Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 285:4031f73fe0e4
access to the raw dicom tags
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 12 Dec 2012 17:53:14 +0100 |
| parents | 81f11fb357f2 |
| children | 4d7469f72a0b |
| rev | line source |
|---|---|
| 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 | |
| 50 #include <dcmtk/dcmdata/dcdicent.h> | |
| 51 #include <dcmtk/dcmdata/dcdict.h> | |
| 52 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 53 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 54 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 55 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 56 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 57 #include <dcmtk/dcmdata/dcvrss.h> | |
| 58 #include <dcmtk/dcmdata/dcvrul.h> | |
| 59 #include <dcmtk/dcmdata/dcvrus.h> | |
| 176 | 60 #include <dcmtk/dcmdata/dcuid.h> |
| 0 | 61 |
| 2 | 62 #include <boost/math/special_functions/round.hpp> |
| 0 | 63 |
| 62 | 64 namespace Orthanc |
| 0 | 65 { |
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66 ParsedDicomFile::ParsedDicomFile(const std::string& content) |
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67 { |
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68 DcmInputBufferStream is; |
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69 if (content.size() > 0) |
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70 { |
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71 is.setBuffer(&content[0], content.size()); |
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72 } |
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73 is.setEos(); |
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74 |
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75 file_.reset(new DcmFileFormat); |
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76 if (!file_->read(is).good()) |
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77 { |
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78 throw OrthancException(ErrorCode_BadFileFormat); |
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79 } |
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80 } |
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81 |
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82 |
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83 static void SendPathValueForDictionary(RestApiOutput& output, |
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84 DcmItem& dicom) |
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85 { |
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86 Json::Value v = Json::arrayValue; |
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87 |
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88 for (unsigned long i = 0; i < dicom.card(); i++) |
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89 { |
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90 DcmElement* element = dicom.getElement(i); |
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91 if (element) |
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92 { |
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93 char buf[16]; |
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94 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); |
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95 v.append(buf); |
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96 } |
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97 } |
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98 |
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99 output.AnswerJson(v); |
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100 } |
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101 |
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102 static inline uint16_t GetCharValue(char c) |
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103 { |
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104 if (c >= '0' && c <= '9') |
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105 return c - '0'; |
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106 else if (c >= 'a' && c <= 'f') |
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107 return c - 'a' + 10; |
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108 else if (c >= 'A' && c <= 'F') |
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109 return c - 'A' + 10; |
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110 else |
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111 return 0; |
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112 } |
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113 |
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114 static inline uint16_t GetTagValue(const char* c) |
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115 { |
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116 return ((GetCharValue(c[0]) << 12) + |
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117 (GetCharValue(c[1]) << 8) + |
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118 (GetCharValue(c[2]) << 4) + |
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119 GetCharValue(c[3])); |
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120 } |
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121 |
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122 static bool ParseTagAndGroup(DcmTagKey& key, |
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123 const std::string& tag) |
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124 { |
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125 if (tag.size() != 9 || |
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126 !isxdigit(tag[0]) || |
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127 !isxdigit(tag[1]) || |
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128 !isxdigit(tag[2]) || |
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129 !isxdigit(tag[3]) || |
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130 tag[4] != '-' || |
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131 !isxdigit(tag[5]) || |
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132 !isxdigit(tag[6]) || |
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133 !isxdigit(tag[7]) || |
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134 !isxdigit(tag[8])) |
