtk/dcmdata/dcvras.h>
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105 #include <dcmtk/dcmdata/dcvrcs.h>
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106 #include <dcmtk/dcmdata/dcvrda.h>
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107 #include <dcmtk/dcmdata/dcvrds.h>
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108 #include <dcmtk/dcmdata/dcvrdt.h>
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109 #include <dcmtk/dcmdata/dcvrfd.h>
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110 #include <dcmtk/dcmdata/dcvrfl.h>
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111 #include <dcmtk/dcmdata/dcvris.h>
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112 #include <dcmtk/dcmdata/dcvrlo.h>
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113 #include <dcmtk/dcmdata/dcvrlt.h>
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114 #include <dcmtk/dcmdata/dcvrpn.h>
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115 #include <dcmtk/dcmdata/dcvrsh.h>
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116 #include <dcmtk/dcmdata/dcvrsl.h>
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117 #include <dcmtk/dcmdata/dcvrss.h>
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118 #include <dcmtk/dcmdata/dcvrst.h>
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119 #include <dcmtk/dcmdata/dcvrtm.h>
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120 #include <dcmtk/dcmdata/dcvrui.h>
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121 #include <dcmtk/dcmdata/dcvrul.h>
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122 #include <dcmtk/dcmdata/dcvrus.h>
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123 #include <dcmtk/dcmdata/dcvrut.h>
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124 #include <dcmtk/dcmdata/dcpixel.h>
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125 #include <dcmtk/dcmdata/dcpixseq.h>
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126 #include <dcmtk/dcmdata/dcpxitem.h>
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129 #include <boost/math/special_functions/round.hpp>
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130 #include <glog/logging.h>
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131 #include <dcmtk/dcmdata/dcostrmb.h>
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132
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133 namespace Orthanc
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134 {
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135 void ParsedDicomFile::Setup(const char* buffer, size_t size)
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136 {
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137 DcmInputBufferStream is;
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138 if (size > 0)
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139 {
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140 is.setBuffer(buffer, size);
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141 }
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142 is.setEos();
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143
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144 file_.reset(new DcmFileFormat);
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145 file_->transferInit();
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146 if (!file_->read(is).good())
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147 {
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148 throw OrthancException(ErrorCode_BadFileFormat);
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149 }
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150 file_->loadAllDataIntoMemory();
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151 file_->transferEnd();
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152 }
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153
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154
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155 static void SendPathValueForDictionary(RestApiOutput& output,
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156 DcmItem& dicom)
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157 {
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158 Json::Value v = Json::arrayValue;
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159
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160 for (unsigned long i = 0; i < dicom.card(); i++)
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161 {
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162 DcmElement* element = dicom.getElement(i);
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163 if (element)
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164 {
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165 char buf[16];
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166 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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167 v.append(buf);
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168 }
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169 }
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170
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171 output.AnswerJson(v);
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172 }
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173
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174 static inline uint16_t GetCharValue(char c)
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175 {
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176 if (c >= '0' && c <= '9')
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177 return c - '0';
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178 else if (c >= 'a' && c <= 'f')
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179 return c - 'a' + 10;
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180 else if (c >= 'A' && c <= 'F')
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181 return c - 'A' + 10;
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182 else
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183 return 0;
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184 }
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185
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186 static inline uint16_t GetTagValue(const char* c)
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187 {
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188 return ((GetCharValue(c[0]) << 12) +
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189 (GetCharValue(c[1]) << 8) +
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190 (GetCharValue(c[2]) << 4) +
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191 GetCharValue(c[3]));
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192 }
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193
304
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194 static void ParseTagAndGroup(DcmTagKey& key,
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195 const std::string& tag)
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196 {
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197 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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198 key = DcmTagKey(t.GetGroup(), t.GetElement());
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199 }
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200
291
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201
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202 static void SendSequence(RestApiOutput& output,
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203 DcmSequenceOfItems& sequence)
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204 {
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205 // This element is a sequence
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206 Json::Value v = Json::arrayValue;
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207
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208 for (unsigned long i = 0; i < sequence.card(); i++)
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209 {
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210 v.append(boost::lexical_cast<std::string>(i));
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211 }
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212
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213 output.AnswerJson(v);
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214 }
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215
676
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216
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217 static void AnswerPixelData(RestApiOutput& output,
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218 DcmPixelData& pixelData,
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219 E_TransferSyntax transferSyntax)
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220 {
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221 DcmPixelSequence* pixelSequence = NULL;
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222 if (pixelData.getEncapsulatedRepresentation
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223 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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224 {
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225 for (unsigned long i = 0; i < pixelSequence->card(); i++)
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226 {
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227 DcmPixelItem* pixelItem = NULL;
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228 if (pixelSequence->getItem(pixelItem, i).good() && pixelItem)
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229 {
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230 Uint8* b = NULL;
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231 if (pixelItem->getUint8Array(b).good() && b)
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232 {
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233 // JPEG-LS (lossless)
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234 // http://gdcm.sourceforge.net/wiki/index.php/Tools/ffmpeg#JPEG_LS
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235 // http://www.stat.columbia.edu/~jakulin/jpeg-ls/
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236 // http://itohws03.ee.noda.sut.ac.jp/~matsuda/mrp/
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237
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238 printf("ITEM: %d %d\n", transferSyntax, pixelItem->getLength());
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239 char buf[64];
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240 sprintf(buf, "/tmp/toto-%06ld.jpg", i);
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241 FILE* fp = fopen(buf, "wb");
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242 fwrite(b, pixelItem->getLength(), 1, fp);
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243 fclose(fp);
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244 }
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245 }
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246 }
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247 }
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248 }
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249
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250
302
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251 static void AnswerDicomField(RestApiOutput& output,
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252 DcmElement& element,
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253 E_TransferSyntax transferSyntax)
291
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254 {
676
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255 // This element is not a sequence. Test if it is pixel data.
