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790
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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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 #ifndef NOMINMAX
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76 #define NOMINMAX
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77 #endif
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78
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79 #include "ParsedDicomFile.h"
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80
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81 #include "FromDcmtkBridge.h"
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82 #include "ToDcmtkBridge.h"
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83 #include "../Core/Toolbox.h"
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84 #include "../Core/OrthancException.h"
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85 #include "../Core/FileFormats/PngWriter.h"
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86 #include "../Core/Uuid.h"
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87 #include "../Core/DicomFormat/DicomString.h"
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88 #include "../Core/DicomFormat/DicomNullValue.h"
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89 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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90
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91 #include <list>
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92 #include <limits>
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93
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94 #include <boost/lexical_cast.hpp>
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95
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96 #include <dcmtk/dcmdata/dcchrstr.h>
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97 #include <dcmtk/dcmdata/dcdicent.h>
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98 #include <dcmtk/dcmdata/dcdict.h>
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99 #include <dcmtk/dcmdata/dcfilefo.h>
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100 #include <dcmtk/dcmdata/dcistrmb.h>
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101 #include <dcmtk/dcmdata/dcuid.h>
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102 #include <dcmtk/dcmdata/dcmetinf.h>
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103
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104 #include <dcmtk/dcmdata/dcvrae.h>
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105 #include <dcmtk/dcmdata/dcvras.h>
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106 #include <dcmtk/dcmdata/dcvrcs.h>
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107 #include <dcmtk/dcmdata/dcvrda.h>
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108 #include <dcmtk/dcmdata/dcvrds.h>
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109 #include <dcmtk/dcmdata/dcvrdt.h>
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110 #include <dcmtk/dcmdata/dcvrfd.h>
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111 #include <dcmtk/dcmdata/dcvrfl.h>
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112 #include <dcmtk/dcmdata/dcvris.h>
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113 #include <dcmtk/dcmdata/dcvrlo.h>
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114 #include <dcmtk/dcmdata/dcvrlt.h>
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115 #include <dcmtk/dcmdata/dcvrpn.h>
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116 #include <dcmtk/dcmdata/dcvrsh.h>
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117 #include <dcmtk/dcmdata/dcvrsl.h>
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118 #include <dcmtk/dcmdata/dcvrss.h>
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119 #include <dcmtk/dcmdata/dcvrst.h>
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120 #include <dcmtk/dcmdata/dcvrtm.h>
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121 #include <dcmtk/dcmdata/dcvrui.h>
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122 #include <dcmtk/dcmdata/dcvrul.h>
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123 #include <dcmtk/dcmdata/dcvrus.h>
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124 #include <dcmtk/dcmdata/dcvrut.h>
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125 #include <dcmtk/dcmdata/dcpixel.h>
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126 #include <dcmtk/dcmdata/dcpixseq.h>
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127 #include <dcmtk/dcmdata/dcpxitem.h>
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128
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129
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130 #include <boost/math/special_functions/round.hpp>
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131 #include <glog/logging.h>
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132 #include <dcmtk/dcmdata/dcostrmb.h>
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133
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134
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135 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream";
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136
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137
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138
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139 namespace Orthanc
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140 {
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141 void ParsedDicomFile::Setup(const char* buffer, size_t size)
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142 {
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143 DcmInputBufferStream is;
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144 if (size > 0)
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145 {
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146 is.setBuffer(buffer, size);
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147 }
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148 is.setEos();
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149
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150 file_.reset(new DcmFileFormat);
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151 file_->transferInit();
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152 if (!file_->read(is).good())
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153 {
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154 throw OrthancException(ErrorCode_BadFileFormat);
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155 }
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156 file_->loadAllDataIntoMemory();
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157 file_->transferEnd();
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158 }
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159
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160
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161 static void SendPathValueForDictionary(RestApiOutput& output,
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162 DcmItem& dicom)
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163 {
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164 Json::Value v = Json::arrayValue;
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165
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166 for (unsigned long i = 0; i < dicom.card(); i++)
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167 {
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168 DcmElement* element = dicom.getElement(i);
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169 if (element)
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170 {
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171 char buf[16];
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172 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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173 v.append(buf);
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174 }
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175 }
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176
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177 output.AnswerJson(v);
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178 }
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179
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180 static inline uint16_t GetCharValue(char c)
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181 {
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182 if (c >= '0' && c <= '9')
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183 return c - '0';
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184 else if (c >= 'a' && c <= 'f')
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185 return c - 'a' + 10;
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186 else if (c >= 'A' && c <= 'F')
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187 return c - 'A' + 10;
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188 else
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189 return 0;
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190 }
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191
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192 static inline uint16_t GetTagValue(const char* c)
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193 {
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194 return ((GetCharValue(c[0]) << 12) +
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195 (GetCharValue(c[1]) << 8) +
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196 (GetCharValue(c[2]) << 4) +
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197 GetCharValue(c[3]));
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198 }
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199
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200 static void ParseTagAndGroup(DcmTagKey& key,
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201 const std::string& tag)
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202 {
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203 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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204 key = DcmTagKey(t.GetGroup(), t.GetElement());
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205 }
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206
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207
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208 static void SendSequence(RestApiOutput& output,
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209 DcmSequenceOfItems& sequence)
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210 {
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211 // This element is a sequence
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212 Json::Value v = Json::arrayValue;
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213
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214 for (unsigned long i = 0; i < sequence.card(); i++)
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215 {
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216 v.append(boost::lexical_cast<std::string>(i));
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217 }
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218
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219 output.AnswerJson(v);
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220 }
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221
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222
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223 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData,
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224 E_TransferSyntax transferSyntax)
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225 {
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226 DcmPixelSequence* pixelSequence = NULL;
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227 if (pixelData.getEncapsulatedRepresentation
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228 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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229 {
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230 return pixelSequence->card();
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231 }
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232 else
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233 {
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234 return 1;
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235 }
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236 }
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237
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238
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239 static void AnswerDicomField(RestApiOutput& output,
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240 DcmElement& element,
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241 E_TransferSyntax transferSyntax)
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242 {
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243 // This element is nor a sequence, neither a pixel-data
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244 std::string buffer;
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245 buffer.resize(65536);
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246 Uint32 length = element.getLength(transferSyntax);
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247 Uint32 offset = 0;
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248
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249 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL);
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250
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251 while (offset < length)
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252 {
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253 Uint32 nbytes;
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254 if (length - offset < buffer.size())
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255 {
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256 nbytes = length - offset;
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257 }
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258 else
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259 {
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260 nbytes = buffer.size();
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261 }
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262
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263 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes);
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264
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265 if (cond.good())
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266 {
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267 output.GetLowLevelOutput().Send(&buffer[0], nbytes);
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268 offset += nbytes;
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269 }
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270 else
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271 {
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272 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text();
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273 return;
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274 }
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275 }
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276
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277 output.MarkLowLevelOutputDone();
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278 }
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279
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280
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281 static bool AnswerPixelData(RestApiOutput& output,
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282 DcmItem& dicom,
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283 E_TransferSyntax transferSyntax,
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284 const std::string* blockUri)
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285 {
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286 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(),
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287 DICOM_TAG_PIXEL_DATA.GetElement());
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288
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289 DcmElement *element = NULL;
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290 if (!dicom.findAndGetElement(k, element).good() ||
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291 element == NULL)
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292 {
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293 return false;
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294 }
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295
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296 try
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297 {
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298 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
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299 if (blockUri == NULL)
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300 {
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301 // The user asks how many blocks are presents in this pixel data
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302 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax);
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303
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304 Json::Value result(Json::arrayValue);
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305 for (unsigned int i = 0; i < blocks; i++)
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306 {
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307 result.append(boost::lexical_cast<std::string>(i));
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308 }
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309
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310 output.AnswerJson(result);
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311 return true;
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312 }
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313
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314
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315 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri);
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316
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317 if (block < GetPixelDataBlockCount(pixelData, transferSyntax))
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318 {
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319 DcmPixelSequence* pixelSequence = NULL;
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320 if (pixelData.getEncapsulatedRepresentation
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321 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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322 {
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323 // This is the case for JPEG transfer syntaxes
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324 if (block < pixelSequence->card())
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325 {
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326 DcmPixelItem* pixelItem = NULL;
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327 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem)
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328 {
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329 if (pixelItem->getLength() == 0)
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330 {
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331 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM);
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332 return true;
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333 }
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334
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335 Uint8* buffer = NULL;
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336 if (pixelItem->getUint8Array(buffer).good() && buffer)
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337 {
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338 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM);
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339 return true;
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340 }
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341 }
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342 }
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343 }
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344 else
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345 {
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346 // This is the case for raw, uncompressed image buffers
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347 assert(*blockUri == "0");
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348 AnswerDicomField(output, *element, transferSyntax);
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349 }
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350 }
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351 }
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352 catch (boost::bad_lexical_cast&)
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353 {
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354 // The URI entered by the user is not a number
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355 }
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356 catch (std::bad_cast&)
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357 {
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358 // This should never happen
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359 }
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360
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361 return false;
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362 }
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363
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364
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365
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366 static void SendPathValueForLeaf(RestApiOutput& output,
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367 const std::string& tag,
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368 DcmItem& dicom,
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369 E_TransferSyntax transferSyntax)
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370 {
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371 DcmTagKey k;
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372 ParseTagAndGroup(k, tag);
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373
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374 DcmSequenceOfItems* sequence = NULL;
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375 if (dicom.findAndGetSequence(k, sequence).good() &&
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376 sequence != NULL &&
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377 sequence->getVR() == EVR_SQ)
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378 {
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379 SendSequence(output, *sequence);
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380 return;
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381 }
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382
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383 DcmElement* element = NULL;
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384 if (dicom.findAndGetElement(k, element).good() &&
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385 element != NULL &&
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386 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags
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387 element->getVR() != EVR_SQ)
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388 {
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389 AnswerDicomField(output, *element, transferSyntax);
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390 }
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391 }
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392
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393 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
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394 const UriComponents& uri)
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395 {
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396 DcmItem* dicom = file_->getDataset();
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397 E_TransferSyntax transferSyntax = file_->getDataset()->getOriginalXfer();
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398
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399 // Special case: Accessing the pixel data
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400 if (uri.size() == 1 ||
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401 uri.size() == 2)
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402 {
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403 DcmTagKey tag;
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404 ParseTagAndGroup(tag, uri[0]);
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405
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406 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() &&
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407 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement())
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408 {
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409 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]);
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410 return;
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411 }
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412 }
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413
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414 // Go down in the tag hierarchy according to the URI
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|
|
415 for (size_t pos = 0; pos < uri.size() / 2; pos++)
|
|
|
416 {
|
|
|
417 size_t index;
|
|
|
418 try
|
|
|
419 {
|
|
|
420 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
|
|
|
421 }
|
|
|
422 catch (boost::bad_lexical_cast&)
|
|
|
423 {
|
|
|
424 return;
|
|
|
425 }
|
|
|
426
|
|
|
427 DcmTagKey k;
|
|
|
428 DcmItem *child = NULL;
|
|
|
429 ParseTagAndGroup(k, uri[2 * pos]);
|
|
|
430 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
|
|
|
431 child == NULL)
|
|
|
432 {
|
|
|
433 return;
|
|
|
434 }
|
|
|
435
|
|
|
436 dicom = child;
|
|
|
437 }
|
|
|
438
|
|
|
439 // We have reached the end of the URI
|
|
|
440 if (uri.size() % 2 == 0)
|
|
|
441 {
|
|
|
442 SendPathValueForDictionary(output, *dicom);
|
|
|
443 }
|
|
|
444 else
|
|
|
445 {
|
|
|
446 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax);
|
|
|
447 }
|
|
|
448 }
|
|
|
449
|
|
|
450
|
|
|
451
|
|
|
452
|
|
|
453
|
|
|
454 static DcmElement* CreateElementForTag(const DicomTag& tag)
|
|
|
455 {
|
|
|
456 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
457
|
|
|
458 switch (key.getEVR())
|
|
|
459 {
|
|
|
460 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
461
|
|
|
462 /**
|
|
|
463 * TODO.
|
|
|
464 **/
|
|
|
465
|
|
|
466 case EVR_OB: // other byte
|
|
|
467 case EVR_OF: // other float
|
|
|
468 case EVR_OW: // other word
|
|
|
469 case EVR_AT: // attribute tag
|
|
|
470 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
471
|
|
|
472 case EVR_UN: // unknown value representation
|
|
|
473 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
474
|
|
|
475
|
|
|
476 /**
|
|
|
477 * String types.
