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SeriesMetadata and StudiesMetadata in DICOMweb
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 17 Feb 2020 16:14:33 +0100
parents 0078d465c768
children 42104307e838
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1 .. _dicomweb:
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4 DICOMweb plugin
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5 ===============
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6
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7 .. contents::
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8
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9 This **official** plugin extends Orthanc with support of the `DICOMweb
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10 protocols <https://en.wikipedia.org/wiki/DICOMweb>`__. More precisely,
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11 the plugin introduces a basic, reference implementation of WADO-URI,
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12 WADO-RS, QIDO-RS and STOW-RS, following `DICOM PS3.18
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13 <http://dicom.nema.org/medical/dicom/current/output/html/part18.html>`__.
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14 The plugin simultaneously turns Orthanc into a **DICOMweb server** and
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15 into a **DICOMweb client**.
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17 For general information, check out the `official homepage of the
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18 plugins <http://www.orthanc-server.com/static.php?page=dicomweb>`__.
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20 The full standard is not implemented yet, the supported features are
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21 `tracked in the repository
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22 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Status.txt>`__.
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25 Compilation
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26 -----------
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27
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28 .. highlight:: text
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30 The procedure to compile this plugin is similar of that for the
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31 :ref:`core of Orthanc <compiling>`. The following commands should work
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32 for every UNIX-like distribution (including GNU/Linux)::
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33
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34 $ mkdir Build
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35 $ cd Build
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36 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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37 $ make
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39 The compilation will produce a shared library ``OrthancDicomWeb`` that
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40 contains the DICOMweb plugin. Pre-compiled binaries for Microsoft
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41 Windows `are also available
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42 <http://www.orthanc-server.com/browse.php?path=/plugin-dicom-web>`__,
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43 and are included in the `Windows installers
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44 <https://www.orthanc-server.com/download-windows.php>`__. A package
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45 for `Apple's Mac OS X
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46 <http://localhost/~jodogne/orthanc/static.php?page=download-mac>`__ is
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47 available courtesy of `Osimis <http://osimis.io/>`__.
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48
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49 *Remark:* Some older build instructions are also available in the
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50 `source distribution
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51 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/BuildInstructions.txt>`__.
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52
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53
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54 Installation
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55 ------------
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57 .. highlight:: json
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58
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59 You of course first have to :ref:`install Orthanc <binaries>`. Once
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60 Orthanc is installed, you must change the :ref:`configuration file
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61 <configuration>` to tell Orthanc where it can find the plugin: This is
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62 done by properly modifying the ``Plugins`` option. For GNU/Linux, you
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63 could for instance use the following configuration file::
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65 {
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66 "Name" : "MyOrthanc",
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67 [...]
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68 "Plugins" : [
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69 "/home/user/OrthancDicomWeb/Build/libOrthancDicomWeb.so"
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70 ]
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71 }
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72
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73 Or, for Windows::
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74
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75 {
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76 "Name" : "MyOrthanc",
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77 [...]
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78 "Plugins" : [
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79 "c:/Temp/OrthancDicomWeb.dll"
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80 ]
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81 }
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82
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83 Note that the DICOMweb server will share all the parameters of the
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84 Orthanc HTTP server, notably wrt. authentication and HTTPS
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85 encryption. For this reason, you will most probably have to enable the
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86 remote access to the Orthanc HTTP server::
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87
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88 {
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89 [...]
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90 "RemoteAccessEnabled" : true,
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91 [...]
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92 }
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93
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94 Once Orthanc has restarted, the root of the DICOMweb REST API is
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95 accessible at ``http://localhost:8042/dicom-web/``.
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97
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98 Options
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99 -------
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100
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101
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102 .. _dicomweb-server-config:
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103
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104 Server-related options
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105 ^^^^^^^^^^^^^^^^^^^^^^
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106
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107 .. highlight:: json
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108
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109 There are several configuration options that can be set to fine-tune
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110 the Orthanc DICOMweb server. Here is the full list of the available
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111 options, all of them must be grouped inside the ``DicomWeb`` section of
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112 the Orthanc configuration file::
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113
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114 {
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115 [...]
