Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 302:238134081136
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 18 Dec 2012 17:29:30 +0100 |
parents | 4d7469f72a0b |
children | c76a35a85c69 |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
0 | 3 * Copyright (C) 2012 Medical Physics Department, CHU of Liege, |
4 * Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
136 | 10 * |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
0 | 22 * |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
71 | 32 #ifndef NOMINMAX |
33 #define NOMINMAX | |
34 #endif | |
0 | 35 |
36 #include "FromDcmtkBridge.h" | |
37 | |
38 #include "ToDcmtkBridge.h" | |
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39 #include "../Core/Toolbox.h" |
62 | 40 #include "../Core/OrthancException.h" |
0 | 41 #include "../Core/PngWriter.h" |
42 #include "../Core/DicomFormat/DicomString.h" | |
43 #include "../Core/DicomFormat/DicomNullValue.h" | |
79 | 44 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
0 | 45 |
71 | 46 #include <limits> |
47 | |
0 | 48 #include <boost/lexical_cast.hpp> |
49 | |
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50 #include <dcmtk/dcmdata/dcchrstr.h> |
0 | 51 #include <dcmtk/dcmdata/dcdicent.h> |
52 #include <dcmtk/dcmdata/dcdict.h> | |
53 #include <dcmtk/dcmdata/dcfilefo.h> | |
54 #include <dcmtk/dcmdata/dcistrmb.h> | |
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55 #include <dcmtk/dcmdata/dcuid.h> |
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56 |
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57 #include <dcmtk/dcmdata/dcvrae.h> |
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58 #include <dcmtk/dcmdata/dcvras.h> |
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59 #include <dcmtk/dcmdata/dcvrcs.h> |
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60 #include <dcmtk/dcmdata/dcvrda.h> |
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61 #include <dcmtk/dcmdata/dcvrds.h> |
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62 #include <dcmtk/dcmdata/dcvrdt.h> |
0 | 63 #include <dcmtk/dcmdata/dcvrfd.h> |
64 #include <dcmtk/dcmdata/dcvrfl.h> | |
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65 #include <dcmtk/dcmdata/dcvris.h> |
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66 #include <dcmtk/dcmdata/dcvrlo.h> |
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67 #include <dcmtk/dcmdata/dcvrlt.h> |
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68 #include <dcmtk/dcmdata/dcvrpn.h> |
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69 #include <dcmtk/dcmdata/dcvrsh.h> |
0 | 70 #include <dcmtk/dcmdata/dcvrsl.h> |
71 #include <dcmtk/dcmdata/dcvrss.h> | |
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72 #include <dcmtk/dcmdata/dcvrst.h> |
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73 #include <dcmtk/dcmdata/dcvrtm.h> |
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74 #include <dcmtk/dcmdata/dcvrui.h> |
0 | 75 #include <dcmtk/dcmdata/dcvrul.h> |
76 #include <dcmtk/dcmdata/dcvrus.h> | |
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77 #include <dcmtk/dcmdata/dcvrut.h> |
0 | 78 |
2 | 79 #include <boost/math/special_functions/round.hpp> |
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80 #include <glog/logging.h> |
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81 #include <dcmtk/dcmdata/dcostrmb.h> |
0 | 82 |
62 | 83 namespace Orthanc |
0 | 84 { |
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85 ParsedDicomFile::ParsedDicomFile(const std::string& content) |
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86 { |
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87 DcmInputBufferStream is; |
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88 if (content.size() > 0) |
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89 { |
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90 is.setBuffer(&content[0], content.size()); |
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91 } |
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92 is.setEos(); |
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93 |
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94 file_.reset(new DcmFileFormat); |
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95 file_->transferInit(); |
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96 if (!file_->read(is).good()) |
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97 { |
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98 throw OrthancException(ErrorCode_BadFileFormat); |
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99 } |
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100 file_->loadAllDataIntoMemory(); |
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101 file_->transferEnd(); |
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102 } |
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103 |
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104 |
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105 static void SendPathValueForDictionary(RestApiOutput& output, |
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106 DcmItem& dicom) |
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107 { |
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108 Json::Value v = Json::arrayValue; |
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109 |
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110 for (unsigned long i = 0; i < dicom.card(); i++) |
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111 { |
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112 DcmElement* element = dicom.getElement(i); |
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113 if (element) |
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114 { |
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115 char buf[16]; |
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116 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); |
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117 v.append(buf); |
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118 } |
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119 } |
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120 |
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121 output.AnswerJson(v); |
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122 } |
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123 |
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124 static inline uint16_t GetCharValue(char c) |
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125 { |
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126 if (c >= '0' && c <= '9') |
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127 return c - '0'; |
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128 else if (c >= 'a' && c <= 'f') |
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129 return c - 'a' + 10; |
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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 |
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133 return 0; |
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134 } |
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135 |
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136 static inline uint16_t GetTagValue(const char* c) |
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137 { |
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138 return ((GetCharValue(c[0]) << 12) + |
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139 (GetCharValue(c[1]) << 8) + |
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140 (GetCharValue(c[2]) << 4) + |
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141 GetCharValue(c[3])); |
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142 } |
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143 |
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144 static bool ParseTagAndGroup(DcmTagKey& key, |
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145 const std::string& tag) |
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146 { |
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147 if (tag.size() != 9 || |
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148 !isxdigit(tag[0]) || |
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149 !isxdigit(tag[1]) || |
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150 !isxdigit(tag[2]) || |
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151 !isxdigit(tag[3]) || |
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152 tag[4] != '-' || |
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153 !isxdigit(tag[5]) || |
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154 !isxdigit(tag[6]) || |
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155 !isxdigit(tag[7]) || |
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156 !isxdigit(tag[8])) |
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157 { |
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158 return false; |
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159 } |
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160 |
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161 uint16_t group = GetTagValue(tag.c_str()); |
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162 uint16_t element = GetTagValue(tag.c_str() + 5); |
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163 |
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164 key = DcmTagKey(group, element); |
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165 |
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166 return true; |
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167 } |
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168 |
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169 |
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170 static void SendSequence(RestApiOutput& output, |
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171 DcmSequenceOfItems& sequence) |
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172 { |
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173 // This element is a sequence |
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174 Json::Value v = Json::arrayValue; |
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175 |
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176 for (unsigned long i = 0; i < sequence.card(); i++) |
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177 { |
