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annotate Sphinx/source/plugins/ohif.rst @ 1071:63a3d4e82c2a

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correct extensions of Nexus
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 22 May 2024 17:08:31 +0200
parents ccba1d561379
children f8a335fdeae7
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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://orthanc.uclouvain.be/>`__ extends Orthanc with the `OHIF
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11 <https://ohif.org/>`__ extensible Web imaging platform.
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12
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13 The plugin greatly simplifies the deployment of OHIF, as it does not
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14 necessitate the setup of any reverse proxy.
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15
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16 If you face difficulties in using OHIF, please get in touch with the
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17 `OHIF community <https://ohif.org/collaborate>`__ in the first place.
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18 Indeed, the OHIF and Orthanc communities are entirely distinct.
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19
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20 **For researchers**: `Please cite this paper
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21 <https://dial.uclouvain.be/pr/boreal/object/boreal:257257>`__.
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24 .. _orthanc_vs_ohif:
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25
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26 Orthanc project vs. OHIF project
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27 --------------------------------
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28
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29 The Orthanc server and the OHIF viewer are **fully separate projects,
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30 with distinct communities**. The OHIF plugin for Orthanc only aims at
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31 facilitating the deployment of OHIF through Orthanc.
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32
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33 As a consequence, the OHIF plugin for Orthanc **only packages official
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34 releases of OHIF**.
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35
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36 Furthermore, any question or issue that is related to OHIF must be
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37 directly `asked to the OHIF community
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38 <https://github.com/OHIF/Viewers/issues>`__, *not* to the Orthanc
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39 discussion group.
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41
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42 Usage
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43 -----
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44
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45 This plugin adds a dedicated button to Orthanc Explorer, which
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46 provides an easy, fast access to the OHIF viewers (click on the image
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47 to view a demo video):
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48
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49 .. image:: ../images/OHIF.png
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50 :align: center
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51 :width: 800
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52 :target: https://www.youtube.com/watch?v=-lzddzq9iT4
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54 |
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57 Compilation
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58 -----------
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59
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60 .. highlight:: bash
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61
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62 Official releases can be `downloaded from the Orthanc homepage
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63 <https://orthanc.uclouvain.be/downloads/sources/orthanc-ohif/index.html>`__. As
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64 an alternative, the `repository containing the source code
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65 <https://orthanc.uclouvain.be/hg/orthanc-ohif/>`__ can be accessed
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66 using Mercurial.
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67
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68 The procedure to compile this plugin is similar of that for the
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69 :ref:`core of Orthanc <binaries>`. The following commands should work
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70 on most GNU/Linux distributions, provided Docker is installed::
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71
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72 $ mkdir Build
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73 $ cd Build
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74 $ ../Resources/CreateOHIFDist.sh
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75 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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76 $ make
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77
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78 The compilation will produce a shared library ``libOrthancOHIF.so``
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79 that contains the OHIF plugin for Orthanc.
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80
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81 Pre-compiled Linux Standard Base (LSB) binaries `are available for
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82 download <https://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-ohif/index.html>`__.
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83
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84 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-ohif/index.html>`__
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85 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-ohif/index.html>`__ are available as well.
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87 Furthermore, the :ref:`Docker images <docker>`
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88 ``jodogne/orthanc-plugins`` and ``orthancteam/orthanc`` also contain the
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89 plugin. Debian and Ubuntu packages can be found in the
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90 :ref:`standalone repository <binaries>`
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91 ``https://debian.orthanc-labs.com/``.
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94 Configuration
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95 -------------
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96
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97 .. highlight:: json
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98
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99 Here is a minimal sample :ref:`configuration file <configuration>` to
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100 use this plugin::
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101
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102 {
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103 "Plugins" : [
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104 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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105 ]
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106 }
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107
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108 Orthanc must of course be restarted after the modification of its
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109 configuration file.
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110
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111
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112 Using DICOMweb
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113 ^^^^^^^^^^^^^^
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114
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115 .. highlight:: json
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116
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117 By default, the plugin uses the `DICOM JSON data source
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118 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__ of
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119 OHIF. This data source is optimized to provide the fastest access to
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120 the DICOM images, while requiring no additional plugin. However, in
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121 order to deliver fast access, the OHIF plugin will cache additional
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122 information about each DICOM instance as :ref:`metadata <metadata>` in
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123 the Orthanc database, which results in a larger size of the Orthanc
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124 database (an additional 1KB is roughly needed per instance).