|
|
|
478 * http://support.dcmtk.org/docs/classDcmByteString.html
|
|
|
479 **/
|
|
|
480
|
|
|
481 case EVR_AS: // age string
|
|
|
482 return new DcmAgeString(key);
|
|
|
483
|
|
|
484 case EVR_AE: // application entity title
|
|
|
485 return new DcmApplicationEntity(key);
|
|
|
486
|
|
|
487 case EVR_CS: // code string
|
|
|
488 return new DcmCodeString(key);
|
|
|
489
|
|
|
490 case EVR_DA: // date string
|
|
|
491 return new DcmDate(key);
|
|
|
492
|
|
|
493 case EVR_DT: // date time string
|
|
|
494 return new DcmDateTime(key);
|
|
|
495
|
|
|
496 case EVR_DS: // decimal string
|
|
|
497 return new DcmDecimalString(key);
|
|
|
498
|
|
|
499 case EVR_IS: // integer string
|
|
|
500 return new DcmIntegerString(key);
|
|
|
501
|
|
|
502 case EVR_TM: // time string
|
|
|
503 return new DcmTime(key);
|
|
|
504
|
|
|
505 case EVR_UI: // unique identifier
|
|
|
506 return new DcmUniqueIdentifier(key);
|
|
|
507
|
|
|
508 case EVR_ST: // short text
|
|
|
509 return new DcmShortText(key);
|
|
|
510
|
|
|
511 case EVR_LO: // long string
|
|
|
512 return new DcmLongString(key);
|
|
|
513
|
|
|
514 case EVR_LT: // long text
|
|
|
515 return new DcmLongText(key);
|
|
|
516
|
|
|
517 case EVR_UT: // unlimited text
|
|
|
518 return new DcmUnlimitedText(key);
|
|
|
519
|
|
|
520 case EVR_SH: // short string
|
|
|
521 return new DcmShortString(key);
|
|
|
522
|
|
|
523 case EVR_PN: // person name
|
|
|
524 return new DcmPersonName(key);
|
|
|
525
|
|
|
526
|
|
|
527 /**
|
|
|
528 * Numerical types
|
|
|
529 **/
|
|
|
530
|
|
|
531 case EVR_SL: // signed long
|
|
|
532 return new DcmSignedLong(key);
|
|
|
533
|
|
|
534 case EVR_SS: // signed short
|
|
|
535 return new DcmSignedShort(key);
|
|
|
536
|
|
|
537 case EVR_UL: // unsigned long
|
|
|
538 return new DcmUnsignedLong(key);
|
|
|
539
|
|
|
540 case EVR_US: // unsigned short
|
|
|
541 return new DcmUnsignedShort(key);
|
|
|
542
|
|
|
543 case EVR_FL: // float single-precision
|
|
|
544 return new DcmFloatingPointSingle(key);
|
|
|
545
|
|
|
546 case EVR_FD: // float double-precision
|
|
|
547 return new DcmFloatingPointDouble(key);
|
|
|
548
|
|
|
549
|
|
|
550 /**
|
|
|
551 * Sequence types, should never occur at this point.
|
|
|
552 **/
|
|
|
553
|
|
|
554 case EVR_SQ: // sequence of items
|
|
|
555 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
556
|
|
|
557
|
|
|
558 /**
|
|
|
559 * Internal to DCMTK.
|
|
|
560 **/
|
|
|
561
|
|
|
562 case EVR_ox: // OB or OW depending on context
|
|
|
563 case EVR_xs: // SS or US depending on context
|
|
|
564 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
565 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
566 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
567 case EVR_item: // used internally for items
|
|
|
568 case EVR_metainfo: // used internally for meta info datasets
|
|
|
569 case EVR_dataset: // used internally for datasets
|
|
|
570 case EVR_fileFormat: // used internally for DICOM files
|
|
|
571 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
572 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
573 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
574 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
575 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
576 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
577 case EVR_OverlayData: // used internally for overlay data
|
|
|
578 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
579 default:
|
|
|
580 break;
|
|
|
581 }
|
|
|
582
|
|
|
583 throw OrthancException(ErrorCode_InternalError);
|
|
|
584 }
|
|
|
585
|
|
|
586
|
|
|
587
|
|
|
588 static void FillElementWithString(DcmElement& element,
|
|
|
589 const DicomTag& tag,
|
|
|
590 const std::string& value)
|
|
|
591 {
|
|
|
592 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
593 bool ok = false;
|
|
|
594
|
|
|
595 try
|
|
|
596 {
|
|
|
597 switch (key.getEVR())
|
|
|
598 {
|
|
|
599 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
600
|
|
|
601 /**
|
|
|
602 * TODO.
|
|
|
603 **/
|
|
|
604
|
|
|
605 case EVR_OB: // other byte
|
|
|
606 case EVR_OF: // other float
|
|
|
607 case EVR_OW: // other word
|
|
|
608 case EVR_AT: // attribute tag
|
|
|
609 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
610
|
|
|
611 case EVR_UN: // unknown value representation
|
|
|
612 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
613
|
|
|
614
|
|
|
615 /**
|
|
|
616 * String types.
