Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 291:4d7469f72a0b
embedding of dicom dictionaries
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 14 Dec 2012 15:15:48 +0100 |
| parents | 4031f73fe0e4 |
| children | 238134081136 |
| 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> |
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63 #include <glog/logging.h> |
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64 #include <dcmtk/dcmdata/dcostrmb.h> |
| 0 | 65 |
| 62 | 66 namespace Orthanc |
| 0 | 67 { |
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68 ParsedDicomFile::ParsedDicomFile(const std::string& content) |
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69 { |
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70 DcmInputBufferStream is; |
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71 if (content.size() > 0) |
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72 { |
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73 is.setBuffer(&content[0], content.size()); |
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74 } |
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75 is.setEos(); |
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76 |
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77 file_.reset(new DcmFileFormat); |
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78 file_->transferInit(); |
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79 if (!file_->read(is).good()) |
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80 { |
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81 throw OrthancException(ErrorCode_BadFileFormat); |
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82 } |
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83 file_->loadAllDataIntoMemory(); |
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84 file_->transferEnd(); |
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85 } |
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86 |
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87 |
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88 static void SendPathValueForDictionary(RestApiOutput& output, |
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89 DcmItem& dicom) |
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90 { |
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91 Json::Value v = Json::arrayValue; |
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92 |
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93 for (unsigned long i = 0; i < dicom.card(); i++) |
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94 { |
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95 DcmElement* element = dicom.getElement(i); |
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96 if (element) |
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97 { |
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98 char buf[16]; |
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99 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); |
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100 v.append(buf); |
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101 } |
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102 } |
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103 |
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104 output.AnswerJson(v); |
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105 } |
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106 |
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107 static inline uint16_t GetCharValue(char c) |
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108 { |
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109 if (c >= '0' && c <= '9') |
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110 return c - '0'; |
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111 else if (c >= 'a' && c <= 'f') |
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112 return c - 'a' + 10; |
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113 else if (c >= 'A' && c <= 'F') |
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114 return c - 'A' + 10; |
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115 else |
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116 return 0; |
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117 } |
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118 |
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119 static inline uint16_t GetTagValue(const char* c) |
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120 { |
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121 return ((GetCharValue(c[0]) << 12) + |
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122 (GetCharValue(c[1]) << 8) + |
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123 (GetCharValue(c[2]) << 4) + |
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124 GetCharValue(c[3])); |
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125 } |
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126 |
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127 static bool ParseTagAndGroup(DcmTagKey& key, |
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128 const std::string& tag) |
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129 { |
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130 if (tag.size() != 9 || |
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131 !isxdigit(tag[0]) || |
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132 !isxdigit(tag[1]) || |
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133 !isxdigit(tag[2]) || |
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134 !isxdigit(tag[3]) || |
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135 tag[4] != '-' || |
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136 !isxdigit(tag[5]) || |
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137 !isxdigit(tag[6]) || |
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138 !isxdigit(tag[7]) || |
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139 !isxdigit(tag[8])) |
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140 { |
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141 return false; |
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142 } |
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143 |
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144 uint16_t group = GetTagValue(tag.c_str()); |
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145 uint16_t element = GetTagValue(tag.c_str() + 5); |
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146 |
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147 key = DcmTagKey(group, element); |
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148 |
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149 return true; |
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150 } |
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151 |
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152 |
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153 static void SendSequence(RestApiOutput& output, |
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154 DcmSequenceOfItems& sequence) |
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155 { |
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156 // This element is a sequence |
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157 Json::Value v = Json::arrayValue; |
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158 |
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159 for (unsigned long i = 0; i < sequence.card(); i++) |
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160 { |
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161 v.append(boost::lexical_cast<std::string>(i)); |
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162 } |
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163 |
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164 output.AnswerJson(v); |
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165 } |
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166 |
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167 static void SendField(RestApiOutput& output, |
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168 DcmElement& element) |
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169 { |
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170 // This element is not a sequence |
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171 std::string buffer; |
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172 buffer.resize(65536); |
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173 Uint32 length = element.getLength(); |
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174 Uint32 offset = 0; |
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175 |
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176 output.GetLowLevelOutput().SendOkHeader("application/octet-stream", true, length, NULL); |
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177 |
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178 while (offset < length) |
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179 { |
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180 Uint32 nbytes; |
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181 if (length - offset < buffer.size()) |
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182 { |
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183 nbytes = length - offset; |
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184 } |
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185 else |
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186 { |
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187 nbytes = buffer.size(); |
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188 } |
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189 |
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190 if (element.getPartialValue(&buffer[0], offset, nbytes).good()) |
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191 { |
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192 output.GetLowLevelOutput().Send(&buffer[0], nbytes); |
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193 offset += nbytes; |
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194 } |
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195 else |
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196 { |
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197 return; |
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198 } |
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199 } |
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200 |
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201 output.MarkLowLevelOutputDone(); |
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202 } |
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203 |
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204 static void SendPathValueForLeaf(RestApiOutput& output, |
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205 const std::string& tag, |
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206 DcmItem& dicom) |
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207 { |
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208 DcmTagKey k; |
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209 if (!ParseTagAndGroup(k, tag)) |
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210 { |
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211 return; |
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212 } |
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213 |
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214 DcmSequenceOfItems* sequence = NULL; |
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215 if (dicom.findAndGetSequence(k, sequence).good() && |
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216 sequence != NULL && |
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217 sequence->getVR() == EVR_SQ) |
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218 { |
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219 SendSequence(output, *sequence); |
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220 return; |
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221 } |
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222 |
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223 DcmElement* element = NULL; |
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224 if (dicom.findAndGetElement(k, element).good() && |
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225 element != NULL && |
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226 element->getVR() != EVR_UNKNOWN && |
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227 element->getVR() != EVR_SQ) |
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228 { |
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229 SendField(output, *element); |
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230 } |
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231 } |
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232 |
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233 void ParsedDicomFile::SendPathValue(RestApiOutput& output, |
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234 const UriComponents& uri) |
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235 { |
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236 DcmItem* dicom = file_->getDataset(); |
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237 |
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238 // Go down in the tag hierarchy according to the URI |
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239 for (size_t pos = 0; pos < uri.size() / 2; pos++) |
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240 { |
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241 size_t index; |
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242 try |
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243 { |
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244 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); |
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245 } |
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246 catch (boost::bad_lexical_cast&) |
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247 { |
