Commit 9080e9e1035fe19833dcad76a2d4e6d9f112a9f4

Authored by Erwan Motte
1 parent d62bb603
Exists in master

Changed to Sphinx format.. started to populate the Ground truth section

INS/index.md
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1   -Index of GLORI INS Subsystem Documentation
2   -==========================================
3   -
4   -*pour la documentation en français, cliquer ici*
5   -
6   -Test insertion png
7   -
8   -Test insertion SVG
9   -
10   -
11   -Test link interne
12   -
13   -Test link externe
14 0 \ No newline at end of file
img/image3_new.png

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1   -Index of GLORI Documentation
2   -============================
3   -
4   -*pour la documentation en français, cliquer [ici](index_fr.md)*
5   -
6   -Test insertion png
7   -
8   -![Figure GNSS-R png](img/image3_new.png)
9   -
10   -Test insertion SVG
11   -
12   -![Figure spyder svg](http://tully.ups-tlse.fr/mottee/GLORI_doc/raw/master/img/spyder_light.svg)
13   -
14   -
15   -
16   -
17   -Test link interne
18   -
19   -[INS Subsystem documentation](INS/index.md)
20   -
21   -Test link externe
22   -
23   -[google.com](http://www.google.com)
24 0 \ No newline at end of file
source/FWD/index.rst 0 → 100644
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  1 +*************
  2 +Forward Model
  3 +*************
  4 +
... ...
source/GTD/GTD_campaigns.rst 0 → 100644
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  1 +*********************
  2 +Campaigns Description
  3 +*********************
  4 +
  5 +
  6 +GLORI 2014 Campaign
  7 +===================
  8 +
  9 +
  10 +
  11 +
  12 +GLORIE 2015 Campaign
  13 +====================
  14 +
  15 +The in situ data of the GLORIE 2015 Campaign was collected in different ways
  16 +according to the sites. The following sections describe the methods and
  17 +available data for each of the sites.
  18 +
  19 +.. figure:: /img/zones.png
  20 + :align: center
  21 + :alt:
  22 +
  23 + Description of the GLORIE 2015 zones (build from qgis)
  24 +
  25 +
  26 +Lamasquère
  27 +----------
  28 +
  29 +The Lamasquère area
  30 +
  31 +.. figure:: /img/lamasquere.png
  32 + :align: center
  33 + :alt:
  34 +
  35 + Description of the Lamasquère area (build from qgis)
  36 +
  37 +
  38 +Auch
  39 +----
  40 +
  41 +
  42 +
  43 +Marcheprime
  44 +-----------
  45 +
  46 +
  47 +Nezer
  48 +-----
0 49 \ No newline at end of file
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source/GTD/GTD_data_format.rst 0 → 100644
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  1 +Ground Truth data format
  2 +========================
  3 +
  4 +The ground truth is stored in the [campaign]_gt shapefile_.
  5 +The polygon delimiting the plots can either be given by partners
  6 +or created by geo-interpretation of *correctly geo-referenced* satellite data.
  7 +They are managed using GIS software such as the freely available QGIS_.