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135 { |
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136 return false; |
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137 } |
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138 |
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139 uint16_t group = GetTagValue(tag.c_str()); |
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140 uint16_t element = GetTagValue(tag.c_str() + 5); |
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141 |
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142 key = DcmTagKey(group, element); |
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143 |
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144 return true; |
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145 } |
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146 |
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147 static void SendPathValueForLeaf(RestApiOutput& output, |
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148 const std::string& tag, |
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149 DcmItem& dicom) |
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150 { |
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151 DcmTagKey k; |
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152 if (!ParseTagAndGroup(k, tag)) |
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153 { |
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154 return; |
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155 } |
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156 |
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157 DcmElement* element = NULL; |
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158 if (dicom.findAndGetElement(k, element).good() && element != NULL) |
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159 { |
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160 if (element->getVR() == EVR_SQ) |
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161 { |
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162 // This element is a sequence |
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163 Json::Value v = Json::arrayValue; |
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164 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(*element); |
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165 |
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166 for (unsigned long i = 0; i < sequence.card(); i++) |
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167 { |
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168 v.append(boost::lexical_cast<std::string>(i)); |
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169 } |
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170 |
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171 output.AnswerJson(v); |
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172 } |
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173 else |
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174 { |
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175 // This element is not a sequence |
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176 std::string buffer; |
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177 buffer.resize(65536); |
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178 Uint32 length = element->getLength(); |
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179 Uint32 offset = 0; |
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180 |
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181 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL); |
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182 |
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183 while (offset < length) |
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184 { |
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185 Uint32 nbytes; |
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186 if (length - offset < buffer.size()) |
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187 { |
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188 nbytes = length - offset; |
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189 } |
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190 else |
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191 { |
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192 nbytes = buffer.size(); |
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193 } |
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194 |
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195 if (element->getPartialValue(&buffer[0], offset, nbytes).good()) |
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196 { |
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197 output.GetLowLevelOutput().Send(&buffer[0], nbytes); |
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198 offset += nbytes; |
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199 } |
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200 else |
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201 { |
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202 return; |
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203 } |
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204 } |
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205 |
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206 output.MarkLowLevelOutputDone(); |
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207 } |
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208 } |
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209 } |
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210 |
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211 void ParsedDicomFile::SendPathValue(RestApiOutput& output, |
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212 const UriComponents& uri) |
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213 { |
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214 DcmItem* dicom = file_->getDataset(); |
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215 |
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216 // Go down in the tag hierarchy according to the URI |