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256 if (element.getTag().getGTag() == DICOM_TAG_PIXEL_DATA.GetGroup() &&
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257 element.getTag().getETag() == DICOM_TAG_PIXEL_DATA.GetElement())
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258 {
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259 try
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260 {
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261 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(element);
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262 AnswerPixelData(output, pixelData, transferSyntax);
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263 //return;
676
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264 }
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265 catch (std::bad_cast&)
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266 {
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267 }
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268 }
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269
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270
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271 // This element is nor a sequence, neither a pixel-data
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272 std::string buffer;
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273 buffer.resize(65536);
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274 Uint32 length = element.getLength(transferSyntax);
291
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275 Uint32 offset = 0;
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276
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277 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL);
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278
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279 while (offset < length)
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280 {
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281 Uint32 nbytes;
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282 if (length - offset < buffer.size())
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283 {
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284 nbytes = length - offset;
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285 }
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286 else
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287 {
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288 nbytes = buffer.size();
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289 }
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290
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291 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes);
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292
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293 if (cond.good())
291
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294 {
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295 output.GetLowLevelOutput().Send(&buffer[0], nbytes);
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296 offset += nbytes;
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297 }
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298 else
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299 {
676
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300 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text();
291
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301 return;
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302 }
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303 }
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304
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305 output.MarkLowLevelOutputDone();
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306 }
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307
285
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308 static void SendPathValueForLeaf(RestApiOutput& output,
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309 const std::string& tag,
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310 DcmItem& dicom,
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311 E_TransferSyntax transferSyntax)
285
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312 {
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313 DcmTagKey k;
304
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314 ParseTagAndGroup(k, tag);
285
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315
291
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316 DcmSequenceOfItems* sequence = NULL;
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317 if (dicom.findAndGetSequence(k, sequence).good() &&
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318 sequence != NULL &&
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319 sequence->getVR() == EVR_SQ)
285
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320 {
291
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321 SendSequence(output, *sequence);
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322 return;
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323 }
285
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324
291
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325 DcmElement* element = NULL;
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326 if (dicom.findAndGetElement(k, element).good() &&
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327 element != NULL &&
318
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328 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags
291
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329 element->getVR() != EVR_SQ)
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330 {
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331 AnswerDicomField(output, *element, transferSyntax);
285
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332 }
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333 }
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334
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335 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
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336 const UriComponents& uri)
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337 {
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338 DcmItem* dicom = file_->getDataset();
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339
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340 // Go down in the tag hierarchy according to the URI
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341 for (size_t pos = 0; pos < uri.size() / 2; pos++)
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342 {
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343 size_t index;
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344 try
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345 {
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346 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
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347 }
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348 catch (boost::bad_lexical_cast&)
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349 {
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350 return;
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351 }
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352
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353 DcmTagKey k;
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354 DcmItem *child = NULL;
304
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355 ParseTagAndGroup(k, uri[2 * pos]);
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356 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
285
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357 child == NULL)
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358 {
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359 return;
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360 }
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361
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362 dicom = child;
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363 }
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364
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365 // We have reached the end of the URI
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366 if (uri.size() % 2 == 0)
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367 {
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368 SendPathValueForDictionary(output, *dicom);
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369 }
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370 else
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371 {
676
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372 SendPathValueForLeaf(output, uri.back(), *dicom, file_->getDataset()->getOriginalXfer());
285
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373 }
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374 }
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375
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376
302
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377
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378
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379
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380 static DcmElement* CreateElementForTag(const DicomTag& tag)
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381 {
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382 DcmTag key(tag.GetGroup(), tag.GetElement());
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383
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384 switch (key.getEVR())
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385 {
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386 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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387
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388 /**
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389 * TODO.
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390 **/
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391
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392 case EVR_OB: // other byte
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393 case EVR_OF: // other float
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394 case EVR_OW: // other word
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395 case EVR_AT: // attribute tag
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396 throw OrthancException(ErrorCode_NotImplemented);
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397
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398 case EVR_UN: // unknown value representation
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399 throw OrthancException(ErrorCode_ParameterOutOfRange);
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400
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401
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402 /**
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403 * String types.
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404 * http://support.dcmtk.org/docs/classDcmByteString.html
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405 **/
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406
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407 case EVR_AS: // age string
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408 return new DcmAgeString(key);
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409
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410 case EVR_AE: // application entity title
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411 return new DcmApplicationEntity(key);
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412
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413 case EVR_CS: // code string
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414 return new DcmCodeString(key);
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415
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416 case EVR_DA: // date string
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417 return new DcmDate(key);
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418
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419 case EVR_DT: // date time string
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420 return new DcmDateTime(key);
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421
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422 case EVR_DS: // decimal string
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423 return new DcmDecimalString(key);
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424
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425 case EVR_IS: // integer string
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426 return new DcmIntegerString(key);
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427
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428 case EVR_TM: // time string
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429 return new DcmTime(key);
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430
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431 case EVR_UI: // unique identifier
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432 return new DcmUniqueIdentifier(key);
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433
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434 case EVR_ST: // short text
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435 return new DcmShortText(key);
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436
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437 case EVR_LO: // long string
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438 return new DcmLongString(key);
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439
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440 case EVR_LT: // long text
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441 return new DcmLongText(key);
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442
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443 case EVR_UT: // unlimited text
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444 return new DcmUnlimitedText(key);
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445
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446 case EVR_SH: // short string
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447 return new DcmShortString(key);
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448
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449 case EVR_PN: // person name
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450 return new DcmPersonName(key);
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451
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452
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453 /**
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454 * Numerical types
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455 **/
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456
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457 case EVR_SL: // signed long
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458 return new DcmSignedLong(key);
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459
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460 case EVR_SS: // signed short
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461 return new DcmSignedShort(key);
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462
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463 case EVR_UL: // unsigned long
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464 return new DcmUnsignedLong(key);
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465
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466 case EVR_US: // unsigned short
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467 return new DcmUnsignedShort(key);
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468
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469 case EVR_FL: // float single-precision
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470 return new DcmFloatingPointSingle(key);
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471
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472 case EVR_FD: // float double-precision
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473 return new DcmFloatingPointDouble(key);
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474
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475
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476 /**
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477 * Sequence types, should never occur at this point.
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478 **/
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479
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480 case EVR_SQ: // sequence of items
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481 throw OrthancException(ErrorCode_ParameterOutOfRange);
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482
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483
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484 /**
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485 * Internal to DCMTK.