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178 v.append(boost::lexical_cast<std::string>(i)); |
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179 } |
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180 |
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181 output.AnswerJson(v); |
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182 } |
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183 |
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184 static void AnswerDicomField(RestApiOutput& output, |
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185 DcmElement& element) |
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186 { |
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187 // This element is not a sequence |
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188 std::string buffer; |
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189 buffer.resize(65536); |
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190 Uint32 length = element.getLength(); |
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191 Uint32 offset = 0; |
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192 |
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193 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL); |
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194 |
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195 while (offset < length) |
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196 { |
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197 Uint32 nbytes; |
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198 if (length - offset < buffer.size()) |
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199 { |
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200 nbytes = length - offset; |
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201 } |
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202 else |
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203 { |
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204 nbytes = buffer.size(); |
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205 } |
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206 |
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207 if (element.getPartialValue(&buffer[0], offset, nbytes).good()) |
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208 { |
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209 output.GetLowLevelOutput().Send(&buffer[0], nbytes); |
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210 offset += nbytes; |
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211 } |
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212 else |
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213 { |
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214 LOG(ERROR) << "Error while sending a DICOM field"; |
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215 return; |
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216 } |
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217 } |
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218 |
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219 output.MarkLowLevelOutputDone(); |
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220 } |
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221 |
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222 static void SendPathValueForLeaf(RestApiOutput& output, |
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223 const std::string& tag, |
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224 DcmItem& dicom) |
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225 { |
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226 DcmTagKey k; |
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227 if (!ParseTagAndGroup(k, tag)) |
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228 { |
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229 return; |
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230 } |
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231 |
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232 DcmSequenceOfItems* sequence = NULL; |
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233 if (dicom.findAndGetSequence(k, sequence).good() && |
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234 sequence != NULL && |
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235 sequence->getVR() == EVR_SQ) |
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236 { |
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237 SendSequence(output, *sequence); |
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238 return; |
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239 } |
285
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240 |
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241 DcmElement* element = NULL; |
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242 if (dicom.findAndGetElement(k, element).good() && |
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243 element != NULL && |
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244 element->getVR() != EVR_UNKNOWN && |
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245 element->getVR() != EVR_SQ) |
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246 { |
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247 AnswerDicomField(output, *element); |
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248 } |
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249 } |
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250 |
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251 void ParsedDicomFile::SendPathValue(RestApiOutput& output, |
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252 const UriComponents& uri) |
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253 { |
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254 DcmItem* dicom = file_->getDataset(); |
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255 |
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256 // Go down in the tag hierarchy according to the URI |
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257 for (size_t pos = 0; pos < uri.size() / 2; pos++) |
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258 { |
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259 size_t index; |
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260 try |
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261 { |
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262 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); |
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263 } |
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264 catch (boost::bad_lexical_cast&) |
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265 { |
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266 return; |
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267 } |
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268 |
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269 DcmTagKey k; |
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270 DcmItem *child = NULL; |
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271 if (!ParseTagAndGroup(k, uri[2 * pos]) || |
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272 !dicom->findAndGetSequenceItem(k, child, index).good() || |
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273 child == NULL) |
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274 { |
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275 return; |
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276 } |
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277 |
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278 dicom = child; |
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279 } |
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280 |
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281 // We have reached the end of the URI |
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282 if (uri.size() % 2 == 0) |
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283 { |
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284 SendPathValueForDictionary(output, *dicom); |
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285 } |
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286 else |
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287 { |
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288 SendPathValueForLeaf(output, uri.back(), *dicom); |
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289 } |
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290 } |
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291 |
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292 |
302
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293 |
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294 |
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295 |
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296 static DcmElement* CreateElementForTag(const DicomTag& tag) |
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297 { |
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298 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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299 |
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300 switch (key.getEVR()) |
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301 { |
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302 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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303 |
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304 /** |
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305 * TODO. |
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306 **/ |
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307 |
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308 case EVR_OB: // other byte |
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309 case EVR_OF: // other float |
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310 case EVR_OW: // other word |
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311 case EVR_AT: // attribute tag |
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312 throw OrthancException(ErrorCode_NotImplemented); |
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313 |
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314 case EVR_UN: // unknown value representation |