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217 for (size_t pos = 0; pos < uri.size() / 2; pos++) |
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218 { |
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219 size_t index; |
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220 try |
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221 { |
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222 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); |
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223 } |
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224 catch (boost::bad_lexical_cast&) |
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225 { |
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226 return; |
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227 } |
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228 |
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229 DcmTagKey k; |
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230 DcmItem *child = NULL; |
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231 if (!ParseTagAndGroup(k, uri[2 * pos]) || |
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232 !dicom->findAndGetSequenceItem(k, child, index).good() || |
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233 child == NULL) |
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234 { |
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235 return; |
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236 } |
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237 |
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238 dicom = child; |
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239 } |
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240 |
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241 // We have reached the end of the URI |
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242 if (uri.size() % 2 == 0) |
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243 { |
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244 SendPathValueForDictionary(output, *dicom); |
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245 } |
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246 else |
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247 { |
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248 SendPathValueForLeaf(output, uri.back(), *dicom); |
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249 } |
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250 } |
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251 |
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252 |
| 0 | 253 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 254 { | |
| 255 target.Clear(); | |
| 256 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 257 { | |
| 258 DcmElement* element = dataset.getElement(i); | |
| 259 if (element && element->isLeaf()) | |
| 260 { | |
| 261 target.SetValue(element->getTag().getGTag(), | |
| 262 element->getTag().getETag(), | |
| 263 ConvertLeafElement(*element)); | |
| 264 } | |
| 265 } | |
| 266 } | |
| 267 | |
| 268 | |
| 269 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 270 { | |
| 271 return DicomTag(element.getGTag(), element.getETag()); | |
| 272 } | |
| 273 | |
| 274 | |
| 275 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 276 { | |
| 277 if (!element.isLeaf()) | |
| 278 { | |
| 62 | 279 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 280 } |
| 281 | |
| 282 if (element.isaString()) | |
| 283 { | |
| 284 char *c; | |
| 285 if (element.getString(c).good() && | |
| 286 c != NULL) | |
| 287 { | |
| 288 std::string s(c); | |
|
107
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289 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 290 return new DicomString(utf8); |
| 291 } | |
| 292 else | |
| 293 { | |
| 294 return new DicomNullValue; | |
| 295 } | |
| 296 } | |
| 297 | |
| 298 try | |
| 299 { | |
| 300 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 301 switch (element.getVR()) | |
| 302 { | |
| 303 | |
| 304 /** | |
| 305 * TODO. | |
| 306 **/ | |
| 307 | |
| 308 case EVR_DS: // decimal string | |
| 309 case EVR_IS: // integer string | |
| 310 case EVR_OB: // other byte | |
| 311 case EVR_OF: // other float | |
| 312 case EVR_OW: // other word | |
| 313 case EVR_AS: // age string | |
| 314 case EVR_AT: // attribute tag | |
| 315 case EVR_DA: // date string | |
| 316 case EVR_DT: // date time string | |
| 317 case EVR_TM: // time string | |
| 318 case EVR_UN: // unknown value representation | |
| 319 return new DicomNullValue(); | |
| 320 | |
| 321 | |
| 322 /** | |
| 323 * String types, should never happen at this point because of | |
| 324 * "element.isaString()". | |
| 325 **/ | |
| 326 | |
| 327 case EVR_AE: // application entity title | |
| 328 case EVR_CS: // code string | |
| 329 case EVR_SH: // short string | |
| 330 case EVR_LO: // long string | |
| 331 case EVR_ST: // short text | |
| 332 case EVR_LT: // long text | |
| 333 case EVR_UT: // unlimited text | |
| 334 case EVR_PN: // person name | |
| 335 case EVR_UI: // unique identifier | |
| 336 return new DicomNullValue(); | |
| 337 | |
| 338 | |
| 339 /** | |
| 340 * Numerical types | |
| 341 **/ | |
| 342 | |
| 343 case EVR_SL: // signed long | |
| 344 { | |
| 345 Sint32 f; | |
| 346 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
| 347 { | |
| 348 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 349 } | |
| 350 else | |
| 351 { | |
| 352 return new DicomNullValue(); | |
| 353 } | |
| 354 } | |
| 355 | |
| 356 case EVR_SS: // signed short | |
| 357 { | |
| 358 Sint16 f; | |
| 359 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
| 360 { | |
| 361 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 362 } | |
| 363 else | |
| 364 { | |
| 365 return new DicomNullValue(); | |
| 366 } | |
| 367 } | |
| 368 | |
| 369 case EVR_UL: // unsigned long | |
| 370 { | |
| 371 Uint32 f; | |
| 372 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
| 373 { | |
| 374 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 375 } | |
| 376 else | |
| 377 { | |
| 378 return new DicomNullValue(); | |
| 379 } | |
| 380 } | |
| 381 | |
| 382 case EVR_US: // unsigned short | |
| 383 { | |
| 384 Uint16 f; | |
| 385 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
| 386 { | |