|
|
|
617 **/
|
|
|
618
|
|
|
619 case EVR_DS: // decimal string
|
|
|
620 case EVR_IS: // integer string
|
|
|
621 case EVR_AS: // age string
|
|
|
622 case EVR_DA: // date string
|
|
|
623 case EVR_DT: // date time string
|
|
|
624 case EVR_TM: // time string
|
|
|
625 case EVR_AE: // application entity title
|
|
|
626 case EVR_CS: // code string
|
|
|
627 case EVR_SH: // short string
|
|
|
628 case EVR_LO: // long string
|
|
|
629 case EVR_ST: // short text
|
|
|
630 case EVR_LT: // long text
|
|
|
631 case EVR_UT: // unlimited text
|
|
|
632 case EVR_PN: // person name
|
|
|
633 case EVR_UI: // unique identifier
|
|
|
634 {
|
|
|
635 ok = element.putString(value.c_str()).good();
|
|
|
636 break;
|
|
|
637 }
|
|
|
638
|
|
|
639
|
|
|
640 /**
|
|
|
641 * Numerical types
|
|
|
642 **/
|
|
|
643
|
|
|
644 case EVR_SL: // signed long
|
|
|
645 {
|
|
|
646 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
|
|
|
647 break;
|
|
|
648 }
|
|
|
649
|
|
|
650 case EVR_SS: // signed short
|
|
|
651 {
|
|
|
652 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
|
|
|
653 break;
|
|
|
654 }
|
|
|
655
|
|
|
656 case EVR_UL: // unsigned long
|
|
|
657 {
|
|
|
658 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
|
|
|
659 break;
|
|
|
660 }
|
|
|
661
|
|
|
662 case EVR_US: // unsigned short
|
|
|
663 {
|
|
|
664 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
|
|
|
665 break;
|
|
|
666 }
|
|
|
667
|
|
|
668 case EVR_FL: // float single-precision
|
|
|
669 {
|
|
|
670 ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
|
|
|
671 break;
|
|
|
672 }
|
|
|
673
|
|
|
674 case EVR_FD: // float double-precision
|
|
|
675 {
|
|
|
676 ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
|
|
|
677 break;
|
|
|
678 }
|
|
|
679
|
|
|
680
|
|
|
681 /**
|
|
|
682 * Sequence types, should never occur at this point.
|
|
|
683 **/
|
|
|
684
|
|
|
685 case EVR_SQ: // sequence of items
|
|
|
686 {
|
|
|
687 ok = false;
|
|
|
688 break;
|
|
|
689 }
|
|
|
690
|
|
|
691
|
|
|
692 /**
|
|
|
693 * Internal to DCMTK.
|
|
|
694 **/
|
|
|
695
|
|
|
696 case EVR_ox: // OB or OW depending on context
|
|
|
697 case EVR_xs: // SS or US depending on context
|
|
|
698 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
699 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
700 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
701 case EVR_item: // used internally for items
|
|
|
702 case EVR_metainfo: // used internally for meta info datasets
|
|
|
703 case EVR_dataset: // used internally for datasets
|
|
|
704 case EVR_fileFormat: // used internally for DICOM files
|
|
|
705 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
706 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
707 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
708 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
709 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
710 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
711 case EVR_OverlayData: // used internally for overlay data
|
|
|
712 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
713 default:
|
|
|
714 break;
|
|
|
715 }
|
|
|
716 }
|
|
|
