annotate OrthancServer/FromDcmtkBridge.cpp @ 315:fc856d175d18

modifications
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 21 Dec 2012 17:18:04 +0100
parents 26efccdff583
children b83d85a85d69
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012 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 #ifndef NOMINMAX
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33 #define NOMINMAX
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34 #endif
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36 #include "FromDcmtkBridge.h"
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38 #include "ToDcmtkBridge.h"
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39 #include "../Core/Toolbox.h"
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40 #include "../Core/OrthancException.h"
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41 #include "../Core/PngWriter.h"
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42 #include "../Core/Uuid.h"
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43 #include "../Core/DicomFormat/DicomString.h"
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44 #include "../Core/DicomFormat/DicomNullValue.h"
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45 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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47 #include <list>
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48 #include <limits>
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49
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50 #include <boost/lexical_cast.hpp>
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51
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52 #include <dcmtk/dcmdata/dcchrstr.h>
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53 #include <dcmtk/dcmdata/dcdicent.h>
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54 #include <dcmtk/dcmdata/dcdict.h>
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55 #include <dcmtk/dcmdata/dcfilefo.h>
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56 #include <dcmtk/dcmdata/dcistrmb.h>
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57 #include <dcmtk/dcmdata/dcuid.h>
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58
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59 #include <dcmtk/dcmdata/dcvrae.h>
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60 #include <dcmtk/dcmdata/dcvras.h>
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61 #include <dcmtk/dcmdata/dcvrcs.h>
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62 #include <dcmtk/dcmdata/dcvrda.h>
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63 #include <dcmtk/dcmdata/dcvrds.h>
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64 #include <dcmtk/dcmdata/dcvrdt.h>
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65 #include <dcmtk/dcmdata/dcvrfd.h>
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66 #include <dcmtk/dcmdata/dcvrfl.h>
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67 #include <dcmtk/dcmdata/dcvris.h>
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68 #include <dcmtk/dcmdata/dcvrlo.h>
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69 #include <dcmtk/dcmdata/dcvrlt.h>
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70 #include <dcmtk/dcmdata/dcvrpn.h>
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71 #include <dcmtk/dcmdata/dcvrsh.h>
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72 #include <dcmtk/dcmdata/dcvrsl.h>
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73 #include <dcmtk/dcmdata/dcvrss.h>
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74 #include <dcmtk/dcmdata/dcvrst.h>
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75 #include <dcmtk/dcmdata/dcvrtm.h>
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76 #include <dcmtk/dcmdata/dcvrui.h>
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77 #include <dcmtk/dcmdata/dcvrul.h>
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78 #include <dcmtk/dcmdata/dcvrus.h>
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79 #include <dcmtk/dcmdata/dcvrut.h>
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81 #include <boost/math/special_functions/round.hpp>
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82 #include <glog/logging.h>
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83 #include <dcmtk/dcmdata/dcostrmb.h>
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84
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85 namespace Orthanc
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86 {
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87 void ParsedDicomFile::Setup(const char* buffer, size_t size)
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88 {
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89 DcmInputBufferStream is;
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90 if (size > 0)
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91 {
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92 is.setBuffer(buffer, size);
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93 }
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94 is.setEos();
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95
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96 file_.reset(new DcmFileFormat);
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97 file_->transferInit();
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98 if (!file_->read(is).good())
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99 {
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100 throw OrthancException(ErrorCode_BadFileFormat);
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101 }
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102 file_->loadAllDataIntoMemory();
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103 file_->transferEnd();
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104 }
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105
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106
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107 static void SendPathValueForDictionary(RestApiOutput& output,
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108 DcmItem& dicom)
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109 {
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110 Json::Value v = Json::arrayValue;
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111
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112 for (unsigned long i = 0; i < dicom.card(); i++)
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113 {
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114 DcmElement* element = dicom.getElement(i);
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115 if (element)
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116 {
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117 char buf[16];
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118 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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119 v.append(buf);
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120 }
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121 }
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122
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123 output.AnswerJson(v);
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124 }
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125
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126 static inline uint16_t GetCharValue(char c)
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127 {
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128 if (c >= '0' && c <= '9')
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129 return c - '0';
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130 else if (c >= 'a' && c <= 'f')
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131 return c - 'a' + 10;
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132 else if (c >= 'A' && c <= 'F')
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133 return c - 'A' + 10;
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134 else
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135 return 0;
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136 }
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137
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138 static inline uint16_t GetTagValue(const char* c)
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139 {
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140 return ((GetCharValue(c[0]) << 12) +
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141 (GetCharValue(c[1]) << 8) +
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142 (GetCharValue(c[2]) << 4) +
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143 GetCharValue(c[3]));
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144 }
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145
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146 static void ParseTagAndGroup(DcmTagKey& key,
285
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147 const std::string& tag)
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148 {
304
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149 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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150 key = DcmTagKey(t.GetGroup(), t.GetElement());
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151 }
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152
291
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153
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154 static void SendSequence(RestApiOutput& output,
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155 DcmSequenceOfItems& sequence)
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156 {
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157 // This element is a sequence
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158 Json::Value v = Json::arrayValue;
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159
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160 for (unsigned long i = 0; i < sequence.card(); i++)
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161 {
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162 v.append(boost::lexical_cast<std::string>(i));
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163 }
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164
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165 output.AnswerJson(v);
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166 }
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167
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168 static void AnswerDicomField(RestApiOutput& output,
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169 DcmElement& element)
291
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170 {
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171 // This element is not a sequence
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172 std::string buffer;
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173 buffer.resize(65536);
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174 Uint32 length = element.getLength();
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175 Uint32 offset = 0;
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176
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177 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL);
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178
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179 while (offset < length)
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180 {
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181 Uint32 nbytes;
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182 if (length - offset < buffer.size())
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183 {
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184 nbytes = length - offset;
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185 }
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186 else
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187 {
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188 nbytes = buffer.size();
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189 }
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190
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191 if (element.getPartialValue(&buffer[0], offset, nbytes).good())
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192 {
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193 output.GetLowLevelOutput().Send(&buffer[0], nbytes);
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194 offset += nbytes;
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195 }
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196 else
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197 {
302
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198 LOG(ERROR) << "Error while sending a DICOM field";
291
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199 return;
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200 }
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201 }
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202
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203 output.MarkLowLevelOutputDone();
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204 }