| 387 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 388 } | |
| 389 else | |
| 390 { | |
| 391 return new DicomNullValue(); | |
| 392 } | |
| 393 } | |
| 394 | |
| 395 case EVR_FL: // float single-precision | |
| 396 { | |
| 397 Float32 f; | |
| 398 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
| 399 { | |
| 400 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 401 } | |
| 402 else | |
| 403 { | |
| 404 return new DicomNullValue(); | |
| 405 } | |
| 406 } | |
| 407 | |
| 408 case EVR_FD: // float double-precision | |
| 409 { | |
| 410 Float64 f; | |
| 411 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
| 412 { | |
| 413 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 414 } | |
| 415 else | |
| 416 { | |
| 417 return new DicomNullValue(); | |
| 418 } | |
| 419 } | |
| 420 | |
| 421 | |
| 422 /** | |
| 423 * Sequence types, should never occur at this point because of | |
| 424 * "element.isLeaf()". | |
| 425 **/ | |
| 426 | |
| 427 case EVR_SQ: // sequence of items | |
| 428 return new DicomNullValue; | |
| 429 | |
| 430 | |
| 431 /** | |
| 432 * Internal to DCMTK. | |
| 433 **/ | |
| 434 | |
| 435 case EVR_ox: // OB or OW depending on context | |
| 436 case EVR_xs: // SS or US depending on context | |
| 437 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 438 case EVR_na: // na="not applicable", for data which has no VR | |
| 439 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 440 case EVR_item: // used internally for items | |
| 441 case EVR_metainfo: // used internally for meta info datasets | |
| 442 case EVR_dataset: // used internally for datasets | |
| 443 case EVR_fileFormat: // used internally for DICOM files | |
| 444 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 445 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 446 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 447 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 448 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 449 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 450 case EVR_OverlayData: // used internally for overlay data | |
| 451 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 452 return new DicomNullValue; | |
| 453 | |
| 454 | |
| 455 /** | |
| 456 * Default case. | |
| 457 **/ | |
| 458 | |
| 459 default: | |
| 460 return new DicomNullValue; | |
| 461 } | |
| 462 } | |
| 463 catch (boost::bad_lexical_cast) | |
| 464 { | |
| 465 return new DicomNullValue; | |
| 466 } | |
| 467 } | |
| 468 | |
| 469 | |
| 470 static void StoreElement(Json::Value& target, | |
| 471 DcmElement& element, | |
| 472 unsigned int maxStringLength); | |
| 473 | |
| 474 static void StoreItem(Json::Value& target, | |
| 475 DcmItem& item, | |
| 476 unsigned int maxStringLength) | |
| 477 { | |
| 478 target = Json::Value(Json::objectValue); | |
| 479 | |
| 480 for (unsigned long i = 0; i < item.card(); i++) | |
| 481 { | |
| 482 DcmElement* element = item.getElement(i); | |
| 483 StoreElement(target, *element, maxStringLength); | |
| 484 } | |
| 485 } | |
| 486 | |
| 487 | |
| 488 static void StoreElement(Json::Value& target, | |
| 489 DcmElement& element, | |
| 490 unsigned int maxStringLength) | |
| 491 { | |
| 492 assert(target.type() == Json::objectValue); | |
| 493 | |
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494 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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495 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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496 const std::string formattedTag = tag.Format(); |
| 0 | 497 |
| 498 if (element.isLeaf()) | |
| 499 { | |
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500 Json::Value value(Json::objectValue); |
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501 value["Name"] = tagName; |
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502 |
| 0 | 503 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 504 if (v->IsNull()) | |
| 505 { | |
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506 value["Type"] = "Null"; |
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507 value["Value"] = Json::nullValue; |
| 0 | 508 } |
| 509 else | |
| 510 { | |
| 511 std::string s = v->AsString(); | |
| 512 if (maxStringLength == 0 || | |
| 513 s.size() <= maxStringLength) | |
| 514 { | |
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515 value["Type"] = "String"; |
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516 value["Value"] = s; |
| 0 | 517 } |
| 518 else | |
| 519 { | |
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520 value["Type"] = "TooLong"; |
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521 value["Value"] = Json::nullValue; |
| 0 | 522 } |
| 523 } | |
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524 |
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525 target[formattedTag] = value; |
| 0 | 526 } |
| 527 else | |
| 528 { | |
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529 Json::Value children(Json::arrayValue); |
| 0 | 530 |
| 531 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 532 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 533 // etc. are not." The following cast is thus OK. | |
| 534 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 535 | |
| 536 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 537 { | |
| 538 DcmItem* child = sequence.getItem(i); | |
|
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539 Json::Value& v = children.append(Json::objectValue); |
| 0 | 540 StoreItem(v, *child, maxStringLength); |
| 541 } | |
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542 |
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543 target[formattedTag]["Name"] = tagName; |
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544 target[formattedTag]["Type"] = "Sequence"; |
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545 target[formattedTag]["Value"] = children; |
| 0 | 546 } |
| 547 } | |
| 548 | |
| 549 | |
| 550 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 551 DcmDataset& dataset, | |
| 552 unsigned int maxStringLength) | |
| 553 { | |
| 554 StoreItem(root, dataset, maxStringLength); | |
| 555 } | |
| 556 | |
| 557 | |
| 558 | |
| 559 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 560 const std::string& path, | |
