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annotate Sphinx/source/plugins/tcia.rst @ 770:9978fb958ee2

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precisions about tcia
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 Sep 2021 13:15:14 +0200
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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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22
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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://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__. As
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30 an alternative, the `repository containing the source code
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31 <https://hg.orthanc-server.com/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://lsb.orthanc-server.com/plugin-tcia/>`__.
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48
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49 Pre-compiled binaries for Microsoft Windows and macOS `are also
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50 available
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51 <https://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__.
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52
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53 Furthermore, the :ref:`Docker images <docker>`
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54 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
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55 plugin.
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57
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58 Configuration
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59 -------------
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60
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61 You of course first have to :ref:`install Orthanc <compiling>`. Once
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62 Orthanc is installed, you must change the :ref:`configuration file
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63 <configuration>` to tell Orthanc where it can find the plugin: This is
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64 done by properly modifying the ``Plugins`` option.
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65
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66 You then have to set the two following options:
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67
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68 * The setting ``Enable`` in section ``Tcia`` must be set to ``true``
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69 to enable the TCIA plugin.
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70
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71 * The setting ``HttpsCACertificates`` must contain a path to a file
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72 containing a list of `trusted Certificate Authorities (CA)
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73 <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your
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74 operating system, this file can be found as follows:
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75
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76 - On Debian-based system, the standard file
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77 ``/etc/ssl/certs/ca-certificates.crt`` can be used.
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78 - On other systems (including Microsoft Windows), the cURL project
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79 provides `CA certificates
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80 <https://curl.haxx.se/docs/caextract.html>`__ that are extracted
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81 from Mozilla.
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82
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83 .. highlight:: json
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84
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85 On Ubuntu, you could for instance use the following minimalist
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86 configuration file::
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87
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88 {
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89 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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90 "Plugins" : [
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91 "/home/user/OrthancTcia/Build/libOrthancTcia.so"
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92 ],
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93 "Tcia" : {
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94 "Enable" : true
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95 }
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96 }
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97
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98 .. highlight:: text
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99
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100 Orthanc must of course be restarted after the modification of its
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101 configuration file.
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102
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103
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104 Usage
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105 -----
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106
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107 Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging
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108 Archive" will show up at the bottom of the page. Clicking on this
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109 button will open the TCIA interface for Orthanc:
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110
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111 .. image:: ../images/tcia-interface.png
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112 :align: center
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113 :width: 640
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114
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115 As can be seen, this Web application allows to both import a cart from
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116 the NBIA Search Client, and to browse the various collections of
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117 medical images from TCIA.
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118
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119 The following screenshot illustrates how to export a cart using the
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120 NBIA Search Client, that can then be imported using this plugin:
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121
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122 .. image:: ../images/tcia-nbia-export.png
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123 :align: center
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124 :width: 640
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125
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126 The TCIA plugin creates a job to do the import. This implies that an
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127 import can be monitored, paused or stopped using the :ref:`REST API
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128 for Orthanc jobs <jobs>`.
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129