annotate OrthancServer/ParsedDicomFile.cpp @ 1858:483f26479743 dcmtk-3.6.1

update to latest dcmtk snapshot
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 02 Dec 2015 10:05:45 +0100
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, 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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32
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33
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34 /*=========================================================================
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35
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36 This file is based on portions of the following project:
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37
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38 Program: GDCM (Grassroots DICOM). A DICOM library
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39 Module: http://gdcm.sourceforge.net/Copyright.html
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40
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41 Copyright (c) 2006-2011 Mathieu Malaterre
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42 Copyright (c) 1993-2005 CREATIS
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43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image)
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44 All rights reserved.
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45
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46 Redistribution and use in source and binary forms, with or without
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47 modification, are permitted provided that the following conditions are met:
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48
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49 * Redistributions of source code must retain the above copyright notice,
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50 this list of conditions and the following disclaimer.
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51
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52 * Redistributions in binary form must reproduce the above copyright notice,
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53 this list of conditions and the following disclaimer in the documentation
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54 and/or other materials provided with the distribution.
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55
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56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any
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57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to
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58 endorse or promote products derived from this software without specific
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59 prior written permission.
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60
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61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
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62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
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65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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71
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72 =========================================================================*/
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73
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74
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75 #include "PrecompiledHeadersServer.h"
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76
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77 #ifndef NOMINMAX
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78 #define NOMINMAX
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79 #endif
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80
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81 #include "ParsedDicomFile.h"
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82
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83 #include "OrthancInitialization.h"
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84 #include "ServerToolbox.h"
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85 #include "FromDcmtkBridge.h"
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86 #include "ToDcmtkBridge.h"
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87 #include "Internals/DicomImageDecoder.h"
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88 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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89 #include "../Core/Images/JpegWriter.h"
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90 #include "../Core/Images/JpegReader.h"
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91 #include "../Core/Images/PngReader.h"
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92 #include "../Core/Images/PngWriter.h"
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93 #include "../Core/Logging.h"
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94 #include "../Core/OrthancException.h"
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95 #include "../Core/Toolbox.h"
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96 #include "../Core/Uuid.h"
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97
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98 #include <list>
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99 #include <limits>
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100
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101 #include <boost/lexical_cast.hpp>
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102
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103 #include <dcmtk/dcmdata/dcchrstr.h>
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104 #include <dcmtk/dcmdata/dcdicent.h>
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105 #include <dcmtk/dcmdata/dcdict.h>
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106 #include <dcmtk/dcmdata/dcfilefo.h>
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107 #include <dcmtk/dcmdata/dcistrmb.h>
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108 #include <dcmtk/dcmdata/dcuid.h>
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109 #include <dcmtk/dcmdata/dcmetinf.h>
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110 #include <dcmtk/dcmdata/dcdeftag.h>
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111
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112 #include <dcmtk/dcmdata/dcvrae.h>
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113 #include <dcmtk/dcmdata/dcvras.h>
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114 #include <dcmtk/dcmdata/dcvrcs.h>
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115 #include <dcmtk/dcmdata/dcvrda.h>
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116 #include <dcmtk/dcmdata/dcvrds.h>
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117 #include <dcmtk/dcmdata/dcvrdt.h>
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118 #include <dcmtk/dcmdata/dcvrfd.h>
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119 #include <dcmtk/dcmdata/dcvrfl.h>
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120 #include <dcmtk/dcmdata/dcvris.h>
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121 #include <dcmtk/dcmdata/dcvrlo.h>
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122 #include <dcmtk/dcmdata/dcvrlt.h>
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123 #include <dcmtk/dcmdata/dcvrpn.h>
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124 #include <dcmtk/dcmdata/dcvrsh.h>
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125 #include <dcmtk/dcmdata/dcvrsl.h>
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126 #include <dcmtk/dcmdata/dcvrss.h>
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127 #include <dcmtk/dcmdata/dcvrst.h>
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128 #include <dcmtk/dcmdata/dcvrtm.h>
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129 #include <dcmtk/dcmdata/dcvrui.h>
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130 #include <dcmtk/dcmdata/dcvrul.h>
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131 #include <dcmtk/dcmdata/dcvrus.h>
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132 #include <dcmtk/dcmdata/dcvrut.h>
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133 #include <dcmtk/dcmdata/dcpixel.h>
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134 #include <dcmtk/dcmdata/dcpixseq.h>
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135 #include <dcmtk/dcmdata/dcpxitem.h>
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136
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137
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138 #include <boost/math/special_functions/round.hpp>
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139 #include <dcmtk/dcmdata/dcostrmb.h>
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140 #include <boost/algorithm/string/predicate.hpp>
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141
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142
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143 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream";
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144
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145
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146
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147 namespace Orthanc
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148 {
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149 struct ParsedDicomFile::PImpl
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150 {
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151 std::auto_ptr<DcmFileFormat> file_;
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152 };
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153
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154
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155 // This method can only be called from the constructors!
