Mercurial > hg > orthanc
annotate OrthancServer/Sources/DicomInstanceToStore.cpp @ 4834:bec432ee1094
download of numpy arrays from the REST API
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 26 Nov 2021 19:03:32 +0100 |
parents | 7053502fbf97 |
children | 2e71a08eea15 43e613a7756b |
rev | line source |
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1003 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
1003 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU General Public License as | |
10 * published by the Free Software Foundation, either version 3 of the | |
11 * License, or (at your option) any later version. | |
12 * | |
13 * In addition, as a special exception, the copyright holders of this | |
14 * program give permission to link the code of its release with the | |
15 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
16 * that use the same license as the "OpenSSL" library), and distribute | |
17 * the linked executables. You must obey the GNU General Public License | |
18 * in all respects for all of the code used other than "OpenSSL". If you | |
19 * modify file(s) with this exception, you may extend this exception to | |
20 * your version of the file(s), but you are not obligated to do so. If | |
21 * you do not wish to do so, delete this exception statement from your | |
22 * version. If you delete this exception statement from all source files | |
23 * in the program, then also delete it here. | |
24 * | |
25 * This program is distributed in the hope that it will be useful, but | |
26 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
27 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
28 * General Public License for more details. | |
29 * | |
30 * You should have received a copy of the GNU General Public License | |
31 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
32 **/ | |
33 | |
34 | |
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35 #include "PrecompiledHeadersServer.h" |
1003 | 36 #include "DicomInstanceToStore.h" |
37 | |
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38 #include "OrthancConfiguration.h" |
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39 |
4045 | 40 #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" |
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41 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.h" |
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42 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.h" |
4045 | 43 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h" |
44 #include "../../OrthancFramework/Sources/Logging.h" | |
45 #include "../../OrthancFramework/Sources/OrthancException.h" | |
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46 |
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47 #include <dcmtk/dcmdata/dcfilefo.h> |
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48 #include <dcmtk/dcmdata/dcdeftag.h> |
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49 |
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50 |
1003 | 51 namespace Orthanc |
52 { | |
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53 class DicomInstanceToStore::FromBuffer : public DicomInstanceToStore |
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54 { |
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55 private: |
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56 const void* buffer_; |
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57 size_t size_; |
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58 std::unique_ptr<ParsedDicomFile> parsed_; |
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59 |
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60 public: |
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61 FromBuffer(const void* buffer, |
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62 size_t size) : |
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63 buffer_(buffer), |
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64 size_(size) |
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65 { |
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66 } |
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67 |
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68 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE |
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69 { |
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70 if (parsed_.get() == NULL) |
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71 { |
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72 const_cast<FromBuffer&>(*this).parsed_.reset(new ParsedDicomFile(buffer_, size_)); |
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73 } |
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74 |
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75 return *parsed_; |
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76 } |
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77 |
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78 virtual const void* GetBufferData() const ORTHANC_OVERRIDE |
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79 { |
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80 return buffer_; |
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81 } |
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82 |
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83 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE |
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84 { |
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85 return size_; |
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86 } |
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87 }; |
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88 |
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89 |
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90 class DicomInstanceToStore::FromParsedDicomFile : public DicomInstanceToStore |
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91 { |
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92 private: |
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93 ParsedDicomFile& parsed_; |
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94 std::unique_ptr<std::string> buffer_; |
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95 |
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96 void SerializeToBuffer() |
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97 { |
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98 if (buffer_.get() == NULL) |
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99 { |
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100 buffer_.reset(new std::string); |
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101 parsed_.SaveToMemoryBuffer(*buffer_); |
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102 } |
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103 } |
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104 |
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105 public: |
4519 | 106 explicit FromParsedDicomFile(ParsedDicomFile& parsed) : |
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107 parsed_(parsed) |
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108 { |
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109 } |
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110 |
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111 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE |
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112 { |
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113 return parsed_; |
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114 } |
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116 virtual const void* GetBufferData() const ORTHANC_OVERRIDE |
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117 { |
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118 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer(); |
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119 |
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120 assert(buffer_.get() != NULL); |
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121 return (buffer_->empty() ? NULL : buffer_->c_str()); |
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122 } |
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123 |
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124 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE |
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125 { |
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126 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer(); |
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127 |
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128 assert(buffer_.get() != NULL); |
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129 return buffer_->size(); |
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130 } |
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131 }; |
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133 |
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134 class DicomInstanceToStore::FromDcmDataset : public DicomInstanceToStore |
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135 { |
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136 private: |
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137 DcmDataset& dataset_; |
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138 std::unique_ptr<std::string> buffer_; |
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139 std::unique_ptr<ParsedDicomFile> parsed_; |
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140 |
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141 void SerializeToBuffer() |
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142 { |
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143 if (buffer_.get() == NULL) |
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144 { |
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145 buffer_.reset(new std::string); |
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146 |
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147 if (!FromDcmtkBridge::SaveToMemoryBuffer(*buffer_, dataset_)) |
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148 { |
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149 throw OrthancException(ErrorCode_InternalError, "Cannot write DICOM file to memory"); |
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150 } |
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151 } |
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152 } |
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153 |
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154 public: |
4519 | 155 explicit FromDcmDataset(DcmDataset& dataset) : |
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156 dataset_(dataset) |
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157 { |
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158 } |
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159 |
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160 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE |
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161 { |
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162 if (parsed_.get() == NULL) |
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163 { |
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164 // This operation is costly, as it creates a clone of the |
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165 // dataset. This explains why the default implementations |
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166 // are overridden below to use "dataset_" as much as possible |
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167 const_cast<FromDcmDataset&>(*this).parsed_.reset(new ParsedDicomFile(dataset_)); |
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168 } |
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169 |
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170 return *parsed_; |
