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annotate Sphinx/source/plugins/dicomweb.rst @ 247:325dd3901547

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 19 May 2019 10:08:52 +0200
parents 57ecb27d1851
children 949a13b92195
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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
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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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27
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28 The procedure to compile these plugins 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 A package for `Apple's Mac OS X
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42 <http://localhost/~jodogne/orthanc/static.php?page=download-mac>`__ is
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43 available courtesy of `Osimis <http://osimis.io/>`__.
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44
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45 *Remark:* Some older build instructions are also available in the
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46 `source distribution
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47 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/BuildInstructions.txt>`__.
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49
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50 Usage
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51 -----
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52
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53 .. highlight:: json
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54
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55 You of course first have to :ref:`install Orthanc <binaries>`. Once
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56 Orthanc is installed, you must change the :ref:`configuration file
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57 <configuration>` to tell Orthanc where it can find the plugin: This is
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58 done by properly modifying the ``Plugins`` option. For GNU/Linux, you
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59 could for instance use the following configuration file::
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60
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61 {
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62 "Name" : "MyOrthanc",
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63 [...]
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64 "Plugins" : [
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65 "/home/user/OrthancDicomWeb/Build/libOrthancDicomWeb.so"
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66 ]
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67 }
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68
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69 Or, for Windows::
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70
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71 {
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72 "Name" : "MyOrthanc",
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73 [...]
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74 "Plugins" : [
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75 "c:/Temp/OrthancDicomWeb.dll"
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76 ]
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77 }
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78
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79 Note that the DICOMweb server will share all the parameters of the
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80 Orthanc HTTP server, notably wrt. authentication and HTTPS
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81 encryption. For this reason, you will most probably have to enable the
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82 remote access to the Orthanc HTTP server::
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83
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84 {
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85 [...]
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86 "RemoteAccessEnabled" : true,
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87 [...]
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88 }
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89
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90 Once Orthanc has restarted, the root of the DICOMweb REST API is
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91 accessible at ``http://localhost:8042/dicom-web/``.
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93
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94 Options
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95 -------
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96
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97 Server-related options
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98 ^^^^^^^^^^^^^^^^^^^^^^
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99
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100 .. highlight:: json
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101
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102 There are several configuration options that can be set to fine-tune
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103 the Orthanc DICOMweb server. Here is the full list of the available
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104 options, all of them must be grouped inside the ``DicomWeb`` section of
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105 the Orthanc configuration file::
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106
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107 {
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108 [...]
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109 "DicomWeb" : {
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110 "Enable" : true, // Whether DICOMweb support is enabled
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111 "Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
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112 "EnableWado" : true, // Whether WADO-URI (previously known as WADO) support is enabled
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113 "WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
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114 "Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
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115 "StowMaxInstances" : 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
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116 "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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117 "QidoCaseSensitive" : true, // For QIDO-RS server, whether search is case sensitive (since release 0.5)
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118 "Host" : "localhost" // Hard-codes the name of the host for subsequent WADO-RS requests (deprecated)
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119 }
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120 }
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121
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122 **Remark:** The option ``Host`` is deprecated. Starting with release
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123 0.7 of the DICOMweb plugin, its value are computed from the standard
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124 HTTP headers ``Forwarded`` and ``Host``, as provided by the HTTP
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125 clients.
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126
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127
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128
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129 Client-related options
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130 ^^^^^^^^^^^^^^^^^^^^^^
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131
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132 .. highlight:: json
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133
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134 If you want to connect Orthanc as a client to remote DICOMweb servers
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135 (cf. below), you need to modify the configuration file so as to define
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136 each of them in the option ``DicomWeb.Servers``. The syntax is
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137 identical to the ``OrthancPeers`` option of the :ref:`configuration of
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138 the Orthanc core <configuration>`.
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139
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140 In the most simple case, here is how to instruct Orthanc about the
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141 existence of a password-less DICOMweb server that will be referred to
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142 as "sample" in Orthanc::
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143
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144 {
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145 [...]
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146 "DicomWeb" : {
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147 "Servers" : {
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148 "sample" : [ "http://192.168.1.1/dicom-web/" ]
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149 }
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150 }
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151 }
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152
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153 You are of course free to add as many DICOMweb servers as you need. If
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154 the DICOMweb server is protected by a password (with `HTTP Basic
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155 access authentication
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156 <https://en.wikipedia.org/wiki/Basic_access_authentication>`__)::
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157
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158 {
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159 [...]
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160 "DicomWeb" : {
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161 "Servers" : {
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162 "sample" : [ "http://192.168.1.1/dicom-web/", "username", "password" ]
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163 }
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164 }
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165 }
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166
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167 If the DICOMweb server is protected with HTTPS client authentication,
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168 you must provide your client certificate (in the `PEM format
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169 <https://en.wikipedia.org/wiki/Privacy-enhanced_Electronic_Mail>`__),
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170 your client private key (also in the PEM format), together with the
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171 password protecting the private key::
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172
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173 {
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174 [...]