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156 void ParsedDicomFile::Setup(const void* buffer,
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157 size_t size)
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158 {
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159 DcmInputBufferStream is;
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160 if (size > 0)
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161 {
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162 is.setBuffer(buffer, size);
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163 }
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164 is.setEos();
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165
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166 pimpl_->file_.reset(new DcmFileFormat);
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167 pimpl_->file_->transferInit();
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168 if (!pimpl_->file_->read(is).good())
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169 {
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170 delete pimpl_; // Avoid a memory leak due to exception
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171 // throwing, as we are in the constructor
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172
790
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173 throw OrthancException(ErrorCode_BadFileFormat);
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174 }
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175 pimpl_->file_->loadAllDataIntoMemory();
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176 pimpl_->file_->transferEnd();
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177 }
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178
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179
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180 static void SendPathValueForDictionary(RestApiOutput& output,
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181 DcmItem& dicom)
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182 {
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183 Json::Value v = Json::arrayValue;
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184
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185 for (unsigned long i = 0; i < dicom.card(); i++)
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186 {
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187 DcmElement* element = dicom.getElement(i);
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188 if (element)
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189 {
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190 char buf[16];
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191 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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192 v.append(buf);
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193 }
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194 }
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195
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196 output.AnswerJson(v);
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197 }
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198
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199 static inline uint16_t GetCharValue(char c)
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200 {
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201 if (c >= '0' && c <= '9')
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202 return c - '0';
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203 else if (c >= 'a' && c <= 'f')
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204 return c - 'a' + 10;
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205 else if (c >= 'A' && c <= 'F')
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206 return c - 'A' + 10;
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207 else
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208 return 0;
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209 }
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210
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211 static inline uint16_t GetTagValue(const char* c)
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212 {
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213 return ((GetCharValue(c[0]) << 12) +
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214 (GetCharValue(c[1]) << 8) +
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215 (GetCharValue(c[2]) << 4) +
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216 GetCharValue(c[3]));
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217 }
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218
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219 static void ParseTagAndGroup(DcmTagKey& key,
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220 const std::string& tag)
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221 {
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222 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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223 key = DcmTagKey(t.GetGroup(), t.GetElement());
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224 }
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225
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226
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227 static void SendSequence(RestApiOutput& output,
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228 DcmSequenceOfItems& sequence)
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229 {
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230 // This element is a sequence
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231 Json::Value v = Json::arrayValue;
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232
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233 for (unsigned long i = 0; i < sequence.card(); i++)
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234 {
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235 v.append(boost::lexical_cast<std::string>(i));
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236 }
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237
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238 output.AnswerJson(v);
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239 }
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240
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241
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242 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData,
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243 E_TransferSyntax transferSyntax)
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244 {
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245 DcmPixelSequence* pixelSequence = NULL;
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246 if (pixelData.getEncapsulatedRepresentation
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247 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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248 {
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249 return pixelSequence->card();
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250 }
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251 else
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252 {
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253 return 1;
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254 }
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255 }
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256
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257
1519
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diff changeset
258 namespace
790
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259 {
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260 class DicomFieldStream : public IHttpStreamAnswer
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261 {
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262 private:
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263 DcmElement& element_;
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diff changeset
264 uint32_t length_;
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265 uint32_t offset_;
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266 std::string chunk_;
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267 size_t chunkSize_;
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268
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269 public:
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270 DicomFieldStream(DcmElement& element,
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271 E_TransferSyntax transferSyntax) :
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272 element_(element),
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diff changeset
273 length_(element.getLength(transferSyntax)),
1616
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diff changeset
274 offset_(0),
644c32c07306 cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1612
diff changeset
275 chunkSize_(0)
1519
8bd0d897763f refactoring: IHttpStreamAnswer
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diff changeset
276 {
1521
3606278d305e refactoring
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diff changeset
277 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB
1519
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diff changeset
278 chunk_.resize(CHUNK_SIZE);
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
279 }
790
331eaf9d9d69 ParsedDicomFile
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parents:
diff changeset
280
1523
c388502a066d testing FilesystemHttpSender
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
281 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/,
c388502a066d testing FilesystemHttpSender
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parents: 1521
diff changeset
282 bool /*deflateAllowed*/)
1519
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diff changeset
283 {
8bd0d897763f refactoring: IHttpStreamAnswer
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diff changeset
284 // No support for compression
8bd0d897763f refactoring: IHttpStreamAnswer
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parents: 1486
diff changeset
285 return HttpCompression_None;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
286 }
790
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
288 virtual bool HasContentFilename(std::string& filename)
790
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289 {
1519
8bd0d897763f refactoring: IHttpStreamAnswer
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parents: 1486
diff changeset
290 return false;
790
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 }
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
292
8bd0d897763f refactoring: IHttpStreamAnswer
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diff changeset
293 virtual std::string GetContentType()
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
294 {
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
295 return "";
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
296 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
297
1519
8bd0d897763f refactoring: IHttpStreamAnswer
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diff changeset
298 virtual uint64_t GetContentLength()
790
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299 {
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
300 return length_;
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
301 }
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
302
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
303 virtual bool ReadNextChunk()
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
304 {
1520
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1519
diff changeset
305 assert(offset_ <= length_);
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
306
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
307 if (offset_ == length_)
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
308 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
309 return false;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
310 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
311 else
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
312 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
313 if (length_ - offset_ < chunk_.size())
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
314 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
315 chunkSize_ = length_ - offset_;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
316 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
317 else
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
318 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
319 chunkSize_ = chunk_.size();
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
320 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
321
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
322 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_);
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
323
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
324 offset_ += chunkSize_;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