717 catch (boost::bad_lexical_cast&)
|
|
|
718 {
|
|
|
719 ok = false;
|
|
|
720 }
|
|
|
721
|
|
|
722 if (!ok)
|
|
|
723 {
|
|
|
724 throw OrthancException(ErrorCode_InternalError);
|
|
|
725 }
|
|
|
726 }
|
|
|
727
|
|
|
728
|
|
|
729 void ParsedDicomFile::Remove(const DicomTag& tag)
|
|
|
730 {
|
|
|
731 DcmTagKey key(tag.GetGroup(), tag.GetElement());
|
|
|
732 DcmElement* element = file_->getDataset()->remove(key);
|
|
|
733 if (element != NULL)
|
|
|
734 {
|
|
|
735 delete element;
|
|
|
736 }
|
|
|
737 }
|
|
|
738
|
|
|
739
|
|
|
740
|
|
|
741 void ParsedDicomFile::RemovePrivateTags()
|
|
|
742 {
|
|
|
743 typedef std::list<DcmElement*> Tags;
|
|
|
744
|
|
|
745 Tags privateTags;
|
|
|
746
|
|
|
747 DcmDataset& dataset = *file_->getDataset();
|
|
|
748 for (unsigned long i = 0; i < dataset.card(); i++)
|
|
|
749 {
|
|
|
750 DcmElement* element = dataset.getElement(i);
|
|
|
751 DcmTag tag(element->getTag());
|
|
|
752 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK
|
|
|
753 tag.getPrivateCreator() != NULL)
|
|
|
754 {
|
|
|
755 privateTags.push_back(element);
|
|
|
756 }
|
|
|
757 }
|
|
|
758
|
|
|
759 for (Tags::iterator it = privateTags.begin();
|
|
|
760 it != privateTags.end(); ++it)
|
|
|
761 {
|
|
|
762 DcmElement* tmp = dataset.remove(*it);
|
|
|
763 if (tmp != NULL)
|
|
|
764 {
|
|
|
765 delete tmp;
|
|
|
766 }
|
|
|
767 }
|
|
|
768 }
|
|
|
769
|
|
|
770
|
|
|
771
|
|
|
772 void ParsedDicomFile::Insert(const DicomTag& tag,
|
|
|
773 const std::string& value)
|
|
|
774 {
|
|
|
775 std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
|
|
|
776 FillElementWithString(*element, tag, value);
|
|
|
777
|
|
|
778 if (!file_->getDataset()->insert(element.release(), false, false).good())
|
|
|
779 {
|
|
|
780 // This field already exists
|
|
|
781 throw OrthancException(ErrorCode_InternalError);
|
|
|
782 }
|
|
|
783 }
|
|
|
784
|
|
|
785
|
|
|
786 void ParsedDicomFile::Replace(const DicomTag& tag,
|
|
|
787 const std::string& value,
|
|
|
788 DicomReplaceMode mode)
|
|
|
789 {
|
|
|
790 DcmTagKey key(tag.GetGroup(), tag.GetElement());
|
|
|
791 DcmElement* element = NULL;
|
|
|
792
|
|
|
793 if (!file_->getDataset()->findAndGetElement(key, element).good() ||
|
|
|
794 element == NULL)
|
|
|
795 {
|
|
|
796 // This field does not exist, act wrt. the specified "mode"
|
|
|
797 switch (mode)
|
|
|
798 {
|
|
|
799 case DicomReplaceMode_InsertIfAbsent:
|
|
|
800 Insert(tag, value);
|
|
|
801 break;
|
|
|
802
|
|
|
803 case DicomReplaceMode_ThrowIfAbsent:
|
|
|
804 throw OrthancException(ErrorCode_InexistentItem);
|
|
|
805
|
|
|
806 case DicomReplaceMode_IgnoreIfAbsent:
|
|
|
807 return;
|
|
|
808 }
|
|
|
809 }
|
|
|
810 else
|
|
|
811 {
|
|
|
812 FillElementWithString(*element, tag, value);
|
|
|
813 }
|
|
|
814
|
|
|
815
|
|
|
816 /**
|
|
|
817 * dcmodify will automatically correct 'Media Storage SOP Class
|
|
|
818 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
|
|
|
819 * you make changes to the related tags in the dataset ('SOP Class
|
|
|
820 * UID' and 'SOP Instance UID') via insert or modify mode
|
|
|
821 * options. You can disable this behaviour by using the -nmu
|
|
|
822 * option.
