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Merge pull request #91 from HYPERNETS/flag_ops
update docs
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docs/sphinx/atbd.rst

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.. atbd - algorithm theoretical basis
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Author: seh2
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Email: sam.hunt@npl.co.uk
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Created: 23/3/20
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.. _atbd:
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Algorithm Theoretical Basis
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===========================
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.. include:: content/atbd/atbd.rst

docs/sphinx/conf.py

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# The master toctree document.
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master_doc = 'index'
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atbd = 'atbd'
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userguide = 'userguide'
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# General information about the project.
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project = u'hypernets_processor'
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'hypernets_processor.tex', u'Hypernets Processor Documentation',
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(userguide, 'hypernets_processor_userguide.tex', u'Hypernets Processor User Guide',
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u'Hypernets Project Team', 'manual'),
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(atbd, 'hypernets_processor_atbd.tex', u'Hypernets Processor Algorithm Theoretical Basis Document',
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u'Hypernets Project Team', 'manual'),
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]
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'hypernets_processor', u'hypernets_processor Documentation',
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(master_doc, 'hypernets_processor', u'Hypernets Processor User Guide',
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author, 'hypernets_processor', 'One line description of project.',
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'Miscellaneous'),
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]

docs/sphinx/content/atbd/atbd.rst

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.. atbd - algorithm theoretical basis
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Author: seh2
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Email: sam.hunt@npl.co.uk
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Created: 23/3/20
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Created: 6/11/20
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.. _atbd:
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Algorithm Theoretical Basis
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===========================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For more information see the project document.
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TBC

docs/sphinx/content/developers/developers.rst

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docs/sphinx/content/users/user_adhoc.rst renamed to docs/sphinx/content/users/adhoc.rst

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.. _user_adhoc:
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User Guide - Ad-hoc Sequence Processing
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=======================================
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Ad-hoc Sequence Processing
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==========================
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This section provides a user guide for running the **hypernets_processor** module to process specified field acquisitions, or sequences, on an ad-hoc basis outside of any automated processing.
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* `input_directory` - directory of raw sequence product, or directory containing a number of raw sequence products, to process.
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* `output_directory` - directory to write output data to.
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* `network` - network name, land or water. The default configuration for this network is applied for the processing.
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* `network` - network name, `land` or `water`. The default configuration for this network is applied for the processing.
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To see more options, try::
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docs/sphinx/content/users/user_automated.rst renamed to docs/sphinx/content/users/automated.rst

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.. _user_automated:
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User Guide - Automated Processing
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=================================
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Automated Processing
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====================
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This section provides a user guide for running the **hypernets_processor** module as an automated processor of incoming field data. In this scenario, a set of field hypstar systems are regularly syncing raw data to a server. Running on this server, the **hypernets_processor** processes the data and adds it to an archive that can be accessed through a user portal.
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docs/sphinx/index.rst

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The **hypernets_processor** module is a Python software package to process the `Hypernets <http://hypernets.eu/from_cms/summary>`_ land and water network in-situ hyperspectral data to surface reflectance products for distribution to users.
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There are two main use cases for the **hypernets_processor** module. The primary function of the software is the automated preparation of data retrieved from network sites for distribution to users. Additionally, the software may also be used for ad-hoc processing of particular field acquisitions, for example for testing instrument operation in the field.
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This documentation aimed at both users and developers of the software, find the relevant sections below.
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For Users:
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~~~~~~~~~~
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.. toctree::
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:maxdepth: 1
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:caption: User Guide
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content/users/adhoc
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content/users/automated
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.. toctree::
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:maxdepth: 2
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:maxdepth: 1
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:caption: ATBD
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content/users/users
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content/atbd/atbd
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For Developers:
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~~~~~~~~~~~~~~~
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.. toctree::
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:maxdepth: 2
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content/developers/developers
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:maxdepth: 1
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:caption: Developer Guide
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API Documentation
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~~~~~~~~~~~~~~~~~
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content/developers/getting_started
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content/developers/software_design
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.. toctree::
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:maxdepth: 2
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:caption: API Documentation
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content/API/hypernets_processor
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`
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content/API/hypernets_processor

docs/sphinx/content/users/users.rst renamed to docs/sphinx/userguide.rst

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.. toctree::
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:maxdepth: 1
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user_adhoc
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user_automated
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content/users/adhoc
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content/users/automated

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