325
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
326 if (!cond.good())
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
327 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
328 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text();
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
329 throw OrthancException(ErrorCode_InternalError);
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
330 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
331
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
332 return true;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
333 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 }
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
335
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
336 virtual const char *GetChunkContent()
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
337 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
338 return chunk_.c_str();
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
339 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
340
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
341 virtual size_t GetChunkSize()
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
342 {
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
343 return chunkSize_;
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
344 }
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
345 };
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
348
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349 static bool AnswerPixelData(RestApiOutput& output,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 DcmItem& dicom,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
351 E_TransferSyntax transferSyntax,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 const std::string* blockUri)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
353 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(),
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 DICOM_TAG_PIXEL_DATA.GetElement());
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 DcmElement *element = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 if (!dicom.findAndGetElement(k, element).good() ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359 element == NULL)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 return false;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364 try
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
365 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 if (blockUri == NULL)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369 // The user asks how many blocks are presents in this pixel data
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
371
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
372 Json::Value result(Json::arrayValue);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
373 for (unsigned int i = 0; i < blocks; i++)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
374 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375 result.append(boost::lexical_cast<std::string>(i));
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
377
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
378 output.AnswerJson(result);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379 return true;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
380 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
385 if (block < GetPixelDataBlockCount(pixelData, transferSyntax))
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
386 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
387 DcmPixelSequence* pixelSequence = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
388 if (pixelData.getEncapsulatedRepresentation
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
391 // This is the case for JPEG transfer syntaxes
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
392 if (block < pixelSequence->card())
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
393 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 DcmPixelItem* pixelItem = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
395 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
396 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
397 if (pixelItem->getLength() == 0)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
398 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400 return true;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 Uint8* buffer = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404 if (pixelItem->getUint8Array(buffer).good() && buffer)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 return true;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412 else
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
414 // This is the case for raw, uncompressed image buffers
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
415 assert(*blockUri == "0");
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
416 DicomFieldStream stream(*element, transferSyntax);
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
417 output.AnswerStream(stream);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
418 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
419 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
420 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
421 catch (boost::bad_lexical_cast&)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
423 // The URI entered by the user is not a number
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
424 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425 catch (std::bad_cast&)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
426 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
427 // This should never happen
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
428 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
430 return false;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
431 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
432
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
433
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
434
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
435 static void SendPathValueForLeaf(RestApiOutput& output,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
436 const std::string& tag,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
437 DcmItem& dicom,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
438 E_TransferSyntax transferSyntax)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440 DcmTagKey k;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 ParseTagAndGroup(k, tag);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 DcmSequenceOfItems* sequence = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 if (dicom.findAndGetSequence(k, sequence).good() &&
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 sequence != NULL &&
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 sequence->getVR() == EVR_SQ)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
447 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
448 SendSequence(output, *sequence);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
449 return;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
452 DcmElement* element = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
453 if (dicom.findAndGetElement(k, element).good() &&
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
454 element != NULL &&
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
455 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
456 element->getVR() != EVR_SQ)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
457 {
1519
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
458 DicomFieldStream stream(*element, transferSyntax);
8bd0d897763f refactoring: IHttpStreamAnswer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
459 output.AnswerStream(stream);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
460 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 const UriComponents& uri)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 {
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
466 DcmItem* dicom = pimpl_->file_->getDataset();
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
467 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer();
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
468
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
469 // Special case: Accessing the pixel data
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
470 if (uri.size() == 1 ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471 uri.size() == 2)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
472 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
473 DcmTagKey tag;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
474 ParseTagAndGroup(tag, uri[0]);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
475
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
476 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() &&
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement())
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
478 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
479 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
480 return;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
481 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
482 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
483
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
484 // Go down in the tag hierarchy according to the URI
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
485 for (size_t pos = 0; pos < uri.size() / 2; pos++)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
486 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
487 size_t index;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
488 try
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
489 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
490 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
491 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
492 catch (boost::bad_lexical_cast&)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
493 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
494 return;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
496
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
497 DcmTagKey k;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
498 DcmItem *child = NULL;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
499 ParseTagAndGroup(k, uri[2 * pos]);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
500 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
501 child == NULL)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
502 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
503 return;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
504 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
505
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
506 dicom = child;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
507 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
508
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
509 // We have reached the end of the URI
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
510 if (uri.size() % 2 == 0)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512 SendPathValueForDictionary(output, *dicom);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
513 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
514 else
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
515 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
517 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
518 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 void ParsedDicomFile::Remove(const DicomTag& tag)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 DcmTagKey key(tag.GetGroup(), tag.GetElement());
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
524 DcmElement* element = pimpl_->file_->getDataset()->remove(key);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
525 if (element != NULL)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
527 delete element;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
528 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
531
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532
991
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
533 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 {
991
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
535 DcmDataset& dataset = *pimpl_->file_->getDataset();
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
536
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
537 // Loop over the dataset to detect its private tags
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
538 typedef std::list<DcmElement*> Tags;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 Tags privateTags;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
540
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
541 for (unsigned long i = 0; i < dataset.card(); i++)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
542 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
543 DcmElement* element = dataset.getElement(i);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
544 DcmTag tag(element->getTag());
991
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
545
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
546 // Is this a private tag?