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315 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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316 |
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317 |
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318 /** |
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319 * String types. |
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320 * http://support.dcmtk.org/docs/classDcmByteString.html |
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321 **/ |
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322 |
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323 case EVR_AS: // age string |
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324 return new DcmAgeString(key); |
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325 |
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326 case EVR_AE: // application entity title |
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327 return new DcmApplicationEntity(key); |
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328 |
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329 case EVR_CS: // code string |
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330 return new DcmCodeString(key); |
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331 |
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332 case EVR_DA: // date string |
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333 return new DcmDate(key); |
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334 |
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335 case EVR_DT: // date time string |
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336 return new DcmDateTime(key); |
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337 |
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338 case EVR_DS: // decimal string |
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339 return new DcmDecimalString(key); |
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340 |
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341 case EVR_IS: // integer string |
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342 return new DcmIntegerString(key); |
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343 |
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344 case EVR_TM: // time string |
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345 return new DcmTime(key); |
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346 |
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347 case EVR_UI: // unique identifier |
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348 return new DcmUniqueIdentifier(key); |
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349 |
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350 case EVR_ST: // short text |
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351 return new DcmShortText(key); |
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352 |
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353 case EVR_LO: // long string |
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354 return new DcmLongString(key); |
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355 |
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356 case EVR_LT: // long text |
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357 return new DcmLongText(key); |
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358 |
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359 case EVR_UT: // unlimited text |
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360 return new DcmUnlimitedText(key); |
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361 |
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362 case EVR_SH: // short string |
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363 return new DcmShortString(key); |
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364 |
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365 case EVR_PN: // person name |
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366 return new DcmPersonName(key); |
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367 |
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368 |
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369 /** |
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370 * Numerical types |
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371 **/ |
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372 |
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373 case EVR_SL: // signed long |
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374 return new DcmSignedLong(key); |
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375 |
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376 case EVR_SS: // signed short |
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377 return new DcmSignedShort(key); |
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378 |
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379 case EVR_UL: // unsigned long |
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380 return new DcmUnsignedLong(key); |
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381 |
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382 case EVR_US: // unsigned short |
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383 return new DcmUnsignedShort(key); |
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384 |
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385 case EVR_FL: // float single-precision |
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386 return new DcmFloatingPointSingle(key); |
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387 |
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388 case EVR_FD: // float double-precision |
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389 return new DcmFloatingPointDouble(key); |
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390 |
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391 |
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392 /** |
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393 * Sequence types, should never occur at this point. |
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394 **/ |
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395 |
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396 case EVR_SQ: // sequence of items |
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397 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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398 |
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399 |
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400 /** |
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401 * Internal to DCMTK. |
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402 **/ |
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403 |
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404 case EVR_ox: // OB or OW depending on context |
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405 case EVR_xs: // SS or US depending on context |
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406 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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407 case EVR_na: // na="not applicable", for data which has no VR |
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408 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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409 case EVR_item: // used internally for items |
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410 case EVR_metainfo: // used internally for meta info datasets |
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411 case EVR_dataset: // used internally for datasets |
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412 case EVR_fileFormat: // used internally for DICOM files |
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413 case EVR_dicomDir: // used internally for DICOMDIR objects |
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414 case EVR_dirRecord: // used internally for DICOMDIR records |
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415 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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416 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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417 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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418 case EVR_PixelData: // used internally for uncompressed pixeld data |
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419 case EVR_OverlayData: // used internally for overlay data |
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420 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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421 default: |
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422 break; |
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423 } |
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424 |
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425 throw OrthancException(ErrorCode_InternalError); |
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426 } |
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427 |
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428 |
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429 |
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430 static void FillElementWithString(DcmElement& element, |
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431 const DicomTag& tag, |
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432 const std::string& value) |
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433 { |
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434 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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435 bool ok = false; |
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436 |
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437 try |
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438 { |
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439 switch (key.getEVR()) |
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440 { |
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441 // http://support.dcmtk.org/docs/dcvr_8h-source.html |
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442 |
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443 /** |
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444 * TODO. |