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175 "DicomWeb" : {
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176 "Servers" : {
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177 "sample" : {
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178 "Url" : "http://192.168.1.1/dicom-web/",
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179 "CertificateFile" : "client.crt",
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180 "CertificateKeyFile" : "client.key",
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181 "CertificateKeyPassword" : "password"
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182 }
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183 }
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184 }
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185 }
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186
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187 Finally, it is also possible to use client authentication with
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188 hardware security modules and smart cards through `PKCS#11
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189 <https://en.wikipedia.org/wiki/PKCS_11>`__ (this feature is only
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190 available is the core of Orthanc was compiled with the
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191 ``-DENABLE_PKCS11=ON`` option in CMake, and if the Orthanc
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192 configuration file has a proper ``Pkcs11`` section)::
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193
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194 {
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195 [...]
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196 "DicomWeb" : {
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197 "Servers" : {
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198 "sample" : {
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199 "Url" : "http://192.168.1.1/dicom-web/",
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200 "Pkcs11" : true
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201 }
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202 }
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203 }
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204 }
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205
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206 **Important remark:** When querying a DICOMweb server, Orthanc will
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207 automatically use the global configuration options ``HttpProxy``,
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208 ``HttpTimeout``, ``HttpsVerifyPeers``, ``HttpsCACertificates``, and
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209 ``Pkcs11``. Make sure to adapt them if need be.
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210
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211
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212 Quickstart
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213 ----------
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214
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215 Once your Orthanc is properly configured (see above), you can make
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216 REST calls to the DICOMweb API. For demonstration purpose, this
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217 section makes the assumption that the ``VIX`` dataset provided by
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218 `OsiriX <http://www.osirix-viewer.com/datasets/>`__ has been uploaded
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219 to Orthanc.
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220
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221 WADO-URI
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222 ^^^^^^^^
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223
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224 .. highlight:: text
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225
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226 Here is a proper WADO-URI (previously known simply as WADO) request to
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227 render one slice of the VIX dataset as a JPEG image::
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228
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229 http://localhost:8042/wado?objectUID=1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466&requestType=WADO
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230
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231 The ``objectUID`` corresponds to the ``SOPInstanceUID`` DICOM tag of
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232 some instance in the ``VIX`` dataset. Given the Orthanc identifier of
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233 an instance from VIX
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234 (e.g. ``14b4db2c-065edecb-6a767936-7068293a-92fcb080``), the latter
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235 tag can be obtained from the ``MainDicomTags`` field::
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236
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237 # curl http://localhost:8042/instances/14b4db2c-065edecb-6a767936-7068293a-92fcb080
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238
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239
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240 WADO-RS
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241 ^^^^^^^
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242
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243 .. highlight:: text
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244
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245 Regarding WADO-RS (i.e. DICOMweb RESTful services), here is how to
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246 obtain the tags of all the instances stored by Orthanc::
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247
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248 # curl http://localhost:8042/dicom-web/instances
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249
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250 Note that, as the MIME type of this answer is a multipart
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251 ``application/dicom+xml``, a Web browser will not be able to display
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252 it. You will have to use either AJAX (JavaScript) or a command-line
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253 tool (such as curl).
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254
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255 Here is how to generate a JPEG preview of one instance with WADO-RS
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256 (through the RetrieveFrames primitive)::
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257
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258 # 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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259
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260
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261
238
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262 .. _dicomweb-client:
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263
32
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264 Querying a remote DICOMweb server with Orthanc
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265 ----------------------------------------------
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266
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267 Listing the available servers
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268 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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269
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270 .. highlight:: text
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271
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272 The list of the remote DICOMweb servers that are known to the DICOMweb
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273 plugin can be obtained as follows::
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274
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275 # curl http://localhost:8042/dicom-web/servers/
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276 [ "sample" ]
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277
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278 Here, a single server called ``sample`` is configured.
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279
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280
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281 Making a call to QIDO-RS or WADO-RS
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282 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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283
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284 .. highlight:: text
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285
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286 In Orthanc, the URI ``/{dicom-web-root}/servers/{name}/get`` allows to
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287 make a HTTP GET call against a DICOMweb server. This can be used to
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288 issue a QIDO-RS or WADO-RS command. Orthanc will take care of properly
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289 encoding the URL and authenticating the client.
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290
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291 For instance, here is a sample QIDO-RS search to query all the studies
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292 (using a bash command-line)::
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293
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294 # curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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295 {
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296 "Uri" : "/studies"
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297 }
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298 EOF
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299
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300 You do not have to specify the base URL of the remote DICOMweb server,
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301 as it is encoded in the configuration file.