1694
06d579e82bb8 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1693
diff changeset
547 if (tag.isPrivate())
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
548 {
991
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
549 bool remove = true;
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
550
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
551 // Check whether this private tag is to be kept
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
552 if (toKeep != NULL)
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
553 {
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
554 DicomTag tmp = FromDcmtkBridge::Convert(tag);
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
555 if (toKeep->find(tmp) != toKeep->end())
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
556 {
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
557 remove = false; // Keep it
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
558 }
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
559 }
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
560
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
561 if (remove)
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
562 {
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
563 privateTags.push_back(element);
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
564 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
565 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
566 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
567
991
2f76b92addd4 keep private tags during anonymization
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
568 // Loop over the detected private tags to remove them
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
569 for (Tags::iterator it = privateTags.begin();
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
570 it != privateTags.end(); ++it)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
571 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
572 DcmElement* tmp = dataset.remove(*it);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
573 if (tmp != NULL)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
574 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
575 delete tmp;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
576 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
577 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
578 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
579
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
580
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
581 static void InsertInternal(DcmDataset& dicom,
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
582 DcmElement* element)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
583 {
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
584 OFCondition cond = dicom.insert(element, false, false);
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
585 if (!cond.good())
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
586 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
587 // This field already exists
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
588 delete element;
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
589 throw OrthancException(ErrorCode_InternalError);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
590 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
591 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
592
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
593
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
594 void ParsedDicomFile::Insert(const DicomTag& tag,
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
595 const Json::Value& value,
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
596 bool decodeDataUriScheme)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
597 {
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
598 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding()));
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
599 InsertInternal(*pimpl_->file_->getDataset(), element.release());
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
600 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
601
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
602
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
603 static void ReplaceInternal(DcmDataset& dicom,
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
604 std::auto_ptr<DcmElement>& element,
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
605 DicomReplaceMode mode)
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
606 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
607 const DcmTagKey& tag = element->getTag();
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
608
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
609 if (!dicom.findAndDeleteElement(tag).good())
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
610 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
611 // This field does not exist, act wrt. the specified "mode"
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
612 switch (mode)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
613 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
614 case DicomReplaceMode_InsertIfAbsent:
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
615 break;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
616
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
617 case DicomReplaceMode_ThrowIfAbsent:
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
618 throw OrthancException(ErrorCode_InexistentItem);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
619
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
620 case DicomReplaceMode_IgnoreIfAbsent:
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
621 return;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
622 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
623 }
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
624
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
625 // Either the tag was not existing, or the replace mode was set to
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
626 // "InsertIfAbsent"
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
627 InsertInternal(dicom, element.release());
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
628 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
629
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
630
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
631 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag,
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
632 const std::string& utf8Value,
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
633 bool decodeDataUriScheme)
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
634 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
635 if (tag != DICOM_TAG_SOP_CLASS_UID &&
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
636 tag != DICOM_TAG_SOP_INSTANCE_UID)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
637 {
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
638 return;
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
639 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
640
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
641 std::string binary;
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
642 const std::string* decoded = &utf8Value;
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
643
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
644 if (decodeDataUriScheme &&
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
645 boost::starts_with(utf8Value, "data:application/octet-stream;base64,"))
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
646 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
647 std::string mime;
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
648 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value);
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
649 decoded = &binary;
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
650 }
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
651 else
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
652 {
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
653 Encoding encoding = GetEncoding();
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
654 if (GetEncoding() != Encoding_Utf8)
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
655 {
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
656 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding);
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
657 decoded = &binary;
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
658 }
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
659 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
660
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
661 /**
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
662 * dcmodify will automatically correct 'Media Storage SOP Class
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
663 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
664 * you make changes to the related tags in the dataset ('SOP Class
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
665 * UID' and 'SOP Instance UID') via insert or modify mode
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
666 * options. You can disable this behaviour by using the -nmu
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
667 * option.
