.. _tcia:


TCIA plugin
===========

.. contents::

This **official** plugin by the `ICTEAM institute of UCLouvain
<https://uclouvain.be/en/research-institutes/icteam>`__ 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

Official releases can be `downloaded from the Orthanc homepage
<https://orthanc.uclouvain.be/downloads/sources/orthanc-tcia/index.html>`__. As
an alternative, the `repository containing the source code
<https://orthanc.uclouvain.be/hg/orthanc-tcia/>`__ can be accessed using
Mercurial.

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://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-tcia/index.html>`__.

Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-tcia/index.html>`__
and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-tcia/index.html>`__ are available as well.

Furthermore, the ``jodogne/orthanc-plugins`` :ref:`Docker images
<docker>` and ``osimis/orthanc`` :ref:`Docker images <docker-osimis>`
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

The TCIA plugin creates a job to do the import. This implies that an
import can be monitored, paused or stopped using the :ref:`REST API
for Orthanc jobs <jobs>`.