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annotate OrthancServer/Sources/DicomInstanceToStore.cpp @ 4988:8fba26292a9f

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Housekeeper plugin: finalizing + integration tests ok
author Alain Mazy <am@osimis.io>
date Sat, 30 Apr 2022 19:39:40 +0200
parents 6eff25f70121
children 877bc3b96476
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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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) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation, either version 3 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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23 #include "PrecompiledHeadersServer.h"
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24 #include "DicomInstanceToStore.h"
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25
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26 #include "OrthancConfiguration.h"
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28 #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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29 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.h"
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30 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.h"
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31 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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32 #include "../../OrthancFramework/Sources/Logging.h"
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33 #include "../../OrthancFramework/Sources/OrthancException.h"
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35 #include <dcmtk/dcmdata/dcfilefo.h>
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36 #include <dcmtk/dcmdata/dcdeftag.h>
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38
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39 namespace Orthanc
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40 {
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41 class DicomInstanceToStore::FromBuffer : public DicomInstanceToStore
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42 {
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43 private:
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44 const void* buffer_;
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45 size_t size_;
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46 std::unique_ptr<ParsedDicomFile> parsed_;
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47
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48 public:
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49 FromBuffer(const void* buffer,
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50 size_t size) :
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51 buffer_(buffer),
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52 size_(size)
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53 {
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54 }
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55
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56 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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57 {
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58 if (parsed_.get() == NULL)
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59 {
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60 const_cast<FromBuffer&>(*this).parsed_.reset(new ParsedDicomFile(buffer_, size_));
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61 }
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62
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63 return *parsed_;
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64 }
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66 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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67 {
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68 return buffer_;
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69 }
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71 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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72 {
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73 return size_;
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74 }
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75 };
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78 class DicomInstanceToStore::FromParsedDicomFile : public DicomInstanceToStore
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79 {
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80 private:
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81 ParsedDicomFile& parsed_;
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82 std::unique_ptr<std::string> buffer_;
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84 void SerializeToBuffer()
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85 {
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86 if (buffer_.get() == NULL)
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87 {
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88 buffer_.reset(new std::string);
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89 parsed_.SaveToMemoryBuffer(*buffer_);
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90 }
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91 }
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93 public:
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94 explicit FromParsedDicomFile(ParsedDicomFile& parsed) :
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95 parsed_(parsed)
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96 {
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97 }
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99 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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100 {
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101 return parsed_;
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102 }
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103
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104 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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105 {
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106 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer();
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107
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108 assert(buffer_.get() != NULL);
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109 return (buffer_->empty() ? NULL : buffer_->c_str());
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110 }
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112 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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113 {
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114 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer();
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116 assert(buffer_.get() != NULL);
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117 return buffer_->size();
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118 }
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119 };
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120
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121
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122 class DicomInstanceToStore::FromDcmDataset : public DicomInstanceToStore
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123 {
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124 private:
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125 DcmDataset& dataset_;
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126 std::unique_ptr<std::string> buffer_;
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127 std::unique_ptr<ParsedDicomFile> parsed_;
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128
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129 void SerializeToBuffer()
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130 {
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131 if (buffer_.get() == NULL)
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132 {
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133 buffer_.reset(new std::string);
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134
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135 if (!FromDcmtkBridge::SaveToMemoryBuffer(*buffer_, dataset_))
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136 {
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137 throw OrthancException(ErrorCode_InternalError, "Cannot write DICOM file to memory");
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138 }
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139 }
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140 }
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141
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142 public:
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143 explicit FromDcmDataset(DcmDataset& dataset) :
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144 dataset_(dataset)
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145 {
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146 }
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147
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148 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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149 {
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150 if (parsed_.get() == NULL)
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151 {
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152 // This operation is costly, as it creates a clone of the
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153 // dataset. This explains why the default implementations
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154 // are overridden below to use "dataset_" as much as possible
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155 const_cast<FromDcmDataset&>(*this).parsed_.reset(new ParsedDicomFile(dataset_));
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156 }
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157
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158 return *parsed_;
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159 }
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160
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161 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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162 {
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163 const_cast<FromDcmDataset&>(*this).SerializeToBuffer();
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164
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165 assert(buffer_.get() != NULL);
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166 return (buffer_->empty() ? NULL : buffer_->c_str());
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167 }
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168
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169 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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170 {
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171 const_cast<FromDcmDataset&>(*this).SerializeToBuffer();