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
668 **/
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
669
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
670 if (tag == DICOM_TAG_SOP_CLASS_UID)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
671 {
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
672 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
673 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
674
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
675 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
676 {
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
677 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent);
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
678 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
679 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
680
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
681
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
682 void ParsedDicomFile::Replace(const DicomTag& tag,
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
683 const std::string& utf8Value,
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
684 DicomReplaceMode mode)
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
685 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
686 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag));
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
687 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding());
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
688 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode);
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
689 UpdateStorageUid(tag, utf8Value, false);
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
690 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
691
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
692
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
693 void ParsedDicomFile::Replace(const DicomTag& tag,
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
694 const Json::Value& value,
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
695 bool decodeDataUriScheme,
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
696 DicomReplaceMode mode)
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
697 {
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
698 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding()));
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
699 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode);
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
700
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
701 if (tag == DICOM_TAG_SOP_CLASS_UID ||
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
702 tag == DICOM_TAG_SOP_INSTANCE_UID)
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
703 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
704 if (value.type() != Json::stringValue)
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
705 {
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
706 throw OrthancException(ErrorCode_BadParameterType);
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
707 }
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
708
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
709 UpdateStorageUid(tag, value.asString(), decodeDataUriScheme);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
710 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
711 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
712
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
713
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
714 void ParsedDicomFile::Answer(RestApiOutput& output)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
715 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
716 std::string serialized;
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 991
diff changeset
717 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset()))
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
718 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
719 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
720 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
721 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
722
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
723
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
724
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
725 bool ParsedDicomFile::GetTagValue(std::string& value,
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
726 const DicomTag& tag)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
727 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
728 DcmTagKey k(tag.GetGroup(), tag.GetElement());
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
729 DcmDataset& dataset = *pimpl_->file_->getDataset();
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
730
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
731 if (tag.IsPrivate() ||
1655
e40fd0d925c5 /tools/create-dicom can create tags with unknown VR
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1641
diff changeset
732 FromDcmtkBridge::IsUnknownTag(tag) ||
1556
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
733 tag == DICOM_TAG_PIXEL_DATA ||
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
734 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
735 {
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
736 const Uint8* data = NULL; // This is freed in the destructor of the dataset
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
737 long unsigned int count = 0;
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
738
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
739 if (dataset.findAndGetUint8Array(k, data, &count).good())
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
740 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
741 if (count > 0)
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
742 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
743 assert(data != NULL);
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
744 value.assign(reinterpret_cast<const char*>(data), count);
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
745 }
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
746 else
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
747 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
748 value.clear();
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
749 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
750
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
751 return true;
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
752 }
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
753 else
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
754 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
755 return false;
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
756 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
757 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
758 else
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
759 {
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
760 DcmElement* element = NULL;
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
761 if (!dataset.findAndGetElement(k, element).good() ||
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
762 element == NULL)
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
763 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
764 return false;
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
765 }
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
766
1736
b953c6eef28d ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1735
diff changeset
767 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement
b953c6eef28d ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1735
diff changeset
768 (*element, DicomToJsonFlags_Default, GetEncoding()));
1556
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
769
1737
ec66a16aa398 removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1736
diff changeset
770 if (v.get() == NULL ||
ec66a16aa398 removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1736
diff changeset
771 v->IsNull())
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
772 {
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
773 value = "";
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
774 }
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
775 else
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
776 {
1737
ec66a16aa398 removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1736
diff changeset
777 // TODO v->IsBinary()
ec66a16aa398 removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1736
diff changeset
778 value = v->GetContent();
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
779 }
1556
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
780
1307
f796207e3df1 Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
781 return true;
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
782 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
783 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
784
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
785
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
786 DicomInstanceHasher ParsedDicomFile::GetHasher()
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
787 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
788 std::string patientId, studyUid, seriesUid, instanceUid;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
789
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
790 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
791 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
792 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
793 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
794 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
795 throw OrthancException(ErrorCode_BadFileFormat);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
796 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
797
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
798 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
799 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
800
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
801
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
802 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
803 {
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 991
diff changeset
804 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset());
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
805 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
806
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
807
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
808 void ParsedDicomFile::SaveToFile(const std::string& path)
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
809 {
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
810 // TODO Avoid using a temporary memory buffer, write directly on disk
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
811 std::string content;
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
812 SaveToMemoryBuffer(content);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
813 Toolbox::WriteFile(content, path);
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
814 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
815
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
816
1805
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
817 ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl)
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
818 {
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
819 pimpl_->file_.reset(new DcmFileFormat);
1805
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
820
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
821 if (createIdentifiers)
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
822 {
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
823 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient));
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
824 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study));
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
825 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series));
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
826 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
f08978b1f45b c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1800
diff changeset
827 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
828 }
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
829
791
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
830
1787
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
831 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : pimpl_(new PImpl)
1786
164d78911382 primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1781
diff changeset
832 {
1787
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
833 std::auto_ptr<DcmDataset> dataset(ToDcmtkBridge::Convert(map));
