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annotate Sphinx/source/plugins/dicomweb.rst @ 258:a073419272c7

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 26 Jun 2019 22:41:33 +0200
parents 949a13b92195
children f9e7036d81d0
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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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15 For general information, check out the `official homepage of the
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16 plugins <http://www.orthanc-server.com/static.php?page=dicomweb>`__.
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18 The full standard is not implemented yet, the supported features are
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19 `tracked in the repository
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20 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Status.txt>`__.
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23 Compilation
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24 -----------
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25
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26 .. highlight:: text
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28 The procedure to compile this plugin is similar of that for the
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29 :ref:`core of Orthanc <compiling>`. The following commands should work
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30 for every UNIX-like distribution (including GNU/Linux)::
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31
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32 $ mkdir Build
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33 $ cd Build
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34 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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35 $ make
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37 The compilation will produce a shared library ``OrthancDicomWeb`` that
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38 contains the DICOMweb plugin. Pre-compiled binaries for Microsoft
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39 Windows `are also available
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40 <http://www.orthanc-server.com/browse.php?path=/plugin-dicom-web>`__,
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41 and are included in the `Windows installers
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42 <https://www.orthanc-server.com/download-windows.php>`__. A package
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43 for `Apple's Mac OS X
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44 <http://localhost/~jodogne/orthanc/static.php?page=download-mac>`__ is
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45 available courtesy of `Osimis <http://osimis.io/>`__.
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46
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47 *Remark:* Some older build instructions are also available in the
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48 `source distribution
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49 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/BuildInstructions.txt>`__.
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52 Usage
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53 -----
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54
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55 .. highlight:: json
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56
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57 You of course first have to :ref:`install Orthanc <binaries>`. Once
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58 Orthanc is installed, you must change the :ref:`configuration file
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59 <configuration>` to tell Orthanc where it can find the plugin: This is
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60 done by properly modifying the ``Plugins`` option. For GNU/Linux, you
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61 could for instance use the following configuration file::
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63 {
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64 "Name" : "MyOrthanc",
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65 [...]
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66 "Plugins" : [
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67 "/home/user/OrthancDicomWeb/Build/libOrthancDicomWeb.so"
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68 ]
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69 }
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70
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71 Or, for Windows::
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72
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73 {
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74 "Name" : "MyOrthanc",
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75 [...]
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76 "Plugins" : [
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77 "c:/Temp/OrthancDicomWeb.dll"
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78 ]
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79 }
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80
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81 Note that the DICOMweb server will share all the parameters of the
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82 Orthanc HTTP server, notably wrt. authentication and HTTPS
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83 encryption. For this reason, you will most probably have to enable the
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84 remote access to the Orthanc HTTP server::
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85
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86 {
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87 [...]
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88 "RemoteAccessEnabled" : true,
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89 [...]
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90 }
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91
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92 Once Orthanc has restarted, the root of the DICOMweb REST API is
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93 accessible at ``http://localhost:8042/dicom-web/``.
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96 Options
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97 -------
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98
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99 Server-related options
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100 ^^^^^^^^^^^^^^^^^^^^^^
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101
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102 .. highlight:: json
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103
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104 There are several configuration options that can be set to fine-tune
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105 the Orthanc DICOMweb server. Here is the full list of the available
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106 options, all of them must be grouped inside the ``DicomWeb`` section of
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107 the Orthanc configuration file::
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108
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109 {
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110 [...]
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111 "DicomWeb" : {
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112 "Enable" : true, // Whether DICOMweb support is enabled
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113 "Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
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114 "EnableWado" : true, // Whether WADO-URI (previously known as WADO) support is enabled
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115 "WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
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116 "Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
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117 "StowMaxInstances" : 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
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118 "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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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 **Remark:** The option ``Host`` is deprecated. Starting with release
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125 0.7 of the DICOMweb plugin, its value are computed from the standard
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126 HTTP headers ``Forwarded`` and ``Host``, as provided by the HTTP
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127 clients.