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125
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126 As an alternative, it is possible to enable the `DICOMweb data source
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127 <https://v3-docs.ohif.org/configuration/dataSources/dicom-web>`__. In
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128 this case, the :ref:`DICOMweb plugin of Orthanc <dicomweb>` must also
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129 be loaded. It can also be useful to load the :ref:`GDCM plugin <gdcm>`
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130 if the DICOM images are encoded using a JPEG2k compressed transfer
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131 syntax.
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132
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133 The advantages of using DICOMweb over the default DICOM JSON are:
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134
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135 * More standard-compliant.
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136
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137 * The OHIF study list is accessible, notably as a button on the
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138 welcome screen of Orthanc Explorer. The study list is not available
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139 if using the DICOM JSON data source.
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140
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141 * No additional space is used in the Orthanc database.
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142
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143 Here is a minimal configuration file to use DICOMweb::
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144
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145 {
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146 "Plugins" : [
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147 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so",
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148 "/home/user/orthanc-dicomweb/Build/libOrthancDicomWeb.so"
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149 ],
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150 "OHIF" : {
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151 "DataSource" : "dicom-web"
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152 }
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153 }
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154
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155
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156 User configuration of OHIF
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157 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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158
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159 .. highlight:: json
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160
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161 OHIF comes with a number of `configuration options
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162 <https://v3-docs.ohif.org/configuration/configurationfiles/#configuration-options>`__
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163 that can be fine-tuned by the user. User settings can be injected
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164 using the ``UserConfiguration`` option as follows::
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165
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166 {
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167 "Plugins" : [
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168 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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169 ],
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170 "OHIF" : {
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171 "UserConfiguration" : "ohif.js"
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172 }
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173 }
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174
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175 .. highlight:: javascript
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176
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177 A minimal ``ohif.js`` would be::
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178
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179 window.config = {
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180 extensions: [],
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181 modes: []
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182 }
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183
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184 Note that the following configuration options will be overridden by
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185 the OHIF plugin to properly configure the data source and the
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186 integration with the Orthanc Web server:
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187
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188 * ``window.config.dataSources``
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189 * ``window.config.defaultDataSourceName``
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190 * ``window.config.routerBasename``
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191 * ``window.config.showStudyList`` (set to ``false`` if using the DICOM
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192 JSON data source)
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193
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194
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195 .. _ohif-router-basename:
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196
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197 Router basename
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198 ^^^^^^^^^^^^^^^
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199
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200 .. highlight:: json
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201
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202 If Orthanc is not branched at the root of a Web server thanks of the
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203 presence of a reverse proxy, the configuration option
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204 ``RouterBasename`` must be adapted.
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205
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206 For instance, if Orthanc is running at address
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207 ``https://host.com/imaging/demo/orthanc/``, the following
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208 configuration file must be used for OHIF to work::
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209
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210 {
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211 "Plugins" : [
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212 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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213 ],
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214 "OHIF" : {
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215 "RouterBasename" : "/imaging/demo/orthanc/ohif/"
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216 }
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217 }
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218
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219 The default value of ``RouterBasename`` is ``/ohif/``.
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220
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221
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222 .. _ohif-preloading:
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223
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224 Preloading
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225 ^^^^^^^^^^
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226
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227 .. highlight:: json
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228
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229 If using the DICOM JSON data source, whenever a new DICOM instance is
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230 received by Orthanc, the OHIF plugin will compute a summary of the
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231 DICOM tags of interest to OHIF, and will store it as :ref:`metadata
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232 <metadata>` in the Orthanc database. This process has the advantage of
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233 speeding up even the first opening of the DICOM study by OHIF, which
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234 probably corresponds to the expectations of most radiologists.
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235
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236 However, if your Orthanc deployment is focused on speed, this
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237 preloading might be undesirable, as it slows down the ingestion of new
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238 DICOM instances by Orthanc. Furthermore, if your Orthanc server will
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239 contain a large number of DICOM studies that will never be displayed
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240 using OHIF, this can result in a waste of space in the Orthanc
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241 database because of the metadata that will be preloaded, but that will
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242 never be read.