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116 "DicomWeb" : {
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117 "Enable" : true, // Whether DICOMweb support is enabled
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118 "Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
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119 "EnableWado" : true, // Whether WADO-URI (previously known as WADO) support is enabled
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120 "WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
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121 "Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
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122 "QidoCaseSensitive" : true, // For QIDO-RS server, whether search is case sensitive (since release 0.5)
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123 "Host" : "localhost", // Hard-codes the name of the host for subsequent WADO-RS requests (deprecated)
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124 "StudiesMetadata" : "Full", // How study-level metadata is retrieved ("Full" or "MainDicomTags", since 1.1)
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125 "SeriesMetadata" : "Full" // How series-level metadata is retrieved ("Full" or "MainDicomTags", since 1.1)
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126 }
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127 }
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128
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129 Furthermore, the global option ``DefaultEncoding`` specifies the
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130 encoding (specific character set) that will be used when answering a
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131 QIDO-RS request. It might be a good idea to set this option to
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132 ``Utf8`` if you are dealing with an international environment.
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135 The options ``StudiesMetadata`` and ``SeriesMetadata`` were introduced
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136 in release 1.1 of the DICOMweb plugin. These options specify how the
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137 calls to ``/dicom-web/studies/.../metadata`` and
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138 ``/dicom-web/studies/.../series/.../metadata`` (i.e. `WADO-RS Retrieve
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139 Metadata
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140 <http://dicom.nema.org/medical/dicom/2019a/output/chtml/part18/sect_6.5.6.html>`__)
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141 are processed:
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142
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143 * If ``Full`` mode is used, the plugin will have to read all the DICOM
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144 instances of the study/series from the :ref:`storage area
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145 <orthanc-storage>`, which gives exact results but requires all the
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146 individual instances to be read and parsed from the filesystem,
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147 leading to bad performance (cf. `issue 162
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148 <https://bitbucket.org/sjodogne/orthanc/issues/162/dicomweb-metadata-resource-reads-all>`__).
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149 This is the default mode.
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150
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151 * If ``MainDicomTags`` mode is used, the plugin will only report the
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152 main DICOM tags that are stored inside the Orthanc database index.
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153 The DICOM files are not read from the disk, which provides very good
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154 performance. However, this is a small subset of all the tags that
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155 would be retrieved if using the ``Full`` mode: A DICOMweb viewer
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156 might need more tags.
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157
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158 * *Work-in-progress:* In the future, another mode might be introduced
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159 for the series level, that would assume that the value of some
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160 non-main DICOM tags is constant across all the instances of the
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161 series. It would then be sufficient for the DICOMweb plugin to only
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162 read one instance from the series. This mode would be a compromise
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163 between ``MainDicomTags`` (focus on speed) and ``Full`` (focus on
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164 accuracy). This mode is still under active investigation, as it
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165 might silently break DICOMweb viewers.
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166
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167 * If you are using a DICOMweb viewer (such as forthcoming Stone Web
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168 viewer or OHIF viewer) in a setup where performance is important,
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169 you should most probably set ``StudiesMetadata`` to
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170 ``MainDicomTags`` and ``SeriesMetadata`` to ``Full``.
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171
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172
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173 **Remark 1:** The following configuration options were present in
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174 releases <= 0.6 of the plugin, but are not used anymore::
260
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175
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176 {
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177 [...]
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178 "DicomWeb" : {
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179 "StowMaxInstances" : 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
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180 "StowMaxSize" : 10, // For STOW-RS client, the maximum size of the body in one single HTTP query (in MB, 0 = no limit)
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181 }
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182 }
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183
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184 These older configuration options were used to limit the size of the
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185 HTTP requests, by issuing multiple calls to STOW-RS (set both options
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186 to 0 to send one single request).