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486 **/
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487
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488 case EVR_ox: // OB or OW depending on context
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489 case EVR_xs: // SS or US depending on context
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490 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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491 case EVR_na: // na="not applicable", for data which has no VR
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492 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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493 case EVR_item: // used internally for items
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494 case EVR_metainfo: // used internally for meta info datasets
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495 case EVR_dataset: // used internally for datasets
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496 case EVR_fileFormat: // used internally for DICOM files
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497 case EVR_dicomDir: // used internally for DICOMDIR objects
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498 case EVR_dirRecord: // used internally for DICOMDIR records
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499 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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500 case EVR_pixelItem: // used internally for pixel items in a compressed image
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501 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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502 case EVR_PixelData: // used internally for uncompressed pixeld data
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503 case EVR_OverlayData: // used internally for overlay data
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504 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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505 default:
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506 break;
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507 }
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508
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509 throw OrthancException(ErrorCode_InternalError);
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510 }
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511
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512
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513
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514 static void FillElementWithString(DcmElement& element,
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515 const DicomTag& tag,
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516 const std::string& value)
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517 {
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518 DcmTag key(tag.GetGroup(), tag.GetElement());
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519 bool ok = false;
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520
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521 try
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522 {
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523 switch (key.getEVR())
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524 {
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525 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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526
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527 /**
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528 * TODO.
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529 **/
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530
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531 case EVR_OB: // other byte
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532 case EVR_OF: // other float
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533 case EVR_OW: // other word
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534 case EVR_AT: // attribute tag
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535 throw OrthancException(ErrorCode_NotImplemented);
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536
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537 case EVR_UN: // unknown value representation
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538 throw OrthancException(ErrorCode_ParameterOutOfRange);
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539
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540
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541 /**
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542 * String types.
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543 **/
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544
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545 case EVR_DS: // decimal string
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546 case EVR_IS: // integer string
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547 case EVR_AS: // age string
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548 case EVR_DA: // date string
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549 case EVR_DT: // date time string
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550 case EVR_TM: // time string
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551 case EVR_AE: // application entity title
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552 case EVR_CS: // code string
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553 case EVR_SH: // short string
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554 case EVR_LO: // long string
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555 case EVR_ST: // short text
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556 case EVR_LT: // long text
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557 case EVR_UT: // unlimited text
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558 case EVR_PN: // person name
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559 case EVR_UI: // unique identifier
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560 {
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561 ok = element.putString(value.c_str()).good();
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562 break;
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563 }
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564
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565
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566 /**
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diff changeset
567 * Numerical types
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568 **/
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569
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570 case EVR_SL: // signed long
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571 {
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572 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
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573 break;
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diff changeset
574 }
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diff changeset
575
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576 case EVR_SS: // signed short
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577 {
238134081136 modification of dicom files
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578 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
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diff changeset
579 break;
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580 }
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581
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582 case EVR_UL: // unsigned long
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583 {
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584 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
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diff changeset
585 break;
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parents: 291
diff changeset
586 }
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587
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588 case EVR_US: // unsigned short
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589 {
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590 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
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591 break;
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diff changeset
592 }
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593
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594 case EVR_FL: // float single-precision
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595 {
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596 ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
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diff changeset
597 break;
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diff changeset
598 }
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599
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600 case EVR_FD: // float double-precision
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601 {
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602 ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
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diff changeset
603 break;
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diff changeset
604 }
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parents: 291
diff changeset
605
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diff changeset
606
238134081136 modification of dicom files
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diff changeset
607 /**
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diff changeset
608 * Sequence types, should never occur at this point.
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diff changeset
609 **/
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diff changeset
610
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diff changeset
611 case EVR_SQ: // sequence of items
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diff changeset
612 {
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613 ok = false;
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diff changeset
614 break;
238134081136 modification of dicom files
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diff changeset
615 }
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diff changeset
616
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diff changeset
617
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diff changeset
618 /**
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diff changeset
619 * Internal to DCMTK.
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diff changeset
620 **/
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621
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diff changeset
622 case EVR_ox: // OB or OW depending on context
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diff changeset
623 case EVR_xs: // SS or US depending on context
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624 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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625 case EVR_na: // na="not applicable", for data which has no VR
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626 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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diff changeset
627 case EVR_item: // used internally for items
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628 case EVR_metainfo: // used internally for meta info datasets
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629 case EVR_dataset: // used internally for datasets
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diff changeset
630 case EVR_fileFormat: // used internally for DICOM files
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diff changeset
631 case EVR_dicomDir: // used internally for DICOMDIR objects
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diff changeset
632 case EVR_dirRecord: // used internally for DICOMDIR records
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diff changeset
633 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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634 case EVR_pixelItem: // used internally for pixel items in a compressed image
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diff changeset
635 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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636 case EVR_PixelData: // used internally for uncompressed pixeld data
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637 case EVR_OverlayData: // used internally for overlay data
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638 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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diff changeset
639 default:
238134081136 modification of dicom files
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diff changeset
640 break;
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641 }
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642 }
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diff changeset
643 catch (boost::bad_lexical_cast&)
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diff changeset
644 {
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645 ok = false;
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diff changeset
646 }
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647
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648 if (!ok)
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diff changeset
649 {
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650 throw OrthancException(ErrorCode_InternalError);
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diff changeset
651 }
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652 }
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diff changeset
653
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654
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655 void ParsedDicomFile::Remove(const DicomTag& tag)
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656 {
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diff changeset
657 DcmTagKey key(tag.GetGroup(), tag.GetElement());
306
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diff changeset
658 DcmElement* element = file_->getDataset()->remove(key);
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659 if (element != NULL)
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660 {
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diff changeset
661 delete element;
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662 }
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663 }
302
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diff changeset
664
306
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diff changeset
665
326d5a4a5af3 modification of instances
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diff changeset
666
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667 void ParsedDicomFile::RemovePrivateTags()
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668 {
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diff changeset
669 typedef std::list<DcmElement*> Tags;
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diff changeset
670
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671 Tags privateTags;
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diff changeset
672
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673 DcmDataset& dataset = *file_->getDataset();
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diff changeset
674 for (unsigned long i = 0; i < dataset.card(); i++)
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675 {
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diff changeset
676 DcmElement* element = dataset.getElement(i);
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diff changeset
677 DcmTag tag(element->getTag());
311