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171 } |
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172 |
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173 virtual const void* GetBufferData() const ORTHANC_OVERRIDE |
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174 { |
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175 const_cast<FromDcmDataset&>(*this).SerializeToBuffer(); |
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176 |
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177 assert(buffer_.get() != NULL); |
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178 return (buffer_->empty() ? NULL : buffer_->c_str()); |
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179 } |
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180 |
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181 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE |
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182 { |
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183 const_cast<FromDcmDataset&>(*this).SerializeToBuffer(); |
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184 |
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185 assert(buffer_.get() != NULL); |
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186 return buffer_->size(); |
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187 } |
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188 |
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189 virtual bool HasPixelData() const ORTHANC_OVERRIDE |
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190 { |
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191 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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192 DICOM_TAG_PIXEL_DATA.GetElement()); |
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193 return dataset_.tagExists(key); |
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194 } |
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195 |
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196 virtual void GetSummary(DicomMap& summary) const ORTHANC_OVERRIDE |
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197 { |
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198 OrthancConfiguration::DefaultExtractDicomSummary(summary, dataset_); |
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199 } |
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200 |
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201 virtual void GetDicomAsJson(Json::Value& dicomAsJson) const ORTHANC_OVERRIDE |
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202 { |
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203 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, dataset_); |
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204 } |
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205 |
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206 virtual void DatasetToJson(Json::Value& target, |
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207 DicomToJsonFormat format, |
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208 DicomToJsonFlags flags, |
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209 unsigned int maxStringLength) const ORTHANC_OVERRIDE |
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210 { |
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211 std::set<DicomTag> ignoreTagLength; |
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212 FromDcmtkBridge::ExtractDicomAsJson( |
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213 target, dataset_, format, flags, maxStringLength, ignoreTagLength); |
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214 } |
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215 |
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216 virtual unsigned int GetFramesCount() const ORTHANC_OVERRIDE |
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217 { |
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218 return DicomFrameIndex::GetFramesCount(dataset_); |
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219 } |
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220 |
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221 virtual ImageAccessor* DecodeFrame(unsigned int frame) const ORTHANC_OVERRIDE |
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222 { |
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223 return DicomImageDecoder::Decode(dataset_, frame); |
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224 } |
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225 }; |
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226 |
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227 |
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228 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const void* buffer, |
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229 size_t size) |
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230 { |
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231 return new FromBuffer(buffer, size); |
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232 } |
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233 |
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234 |
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235 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const std::string& buffer) |
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236 { |
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237 return new FromBuffer(buffer.empty() ? NULL : buffer.c_str(), buffer.size()); |
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238 } |
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239 |
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240 |
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241 DicomInstanceToStore* DicomInstanceToStore::CreateFromParsedDicomFile(ParsedDicomFile& dicom) |
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242 { |
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243 return new FromParsedDicomFile(dicom); |
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244 } |
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245 |
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246 |
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247 DicomInstanceToStore* DicomInstanceToStore::CreateFromDcmDataset(DcmDataset& dataset) |
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248 { |
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249 return new FromDcmDataset(dataset); |
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250 } |
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251 |
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252 |
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253 bool DicomInstanceToStore::LookupTransferSyntax(DicomTransferSyntax& result) const |
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254 { |
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255 DicomMap header; |
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256 if (DicomMap::ParseDicomMetaInformation(header, GetBufferData(), GetBufferSize())) |
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257 { |
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258 const DicomValue* value = header.TestAndGetValue(DICOM_TAG_TRANSFER_SYNTAX_UID); |
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259 if (value != NULL && |
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260 !value->IsBinary() && |
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261 !value->IsNull()) |
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262 { |
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263 return ::Orthanc::LookupTransferSyntax(result, Toolbox::StripSpaces(value->GetContent())); |
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264 } |
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265 } |
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266 else |
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267 { |
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268 // This is a DICOM file without a proper meta-header. Fallback |
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269 // to DCMTK, which will fully parse the dataset to retrieve |
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270 // the transfer syntax. Added in Orthanc 1.8.2. |
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271 return GetParsedDicomFile().LookupTransferSyntax(result); |
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272 } |
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273 |
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274 return false; |
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275 } |
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276 |
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277 |
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278 bool DicomInstanceToStore::HasPixelData() const |
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279 { |
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280 return GetParsedDicomFile().HasTag(DICOM_TAG_PIXEL_DATA); |
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281 } |
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282 |
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283 |
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284 void DicomInstanceToStore::GetSummary(DicomMap& summary) const |
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285 { |
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286 OrthancConfiguration::DefaultExtractDicomSummary(summary, GetParsedDicomFile()); |
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287 } |
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288 |
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289 |
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290 void DicomInstanceToStore::GetDicomAsJson(Json::Value& dicomAsJson) const |
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291 { |
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292 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, GetParsedDicomFile()); |
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293 } |
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294 |
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295 |
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296 void DicomInstanceToStore::DatasetToJson(Json::Value& target, |
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297 DicomToJsonFormat format, |
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298 DicomToJsonFlags flags, |
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299 unsigned int maxStringLength) const |
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300 { |
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301 return GetParsedDicomFile().DatasetToJson(target, format, flags, maxStringLength); |
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302 } |
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303 |
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304 |
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305 unsigned int DicomInstanceToStore::GetFramesCount() const |
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306 { |
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307 return GetParsedDicomFile().GetFramesCount(); |
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308 } |
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309 |
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310 |
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311 ImageAccessor* DicomInstanceToStore::DecodeFrame(unsigned int frame) const |
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312 { |
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313 return GetParsedDicomFile().DecodeFrame(frame); |
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314 } |
1003 | 315 } |