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annotate OrthancServer/Sources/DicomInstanceToStore.cpp @ 5656:a3c244090f67 find-refactoring

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integration mainline->find-refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 06 Jun 2024 13:24:04 +0200
parents f7adfb22e20e
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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) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU General Public License as
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11 * published by the Free Software Foundation, either version 3 of the
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12 * License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU General Public License
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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21 **/
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24 #include "PrecompiledHeadersServer.h"
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25 #include "DicomInstanceToStore.h"
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26
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27 #include "OrthancConfiguration.h"
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28
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29 #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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30 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.h"
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31 #include "../../OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.h"
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32 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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33 #include "../../OrthancFramework/Sources/Logging.h"
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34 #include "../../OrthancFramework/Sources/OrthancException.h"
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36 #include <dcmtk/dcmdata/dcfilefo.h>
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37 #include <dcmtk/dcmdata/dcdeftag.h>
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40 namespace Orthanc
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41 {
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42 class DicomInstanceToStore::FromBuffer : public DicomInstanceToStore
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43 {
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44 private:
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45 const void* buffer_;
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46 size_t size_;
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47 std::unique_ptr<ParsedDicomFile> parsed_;
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48
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49 public:
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50 FromBuffer(const void* buffer,
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51 size_t size) :
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52 buffer_(buffer),
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53 size_(size)
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54 {
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55 }
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56
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57 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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58 {
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59 if (parsed_.get() == NULL)
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60 {
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61 const_cast<FromBuffer&>(*this).parsed_.reset(new ParsedDicomFile(buffer_, size_));
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62 }
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64 return *parsed_;
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65 }
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67 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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68 {
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69 return buffer_;
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70 }
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71
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72 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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73 {
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74 return size_;
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75 }
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76 };
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79 class DicomInstanceToStore::FromParsedDicomFile : public DicomInstanceToStore
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80 {
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81 private:
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82 ParsedDicomFile& parsed_;
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83 std::unique_ptr<std::string> buffer_;
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84
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85 void SerializeToBuffer()
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86 {
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87 if (buffer_.get() == NULL)
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88 {
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89 buffer_.reset(new std::string);
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90 parsed_.SaveToMemoryBuffer(*buffer_);
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91 }
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92 }
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94 public:
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95 explicit FromParsedDicomFile(ParsedDicomFile& parsed) :
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96 parsed_(parsed)
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97 {
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98 }
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100 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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101 {
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102 return parsed_;
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103 }
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105 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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106 {
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107 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer();
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108
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109 assert(buffer_.get() != NULL);
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110 return (buffer_->empty() ? NULL : buffer_->c_str());
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111 }
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113 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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114 {
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115 const_cast<FromParsedDicomFile&>(*this).SerializeToBuffer();
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116
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117 assert(buffer_.get() != NULL);
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118 return buffer_->size();
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119 }
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120 };
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121
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122
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123 class DicomInstanceToStore::FromDcmDataset : public DicomInstanceToStore
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124 {
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125 private:
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126 DcmDataset& dataset_;
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127 std::unique_ptr<std::string> buffer_;
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128 std::unique_ptr<ParsedDicomFile> parsed_;
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129
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130 void SerializeToBuffer()
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131 {
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132 if (buffer_.get() == NULL)
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133 {
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134 buffer_.reset(new std::string);
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135
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136 std::string errorMessage;
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137 if (!FromDcmtkBridge::SaveToMemoryBuffer(*buffer_, dataset_, errorMessage))
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138 {
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139 throw OrthancException(ErrorCode_InternalError, "Cannot write DICOM file to memory: " + errorMessage);
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140 }
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141 }
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142 }
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143
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144 public:
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145 explicit FromDcmDataset(DcmDataset& dataset) :
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146 dataset_(dataset)
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147 {
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148 }
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149
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150 virtual ParsedDicomFile& GetParsedDicomFile() const ORTHANC_OVERRIDE
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151 {
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152 if (parsed_.get() == NULL)
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153 {
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154 // This operation is costly, as it creates a clone of the
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155 // dataset. This explains why the default implementations
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156 // are overridden below to use "dataset_" as much as possible
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157 const_cast<FromDcmDataset&>(*this).parsed_.reset(new ParsedDicomFile(dataset_));
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158 }
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159
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160 return *parsed_;
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161 }
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162
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163 virtual const void* GetBufferData() const ORTHANC_OVERRIDE
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164 {
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165 const_cast<FromDcmDataset&>(*this).SerializeToBuffer();
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166
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167 assert(buffer_.get() != NULL);
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168 return (buffer_->empty() ? NULL : buffer_->c_str());
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169 }
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170
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171 virtual size_t GetBufferSize() const ORTHANC_OVERRIDE