26efccdff583 anonymisation
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678 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK
26efccdff583 anonymisation
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diff changeset
679 tag.getPrivateCreator() != NULL)
306
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diff changeset
680 {
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diff changeset
681 privateTags.push_back(element);
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682 }
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diff changeset
683 }
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684
326d5a4a5af3 modification of instances
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685 for (Tags::iterator it = privateTags.begin();
656
08eca5d86aad fixes to cppcheck
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diff changeset
686 it != privateTags.end(); ++it)
306
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diff changeset
687 {
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688 DcmElement* tmp = dataset.remove(*it);
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689 if (tmp != NULL)
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690 {
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diff changeset
691 delete tmp;
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692 }
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diff changeset
693 }
302
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694 }
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695
238134081136 modification of dicom files
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diff changeset
696
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697
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698 void ParsedDicomFile::Insert(const DicomTag& tag,
238134081136 modification of dicom files
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diff changeset
699 const std::string& value)
238134081136 modification of dicom files
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diff changeset
700 {
238134081136 modification of dicom files
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diff changeset
701 std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
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diff changeset
702 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
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703
238134081136 modification of dicom files
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704 if (!file_->getDataset()->insert(element.release(), false, false).good())
238134081136 modification of dicom files
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diff changeset
705 {
238134081136 modification of dicom files
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diff changeset
706 // This field already exists
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707 throw OrthancException(ErrorCode_InternalError);
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708 }
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diff changeset
709 }
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parents: 291
diff changeset
710
238134081136 modification of dicom files
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711
305
86bb79522f19 name of the private tags
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712 void ParsedDicomFile::Replace(const DicomTag& tag,
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diff changeset
713 const std::string& value,
86bb79522f19 name of the private tags
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diff changeset
714 DicomReplaceMode mode)
302
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diff changeset
715 {
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716 DcmTagKey key(tag.GetGroup(), tag.GetElement());
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717 DcmElement* element = NULL;
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718
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diff changeset
719 if (!file_->getDataset()->findAndGetElement(key, element).good() ||
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diff changeset
720 element == NULL)
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diff changeset
721 {
305
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722 // This field does not exist, act wrt. the specified "mode"
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diff changeset
723 switch (mode)
302
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724 {
305
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diff changeset
725 case DicomReplaceMode_InsertIfAbsent:
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parents: 304
diff changeset
726 Insert(tag, value);
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
727 break;
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
728
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
729 case DicomReplaceMode_ThrowIfAbsent:
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
730 throw OrthancException(ErrorCode_InexistentItem);
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
731
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
732 case DicomReplaceMode_IgnoreIfAbsent:
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
733 return;
302
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
734 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
735 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
736 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
737 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
738 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
739 }
303
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
740
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
741
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
742 /**
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
743 * dcmodify will automatically correct 'Media Storage SOP Class
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
744 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
745 * you make changes to the related tags in the dataset ('SOP Class
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
746 * UID' and 'SOP Instance UID') via insert or modify mode
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
747 * options. You can disable this behaviour by using the -nmu
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
748 * option.
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
749 **/
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
750 if (tag == DICOM_TAG_SOP_CLASS_UID)
305
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
751 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent);
303
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
752
c76a35a85c69 ready for anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 302
diff changeset
753 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
754 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent);
302
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
755 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
756
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
757
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
758 void ParsedDicomFile::Answer(RestApiOutput& output)
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parents: 291
diff changeset
759 {
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parents: 291
diff changeset
760 std::string serialized;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
761 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset()))
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
762 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
763 output.AnswerBuffer(serialized, "application/octet-stream");
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
764 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
765 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
766
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
767
308
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
768
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
769 bool ParsedDicomFile::GetTagValue(std::string& value,
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
770 const DicomTag& tag)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
771 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
772 DcmTagKey k(tag.GetGroup(), tag.GetElement());
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
773 DcmDataset& dataset = *file_->getDataset();
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
774 DcmElement* element = NULL;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
775 if (!dataset.findAndGetElement(k, element).good() ||
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
776 element == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
777 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
778 return false;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
779 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
780
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
781 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
782
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
783 if (v.get() == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
784 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
785 value = "";
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
786 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
787 else
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
788 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
789 value = v->AsString();
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
790 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
791
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
792 return true;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
793 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
794
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
795
315
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
796
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
797 DicomInstanceHasher ParsedDicomFile::GetHasher()
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
798 {
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
799 std::string patientId, studyUid, seriesUid, instanceUid;
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
800
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
801 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
802 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
803 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
804 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
805 {
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
806 throw OrthancException(ErrorCode_BadFileFormat);
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
807 }
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
808
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
809 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
810 }
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
811
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
812
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
813 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
814 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
815 target.Clear();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
816 for (unsigned long i = 0; i < dataset.card(); i++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
817 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
818 DcmElement* element = dataset.getElement(i);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
819 if (element && element->isLeaf())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
820 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
821 target.SetValue(element->getTag().getGTag(),
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
822 element->getTag().getETag(),
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
823 ConvertLeafElement(*element));
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
824 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
825 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
826 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
827
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
828
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
829 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
830 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
831 return DicomTag(element.getGTag(), element.getETag());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
832 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
833
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
834
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
835 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
836 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
837 if (!element.isLeaf())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
838 {
62
a70bb32802ae renaming Server
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parents: 57
diff changeset
839 throw OrthancException("Only applicable to leaf elements");
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
840 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
841
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
842 if (element.isaString())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
843 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
844 char *c;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
845 if (element.getString(c).good() &&
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
846 c != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
847 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
848 std::string s(c);
107
3b45473c0a73 replace boost::locale with iconv for debian
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parents: 106
diff changeset
849 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter?
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
850 return new DicomString(utf8);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
851 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
852 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
853 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
854 return new DicomNullValue;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
855 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
856 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
857
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
858 try
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
859 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
860 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
861 switch (element.getVR())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
862 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
863
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
864 /**
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
865 * TODO.
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
866 **/
306
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
867
302
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parents: 291
diff changeset
868 case EVR_OB: // other byte
238134081136 modification of dicom files
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parents: 291
diff changeset
869 case EVR_OF: // other float
238134081136 modification of dicom files
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parents: 291
diff changeset
870 case EVR_OW: // other word
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parents: 291
diff changeset
871 case EVR_AT: // attribute tag
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parents: 291
diff changeset
872 case EVR_UN: // unknown value representation
238134081136 modification of dicom files
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parents: 291
diff changeset
873 return new DicomNullValue();
306
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
874
302
238134081136 modification of dicom files
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parents: 291
diff changeset
875 /**
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parents: 291
diff changeset
876 * String types, should never happen at this point because of
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diff changeset
877 * "element.isaString()".