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187
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188
318
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189 **Remark 2:** The option ``Host`` is deprecated. Starting with release
243
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190 0.7 of the DICOMweb plugin, its value are computed from the standard
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191 HTTP headers ``Forwarded`` and ``Host``, as provided by the HTTP
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192 clients.
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193
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194
32
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195
255
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196 .. _dicomweb-client-config:
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197
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198 Client-related options
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199 ^^^^^^^^^^^^^^^^^^^^^^
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200
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201 .. highlight:: json
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202
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203 If you want to connect Orthanc as a client to remote DICOMweb servers
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204 (cf. below), you need to modify the configuration file so as to define
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205 each of them in the option ``DicomWeb.Servers``. The syntax is
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206 identical to the ``OrthancPeers`` option of the :ref:`configuration of
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207 the Orthanc core <configuration>`.
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208
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209 In the most simple case, here is how to instruct Orthanc about the
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210 existence of a password-less DICOMweb server that will be referred to
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211 as "sample" in Orthanc::
30
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212
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213 {
32
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214 [...]
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215 "DicomWeb" : {
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216 "Servers" : {
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217 "sample" : [ "http://192.168.1.1/dicom-web/" ]
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218 }
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219 }
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220 }
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221
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222 You are of course free to add as many DICOMweb servers as you need. If
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223 the DICOMweb server is protected by a password (with `HTTP Basic
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224 access authentication
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225 <https://en.wikipedia.org/wiki/Basic_access_authentication>`__)::
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226
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227 {
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228 [...]
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229 "DicomWeb" : {
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230 "Servers" : {
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231 "sample" : [ "http://192.168.1.1/dicom-web/", "username", "password" ]
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232 }
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233 }
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234 }
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235
260
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236 Two important options can be provided for individual remote DICOMweb servers:
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237
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238 * ``HasDelete`` can be set to ``true`` to indicate that the HTTP
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239 DELETE method can be used to delete remote studies/series/instances.
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240 This notably adds a "delete" button on the Web interface of the
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241 DICOMweb client, and creates a route
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242 ``/dicom-web/servers/sample/delete`` in the REST API.
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243
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244 * ``ChunkedTransfers`` must be set to ``false`` if the remote DICOMweb
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245 server does not support `HTTP chunked transfer encoding
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246 <https://en.wikipedia.org/wiki/Chunked_transfer_encoding>`__. Setting
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247 this option to ``true`` is the best choice to reduce memory
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248 consumption. However, it must be set to ``false`` if the remote
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249 DICOMweb server is Orthanc <= 1.5.6, as chunked transfer encoding is
293
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250 only supported starting with Orthanc 1.5.8. Beware setting ``ChunkedTransfers``
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251 to ``true`` utilizes all CPU resources which results in extremely low throughput
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252 as of version 1.0 of the DICOMweb plugin (see
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253 `issue 156 <https://bitbucket.org/sjodogne/orthanc/issues/156/>`__ for status).
260
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254
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255 You'll have to convert the JSON array into a JSON object to set these
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256 options::
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257
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258 {
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259 [...]
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260 "DicomWeb" : {
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261 "Servers" : {
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262 "sample" : {
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263 "Url" : "http://192.168.1.1/dicom-web/",
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264 "Username" : "username",
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265 "Password" : "password",
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266 "HasDelete" : true,
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267 "ChunkedTransfers" : true // Set to "false" if "sample" is Orthanc <= 1.5.6
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268 }
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269 }
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270 }
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271 }
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272
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273
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274 Furthermore, if the DICOMweb server is protected with HTTPS client
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275 authentication, you must provide your client certificate (in the `PEM
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276 format
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277 <https://en.wikipedia.org/wiki/Privacy-enhanced_Electronic_Mail>`__),
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278 your client private key (also in the PEM format), together with the
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279 password protecting the private key::
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280
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281 {
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282 [...]