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205
285
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206 static void SendPathValueForLeaf(RestApiOutput& output,
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207 const std::string& tag,
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208 DcmItem& dicom)
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209 {
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210 DcmTagKey k;
304
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211 ParseTagAndGroup(k, tag);
285
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212
291
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213 DcmSequenceOfItems* sequence = NULL;
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214 if (dicom.findAndGetSequence(k, sequence).good() &&
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215 sequence != NULL &&
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216 sequence->getVR() == EVR_SQ)
285
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217 {
291
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218 SendSequence(output, *sequence);
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219 return;
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220 }
285
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221
291
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222 DcmElement* element = NULL;
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223 if (dicom.findAndGetElement(k, element).good() &&
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224 element != NULL &&
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225 element->getVR() != EVR_UNKNOWN &&
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226 element->getVR() != EVR_SQ)
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227 {
302
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228 AnswerDicomField(output, *element);
285
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229 }
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230 }
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231
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232 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
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233 const UriComponents& uri)
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234 {
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235 DcmItem* dicom = file_->getDataset();
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236
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237 // Go down in the tag hierarchy according to the URI
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238 for (size_t pos = 0; pos < uri.size() / 2; pos++)
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239 {
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240 size_t index;
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241 try
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242 {
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243 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
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244 }
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245 catch (boost::bad_lexical_cast&)
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246 {
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247 return;
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248 }
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249
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250 DcmTagKey k;
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251 DcmItem *child = NULL;
304
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252 ParseTagAndGroup(k, uri[2 * pos]);
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253 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
285
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254 child == NULL)
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255 {
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256 return;
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257 }
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258
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259 dicom = child;
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260 }
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261
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262 // We have reached the end of the URI
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263 if (uri.size() % 2 == 0)
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264 {
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265 SendPathValueForDictionary(output, *dicom);
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266 }
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267 else
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268 {
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269 SendPathValueForLeaf(output, uri.back(), *dicom);
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270 }
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271 }
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272
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273
302
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274
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275
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276
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277 static DcmElement* CreateElementForTag(const DicomTag& tag)
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278 {
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279 DcmTag key(tag.GetGroup(), tag.GetElement());
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280
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281 switch (key.getEVR())
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282 {
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283 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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284
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285 /**
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286 * TODO.
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287 **/
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288
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289 case EVR_OB: // other byte
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290 case EVR_OF: // other float
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291 case EVR_OW: // other word
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292 case EVR_AT: // attribute tag
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293 throw OrthancException(ErrorCode_NotImplemented);
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294
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295 case EVR_UN: // unknown value representation
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296 throw OrthancException(ErrorCode_ParameterOutOfRange);
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297
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298
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299 /**
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300 * String types.
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301 * http://support.dcmtk.org/docs/classDcmByteString.html
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302 **/
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303
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304 case EVR_AS: // age string
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305 return new DcmAgeString(key);
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306
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307 case EVR_AE: // application entity title
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308 return new DcmApplicationEntity(key);
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309
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310 case EVR_CS: // code string
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311 return new DcmCodeString(key);
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312
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313 case EVR_DA: // date string
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314 return new DcmDate(key);
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315
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316 case EVR_DT: // date time string
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317 return new DcmDateTime(key);
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318
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319 case EVR_DS: // decimal string
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320 return new DcmDecimalString(key);
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321
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322 case EVR_IS: // integer string
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323 return new DcmIntegerString(key);
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324
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325 case EVR_TM: // time string
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326 return new DcmTime(key);
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327
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328 case EVR_UI: // unique identifier
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329 return new DcmUniqueIdentifier(key);
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330
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331 case EVR_ST: // short text
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332 return new DcmShortText(key);
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333
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334 case EVR_LO: // long string
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335 return new DcmLongString(key);
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336
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337 case EVR_LT: // long text
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338 return new DcmLongText(key);
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339
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340 case EVR_UT: // unlimited text
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341 return new DcmUnlimitedText(key);
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342
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343 case EVR_SH: // short string
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344 return new DcmShortString(key);
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345
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346 case EVR_PN: // person name
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347 return new DcmPersonName(key);
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348
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349
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350 /**
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351 * Numerical types
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352 **/
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353
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354 case EVR_SL: // signed long
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355 return new DcmSignedLong(key);
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356
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357 case EVR_SS: // signed short
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358 return new DcmSignedShort(key);
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359
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360 case EVR_UL: // unsigned long
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361 return new DcmUnsignedLong(key);
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362
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363 case EVR_US: // unsigned short
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364 return new DcmUnsignedShort(key);
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365
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366 case EVR_FL: // float single-precision
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367 return new DcmFloatingPointSingle(key);
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368
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369 case EVR_FD: // float double-precision
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370 return new DcmFloatingPointDouble(key);
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371
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372
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373 /**
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374 * Sequence types, should never occur at this point.
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375 **/
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376
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377 case EVR_SQ: // sequence of items
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378 throw OrthancException(ErrorCode_ParameterOutOfRange);
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379
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380
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381 /**
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382 * Internal to DCMTK.
