changeset 760:e9da78572539

documentation of tcia
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 29 Aug 2021 13:31:57 +0200
parents 94f5fc38b927
children 525d59a7c198
files Sphinx/source/images/tcia-interface.png Sphinx/source/images/tcia-nbia-export.png Sphinx/source/plugins/tcia.rst
diffstat 3 files changed, 107 insertions(+), 1 deletions(-) [+]
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Binary file Sphinx/source/images/tcia-interface.png has changed
Binary file Sphinx/source/images/tcia-nbia-export.png has changed
--- a/Sphinx/source/plugins/tcia.rst	Sat Aug 28 10:21:27 2021 +0200
+++ b/Sphinx/source/plugins/tcia.rst	Sun Aug 29 13:31:57 2021 +0200
@@ -6,4 +6,110 @@
 
 .. contents::
 
-Soon available.
+This **official** plugin extends Orthanc with a Web interface that can
+be used to import open-data medical images from `The Cancer Imaging
+Archive (TCIA) <https://www.cancerimagingarchive.net/>`__, and serve
+them immediately using Orthanc.
+
+The plugin can be used to import so-called "cart spreadsheet"
+generated by the `NBIA Search Client
+<https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse
+the image collections of TCIA thanks to its `REST API
+<https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__.
+
+
+Compilation
+-----------
+
+.. highlight:: bash
+
+The procedure to compile this plugin is similar of that for the
+:ref:`core of Orthanc <binaries>`. The following commands should work
+for most UNIX-like distribution (including GNU/Linux)::
+
+  $ mkdir Build
+  $ cd Build
+  $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
+  $ make
+
+The compilation will produce a shared library ``OrthancTcia``
+that contains the TCIA plugin for Orthanc.
+
+Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
+<https://lsb.orthanc-server.com/plugin-tcia/>`__.
+
+Pre-compiled binaries for Microsoft Windows and macOS `are also
+available
+<https://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__.
+
+Furthermore, the :ref:`Docker images <docker>`
+``jodogne/orthanc-plugins`` also contain the plugin.
+
+
+Configuration
+-------------
+
+You of course first have to :ref:`install Orthanc <compiling>`. Once
+Orthanc is installed, you must change the :ref:`configuration file
+<configuration>` to tell Orthanc where it can find the plugin: This is
+done by properly modifying the ``Plugins`` option.
+
+You then have to set the two following options:
+
+* The setting ``Enable`` in section ``Tcia`` must be set to ``true``
+  to enable the TCIA plugin.
+
+* The setting ``HttpsCACertificates`` must contain a path to a file
+  containing a list of `trusted Certificate Authorities (CA)
+  <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your
+  operating system, this file can be found as follows:
+
+  - On Debian-based system, the standard file
+    ``/etc/ssl/certs/ca-certificates.crt`` can be used.
+  - On other systems (including Microsoft Windows), the cURL project
+    provides `CA certificates
+    <https://curl.haxx.se/docs/caextract.html>`__ that are extracted
+    from Mozilla.
+
+.. highlight:: json
+
+On Ubuntu, you could for instance use the following minimalist
+configuration file::
+
+  {
+    "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
+    "Plugins" : [
+      "/home/user/OrthancTcia/Build/libOrthancTcia.so"
+    ],
+    "Tcia" : {
+      "Enable" : true
+    }
+  }
+
+.. highlight:: text
+
+Orthanc must of course be restarted after the modification of its
+configuration file.
+
+
+Usage
+-----
+
+Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging
+Archive" will show up at the bottom of the page. Clicking on this
+button will open the TCIA interface for Orthanc:
+
+.. image:: ../images/tcia-interface.png
+           :align: center
+           :width: 640
+
+As can be seen, this Web application allows to both import a cart from
+the NBIA Search Client, and to browse the various collections of
+medical images from TCIA.
+
+The following screenshot illustrates how to export a cart using the
+NBIA Search Client, that can then be imported using this plugin:
+
+.. image:: ../images/tcia-nbia-export.png
+           :align: center
+           :width: 640