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annotate Sphinx/source/plugins/dicomweb.rst @ 262:3391edf37359

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note for packagers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 06 Aug 2019 09:51:59 +0200
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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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64
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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 Server-related options
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102 ^^^^^^^^^^^^^^^^^^^^^^
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103
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104 .. highlight:: json
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105
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106 There are several configuration options that can be set to fine-tune
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107 the Orthanc DICOMweb server. Here is the full list of the available
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108 options, all of them must be grouped inside the ``DicomWeb`` section of
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109 the Orthanc configuration file::
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110
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111 {
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112 [...]
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113 "DicomWeb" : {
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114 "Enable" : true, // Whether DICOMweb support is enabled
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115 "Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
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116 "EnableWado" : true, // Whether WADO-URI (previously known as WADO) support is enabled
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117 "WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
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118 "Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
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119 "QidoCaseSensitive" : true, // For QIDO-RS server, whether search is case sensitive (since release 0.5)
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120 "Host" : "localhost" // Hard-codes the name of the host for subsequent WADO-RS requests (deprecated)
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121 }
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122 }
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123
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124 Furthermore, the global option ``DefaultEncoding`` specifies the
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125 encoding (specific character set) that will be used when answering a
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126 QIDO-RS request. It might be a good idea to set this option to
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127 ``Utf8`` if you are dealing with an international environment.
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128
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129 The following configuration options were present in releases <= 0.6 of the plugin,
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130 but are not used anymore::
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131
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132 {
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133 [...]
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134 "DicomWeb" : {
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135 "StowMaxInstances" : 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
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136 "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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137 }
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138 }
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139
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140 These older configuration options were used to limit the size of the
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141 HTTP requests, by issuing multiple calls to STOW-RS (set both options
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142 to 0 to send one single request).
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143
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144
243
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145 **Remark:** The option ``Host`` is deprecated. Starting with release
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146 0.7 of the DICOMweb plugin, its value are computed from the standard
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147 HTTP headers ``Forwarded`` and ``Host``, as provided by the HTTP
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148 clients.
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149
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150
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151
255
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152 .. _dicomweb-client-config:
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153
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154 Client-related options
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155 ^^^^^^^^^^^^^^^^^^^^^^
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156
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157 .. highlight:: json
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158
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159 If you want to connect Orthanc as a client to remote DICOMweb servers
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160 (cf. below), you need to modify the configuration file so as to define
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161 each of them in the option ``DicomWeb.Servers``. The syntax is
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162 identical to the ``OrthancPeers`` option of the :ref:`configuration of
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163 the Orthanc core <configuration>`.
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164
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165 In the most simple case, here is how to instruct Orthanc about the
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166 existence of a password-less DICOMweb server that will be referred to
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167 as "sample" in Orthanc::
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168
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169 {
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170 [...]
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171 "DicomWeb" : {
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172 "Servers" : {
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173 "sample" : [ "http://192.168.1.1/dicom-web/" ]
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174 }
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175 }
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176 }
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177
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178 You are of course free to add as many DICOMweb servers as you need. If
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179 the DICOMweb server is protected by a password (with `HTTP Basic
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180 access authentication
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181 <https://en.wikipedia.org/wiki/Basic_access_authentication>`__)::
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182
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183 {
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184 [...]
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185 "DicomWeb" : {
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186 "Servers" : {
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187 "sample" : [ "http://192.168.1.1/dicom-web/", "username", "password" ]
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188 }
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189 }
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190 }
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191
260
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192 Two important options can be provided for individual remote DICOMweb servers:
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193
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194 * ``HasDelete`` can be set to ``true`` to indicate that the HTTP
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195 DELETE method can be used to delete remote studies/series/instances.
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196 This notably adds a "delete" button on the Web interface of the
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197 DICOMweb client, and creates a route
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198 ``/dicom-web/servers/sample/delete`` in the REST API.
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199
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200 * ``ChunkedTransfers`` must be set to ``false`` if the remote DICOMweb
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201 server does not support `HTTP chunked transfer encoding
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202 <https://en.wikipedia.org/wiki/Chunked_transfer_encoding>`__. Setting
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203 this option to ``true`` is the best choice to reduce memory
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204 consumption. However, it must be set to ``false`` if the remote
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205 DICOMweb server is Orthanc <= 1.5.6, as chunked transfer encoding is
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206 only supported starting with Orthanc 1.5.7.