  8 +
  9 +.. _QGIS: http://www.qgis.org/
  10 +
  11 +The following fields were selected in order to build a unified ground truth
  12 + database:
  13 +
  14 +Soil
  15 +----
  16 +
  17 +Values related to soil structure and considered as constant
  18 +for the whole duration of the campaign:
  19 +
  20 ++------------------------------+------+-----------+
  21 +| Parameter | unit | variable |
  22 ++==============================+======+===========+
  23 +| Roughness Standard deviation | [m] | rough_std |
  24 ++------------------------------+------+-----------+
  25 +| Roughness Correlation length | [m] | rough_L |
  26 ++------------------------------+------+-----------+
  27 +| Soil Sand content | [%] | soil_sand |
  28 ++------------------------------+------+-----------+
  29 +| Soil Silt content | [%] | soil_silt |
  30 ++------------------------------+------+-----------+
  31 +| Soil Clay content | [%] | soil_clay |
  32 ++------------------------------+------+-----------+
  33 +
  34 +
  35 +Crop meta data
  36 +--------------
  37 +
  38 +Values related to crops and considered as constant for the whole
  39 +duration of the campaign:
  40 +
  41 ++------------------------------+--------+-----------+
  42 +| Parameter | unit | variable |
  43 ++==============================+========+===========+
  44 +| Crop Type | [N/A] | crop_type |
  45 ++------------------------------+--------+-----------+
  46 +| Seeding date | [date] | date_seed |
  47 ++------------------------------+--------+-----------+
  48 +| Harvest date | [date] | date_harv |
  49 ++------------------------------+--------+-----------+
  50 +| Irrigated | [Y/N] | if_irrig |
  51 ++------------------------------+--------+-----------+
  52 +
  53 +
  54 +Plot shape
  55 +----------
  56 +
  57 +The plot shape field is shapefile_ polygon defined as a series of x/y
  58 +coordinates representing a closed geometry. The reference system to be used
  59 +is Lambert 93
  60 +(`EPSG 2154`_)
  61 +
  62 +.. _`EPSG 2154`: http://spatialreference.org/ref/epsg/rgf93-lambert-93/
  63 +
  64 +.. _shapefile: https://en.wikipedia.org/wiki/Shapefile
  65 +
  66 ++------------------------------+--------+-----------+
  67 +| Parameter | unit | variable |
  68 ++==============================+========+===========+
  69 +| Plot shape | shp | geometry |
  70 ++------------------------------+--------+-----------+
  71 +
  72 +
  73 +Soil Moisture
  74 +-------------
  75 +
  76 +Values related to soil moisture are stored for each flight date.
  77 +For flights spanning over two days, the date of the second day is given.
  78 +
  79 ++----------------------------------+---------+---------------+
  80 +| Parameter | unit | variable |
  81 ++==================================+=========+===============+
  82 +| Mean volumetric soil moisture | [m3/m3] | SM_avg_[MMDD] |
  83 ++----------------------------------+---------+---------------+
  84 +| Std dev volumetric soil moisture | [m3/m3] | SM_std_[MMDD] |
  85 ++----------------------------------+---------+---------------+
  86 +
  87 +
  88 +Vegetation
  89 +----------
  90 +
  91 +Values related to vegetation cover for each flight date
  92 +
  93 ++------------------------------+---------+-----------------+
  94 +| Parameter | unit | variable |
  95 ++==============================+=========+=================+
  96 +| Leaf Area Index | [m2/m2] | crop_LAI_[MMDD] |
  97 ++------------------------------+---------+-----------------+
  98 +| Crop height | [m] | crop_h_[MMDD] |
  99 ++------------------------------+---------+-----------------+
  100 +| Vegetation Water Content | [kg/m2] | crop_VWC_[MMDD] |
  101 ++------------------------------+---------+-----------------+
  102 +| Vegetation Relative Humidity | [%] | crop_VRH_[MMDD] |
  103 ++------------------------------+---------+-----------------+
  104 +
  105 +
  106 +
  107 +Biomass
  108 +-------
  109 +
  110 +Values related to biomass description. Considered as constant for the whole
  111 +campaign duration.
  112 +
  113 ++------------------------------+---------+-----------------+
  114 +| Parameter | unit | variable |
  115 ++==============================+=========+=================+
  116 +| Biomass Density | [t/ha] | biom_dens |
  117 ++------------------------------+---------+-----------------+
  118 +| Biomass height | [m] | biom_h |
  119 ++------------------------------+---------+-----------------+
  120 +| Stand plantation year | [year] | biom_year |
  121 ++------------------------------+---------+-----------------+
... ...
source/GTD/GTD_index.rst 0 → 100644
... ... @@ -0,0 +1,10 @@
  1 +************
  2 +Ground Truth
  3 +************
  4 +
  5 +.. toctree::
  6 + :maxdepth: 2
  7 +
  8 + GTD_campaigns
  9 + GTD_data_format
  10 +
... ...
source/INS/index.rst 0 → 100644
... ... @@ -0,0 +1,4 @@
  1 +********************
  2 +Instrument subsystem
  3 +********************
  4 +
... ...
source/INV/index.rst 0 → 100644
... ... @@ -0,0 +1,4 @@
  1 +*******************
  2 +Inversion subsystem
  3 +*******************
  4 +
... ...
source/Introduction.rst 0 → 100644
... ... @@ -0,0 +1,2 @@
  1 +Introduction to GLORI Documentation
  2 +===================================
0 3 \ No newline at end of file
... ...