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
834
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
835 // NOTE: This implies an unnecessary memory copy of the dataset, but no way to get around
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
836 // http://support.dcmtk.org/redmine/issues/544
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
837 std::auto_ptr<DcmFileFormat> fileFormat(new DcmFileFormat(dataset.get()));
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
838
1b1d5470233f refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1786
diff changeset
839 pimpl_->file_.reset(fileFormat.release());
1786
164d78911382 primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1781
diff changeset
840 }
164d78911382 primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1781
diff changeset
841
164d78911382 primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1781
diff changeset
842
1800
30e97a1f4093 callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1788
diff changeset
843 ParsedDicomFile::ParsedDicomFile(const void* content,
30e97a1f4093 callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1788
diff changeset
844 size_t size) : pimpl_(new PImpl)
791
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
845 {
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
846 Setup(content, size);
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
847 }
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
848
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
849 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl)
791
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
850 {
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
851 if (content.size() == 0)
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
852 {
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
853 Setup(NULL, 0);
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
854 }
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
855 else
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
856 {
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
857 Setup(&content[0], content.size());
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
858 }
381f90e2b69d refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 790
diff changeset
859 }
792
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
860
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
861
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
862 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) :
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
863 pimpl_(new PImpl)
792
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
864 {
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
865 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone()));
956
2fd5a163776d primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 874
diff changeset
866
1564
1b7def486e62 creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1562
diff changeset
867 // Create a new instance-level identifier
1b7def486e62 creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1562
diff changeset
868 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
792
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
869 }
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
870
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
871
1788
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
872 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl)
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
873 {
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
874 pimpl_->file_.reset(new DcmFileFormat(&dicom));
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
875 }
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
876
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
877
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
878 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl)
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
879 {
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
880 pimpl_->file_.reset(new DcmFileFormat(dicom));
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
881 }
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
882
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
883
792
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
884 ParsedDicomFile::~ParsedDicomFile()
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
885 {
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
886 delete pimpl_;
792
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
887 }
111a1738e11e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 791
diff changeset
888
793
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
889
1824
b530c3dfe2a6 refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1818
diff changeset
890 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const
793
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
891 {
1788
6a2d507ef064 getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1787
diff changeset
892 return *pimpl_->file_.get();
793
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
893 }
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
894
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
895
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
896 ParsedDicomFile* ParsedDicomFile::Clone()
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
897 {
794
437c4a83d2cc refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 793
diff changeset
898 return new ParsedDicomFile(*this);
793
145604a97914 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 792
diff changeset
899 }
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
900
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
901
1562
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
902 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme)
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
903 {
1641
4e56b5a206b7 Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1616
diff changeset
904 std::string mime, content;
4e56b5a206b7 Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1616
diff changeset
905 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme);
1562
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
906 Toolbox::ToLowerCase(mime);
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
907
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
908 if (mime == "image/png" ||
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
909 mime == "image/jpeg")
1562
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
910 {
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
911 EmbedImage(mime, content);
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
912 }
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
913 else if (mime == "application/pdf")
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
914 {
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
915 EmbedPdf(content);
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
916 }
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
917 else
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
918 {
1693
558b25228a23 creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1689
diff changeset
919 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime;
1562
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
920 throw OrthancException(ErrorCode_NotImplemented);
2084b7c20478 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1558
diff changeset
921 }
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
922 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
923
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
924
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
925 void ParsedDicomFile::EmbedImage(const std::string& mime,
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
926 const std::string& content)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
927 {
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
928 if (mime == "image/png")
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
929 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
930 PngReader reader;
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
931 reader.ReadFromMemory(content);
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
932 EmbedImage(reader);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
933 }
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
934 else if (mime == "image/jpeg")
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
935 {
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
936 JpegReader reader;
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
937 reader.ReadFromMemory(content);
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
938 EmbedImage(reader);
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
939 }
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
940 else
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
941 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
942 throw OrthancException(ErrorCode_NotImplemented);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
943 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
944 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
945
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
946
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
947 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor)
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
948 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
949 if (accessor.GetFormat() != PixelFormat_Grayscale8 &&
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
950 accessor.GetFormat() != PixelFormat_Grayscale16 &&
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
951 accessor.GetFormat() != PixelFormat_RGB24 &&
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
952 accessor.GetFormat() != PixelFormat_RGBA32)
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
953 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
954 throw OrthancException(ErrorCode_NotImplemented);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
955 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
956
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
957 if (accessor.GetFormat() == PixelFormat_RGBA32)
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
958 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
959 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM";
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
960 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
961
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
962 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
963
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
964 Remove(DICOM_TAG_PIXEL_DATA);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
965 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth()));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
966 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight()));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
967 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
968 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
969 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
970 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
971 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
972 Replace(DICOM_TAG_BITS_ALLOCATED, "8");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
973 Replace(DICOM_TAG_BITS_STORED, "8");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
974 Replace(DICOM_TAG_HIGH_BIT, "7");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
975
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
976 unsigned int bytesPerPixel = 1;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
977
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
978 switch (accessor.GetFormat())
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
979 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
980 case PixelFormat_RGB24:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
981 case PixelFormat_RGBA32:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
982 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
983 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
984 bytesPerPixel = 3;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
985 break;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
986
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
987 case PixelFormat_Grayscale8:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
988 break;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
989
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
990 case PixelFormat_Grayscale16:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
991 Replace(DICOM_TAG_BITS_ALLOCATED, "16");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
992 Replace(DICOM_TAG_BITS_STORED, "16");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
993 Replace(DICOM_TAG_HIGH_BIT, "15");
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