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diff changeset
878 **/
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diff changeset
879
306
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diff changeset
880 case EVR_DS: // decimal string
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diff changeset
881 case EVR_IS: // integer string
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882 case EVR_AS: // age string
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diff changeset
883 case EVR_DA: // date string
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diff changeset
884 case EVR_DT: // date time string
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diff changeset
885 case EVR_TM: // time string
302
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diff changeset
886 case EVR_AE: // application entity title
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diff changeset
887 case EVR_CS: // code string
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diff changeset
888 case EVR_SH: // short string
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diff changeset
889 case EVR_LO: // long string
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diff changeset
890 case EVR_ST: // short text
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diff changeset
891 case EVR_LT: // long text
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diff changeset
892 case EVR_UT: // unlimited text
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diff changeset
893 case EVR_PN: // person name
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diff changeset
894 case EVR_UI: // unique identifier
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diff changeset
895 return new DicomNullValue();
0
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parents:
diff changeset
896
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parents:
diff changeset
897
302
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diff changeset
898 /**
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diff changeset
899 * Numerical types
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diff changeset
900 **/
0
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parents:
diff changeset
901
302
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diff changeset
902 case EVR_SL: // signed long
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903 {
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diff changeset
904 Sint32 f;
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905 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
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diff changeset
906 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
907 else
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908 return new DicomNullValue();
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909 }
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910
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911 case EVR_SS: // signed short
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912 {
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diff changeset
913 Sint16 f;
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914 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
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diff changeset
915 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
916 else
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diff changeset
917 return new DicomNullValue();
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918 }
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919
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920 case EVR_UL: // unsigned long
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921 {
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922 Uint32 f;
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923 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
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diff changeset
924 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
925 else
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diff changeset
926 return new DicomNullValue();
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diff changeset
927 }
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diff changeset
928
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929 case EVR_US: // unsigned short
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930 {
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diff changeset
931 Uint16 f;
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diff changeset
932 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
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diff changeset
933 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
934 else
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diff changeset
935 return new DicomNullValue();
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936 }
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937
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938 case EVR_FL: // float single-precision
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939 {
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940 Float32 f;
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941 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
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942 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
943 else
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944 return new DicomNullValue();
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945 }
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diff changeset
946
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947 case EVR_FD: // float double-precision
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948 {
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diff changeset
949 Float64 f;
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950 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
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diff changeset
951 return new DicomString(boost::lexical_cast<std::string>(f));
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952 else
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953 return new DicomNullValue();
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954 }
0
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parents:
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955
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parents:
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956
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parents:
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957 /**
302
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diff changeset
958 * Sequence types, should never occur at this point because of
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diff changeset
959 * "element.isLeaf()".
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diff changeset
960 **/
0
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diff changeset
961
302
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diff changeset
962 case EVR_SQ: // sequence of items
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963 return new DicomNullValue;
0
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964
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965
302
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diff changeset
966 /**
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diff changeset
967 * Internal to DCMTK.
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diff changeset
968 **/
0
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diff changeset
969
302
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diff changeset
970 case EVR_ox: // OB or OW depending on context
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diff changeset
971 case EVR_xs: // SS or US depending on context
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diff changeset
972 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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diff changeset
973 case EVR_na: // na="not applicable", for data which has no VR
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diff changeset
974 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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diff changeset
975 case EVR_item: // used internally for items
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diff changeset
976 case EVR_metainfo: // used internally for meta info datasets
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diff changeset
977 case EVR_dataset: // used internally for datasets
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diff changeset
978 case EVR_fileFormat: // used internally for DICOM files
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diff changeset
979 case EVR_dicomDir: // used internally for DICOMDIR objects
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diff changeset
980 case EVR_dirRecord: // used internally for DICOMDIR records
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diff changeset
981 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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diff changeset
982 case EVR_pixelItem: // used internally for pixel items in a compressed image
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diff changeset
983 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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diff changeset
984 case EVR_PixelData: // used internally for uncompressed pixeld data
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diff changeset
985 case EVR_OverlayData: // used internally for overlay data
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diff changeset
986 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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diff changeset
987 return new DicomNullValue;
0
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parents:
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988
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diff changeset
989
302
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diff changeset
990 /**
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diff changeset
991 * Default case.
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diff changeset
992 **/
0
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diff changeset
993
302
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diff changeset
994 default:
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995 return new DicomNullValue;
0
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parents:
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996 }
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parents:
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997 }
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parents:
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998 catch (boost::bad_lexical_cast)
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parents:
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999 {
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parents:
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1000 return new DicomNullValue;
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parents:
diff changeset
1001 }
306
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diff changeset
1002 catch (std::bad_cast)
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1003 {
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1004 return new DicomNullValue;
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1005 }
0
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parents:
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1006 }
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parents:
diff changeset
1007
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parents:
diff changeset
1008
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parents:
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1009 static void StoreElement(Json::Value& target,
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1010 DcmElement& element,
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1011 unsigned int maxStringLength);
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1012
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1013 static void StoreItem(Json::Value& target,
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1014 DcmItem& item,
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parents:
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1015 unsigned int maxStringLength)
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parents:
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1016 {
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1017 target = Json::Value(Json::objectValue);
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parents:
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1018
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1019 for (unsigned long i = 0; i < item.card(); i++)
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parents:
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1020 {
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1021 DcmElement* element = item.getElement(i);
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1022 StoreElement(target, *element, maxStringLength);
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parents:
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1023 }
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parents:
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1024 }
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parents:
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1025
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parents:
diff changeset
1026
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1027 static void StoreElement(Json::Value& target,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1028 DcmElement& element,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1029 unsigned int maxStringLength)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1030 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1031 assert(target.type() == Json::objectValue);
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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 DicomTag tag(FromDcmtkBridge::GetTag(element));
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
1034 const std::string formattedTag = tag.Format();
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1035
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1036 #if 0
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
1037 const std::string tagName = FromDcmtkBridge::GetName(tag);
305
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1038 #else
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parents: 304
diff changeset
1039 // This version of the code gives access to the name of the private tags
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parents: 304
diff changeset
1040 DcmTag tagbis(element.getTag());
306
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diff changeset
1041 const std::string tagName(tagbis.getTagName());
305
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parents: 304
diff changeset
1042 #endif
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1043
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1044 if (element.isLeaf())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1045 {
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1046 Json::Value value(Json::objectValue);
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1047 value["Name"] = tagName;
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1048
306
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1049 if (tagbis.getPrivateCreator() != NULL)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1050 {
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parents: 305
diff changeset
1051 value["PrivateCreator"] = tagbis.getPrivateCreator();
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parents: 305
diff changeset
1052 }
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parents: 305
diff changeset
1053
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1054 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1055 if (v->IsNull())
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1056 {
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
1057 value["Type"] = "Null";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1058 value["Value"] = Json::nullValue;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1059 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1060 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1061 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1062 std::string s = v->AsString();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1063 if (maxStringLength == 0 ||
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1064 s.size() <= maxStringLength)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1065 {
35
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diff changeset
1066 value["Type"] = "String";
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parents: 2
diff changeset
1067 value["Value"] = s;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1068 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1069 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1070 {
35
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diff changeset
1071 value["Type"] = "TooLong";
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
1072 value["Value"] = Json::nullValue;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1073 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1074 }
35
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parents: 2
diff changeset
1075
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parents: 2
diff changeset
1076 target[formattedTag] = value;
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1077 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1078 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1079 {
35
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parents: 2
diff changeset
1080 Json::Value children(Json::arrayValue);
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1081
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1082 // "All subclasses of DcmElement except for DcmSequenceOfItems
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1083 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1084 // etc. are not." The following cast is thus OK.