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445 **/ |
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446 |
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447 case EVR_OB: // other byte |
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448 case EVR_OF: // other float |
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449 case EVR_OW: // other word |
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450 case EVR_AT: // attribute tag |
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451 throw OrthancException(ErrorCode_NotImplemented); |
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452 |
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453 case EVR_UN: // unknown value representation |
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454 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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455 |
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456 |
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457 /** |
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458 * String types. |
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459 **/ |
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460 |
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461 case EVR_DS: // decimal string |
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462 case EVR_IS: // integer string |
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463 case EVR_AS: // age string |
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464 case EVR_DA: // date string |
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465 case EVR_DT: // date time string |
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466 case EVR_TM: // time string |
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467 case EVR_AE: // application entity title |
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468 case EVR_CS: // code string |
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469 case EVR_SH: // short string |
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470 case EVR_LO: // long string |
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471 case EVR_ST: // short text |
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472 case EVR_LT: // long text |
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473 case EVR_UT: // unlimited text |
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474 case EVR_PN: // person name |
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475 case EVR_UI: // unique identifier |
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476 { |
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477 ok = element.putString(value.c_str()).good(); |
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478 break; |
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479 } |
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480 |
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481 |
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482 /** |
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483 * Numerical types |
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484 **/ |
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485 |
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486 case EVR_SL: // signed long |
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487 { |
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488 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); |
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489 break; |
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490 } |
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491 |
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492 case EVR_SS: // signed short |
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493 { |
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494 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); |
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495 break; |
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496 } |
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497 |
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498 case EVR_UL: // unsigned long |
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499 { |
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500 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); |
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501 break; |
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502 } |
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503 |
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504 case EVR_US: // unsigned short |
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505 { |
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506 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); |
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507 break; |
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508 } |
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509 |
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510 case EVR_FL: // float single-precision |
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511 { |
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512 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); |
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513 break; |
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514 } |
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515 |
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516 case EVR_FD: // float double-precision |
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517 { |
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518 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); |
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519 break; |
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520 } |
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521 |
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522 |
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523 /** |
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524 * Sequence types, should never occur at this point. |
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525 **/ |
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526 |
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527 case EVR_SQ: // sequence of items |
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528 { |
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529 ok = false; |
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530 break; |
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531 } |
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532 |
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533 |
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534 /** |
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535 * Internal to DCMTK. |
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536 **/ |
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537 |
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538 case EVR_ox: // OB or OW depending on context |
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539 case EVR_xs: // SS or US depending on context |
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540 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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541 case EVR_na: // na="not applicable", for data which has no VR |
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542 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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543 case EVR_item: // used internally for items |
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544 case EVR_metainfo: // used internally for meta info datasets |
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545 case EVR_dataset: // used internally for datasets |
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546 case EVR_fileFormat: // used internally for DICOM files |
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547 case EVR_dicomDir: // used internally for DICOMDIR objects |
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548 case EVR_dirRecord: // used internally for DICOMDIR records |
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549 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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550 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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551 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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552 case EVR_PixelData: // used internally for uncompressed pixeld data |
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553 case EVR_OverlayData: // used internally for overlay data |
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554 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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555 default: |
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556 break; |
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557 } |
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558 } |
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559 catch (boost::bad_lexical_cast&) |
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560 { |
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561 ok = false; |
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562 } |
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563 |
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564 if (!ok) |
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565 { |
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566 throw OrthancException(ErrorCode_InternalError); |
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567 } |
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568 } |
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569 |
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570 |
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571 void ParsedDicomFile::Remove(const DicomTag& tag) |
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572 { |
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573 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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574 |
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575 // TODO This call results in memory leaks inside DCMTK |