994 bytesPerPixel = 2;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
995 break;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
996
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
997 default:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
998 throw OrthancException(ErrorCode_NotImplemented);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
999 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1000
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1001 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(),
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1002 DICOM_TAG_PIXEL_DATA.GetElement());
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1003
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1004 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1005
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1006 unsigned int pitch = accessor.GetWidth() * bytesPerPixel;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1007 Uint8* target = NULL;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1008 pixels->createUint8Array(accessor.GetHeight() * pitch, target);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1009
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1010 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1011 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1012 switch (accessor.GetFormat())
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1013 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1014 case PixelFormat_RGB24:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1015 case PixelFormat_Grayscale8:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1016 case PixelFormat_Grayscale16:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1017 case PixelFormat_SignedGrayscale16:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1018 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1019 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1020 target += pitch;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1021 break;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1022 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1023
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1024 case PixelFormat_RGBA32:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1025 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1026 // The alpha channel is not supported by the DICOM standard
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1027 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1028 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4)
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1029 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1030 target[0] = source[0];
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1031 target[1] = source[1];
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1032 target[2] = source[2];
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1033 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1034
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1035 break;
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1036 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1037
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1038 default:
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1039 throw OrthancException(ErrorCode_NotImplemented);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1040 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1041 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1042
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1043 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good())
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1044 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1045 throw OrthancException(ErrorCode_InternalError);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1046 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 799
diff changeset
1047 }
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1048
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1049
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1050 ImageAccessor* ParsedDicomFile::ExtractImage(IDicomImageDecoder& decoder,
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1051 unsigned int frame)
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1052 {
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1053 std::auto_ptr<ImageAccessor> decoded(decoder.Decode(*this, frame));
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1054
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1055 if (decoded.get() == NULL)
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1056 {
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1057 LOG(ERROR) << "Cannot decode a DICOM image";
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1058 throw OrthancException(ErrorCode_BadFileFormat);
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1059 }
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1060 else
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1061 {
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1062 return decoded.release();
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1063 }
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1064 }
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1065
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1066
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1067 ImageAccessor* ParsedDicomFile::ExtractImage(IDicomImageDecoder& decoder,
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1068 unsigned int frame,
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1069 ImageExtractionMode mode)
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1070 {
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1071 std::auto_ptr<ImageAccessor> decoded(ExtractImage(decoder, frame));
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1072
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1073 bool ok = false;
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1074
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1075 switch (mode)
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1076 {
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1077 case ImageExtractionMode_UInt8:
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1078 ok = DicomImageDecoder::TruncateDecodedImage(decoded, PixelFormat_Grayscale8, false);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1079 break;
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1080
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1081 case ImageExtractionMode_UInt16:
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1082 ok = DicomImageDecoder::TruncateDecodedImage(decoded, PixelFormat_Grayscale16, false);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1083 break;
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1084
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1085 case ImageExtractionMode_Int16:
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1086 ok = DicomImageDecoder::TruncateDecodedImage(decoded, PixelFormat_SignedGrayscale16, false);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1087 break;
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1088
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1089 case ImageExtractionMode_Preview:
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1090 ok = DicomImageDecoder::PreviewDecodedImage(decoded);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1091 break;
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1092
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1093 default:
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1094 throw OrthancException(ErrorCode_ParameterOutOfRange);
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1095 }
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1096
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1097 if (ok)
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1098 {
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1099 assert(decoded.get() != NULL);
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1100 return decoded.release();
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1101 }
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1102 else
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1103 {
1824
b530c3dfe2a6 refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1818
diff changeset
1104 throw OrthancException(ErrorCode_NotImplemented);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1105 }
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1106 }
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1107
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1108
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1109 void ParsedDicomFile::ExtractPngImage(std::string& result,
1824
b530c3dfe2a6 refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1818
diff changeset
1110 IDicomImageDecoder& decoder,
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1111 unsigned int frame,
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1112 ImageExtractionMode mode)
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1113 {
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1114 std::auto_ptr<ImageAccessor> decoded(ExtractImage(decoder, frame, mode));
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1115 assert(decoded.get() != NULL);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1116
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1117 PngWriter writer;
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1118 writer.WriteToMemory(result, *decoded);
874
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1119 }
87791ebc1f50 download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
1120
956
2fd5a163776d primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 874
diff changeset
1121
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1122 void ParsedDicomFile::ExtractJpegImage(std::string& result,
1824
b530c3dfe2a6 refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1818
diff changeset
1123 IDicomImageDecoder& decoder,
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1124 unsigned int frame,
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1125 ImageExtractionMode mode,
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1126 uint8_t quality)
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1127 {
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1128 if (mode != ImageExtractionMode_UInt8 &&
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1129 mode != ImageExtractionMode_Preview)
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1130 {
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1131 throw OrthancException(ErrorCode_ParameterOutOfRange);
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1132 }
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1133
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1134 std::auto_ptr<ImageAccessor> decoded(ExtractImage(decoder, frame, mode));
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1135 assert(decoded.get() != NULL);
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1136
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1137 JpegWriter writer;
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1138 writer.SetQuality(quality);
1826
ac5b0b4e2434 refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1824
diff changeset
1139 writer.WriteToMemory(result, *decoded);
1781
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1140 }
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1141
5ad4e4d92ecb AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1737
diff changeset
1142
956
2fd5a163776d primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 874
diff changeset
1143 Encoding ParsedDicomFile::GetEncoding() const
2fd5a163776d primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 874
diff changeset
1144 {
1695
18c02c6987d5 fix for encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1694
diff changeset
1145 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset());
956
2fd5a163776d primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 874
diff changeset
1146 }
1090
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1147
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1148
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1149 void ParsedDicomFile::SetEncoding(Encoding encoding)
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1150 {
1558
124de28b32ed fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1556
diff changeset
1151 if (encoding == Encoding_Windows1251)
1090
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1152 {
1558
124de28b32ed fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1556
diff changeset
1153 // This Cyrillic codepage is not officially supported by the
124de28b32ed fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1556
diff changeset
1154 // DICOM standard. Do not set the SpecificCharacterSet tag.