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302
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303 The result of the command above is a multipart
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304 ``application/dicom+xml`` document. It is possible to request a more
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305 human-friendly JSON answer by adding the ``Accept`` HTTP header. Here
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306 is how to search for a given patient name, while requesting a JSON
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307 answer and pretty-printing through the ``json_pp`` command-line tool::
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308
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309 # curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF | json_pp
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310 {
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311 "Uri" : "/studies",
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312 "HttpHeaders" : {
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313 "Accept" : "application/json"
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314 },
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315 "Arguments" : {
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316 "00100010" : "*JODOGNE*"
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317 }
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318 }
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319 EOF
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320
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321 Note how all the GET arguments for the QIDO-RS request must be
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322 specified in the ``Arguments`` field. Orthanc will take care of
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323 properly encoding it to a URL.
32
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324
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325 An user-friendly reference of the features available in QIDO-RS and
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326 WADO-RS `can be found on this site <http://www.dicomweb.org/>`__.
32
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327
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328
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329 Sending DICOM resources to a STOW-RS server
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330 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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331
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332 .. highlight:: text
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333
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334 STOW-RS allows to send local DICOM resources to a remote DICOMweb
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335 server. In Orthanc, the STOW-RS client primitive is available at URI
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336 ``/{dicom-web-root}/servers/{name}/stow``. Here is a sample call::
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337
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338 # curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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339 {
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340 "Resources" : [
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341 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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342 ]
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343 }
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344 EOF
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345
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346 Note that this primitive takes as its input a list of :ref:`Orthanc
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347 identifiers <orthanc-ids>` corresponding to the resources (patients,
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348 studies, series and/or instances) to be exported.
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349
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350 Remark 1: Additional HTTP headers can be added with an optional
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351 ``HttpHeaders`` argument as for QIDO-RS and WADO-RS. This might be
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352 useful e.g. for cookie-based session management.
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353
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354 Remark 2: One call to this ``.../stow`` primitive will possibly result
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355 in several HTTP requests to the DICOMweb server, in order to limit the
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356 size of the HTTP messages. The configuration options
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357 ``DicomWeb.StowMaxInstances`` and ``DicomWeb.StowMaxSize`` can be used
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358 to tune this behavior (set both options to 0 to send one single
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359 request).
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360
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361
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362 Retrieving DICOM resources from a WADO-RS server
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363 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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364
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365 .. highlight:: text
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366
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367 Once DICOM resources of interest have been identified through a
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368 QIDO-RS call to a remote DICOMweb server (cf. above), it is
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369 interesting to download them locally with a WADO-RS call. You could do
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370 it manually with a second call to the
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371 ``/{dicom-web-root}/servers/{name}/get`` URI, but Orthanc provides
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372 another primitive ``.../retrieve`` to automate this process.
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373
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374 Here is how you would download one study, one series and one instance
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375 whose StudyInstanceUID (0020,000d), SeriesInstanceUID (0020,000e) are
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376 SOPInstanceUID (0008,0018) have been identified through a former
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377 QIDO-RS call::
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378
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379 # curl http://localhost:8042/dicom-web/servers/sample/retrieve -X POST -d @- << EOF
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380 {
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381 "Resources" : [
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382 {
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383 "Study" : "1.3.51.0.1.1.192.168.29.133.1688840.1688819"
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384 },
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385 {
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386 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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387 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041613040617636372171.0.0.0"
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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" : "1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0",
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392 "Instance" : "1.3.12.2.1107.5.2.33.37097.2012041612485540185869716"
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393 }
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394 ]
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395 }
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396 EOF
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397
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398 Orthanc will reply with the list of the Orthanc identifiers of all the
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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399 DICOM instances that were downloaded from the remote server.
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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400
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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401 Remark 1: Contrarily to the ``.../stow`` URI that uses :ref:`Orthanc
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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402 identifiers <orthanc-ids>`, the ``.../retrieve`` URI uses DICOM
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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403 identifiers.
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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404
89
c9a33e4a0577 fix mixup between HttpArguments and HttpHeaders in WADO-RS
Sebastien Jodogne <s.jodogne@gmail.com>
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405 Remark 2: The ``HttpHeaders`` and ``Arguments`` arguments are also
c9a33e4a0577 fix mixup between HttpArguments and HttpHeaders in WADO-RS
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406 available, as for QIDO-RS.
32
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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407
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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408
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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409
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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410 Additional samples
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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411 ------------------
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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412
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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413 Samples of how to call DICOMweb services from standalone applications
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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414 are available for `Python
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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415 <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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416 and for `JavaScript
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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417 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/JavaScript>`__.
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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418
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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419 Some integration tests are also `available separately
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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420 <https://bitbucket.org/sjodogne/orthanc-tests/src/default/Plugins/DicomWeb/Run.py>`__
03b32d0e49f2 documentation of the dicomweb plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
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421 (work in progress).