source/PRO/index.rst 0 → 100644
... ... @@ -0,0 +1,4 @@
  1 +********************
  2 +Processing subsystem
  3 +********************
  4 +
... ...
source/Subsystems.rst 0 → 100644
... ... @@ -0,0 +1,27 @@
  1 +Definition of GLORI'S Subsystems
  2 +********************************
  3 +
  4 +Test png
  5 +========
  6 +
  7 +.. figure:: /img/image3_new.png
  8 + :align: center
  9 +
  10 + test png
  11 +
  12 +Test svg
  13 +========
  14 +
  15 +.. figure:: /img/spyder_light.svg
  16 + :align: center
  17 +
  18 + test svg
  19 +
  20 +Test lien interne
  21 +=================
  22 +
  23 +
  24 +
  25 +
  26 +Test lien externe
  27 +=================
... ...
source/VAL/index.rst 0 → 100644
... ... @@ -0,0 +1,4 @@
  1 +********************
  2 +Validation subsystem
  3 +********************
  4 +
... ...
source/conf.py 0 → 100644
... ... @@ -0,0 +1,368 @@
  1 +# -*- coding: utf-8 -*-
  2 +#
  3 +# GLORI_doc documentation build configuration file, created by
  4 +# sphinx-quickstart on Mon May 30 11:28:04 2016.
  5 +#
  6 +# This file is execfile()d with the current directory set to its
  7 +# containing dir.
  8 +#
  9 +# Note that not all possible configuration values are present in this
  10 +# autogenerated file.
  11 +#
  12 +# All configuration values have a default; values that are commented out
  13 +# serve to show the default.
  14 +
  15 +import sys
  16 +import os
  17 +
  18 +# If extensions (or modules to document with autodoc) are in another directory,
  19 +# add these directories to sys.path here. If the directory is relative to the
  20 +# documentation root, use os.path.abspath to make it absolute, like shown here.
  21 +#sys.path.insert(0, os.path.abspath('.'))
  22 +
  23 +# -- General configuration ------------------------------------------------
  24 +
  25 +# If your documentation needs a minimal Sphinx version, state it here.
  26 +#needs_sphinx = '1.0'
  27 +
  28 +# Add any Sphinx extension module names here, as strings. They can be
  29 +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
  30 +# ones.
  31 +extensions = [
  32 + 'sphinx.ext.autodoc',
  33 + 'sphinx.ext.doctest',
  34 + 'sphinx.ext.intersphinx',
  35 + 'sphinx.ext.todo',
  36 + 'sphinx.ext.coverage',
  37 + 'sphinx.ext.mathjax',
  38 + 'sphinx.ext.ifconfig',
  39 + 'rst2pdf.pdfbuilder',
  40 +]
  41 +
  42 +# Add any paths that contain templates here, relative to this directory.
  43 +templates_path = ['_templates']
  44 +
  45 +# The suffix(es) of source filenames.
  46 +# You can specify multiple suffix as a list of string:
  47 +# source_suffix = ['.rst', '.md']
  48 +source_suffix = '.rst'
  49 +
  50 +# The encoding of source files.
  51 +#source_encoding = 'utf-8-sig'
  52 +
  53 +# The master toctree document.
  54 +master_doc = 'index'
  55 +
  56 +# General information about the project.
  57 +project = u'GLORI_doc'
  58 +copyright = u'2016, Erwan Motte'
  59 +author = u'Erwan Motte'
  60 +
  61 +# The version info for the project you're documenting, acts as replacement for
  62 +# |version| and |release|, also used in various other places throughout the
  63 +# built documents.
  64 +#
  65 +# The short X.Y version.
  66 +version = u'1.0'
  67 +# The full version, including alpha/beta/rc tags.
  68 +release = u'1.0'
  69 +
  70 +# The language for content autogenerated by Sphinx. Refer to documentation
  71 +# for a list of supported languages.
  72 +#
  73 +# This is also used if you do content translation via gettext catalogs.
  74 +# Usually you set "language" from the command line for these cases.
  75 +language = None
  76 +
  77 +# There are two options for replacing |today|: either, you set today to some
  78 +# non-false value, then it is used:
  79 +#today = ''
  80 +# Else, today_fmt is used as the format for a strftime call.