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248 return; |
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249 } |
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250 |
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251 DcmTagKey k; |
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252 DcmItem *child = NULL; |
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253 if (!ParseTagAndGroup(k, uri[2 * pos]) || |
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254 !dicom->findAndGetSequenceItem(k, child, index).good() || |
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255 child == NULL) |
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256 { |
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257 return; |
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258 } |
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259 |
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260 dicom = child; |
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261 } |
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262 |
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263 // We have reached the end of the URI |
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264 if (uri.size() % 2 == 0) |
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265 { |
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266 SendPathValueForDictionary(output, *dicom); |
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267 } |
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268 else |
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269 { |
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270 SendPathValueForLeaf(output, uri.back(), *dicom); |
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271 } |
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272 } |
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273 |
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274 |
| 0 | 275 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) |
| 276 { | |
| 277 target.Clear(); | |
| 278 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 279 { | |
| 280 DcmElement* element = dataset.getElement(i); | |
| 281 if (element && element->isLeaf()) | |
| 282 { | |
| 283 target.SetValue(element->getTag().getGTag(), | |
| 284 element->getTag().getETag(), | |
| 285 ConvertLeafElement(*element)); | |
| 286 } | |
| 287 } | |
| 288 } | |
| 289 | |
| 290 | |
| 291 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 292 { | |
| 293 return DicomTag(element.getGTag(), element.getETag()); | |
| 294 } | |
| 295 | |
| 296 | |
| 297 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 298 { | |
| 299 if (!element.isLeaf()) | |
| 300 { | |
| 62 | 301 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 302 } |
| 303 | |
| 304 if (element.isaString()) | |
| 305 { | |
| 306 char *c; | |
| 307 if (element.getString(c).good() && | |
| 308 c != NULL) | |
| 309 { | |
| 310 std::string s(c); | |
|
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311 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 312 return new DicomString(utf8); |
| 313 } | |
| 314 else | |
| 315 { | |
| 316 return new DicomNullValue; | |
| 317 } | |
| 318 } | |
| 319 | |
| 320 try | |
| 321 { | |
| 322 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 323 switch (element.getVR()) | |
| 324 { | |
| 325 | |
| 326 /** | |
| 327 * TODO. | |
| 328 **/ | |
| 329 | |
| 330 case EVR_DS: // decimal string | |
| 331 case EVR_IS: // integer string | |
| 332 case EVR_OB: // other byte | |
| 333 case EVR_OF: // other float | |
| 334 case EVR_OW: // other word | |
| 335 case EVR_AS: // age string | |
| 336 case EVR_AT: // attribute tag | |
| 337 case EVR_DA: // date string | |
| 338 case EVR_DT: // date time string | |
| 339 case EVR_TM: // time string | |
| 340 case EVR_UN: // unknown value representation | |
| 341 return new DicomNullValue(); | |
| 342 | |
| 343 | |
| 344 /** | |
| 345 * String types, should never happen at this point because of | |
| 346 * "element.isaString()". | |
| 347 **/ | |
| 348 | |
| 349 case EVR_AE: // application entity title | |
| 350 case EVR_CS: // code string | |
| 351 case EVR_SH: // short string | |
| 352 case EVR_LO: // long string | |
| 353 case EVR_ST: // short text | |
| 354 case EVR_LT: // long text | |
| 355 case EVR_UT: // unlimited text | |
| 356 case EVR_PN: // person name | |
| 357 case EVR_UI: // unique identifier | |
| 358 return new DicomNullValue(); | |
| 359 | |
| 360 | |
| 361 /** | |
| 362 * Numerical types | |
| 363 **/ | |
| 364 | |
| 365 case EVR_SL: // signed long | |
| 366 { | |
| 367 Sint32 f; | |
| 368 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
| 369 { | |
| 370 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 371 } | |
| 372 else | |
| 373 { | |
| 374 return new DicomNullValue(); | |
| 375 } | |
| 376 } | |
| 377 | |
| 378 case EVR_SS: // signed short | |
| 379 { | |
| 380 Sint16 f; | |
| 381 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
| 382 { | |
| 383 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 384 } | |
| 385 else | |
| 386 { | |
| 387 return new DicomNullValue(); | |
| 388 } | |
| 389 } | |
| 390 | |
| 391 case EVR_UL: // unsigned long | |
| 392 { | |
| 393 Uint32 f; | |
| 394 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
| 395 { | |
| 396 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 397 } | |
| 398 else | |
| 399 { | |
| 400 return new DicomNullValue(); | |
| 401 } | |
| 402 } | |
| 403 | |
| 404 case EVR_US: // unsigned short | |
| 405 { | |
| 406 Uint16 f; | |
| 407 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
| 408 { | |
| 409 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 410 } | |
| 411 else | |
| 412 { | |
| 413 return new DicomNullValue(); | |
| 414 } | |
| 415 } | |
| 416 | |
| 417 case EVR_FL: // float single-precision | |
| 418 { | |
| 419 Float32 f; | |
| 420 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
| 421 { | |
| 422 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 423 } | |
| 424 else | |
| 425 { | |
| 426 return new DicomNullValue(); | |
| 427 } | |
| 428 } | |
| 429 | |
| 430 case EVR_FD: // float double-precision | |
| 431 { | |
| 432 Float64 f; | |
| 433 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
| 434 { | |
| 435 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 436 } | |
| 437 else | |
| 438 { | |
| 439 return new DicomNullValue(); | |
| 440 } | |
| 441 } | |
| 442 | |
| 443 | |
| 444 /** | |
| 445 * Sequence types, should never occur at this point because of | |
| 446 * "element.isLeaf()". | |
| 447 **/ | |
| 448 | |
| 449 case EVR_SQ: // sequence of items | |
| 450 return new DicomNullValue; | |
| 451 | |
| 452 | |
| 453 /** | |
| 454 * Internal to DCMTK. | |
| 455 **/ | |
| 456 | |
| 457 case EVR_ox: // OB or OW depending on context | |
| 458 case EVR_xs: // SS or US depending on context | |
| 459 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 460 case EVR_na: // na="not applicable", for data which has no VR | |
| 461 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 462 case EVR_item: // used internally for items | |
| 463 case EVR_metainfo: // used internally for meta info datasets | |