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172
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173 assert(buffer_.get() != NULL);
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174 return buffer_->size();
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175 }
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176
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177 virtual bool HasPixelData() const ORTHANC_OVERRIDE
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178 {
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179 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(),
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180 DICOM_TAG_PIXEL_DATA.GetElement());
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181 return dataset_.tagExists(key);
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182 }
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183
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184 virtual void GetSummary(DicomMap& summary) const ORTHANC_OVERRIDE
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185 {
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186 OrthancConfiguration::DefaultExtractDicomSummary(summary, dataset_);
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187 }
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188
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189 virtual void GetDicomAsJson(Json::Value& dicomAsJson) const ORTHANC_OVERRIDE
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190 {
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191 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, dataset_);
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192 }
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193
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194 virtual void DatasetToJson(Json::Value& target,
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195 DicomToJsonFormat format,
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196 DicomToJsonFlags flags,
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197 unsigned int maxStringLength) const ORTHANC_OVERRIDE
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198 {
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199 std::set<DicomTag> ignoreTagLength;
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200 FromDcmtkBridge::ExtractDicomAsJson(
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201 target, dataset_, format, flags, maxStringLength, ignoreTagLength);
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202 }
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203
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204 virtual unsigned int GetFramesCount() const ORTHANC_OVERRIDE
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205 {
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206 return DicomFrameIndex::GetFramesCount(dataset_);
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207 }
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208
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209 virtual ImageAccessor* DecodeFrame(unsigned int frame) const ORTHANC_OVERRIDE
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210 {
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211 return DicomImageDecoder::Decode(dataset_, frame);
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212 }
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213 };
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214
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215
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216 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const void* buffer,
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217 size_t size)
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218 {
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219 return new FromBuffer(buffer, size);
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220 }
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221
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222
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223 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const std::string& buffer)
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224 {
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225 return new FromBuffer(buffer.empty() ? NULL : buffer.c_str(), buffer.size());
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226 }
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227
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228
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229 DicomInstanceToStore* DicomInstanceToStore::CreateFromParsedDicomFile(ParsedDicomFile& dicom)
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230 {
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231 return new FromParsedDicomFile(dicom);
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232 }
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233
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234
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235 DicomInstanceToStore* DicomInstanceToStore::CreateFromDcmDataset(DcmDataset& dataset)
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236 {
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237 return new FromDcmDataset(dataset);
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238 }
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239
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240
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241 bool DicomInstanceToStore::LookupTransferSyntax(DicomTransferSyntax& result) const
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242 {
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243 DicomMap header;
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244 if (DicomMap::ParseDicomMetaInformation(header, GetBufferData(), GetBufferSize()))
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245 {
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246 const DicomValue* value = header.TestAndGetValue(DICOM_TAG_TRANSFER_SYNTAX_UID);
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247 if (value != NULL &&
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248 !value->IsBinary() &&
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249 !value->IsNull())
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250 {
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251 return ::Orthanc::LookupTransferSyntax(result, Toolbox::StripSpaces(value->GetContent()));
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252 }
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253 }
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254 else
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255 {
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256 // This is a DICOM file without a proper meta-header. Fallback
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257 // to DCMTK, which will fully parse the dataset to retrieve
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258 // the transfer syntax. Added in Orthanc 1.8.2.
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259 return GetParsedDicomFile().LookupTransferSyntax(result);
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260 }
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261
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262 return false;
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263 }
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264
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265
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266 bool DicomInstanceToStore::HasPixelData() const
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267 {
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268 return GetParsedDicomFile().HasTag(DICOM_TAG_PIXEL_DATA);
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269 }
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270
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271
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272 void DicomInstanceToStore::GetSummary(DicomMap& summary) const
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273 {
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274 OrthancConfiguration::DefaultExtractDicomSummary(summary, GetParsedDicomFile());
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275 }
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276
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277
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278 void DicomInstanceToStore::GetDicomAsJson(Json::Value& dicomAsJson) const
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279 {
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280 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, GetParsedDicomFile());
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281 }
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282
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283
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284 void DicomInstanceToStore::DatasetToJson(Json::Value& target,
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285 DicomToJsonFormat format,
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286 DicomToJsonFlags flags,
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287 unsigned int maxStringLength) const
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288 {
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289 return GetParsedDicomFile().DatasetToJson(target, format, flags, maxStringLength);
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290 }
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291
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292
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293 unsigned int DicomInstanceToStore::GetFramesCount() const
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294 {
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295 return GetParsedDicomFile().GetFramesCount();
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296 }
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297
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298
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299 ImageAccessor* DicomInstanceToStore::DecodeFrame(unsigned int frame) const
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300 {
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301 return GetParsedDicomFile().DecodeFrame(frame);
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302 }
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303
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304 void DicomInstanceToStore::CopyMetadata(const DicomInstanceToStore::MetadataMap& metadata)
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305 {
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306 for (MetadataMap::const_iterator it = metadata.begin();
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307 it != metadata.end(); ++it)
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308 {
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309 AddMetadata(it->first.first, it->first.second, it->second);
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310 }
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311 }
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312
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313 }