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annotate Sphinx/source/plugins/tcia.rst @ 993:05b106383b2a

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migration to UCLouvain servers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 21 Nov 2023 21:39:40 +0100
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1 .. _tcia:
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4 TCIA 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 a Web interface that can be used to import open-data
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12 medical images from `The Cancer Imaging Archive (TCIA)
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13 <https://www.cancerimagingarchive.net/>`__, and serve them immediately
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14 using Orthanc.
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15
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16 The plugin can be used to import so-called "cart spreadsheet"
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17 generated by the `NBIA Search Client
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18 <https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse
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19 the image collections of TCIA thanks to its `REST API
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20 <https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__.
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21
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23 Compilation
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24 -----------
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25
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26 .. highlight:: bash
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27
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28 Official releases can be `downloaded from the Orthanc homepage
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29 <https://orthanc.uclouvain.be/downloads/sources/orthanc-tcia/index.html>`__. As
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30 an alternative, the `repository containing the source code
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31 <https://orthanc.uclouvain.be/hg/orthanc-tcia/>`__ can be accessed using
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32 Mercurial.
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33
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34 The procedure to compile this plugin is similar of that for the
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35 :ref:`core of Orthanc <binaries>`. The following commands should work
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36 for most UNIX-like distribution (including GNU/Linux)::
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37
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38 $ mkdir Build
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39 $ cd Build
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40 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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41 $ make
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42
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43 The compilation will produce a shared library ``OrthancTcia``
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44 that contains the TCIA plugin for Orthanc.
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45
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46 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
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47 <https://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-tcia/index.html>`__.
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48
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49 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-tcia/index.html>`__
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50 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-tcia/index.html>`__ are available as well.
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51
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52 Furthermore, the ``jodogne/orthanc-plugins`` :ref:`Docker images
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53 <docker>` and ``osimis/orthanc`` :ref:`Docker images <docker-osimis>`
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54 also contain the plugin.
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56
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57 Configuration
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58 -------------
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59
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60 You of course first have to :ref:`install Orthanc <compiling>`. Once
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61 Orthanc is installed, you must change the :ref:`configuration file
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62 <configuration>` to tell Orthanc where it can find the plugin: This is
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63 done by properly modifying the ``Plugins`` option.
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64
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65 You then have to set the two following options:
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66
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67 * The setting ``Enable`` in section ``Tcia`` must be set to ``true``
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68 to enable the TCIA plugin.
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69
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70 * The setting ``HttpsCACertificates`` must contain a path to a file
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71 containing a list of `trusted Certificate Authorities (CA)
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72 <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your
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73 operating system, this file can be found as follows:
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74
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75 - On Debian-based system, the standard file
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76 ``/etc/ssl/certs/ca-certificates.crt`` can be used.
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77 - On other systems (including Microsoft Windows), the cURL project
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78 provides `CA certificates
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79 <https://curl.haxx.se/docs/caextract.html>`__ that are extracted
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80 from Mozilla.
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81
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82 .. highlight:: json
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83
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84 On Ubuntu, you could for instance use the following minimalist
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85 configuration file::
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86
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87 {
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88 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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89 "Plugins" : [
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90 "/home/user/OrthancTcia/Build/libOrthancTcia.so"
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91 ],
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92 "Tcia" : {
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93 "Enable" : true
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94 }
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95 }
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96
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97 .. highlight:: text
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98
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99 Orthanc must of course be restarted after the modification of its
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100 configuration file.
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101
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102
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103 Usage
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104 -----
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105
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106 Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging
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107 Archive" will show up at the bottom of the page. Clicking on this
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108 button will open the TCIA interface for Orthanc:
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109
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110 .. image:: ../images/tcia-interface.png
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111 :align: center
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112 :width: 640
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113
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114 As can be seen, this Web application allows to both import a cart from
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115 the NBIA Search Client, and to browse the various collections of
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116 medical images from TCIA.
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117
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118 The following screenshot illustrates how to export a cart using the
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119 NBIA Search Client, that can then be imported using this plugin:
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120
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121 .. image:: ../images/tcia-nbia-export.png
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122 :align: center
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123 :width: 640
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124
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125 The TCIA plugin creates a job to do the import. This implies that an
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126 import can be monitored, paused or stopped using the :ref:`REST API
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127 for Orthanc jobs <jobs>`.
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128