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207
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208 You'll have to convert the JSON array into a JSON object to set these
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209 options::
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210
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211 {
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212 [...]
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213 "DicomWeb" : {
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214 "Servers" : {
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215 "sample" : {
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216 "Url" : "http://192.168.1.1/dicom-web/",
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217 "Username" : "username",
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218 "Password" : "password",
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219 "HasDelete" : true,
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220 "ChunkedTransfers" : true // Set to "false" if "sample" is Orthanc <= 1.5.6
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221 }
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222 }
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223 }
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224 }
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225
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226
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227 Furthermore, if the DICOMweb server is protected with HTTPS client
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228 authentication, you must provide your client certificate (in the `PEM
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229 format
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230 <https://en.wikipedia.org/wiki/Privacy-enhanced_Electronic_Mail>`__),
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231 your client private key (also in the PEM format), together with the
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232 password protecting the private key::
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233
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234 {
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235 [...]
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236 "DicomWeb" : {
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237 "Servers" : {
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238 "sample" : {
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239 "Url" : "http://192.168.1.1/dicom-web/",
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240 "CertificateFile" : "client.crt",
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241 "CertificateKeyFile" : "client.key",
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242 "CertificateKeyPassword" : "password"
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243 }
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244 }
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245 }
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246 }
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247
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248 Finally, it is also possible to use client authentication with
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249 hardware security modules and smart cards through `PKCS#11
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250 <https://en.wikipedia.org/wiki/PKCS_11>`__ (this feature is only
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251 available is the core of Orthanc was compiled with the
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252 ``-DENABLE_PKCS11=ON`` option in CMake, and if the Orthanc
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253 configuration file has a proper ``Pkcs11`` section)::
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254
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255 {
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256 [...]
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257 "DicomWeb" : {
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258 "Servers" : {
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259 "sample" : {
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260 "Url" : "http://192.168.1.1/dicom-web/",
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261 "Pkcs11" : true
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262 }
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263 }
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264 }
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265 }
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266
260
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267 **Remark:** A :ref:`plugin by Osimis <google>` is available to
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268 dynamically create authenticated connections to Google Cloud Platform.
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269
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270 **Important remark:** When querying a DICOMweb server, Orthanc will
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271 automatically use the global configuration options ``HttpProxy``,
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272 ``HttpTimeout``, ``HttpsVerifyPeers``, ``HttpsCACertificates``, and
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273 ``Pkcs11``. Make sure to adapt them if need be.
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274
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275
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276 Quickstart - DICOMweb client
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277 ----------------------------
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278
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279 Starting with version 1.0 of the DICOMweb plugin, a Web interface is
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280 provided to use Orthanc as a DICOMweb client. Simply click on the
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281 "Open DICOMweb client" button at the bottom of the welcome screen of
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282 :ref:`Orthanc Explorer <orthanc-explorer>`.
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283
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284 Here is a direct link to the DICOMweb client running on our demo
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285 server:
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286 `http://demo.orthanc-server.com/dicom-web/app/client/index.html
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287 <http://demo.orthanc-server.com/dicom-web/app/client/index.html>`__
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288
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289
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290
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291 Quickstart - DICOMweb server
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292 ----------------------------
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293
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294 Once your Orthanc server is properly configured (see above), you can
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295 make REST calls to the API of the DICOMweb server. For demonstration
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296 purpose, this section makes the assumption that the ``VIX`` dataset
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297 provided by `OsiriX <http://www.osirix-viewer.com/datasets/>`__ has
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298 been uploaded to Orthanc.
