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updated docker osimis plugins
author Alain Mazy <am@osimis.io>
date Mon, 06 Sep 2021 19:35:17 +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
760
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9 This **official** plugin extends Orthanc with a Web interface that can
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10 be used to import open-data medical images from `The Cancer Imaging
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11 Archive (TCIA) <https://www.cancerimagingarchive.net/>`__, and serve
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12 them immediately using Orthanc.
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13
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14 The plugin can be used to import so-called "cart spreadsheet"
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15 generated by the `NBIA Search Client
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16 <https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse
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17 the image collections of TCIA thanks to its `REST API
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18 <https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__.
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20
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21 Compilation
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22 -----------
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23
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24 .. highlight:: bash
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25
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26 The procedure to compile this plugin is similar of that for the
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27 :ref:`core of Orthanc <binaries>`. The following commands should work
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28 for most UNIX-like distribution (including GNU/Linux)::
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29
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30 $ mkdir Build
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31 $ cd Build
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32 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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33 $ make
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34
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35 The compilation will produce a shared library ``OrthancTcia``
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36 that contains the TCIA plugin for Orthanc.
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37
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38 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
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39 <https://lsb.orthanc-server.com/plugin-tcia/>`__.
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40
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41 Pre-compiled binaries for Microsoft Windows and macOS `are also
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42 available
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43 <https://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__.
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44
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45 Furthermore, the :ref:`Docker images <docker>`
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46 ``jodogne/orthanc-plugins`` also contain the plugin.
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47
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48
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49 Configuration
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50 -------------
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51
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52 You of course first have to :ref:`install Orthanc <compiling>`. Once
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53 Orthanc is installed, you must change the :ref:`configuration file
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54 <configuration>` to tell Orthanc where it can find the plugin: This is
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55 done by properly modifying the ``Plugins`` option.
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56
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57 You then have to set the two following options:
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58
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59 * The setting ``Enable`` in section ``Tcia`` must be set to ``true``
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60 to enable the TCIA plugin.
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61
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62 * The setting ``HttpsCACertificates`` must contain a path to a file
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63 containing a list of `trusted Certificate Authorities (CA)
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64 <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your
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65 operating system, this file can be found as follows:
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66
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67 - On Debian-based system, the standard file
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68 ``/etc/ssl/certs/ca-certificates.crt`` can be used.
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69 - On other systems (including Microsoft Windows), the cURL project
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70 provides `CA certificates
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71 <https://curl.haxx.se/docs/caextract.html>`__ that are extracted
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72 from Mozilla.
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73
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74 .. highlight:: json
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75
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76 On Ubuntu, you could for instance use the following minimalist
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77 configuration file::
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78
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79 {
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80 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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81 "Plugins" : [
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82 "/home/user/OrthancTcia/Build/libOrthancTcia.so"
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83 ],
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84 "Tcia" : {
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85 "Enable" : true
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86 }
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87 }
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88
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89 .. highlight:: text
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90
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91 Orthanc must of course be restarted after the modification of its
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92 configuration file.
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93
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94
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95 Usage
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96 -----
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97
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98 Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging
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99 Archive" will show up at the bottom of the page. Clicking on this
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100 button will open the TCIA interface for Orthanc:
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101
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102 .. image:: ../images/tcia-interface.png
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103 :align: center
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104 :width: 640
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105
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106 As can be seen, this Web application allows to both import a cart from
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107 the NBIA Search Client, and to browse the various collections of
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108 medical images from TCIA.
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109
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110 The following screenshot illustrates how to export a cart using the
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111 NBIA Search Client, that can then be imported using this plugin:
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112
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113 .. image:: ../images/tcia-nbia-export.png
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114 :align: center
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115 :width: 640