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1085 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1086
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1087 for (unsigned long i = 0; i < sequence.card(); i++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1088 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1089 DcmItem* child = sequence.getItem(i);
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
1090 Json::Value& v = children.append(Json::objectValue);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1091 StoreItem(v, *child, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1092 }
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1093
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1094 target[formattedTag]["Name"] = tagName;
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1095 target[formattedTag]["Type"] = "Sequence";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
1096 target[formattedTag]["Value"] = children;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1097 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1098 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1099
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1100
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1101 void FromDcmtkBridge::ToJson(Json::Value& root,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1102 DcmDataset& dataset,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1103 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1104 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1105 StoreItem(root, dataset, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1106 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1107
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1108
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1109
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1110 void FromDcmtkBridge::ToJson(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1111 const std::string& path,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1112 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1113 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1114 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1115 if (!dicom.loadFile(path.c_str()).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1116 {
62
a70bb32802ae renaming Server
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parents: 57
diff changeset
1117 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1118 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1119 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1120 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1121 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1122 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1123 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1124
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1125
368
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parents: 319
diff changeset
1126 static void ExtractPngImageColorPreview(std::string& result,
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1127 DicomIntegerPixelAccessor& accessor)
42
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1128 {
368
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parents: 319
diff changeset
1129 assert(accessor.GetChannelCount() == 3);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1130 PngWriter w;
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1131
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1132 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight() * 3, 0);
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parents: 319
diff changeset
1133 uint8_t* pixel = &image[0];
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parents: 319
diff changeset
1134
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1135 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1136 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1137 for (unsigned int x = 0; x < accessor.GetWidth(); x++)
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parents: 319
diff changeset
1138 {
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parents: 319
diff changeset
1139 for (unsigned int c = 0; c < 3; c++, pixel++)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1140 {
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parents: 319
diff changeset
1141 int32_t v = accessor.GetValue(x, y, c);
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parents: 319
diff changeset
1142 if (v < 0)
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parents: 319
diff changeset
1143 *pixel = 0;
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parents: 319
diff changeset
1144 else if (v > 255)
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1145 *pixel = 255;
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parents: 319
diff changeset
1146 else
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parents: 319
diff changeset
1147 *pixel = v;
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1148 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1149 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1150 }
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1151
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1152 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1153 accessor.GetWidth() * 3, PixelFormat_RGB24, &image[0]);
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parents: 319
diff changeset
1154 }
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parents: 319
diff changeset
1155
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1156
80011cd589e6 support of rgb images
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parents: 319
diff changeset
1157 static void ExtractPngImageGrayscalePreview(std::string& result,
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1158 DicomIntegerPixelAccessor& accessor)
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parents: 319
diff changeset
1159 {
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parents: 319
diff changeset
1160 assert(accessor.GetChannelCount() == 1);
42
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1161 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1162
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1163 int32_t min, max;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1164 accessor.GetExtremeValues(min, max);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1165
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1166 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1167 if (min != max)
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1168 {
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1169 uint8_t* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1170 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1171 {
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1172 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
1173 {
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1174 int32_t v = accessor.GetValue(x, y);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1175 *pixel = static_cast<uint8_t>(
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1176 boost::math::lround(static_cast<float>(v - min) /
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1177 static_cast<float>(max - min) * 255.0f));
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1178 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1179 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1180 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1181
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1182 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1183 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1184 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1185
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1186
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1187 template <typename T>
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1188 static void ExtractPngImageTruncate(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1189 DicomIntegerPixelAccessor& accessor,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1190 PixelFormat format)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1191 {
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1192 assert(accessor.GetChannelCount() == 1);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1193
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1194 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1195
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1196 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1197 T* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1198 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1199 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1200 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
1201 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1202 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
1203 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
1204 *pixel = std::numeric_limits<T>::min();
464
5987dd8e0776 fix reading signed values in dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 454
diff changeset
1205 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
1206 *pixel = std::numeric_limits<T>::max();
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1207 else
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1208 *pixel = static_cast<T>(v);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1209 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1210 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1211
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1212 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1213 accessor.GetWidth() * sizeof(T), format, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1214 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1215
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1216
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1217 static bool DecodePsmctRle1(std::string& output,
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1218 DcmDataset& dataset)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1219 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1220 static const DicomTag tagContent(0x07a1, 0x100a);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1221 static const DicomTag tagCompressionType(0x07a1, 0x1011);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1222
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1223 DcmElement* e;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1224 char* c;
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 // Check whether the DICOM instance contains an image encoded with
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1227 // the PMSCT_RLE1 scheme.
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1228 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagCompressionType), e).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1229 e == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1230 !e->isaString() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1231 !e->getString(c).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1232 c == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1233 strcmp("PMSCT_RLE1", c))
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 return false;
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 // 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
1239 // data from the appropriate private DICOM tag.
