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documentation of IIIF support
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 13 Jul 2023 16:26:49 +0200
parents dfd33c9624d8
children 1316bc62b5d5
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1 .. _ohif:
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2
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3
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4 OHIF 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 by the `ICTEAM institute of UCLouvain
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10 <https://uclouvain.be/en/research-institutes/icteam>`__ extends
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11 Orthanc with the `OHIF <https://ohif.org/>`__ extensible Web imaging
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12 platform.
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13
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14 The plugin greatly simplifies the deployment of OHIF, as it does not
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15 necessitate the setup of any reverse proxy.
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16
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17 If you face difficulties in using OHIF, please get in touch with the
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18 `OHIF community <https://ohif.org/collaborate>`__ in the first place.
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19 Indeed, the OHIF and Orthanc communities are entirely distinct.
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20
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21
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22 Usage
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23 -----
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24
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25 This plugin adds a dedicated button to Orthanc Explorer, which
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26 provides an easy, fast access to the OHIF viewers (click on the image
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27 to view a demo video):
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28
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29 .. image:: ../images/OHIF.png
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30 :align: center
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31 :width: 800
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32 :target: https://www.youtube.com/watch?v=-lzddzq9iT4
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33
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34 |
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36
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37 Compilation
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38 -----------
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39
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40 .. highlight:: bash
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41
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42 Official releases can be `downloaded from the Orthanc homepage
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43 <https://www.orthanc-server.com/browse.php?path=/plugin-ohif>`__. As
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44 an alternative, the `repository containing the source code
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45 <https://orthanc.uclouvain.be/hg/orthanc-ohif/>`__ can be accessed
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46 using Mercurial.
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47
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48 The procedure to compile this plugin is similar of that for the
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49 :ref:`core of Orthanc <binaries>`. The following commands should work
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50 on most GNU/Linux distributions, provided Docker is installed::
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51
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52 $ mkdir Build
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53 $ cd Build
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54 $ ../Resources/CreateOHIFDist.sh
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55 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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56 $ make
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57
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58 The compilation will produce a shared library ``libOrthancOHIF.so``
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59 that contains the OHIF plugin for Orthanc.
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60
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61 Pre-compiled Linux Standard Base (LSB) binaries `are available for
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62 download <https://lsb.orthanc-server.com/plugin-ohif/>`__.
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63
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64 Pre-compiled binaries for Microsoft Windows and macOS `are also
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65 available
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66 <https://www.orthanc-server.com/browse.php?path=/plugin-ohif>`__.
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67
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68 Furthermore, the :ref:`Docker images <docker>`
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69 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
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70 plugin. Debian and Ubuntu packages can be found in the
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71 :ref:`standalone repository <binaries>`
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72 ``https://debian.orthanc-labs.com/``.
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75 Configuration
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76 -------------
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77
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78 .. highlight:: json
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79
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80 Here is a minimal sample :ref:`configuration file <configuration>` to
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81 use this plugin::
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82
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83 {
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84 "Plugins" : [
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85 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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86 ]
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87 }
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88
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89 Orthanc must of course be restarted after the modification of its
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90 configuration file.
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91
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92
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93 Using DICOMweb
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94 ^^^^^^^^^^^^^^
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95
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96 .. highlight:: json
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97
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98 By default, the plugin uses the `DICOM JSON data source
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99 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__ of
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100 OHIF. This data source is optimized to provide the fastest access to
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101 the DICOM images, while requiring no additional plugin. However, in
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102 order to deliver fast access, the OHIF plugin will cache additional
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103 information about each DICOM instance as :ref:`metadata <metadata>` in
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104 the Orthanc database, which results in a larger size of the Orthanc
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105 database (an additional 1KB is roughly needed per instance).