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383 **/
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384
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385 case EVR_ox: // OB or OW depending on context
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386 case EVR_xs: // SS or US depending on context
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387 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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388 case EVR_na: // na="not applicable", for data which has no VR
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389 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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390 case EVR_item: // used internally for items
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391 case EVR_metainfo: // used internally for meta info datasets
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392 case EVR_dataset: // used internally for datasets
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393 case EVR_fileFormat: // used internally for DICOM files
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394 case EVR_dicomDir: // used internally for DICOMDIR objects
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395 case EVR_dirRecord: // used internally for DICOMDIR records
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396 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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397 case EVR_pixelItem: // used internally for pixel items in a compressed image
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398 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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399 case EVR_PixelData: // used internally for uncompressed pixeld data
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400 case EVR_OverlayData: // used internally for overlay data
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401 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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402 default:
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403 break;
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404 }
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405
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406 throw OrthancException(ErrorCode_InternalError);
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407 }
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408
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409
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410
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411 static void FillElementWithString(DcmElement& element,
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412 const DicomTag& tag,
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413 const std::string& value)
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414 {
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415 DcmTag key(tag.GetGroup(), tag.GetElement());
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416 bool ok = false;
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417
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418 try
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419 {
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420 switch (key.getEVR())
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421 {
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422 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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423
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424 /**
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425 * TODO.
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426 **/
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427
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428 case EVR_OB: // other byte
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429 case EVR_OF: // other float
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430 case EVR_OW: // other word
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431 case EVR_AT: // attribute tag
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432 throw OrthancException(ErrorCode_NotImplemented);
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433
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434 case EVR_UN: // unknown value representation
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435 throw OrthancException(ErrorCode_ParameterOutOfRange);
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436
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437
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438 /**
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439 * String types.
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440 **/
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441
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442 case EVR_DS: // decimal string
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443 case EVR_IS: // integer string
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444 case EVR_AS: // age string
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445 case EVR_DA: // date string
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446 case EVR_DT: // date time string
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447 case EVR_TM: // time string
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diff changeset
448 case EVR_AE: // application entity title
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449 case EVR_CS: // code string
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450 case EVR_SH: // short string
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451 case EVR_LO: // long string
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452 case EVR_ST: // short text
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453 case EVR_LT: // long text
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454 case EVR_UT: // unlimited text
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455 case EVR_PN: // person name
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456 case EVR_UI: // unique identifier
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457 {
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458 ok = element.putString(value.c_str()).good();
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diff changeset
459 break;
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diff changeset
460 }
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461
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462
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463 /**
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diff changeset
464 * Numerical types
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465 **/
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466
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467 case EVR_SL: // signed long
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468 {
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469 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
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470 break;
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471 }
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472
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473 case EVR_SS: // signed short
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474 {
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475 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
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476 break;
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diff changeset
477 }
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478
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479 case EVR_UL: // unsigned long
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480 {
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481 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
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482 break;
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483 }
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484
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485 case EVR_US: // unsigned short
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486 {
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487 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
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488 break;
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489 }
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490
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491 case EVR_FL: // float single-precision
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492 {
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493 ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
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494 break;
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495 }
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496
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497 case EVR_FD: // float double-precision
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498 {
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499 ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
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500 break;
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501 }
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502
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503
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504 /**
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505 * Sequence types, should never occur at this point.
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506 **/
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507
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508 case EVR_SQ: // sequence of items
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509 {
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diff changeset
510 ok = false;
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diff changeset
511 break;
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diff changeset
512 }
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diff changeset
513
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diff changeset
514
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515 /**
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516 * Internal to DCMTK.
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517 **/
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518
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519 case EVR_ox: // OB or OW depending on context
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520 case EVR_xs: // SS or US depending on context
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521 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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522 case EVR_na: // na="not applicable", for data which has no VR
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diff changeset
523 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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diff changeset
524 case EVR_item: // used internally for items
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525 case EVR_metainfo: // used internally for meta info datasets
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diff changeset
526 case EVR_dataset: // used internally for datasets
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diff changeset
527 case EVR_fileFormat: // used internally for DICOM files
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diff changeset
528 case EVR_dicomDir: // used internally for DICOMDIR objects
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diff changeset
529 case EVR_dirRecord: // used internally for DICOMDIR records
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diff changeset
530 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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diff changeset
531 case EVR_pixelItem: // used internally for pixel items in a compressed image
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diff changeset
532 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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533 case EVR_PixelData: // used internally for uncompressed pixeld data
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diff changeset
534 case EVR_OverlayData: // used internally for overlay data
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diff changeset
535 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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diff changeset
536 default:
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diff changeset
537 break;
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diff changeset
538 }
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diff changeset
539 }
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diff changeset
540 catch (boost::bad_lexical_cast&)
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diff changeset
541 {
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diff changeset
542 ok = false;
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diff changeset
543 }
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544
238134081136 modification of dicom files
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545 if (!ok)
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diff changeset
546 {
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diff changeset
547 throw OrthancException(ErrorCode_InternalError);
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548 }
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diff changeset
549 }
238134081136 modification of dicom files
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diff changeset
550
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551
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diff changeset
552 void ParsedDicomFile::Remove(const DicomTag& tag)
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diff changeset
553 {
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diff changeset
554 DcmTagKey key(tag.GetGroup(), tag.GetElement());
306
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diff changeset
555 DcmElement* element = file_->getDataset()->remove(key);
326d5a4a5af3 modification of instances
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diff changeset
556 if (element != NULL)
326d5a4a5af3 modification of instances
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diff changeset
557 {
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
558 delete element;
326d5a4a5af3 modification of instances
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diff changeset
559 }
326d5a4a5af3 modification of instances
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diff changeset
560 }
302
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diff changeset
561
306
326d5a4a5af3 modification of instances
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diff changeset
562
326d5a4a5af3 modification of instances
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diff changeset
563
326d5a4a5af3 modification of instances
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diff changeset
564 void ParsedDicomFile::RemovePrivateTags()
326d5a4a5af3 modification of instances
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diff changeset
565 {
326d5a4a5af3 modification of instances
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diff changeset
566 typedef std::list<DcmElement*> Tags;
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diff changeset
567
326d5a4a5af3 modification of instances
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diff changeset
568 Tags privateTags;
326d5a4a5af3 modification of instances
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diff changeset
569
326d5a4a5af3 modification of instances
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diff changeset
570 DcmDataset& dataset = *file_->getDataset();
326d5a4a5af3 modification of instances
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diff changeset
571 for (unsigned long i = 0; i < dataset.card(); i++)