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1240 Uint8* pixData = NULL;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1241 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(tagContent), e).good() ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1242 e == NULL ||
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1243 e->getUint8Array(pixData) != EC_Normal)
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 return false;
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 // The "unsigned" below IS VERY IMPORTANT
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1249 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1250 const size_t length = e->getLength();
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1251
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1252 /**
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1253 * 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
1254 * Mathieu Malaterre (under a BSD license).
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1255 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1256 **/
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1257
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1258 // RLE pass
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1259 std::vector<uint8_t> temp;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1260 temp.reserve(length);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1261 for (size_t i = 0; i < length; i++)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1262 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1263 if (inbuffer[i] == 0xa5)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1264 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1265 temp.push_back(inbuffer[i+2]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1266 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1267 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1268 temp.push_back(inbuffer[i+2]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1269 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1270 i += 2;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1271 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1272 else
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1273 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1274 temp.push_back(inbuffer[i]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1275 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1276 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1277
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1278 // Delta encoding pass
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1279 uint16_t delta = 0;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1280 output.clear();
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1281 output.reserve(temp.size());
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1282 for (size_t i = 0; i < temp.size(); i++)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1283 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1284 uint16_t value;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1285
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1286 if (temp[i] == 0x5a)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1287 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1288 uint16_t v1 = temp[i + 1];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1289 uint16_t v2 = temp[i + 2];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1290 value = (v2 << 8) + v1;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1291 i += 2;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1292 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1293 else
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1294 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1295 value = delta + (int8_t) temp[i];
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1296 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1297
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1298 output.push_back(value & 0xff);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1299 output.push_back(value >> 8);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1300 delta = value;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1301 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1302
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1303 if (output.size() % 2)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1304 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1305 output.resize(output.size() - 1);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1306 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1307
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1308 return true;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1309 }
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1310
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1311
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1312 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1313 DcmDataset& dataset,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1314 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1315 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1316 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1317 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1318
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1319 std::auto_ptr<DicomIntegerPixelAccessor> accessor;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1320
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1321 DicomMap m;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1322 FromDcmtkBridge::Convert(m, dataset);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1323
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1324 std::string privateContent;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1325
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1326 DcmElement* e;
80
6212bf978584 status of series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 79
diff changeset
1327 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() &&
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1328 e != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1329 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1330 Uint8* pixData = NULL;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1331 if (e->getUint8Array(pixData) == EC_Normal)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1332 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1333 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
1334 accessor->SetCurrentFrame(frame);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1335 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1336 }
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1337 else if (DecodePsmctRle1(privateContent, dataset))
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1338 {
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1339 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded";
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1340 Uint8* pixData = NULL;
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1341 if (privateContent.size() > 0)
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1342 pixData = reinterpret_cast<Uint8*>(&privateContent[0]);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1343 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, privateContent.size()));
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1344 accessor->SetCurrentFrame(frame);
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1345 }
419
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1346
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1347 if (accessor.get() == NULL)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1348 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1349 throw OrthancException(ErrorCode_BadFileFormat);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 399
diff changeset
1350 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1351
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1352 PixelFormat format;
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1353 bool supported = false;
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1354
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1355 if (accessor->GetChannelCount() == 1)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1356 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1357 switch (mode)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1358 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1359 case ImageExtractionMode_Preview:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1360 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1361 format = PixelFormat_Grayscale8;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1362 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1363
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1364 case ImageExtractionMode_UInt8:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1365 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1366 format = PixelFormat_Grayscale8;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1367 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1368
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1369 case ImageExtractionMode_UInt16:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1370 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1371 format = PixelFormat_Grayscale16;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1372 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1373
465
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1374 case ImageExtractionMode_Int16:
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1375 supported = true;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1376 format = PixelFormat_SignedGrayscale16;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1377 break;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1378
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1379 default:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1380 supported = false;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1381 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1382 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1383 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1384 else if (accessor->GetChannelCount() == 3)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1385 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1386 switch (mode)
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1387 {
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1388 case ImageExtractionMode_Preview:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1389 supported = true;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1390 format = PixelFormat_RGB24;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1391 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1392
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1393 default:
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1394 supported = false;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1395 break;
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1396 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1397 }
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1398
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1399 if (!supported)
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1400 {
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1401 throw OrthancException(ErrorCode_NotImplemented);
369
4632a044746e simplification of the code
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 368
diff changeset
1402 }
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1403
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1404 if (accessor.get() == NULL ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1405 accessor->GetWidth() == 0 ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1406 accessor->GetHeight() == 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1407 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1408 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1409 w.WriteToMemory(result, 0, 0, 0, format, NULL);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1410 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1411 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1412 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1413 switch (mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1414 {
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1415 case ImageExtractionMode_Preview:
368
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1416 if (format == PixelFormat_Grayscale8)
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1417 ExtractPngImageGrayscalePreview(result, *accessor);
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1418 else
80011cd589e6 support of rgb images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 319
diff changeset
1419 ExtractPngImageColorPreview(result, *accessor);
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1420 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1421
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1422 case ImageExtractionMode_UInt8:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1423 ExtractPngImageTruncate<uint8_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1424 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1425
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1426 case ImageExtractionMode_UInt16:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1427 ExtractPngImageTruncate<uint16_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1428 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1429
465
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1430 case ImageExtractionMode_Int16:
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1431 ExtractPngImageTruncate<int16_t>(result, *accessor, format);
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1432 break;
7a966b440f19 signed images to PNG
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 464
diff changeset
1433
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1434 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1435 throw OrthancException(ErrorCode_NotImplemented);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1436 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1437 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1438 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1439
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1440
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1441 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1442 const std::string& dicomContent,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1443 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1444 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1445 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1446 DcmInputBufferStream is;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1447 if (dicomContent.size() > 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1448 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1449 is.setBuffer(&dicomContent[0], dicomContent.size());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1450 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1451 is.setEos();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1452
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1453 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1454 if (dicom.read(is).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1455 {