| 464 case EVR_dataset: // used internally for datasets | |
| 465 case EVR_fileFormat: // used internally for DICOM files | |
| 466 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 467 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 468 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 469 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 470 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 471 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 472 case EVR_OverlayData: // used internally for overlay data | |
| 473 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 474 return new DicomNullValue; | |
| 475 | |
| 476 | |
| 477 /** | |
| 478 * Default case. | |
| 479 **/ | |
| 480 | |
| 481 default: | |
| 482 return new DicomNullValue; | |
| 483 } | |
| 484 } | |
| 485 catch (boost::bad_lexical_cast) | |
| 486 { | |
| 487 return new DicomNullValue; | |
| 488 } | |
| 489 } | |
| 490 | |
| 491 | |
| 492 static void StoreElement(Json::Value& target, | |
| 493 DcmElement& element, | |
| 494 unsigned int maxStringLength); | |
| 495 | |
| 496 static void StoreItem(Json::Value& target, | |
| 497 DcmItem& item, | |
| 498 unsigned int maxStringLength) | |
| 499 { | |
| 500 target = Json::Value(Json::objectValue); | |
| 501 | |
| 502 for (unsigned long i = 0; i < item.card(); i++) | |
| 503 { | |
| 504 DcmElement* element = item.getElement(i); | |
| 505 StoreElement(target, *element, maxStringLength); | |
| 506 } | |
| 507 } | |
| 508 | |
| 509 | |
| 510 static void StoreElement(Json::Value& target, | |
| 511 DcmElement& element, | |
| 512 unsigned int maxStringLength) | |
| 513 { | |
| 514 assert(target.type() == Json::objectValue); | |
| 515 | |
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516 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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517 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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518 const std::string formattedTag = tag.Format(); |
| 0 | 519 |
| 520 if (element.isLeaf()) | |
| 521 { | |
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522 Json::Value value(Json::objectValue); |
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523 value["Name"] = tagName; |
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524 |
| 0 | 525 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 526 if (v->IsNull()) | |
| 527 { | |
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528 value["Type"] = "Null"; |
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529 value["Value"] = Json::nullValue; |
| 0 | 530 } |
| 531 else | |
| 532 { | |
| 533 std::string s = v->AsString(); | |
| 534 if (maxStringLength == 0 || | |
| 535 s.size() <= maxStringLength) | |
| 536 { | |
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537 value["Type"] = "String"; |
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538 value["Value"] = s; |
| 0 | 539 } |
| 540 else | |
| 541 { | |
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542 value["Type"] = "TooLong"; |
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543 value["Value"] = Json::nullValue; |
| 0 | 544 } |
| 545 } | |
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546 |
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547 target[formattedTag] = value; |
| 0 | 548 } |
| 549 else | |
| 550 { | |
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551 Json::Value children(Json::arrayValue); |
| 0 | 552 |
| 553 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 554 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 555 // etc. are not." The following cast is thus OK. | |
| 556 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 557 | |
| 558 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 559 { | |
| 560 DcmItem* child = sequence.getItem(i); | |
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561 Json::Value& v = children.append(Json::objectValue); |
| 0 | 562 StoreItem(v, *child, maxStringLength); |
| 563 } | |
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564 |
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565 target[formattedTag]["Name"] = tagName; |
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566 target[formattedTag]["Type"] = "Sequence"; |
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567 target[formattedTag]["Value"] = children; |
| 0 | 568 } |
| 569 } | |
| 570 | |
| 571 | |
| 572 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 573 DcmDataset& dataset, | |
| 574 unsigned int maxStringLength) | |
| 575 { | |
| 576 StoreItem(root, dataset, maxStringLength); | |
| 577 } | |
| 578 | |
| 579 | |
| 580 | |
| 581 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 582 const std::string& path, | |
| 583 unsigned int maxStringLength) | |
| 584 { | |
| 585 DcmFileFormat dicom; | |
| 586 if (!dicom.loadFile(path.c_str()).good()) | |
| 587 { | |
| 62 | 588 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 589 } |
| 590 else | |
| 591 { | |
| 592 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 593 } | |
| 594 } | |
| 595 | |
| 596 | |
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597 static void ExtractPngImagePreview(std::string& result, |
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598 DicomIntegerPixelAccessor& accessor) |
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599 { |
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600 PngWriter w; |
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601 |
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602 int32_t min, max; |
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603 accessor.GetExtremeValues(min, max); |
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604 |
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605 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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606 if (min != max) |
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607 { |
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608 uint8_t* pixel = &image[0]; |
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609 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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610 { |
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611 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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612 { |
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613 int32_t v = accessor.GetValue(x, y); |
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614 *pixel = static_cast<uint8_t>( |
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615 boost::math::lround(static_cast<float>(v - min) / |
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616 static_cast<float>(max - min) * 255.0f)); |
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617 } |
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618 } |
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619 } |
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620 |
