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ENH: removed old Dashboard text. Added commandline help
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FBerendsen committed Feb 2, 2018
1 parent 09a7c38 commit db67d9f
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74 changes: 2 additions & 72 deletions source/Dashboard.rst
@@ -1,76 +1,6 @@
Dashboard
=========

Mac OS X
--------
All branches and pull requests are build and unit tested by Continuous Integration: see our CDash for the latest status:

- Install docker

::
$ https://github.com/boot2docker/osx-installer/releases


- Install pip

::
$ sudo easy_install pip

- Install docker-compose

::
$ sudo pip install -U docker-compose

- Build elastix with ELASTIX_BUILD_DASHBOARD set to ON.

- To fire up the dashboard server, run the following command in the Testing/Dashboard build directory.

::
$ docker-compose up

Go to http://elastix to see the dashboard.

- Download the logstash forwarder from https://download.elastic.co/logstash-forwarder/binaries/logstash-forwarder_darwin_amd64 and run the executable with the associated configuration file

::
$ curl -O https://download.elastic.co/logstash-forwarder/binaries/logstash-forwarder_darwin_amd64
$ chmod +x logstash-forwarder_darwin_amd64
$ ./logstash-forwarder_darwin_amd64 -config elxLogstashForwarder.conf

- If you see "code:`DNS lookup failure "elastix": lookup elastix: no such host` add the elastix domain and associated boot2docker ip to the /etc/hosts file. For example, if :code:`$ boot2docker ip` shows you :code:`192.168.59.103`, you would the following line:

::
192.168.59.103 elastix



- We provide a key and certificate pair for testing purposes. DO NOT use this in production as they can be viewed by everybody (they are in public repository). To generate a new certificate, use the following command:

::
openssl req -subj "/CN=elastix/" -x509 -batch -nodes -newkey rsa:2048 -keyout elxLogstashForwarder.key -out elxLogstashForwarder.crt

Replace elastix with the domain name where you host the dashboard (e.g. elastix.isi.uu.nl). In production, point the ELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY and ELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE CMake variables to the new files in order for CMake to update the docker, logstash and logstash forwader configuration files with the new values.

Docker Cheat Sheet
------------------

- To stop containers run

::
$ docker stop $(docker ps -aq)

- To delete containers run

::
$ docker rm $(docker ps -aq)

- To delete images run

::
$ docker rmi $(docker ps -q)

- Bash into docker container

::
$ docker exec -i -t dashboard_elastix_1 bash

where dashboard_elastix_1 is the name of the container (could be different on your machine). Persisted data is located in the :code:`/data` directory and logs are located in the :code:`/var/log/elasticsearch`, :code:`/var/log/logstash` and :code:`/var/log/kibana` directories.
`<https://my.cdash.org/index.php?project=SuperElastix>`_
19 changes: 19 additions & 0 deletions source/Usage.rst
Expand Up @@ -14,6 +14,25 @@ The SuperElastix commandline tool can be found at:

- Linux: :code:`<build-path>/Applications-build/CommandLineInterface/`


By calling :code:`SuperElastix --help` its options are shown.

::

Allowed options:
--help produce help message
--conf arg Configuration file: single or multiple Blueprints
[.xml|.json]
--in arg Input data: images, labels, meshes, etc. Usage arg:
<name>=<path> (or multiple pairs)
--out arg Output data: images, labels, meshes, etc. Usage arg:
<name>=<path> (or multiple pairs)
--graphout arg Output Graphviz dot file
--logfile arg Log output file
--loglevel arg Log level [off|critical|error|warning|info|debug|trace]

The file format of a Blueprint is described in :ref:`design_configuring`, where the :code:`<name>`-s of the :code:`--in` and :code:`--out` arguments must correspond to the sinking and sourcing component identifier names as defined in the Blueprint, respectively.

Demo Experiments
----------------

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