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283 "DicomWeb" : {
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284 "Servers" : {
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285 "sample" : {
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286 "Url" : "http://192.168.1.1/dicom-web/",
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287 "CertificateFile" : "client.crt",
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288 "CertificateKeyFile" : "client.key",
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289 "CertificateKeyPassword" : "password"
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290 }
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291 }
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292 }
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293 }
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294
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295 Finally, it is also possible to use client authentication with
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296 hardware security modules and smart cards through `PKCS#11
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297 <https://en.wikipedia.org/wiki/PKCS_11>`__ (this feature is only
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298 available is the core of Orthanc was compiled with the
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299 ``-DENABLE_PKCS11=ON`` option in CMake, and if the Orthanc
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300 configuration file has a proper ``Pkcs11`` section)::
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301
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302 {
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303 [...]
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304 "DicomWeb" : {
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305 "Servers" : {
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306 "sample" : {
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307 "Url" : "http://192.168.1.1/dicom-web/",
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308 "Pkcs11" : true
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309 }
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310 }
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311 }
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312 }
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313
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314 **Remark:** A :ref:`plugin by Osimis <google>` is available to
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315 dynamically create authenticated connections to Google Cloud Platform.
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316
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317 **Important remark:** When querying a DICOMweb server, Orthanc will
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318 automatically use the global configuration options ``HttpProxy``,
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319 ``HttpTimeout``, ``HttpsVerifyPeers``, ``HttpsCACertificates``, and
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320 ``Pkcs11``. Make sure to adapt them if need be.
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321
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322
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323 Quickstart - DICOMweb client
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324 ----------------------------
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325
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326 Starting with version 1.0 of the DICOMweb plugin, a Web interface is
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327 provided to use Orthanc as a DICOMweb client. Simply click on the
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328 "Open DICOMweb client" button at the bottom of the welcome screen of
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329 :ref:`Orthanc Explorer <orthanc-explorer>`.
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330
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331 Here is a direct link to the DICOMweb client running on our demo
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332 server:
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333 `http://demo.orthanc-server.com/dicom-web/app/client/index.html
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334 <http://demo.orthanc-server.com/dicom-web/app/client/index.html>`__
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335
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336
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337
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338 Quickstart - DICOMweb server
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339 ----------------------------
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340
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341 Once your Orthanc server is properly configured (see above), you can
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342 make REST calls to the API of the DICOMweb server. For demonstration
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343 purpose, this section makes the assumption that the ``VIX`` dataset
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344 provided by `OsiriX <http://www.osirix-viewer.com/datasets/>`__ has
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345 been uploaded to Orthanc.
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346
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347 WADO-URI
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348 ^^^^^^^^
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349
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350 .. highlight:: text
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351
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352 Here is a proper WADO-URI (previously known simply as WADO) request to
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353 render one slice of the VIX dataset as a JPEG image::
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354
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355 http://localhost:8042/wado?objectUID=1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466&requestType=WADO
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356
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357
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358 .. highlight:: bash
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359
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360 The ``objectUID`` corresponds to the ``SOPInstanceUID`` DICOM tag of
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361 some instance in the ``VIX`` dataset. Given the Orthanc identifier of
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362 an instance from VIX
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363 (e.g. ``14b4db2c-065edecb-6a767936-7068293a-92fcb080``), the latter
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364 tag can be obtained from the ``MainDicomTags`` field::
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365
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366 $ curl http://localhost:8042/instances/14b4db2c-065edecb-6a767936-7068293a-92fcb080
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367
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368
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369 QIDO-RS
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370 ^^^^^^^
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371
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372 .. highlight:: bash
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373
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374 Regarding QIDO-RS (querying the content of a remote DICOMweb server),
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375 here is how to obtain the list of studies stored by Orthanc::
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376
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377 $ curl http://localhost:8042/dicom-web/studies
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378
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379 Note that the ``/dicom-web/`` prefix comes from the configuration
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380 option ``Root`` of the ``DicomWeb`` section. Filtering the studies is
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381 possible as follows::
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382
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383 $ curl http://localhost:8042/dicom-web/studies?PatientName=VIX
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384
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385
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386
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387 WADO-RS
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388 ^^^^^^^
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389
311
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390 A study can be retrieved through WADO-RS. Here is a sample using the VIX dataset::
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391
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392 $ curl http://localhost:8042/dicom-web/studies/2.16.840.1.113669.632.20.1211.10000315526/
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393
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394 This answer is a `multipart stream
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395 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of
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396 ``application/dicom`` DICOM instances, so a Web browser will not be
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397 able to display it (. You will have to use either AJAX (JavaScript) or a
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398 command-line tool (such as cURL).