326d5a4a5af3 modification of instances
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diff changeset
572 {
326d5a4a5af3 modification of instances
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diff changeset
573 DcmElement* element = dataset.getElement(i);
326d5a4a5af3 modification of instances
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diff changeset
574 DcmTag tag(element->getTag());
311
26efccdff583 anonymisation
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diff changeset
575 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK
26efccdff583 anonymisation
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diff changeset
576 tag.getPrivateCreator() != NULL)
306
326d5a4a5af3 modification of instances
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diff changeset
577 {
326d5a4a5af3 modification of instances
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diff changeset
578 privateTags.push_back(element);
326d5a4a5af3 modification of instances
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diff changeset
579 }
326d5a4a5af3 modification of instances
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diff changeset
580 }
326d5a4a5af3 modification of instances
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diff changeset
581
326d5a4a5af3 modification of instances
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diff changeset
582 for (Tags::iterator it = privateTags.begin();
326d5a4a5af3 modification of instances
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diff changeset
583 it != privateTags.end(); it++)
326d5a4a5af3 modification of instances
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diff changeset
584 {
326d5a4a5af3 modification of instances
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diff changeset
585 DcmElement* tmp = dataset.remove(*it);
326d5a4a5af3 modification of instances
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diff changeset
586 if (tmp != NULL)
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parents: 305
diff changeset
587 {
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
588 delete tmp;
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
589 }
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
590 }
302
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diff changeset
591 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
592
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
593
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
594
238134081136 modification of dicom files
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parents: 291
diff changeset
595 void ParsedDicomFile::Insert(const DicomTag& tag,
238134081136 modification of dicom files
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diff changeset
596 const std::string& value)
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
597 {
238134081136 modification of dicom files
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diff changeset
598 std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
238134081136 modification of dicom files
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diff changeset
599 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
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diff changeset
600
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
601 if (!file_->getDataset()->insert(element.release(), false, false).good())
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
602 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
603 // This field already exists
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
604 throw OrthancException(ErrorCode_InternalError);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
605 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
606 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
607
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
608
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
609 void ParsedDicomFile::Replace(const DicomTag& tag,
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
610 const std::string& value,
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
611 DicomReplaceMode mode)
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
612 {
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
613 DcmTagKey key(tag.GetGroup(), tag.GetElement());
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
614 DcmElement* element = NULL;
238134081136 modification of dicom files
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parents: 291
diff changeset
615
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
616 if (!file_->getDataset()->findAndGetElement(key, element).good() ||
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
617 element == NULL)
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
618 {
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
619 // This field does not exist, act wrt. the specified "mode"
86bb79522f19 name of the private tags
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parents: 304
diff changeset
620 switch (mode)
302
238134081136 modification of dicom files
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diff changeset
621 {
305
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parents: 304
diff changeset
622 case DicomReplaceMode_InsertIfAbsent:
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diff changeset
623 Insert(tag, value);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
624 break;
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
625
86bb79522f19 name of the private tags
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parents: 304
diff changeset
626 case DicomReplaceMode_ThrowIfAbsent:
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parents: 304
diff changeset
627 throw OrthancException(ErrorCode_InexistentItem);
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
628
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parents: 304
diff changeset
629 case DicomReplaceMode_IgnoreIfAbsent:
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diff changeset
630 return;
302
238134081136 modification of dicom files
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parents: 291
diff changeset
631 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
632 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
633 else
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
634 {
238134081136 modification of dicom files
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parents: 291
diff changeset
635 FillElementWithString(*element, tag, value);
238134081136 modification of dicom files
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parents: 291
diff changeset
636 }
303
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
637
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
638
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
639 /**
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parents: 302
diff changeset
640 * dcmodify will automatically correct 'Media Storage SOP Class
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
641 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
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parents: 302
diff changeset
642 * you make changes to the related tags in the dataset ('SOP Class
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
643 * UID' and 'SOP Instance UID') via insert or modify mode
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parents: 302
diff changeset
644 * options. You can disable this behaviour by using the -nmu
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
645 * option.
c76a35a85c69 ready for anonymization
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diff changeset
646 **/
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diff changeset
647 if (tag == DICOM_TAG_SOP_CLASS_UID)
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
648 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent);
303
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parents: 302
diff changeset
649
c76a35a85c69 ready for anonymization
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parents: 302
diff changeset
650 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
305
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parents: 304
diff changeset
651 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent);
302
238134081136 modification of dicom files
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parents: 291
diff changeset
652 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
653
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
654
238134081136 modification of dicom files
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parents: 291
diff changeset
655 void ParsedDicomFile::Answer(RestApiOutput& output)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
656 {
238134081136 modification of dicom files
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parents: 291
diff changeset
657 std::string serialized;
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
658 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset()))
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
659 {
238134081136 modification of dicom files
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parents: 291
diff changeset
660 output.AnswerBuffer(serialized, "application/octet-stream");
238134081136 modification of dicom files
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parents: 291
diff changeset
661 }
238134081136 modification of dicom files
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parents: 291
diff changeset
662 }
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
663
238134081136 modification of dicom files
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parents: 291
diff changeset
664
308
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
665
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
666 bool ParsedDicomFile::GetTagValue(std::string& value,
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parents: 306
diff changeset
667 const DicomTag& tag)
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
668 {
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
669 DcmTagKey k(tag.GetGroup(), tag.GetElement());
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
670 DcmDataset& dataset = *file_->getDataset();
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
671 DcmElement* element = NULL;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
672 if (!dataset.findAndGetElement(k, element).good() ||
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
673 element == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
674 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
675 return false;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
676 }
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
677
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
678 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element));
fbf2b2282086 inplace modification of series and studies
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parents: 306
diff changeset
679
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
680 if (v.get() == NULL)
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
681 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
682 value = "";
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
683 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
684 else
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
685 {
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
686 value = v->AsString();
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
687 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
688
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
689 return true;
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
690 }
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
691
fbf2b2282086 inplace modification of series and studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 306
diff changeset
692
315
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
693
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
694 DicomInstanceHasher ParsedDicomFile::GetHasher()
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
695 {
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
696 std::string patientId, studyUid, seriesUid, instanceUid;
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
697
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
698 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
699 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
700 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
701 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
702 {
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
703 throw OrthancException(ErrorCode_BadFileFormat);
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
704 }
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
705
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
706 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
707 }
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
708
fc856d175d18 modifications
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 311
diff changeset
709
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
710 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
711 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
712 target.Clear();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
713 for (unsigned long i = 0; i < dataset.card(); i++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
714 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
715 DcmElement* element = dataset.getElement(i);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
716 if (element && element->isLeaf())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
717 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
718 target.SetValue(element->getTag().getGTag(),
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
719 element->getTag().getETag(),
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
720 ConvertLeafElement(*element));
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
721 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
722 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
723 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
724
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
725
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
726 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
727 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
728 return DicomTag(element.getGTag(), element.getETag());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
729 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
730
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
731
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
732 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
733 {
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parents:
diff changeset
734 if (!element.isLeaf())
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parents:
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735 {
62
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736 throw OrthancException("Only applicable to leaf elements");
0
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parents:
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737 }
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parents:
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738
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parents:
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739 if (element.isaString())
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parents:
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740 {
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parents:
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741 char *c;
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parents:
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742 if (element.getString(c).good() &&
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743 c != NULL)
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parents:
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744 {
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745 std::string s(c);
107
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746 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter?
