.. _docker:
.. highlight:: bash


Orthanc for Docker
==================

.. contents::
   :depth: 3


Introduction
------------

`Docker images <https://en.wikipedia.org/wiki/Docker_(software)>`__
for the Orthanc core and its official plugins are freely available on
the `DockerHub platform <https://hub.docker.com/u/jodogne/>`__. The
source code of the corresponding Docker images is available on `GitHub
<https://github.com/jodogne/OrthancDocker>`__.

*Note for CentOS users:* The Docker environment might be difficult to
configure on your platform. Hints are available on the `Orthanc Users
discussion group
<https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__.


Running the Orthanc core
------------------------

The following command will start the core of Orthanc, with all the
plugins disabled::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc

Once Orthanc is running, use Mozilla Firefox at URL
http://localhost:8042/ to interact with Orthanc. The default username
is ``orthanc`` and its password is ``orthanc``.

The command above starts the mainline version of Orthanc, whose
development is in continuous progress. This gives you access to the
latest features. If more stability is required, you can select the
release of Orthanc to be run::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.1.0

Passing additional command-line options (e.g. to make Orthanc verbose)
can be done as follows (note the ``/etc/orthanc`` option that is
required for Orthanc to find its configuration files)::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose


Usage, with plugins enabled
---------------------------

The following command will run the mainline version of the Orthanc
core, together with its :ref:`Web viewer <webviewer>`, its
:ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb
implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer
<wsi>`::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins


Fine-tuning the configuration
-----------------------------

For security reasons, you should at least protect your instance of
Orthanc by changing this default user, in the ``RegisteredUsers``
:ref:`configuration option <configuration>`. You will also probably
need to fine-tune other parameters, notably the list of the DICOM
modalities Orthanc knows about.

You can generate a custom configuration file for Orthanc as follows::

  $ sudo docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json

Then, edit the just-generated file ``/tmp/orthanc.json`` and restart
Orthanc with your updated configuration::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc


Making the Orthanc database persistent
--------------------------------------

The filesystem of Docker containers is volatile (its content is
deleted once the container stops). You can make the Orthanc database
persistent by mapping the ``/var/lib/orthanc/db`` folder of the
container to some path in the filesystem of your Linux host, e.g.::

  $ mkdir /tmp/orthanc-db
  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.1.0 


Whole-slide imaging support
---------------------------

The ``orthanc-plugins`` image includes support for :ref:`microscopic
whole-slide imaging (WSI) <wsi>`. For instance, the following command
will start the WSI viewer plugin transparently together with Orthanc::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins

Note that we gave the name ``orthanc-wsi`` to this new Docker
container. Then, the Dicomizer command-line tool can be invoked as
follows::

  $ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif

This command needs a few explanations:

* ``--link=orthanc-wsi:orthanc`` links the container running the
  Dicomizer, to the Docker container running Orthanc that we started
  just before.
* ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer
  must be run instead of the Orthanc server.
* ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image
  ``/tmp/Source.tif`` on the host computer into the Orthanc container
  as read-only file ``/tmp/Source.tif``.
* ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push
  images through the ``--link`` created above.
* ``--username=orthanc --password=orthanc`` correspond to the default
  credentials of the ``orthanc-plugins`` image.

Obviously, you are free to add all the options you wish (check out the
``--help`` flag to list these options). In particular, the
``--dataset`` option allows to specify DICOM tags, in the JSON file
format, so as to include them in the resulting DICOM series (the
option ``--sample-dataset`` prints a sample JSON file that has the
expected format).

If you have a source image that is not a hierarchical TIFF, you must
instruct the Dicomizer to use `OpenSlide <http://openslide.org/>`__ to
decode it by adding the ``--openslide`` option::

  $ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs


PostgreSQL and Orthanc inside Docker
------------------------------------

It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container::

  $ sudo docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres

Open another shell, and create a database to host the Orthanc database::

  $ sudo docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres'

You will have to type the password (cf. the environment variable
``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then,
retrieve the IP and the port of the PostgreSQL container, together
with the default Orthanc configuration file::

  $ sudo docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres
  $ sudo docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres
  $ sudo docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json

.. highlight:: json

Add the following section to ``/tmp/orthanc.json`` (adapting the
values Host and Port to what docker inspect said above)::

  "PostgreSQL" : {
    "EnableIndex" : true,
    "EnableStorage" : true,
    "Host" : "172.17.0.38",
    "Port" : 5432,
    "Database" : "orthanc",
    "Username" : "postgres",
    "Password" : "pgpassword"
  }

.. highlight:: bash

Finally, you can start Orthanc::

  $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins


Debugging
---------

For debugging purpose, you can start an interactive bash session as
follows::

  $ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc
  $ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins