Mercurial > hg > orthanc-book

annotate Sphinx/source/plugins/ohif.rst @ 953:2038eb1f55bb

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finalized ohif documentation
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 19 Jun 2023 08:00:51 +0200
parents 4a76327e83fb
children 19fd9eab4ec0
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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. It also speeds up the
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16 loading of
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17
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18
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19 Usage
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20 -----
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21
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22 This plugin adds a dedicated button to Orthanc Explorer, which
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23 provides an easy, fast access to the OHIF viewers (click on the image
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24 to view a demo video):
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25
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26 .. image:: ../images/OHIF.png
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27 :align: center
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28 :width: 800
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29 :target: https://www.youtube.com/watch?v=-lzddzq9iT4
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30 |
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33 Compilation
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34 -----------
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35
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36 .. highlight:: bash
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37
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38 Official releases can be `downloaded from the Orthanc homepage
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39 <https://www.orthanc-server.com/browse.php?path=/plugin-ohif>`__. As
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40 an alternative, the `repository containing the source code
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41 <https://orthanc.uclouvain.be/hg/orthanc-ohif/>`__ can be accessed
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42 using Mercurial.
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43
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44 The procedure to compile this plugin is similar of that for the
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45 :ref:`core of Orthanc <binaries>`. The following commands should work
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46 on most GNU/Linux distributions, provided Docker is installed::
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47
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48 $ mkdir Build
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49 $ cd Build
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50 $ ../Resources/CreateOHIFDist.sh
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51 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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52 $ make
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53
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54 The compilation will produce a shared library ``libOrthancOHIF.so``
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55 that contains the OHIF plugin for Orthanc.
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56
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57 Pre-compiled Linux Standard Base (LSB) binaries `are available for
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58 download <https://lsb.orthanc-server.com/plugin-ohif/>`__.
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59
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60 Pre-compiled binaries for Microsoft Windows and macOS `are also
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61 available
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62 <https://www.orthanc-server.com/browse.php?path=/plugin-ohif>`__.
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63
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64 Furthermore, the :ref:`Docker images <docker>`
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65 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
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66 plugin. Debian and Ubuntu packages can be found in the
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67 :ref:`standalone repository <binaries>`
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68 ``https://debian.orthanc-labs.com/``.
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71 Configuration
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72 -------------
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73
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74 .. highlight:: json
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75
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76 Here is a minimal sample :ref:`configuration file <configuration>` to
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77 use this plugin::
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78
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79 {
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80 "Plugins" : [
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81 "/home/user/orthanc-ohif/Build/libOHIF.so"
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82 ]
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83 }
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84
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85 Orthanc must of course be restarted after the modification of its
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86 configuration file.
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87
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88
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89 Using DICOMweb
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90 ^^^^^^^^^^^^^^
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91
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92 .. highlight:: json
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93
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94 By default, the plugin uses the `DICOM JSON data source
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95 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__ of
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96 OHIF. This data source is optimized to provide the fastest access to
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97 the DICOM images, while requiring no additional plugin. However, in
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98 order to deliver fast access, the OHIF plugin will cache additional
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99 information about each DICOM instance as :ref:`metadata <metadata>` in
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100 the Orthanc database, which results in a larger size of the Orthanc
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101 database (an additional 1KB is roughly needed per instance).
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102
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103 As an alternative, it is possible to enable the `DICOMweb data source
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104 <https://v3-docs.ohif.org/configuration/dataSources/dicom-web>`__. In
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105 this case, the :ref:`DICOMweb plugin of Orthanc <dicomweb>` must also
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106 be loaded. It can also be useful to load the :ref:`GDCM plugin <gdcm>`
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107 if the DICOM images are encoded using a JPEG2k compressed transfer
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108 syntax.
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109
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110 The advantages of using DICOMweb over the default DICOM JSON are:
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111
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112 * More standard-compliant.
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113
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114 * The OHIF study list is accessible, notably as a button on the
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115 welcome screen of Orthanc Explorer. The study list is not available
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116 if using the DICOM JSON data source.
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117
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118 * No additional space is used in the Orthanc database.