124de28b32ed fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1556
diff changeset
1155 return;
1090
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1156 }
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1157
1565
4b23310eb7e8 add tags per instances in a series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1564
diff changeset
1158 std::string s = GetDicomSpecificCharacterSet(encoding);
1091
a66224eec125 encoding tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1090
diff changeset
1159 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent);
1090
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1160 }
e494ceb8d763 support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1018
diff changeset
1161
1686
14a32b2fa63e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1662
diff changeset
1162 void ParsedDicomFile::ToJson(Json::Value& target,
14a32b2fa63e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1662
diff changeset
1163 DicomToJsonFormat format,
1735
a001f6226c7c primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1701
diff changeset
1164 DicomToJsonFlags flags,
1686
14a32b2fa63e refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1662
diff changeset
1165 unsigned int maxStringLength)
1160
80671157d051 generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1113
diff changeset
1166 {
1735
a001f6226c7c primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1701
diff changeset
1167 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, flags, maxStringLength);
1160
80671157d051 generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1113
diff changeset
1168 }
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1169
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1170
1831
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1171 void ParsedDicomFile::HeaderToJson(Json::Value& target,
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1172 DicomToJsonFormat format)
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1173 {
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1174 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0);
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1175 }
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1176
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1827
diff changeset
1177
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1178 bool ParsedDicomFile::HasTag(const DicomTag& tag) const
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1179 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1180 DcmTag key(tag.GetGroup(), tag.GetElement());
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1181 return pimpl_->file_->getDataset()->tagExists(key);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1182 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1183
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1184
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1185 void ParsedDicomFile::EmbedPdf(const std::string& pdf)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1186 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1187 if (pdf.size() < 5 || // (*)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1188 strncmp("%PDF-", pdf.c_str(), 5) != 0)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1189 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1190 LOG(ERROR) << "Not a PDF file";
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1191 throw OrthancException(ErrorCode_BadFileFormat);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1192 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1193
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1194 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1195 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT");
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1196 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD");
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1197 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf");
1566
3be6eb3757c8 error handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1565
diff changeset
1198 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1");
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1199
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1200 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument));
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1201
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1202 size_t s = pdf.size();
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1203 if (s & 1)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1204 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1205 // The size of the buffer must be even
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1206 s += 1;
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1207 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1208
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1209 Uint8* bytes = NULL;
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1210 OFCondition result = element->createUint8Array(s, bytes);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1211 if (!result.good() || bytes == NULL)
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1212 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1213 throw OrthancException(ErrorCode_NotEnoughMemory);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1214 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1215
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1216 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) )
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1217 bytes[s - 1] = 0;
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1218
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1219 memcpy(bytes, pdf.c_str(), pdf.size());
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1220
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1221 DcmPolymorphOBOW* obj = element.release();
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1222 result = pimpl_->file_->getDataset()->insert(obj);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1223
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1224 if (!result.good())
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1225 {
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1226 delete obj;
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1227 throw OrthancException(ErrorCode_NotEnoughMemory);
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1228 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1229 }
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1523
diff changeset
1230
1556
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1231
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1232 bool ParsedDicomFile::ExtractPdf(std::string& pdf)
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1233 {
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1234 std::string sop, mime;
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1235
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1236 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) ||
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1237 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) ||
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1238 sop != UID_EncapsulatedPDFStorage ||
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1239 mime != "application/pdf")
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1240 {
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1241 return false;
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1242 }
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1243
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1244 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT))
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1245 {
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1246 return false;
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1247 }
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1248
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1249 // Strip the possible pad byte at the end of file, because the
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1250 // encapsulated documents must always have an even length. The PDF
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1251 // format expects files to end with %%EOF followed by CR/LF. If
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1252 // the last character of the file is not a CR or LF, we assume it
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1253 // is a pad byte and remove it.
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1254 if (pdf.size() > 0)
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1255 {
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1256 char last = *pdf.rbegin();
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1257
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1258 if (last != 10 && last != 13)
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1259 {
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1260 pdf.resize(pdf.size() - 1);
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1261 }
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1262 }
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1263
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1264 return true;
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
1265 }
1662
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1266
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1267
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1268 void ParsedDicomFile::Convert(DicomMap& tags)
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1269 {
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1270 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset());
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1655
diff changeset
1271 }
1818
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1272
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1273
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1274 ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json,
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1275 DicomFromJsonFlags flags)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1276 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1277 std::string tmp = Configuration::GetGlobalStringParameter("DefaultEncoding", "Latin1");
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1278 Encoding encoding = StringToEncoding(tmp.c_str());
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1279
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1280 Json::Value::Members tags = json.getMemberNames();
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1281
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1282 for (size_t i = 0; i < tags.size(); i++)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1283 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1284 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1285 if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1286 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1287 const Json::Value& value = json[tags[i]];
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1288 if (value.type() != Json::stringValue ||
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1289 !GetDicomEncoding(encoding, value.asCString()))
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1290 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1291 LOG(ERROR) << "Unknown encoding while creating DICOM from JSON: " << value;
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1292 throw OrthancException(ErrorCode_BadRequest);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1293 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1294 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1295 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1296
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1297 const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1298 const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1299
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1300 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers));
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1301 result->SetEncoding(encoding);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1302
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1303 for (size_t i = 0; i < tags.size(); i++)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1304 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1305 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1306 const Json::Value& value = json[tags[i]];
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1307
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1308 if (tag == DICOM_TAG_PIXEL_DATA ||
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1309 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1310 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1311 if (value.type() != Json::stringValue)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1312 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1313 throw OrthancException(ErrorCode_BadRequest);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1314 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1315 else
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1316 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1317 result->EmbedContent(value.asString());
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1318 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1319 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1320 else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET)
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1321 {
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1322 result->Replace(tag, value, decodeDataUriScheme);
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1323 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1324 }
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1325
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1326 return result.release();
1065401501fb ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1805
diff changeset
1327 }
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1328 }