0
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747 return new DicomString(utf8);
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parents:
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748 }
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Sebastien Jodogne <s.jodogne@gmail.com>
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749 else
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parents:
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750 {
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parents:
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751 return new DicomNullValue;
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parents:
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752 }
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parents:
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753 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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754
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
755 try
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parents:
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756 {
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757 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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758 switch (element.getVR())
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parents:
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759 {
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parents:
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760
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parents:
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761 /**
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parents:
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762 * TODO.
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parents:
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763 **/
306
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764
302
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765 case EVR_OB: // other byte
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766 case EVR_OF: // other float
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767 case EVR_OW: // other word
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768 case EVR_AT: // attribute tag
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769 case EVR_UN: // unknown value representation
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770 return new DicomNullValue();
306
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771
302
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772 /**
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diff changeset
773 * String types, should never happen at this point because of
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diff changeset
774 * "element.isaString()".
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775 **/
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776
306
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777 case EVR_DS: // decimal string
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778 case EVR_IS: // integer string
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779 case EVR_AS: // age string
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780 case EVR_DA: // date string
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781 case EVR_DT: // date time string
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782 case EVR_TM: // time string
302
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783 case EVR_AE: // application entity title
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784 case EVR_CS: // code string
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785 case EVR_SH: // short string
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786 case EVR_LO: // long string
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787 case EVR_ST: // short text
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788 case EVR_LT: // long text
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789 case EVR_UT: // unlimited text
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790 case EVR_PN: // person name
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791 case EVR_UI: // unique identifier
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parents: 291
diff changeset
792 return new DicomNullValue();
0
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parents:
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793
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parents:
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794
302
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diff changeset
795 /**
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diff changeset
796 * Numerical types
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parents: 291
diff changeset
797 **/
0
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parents:
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798
302
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799 case EVR_SL: // signed long
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800 {
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diff changeset
801 Sint32 f;
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802 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
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803 return new DicomString(boost::lexical_cast<std::string>(f));
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804 else
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805 return new DicomNullValue();
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parents: 291
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806 }
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parents: 291
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807
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808 case EVR_SS: // signed short
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809 {
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810 Sint16 f;
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811 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
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diff changeset
812 return new DicomString(boost::lexical_cast<std::string>(f));
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813 else
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814 return new DicomNullValue();
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parents: 291
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815 }
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parents: 291
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816
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817 case EVR_UL: // unsigned long
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parents: 291
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818 {
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819 Uint32 f;
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820 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
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diff changeset
821 return new DicomString(boost::lexical_cast<std::string>(f));
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diff changeset
822 else
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parents: 291
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823 return new DicomNullValue();
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parents: 291
diff changeset
824 }
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parents: 291
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825
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826 case EVR_US: // unsigned short
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parents: 291
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827 {
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diff changeset
828 Uint16 f;
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diff changeset
829 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
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830 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
831 else
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parents: 291
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832 return new DicomNullValue();
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parents: 291
diff changeset
833 }
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parents: 291
diff changeset
834
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parents: 291
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835 case EVR_FL: // float single-precision
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parents: 291
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836 {
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diff changeset
837 Float32 f;
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diff changeset
838 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
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parents: 291
diff changeset
839 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
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840 else
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parents: 291
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841 return new DicomNullValue();
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parents: 291
diff changeset
842 }
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parents: 291
diff changeset
843
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parents: 291
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844 case EVR_FD: // float double-precision
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parents: 291
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845 {
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diff changeset
846 Float64 f;
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diff changeset
847 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
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diff changeset
848 return new DicomString(boost::lexical_cast<std::string>(f));
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parents: 291
diff changeset
849 else
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parents: 291
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850 return new DicomNullValue();
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parents: 291
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851 }
0
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parents:
diff changeset
852
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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853
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parents:
diff changeset
854 /**
302
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diff changeset
855 * Sequence types, should never occur at this point because of
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parents: 291
diff changeset
856 * "element.isLeaf()".
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857 **/
0
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parents:
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858
302
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859 case EVR_SQ: // sequence of items
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parents: 291
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860 return new DicomNullValue;
0
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parents:
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861
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parents:
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862
302
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diff changeset
863 /**
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parents: 291
diff changeset
864 * Internal to DCMTK.