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128
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129
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130
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131 .. _dicomweb-client-config:
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132
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133 Client-related options
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134 ^^^^^^^^^^^^^^^^^^^^^^
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135
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136 .. highlight:: json
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137
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138 If you want to connect Orthanc as a client to remote DICOMweb servers
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139 (cf. below), you need to modify the configuration file so as to define
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140 each of them in the option ``DicomWeb.Servers``. The syntax is
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141 identical to the ``OrthancPeers`` option of the :ref:`configuration of
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142 the Orthanc core <configuration>`.
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143
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144 In the most simple case, here is how to instruct Orthanc about the
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145 existence of a password-less DICOMweb server that will be referred to
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146 as "sample" in Orthanc::
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147
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148 {
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149 [...]
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150 "DicomWeb" : {
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151 "Servers" : {
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152 "sample" : [ "http://192.168.1.1/dicom-web/" ]
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153 }
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154 }
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155 }
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156
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157 You are of course free to add as many DICOMweb servers as you need. If
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158 the DICOMweb server is protected by a password (with `HTTP Basic
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159 access authentication
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160 <https://en.wikipedia.org/wiki/Basic_access_authentication>`__)::
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161
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162 {
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163 [...]
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164 "DicomWeb" : {
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165 "Servers" : {
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166 "sample" : [ "http://192.168.1.1/dicom-web/", "username", "password" ]
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167 }
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168 }
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169 }
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170
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171 If the DICOMweb server is protected with HTTPS client authentication,
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172 you must provide your client certificate (in the `PEM format
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173 <https://en.wikipedia.org/wiki/Privacy-enhanced_Electronic_Mail>`__),
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174 your client private key (also in the PEM format), together with the
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175 password protecting the private key::
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176
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177 {
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178 [...]
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179 "DicomWeb" : {
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180 "Servers" : {
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181 "sample" : {
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182 "Url" : "http://192.168.1.1/dicom-web/",
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183 "CertificateFile" : "client.crt",
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184 "CertificateKeyFile" : "client.key",
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185 "CertificateKeyPassword" : "password"
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186 }
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187 }
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188 }
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189 }
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190
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191 Finally, it is also possible to use client authentication with
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192 hardware security modules and smart cards through `PKCS#11
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193 <https://en.wikipedia.org/wiki/PKCS_11>`__ (this feature is only
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194 available is the core of Orthanc was compiled with the
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195 ``-DENABLE_PKCS11=ON`` option in CMake, and if the Orthanc
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196 configuration file has a proper ``Pkcs11`` section)::
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197
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198 {
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199 [...]
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200 "DicomWeb" : {
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201 "Servers" : {
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202 "sample" : {
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203 "Url" : "http://192.168.1.1/dicom-web/",
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204 "Pkcs11" : true
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205 }
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206 }
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207 }
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208 }
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209
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210 **Important remark:** When querying a DICOMweb server, Orthanc will
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211 automatically use the global configuration options ``HttpProxy``,
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212 ``HttpTimeout``, ``HttpsVerifyPeers``, ``HttpsCACertificates``, and
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213 ``Pkcs11``. Make sure to adapt them if need be.
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214
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215
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216 Quickstart
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217 ----------
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218
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219 Once your Orthanc is properly configured (see above), you can make
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220 REST calls to the DICOMweb API. For demonstration purpose, this
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221 section makes the assumption that the ``VIX`` dataset provided by
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222 `OsiriX <http://www.osirix-viewer.com/datasets/>`__ has been uploaded
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223 to Orthanc.