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576 file_->getDataset()->remove(key); |
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577 } |
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578 |
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579 |
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580 |
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581 void ParsedDicomFile::Insert(const DicomTag& tag, |
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582 const std::string& value) |
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583 { |
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584 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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585 FillElementWithString(*element, tag, value); |
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586 |
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587 if (!file_->getDataset()->insert(element.release(), false, false).good()) |
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588 { |
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589 // This field already exists |
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590 throw OrthancException(ErrorCode_InternalError); |
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591 } |
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592 } |
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593 |
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594 |
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595 void ParsedDicomFile::ReplaceInternal(const DicomTag& tag, |
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596 const std::string& value, |
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597 bool insertOnAbsent) |
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598 { |
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599 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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600 DcmElement* element = NULL; |
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601 |
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602 if (!file_->getDataset()->findAndGetElement(key, element).good() || |
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603 element == NULL) |
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604 { |
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605 if (insertOnAbsent) |
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606 { |
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607 // This field does not exist, use "Insert()" instead |
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608 Insert(tag, value); |
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609 } |
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610 else |
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611 { |
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612 throw OrthancException(ErrorCode_InternalError); |
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613 } |
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614 } |
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615 else |
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616 { |
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617 FillElementWithString(*element, tag, value); |
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618 } |
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619 } |
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620 |
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621 |
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622 void ParsedDicomFile::Replace(const DicomTag& tag, |
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623 const std::string& value) |
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624 { |
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625 return ReplaceInternal(tag, value, false); |
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626 } |
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627 |
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628 void ParsedDicomFile::InsertOrReplace(const DicomTag& tag, |
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629 const std::string& value) |
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630 { |
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631 return ReplaceInternal(tag, value, true); |
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632 } |
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633 |
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634 |
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635 |
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636 void ParsedDicomFile::Answer(RestApiOutput& output) |
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637 { |
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638 std::string serialized; |
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639 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset())) |
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640 { |
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641 output.AnswerBuffer(serialized, "application/octet-stream"); |
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642 } |
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643 } |
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644 |
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645 |
0 | 646 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
647 { | |
648 target.Clear(); | |
649 for (unsigned long i = 0; i < dataset.card(); i++) | |
650 { | |
651 DcmElement* element = dataset.getElement(i); | |
652 if (element && element->isLeaf()) | |
653 { | |
654 target.SetValue(element->getTag().getGTag(), | |
655 element->getTag().getETag(), | |
656 ConvertLeafElement(*element)); | |
657 } | |
658 } | |
659 } | |
660 | |
661 | |
662 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
663 { | |
664 return DicomTag(element.getGTag(), element.getETag()); | |
665 } | |
666 | |
667 | |
668 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
669 { | |
670 if (!element.isLeaf()) | |
671 { | |
62 | 672 throw OrthancException("Only applicable to leaf elements"); |
0 | 673 } |
674 | |
675 if (element.isaString()) | |
676 { | |
677 char *c; | |
678 if (element.getString(c).good() && | |
679 c != NULL) | |
680 { | |
681 std::string s(c); | |
107
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682 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 683 return new DicomString(utf8); |
684 } | |
685 else | |
686 { | |
687 return new DicomNullValue; | |
688 } | |
689 } | |
690 | |
691 try | |
692 { | |
693 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
694 switch (element.getVR()) | |
695 { | |
696 | |
697 /** | |
698 * TODO. | |
699 **/ | |
700 | |
302
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701 case EVR_DS: // decimal string |
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702 case EVR_IS: // integer string |
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703 case EVR_OB: // other byte |
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704 case EVR_OF: // other float |
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705 case EVR_OW: // other word |
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706 case EVR_AS: // age string |
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707 case EVR_AT: // attribute tag |
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|
708 case EVR_DA: // date string |
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|
709 case EVR_DT: // date time string |
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diff
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|
710 case EVR_TM: // time string |
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diff
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|
711 case EVR_UN: // unknown value representation |
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diff
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|
712 return new DicomNullValue(); |
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diff
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|
713 |
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diff
changeset
|
714 |
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diff
changeset
|
715 /** |
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|
716 * String types, should never happen at this point because of |
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diff
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|
717 * "element.isaString()". |
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|
718 **/ |
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diff
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|
719 |
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|
720 case EVR_AE: // application entity title |
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diff
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|
721 case EVR_CS: // code string |
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diff
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722 case EVR_SH: // short string |
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|
723 case EVR_LO: // long string |
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diff
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|
724 case EVR_ST: // short text |
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diff
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|
725 case EVR_LT: // long text |
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diff
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|
726 case EVR_UT: // unlimited text |
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diff
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|
727 case EVR_PN: // person name |
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diff
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|
728 case EVR_UI: // unique identifier |
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diff
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|
729 return new DicomNullValue(); |
0 | 730 |
731 | |
302
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|
732 /** |
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|
733 * Numerical types |
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|
734 **/ |
0 | 735 |
302
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|
736 case EVR_SL: // signed long |