|
|
|
823 **/
|
|
|
824
|
|
|
825 if (tag == DICOM_TAG_SOP_CLASS_UID)
|
|
|
826 {
|
|
|
827 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent);
|
|
|
828 }
|
|
|
829
|
|
|
830 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
|
|
|
831 {
|
|
|
832 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent);
|
|
|
833 }
|
|
|
834 }
|
|
|
835
|
|
|
836
|
|
|
837 void ParsedDicomFile::Answer(RestApiOutput& output)
|
|
|
838 {
|
|
|
839 std::string serialized;
|
|
|
840 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset()))
|
|
|
841 {
|
|
|
842 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM);
|
|
|
843 }
|
|
|
844 }
|
|
|
845
|
|
|
846
|
|
|
847
|
|
|
848 bool ParsedDicomFile::GetTagValue(std::string& value,
|
|
|
849 const DicomTag& tag)
|
|
|
850 {
|
|
|
851 DcmTagKey k(tag.GetGroup(), tag.GetElement());
|
|
|
852 DcmDataset& dataset = *file_->getDataset();
|
|
|
853 DcmElement* element = NULL;
|
|
|
854 if (!dataset.findAndGetElement(k, element).good() ||
|
|
|
855 element == NULL)
|
|
|
856 {
|
|
|
857 return false;
|
|
|
858 }
|
|
|
859
|
|
|
860 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element));
|
|
|
861
|
|
|
862 if (v.get() == NULL)
|
|
|
863 {
|
|
|
864 value = "";
|
|
|
865 }
|
|
|
866 else
|
|
|
867 {
|
|
|
868 value = v->AsString();
|
|
|
869 }
|
|
|
870
|
|
|
871 return true;
|
|
|
872 }
|
|
|
873
|
|
|
874
|
|
|
875
|
|
|
876 DicomInstanceHasher ParsedDicomFile::GetHasher()
|
|
|
877 {
|
|
|
878 std::string patientId, studyUid, seriesUid, instanceUid;
|
|
|
879
|
|
|
880 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
|
|
|
881 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
|
|
|
882 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
|
|
|
883 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
|
|
|
884 {
|
|
|
885 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
886 }
|
|
|
887
|
|
|
888 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
|
|
|
889 }
|
|
|
890
|
|
|
891
|
|
|
892 static void StoreElement(Json::Value& target,
|
|
|
893 DcmElement& element,
|
|
|
894 unsigned int maxStringLength);
|
|
|
895
|
|
|
896 static void StoreItem(Json::Value& target,
|
|
|
897 DcmItem& item,
|
|
|
898 unsigned int maxStringLength)
|
|
|
899 {
|
|
|
900 target = Json::Value(Json::objectValue);
|
|
|
901
|
|
|
902 for (unsigned long i = 0; i < item.card(); i++)
|
|
|
903 {
|
|
|
904 DcmElement* element = item.getElement(i);
|
|
|
905 StoreElement(target, *element, maxStringLength);
|
|
|
906 }
|
|
|
907 }
|
|
|
908
|
|
|
909
|
|
|
910 static void StoreElement(Json::Value& target,
|
|
|
911 DcmElement& element,
|
|
|
912 unsigned int maxStringLength)
|
|
|
913 {
|
|
|
914 assert(target.type() == Json::objectValue);
|
|
|
915
|
|
|
916 DicomTag tag(FromDcmtkBridge::GetTag(element));
|
|
|
917 const std::string formattedTag = tag.Format();
|
|
|
918
|
|
|
919 #if 0
|
|
|
920 const std::string tagName = FromDcmtkBridge::GetName(tag);
|
|
|
921 #else
|
|
|
922 // This version of the code gives access to the name of the private tags
|
|
|
923 DcmTag tagbis(element.getTag());
|
|
|
924 const std::string tagName(tagbis.getTagName());
|
|
|
925 #endif
|
|
|
926
|
|
|
927 if (element.isLeaf())
|
|
|
928 {
|
|
|
929 Json::Value value(Json::objectValue);
|
|
|
930 value["Name"] = tagName;
|
|
|
931
|
|
|
932 if (tagbis.getPrivateCreator() != NULL)
|
|
|
933 {
|
|
|
934 value["PrivateCreator"] = tagbis.getPrivateCreator();
|
|
|
935 }
|
|
|
936
|
|
|
937 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
|
|
|
938 if (v->IsNull())
|
|
|
939 {
|
|
|
940 value["Type"] = "Null";
|
|
|
941 value["Value"] = Json::nullValue;
|
|
|
942 }
|
|
|
943 else
|
|
|
944 {
|
|
|
945 std::string s = v->AsString();
|
|
|
946 if (maxStringLength == 0 ||
|
|
|
947 s.size() <= maxStringLength)
|
|
|
948 {
|
|
|
949 value["Type"] = "String";
|
|
|
950 value["Value"] = s;
|
|
|
951 }
|
|
|
952 else
|
|
|
953 {
|
|
|
954 value["Type"] = "TooLong";
|
|
|
955 value["Value"] = Json::nullValue;
|
|
|
956 }
|
|
|
957 }
|
|
|
958
|
|
|
959 target[formattedTag] = value;
|
|
|
960 }
|
|
|
961 else
|
|
|
962 {
|
|
|
963 Json::Value children(Json::arrayValue);
|
|
|
964
|
|
|
965 // "All subclasses of DcmElement except for DcmSequenceOfItems
|
|
|
966 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
|
|
|
967 // etc. are not." The following cast is thus OK.