  81 +#today_fmt = '%B %d, %Y'
  82 +
  83 +# List of patterns, relative to source directory, that match files and
  84 +# directories to ignore when looking for source files.
  85 +exclude_patterns = []
  86 +
  87 +# The reST default role (used for this markup: `text`) to use for all
  88 +# documents.
  89 +#default_role = None
  90 +
  91 +# If true, '()' will be appended to :func: etc. cross-reference text.
  92 +#add_function_parentheses = True
  93 +
  94 +# If true, the current module name will be prepended to all description
  95 +# unit titles (such as .. function::).
  96 +#add_module_names = True
  97 +
  98 +# If true, sectionauthor and moduleauthor directives will be shown in the
  99 +# output. They are ignored by default.
  100 +#show_authors = False
  101 +
  102 +# The name of the Pygments (syntax highlighting) style to use.
  103 +pygments_style = 'sphinx'
  104 +
  105 +# A list of ignored prefixes for module index sorting.
  106 +#modindex_common_prefix = []
  107 +
  108 +# If true, keep warnings as "system message" paragraphs in the built documents.
  109 +#keep_warnings = False
  110 +
  111 +# If true, `todo` and `todoList` produce output, else they produce nothing.
  112 +todo_include_todos = True
  113 +
  114 +
  115 +# -- Options for HTML output ----------------------------------------------
  116 +
  117 +# The theme to use for HTML and HTML Help pages. See the documentation for
  118 +# a list of builtin themes.
  119 +html_theme = 'alabaster'
  120 +
  121 +# Theme options are theme-specific and customize the look and feel of a theme
  122 +# further. For a list of options available for each theme, see the
  123 +# documentation.
  124 +#html_theme_options = {}
  125 +
  126 +# Add any paths that contain custom themes here, relative to this directory.
  127 +#html_theme_path = []
  128 +
  129 +# The name for this set of Sphinx documents. If None, it defaults to
  130 +# "<project> v<release> documentation".
  131 +#html_title = None
  132 +
  133 +# A shorter title for the navigation bar. Default is the same as html_title.
  134 +#html_short_title = None
  135 +
  136 +# The name of an image file (relative to this directory) to place at the top
  137 +# of the sidebar.
  138 +#html_logo = None
  139 +
  140 +# The name of an image file (within the static path) to use as favicon of the
  141 +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
  142 +# pixels large.
  143 +#html_favicon = None
  144 +
  145 +# Add any paths that contain custom static files (such as style sheets) here,
  146 +# relative to this directory. They are copied after the builtin static files,
  147 +# so a file named "default.css" will overwrite the builtin "default.css".
  148 +html_static_path = ['_static']
  149 +
  150 +# Add any extra paths that contain custom files (such as robots.txt or
  151 +# .htaccess) here, relative to this directory. These files are copied
  152 +# directly to the root of the documentation.
  153 +#html_extra_path = []
  154 +
  155 +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
  156 +# using the given strftime format.
  157 +#html_last_updated_fmt = '%b %d, %Y'
  158 +
  159 +# If true, SmartyPants will be used to convert quotes and dashes to
  160 +# typographically correct entities.
  161 +#html_use_smartypants = True
  162 +
  163 +# Custom sidebar templates, maps document names to template names.
  164 +#html_sidebars = {}
  165 +
  166 +# Additional templates that should be rendered to pages, maps page names to
  167 +# template names.
  168 +#html_additional_pages = {}
  169 +
  170 +# If false, no module index is generated.
  171 +#html_domain_indices = True
  172 +
  173 +# If false, no index is generated.
  174 +#html_use_index = True
  175 +
  176 +# If true, the index is split into individual pages for each letter.
  177 +#html_split_index = False
  178 +
  179 +# If true, links to the reST sources are added to the pages.
  180 +#html_show_sourcelink = True
  181 +
  182 +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
  183 +#html_show_sphinx = True
  184 +
  185 +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
  186 +#html_show_copyright = True
  187 +
  188 +# If true, an OpenSearch description file will be output, and all pages will
  189 +# contain a <link> tag referring to it. The value of this option must be the
  190 +# base URL from which the finished HTML is served.
  191 +#html_use_opensearch = ''
  192 +
  193 +# This is the file name suffix for HTML files (e.g. ".xhtml").