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224
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225 WADO-URI
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226 ^^^^^^^^
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227
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228 .. highlight:: text
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229
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230 Here is a proper WADO-URI (previously known simply as WADO) request to
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231 render one slice of the VIX dataset as a JPEG image::
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232
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233 http://localhost:8042/wado?objectUID=1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466&requestType=WADO
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234
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235 The ``objectUID`` corresponds to the ``SOPInstanceUID`` DICOM tag of
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236 some instance in the ``VIX`` dataset. Given the Orthanc identifier of
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237 an instance from VIX
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238 (e.g. ``14b4db2c-065edecb-6a767936-7068293a-92fcb080``), the latter
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239 tag can be obtained from the ``MainDicomTags`` field::
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240
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241 # curl http://localhost:8042/instances/14b4db2c-065edecb-6a767936-7068293a-92fcb080
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242
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243
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244 WADO-RS
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245 ^^^^^^^
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246
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247 .. highlight:: text
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248
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249 Regarding WADO-RS (i.e. DICOMweb RESTful services), here is how to
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250 obtain the tags of all the instances stored by Orthanc::
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251
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252 # curl http://localhost:8042/dicom-web/instances
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253
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254 Note that, as the MIME type of this answer is a multipart
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255 ``application/dicom+xml``, a Web browser will not be able to display
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256 it. You will have to use either AJAX (JavaScript) or a command-line
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257 tool (such as curl).
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258
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259 Here is how to generate a JPEG preview of one instance with WADO-RS
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260 (through the RetrieveFrames primitive)::
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261
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262 # 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 -H 'accept: multipart/related; type=image/dicom+jpeg'
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263
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264
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265
238
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266 .. _dicomweb-client:
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267
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268 Querying a remote DICOMweb server with Orthanc
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269 ----------------------------------------------
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270
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271 Listing the available servers
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272 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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273
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274 .. highlight:: text
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275
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276 The list of the remote DICOMweb servers that are known to the DICOMweb
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277 plugin can be obtained as follows::
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278
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279 # curl http://localhost:8042/dicom-web/servers/
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280 [ "sample" ]
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281
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282 Here, a single server called ``sample`` is configured.
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283
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284
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285 Making a call to QIDO-RS or WADO-RS
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286 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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287
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288 .. highlight:: text
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289
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290 In Orthanc, the URI ``/{dicom-web-root}/servers/{name}/get`` allows to
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291 make a HTTP GET call against a DICOMweb server. This can be used to
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292 issue a QIDO-RS or WADO-RS command. Orthanc will take care of properly
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293 encoding the URL and authenticating the client.
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294
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295 For instance, here is a sample QIDO-RS search to query all the studies
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296 (using a bash command-line)::
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297
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298 # curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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299 {
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300 "Uri" : "/studies"
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301 }
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302 EOF
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303
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304 You do not have to specify the base URL of the remote DICOMweb server,
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305 as it is encoded in the configuration file.
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306
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307 The result of the command above is a multipart
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308 ``application/dicom+xml`` document. It is possible to request a more
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309 human-friendly JSON answer by adding the ``Accept`` HTTP header. Here
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310 is how to search for a given patient name, while requesting a JSON
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311 answer and pretty-printing through the ``json_pp`` command-line tool::
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312
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313 # curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF | json_pp
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314 {
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315 "Uri" : "/studies",
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316 "HttpHeaders" : {
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317 "Accept" : "application/json"
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318 },
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319 "Arguments" : {
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320 "00100010" : "*JODOGNE*"
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321 }
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322 }
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323 EOF
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324
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325 Note how all the GET arguments for the QIDO-RS request must be
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326 specified in the ``Arguments`` field. Orthanc will take care of
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327 properly encoding it to a URL.
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328
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329 An user-friendly reference of the features available in QIDO-RS and
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330 WADO-RS `can be found on this site <http://www.dicomweb.org/>`__.
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331
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332
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333 Sending DICOM resources to a STOW-RS server
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334 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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335
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336 .. highlight:: text
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337
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338 STOW-RS allows to send local DICOM resources to a remote DICOMweb
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339 server. In Orthanc, the STOW-RS client primitive is available at URI
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340 ``/{dicom-web-root}/servers/{name}/stow``. Here is a sample call::
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341
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342 # curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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343 {
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344 "Resources" : [
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345 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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346 ]
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347 }
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348 EOF
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349
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350 Note that this primitive takes as its input a list of :ref:`Orthanc
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351 identifiers <orthanc-ids>` corresponding to the resources (patients,
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352 studies, series and/or instances) to be exported.