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diff
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|
737 { |
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|
738 Sint32 f; |
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739 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) |
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|
740 { |
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741 return new DicomString(boost::lexical_cast<std::string>(f)); |
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742 } |
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|
743 else |
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|
744 { |
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|
745 return new DicomNullValue(); |
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|
746 } |
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|
747 } |
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|
748 |
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749 case EVR_SS: // signed short |
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|
750 { |
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|
751 Sint16 f; |
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752 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) |
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|
753 { |
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754 return new DicomString(boost::lexical_cast<std::string>(f)); |
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|
755 } |
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|
756 else |
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|
757 { |
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|
758 return new DicomNullValue(); |
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|
759 } |
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diff
changeset
|
760 } |
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diff
changeset
|
761 |
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|
762 case EVR_UL: // unsigned long |
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|
763 { |
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|
764 Uint32 f; |
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765 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) |
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|
766 { |
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767 return new DicomString(boost::lexical_cast<std::string>(f)); |
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diff
changeset
|
768 } |
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changeset
|
769 else |
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diff
changeset
|
770 { |
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changeset
|
771 return new DicomNullValue(); |
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diff
changeset
|
772 } |
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diff
changeset
|
773 } |
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diff
changeset
|
774 |
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|
775 case EVR_US: // unsigned short |
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|
776 { |
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changeset
|
777 Uint16 f; |
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778 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) |
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diff
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|
779 { |
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changeset
|
780 return new DicomString(boost::lexical_cast<std::string>(f)); |
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diff
changeset
|
781 } |
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291
diff
changeset
|
782 else |
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291
diff
changeset
|
783 { |
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291
diff
changeset
|
784 return new DicomNullValue(); |
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diff
changeset
|
785 } |
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291
diff
changeset
|
786 } |
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291
diff
changeset
|
787 |
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diff
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|
788 case EVR_FL: // float single-precision |
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diff
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|
789 { |
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diff
changeset
|
790 Float32 f; |
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|
791 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) |
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diff
changeset
|
792 { |
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291
diff
changeset
|
793 return new DicomString(boost::lexical_cast<std::string>(f)); |
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291
diff
changeset
|
794 } |
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291
diff
changeset
|
795 else |
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parents:
291
diff
changeset
|
796 { |
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291
diff
changeset
|
797 return new DicomNullValue(); |
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291
diff
changeset
|
798 } |
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291
diff
changeset
|
799 } |
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291
diff
changeset
|
800 |
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diff
changeset
|
801 case EVR_FD: // float double-precision |
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diff
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|
802 { |
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diff
changeset
|
803 Float64 f; |
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diff
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|
804 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) |
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diff
changeset
|
805 { |
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diff
changeset
|
806 return new DicomString(boost::lexical_cast<std::string>(f)); |
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291
diff
changeset
|
807 } |
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parents:
291
diff
changeset
|
808 else |
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parents:
291
diff
changeset
|
809 { |
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291
diff
changeset
|
810 return new DicomNullValue(); |
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291
diff
changeset
|
811 } |
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291
diff
changeset
|
812 } |
0 | 813 |
814 | |
815 /** | |
302
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diff
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|
816 * Sequence types, should never occur at this point because of |
238134081136
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parents:
291
diff
changeset
|
817 * "element.isLeaf()". |
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diff
changeset
|
818 **/ |
0 | 819 |
302
238134081136
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291
diff
changeset
|
820 case EVR_SQ: // sequence of items |
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diff
changeset
|
821 return new DicomNullValue; |
0 | 822 |
823 | |
302
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diff
changeset
|
824 /** |
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diff
changeset
|
825 * Internal to DCMTK. |
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diff
changeset
|
826 **/ |
0 | 827 |
302
238134081136
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291
diff
changeset
|
828 case EVR_ox: // OB or OW depending on context |
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diff
changeset
|
829 case EVR_xs: // SS or US depending on context |
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291
diff
changeset
|
830 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) |
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diff
changeset
|
831 case EVR_na: // na="not applicable", for data which has no VR |
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291
diff
changeset
|
832 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor |
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diff
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|
833 case EVR_item: // used internally for items |
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diff
changeset
|
834 case EVR_metainfo: // used internally for meta info datasets |
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291
diff
changeset
|
835 case EVR_dataset: // used internally for datasets |
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291
diff
changeset
|
836 case EVR_fileFormat: // used internally for DICOM files |
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291
diff
changeset
|
837 case EVR_dicomDir: // used internally for DICOMDIR objects |
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291
diff
changeset
|
838 case EVR_dirRecord: // used internally for DICOMDIR records |
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291
diff
changeset
|
839 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image |
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291
diff
changeset
|
840 case EVR_pixelItem: // used internally for pixel items in a compressed image |
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parents:
291
diff
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|
841 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) |
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842 case EVR_PixelData: // used internally for uncompressed pixeld data |
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843 case EVR_OverlayData: // used internally for overlay data |
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844 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR |
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845 return new DicomNullValue; |
0 | 846 |
847 | |
302
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848 /** |
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849 * Default case. |
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850 **/ |
0 | 851 |
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852 default: |