| 561 unsigned int maxStringLength) | |
| 562 { | |
| 563 DcmFileFormat dicom; | |
| 564 if (!dicom.loadFile(path.c_str()).good()) | |
| 565 { | |
| 62 | 566 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 567 } |
| 568 else | |
| 569 { | |
| 570 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 571 } | |
| 572 } | |
| 573 | |
| 574 | |
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575 static void ExtractPngImagePreview(std::string& result, |
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576 DicomIntegerPixelAccessor& accessor) |
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577 { |
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578 PngWriter w; |
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579 |
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580 int32_t min, max; |
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581 accessor.GetExtremeValues(min, max); |
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582 |
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583 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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584 if (min != max) |
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585 { |
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586 uint8_t* pixel = &image[0]; |
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587 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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588 { |
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589 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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590 { |
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591 int32_t v = accessor.GetValue(x, y); |
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592 *pixel = static_cast<uint8_t>( |
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593 boost::math::lround(static_cast<float>(v - min) / |
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594 static_cast<float>(max - min) * 255.0f)); |
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595 } |
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596 } |
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597 } |
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598 |
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599 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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600 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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601 } |
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602 |
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603 |
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604 template <typename T> |
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605 static void ExtractPngImageTruncate(std::string& result, |
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606 DicomIntegerPixelAccessor& accessor, |
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607 PixelFormat format) |
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608 { |
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609 PngWriter w; |
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610 |
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611 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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612 T* pixel = &image[0]; |
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613 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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614 { |
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615 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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616 { |
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617 int32_t v = accessor.GetValue(x, y); |
| 73 | 618 if (v < std::numeric_limits<T>::min()) |
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619 *pixel = std::numeric_limits<T>::min(); |
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620 else if (v > std::numeric_limits<T>::max()) |
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621 *pixel = std::numeric_limits<T>::max(); |
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622 else |
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623 *pixel = static_cast<T>(v); |
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624 } |
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625 } |
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626 |
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627 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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628 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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629 } |
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630 |
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631 |
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632 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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633 DcmDataset& dataset, |
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634 unsigned int frame, |
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635 ImageExtractionMode mode) |
| 0 | 636 { |
| 637 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 638 | |
| 639 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 640 | |
| 641 DicomMap m; | |
| 642 FromDcmtkBridge::Convert(m, dataset); | |
| 643 | |
| 644 DcmElement* e; | |
| 80 | 645 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 646 e != NULL) |
| 647 { | |
| 648 Uint8* pixData = NULL; | |
| 649 if (e->getUint8Array(pixData) == EC_Normal) | |
| 650 { | |
| 651 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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652 accessor->SetCurrentFrame(frame); |
| 0 | 653 } |
| 654 } | |
| 655 | |
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656 PixelFormat format; |
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657 switch (mode) |
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658 { |
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659 case ImageExtractionMode_Preview: |
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660 case ImageExtractionMode_UInt8: |