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106
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107 As an alternative, it is possible to enable the `DICOMweb data source
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108 <https://v3-docs.ohif.org/configuration/dataSources/dicom-web>`__. In
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109 this case, the :ref:`DICOMweb plugin of Orthanc <dicomweb>` must also
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110 be loaded. It can also be useful to load the :ref:`GDCM plugin <gdcm>`
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111 if the DICOM images are encoded using a JPEG2k compressed transfer
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112 syntax.
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113
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114 The advantages of using DICOMweb over the default DICOM JSON are:
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115
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116 * More standard-compliant.
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117
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118 * The OHIF study list is accessible, notably as a button on the
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119 welcome screen of Orthanc Explorer. The study list is not available
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120 if using the DICOM JSON data source.
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121
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122 * No additional space is used in the Orthanc database.
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123
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124 Here is a minimal configuration file to use DICOMweb::
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125
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126 {
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127 "Plugins" : [
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128 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so",
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129 "/home/user/orthanc-dicomweb/Build/libOrthancDicomWeb.so"
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130 ],
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131 "OHIF" : {
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132 "DataSource" : "dicom-web"
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133 }
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134 }
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135
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136
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137 User configuration of OHIF
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138 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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139
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140 .. highlight:: json
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141
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142 OHIF comes with a number of `configuration options
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143 <https://v3-docs.ohif.org/configuration/configurationfiles/#configuration-options>`__
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144 that can be fine-tuned by the user. User settings can be injected
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145 using the ``UserConfiguration`` option as follows::
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146
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147 {
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148 "Plugins" : [
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149 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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150 ],
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151 "OHIF" : {
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152 "UserConfiguration" : "ohif.js"
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153 }
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154 }
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155
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156 .. highlight:: javascript
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157
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158 A minimal ``ohif.js`` would be::
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159
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160 window.config = {
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161 extensions: [],
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162 modes: []
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163 }
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164
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165 Note that the following configuration options will be overridden by
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166 the OHIF plugin to properly configure the data source and the
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167 integration with the Orthanc Web server:
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168
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169 * ``window.config.dataSources``
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170 * ``window.config.defaultDataSourceName``
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171 * ``window.config.routerBasename``
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172 * ``window.config.showStudyList`` (set to ``false`` if using the DICOM
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173 JSON data source)
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174
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175
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176 .. _ohif-router-basename:
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177
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178 Router basename
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179 ^^^^^^^^^^^^^^^
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180
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181 .. highlight:: json
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182
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183 If Orthanc is not branched at the root of a Web server thanks of the
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184 presence of a reverse proxy, the configuration option
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185 ``RouterBasename`` must be adapted.
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186
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187 For instance, if Orthanc is running at address
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188 ``https://host.com/imaging/demo/orthanc/``, the following
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189 configuration file must be used for OHIF to work::
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190
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191 {
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192 "Plugins" : [
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193 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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194 ],
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195 "OHIF" : {
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196 "RouterBasename" : "/imaging/demo/orthanc/ohif/"
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197 }
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198 }
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199
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200 The default value of ``RouterBasename`` is ``/ohif/``.
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201
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202
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203 .. _ohif-preloading:
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204
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205 Preloading
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206 ^^^^^^^^^^
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207
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208 .. highlight:: json
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209
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210 If using the DICOM JSON data source, whenever a new DICOM instance is
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211 received by Orthanc, the OHIF plugin will compute a summary of the
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212 DICOM tags of interest to OHIF, and will store it as :ref:`metadata
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213 <metadata>` in the Orthanc database. This process has the advantage of
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214 speeding up even the first opening of the DICOM study by OHIF, which
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215 probably corresponds to the expectations of most radiologists.
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216
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217 However, if your Orthanc deployment is focused on speed, this
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218 preloading might be undesirable, as it slows down the ingestion of new
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219 DICOM instances by Orthanc. Furthermore, if your Orthanc server will
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220 contain a large number of DICOM studies that will never be displayed
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221 using OHIF, this can result in a waste of space in the Orthanc
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222 database because of the metadata that will be preloaded, but that will
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223 never be read.