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853 return new DicomNullValue; |
0 | 854 } |
855 } | |
856 catch (boost::bad_lexical_cast) | |
857 { | |
858 return new DicomNullValue; | |
859 } | |
860 } | |
861 | |
862 | |
863 static void StoreElement(Json::Value& target, | |
864 DcmElement& element, | |
865 unsigned int maxStringLength); | |
866 | |
867 static void StoreItem(Json::Value& target, | |
868 DcmItem& item, | |
869 unsigned int maxStringLength) | |
870 { | |
871 target = Json::Value(Json::objectValue); | |
872 | |
873 for (unsigned long i = 0; i < item.card(); i++) | |
874 { | |
875 DcmElement* element = item.getElement(i); | |
876 StoreElement(target, *element, maxStringLength); | |
877 } | |
878 } | |
879 | |
880 | |
881 static void StoreElement(Json::Value& target, | |
882 DcmElement& element, | |
883 unsigned int maxStringLength) | |
884 { | |
885 assert(target.type() == Json::objectValue); | |
886 | |
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887 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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888 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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889 const std::string formattedTag = tag.Format(); |
0 | 890 |
891 if (element.isLeaf()) | |
892 { | |
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893 Json::Value value(Json::objectValue); |
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894 value["Name"] = tagName; |
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895 |
0 | 896 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
897 if (v->IsNull()) | |
898 { | |
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899 value["Type"] = "Null"; |
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900 value["Value"] = Json::nullValue; |
0 | 901 } |
902 else | |
903 { | |
904 std::string s = v->AsString(); | |
905 if (maxStringLength == 0 || | |
906 s.size() <= maxStringLength) | |
907 { | |
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908 value["Type"] = "String"; |
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909 value["Value"] = s; |
0 | 910 } |
911 else | |
912 { | |
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913 value["Type"] = "TooLong"; |
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914 value["Value"] = Json::nullValue; |
0 | 915 } |
916 } | |
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917 |
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918 target[formattedTag] = value; |
0 | 919 } |
920 else | |
921 { | |
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922 Json::Value children(Json::arrayValue); |
0 | 923 |
924 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
925 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
926 // etc. are not." The following cast is thus OK. | |
927 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
928 | |
929 for (unsigned long i = 0; i < sequence.card(); i++) | |
930 { | |
931 DcmItem* child = sequence.getItem(i); | |
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932 Json::Value& v = children.append(Json::objectValue); |
0 | 933 StoreItem(v, *child, maxStringLength); |
934 } | |
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935 |
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936 target[formattedTag]["Name"] = tagName; |
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937 target[formattedTag]["Type"] = "Sequence"; |
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938 target[formattedTag]["Value"] = children; |
0 | 939 } |
940 } | |
941 | |
942 | |
943 void FromDcmtkBridge::ToJson(Json::Value& root, | |
944 DcmDataset& dataset, | |
945 unsigned int maxStringLength) | |
946 { | |
947 StoreItem(root, dataset, maxStringLength); | |
948 } | |
949 | |
950 | |
951 | |
952 void FromDcmtkBridge::ToJson(Json::Value& target, | |
953 const std::string& path, | |
954 unsigned int maxStringLength) | |
955 { | |
956 DcmFileFormat dicom; | |
957 if (!dicom.loadFile(path.c_str()).good()) | |
958 { | |
62 | 959 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 960 } |
961 else | |
962 { | |
963 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
964 } | |
965 } | |
966 | |
967 | |
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968 static void ExtractPngImagePreview(std::string& result, |
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969 DicomIntegerPixelAccessor& accessor) |
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970 { |
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971 PngWriter w; |
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972 |
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973 int32_t min, max; |
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974 accessor.GetExtremeValues(min, max); |
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975 |
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976 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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977 if (min != max) |
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978 { |
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979 uint8_t* pixel = &image[0]; |
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980 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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981 { |
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982 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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983 { |
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984 int32_t v = accessor.GetValue(x, y); |
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985 *pixel = static_cast<uint8_t>( |
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986 boost::math::lround(static_cast<float>(v - min) / |
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987 static_cast<float>(max - min) * 255.0f)); |
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988 } |
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989 } |
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990 } |
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991 |
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992 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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993 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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994 } |
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995 |
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996 |
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997 template <typename T> |
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998 static void ExtractPngImageTruncate(std::string& result, |
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999 DicomIntegerPixelAccessor& accessor, |
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1000 PixelFormat format) |
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1001 { |
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1002 PngWriter w; |
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1003 |
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1004 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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1005 T* pixel = &image[0]; |
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1006 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1007 { |
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1008 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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1009 { |
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1010 int32_t v = accessor.GetValue(x, y); |
73 | 1011 if (v < std::numeric_limits<T>::min()) |
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1012 *pixel = std::numeric_limits<T>::min(); |
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1013 else if (v > std::numeric_limits<T>::max()) |
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1014 *pixel = std::numeric_limits<T>::max(); |
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1015 else |
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1016 *pixel = static_cast<T>(v); |
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1017 } |
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1018 } |
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1019 |
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1020 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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1021 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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1022 } |
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1023 |
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1024 |
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1025 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1026 DcmDataset& dataset, |
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1027 unsigned int frame, |
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1028 ImageExtractionMode mode) |
0 | 1029 { |
1030 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
1031 | |
1032 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
1033 | |
1034 DicomMap m; | |
1035 FromDcmtkBridge::Convert(m, dataset); | |
1036 | |
1037 DcmElement* e; | |
80 | 1038 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 1039 e != NULL) |
1040 { | |
1041 Uint8* pixData = NULL; | |
1042 if (e->getUint8Array(pixData) == EC_Normal) | |
1043 { | |
1044 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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1045 accessor->SetCurrentFrame(frame); |
0 | 1046 } |
1047 } | |
1048 | |
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1049 PixelFormat format; |
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1050 switch (mode) |
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1051 { |
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1052 case ImageExtractionMode_Preview: |
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1053 case ImageExtractionMode_UInt8: |
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1054 format = PixelFormat_Grayscale8; |
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1055 break; |
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1056 |
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1057 case ImageExtractionMode_UInt16: |