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399
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400 You can render one individual frame as a plain PNG image as follows::
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401
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402 $ curl http://localhost:8042/dicom-web/studies/2.16.840.1.113669.632.20.1211.10000315526/series/1.3.12.2.1107.5.1.4.54693.30000006100507010800000005268/instances/1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466/frames/1/rendered -H 'accept: image/png'
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403
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404
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405 Other endpoints
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406 ^^^^^^^^^^^^^^^
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407
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408 This page only provides some very basic examples about the use of a
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409 DICOMweb server. Please check out `the full reference of the DICOMweb
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410 API <https://www.dicomstandard.org/dicomweb/>`__ for more information.
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411
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412
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413
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414 .. _dicomweb-client:
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415
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416 REST API of the Orthanc DICOMweb client
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417 ---------------------------------------
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418
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419 Listing the available servers
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420 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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421
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422 .. highlight:: bash
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423
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424 The list of the remote DICOMweb servers that are known to the DICOMweb
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425 plugin can be obtained as follows::
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426
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427 $ curl http://localhost:8042/dicom-web/servers/
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428 [ "sample" ]
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429
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430 In this case, a single server called ``sample`` is configured.
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431
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432
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433 Making a call to QIDO-RS or WADO-RS
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434 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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435
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436 .. highlight:: bash
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437
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438 In Orthanc, the URI ``/{dicom-web-root}/servers/{name}/get`` allows to
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439 make a HTTP GET call against a DICOMweb server. This can be used to
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440 issue a QIDO-RS or WADO-RS command. Orthanc will take care of properly
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441 encoding the URL and authenticating the client. For instance, here is
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442 a sample QIDO-RS search to query all the studies (using a bash
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443 command-line)::
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444
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445 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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446 {
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447 "Uri" : "/studies"
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448 }
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449 EOF
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450
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451 The result of this call is a JSON document formatted according to the
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452 DICOMweb standard. You do not have to specify the base URL of the
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453 remote DICOMweb server, as it is encoded in the configuration file.
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454
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455 As a more advanced example, here is how to search all the series
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456 associated with a given patient name, while requesting to use an XML
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457 format::
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458
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459 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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460 {
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461 "Uri" : "/series",
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462 "HttpHeaders" : {
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463 "Accept" : "application/dicom+xml"
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464 },
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465 "Arguments" : {
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466 "00100010" : "KNIX"
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467 }
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468 }
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469 EOF
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470
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471 The result of the command above is a `multipart stream
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472 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of XML
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473 documents describing each series.
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474
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475 Note how all the GET arguments to the QIDO-RS request must be
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476 specified in the ``Arguments`` field. Orthanc will take care of
260
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477 `properly encoding it as an URL
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478 <https://en.wikipedia.org/wiki/Percent-encoding>`__.
32
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479
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480 An user-friendly reference of the features available in QIDO-RS and
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481 WADO-RS `can be found on this site <http://www.dicomweb.org/>`__.
32
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482
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483
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484 Sending DICOM resources to a STOW-RS server
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485 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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486
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487 .. highlight:: bash
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488
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489 STOW-RS allows to send local DICOM resources to a remote DICOMweb
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490 server. In Orthanc, the STOW-RS client primitive is available at URI
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491 ``/{dicom-web-root}/servers/{name}/stow``. Here is a sample call::
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492
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493 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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494 {
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495 "Resources" : [
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496 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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497 ]
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498 }
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499 EOF
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500
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501 Note that this primitive takes as its input a list of :ref:`Orthanc
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502 identifiers <orthanc-ids>` corresponding to the resources (patients,
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503 studies, series and/or instances) to be exported.