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parents: 291
diff changeset
865 **/
0
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parents:
diff changeset
866
302
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diff changeset
867 case EVR_ox: // OB or OW depending on context
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parents: 291
diff changeset
868 case EVR_xs: // SS or US depending on context
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diff changeset
869 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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diff changeset
870 case EVR_na: // na="not applicable", for data which has no VR
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parents: 291
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871 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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parents: 291
diff changeset
872 case EVR_item: // used internally for items
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parents: 291
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873 case EVR_metainfo: // used internally for meta info datasets
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parents: 291
diff changeset
874 case EVR_dataset: // used internally for datasets
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parents: 291
diff changeset
875 case EVR_fileFormat: // used internally for DICOM files
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parents: 291
diff changeset
876 case EVR_dicomDir: // used internally for DICOMDIR objects
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parents: 291
diff changeset
877 case EVR_dirRecord: // used internally for DICOMDIR records
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parents: 291
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878 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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parents: 291
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879 case EVR_pixelItem: // used internally for pixel items in a compressed image
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parents: 291
diff changeset
880 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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parents: 291
diff changeset
881 case EVR_PixelData: // used internally for uncompressed pixeld data
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parents: 291
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882 case EVR_OverlayData: // used internally for overlay data
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parents: 291
diff changeset
883 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
884 return new DicomNullValue;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
885
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
886
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
887 /**
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
888 * Default case.
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
889 **/
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
890
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
891 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
892 return new DicomNullValue;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
893 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
894 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
895 catch (boost::bad_lexical_cast)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
896 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
897 return new DicomNullValue;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
898 }
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
899 catch (std::bad_cast)
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
900 {
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
901 return new DicomNullValue;
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
902 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
903 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
904
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
905
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
906 static void StoreElement(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
907 DcmElement& element,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
908 unsigned int maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
909
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
910 static void StoreItem(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
911 DcmItem& item,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
912 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
913 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
914 target = Json::Value(Json::objectValue);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
915
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
916 for (unsigned long i = 0; i < item.card(); i++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
917 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
918 DcmElement* element = item.getElement(i);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
919 StoreElement(target, *element, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
920 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
921 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
922
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
923
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
924 static void StoreElement(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
925 DcmElement& element,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
926 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
927 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
928 assert(target.type() == Json::objectValue);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
929
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
930 DicomTag tag(FromDcmtkBridge::GetTag(element));
305
86bb79522f19 name of the private tags
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diff changeset
931 const std::string formattedTag = tag.Format();
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
932
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
933 #if 0
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
934 const std::string tagName = FromDcmtkBridge::GetName(tag);
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
935 #else
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
936 // This version of the code gives access to the name of the private tags
86bb79522f19 name of the private tags
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parents: 304
diff changeset
937 DcmTag tagbis(element.getTag());
306
326d5a4a5af3 modification of instances
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diff changeset
938 const std::string tagName(tagbis.getTagName());
305
86bb79522f19 name of the private tags
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parents: 304
diff changeset
939 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
940
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
941 if (element.isLeaf())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
942 {
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
943 Json::Value value(Json::objectValue);
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
944 value["Name"] = tagName;
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
945
306
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
946 if (tagbis.getPrivateCreator() != NULL)
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
947 {
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
948 value["PrivateCreator"] = tagbis.getPrivateCreator();
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
949 }
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
950
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
951 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
952 if (v->IsNull())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
953 {
35
f6d12037f886 full json vs. simplified json
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parents: 2
diff changeset
954 value["Type"] = "Null";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
955 value["Value"] = Json::nullValue;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
956 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
957 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
958 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
959 std::string s = v->AsString();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
960 if (maxStringLength == 0 ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
961 s.size() <= maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
962 {
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
963 value["Type"] = "String";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
964 value["Value"] = s;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
965 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
966 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
967 {
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
968 value["Type"] = "TooLong";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
969 value["Value"] = Json::nullValue;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
970 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
971 }
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
972
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
973 target[formattedTag] = value;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
974 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
975 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
976 {
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
977 Json::Value children(Json::arrayValue);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
978
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
979 // "All subclasses of DcmElement except for DcmSequenceOfItems
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
980 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
981 // etc. are not." The following cast is thus OK.
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
982 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
983
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
984 for (unsigned long i = 0; i < sequence.card(); i++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
985 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
986 DcmItem* child = sequence.getItem(i);
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
987 Json::Value& v = children.append(Json::objectValue);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
988 StoreItem(v, *child, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
989 }
35
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
990
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
991 target[formattedTag]["Name"] = tagName;
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
992 target[formattedTag]["Type"] = "Sequence";
f6d12037f886 full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2
diff changeset
993 target[formattedTag]["Value"] = children;
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
994 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
995 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
996
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
997
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
998 void FromDcmtkBridge::ToJson(Json::Value& root,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
999 DcmDataset& dataset,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1000 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1001 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1002 StoreItem(root, dataset, maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1003 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1004
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1005
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1006
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1007 void FromDcmtkBridge::ToJson(Json::Value& target,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1008 const std::string& path,
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1009 unsigned int maxStringLength)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1010 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1011 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1012 if (!dicom.loadFile(path.c_str()).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1013 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1014 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1015 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1016 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1017 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1018 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1019 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1020 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1021
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1022
42
ea48f38afe5f access to raw images
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parents: 41
diff changeset
1023 static void ExtractPngImagePreview(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1024 DicomIntegerPixelAccessor& accessor)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1025 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1026 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1027
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1028 int32_t min, max;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1029 accessor.GetExtremeValues(min, max);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1030