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661 format = PixelFormat_Grayscale8; |
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662 break; |
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663 |
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664 case ImageExtractionMode_UInt16: |
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665 format = PixelFormat_Grayscale16; |
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666 break; |
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667 |
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668 default: |
| 62 | 669 throw OrthancException(ErrorCode_NotImplemented); |
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670 } |
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671 |
| 0 | 672 if (accessor.get() == NULL || |
| 673 accessor->GetWidth() == 0 || | |
| 674 accessor->GetHeight() == 0) | |
| 675 { | |
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676 PngWriter w; |
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677 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 678 } |
| 679 else | |
| 680 { | |
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681 switch (mode) |
| 0 | 682 { |
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683 case ImageExtractionMode_Preview: |
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684 ExtractPngImagePreview(result, *accessor); |
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685 break; |
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686 |
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687 case ImageExtractionMode_UInt8: |
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688 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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689 break; |
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690 |
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691 case ImageExtractionMode_UInt16: |
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692 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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693 break; |
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694 |
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695 default: |
| 62 | 696 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 697 } |
| 698 } | |
| 699 } | |
| 700 | |
| 701 | |
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702 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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703 const std::string& dicomContent, |
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704 unsigned int frame, |
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705 ImageExtractionMode mode) |
| 0 | 706 { |
| 707 DcmInputBufferStream is; | |
| 708 if (dicomContent.size() > 0) | |
| 709 { | |
| 710 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 711 } | |
| 712 is.setEos(); | |
| 713 | |
| 714 DcmFileFormat dicom; | |
| 715 if (dicom.read(is).good()) | |
| 716 { | |
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717 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 718 } |
| 719 else | |
| 720 { | |
| 62 | 721 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 722 } |
| 723 } | |
| 724 | |
| 725 | |
| 726 | |
| 727 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 728 { | |
| 106 | 729 // Some patches for important tags because of different DICOM |
| 730 // dictionaries between DCMTK versions | |
| 731 if (t == DICOM_TAG_PATIENT_NAME) | |
| 732 return "PatientName"; | |
| 733 | |
| 734 if (t == DicomTag(0x0010, 0x0030)) | |
| 735 return "PatientBirthDate"; | |
| 736 | |
| 737 if (t == DicomTag(0x0010, 0x0040)) | |
| 738 return "PatientSex"; | |
| 739 | |
| 740 // End of patches | |
| 741 | |
| 0 | 742 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 743 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 744 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 745 | |
| 746 std::string s("Unknown"); | |
| 747 if (entry != NULL) | |
| 748 { | |
| 749 s = std::string(entry->getTagName()); | |
| 750 } | |
| 751 | |
| 752 dcmDataDict.unlock(); | |
| 753 return s; | |
| 754 } | |
| 755 | |
| 756 | |
| 757 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
| 758 { | |
| 759 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 760 const DcmDictEntry* entry = dict.findEntry(name); | |
| 761 | |
| 762 if (entry == NULL) | |
| 763 { | |
| 764 dcmDataDict.unlock(); | |
| 62 | 765 throw OrthancException("Unknown DICOM tag"); |
| 0 | 766 } |
| 767 else | |
| 768 { | |
| 769 DcmTagKey key = entry->getKey(); | |
| 770 DicomTag tag(key.getGroup(), key.getElement()); | |
| 771 dcmDataDict.unlock(); | |
| 772 return tag; | |
| 773 } | |
| 774 } | |
| 775 | |
| 776 | |
| 777 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 778 { | |
| 779 for (DicomMap::Map::const_iterator | |
| 780 it = m.map_.begin(); it != m.map_.end(); it++) | |
| 781 { | |
| 782 DicomTag t = it->first; | |
| 783 std::string s = it->second->AsString(); | |
| 784 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
| 785 } | |
| 786 } | |
| 787 | |
| 788 | |
| 789 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 790 const DicomMap& values) | |
| 791 { | |
| 792 if (result.type() != Json::objectValue) | |
| 793 { | |
| 62 | 794 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 795 } |
| 796 | |
| 797 result.clear(); | |
| 798 | |
| 799 for (DicomMap::Map::const_iterator | |
| 800 it = values.map_.begin(); it != values.map_.end(); it++) | |
| 801 { | |
| 802 result[GetName(it->first)] = it->second->AsString(); | |
| 803 } | |
| 804 } | |
| 176 | 805 |
| 806 | |
| 807 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
| 808 { | |
| 809 char uid[100]; | |
| 810 | |
| 811 switch (level) | |
| 812 { | |
| 813 case DicomRootLevel_Instance: | |
| 814 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
| 815 | |
| 816 case DicomRootLevel_Series: | |
| 817 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); | |
| 818 | |
| 819 case DicomRootLevel_Study: | |
| 820 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); | |
| 821 | |
| 822 default: | |
| 823 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 824 } | |
| 825 } | |
| 826 | |
| 0 | 827 } |