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1456 ExtractPngImage(result, *dicom.getDataset(), frame, mode);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1457 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1458 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1459 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1460 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1461 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1462 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1463
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1464
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1465
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1466 std::string FromDcmtkBridge::GetName(const DicomTag& t)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1467 {
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1468 // Some patches for important tags because of different DICOM
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1469 // dictionaries between DCMTK versions
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1470 std::string n = t.GetMainTagsName();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1471 if (n.size() != 0)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1472 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1473 return n;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1474 }
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1475 // End of patches
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1476
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1477 #if 0
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1478 DcmTagKey tag(t.GetGroup(), t.GetElement());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1479 const DcmDataDictionary& dict = dcmDataDict.rdlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1480 const DcmDictEntry* entry = dict.findEntry(tag, NULL);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1481
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1482 std::string s(DcmTag_ERROR_TagName);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1483 if (entry != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1484 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1485 s = std::string(entry->getTagName());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1486 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1487
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1488 dcmDataDict.unlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1489 return s;
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1490 #else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1491 DcmTag tag(t.GetGroup(), t.GetElement());
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1492 const char* name = tag.getTagName();
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1493 if (name == NULL)
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1494 {
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1495 return DcmTag_ERROR_TagName;
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1496 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1497 else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1498 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1499 return std::string(name);
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1500 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1501 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1502 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1503
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1504
304
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1505 DicomTag FromDcmtkBridge::ParseTag(const char* name)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1506 {
304
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1507 if (strlen(name) == 9 &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1508 isxdigit(name[0]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1509 isxdigit(name[1]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1510 isxdigit(name[2]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1511 isxdigit(name[3]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1512 name[4] == '-' &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1513 isxdigit(name[5]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1514 isxdigit(name[6]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1515 isxdigit(name[7]) &&
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1516 isxdigit(name[8]))
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1517 {
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1518 uint16_t group = GetTagValue(name);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1519 uint16_t element = GetTagValue(name + 5);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1520 return DicomTag(group, element);
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1521 }
4eea080e6e7a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1522
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1523 #if 0
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1524 const DcmDataDictionary& dict = dcmDataDict.rdlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1525 const DcmDictEntry* entry = dict.findEntry(name);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1526
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1527 if (entry == NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1528 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1529 dcmDataDict.unlock();
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1530 throw OrthancException("Unknown DICOM tag");
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1531 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1532 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1533 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1534 DcmTagKey key = entry->getKey();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1535 DicomTag tag(key.getGroup(), key.getElement());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1536 dcmDataDict.unlock();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1537 return tag;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1538 }
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1539 #else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1540 DcmTag tag;
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1541 if (DcmTag::findTagFromName(name, tag).good())
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1542 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1543 return DicomTag(tag.getGTag(), tag.getETag());
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1544 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1545 else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1546 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1547 throw OrthancException("Unknown DICOM tag");
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1548 }
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1549 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1550 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1551
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1552
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1553 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1554 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1555 for (DicomMap::Map::const_iterator
656
08eca5d86aad fixes to cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 465
diff changeset
1556 it = m.map_.begin(); it != m.map_.end(); ++it)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1557 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1558 DicomTag t = it->first;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1559 std::string s = it->second->AsString();
319
760d0f32cb34 PMSCT_RLE1
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 318
diff changeset
1560 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
1561 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1562 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1563
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1564
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1565 void FromDcmtkBridge::ToJson(Json::Value& result,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1566 const DicomMap& values)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1567 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1568 if (result.type() != Json::objectValue)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1569 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1570 throw OrthancException(ErrorCode_BadParameterType);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1571 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1572
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1573 result.clear();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1574
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1575 for (DicomMap::Map::const_iterator
656
08eca5d86aad fixes to cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 465
diff changeset
1576 it = values.map_.begin(); it != values.map_.end(); ++it)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1577 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1578 result[GetName(it->first)] = it->second->AsString();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1579 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1580 }
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1581
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1582
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1583 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1584 {
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1585 char uid[100];
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1586
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1587 switch (level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1588 {
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1589 case DicomRootLevel_Patient:
311
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1590 // The "PatientID" field is of type LO (Long String), 64
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1591 // 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
1592 // as a random PatientID.
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
1593 return Toolbox::GenerateUuid();
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1594
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1595 case DicomRootLevel_Instance:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1596 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1597
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1598 case DicomRootLevel_Series:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1599 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1600
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1601 case DicomRootLevel_Study:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1602 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1603
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1604 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1605 throw OrthancException(ErrorCode_ParameterOutOfRange);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1606 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1607 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1608
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1609 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1610 DcmDataset* dataSet)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1611 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1612 // 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
1613 // information to the file. We always switch to the Little Endian
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1614 // syntax, with explicit length.
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1615
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1616 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1617
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1618
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1619 /**
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1620 * Note that up to Orthanc 0.7.1 (inclusive), the
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1621 * "EXS_LittleEndianExplicit" was always used to save the DICOM
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1622 * dataset into memory. We now keep the original transfer syntax
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1623 * (if available).
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1624 **/
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1625 E_TransferSyntax xfer = dataSet->getOriginalXfer();
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1626 if (xfer == EXS_Unknown)
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1627 {
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1628 // No information about the original transfer syntax: This is
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1629 // most probably a DICOM dataset that was read from memory.
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1630 xfer = EXS_LittleEndianExplicit;
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1631 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1632
291
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diff changeset
1633 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
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1634
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
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1635 // Create the meta-header information
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1636 DcmFileFormat ff(dataSet);
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
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1637 ff.validateMetaInfo(xfer);
291
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1638
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
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parents: 656
diff changeset
1639 // Create a memory buffer with the proper size
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1640 uint32_t s = ff.calcElementLength(xfer, encodingType);
291
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1641 buffer.resize(s);
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1642 DcmOutputBufferStream ob(&buffer[0], s);
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1643
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
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parents: 656
diff changeset
1644 // Fill the memory buffer with the meta-header and the dataset
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1645 ff.transferInit();
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1646 OFCondition c = ff.write(ob, xfer, encodingType, NULL,
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1647 /*opt_groupLength*/ EGL_recalcGL,
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1648 /*opt_paddingType*/ EPD_withoutPadding);
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
1649 ff.transferEnd();
291
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1650
661
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1651 // Handle errors
291
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1652 if (c.good())
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1653 {
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1654 return true;
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1655 }
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1656 else
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1657 {
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1658 buffer.clear();
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1659 return false;
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1660 }
4d7469f72a0b embedding of dicom dictionaries
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1661 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1662 }