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224
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225 It is consequently possible to turn off the automated preloading
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226 of metadata using the following configuration::
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227
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228 {
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229 "Plugins" : [
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230 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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231 ],
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232 "OHIF" : {
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233 "DataSource" : "dicom-json",
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234 "Preload" : false
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235 }
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236 }
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237
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238 If the ``Preload`` option is set to ``false``, the first display of a
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239 DICOM study can take several seconds because of the computation of the
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240 metadata, but subsequent displays will run much faster.
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241
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242 Note that preloading is only applied to the newly received instances:
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243 The DICOM instances that were stored in the Orthanc server before the
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244 installation of the OHIF plugin will only benefit from the
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245 optimization starting with their second display using OHIF.
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246
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247
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248 .. _ohif-https:
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249
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250 HTTPS encryption
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251 ^^^^^^^^^^^^^^^^
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252
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253 .. highlight:: bash
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254
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255 In order to use the :ref:`built-in HTTPS encryption <https-builtin>`
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256 of Orthanc together with the OHIF plugin, first generate a proper
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257 X.509 certificate for the ``localhost``::
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258
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259 $ openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
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260 -subj "/C=BE/CN=localhost" -keyout /tmp/private.key -out /tmp/certificate.crt
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261 $ cat /tmp/private.key /tmp/certificate.crt > /tmp/certificate.pem
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262
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263
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264 .. highlight:: json
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265
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266 Secondly, create the following configuration file::
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267
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268 {
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269 "Plugins" : [
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270 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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271 ],
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272 "SslEnabled" : true,
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273 "SslCertificate" : "/tmp/certificate.pem",
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274 "OHIF" : {
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275 "DataSource" : "dicom-json",
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276 "RouterBasename" : "/ohif/"
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277 }
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278 }
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279
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280 If more complex scenarios with reverse proxies are involved, make sure
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281 to properly setup :ref:`CORS in your reverse proxy <nginx-cors>` and
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282 to :ref:`adapt the router basename <ohif-router-basename>`. If you
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283 face difficulties, while the simple setup with the built-in HTTPS
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284 encryption described above works, your issue is related to OHIF, so
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285 please get in touch with the `OHIF community
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286 <https://ohif.org/collaborate>`__.
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287
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288
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289 For developers
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290 --------------
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291
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292 Extensions to the REST API
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293 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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294
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295 .. highlight:: bash
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296
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297 The content of the `DICOM JSON data source
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298 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__
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299 for a DICOM study of interest can be retrieved as follows::
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300
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301 $ curl http://demo.orthanc-server.com/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/ohif-dicom-json
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302
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303 This data source is constructed from the :ref:`metadata 4202
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304 <registry>` associated with the individual DICOM instances of the
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305 DICOM study. The metadata corresponds to the `Base64 encoding
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306 <https://en.wikipedia.org/wiki/Base64>`__ of a gzipped JSON file. For
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307 debugging, the JSON file associated with a DICOM instance can be
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308 inspected using::
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309
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310 $ curl http://demo.orthanc-server.com/instances/1f3c00bd-49df10b7-f416a598-1b3bb5a2-cb791b52/metadata/4202 | base64 -d | gunzip -c
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311
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312
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313 Preloading existing studies
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314 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
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315
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316 :ref:`As explained above <ohif-preloading>`, the metadata associated
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317 with DICOM instances are only preloaded for the newly ingested DICOM
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318 instances. Using the REST API of Orthanc, it is easy to create a
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319 script that would preload the metadata for the already existing DICOM
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320 studies, hereby greatly speeding up the first opening of those studies
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321 as well.
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322
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323 This script would loop over the :ref:`the DICOM studies that are
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324 stored by Orthanc <rest-access>` using ``GET /studies``. For each
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325 study whose :ref:`Orthanc identifier <orthanc-ids>` is ``id``, the
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326 script would simply call ``GET /studies/{id}/ohif-dicom-json``.
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327