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172 {
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173 const_cast<FromDcmDataset&>(*this).SerializeToBuffer();
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174
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175 assert(buffer_.get() != NULL);
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176 return buffer_->size();
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177 }
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178
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179 virtual bool HasPixelData() const ORTHANC_OVERRIDE
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180 {
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181 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(),
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182 DICOM_TAG_PIXEL_DATA.GetElement());
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183 return dataset_.tagExists(key);
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184 }
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185
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186 virtual void GetSummary(DicomMap& summary) const ORTHANC_OVERRIDE
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187 {
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188 OrthancConfiguration::DefaultExtractDicomSummary(summary, dataset_);
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189 }
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190
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191 virtual void GetDicomAsJson(Json::Value& dicomAsJson, const std::set<DicomTag>& ignoreTagLength) const ORTHANC_OVERRIDE
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192 {
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193 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, dataset_, ignoreTagLength);
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194 }
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195
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196 virtual void DatasetToJson(Json::Value& target,
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197 DicomToJsonFormat format,
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198 DicomToJsonFlags flags,
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199 unsigned int maxStringLength) const ORTHANC_OVERRIDE
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200 {
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201 std::set<DicomTag> ignoreTagLength;
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202 FromDcmtkBridge::ExtractDicomAsJson(
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203 target, dataset_, format, flags, maxStringLength, ignoreTagLength);
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204 }
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205
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206 virtual unsigned int GetFramesCount() const ORTHANC_OVERRIDE
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207 {
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208 return DicomFrameIndex::GetFramesCount(dataset_);
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209 }
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210
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211 virtual ImageAccessor* DecodeFrame(unsigned int frame) const ORTHANC_OVERRIDE
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212 {
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213 return DicomImageDecoder::Decode(dataset_, frame);
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214 }
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215 };
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216
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217
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218 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const void* buffer,
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219 size_t size)
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220 {
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221 return new FromBuffer(buffer, size);
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222 }
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223
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224
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225 DicomInstanceToStore* DicomInstanceToStore::CreateFromBuffer(const std::string& buffer)
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226 {
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227 return new FromBuffer(buffer.empty() ? NULL : buffer.c_str(), buffer.size());
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228 }
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229
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230
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231 DicomInstanceToStore* DicomInstanceToStore::CreateFromParsedDicomFile(ParsedDicomFile& dicom)
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232 {
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233 return new FromParsedDicomFile(dicom);
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234 }
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235
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236
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237 DicomInstanceToStore* DicomInstanceToStore::CreateFromDcmDataset(DcmDataset& dataset)
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238 {
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239 return new FromDcmDataset(dataset);
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240 }
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241
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242
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243 bool DicomInstanceToStore::LookupTransferSyntax(DicomTransferSyntax& result) const
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244 {
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245 DicomMap header;
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246 if (DicomMap::ParseDicomMetaInformation(header, GetBufferData(), GetBufferSize()))
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247 {
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248 const DicomValue* value = header.TestAndGetValue(DICOM_TAG_TRANSFER_SYNTAX_UID);
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249 if (value != NULL &&
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250 !value->IsBinary() &&
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251 !value->IsNull())
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252 {
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253 return ::Orthanc::LookupTransferSyntax(result, Toolbox::StripSpaces(value->GetContent()));
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254 }
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255 }
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256 else
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257 {
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258 // This is a DICOM file without a proper meta-header. Fallback
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259 // to DCMTK, which will fully parse the dataset to retrieve
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260 // the transfer syntax. Added in Orthanc 1.8.2.
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261 return GetParsedDicomFile().LookupTransferSyntax(result);
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262 }
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263
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264 return false;
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265 }
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266
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267
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268 bool DicomInstanceToStore::HasPixelData() const
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269 {
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270 return GetParsedDicomFile().HasTag(DICOM_TAG_PIXEL_DATA);
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271 }
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272
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273
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274 void DicomInstanceToStore::GetSummary(DicomMap& summary) const
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275 {
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276 OrthancConfiguration::DefaultExtractDicomSummary(summary, GetParsedDicomFile());
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277 }
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278
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279
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280 void DicomInstanceToStore::GetDicomAsJson(Json::Value& dicomAsJson, const std::set<DicomTag>& ignoreTagLength) const
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281 {
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282 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, GetParsedDicomFile(), ignoreTagLength);
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283 }
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284
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285
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286 void DicomInstanceToStore::DatasetToJson(Json::Value& target,
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287 DicomToJsonFormat format,
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288 DicomToJsonFlags flags,
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289 unsigned int maxStringLength) const
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290 {
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291 return GetParsedDicomFile().DatasetToJson(target, format, flags, maxStringLength);
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292 }
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293
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294
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295 unsigned int DicomInstanceToStore::GetFramesCount() const
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296 {
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297 return GetParsedDicomFile().GetFramesCount();
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298 }
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299
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300
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301 ImageAccessor* DicomInstanceToStore::DecodeFrame(unsigned int frame) const
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302 {
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303 return GetParsedDicomFile().DecodeFrame(frame);
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304 }
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305
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306 void DicomInstanceToStore::CopyMetadata(const DicomInstanceToStore::MetadataMap& metadata)
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307 {
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308 for (MetadataMap::const_iterator it = metadata.begin();
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309 it != metadata.end(); ++it)
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310 {
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311 AddMetadata(it->first.first, it->first.second, it->second);
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312 }
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313 }
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314
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315 }