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1031 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1032 if (min != max)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1033 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1034 uint8_t* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1035 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1036 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1037 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1038 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1039 int32_t v = accessor.GetValue(x, y);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1040 *pixel = static_cast<uint8_t>(
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1041 boost::math::lround(static_cast<float>(v - min) /
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1042 static_cast<float>(max - min) * 255.0f));
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1043 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1044 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1045 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1046
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1047 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1048 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1049 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1050
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1051
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1052 template <typename T>
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1053 static void ExtractPngImageTruncate(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1054 DicomIntegerPixelAccessor& accessor,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1055 PixelFormat format)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1056 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1057 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1058
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1059 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1060 T* pixel = &image[0];
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1061 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1062 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1063 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1064 {
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1065 int32_t v = accessor.GetValue(x, y);
73
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 71
diff changeset
1066 if (v < std::numeric_limits<T>::min())
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1067 *pixel = std::numeric_limits<T>::min();
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1068 else if (v > std::numeric_limits<T>::max())
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1069 *pixel = std::numeric_limits<T>::max();
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1070 else
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1071 *pixel = static_cast<T>(v);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1072 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1073 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1074
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1075 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1076 accessor.GetWidth() * sizeof(T), format, &image[0]);
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1077 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1078
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1079
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1080 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1081 DcmDataset& dataset,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1082 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1083 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1084 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1085 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1086
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1087 std::auto_ptr<DicomIntegerPixelAccessor> accessor;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1088
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1089 DicomMap m;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1090 FromDcmtkBridge::Convert(m, dataset);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1091
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1092 DcmElement* e;
80
6212bf978584 status of series
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 79
diff changeset
1093 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() &&
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1094 e != NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1095 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1096 Uint8* pixData = NULL;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1097 if (e->getUint8Array(pixData) == EC_Normal)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1098 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1099 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength()));
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1100 accessor->SetCurrentFrame(frame);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1101 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1102 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1103
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1104 PixelFormat format;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1105 switch (mode)
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1106 {
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1107 case ImageExtractionMode_Preview:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1108 case ImageExtractionMode_UInt8:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1109 format = PixelFormat_Grayscale8;
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1110 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1111
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1112 case ImageExtractionMode_UInt16:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1113 format = PixelFormat_Grayscale16;
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1114 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1115
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1116 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1117 throw OrthancException(ErrorCode_NotImplemented);
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1118 }
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1119
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1120 if (accessor.get() == NULL ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1121 accessor->GetWidth() == 0 ||
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1122 accessor->GetHeight() == 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1123 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1124 PngWriter w;
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1125 w.WriteToMemory(result, 0, 0, 0, format, NULL);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1126 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1127 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1128 {
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1129 switch (mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1130 {
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1131 case ImageExtractionMode_Preview:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1132 ExtractPngImagePreview(result, *accessor);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1133 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1134
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1135 case ImageExtractionMode_UInt8:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1136 ExtractPngImageTruncate<uint8_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1137 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1138
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1139 case ImageExtractionMode_UInt16:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1140 ExtractPngImageTruncate<uint16_t>(result, *accessor, format);
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1141 break;
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1142
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1143 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1144 throw OrthancException(ErrorCode_NotImplemented);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1145 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1146 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1147 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1148
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1149
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1150 void FromDcmtkBridge::ExtractPngImage(std::string& result,
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1151 const std::string& dicomContent,
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1152 unsigned int frame,
42
ea48f38afe5f access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 41
diff changeset
1153 ImageExtractionMode mode)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1154 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1155 DcmInputBufferStream is;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1156 if (dicomContent.size() > 0)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1157 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1158 is.setBuffer(&dicomContent[0], dicomContent.size());
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1159 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1160 is.setEos();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1161
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1162 DcmFileFormat dicom;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1163 if (dicom.read(is).good())
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1164 {
53
293038baf8f1 access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 50
diff changeset
1165 ExtractPngImage(result, *dicom.getDataset(), frame, mode);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1166 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1167 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1168 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1169 throw OrthancException(ErrorCode_BadFileFormat);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1170 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1171 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1172
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1173
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1174
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1175 std::string FromDcmtkBridge::GetName(const DicomTag& t)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1176 {
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1177 // Some patches for important tags because of different DICOM
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1178 // dictionaries between DCMTK versions
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1179 std::string n = t.GetMainTagsName();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1180 if (n.size() != 0)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1181 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1182 return n;
4d7469f72a0b embedding of dicom dictionaries
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parents: 285
diff changeset
1183 }
106
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1184 // End of patches
332fec038d52 patch for dcmtk dictionaries
jodogne
parents: 80
diff changeset
1185
305
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1186 #if 0
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1187 DcmTagKey tag(t.GetGroup(), t.GetElement());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1188 const DcmDataDictionary& dict = dcmDataDict.rdlock();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1189 const DcmDictEntry* entry = dict.findEntry(tag, NULL);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1190
306
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diff changeset
1191 std::string s(DcmTag_ERROR_TagName);
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1192 if (entry != NULL)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1193 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1194 s = std::string(entry->getTagName());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1195 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1196
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1197 dcmDataDict.unlock();
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parents:
diff changeset
1198 return s;
305
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diff changeset
1199 #else
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parents: 304
diff changeset
1200 DcmTag tag(t.GetGroup(), t.GetElement());
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parents: 304
diff changeset
1201 const char* name = tag.getTagName();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1202 if (name == NULL)
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parents: 304
diff changeset
1203 {
306
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parents: 305
diff changeset
1204 return DcmTag_ERROR_TagName;
305
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1205 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
1206 else
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parents: 304
diff changeset
1207 {
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parents: 304
diff changeset
1208 return std::string(name);
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parents: 304
diff changeset
1209 }
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parents: 304
diff changeset
1210 #endif
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1211 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1212
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1213
304