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243
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244 It is consequently possible to turn off the automated preloading
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245 of metadata using the following configuration::
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246
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247 {
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248 "Plugins" : [
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249 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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250 ],
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251 "OHIF" : {
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252 "DataSource" : "dicom-json",
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253 "Preload" : false
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254 }
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255 }
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256
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257 If the ``Preload`` option is set to ``false``, the first display of a
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258 DICOM study can take several seconds because of the computation of the
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259 metadata, but subsequent displays will run much faster.
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260
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261 Note that preloading is only applied to the newly received instances:
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262 The DICOM instances that were stored in the Orthanc server before the
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263 installation of the OHIF plugin will only benefit from the
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264 optimization starting with their second display using OHIF.
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265
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266
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267 .. _ohif-https:
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268
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269 HTTPS encryption
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270 ^^^^^^^^^^^^^^^^
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271
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272 .. highlight:: bash
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273
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274 In order to use the :ref:`built-in HTTPS encryption <https-builtin>`
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275 of Orthanc together with the OHIF plugin, first generate a proper
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276 X.509 certificate for the ``localhost``::
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277
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278 $ openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
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279 -subj "/C=BE/CN=localhost" -keyout /tmp/private.key -out /tmp/certificate.crt
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280 $ cat /tmp/private.key /tmp/certificate.crt > /tmp/certificate.pem
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281
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282
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283 .. highlight:: json
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284
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285 Secondly, create the following configuration file::
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286
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287 {
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288 "Plugins" : [
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289 "/home/user/orthanc-ohif/Build/libOrthancOHIF.so"
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290 ],
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291 "SslEnabled" : true,
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292 "SslCertificate" : "/tmp/certificate.pem",
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293 "OHIF" : {
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294 "DataSource" : "dicom-json",
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295 "RouterBasename" : "/ohif/"
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296 }
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297 }
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298
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299 If more complex scenarios with reverse proxies are involved, make sure
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300 to properly setup :ref:`CORS in your reverse proxy <nginx-cors>` and
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301 to :ref:`adapt the router basename <ohif-router-basename>`. If you
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302 face difficulties, while the simple setup with the built-in HTTPS
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303 encryption described above works, your issue is related to OHIF, so
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304 please get in touch with the `OHIF community
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305 <https://ohif.org/collaborate>`__.
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306
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307
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308 For developers
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309 --------------
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310
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311 Extensions to the REST API
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312 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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313
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314 .. highlight:: bash
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315
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316 The content of the `DICOM JSON data source
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317 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__
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318 for a DICOM study of interest can be retrieved as follows::
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319
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320 $ curl https://orthanc.uclouvain.be/demo/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/ohif-dicom-json
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321
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322 This data source is constructed from the :ref:`metadata 4202
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323 <registry>` associated with the individual DICOM instances of the
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324 DICOM study. The metadata corresponds to the `Base64 encoding
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325 <https://en.wikipedia.org/wiki/Base64>`__ of a gzipped JSON file. For
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326 debugging, the JSON file associated with a DICOM instance can be
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327 inspected using::
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328
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329 $ curl https://orthanc.uclouvain.be/demo/instances/1f3c00bd-49df10b7-f416a598-1b3bb5a2-cb791b52/metadata/4202 | base64 -d | gunzip -c
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330
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331
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332 Preloading existing studies
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333 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
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334
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335 :ref:`As explained above <ohif-preloading>`, the metadata associated
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336 with DICOM instances are only preloaded for the newly ingested DICOM
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337 instances. Using the REST API of Orthanc, it is easy to create a
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338 script that would preload the metadata for the already existing DICOM
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339 studies, hereby greatly speeding up the first opening of those studies
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340 as well.
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341
954
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342 This script would loop over the :ref:`the DICOM studies that are
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343 stored by Orthanc <rest-access>` using ``GET /studies``. For each
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344 study whose :ref:`Orthanc identifier <orthanc-ids>` is ``id``, the
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345 script would simply call ``GET /studies/{id}/ohif-dicom-json``.
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346