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504
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505 Additional HTTP headers can be added with an optional ``HttpHeaders``
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506 argument as for QIDO-RS and WADO-RS. This might be useful e.g. for
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507 cookie-based session management.
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508
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3391edf37359 note for packagers
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509 Internally, this call results in creating an :ref:`Orthanc job <jobs>`
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510 that is executed synchronously (the REST call only returns once the
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511 STOW-RS request is finished). You can run the job in asynchronous
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512 mode as follows::
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513
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514 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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515 {
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516 "Resources" : [
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517 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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518 ],
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519 "Synchronous" : false,
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520 "Priority" : 10
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521 }
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522 EOF
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523
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524 {
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525 "ID" : "a7bd2a5c-291d-4ca5-977a-66502cab22a1",
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526 "Path" : ".././../jobs/a7bd2a5c-291d-4ca5-977a-66502cab22a1"
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527 }
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528
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529 Such a call ends immediately, and returns the ID of the job created by
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530 Orthanc. The :ref:`status of the job <jobs-monitoring>` can then be
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531 monitored using the Orthanc REST API.
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532
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533
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534
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535 Retrieving DICOM resources from a WADO-RS server
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536 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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537
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538 .. highlight:: bash
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539
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540 Once DICOM resources of interest have been identified through a
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541 QIDO-RS call to a remote DICOMweb server (cf. above), it is
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542 interesting to download them locally with a WADO-RS call. You could do
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543 it manually with a second call to the
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544 ``/{dicom-web-root}/servers/{name}/get`` URI, but Orthanc provides
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545 another primitive ``.../retrieve`` to automate this process, in order
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546 to avoid the manual parsing of the multipart stream.
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547
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548 Here is how you would download one study, one series and one instance
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549 whose StudyInstanceUID (0020,000d), SeriesInstanceUID (0020,000e) are
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550 SOPInstanceUID (0008,0018) have been identified through a former
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551 QIDO-RS call::
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552
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553 $ curl http://localhost:8042/dicom-web/servers/sample/retrieve -X POST -d @- << EOF
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554 {
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555 "Resources" : [
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556 {
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557 "Study" : "1.3.51.0.1.1.192.168.29.133.1688840.1688819"
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558 },
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559 {
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560 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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561 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041613040617636372171.0.0.0"
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562 },
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563 {
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564 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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565 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0",
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566 "Instance" : "1.3.12.2.1107.5.2.33.37097.2012041612485540185869716"
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567 }
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568 ]
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569 }
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570 EOF
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571
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572 Orthanc will reply with the list of the Orthanc identifiers of all the
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573 DICOM instances that were downloaded from the remote server.
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574
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575 Remark 1: Contrarily to the ``.../stow`` URI that uses :ref:`Orthanc
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576 identifiers <orthanc-ids>`, the ``.../retrieve`` URI uses DICOM
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577 identifiers.
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578
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579 Remark 2: The ``HttpHeaders`` and ``Arguments`` arguments are also
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580 available, as for QIDO-RS, to fine-tune the parameters of the WADO-RS
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581 request.
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582
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583 Remark 3: As for QIDO-RS, the request is run synchronously by default.
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584 The ``Synchronous`` and ``Priority`` arguments can be used to
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585 asynchronously run the request.
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586
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587
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588
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589 Additional samples
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590 ------------------
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591
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592 Samples of how to call DICOMweb services from standalone applications
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593 are available for `Python
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594 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/Python/>`__
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595 and for `JavaScript
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596 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/JavaScript>`__.
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597
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598 Integration tests are `available separately
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599 <https://bitbucket.org/sjodogne/orthanc-tests/src/default/Plugins/DicomWeb/Run.py>`__,
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600 and provide samples for more advanced features of the REST API (such
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601 as dynamically adding/updating/removing remote DICOMweb servers using
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602 HTTP PUT and DELETE methods).