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annotate OrthancServer/Sources/DicomInstanceToStore.cpp @ 4834:bec432ee1094

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download of numpy arrays from the REST API
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 26 Nov 2021 19:03:32 +0100
parents 7053502fbf97
children 2e71a08eea15 43e613a7756b
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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) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 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 * In addition, as a special exception, the copyright holders of this
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14 * program give permission to link the code of its release with the
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15 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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16 * that use the same license as the "OpenSSL" library), and distribute
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17 * the linked executables. You must obey the GNU General Public License
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18 * in all respects for all of the code used other than "OpenSSL". If you
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19 * modify file(s) with this exception, you may extend this exception to
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20 * your version of the file(s), but you are not obligated to do so. If
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21 * you do not wish to do so, delete this exception statement from your
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22 * version. If you delete this exception statement from all source files
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23 * in the program, then also delete it here.
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24 *
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25 * This program is distributed in the hope that it will be useful, but
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26 * WITHOUT ANY WARRANTY; without even the implied warranty of
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27 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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28 * General Public License for more details.
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29 *
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30 * You should have received a copy of the GNU General Public License
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31 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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32 **/
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33
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34
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35 #include "PrecompiledHeadersServer.h"
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36 #include "DicomInstanceToStore.h"
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37
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38 #include "OrthancConfiguration.h"
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39
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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"
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43 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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44 #include "../../OrthancFramework/Sources/Logging.h"
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45 #include "../../OrthancFramework/Sources/OrthancException.h"
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47 #include <dcmtk/dcmdata/dcfilefo.h>
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48 #include <dcmtk/dcmdata/dcdeftag.h>
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51 namespace Orthanc
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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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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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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:
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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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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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132
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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:
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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 }
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315 }