|
|
|
968 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
|
|
|
969
|
|
|
970 for (unsigned long i = 0; i < sequence.card(); i++)
|
|
|
971 {
|
|
|
972 DcmItem* child = sequence.getItem(i);
|
|
|
973 Json::Value& v = children.append(Json::objectValue);
|
|
|
974 StoreItem(v, *child, maxStringLength);
|
|
|
975 }
|
|
|
976
|
|
|
977 target[formattedTag]["Name"] = tagName;
|
|
|
978 target[formattedTag]["Type"] = "Sequence";
|
|
|
979 target[formattedTag]["Value"] = children;
|
|
|
980 }
|
|
|
981 }
|
|
|
982
|
|
|
983
|
|
|
984 template <typename T>
|
|
|
985 static void ExtractPngImageTruncate(std::string& result,
|
|
|
986 DicomIntegerPixelAccessor& accessor,
|
|
|
987 PixelFormat format)
|
|
|
988 {
|
|
|
989 assert(accessor.GetChannelCount() == 1);
|
|
|
990
|
|
|
991 PngWriter w;
|
|
|
992
|
|
|
993 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
|
|
|
994 T* pixel = &image[0];
|
|
|
995 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
|
|
|
996 {
|
|
|
997 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
|
|
|
998 {
|
|
|
999 int32_t v = accessor.GetValue(x, y);
|
|
|
1000 if (v < static_cast<int32_t>(std::numeric_limits<T>::min()))
|
|
|
1001 *pixel = std::numeric_limits<T>::min();
|
|
|
1002 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max()))
|
|
|
1003 *pixel = std::numeric_limits<T>::max();
|
|
|
1004 else
|
|
|
1005 *pixel = static_cast<T>(v);
|
|
|
1006 }
|
|
|
1007 }
|
|
|
1008
|
|
|
1009 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
|
|
|
1010 accessor.GetWidth() * sizeof(T), format, &image[0]);
|
|
|
1011 }
|
|
|
1012
|
|
|
1013
|
|
|
1014 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer)
|
|
|
1015 {
|
|
|
1016 FromDcmtkBridge::SaveToMemoryBuffer(buffer, file_->getDataset());
|
|
|
1017 }
|
|
|
1018
|
|
|
1019
|
|
|
1020 void ParsedDicomFile::SaveToFile(const std::string& path)
|
|
|
1021 {
|
|
|
1022 // TODO Avoid using a temporary memory buffer, write directly on disk
|
|
|
1023 std::string content;
|
|
|
1024 SaveToMemoryBuffer(content);
|
|
|
1025 Toolbox::WriteFile(content, path);
|
|
|
1026 }
|
|
|
1027
|
|
|
1028
|
|
|
1029 ParsedDicomFile::ParsedDicomFile()
|
|
|
1030 {
|
|
|
1031 file_.reset(new DcmFileFormat);
|
|
|
1032 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient));
|
|
|
1033 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study));
|
|
|
1034 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series));
|
|
|
1035 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
|
|
|
1036 }
|
|
|
1037
|
|
791
|
1038
|
|
|
1039 ParsedDicomFile::ParsedDicomFile(const char* content,
|
|
|
1040 size_t size)
|
|
|
1041 {
|
|
|
1042 Setup(content, size);
|
|
|
1043 }
|
|
|
1044
|
|
|
1045 ParsedDicomFile::ParsedDicomFile(const std::string& content)
|
|
|
1046 {
|
|
|
1047 if (content.size() == 0)
|
|
|
1048 {
|
|
|
1049 Setup(NULL, 0);
|
|
|
1050 }
|
|
|
1051 else
|
|
|
1052 {
|
|
|
1053 Setup(&content[0], content.size());
|
|
|
1054 }
|
|
|
1055 }
|
|
792
|
1056
|
|
|
1057
|
|
|
1058 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& other) :
|
|
|
1059 file_(dynamic_cast<DcmFileFormat*>(other.clone()))
|
|
|
1060 {
|
|
|
1061 }
|
|
|
1062
|
|
|
1063
|
|
|
1064 ParsedDicomFile::~ParsedDicomFile()
|
|
|
1065 {
|
|
|
1066 }
|
|
|
1067
|
|
790
|
1068 }
|