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299
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300 WADO-URI
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301 ^^^^^^^^
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302
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303 .. highlight:: text
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304
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305 Here is a proper WADO-URI (previously known simply as WADO) request to
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306 render one slice of the VIX dataset as a JPEG image::
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307
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308 http://localhost:8042/wado?objectUID=1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466&requestType=WADO
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309
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310
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311 .. highlight:: bash
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312
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313 The ``objectUID`` corresponds to the ``SOPInstanceUID`` DICOM tag of
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314 some instance in the ``VIX`` dataset. Given the Orthanc identifier of
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315 an instance from VIX
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316 (e.g. ``14b4db2c-065edecb-6a767936-7068293a-92fcb080``), the latter
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317 tag can be obtained from the ``MainDicomTags`` field::
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318
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319 $ curl http://localhost:8042/instances/14b4db2c-065edecb-6a767936-7068293a-92fcb080
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320
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321
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322 QIDO-RS
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323 ^^^^^^^
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324
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325 .. highlight:: bash
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326
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327 Regarding QIDO-RS (querying the content of a remote DICOMweb server),
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328 here is how to obtain the list of studies stored by Orthanc::
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329
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330 $ curl http://localhost:8042/dicom-web/studies
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331
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332 Note that the ``/dicom-web/`` prefix comes from the configuration
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333 option ``Root`` of the ``DicomWeb`` section. Filtering the studies is
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334 possible as follows::
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335
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336 $ curl http://localhost:8042/dicom-web/studies?PatientName=VIX
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337
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338
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339
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340 WADO-RS
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341 ^^^^^^^
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342
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343 A study can be retrieved through WADO-RS. Here is a sample::
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344
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345 $ curl http://localhost:8042/dicom-web/studies/2.16.840.1.113669.632.20.1211.10000315526/
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346
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347 This answer is a `multipart stream
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348 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of
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349 ``application/dicom`` DICOM instances, so a Web browser will not be
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350 able to display it (. You will have to use either AJAX (JavaScript) or a
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351 command-line tool (such as cURL).
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352
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353 You can render one individual frame as a plain PNG image as follows::
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354
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355 $ 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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356
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357
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358 Other endpoints
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359 ^^^^^^^^^^^^^^^
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360
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361 This page only provides some very basic examples about the use of a
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362 DICOMweb server. Please check out `the full reference of the DICOMweb
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363 API <https://www.dicomstandard.org/dicomweb/>`__ for more information.
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364
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365
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366
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367 .. _dicomweb-client:
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368
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369 REST API of the Orthanc DICOMweb client
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370 ---------------------------------------
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371
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372 Listing the available servers
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373 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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374
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375 .. highlight:: bash
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376
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377 The list of the remote DICOMweb servers that are known to the DICOMweb
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378 plugin can be obtained as follows::
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379
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380 $ curl http://localhost:8042/dicom-web/servers/
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381 [ "sample" ]
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382
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383 In this case, a single server called ``sample`` is configured.
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384
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385
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386 Making a call to QIDO-RS or WADO-RS
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387 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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388
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389 .. highlight:: bash
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390
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391 In Orthanc, the URI ``/{dicom-web-root}/servers/{name}/get`` allows to
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392 make a HTTP GET call against a DICOMweb server. This can be used to
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393 issue a QIDO-RS or WADO-RS command. Orthanc will take care of properly
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394 encoding the URL and authenticating the client. For instance, here is
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395 a sample QIDO-RS search to query all the studies (using a bash
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396 command-line)::
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397
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398 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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399 {
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400 "Uri" : "/studies"
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401 }
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402 EOF
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403
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404 The result of this call is a JSON document formatted according to the
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405 DICOMweb standard. You do not have to specify the base URL of the
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406 remote DICOMweb server, as it is encoded in the configuration file.
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407
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408 As a more advanced example, here is how to search all the series
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409 associated with a given patient name, while requesting to use an XML
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410 format::
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411
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412 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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413 {
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414 "Uri" : "/series",
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415 "HttpHeaders" : {
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416 "Accept" : "application/dicom+xml"
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417 },
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418 "Arguments" : {
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419 "00100010" : "KNIX"
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420 }
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421 }
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422 EOF
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423
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424 The result of the command above is a `multipart stream
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425 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of XML
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426 documents describing each series.
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427
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428 Note how all the GET arguments to the QIDO-RS request must be
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429 specified in the ``Arguments`` field. Orthanc will take care of
260
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430 `properly encoding it as an URL
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431 <https://en.wikipedia.org/wiki/Percent-encoding>`__.
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432
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433 An user-friendly reference of the features available in QIDO-RS and
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434 WADO-RS `can be found on this site <http://www.dicomweb.org/>`__.