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1058 format = PixelFormat_Grayscale16; |
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1059 break; |
42
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1060 |
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1061 default: |
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1062 throw OrthancException(ErrorCode_NotImplemented); |
42
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1063 } |
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1064 |
0 | 1065 if (accessor.get() == NULL || |
1066 accessor->GetWidth() == 0 || | |
1067 accessor->GetHeight() == 0) | |
1068 { | |
42
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1069 PngWriter w; |
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1070 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 1071 } |
1072 else | |
1073 { | |
42
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1074 switch (mode) |
0 | 1075 { |
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1076 case ImageExtractionMode_Preview: |
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1077 ExtractPngImagePreview(result, *accessor); |
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1078 break; |
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1079 |
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1080 case ImageExtractionMode_UInt8: |
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1081 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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1082 break; |
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1083 |
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1084 case ImageExtractionMode_UInt16: |
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1085 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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1086 break; |
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1087 |
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1088 default: |
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1089 throw OrthancException(ErrorCode_NotImplemented); |
0 | 1090 } |
1091 } | |
1092 } | |
1093 | |
1094 | |
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1095 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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1096 const std::string& dicomContent, |
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1097 unsigned int frame, |
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1098 ImageExtractionMode mode) |
0 | 1099 { |
1100 DcmInputBufferStream is; | |
1101 if (dicomContent.size() > 0) | |
1102 { | |
1103 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
1104 } | |
1105 is.setEos(); | |
1106 | |
1107 DcmFileFormat dicom; | |
1108 if (dicom.read(is).good()) | |
1109 { | |
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1110 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 1111 } |
1112 else | |
1113 { | |
62 | 1114 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 1115 } |
1116 } | |
1117 | |
1118 | |
1119 | |
1120 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
1121 { | |
106 | 1122 // Some patches for important tags because of different DICOM |
1123 // dictionaries between DCMTK versions | |
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1124 std::string n = t.GetMainTagsName(); |
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1125 if (n.size() != 0) |
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1126 { |
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1127 return n; |
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1128 } |
106 | 1129 // End of patches |
1130 | |
0 | 1131 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
1132 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1133 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
1134 | |
1135 std::string s("Unknown"); | |
1136 if (entry != NULL) | |
1137 { | |
1138 s = std::string(entry->getTagName()); | |
1139 } | |
1140 | |
1141 dcmDataDict.unlock(); | |
1142 return s; | |
1143 } | |
1144 | |
1145 | |
1146 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
1147 { | |
1148 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1149 const DcmDictEntry* entry = dict.findEntry(name); | |
1150 | |
1151 if (entry == NULL) | |
1152 { | |
1153 dcmDataDict.unlock(); | |
62 | 1154 throw OrthancException("Unknown DICOM tag"); |
0 | 1155 } |
1156 else | |
1157 { | |
1158 DcmTagKey key = entry->getKey(); | |
1159 DicomTag tag(key.getGroup(), key.getElement()); | |
1160 dcmDataDict.unlock(); | |
1161 return tag; | |
1162 } | |
1163 } | |
1164 | |
1165 | |
1166 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
1167 { | |
1168 for (DicomMap::Map::const_iterator | |
1169 it = m.map_.begin(); it != m.map_.end(); it++) | |
1170 { | |
1171 DicomTag t = it->first; | |
1172 std::string s = it->second->AsString(); | |
1173 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
1174 } | |
1175 } | |
1176 | |
1177 | |
1178 void FromDcmtkBridge::ToJson(Json::Value& result, | |
1179 const DicomMap& values) | |
1180 { | |
1181 if (result.type() != Json::objectValue) | |
1182 { | |
62 | 1183 throw OrthancException(ErrorCode_BadParameterType); |
0 | 1184 } |
1185 | |
1186 result.clear(); | |
1187 | |
1188 for (DicomMap::Map::const_iterator | |
1189 it = values.map_.begin(); it != values.map_.end(); it++) | |
1190 { | |
1191 result[GetName(it->first)] = it->second->AsString(); | |
1192 } | |
1193 } | |
176 | 1194 |
1195 | |
1196 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
1197 { | |
1198 char uid[100]; | |
1199 | |
1200 switch (level) | |
1201 { | |
302
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1202 case DicomRootLevel_Instance: |
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1203 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); |
176 | 1204 |
302
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1205 case DicomRootLevel_Series: |
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1206 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); |
176 | 1207 |
302
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1208 case DicomRootLevel_Study: |
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1209 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); |
176 | 1210 |
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1211 default: |
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1212 throw OrthancException(ErrorCode_ParameterOutOfRange); |
176 | 1213 } |
1214 } | |
1215 | |
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1216 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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1217 DcmDataset* dataSet) |
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1218 { |
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1219 // Determine the transfer syntax which shall be used to write the |
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1220 // information to the file. We always switch to the Little Endian |
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1221 // syntax, with explicit length. |
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1222 |
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1223 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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1224 E_TransferSyntax xfer = EXS_LittleEndianExplicit; |
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1225 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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1226 |
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1227 uint32_t s = dataSet->getLength(xfer, encodingType); |
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1228 |
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1229 buffer.resize(s); |
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1230 DcmOutputBufferStream ob(&buffer[0], s); |
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1231 |
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1232 dataSet->transferInit(); |
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1233 |
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1234 #if DCMTK_VERSION_NUMBER >= 360 |
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1235 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL, |
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1236 /*opt_groupLength*/ EGL_recalcGL, |
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1237 /*opt_paddingType*/ EPD_withoutPadding); |
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1238 #else |
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1239 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL); |
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1240 #endif |
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1241 |
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1242 dataSet->transferEnd(); |
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1243 if (c.good()) |
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1244 { |
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1245 return true; |
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1246 } |
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1247 else |
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1248 { |
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1249 buffer.clear(); |
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1250 return false; |
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1251 } |
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1252 |
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1253 #if 0 |
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1254 OFCondition cond = cbdata->dcmff->saveFile(fileName.c_str(), xfer, |
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1255 encodingType, |
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1256 /*opt_groupLength*/ EGL_recalcGL, |
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1257 /*opt_paddingType*/ EPD_withoutPadding, |
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1258 OFstatic_cast(Uint32, /*opt_filepad*/ 0), |
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1259 OFstatic_cast(Uint32, /*opt_itempad*/ 0), |
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1260 (opt_useMetaheader) ? EWM_fileformat : EWM_dataset); |
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1261 #endif |
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1262 } |
0 | 1263 } |