  194 +#html_file_suffix = None
  195 +
  196 +# Language to be used for generating the HTML full-text search index.
  197 +# Sphinx supports the following languages:
  198 +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
  199 +# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
  200 +#html_search_language = 'en'
  201 +
  202 +# A dictionary with options for the search language support, empty by default.
  203 +# Now only 'ja' uses this config value
  204 +#html_search_options = {'type': 'default'}
  205 +
  206 +# The name of a javascript file (relative to the configuration directory) that
  207 +# implements a search results scorer. If empty, the default will be used.
  208 +#html_search_scorer = 'scorer.js'
  209 +
  210 +# Output file base name for HTML help builder.
  211 +htmlhelp_basename = 'GLORI_docdoc'
  212 +
  213 +# -- Options for LaTeX output ---------------------------------------------
  214 +
  215 +latex_elements = {
  216 +# The paper size ('letterpaper' or 'a4paper').
  217 +#'papersize': 'letterpaper',
  218 +
  219 +# The font size ('10pt', '11pt' or '12pt').
  220 +#'pointsize': '10pt',
  221 +
  222 +# Additional stuff for the LaTeX preamble.
  223 +#'preamble': '',
  224 +
  225 +# Latex figure (float) alignment
  226 +#'figure_align': 'htbp',
  227 +}
  228 +
  229 +# Grouping the document tree into LaTeX files. List of tuples
  230 +# (source start file, target name, title,
  231 +# author, documentclass [howto, manual, or own class]).
  232 +latex_documents = [
  233 + (master_doc, 'GLORI_doc.tex', u'GLORI\\_doc Documentation',
  234 + u'Erwan Motte', 'manual'),
  235 +]
  236 +
  237 +# The name of an image file (relative to this directory) to place at the top of
  238 +# the title page.
  239 +#latex_logo = None
  240 +
  241 +# For "manual" documents, if this is true, then toplevel headings are parts,
  242 +# not chapters.
  243 +#latex_use_parts = False
  244 +
  245 +# If true, show page references after internal links.
  246 +#latex_show_pagerefs = False
  247 +
  248 +# If true, show URL addresses after external links.
  249 +#latex_show_urls = False
  250 +
  251 +# Documents to append as an appendix to all manuals.
  252 +#latex_appendices = []
  253 +
  254 +# If false, no module index is generated.
  255 +#latex_domain_indices = True
  256 +
  257 +
  258 +# -- Options for manual page output ---------------------------------------
  259 +
  260 +# One entry per manual page. List of tuples
  261 +# (source start file, name, description, authors, manual section).
  262 +man_pages = [
  263 + (master_doc, 'glori_doc', u'GLORI_doc Documentation',
  264 + [author], 1)
  265 +]
  266 +
  267 +# If true, show URL addresses after external links.
  268 +#man_show_urls = False
  269 +
  270 +
  271 +# -- Options for Texinfo output -------------------------------------------
  272 +
  273 +# Grouping the document tree into Texinfo files. List of tuples
  274 +# (source start file, target name, title, author,
  275 +# dir menu entry, description, category)
  276 +texinfo_documents = [
  277 + (master_doc, 'GLORI_doc', u'GLORI_doc Documentation',
  278 + author, 'GLORI_doc', 'One line description of project.',
  279 + 'Miscellaneous'),
  280 +]
  281 +
  282 +# Documents to append as an appendix to all manuals.
  283 +#texinfo_appendices = []
  284 +
  285 +# If false, no module index is generated.
  286 +#texinfo_domain_indices = True
  287 +
  288 +# How to display URL addresses: 'footnote', 'no', or 'inline'.
  289 +#texinfo_show_urls = 'footnote'
  290 +
  291 +# If true, do not generate a @detailmenu in the "Top" node's menu.
  292 +#texinfo_no_detailmenu = False
  293 +
  294 +
  295 +# -- Options for Epub output ----------------------------------------------
  296 +
  297 +# Bibliographic Dublin Core info.
  298 +epub_title = project
  299 +epub_author = author
  300 +epub_publisher = author
  301 +epub_copyright = copyright
  302 +
  303 +# The basename for the epub file. It defaults to the project name.
  304 +#epub_basename = project
  305 +