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435
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436
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437 Sending DICOM resources to a STOW-RS server
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438 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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439
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440 .. highlight:: bash
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441
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442 STOW-RS allows to send local DICOM resources to a remote DICOMweb
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443 server. In Orthanc, the STOW-RS client primitive is available at URI
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444 ``/{dicom-web-root}/servers/{name}/stow``. Here is a sample call::
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445
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446 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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447 {
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448 "Resources" : [
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449 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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450 ]
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451 }
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452 EOF
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453
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454 Note that this primitive takes as its input a list of :ref:`Orthanc
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455 identifiers <orthanc-ids>` corresponding to the resources (patients,
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456 studies, series and/or instances) to be exported.
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457
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458 Additional HTTP headers can be added with an optional ``HttpHeaders``
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459 argument as for QIDO-RS and WADO-RS. This might be useful e.g. for
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460 cookie-based session management.
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461
262
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462 Internally, this call results in creating an :ref:`Orthanc job <jobs>`
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463 that is executed synchronously (the REST call only returns once the
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464 STOW-RS request is finished). You can run the job in asynchronous
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465 mode as follows::
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466
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467 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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468 {
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469 "Resources" : [
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470 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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471 ],
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472 "Synchronous" : false,
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473 "Priority" : 10
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474 }
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475 EOF
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476
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477 {
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478 "ID" : "a7bd2a5c-291d-4ca5-977a-66502cab22a1",
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479 "Path" : ".././../jobs/a7bd2a5c-291d-4ca5-977a-66502cab22a1"
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480 }
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481
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482 Such a call ends immediately, and returns the ID of the job created by
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483 Orthanc. The :ref:`status of the job <jobs-monitoring>` can then be
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484 monitored using the Orthanc REST API.
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485
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486
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487
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488 Retrieving DICOM resources from a WADO-RS server
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489 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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490
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491 .. highlight:: bash
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492
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493 Once DICOM resources of interest have been identified through a
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494 QIDO-RS call to a remote DICOMweb server (cf. above), it is
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495 interesting to download them locally with a WADO-RS call. You could do
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496 it manually with a second call to the
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497 ``/{dicom-web-root}/servers/{name}/get`` URI, but Orthanc provides
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498 another primitive ``.../retrieve`` to automate this process, in order
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499 to avoid the manual parsing of the multipart stream.
32
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500
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501 Here is how you would download one study, one series and one instance
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502 whose StudyInstanceUID (0020,000d), SeriesInstanceUID (0020,000e) are
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503 SOPInstanceUID (0008,0018) have been identified through a former
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504 QIDO-RS call::
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505
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506 $ curl http://localhost:8042/dicom-web/servers/sample/retrieve -X POST -d @- << EOF
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507 {
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508 "Resources" : [
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509 {
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diff changeset
510 "Study" : "1.3.51.0.1.1.192.168.29.133.1688840.1688819"
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511 },
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512 {
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513 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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514 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041613040617636372171.0.0.0"
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515 },
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516 {
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517 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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518 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0",
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519 "Instance" : "1.3.12.2.1107.5.2.33.37097.2012041612485540185869716"
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520 }
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521 ]
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522 }
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523 EOF
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524
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525 Orthanc will reply with the list of the Orthanc identifiers of all the
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526 DICOM instances that were downloaded from the remote server.
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527
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diff changeset
528 Remark 1: Contrarily to the ``.../stow`` URI that uses :ref:`Orthanc
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diff changeset
529 identifiers <orthanc-ids>`, the ``.../retrieve`` URI uses DICOM
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diff changeset
530 identifiers.
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531
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532 Remark 2: The ``HttpHeaders`` and ``Arguments`` arguments are also
260
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533 available, as for QIDO-RS, to fine-tune the parameters of the WADO-RS
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534 request.
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535
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536 Remark 3: As for QIDO-RS, the request is run synchronously by default.
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537 The ``Synchronous`` and ``Priority`` arguments can be used to
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538 asynchronously run the request.
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539
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540
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541
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542 Additional samples
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543 ------------------
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544
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545 Samples of how to call DICOMweb services from standalone applications
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546 are available for `Python
03b32d0e49f2 documentation of the dicomweb plugin
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547 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/Python/>`__
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548 and for `JavaScript
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549 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/JavaScript>`__.
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550
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551 Integration tests are `available separately
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552 <https://bitbucket.org/sjodogne/orthanc-tests/src/default/Plugins/DicomWeb/Run.py>`__,
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553 and provide samples for more advanced features of the REST API (such
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554 as dynamically adding/updating/removing remote DICOMweb servers using
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555 HTTP PUT and DELETE methods).