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119
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120 Here is a minimal configuration file to use DICOMweb::
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121
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122 {
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123 "Plugins" : [
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124 "/home/user/orthanc-ohif/Build/libOHIF.so",
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125 "/home/user/orthanc-dicomweb/Build/libOHIF.so"
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126 ],
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127 "OHIF" : {
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128 "DataSource" : "dicom-web"
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129 }
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130 }
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131
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132
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133 Router basename
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134 ^^^^^^^^^^^^^^^
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135
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136 .. highlight:: json
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137
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138 If Orthanc is not branched at the root of a Web server thanks of the
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139 presence of a reverse proxy, the configuration option
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140 ``RouterBasename`` must be adapted.
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141
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142 For instance, if Orthanc is running at address
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143 ``https://host.com/imaging/demo/orthanc/``, the following
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144 configuration file must be used for OHIF to work::
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145
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146 {
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147 "Plugins" : [
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148 "/home/user/orthanc-ohif/Build/libOHIF.so"
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149 ],
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150 "OHIF" : {
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151 "RouterBasename" : "/imaging/demo/orthanc/ohif/"
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152 }
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153 }
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154
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155 The default value of ``RouterBasename`` is ``/ohif/``.
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156
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157
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158 .. _ohif-preloading:
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159
952
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160 Preloading
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161 ^^^^^^^^^^
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162
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163 .. highlight:: json
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164
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165 If using the DICOM JSON data source, whenever a new DICOM instance is
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166 received by Orthanc, the OHIF plugin will compute a summary of the
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167 DICOM tags of interest to OHIF, and will store it as :ref:`metadata
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168 <metadata>` in the Orthanc database. This process has the advantage of
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169 speeding up even the first opening of the DICOM study by OHIF, which
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170 probably corresponds to the expectations of most radiologists.
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171
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172 However, if your Orthanc deployment is focused on speed, this
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173 preloading might be undesirable, as it slows down the ingestion of new
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174 DICOM instances by Orthanc. Furthermore, if your Orthanc server will
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175 contain a large number of DICOM studies that will never be displayed
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176 using OHIF, this can result in a waste of space in the Orthanc
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177 database because of the metadata that will be preloaded, but that will
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178 never be read.
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179
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180 It is consequently possible to turn off the automated preloading
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181 of metadata using the following configuration::
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182
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183 {
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184 "Plugins" : [
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185 "/home/user/orthanc-ohif/Build/libOHIF.so"
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186 ],
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187 "OHIF" : {
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188 "DataSource" : "dicom-json",
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189 "Preload" : false
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190 }
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191 }
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192
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193 If the ``Preload`` option is set to ``false``, the first display of a
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194 DICOM study can take several seconds because of the computation of the
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195 metadata, but subsequent displays will run much faster.
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196
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197 Note that preloading is only applied to the newly received instances:
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198 The DICOM instances that were stored in the Orthanc server before the
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199 installation of the OHIF plugin will only benefit from the
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200 optimization starting with their second display using OHIF.
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201
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202
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203 For developers
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204 --------------
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205
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206 Extensions to the REST API
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207 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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208
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209 .. highlight:: bash
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210
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211 The content of the `DICOM JSON data source
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212 <https://v3-docs.ohif.org/configuration/datasources/dicom-json/>`__
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213 for a DICOM study of interest can be retrieved as follows::
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214
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215 $ curl http://demo.orthanc-server.com/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/ohif-dicom-json
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216
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217 This data source is constructed from the :ref:`metadata 4202
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218 <registry>` associated with the individual DICOM instances of the
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219 DICOM study. The metadata corresponds to the `Base64 encoding
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220 <https://en.wikipedia.org/wiki/Base64>`__ of a gzipped JSON file. For
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221 debugging, the JSON file associated with a DICOM instance can be
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222 inspected using::
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223
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224 $ curl http://demo.orthanc-server.com/instances/1f3c00bd-49df10b7-f416a598-1b3bb5a2-cb791b52/metadata/4202 | base64 -d | gunzip -c
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225
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226
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227 Preloading existing studies
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228 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
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229
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230 :ref:`As explained above <ohif-preloading>`, the metadata associated
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231 with DICOM instances are only preloaded for the newly ingested DICOM
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232 instances. Using the REST API of Orthanc, it is easy to create a
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233 script that would preload the metadata for the already existing DICOM
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234 studies, hereby greatly speeding up the first opening of those studies
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235 as well.
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236
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237 This script would loop over the :ref:`the DICOM studies that are stored
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238 by Orthanc <rest-access>` using ``GET /studies``. For each study whose
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239 :ref:`Orthanc identifier <orthanc-identifiers>` is ``id``, the script
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240 would simply call ``GET /studies/{id}/ohif-dicom-json``.
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241