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353
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354 Remark 1: Additional HTTP headers can be added with an optional
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355 ``HttpHeaders`` argument as for QIDO-RS and WADO-RS. This might be
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356 useful e.g. for cookie-based session management.
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357
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358 Remark 2: One call to this ``.../stow`` primitive will possibly result
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359 in several HTTP requests to the DICOMweb server, in order to limit the
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360 size of the HTTP messages. The configuration options
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361 ``DicomWeb.StowMaxInstances`` and ``DicomWeb.StowMaxSize`` can be used
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362 to tune this behavior (set both options to 0 to send one single
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363 request).
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364
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365
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366 Retrieving DICOM resources from a WADO-RS server
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367 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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368
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369 .. highlight:: text
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370
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371 Once DICOM resources of interest have been identified through a
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372 QIDO-RS call to a remote DICOMweb server (cf. above), it is
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373 interesting to download them locally with a WADO-RS call. You could do
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374 it manually with a second call to the
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375 ``/{dicom-web-root}/servers/{name}/get`` URI, but Orthanc provides
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376 another primitive ``.../retrieve`` to automate this process.
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377
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378 Here is how you would download one study, one series and one instance
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379 whose StudyInstanceUID (0020,000d), SeriesInstanceUID (0020,000e) are
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380 SOPInstanceUID (0008,0018) have been identified through a former
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381 QIDO-RS call::
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382
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383 # curl http://localhost:8042/dicom-web/servers/sample/retrieve -X POST -d @- << EOF
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384 {
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385 "Resources" : [
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386 {
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387 "Study" : "1.3.51.0.1.1.192.168.29.133.1688840.1688819"
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388 },
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389 {
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390 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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391 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041613040617636372171.0.0.0"
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392 },
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393 {
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394 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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395 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0",
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396 "Instance" : "1.3.12.2.1107.5.2.33.37097.2012041612485540185869716"
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397 }
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398 ]
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399 }
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400 EOF
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401
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402 Orthanc will reply with the list of the Orthanc identifiers of all the
03b32d0e49f2 documentation of the dicomweb plugin
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403 DICOM instances that were downloaded from the remote server.
03b32d0e49f2 documentation of the dicomweb plugin
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parents: 31
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404
03b32d0e49f2 documentation of the dicomweb plugin
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405 Remark 1: Contrarily to the ``.../stow`` URI that uses :ref:`Orthanc
03b32d0e49f2 documentation of the dicomweb plugin
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parents: 31
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406 identifiers <orthanc-ids>`, the ``.../retrieve`` URI uses DICOM
03b32d0e49f2 documentation of the dicomweb plugin
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407 identifiers.
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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408
89
c9a33e4a0577 fix mixup between HttpArguments and HttpHeaders in WADO-RS
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409 Remark 2: The ``HttpHeaders`` and ``Arguments`` arguments are also
c9a33e4a0577 fix mixup between HttpArguments and HttpHeaders in WADO-RS
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410 available, as for QIDO-RS.
32
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411
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412
03b32d0e49f2 documentation of the dicomweb plugin
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413
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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414 Additional samples
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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415 ------------------
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Sebastien Jodogne <s.jodogne@gmail.com>
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416
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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417 Samples of how to call DICOMweb services from standalone applications
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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418 are available for `Python
03b32d0e49f2 documentation of the dicomweb plugin
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419 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/Python/>`__
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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420 and for `JavaScript
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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421 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/JavaScript>`__.
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parents: 31
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422
03b32d0e49f2 documentation of the dicomweb plugin
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423 Some integration tests are also `available separately
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
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424 <https://bitbucket.org/sjodogne/orthanc-tests/src/default/Plugins/DicomWeb/Run.py>`__
03b32d0e49f2 documentation of the dicomweb plugin
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425 (work in progress).