Mercurial > hg > orthanc-book
annotate Sphinx/source/plugins/tcia.rst @ 767:9130cb19dc4d
updated docker osimis plugins
author | Alain Mazy <am@osimis.io> |
---|---|
date | Mon, 06 Sep 2021 19:35:17 +0200 |
parents | e9da78572539 |
children | 9978fb958ee2 |
rev | line source |
---|---|
758 | 1 .. _tcia: |
2 | |
3 | |
4 TCIA plugin | |
5 =========== | |
6 | |
7 .. contents:: | |
8 | |
760
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
9 This **official** plugin extends Orthanc with a Web interface that can |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
10 be used to import open-data medical images from `The Cancer Imaging |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
11 Archive (TCIA) <https://www.cancerimagingarchive.net/>`__, and serve |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
12 them immediately using Orthanc. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
13 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
14 The plugin can be used to import so-called "cart spreadsheet" |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
15 generated by the `NBIA Search Client |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
16 <https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
17 the image collections of TCIA thanks to its `REST API |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
18 <https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
19 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
20 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
21 Compilation |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
22 ----------- |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
23 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
24 .. highlight:: bash |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
25 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
26 The procedure to compile this plugin is similar of that for the |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
27 :ref:`core of Orthanc <binaries>`. The following commands should work |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
28 for most UNIX-like distribution (including GNU/Linux):: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
29 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
30 $ mkdir Build |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
31 $ cd Build |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
32 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
33 $ make |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
34 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
35 The compilation will produce a shared library ``OrthancTcia`` |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
36 that contains the TCIA plugin for Orthanc. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
37 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
38 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
39 <https://lsb.orthanc-server.com/plugin-tcia/>`__. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
40 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
41 Pre-compiled binaries for Microsoft Windows and macOS `are also |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
42 available |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
43 <https://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
44 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
45 Furthermore, the :ref:`Docker images <docker>` |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
46 ``jodogne/orthanc-plugins`` also contain the plugin. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
47 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
48 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
49 Configuration |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
50 ------------- |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
51 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
52 You of course first have to :ref:`install Orthanc <compiling>`. Once |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
53 Orthanc is installed, you must change the :ref:`configuration file |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
54 <configuration>` to tell Orthanc where it can find the plugin: This is |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
55 done by properly modifying the ``Plugins`` option. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
56 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
57 You then have to set the two following options: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
58 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
59 * The setting ``Enable`` in section ``Tcia`` must be set to ``true`` |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
60 to enable the TCIA plugin. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
61 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
62 * The setting ``HttpsCACertificates`` must contain a path to a file |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
63 containing a list of `trusted Certificate Authorities (CA) |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
64 <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
65 operating system, this file can be found as follows: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
66 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
67 - On Debian-based system, the standard file |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
68 ``/etc/ssl/certs/ca-certificates.crt`` can be used. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
69 - On other systems (including Microsoft Windows), the cURL project |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
70 provides `CA certificates |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
71 <https://curl.haxx.se/docs/caextract.html>`__ that are extracted |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
72 from Mozilla. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
73 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
74 .. highlight:: json |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
75 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
76 On Ubuntu, you could for instance use the following minimalist |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
77 configuration file:: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
78 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
79 { |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
80 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt", |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
81 "Plugins" : [ |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
82 "/home/user/OrthancTcia/Build/libOrthancTcia.so" |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
83 ], |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
84 "Tcia" : { |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
85 "Enable" : true |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
86 } |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
87 } |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
88 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
89 .. highlight:: text |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
90 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
91 Orthanc must of course be restarted after the modification of its |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
92 configuration file. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
93 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
94 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
95 Usage |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
96 ----- |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
97 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
98 Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
99 Archive" will show up at the bottom of the page. Clicking on this |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
100 button will open the TCIA interface for Orthanc: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
101 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
102 .. image:: ../images/tcia-interface.png |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
103 :align: center |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
104 :width: 640 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
105 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
106 As can be seen, this Web application allows to both import a cart from |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
107 the NBIA Search Client, and to browse the various collections of |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
108 medical images from TCIA. |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
109 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
110 The following screenshot illustrates how to export a cart using the |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
111 NBIA Search Client, that can then be imported using this plugin: |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
112 |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
113 .. image:: ../images/tcia-nbia-export.png |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
114 :align: center |
e9da78572539
documentation of tcia
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
758
diff
changeset
|
115 :width: 640 |