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diff changeset
1214 DicomTag FromDcmtkBridge::ParseTag(const char* name)
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1215 {
304
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diff changeset
1216 if (strlen(name) == 9 &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1217 isxdigit(name[0]) &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1218 isxdigit(name[1]) &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1219 isxdigit(name[2]) &&
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parents: 303
diff changeset
1220 isxdigit(name[3]) &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1221 name[4] == '-' &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1222 isxdigit(name[5]) &&
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parents: 303
diff changeset
1223 isxdigit(name[6]) &&
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parents: 303
diff changeset
1224 isxdigit(name[7]) &&
4eea080e6e7a refactoring
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parents: 303
diff changeset
1225 isxdigit(name[8]))
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parents: 303
diff changeset
1226 {
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1227 uint16_t group = GetTagValue(name);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1228 uint16_t element = GetTagValue(name + 5);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 303
diff changeset
1229 return DicomTag(group, element);
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parents: 303
diff changeset
1230 }
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parents: 303
diff changeset
1231
305
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parents: 304
diff changeset
1232 #if 0
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1233 const DcmDataDictionary& dict = dcmDataDict.rdlock();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1234 const DcmDictEntry* entry = dict.findEntry(name);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1235
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1236 if (entry == NULL)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1237 {
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parents:
diff changeset
1238 dcmDataDict.unlock();
62
a70bb32802ae renaming Server
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diff changeset
1239 throw OrthancException("Unknown DICOM tag");
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1240 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1241 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1242 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1243 DcmTagKey key = entry->getKey();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1244 DicomTag tag(key.getGroup(), key.getElement());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1245 dcmDataDict.unlock();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1246 return tag;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1247 }
305
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parents: 304
diff changeset
1248 #else
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parents: 304
diff changeset
1249 DcmTag tag;
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diff changeset
1250 if (DcmTag::findTagFromName(name, tag).good())
86bb79522f19 name of the private tags
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parents: 304
diff changeset
1251 {
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diff changeset
1252 return DicomTag(tag.getGTag(), tag.getETag());
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parents: 304
diff changeset
1253 }
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parents: 304
diff changeset
1254 else
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parents: 304
diff changeset
1255 {
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diff changeset
1256 throw OrthancException("Unknown DICOM tag");
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parents: 304
diff changeset
1257 }
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parents: 304
diff changeset
1258 #endif
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1259 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1260
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1261
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1262 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1263 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1264 for (DicomMap::Map::const_iterator
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1265 it = m.map_.begin(); it != m.map_.end(); it++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1266 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1267 DicomTag t = it->first;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1268 std::string s = it->second->AsString();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1269 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1270 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1271 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1272
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1273
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1274 void FromDcmtkBridge::ToJson(Json::Value& result,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1275 const DicomMap& values)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1276 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1277 if (result.type() != Json::objectValue)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1278 {
62
a70bb32802ae renaming Server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
1279 throw OrthancException(ErrorCode_BadParameterType);
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1280 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1281
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1282 result.clear();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1283
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1284 for (DicomMap::Map::const_iterator
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1285 it = values.map_.begin(); it != values.map_.end(); it++)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1286 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1287 result[GetName(it->first)] = it->second->AsString();
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1288 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1289 }
176
81f11fb357f2 uid generation
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parents: 136
diff changeset
1290
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1291
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1292 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level)
81f11fb357f2 uid generation
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parents: 136
diff changeset
1293 {
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1294 char uid[100];
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1295
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1296 switch (level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1297 {
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
1298 case DicomRootLevel_Patient:
311
26efccdff583 anonymisation
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parents: 308
diff changeset
1299 // The "PatientID" field is of type LO (Long String), 64
26efccdff583 anonymisation
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parents: 308
diff changeset
1300 // Bytes Maximum. An UUID is of length 36, thus it can be used
26efccdff583 anonymisation
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parents: 308
diff changeset
1301 // as a random PatientID.
26efccdff583 anonymisation
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parents: 308
diff changeset
1302 return Toolbox::GenerateUuid();
306
326d5a4a5af3 modification of instances
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parents: 305
diff changeset
1303
302
238134081136 modification of dicom files
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parents: 291
diff changeset
1304 case DicomRootLevel_Instance:
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parents: 291
diff changeset
1305 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1306
302
238134081136 modification of dicom files
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parents: 291
diff changeset
1307 case DicomRootLevel_Series:
238134081136 modification of dicom files
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parents: 291
diff changeset
1308 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1309
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1310 case DicomRootLevel_Study:
238134081136 modification of dicom files
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parents: 291
diff changeset
1311 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1312
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
1313 default:
238134081136 modification of dicom files
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parents: 291
diff changeset
1314 throw OrthancException(ErrorCode_ParameterOutOfRange);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1315 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1316 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
1317
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1318 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1319 DcmDataset* dataSet)
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1320 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1321 // Determine the transfer syntax which shall be used to write the
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1322 // information to the file. We always switch to the Little Endian
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1323 // syntax, with explicit length.
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1324
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1325 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1326 E_TransferSyntax xfer = EXS_LittleEndianExplicit;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1327 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1328
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1329 uint32_t s = dataSet->getLength(xfer, encodingType);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1330
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1331 buffer.resize(s);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
1332 DcmOutputBufferStream ob(&buffer[0], s);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1333
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1334 dataSet->transferInit();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1335
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1336 #if DCMTK_VERSION_NUMBER >= 360
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1337 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL,
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Sebastien Jodogne <s.jodogne@gmail.com>
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1338 /*opt_groupLength*/ EGL_recalcGL,
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1339 /*opt_paddingType*/ EPD_withoutPadding);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1340 #else
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1341 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1342 #endif
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1343
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1344 dataSet->transferEnd();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1345 if (c.good())
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1346 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1347 return true;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1348 }
4d7469f72a0b embedding of dicom dictionaries
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1349 else
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Sebastien Jodogne <s.jodogne@gmail.com>
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1350 {
4d7469f72a0b embedding of dicom dictionaries
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1351 buffer.clear();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1352 return false;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
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1353 }
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1354
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1355 #if 0
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1356 OFCondition cond = cbdata->dcmff->saveFile(fileName.c_str(), xfer,
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parents: 285
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1357 encodingType,
4d7469f72a0b embedding of dicom dictionaries
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1358 /*opt_groupLength*/ EGL_recalcGL,
4d7469f72a0b embedding of dicom dictionaries
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1359 /*opt_paddingType*/ EPD_withoutPadding,
4d7469f72a0b embedding of dicom dictionaries
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parents: 285
diff changeset
1360 OFstatic_cast(Uint32, /*opt_filepad*/ 0),
4d7469f72a0b embedding of dicom dictionaries
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parents: 285
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1361 OFstatic_cast(Uint32, /*opt_itempad*/ 0),
4d7469f72a0b embedding of dicom dictionaries
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parents: 285
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1362 (opt_useMetaheader) ? EWM_fileformat : EWM_dataset);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1363 #endif
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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1364 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1365 }