.. |foo| image:: img/tomwer_icon.png
    :scale: 22 %


==============
|foo|   tomwer
==============

tomwer is a solution including:

   * a high level library
      * containing some processing code
      * allowing call and interconnect of several tomography third libraries (nabu)
      * offering gui for each process requiring some interaction.

   * a set of :ref:`stand alone applications`
   * an `orange <https://github.com/biolab/orange3>`_ add-on allowing end-users to define their workflow for tomography data processing

tomwer main goal is to automate tomography treatment once the data has been acquired.

.. figure:: img/tomwer_start_short.gif
    :scale: 100 %

    Workflow processing

.. figure:: img/standalone_example.png
    :scale: 25 %

    nabu standalone application


tomwer has been developed by the `Software group <http://www.esrf.eu/Instrumentation/software>`_ of the `European Synchrotron <https://www.esrf.eu/>`_.

.. toctree::
   :hidden:
   :maxdepth: 3

   applications/index.rst
   convert_hdf5_dataset.rst
   canvas/index.rst
   developer.rst
   install.rst
   language.rst
   other.rst
   settings.rst
   tutorials/index.rst
   user_corner/index.rst
   workflow.rst


=========================
|foo|   Table of contents
=========================


:doc:`install`
    Installation

:doc:`tutorials/index`
    tutorials for using the orange add-on

:doc:`language/index`
    details about the technical language used

:doc:`user_corner/index`
    User corner

:doc:`canvas/index`
    information regarding the canvas

:doc:`applications/index`
    applications

:doc:`settings`
    Settings

:doc:`developer`
    developer information

:doc:`other`
    How to get help, graylog (web logs), environment variables.


for the html help from the GUI we need to keep those in the index.rst file

---------------
Start up videos
---------------

.. include:: tutorials/start_up_videos.rst


-------
Widgets
-------

.. the orange widgets section has to be stored here to fit the orange requirement (and accessing the help from orange-canvas)

This is the list of actual widgets/boxes proposed by the workflow tool:


Control
```````

.. toctree::
  :maxdepth: 1

  widgets/control/datadiscovery.rst
  widgets/control/datalistwidget.rst
  widgets/control/datalistener.rst
  widgets/control/dataselectorwidget.rst
  widgets/control/datatransfertwidget.rst
  widgets/control/datavalidatorwidget.rst
  widgets/control/datawatcherwidget.rst
  widgets/control/emailnotifier.rst
  widgets/control/nxtomoconcatenate.rst
  widgets/control/nxtomomillwidget.rst
  widgets/control/filterwidget.rst
  widgets/control/reducedarkflatselectorwidget.rst
  widgets/control/singletomoobj.rst
  widgets/control/timerwidget.rst
  widgets/control/volumesymlink.rst


Reconstruction
``````````````

.. toctree::
  :maxdepth: 1

  widgets/reconstruction/corwidget.rst
  widgets/reconstruction/darkrefwidget.rst
  widgets/reconstruction/liveslicewidget.rst
  widgets/reconstruction/nabuslicewidget.rst
  widgets/reconstruction/nabuvolumewidget.rst
  widgets/reconstruction/saaxiswidget.rst
  widgets/reconstruction/sadeltabetawidget.rst
  widgets/reconstruction/tofuwidget.rst
  widgets/reconstruction/castvolumewidget.rst
  widgets/reconstruction/intensitynormalization.rst
  widgets/reconstruction/helicalprepareweightsdouble.rst


Cluster
```````

.. toctree::
  :maxdepth: 1

  widgets/cluster/futuresupervisor.rst
  widgets/cluster/slurmcluster.rst


Visualization
`````````````

.. toctree::
  :maxdepth: 1

  widgets/visualization/diffviewer.rst
  widgets/visualization/slicestack.rst
  widgets/visualization/sinogramviewer.rst
  widgets/visualization/volumeviewer.rst
  widgets/visualization/dataviewerwidget.rst
  widgets/visualization/radiostack.rst
  widgets/visualization/samplemovedwidget.rst
  widgets/visualization/nxtomometadataviewer.rst


HDF5 edition - NXTomo
`````````````````````

.. toctree::
  :maxdepth: 1

  widgets/edit/darkrefpatch.rst
  widgets/edit/imagekeyeditor.rst
  widgets/edit/imagekeyupgrader.rst
  widgets/edit/nxtomoeditor.rst


Other
`````

.. toctree::
  :maxdepth: 1

  widgets/other/pythonscript.rst
  widgets/other/tomoobjshub.rst