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621 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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622 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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623 } |
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624 |
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625 |
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626 template <typename T> |
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627 static void ExtractPngImageTruncate(std::string& result, |
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628 DicomIntegerPixelAccessor& accessor, |
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629 PixelFormat format) |
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630 { |
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631 PngWriter w; |
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632 |
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633 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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634 T* pixel = &image[0]; |
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635 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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636 { |
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637 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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638 { |
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639 int32_t v = accessor.GetValue(x, y); |
| 73 | 640 if (v < std::numeric_limits<T>::min()) |
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641 *pixel = std::numeric_limits<T>::min(); |
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642 else if (v > std::numeric_limits<T>::max()) |
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643 *pixel = std::numeric_limits<T>::max(); |
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644 else |
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645 *pixel = static_cast<T>(v); |
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646 } |
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647 } |
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648 |
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649 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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650 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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651 } |
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652 |
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653 |
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654 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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655 DcmDataset& dataset, |
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656 unsigned int frame, |
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657 ImageExtractionMode mode) |
| 0 | 658 { |
| 659 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 660 | |
| 661 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 662 | |
| 663 DicomMap m; | |
| 664 FromDcmtkBridge::Convert(m, dataset); | |
| 665 | |
| 666 DcmElement* e; | |
| 80 | 667 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 668 e != NULL) |
| 669 { | |
| 670 Uint8* pixData = NULL; | |
| 671 if (e->getUint8Array(pixData) == EC_Normal) | |
| 672 { | |
| 673 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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674 accessor->SetCurrentFrame(frame); |
| 0 | 675 } |
| 676 } | |
| 677 | |
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678 PixelFormat format; |
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679 switch (mode) |
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680 { |
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681 case ImageExtractionMode_Preview: |
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682 case ImageExtractionMode_UInt8: |
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683 format = PixelFormat_Grayscale8; |
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684 break; |
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685 |
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686 case ImageExtractionMode_UInt16: |
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687 format = PixelFormat_Grayscale16; |
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688 break; |
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689 |
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690 default: |
| 62 | 691 throw OrthancException(ErrorCode_NotImplemented); |
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692 } |
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693 |
| 0 | 694 if (accessor.get() == NULL || |
| 695 accessor->GetWidth() == 0 || | |
| 696 accessor->GetHeight() == 0) | |
| 697 { | |
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698 PngWriter w; |
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699 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 700 } |
| 701 else | |
| 702 { | |
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703 switch (mode) |
| 0 | 704 { |
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705 case ImageExtractionMode_Preview: |
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706 ExtractPngImagePreview(result, *accessor); |
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707 break; |
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708 |
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709 case ImageExtractionMode_UInt8: |
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710 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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711 break; |
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712 |
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713 case ImageExtractionMode_UInt16: |
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714 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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715 break; |
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716 |
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717 default: |
| 62 | 718 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 719 } |
| 720 } | |
| 721 } | |
| 722 | |
| 723 | |
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724 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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725 const std::string& dicomContent, |
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726 unsigned int frame, |
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727 ImageExtractionMode mode) |
| 0 | 728 { |
| 729 DcmInputBufferStream is; | |
| 730 if (dicomContent.size() > 0) | |
| 731 { | |
| 732 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 733 } | |
| 734 is.setEos(); | |
| 735 | |
| 736 DcmFileFormat dicom; | |
| 737 if (dicom.read(is).good()) | |
| 738 { | |
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739 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 740 } |
| 741 else | |
| 742 { | |
| 62 | 743 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 744 } |
| 745 } | |
| 746 | |
| 747 | |
| 748 | |
| 749 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 750 { | |
| 106 | 751 // Some patches for important tags because of different DICOM |
| 752 // dictionaries between DCMTK versions | |
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753 std::string n = t.GetMainTagsName(); |
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754 if (n.size() != 0) |
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755 { |
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756 return n; |
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757 } |
| 106 | 758 // End of patches |
| 759 | |
| 0 | 760 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 761 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 762 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 763 | |
| 764 std::string s("Unknown"); | |
| 765 if (entry != NULL) | |
| 766 { | |
| 767 s = std::string(entry->getTagName()); | |
| 768 } | |
| 769 | |
| 770 dcmDataDict.unlock(); | |
| 771 return s; | |
| 772 } | |
| 773 | |
| 774 | |
| 775 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
| 776 { | |
| 777 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 778 const DcmDictEntry* entry = dict.findEntry(name); | |
| 779 | |
| 780 if (entry == NULL) | |
| 781 { | |
| 782 dcmDataDict.unlock(); | |
| 62 | 783 throw OrthancException("Unknown DICOM tag"); |
| 0 | 784 } |
| 785 else | |
| 786 { | |
| 787 DcmTagKey key = entry->getKey(); | |
| 788 DicomTag tag(key.getGroup(), key.getElement()); | |
| 789 dcmDataDict.unlock(); | |
| 790 return tag; | |
| 791 } | |
| 792 } | |
| 793 | |
| 794 | |
| 795 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 796 { | |
| 797 for (DicomMap::Map::const_iterator | |
| 798 it = m.map_.begin(); it != m.map_.end(); it++) | |
| 799 { | |
| 800 DicomTag t = it->first; | |
| 801 std::string s = it->second->AsString(); | |
| 802 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
| 803 } | |
| 804 } | |
| 805 | |
| 806 | |
| 807 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 808 const DicomMap& values) | |
| 809 { | |
| 810 if (result.type() != Json::objectValue) | |
| 811 { | |
| 62 | 812 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 813 } |
| 814 | |
| 815 result.clear(); | |
| 816 | |
| 817 for (DicomMap::Map::const_iterator | |
| 818 it = values.map_.begin(); it != values.map_.end(); it++) | |
| 819 { | |
| 820 result[GetName(it->first)] = it->second->AsString(); | |
| 821 } | |
| 822 } | |
| 176 | 823 |
| 824 | |
| 825 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
| 826 { | |
| 827 char uid[100]; | |
| 828 | |
| 829 switch (level) | |
| 830 { | |
| 831 case DicomRootLevel_Instance: | |
| 832 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
| 833 | |
| 834 case DicomRootLevel_Series: | |
| 835 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); | |
| 836 | |
| 837 case DicomRootLevel_Study: | |
| 838 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); | |
| 839 | |
| 840 default: | |
| 841 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 842 } | |
| 843 } | |
| 844 | |
|
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845 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, |
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846 DcmDataset* dataSet) |
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847 { |
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848 // Determine the transfer syntax which shall be used to write the |
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849 // information to the file. We always switch to the Little Endian |
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850 // syntax, with explicit length. |
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851 |
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852 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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853 E_TransferSyntax xfer = EXS_LittleEndianExplicit; |
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854 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; |
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855 |
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856 uint32_t s = dataSet->getLength(xfer, encodingType); |
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857 |
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858 buffer.resize(s); |
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859 DcmOutputBufferStream ob(&buffer[0], s); |
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860 |
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861 dataSet->transferInit(); |
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862 |
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863 #if DCMTK_VERSION_NUMBER >= 360 |
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864 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL, |
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865 /*opt_groupLength*/ EGL_recalcGL, |
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866 /*opt_paddingType*/ EPD_withoutPadding); |
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867 #else |
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868 OFCondition c = dataSet->write(ob, xfer, encodingType, NULL); |
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869 #endif |
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870 |
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871 dataSet->transferEnd(); |
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872 if (c.good()) |
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873 { |
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874 return true; |
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875 } |
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876 else |
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877 { |
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878 buffer.clear(); |
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879 return false; |
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880 } |
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881 |
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882 #if 0 |
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883 OFCondition cond = cbdata->dcmff->saveFile(fileName.c_str(), xfer, |
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884 encodingType, |
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885 /*opt_groupLength*/ EGL_recalcGL, |
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886 /*opt_paddingType*/ EPD_withoutPadding, |
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887 OFstatic_cast(Uint32, /*opt_filepad*/ 0), |
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888 OFstatic_cast(Uint32, /*opt_itempad*/ 0), |
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889 (opt_useMetaheader) ? EWM_fileformat : EWM_dataset); |
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890 #endif |
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891 } |
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892 |
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893 |
| 0 | 894 } |