Merge branch 'feature/sphinx' into develop

.gitignore

@@ -4,7 +4,8 @@
 deploy/
 deploy/*
 temp/
-
+doc/build/
+doc/build/*
 example/*.aux.xml
 timeseriesviewer/ui/tmp.ui
 .*

Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = HUBTimeSeriesViewer
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = HUBTimeSeriesViewer
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

doc/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=HUBTimeSeriesViewer
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

doc/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# HUB TimeSeriesViewer documentation build configuration file, created by
+# sphinx-quickstart on Fri Jan 19 11:57:19 2018.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath('../../'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+#source_suffix = '.rst'
+source_parsers = {
+   '.md': 'recommonmark.parser.CommonMarkParser',
+}
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'HUB TimeSeriesViewer'
+copyright = u'2018, Benjamin Jakimow, Sebastian van der Linden, Patrick Hostert'
+author = u'Benjamin Jakimow'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+import timeseriesviewer
+version = u'{}'.format(timeseriesviewer.VERSION)
+# The full version, including alpha/beta/rc tags.
+release = u'{}'.format(timeseriesviewer.VERSION)
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'HUBTimeSeriesViewerDoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'HUBTimeSeriesViewer.tex', u'HUB TimeSeriesViewer Documentation',
+     u'Benjamin Jakimow', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'hubtimeseriesviewer', u'HUB TimeSeriesViewer Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'HUBTimeSeriesViewer', u'HUB TimeSeriesViewer Documentation',
+     author, 'HUBTimeSeriesViewer', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None,
+                       'python':('https://docs.python.org/2.7', None),
+                       'http://www.pyqtgraph.org/documentation':None}

doc/source/index.rst

+.. HUB TimeSeriesViewer documentation master file, created by
+   sphinx-quickstart on Fri Jan 19 11:57:19 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+HUB Time Series Viewer
+================================================
+
+About
+-----
+The Humboldt-Universität zu Berlin (HUB) Time Series Viewer is a QGIS Plugin to visualize raster based earth observation time series data.
+
+Its major aims are:
+
+* an integrated visualization and labeling of multi-sensor remote-sensing time-series data, based on `QGIS <http://www.qgis.org>`_
+* to minimize the user-interaction ("mouse-clicks") required to optimize different ways of data representation.
+* an (almost) platform independent installation
+
+.. image:: img/screenshot1.png
+
+..  toctree::
+    :maxdepth: 2
+    :caption: Contents:
+    :local:
+
+
+News
+----
+
+2017-06-27: `Poster <https://bitbucket.org/jakimowb/hub-timeseriesviewer/downloads/Jakimow.et.al.TimeSeriesViewer.pdf>`_ & demonstration at `Multitemp 2017, Brugges, Belgium <https://multitemp2017.vito.be>`_.
+
+2017-05-21: many changes, done in development branch "develop", e.g. QGIS MapCanvases for interactive maps, temporal profiles and more.
+
+2017-02-14: first setup for test users in the recent development branch qgis_apo
+
+2016-12-02: Work on this project continued. During the last months I focused on the `EnMAP-Box <https://bitbucket.org/hu-geomatics/enmap-box>`_ where I gained a lot of experience in using Qt and QGIS API.
+
+
+
+Features
+--------
+
+* Raster images can be added to the time series without homogenisation of spatial extent or coordinate reference system. Time stamps are extracted automatically from (i) image meta data ("acquisition date"), (ii) the file name or (iii) the file directory path.
+* Raster IO uses the `Geospatial Data Abstraction Library (GDAL) <http://www.gdal.org>`_, which supports up to 142 `raster image formats <http://www.gdal.org/formats_list.html>`_ different raster formats.
+* Distinguished sensors by pixel size and number of bands and, if available, band wavelength information and sensor name.
+* Spatial-temporal ("maps") visualisation allows to show multiples band combinations in parallel, e.g. True Color and coloured infrared.
+* Color stretches are applied to all raster images of same sensor and band combination. This helps to optimise color stretches for multiple images in a minimum of time.
+* Spectral-temporal ("time profile") visualisation shows raw or scaled, sensor specific band values.
+
+Missing Features / Outlook
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* a lot of debugging, making the small errors gone.
+* 3D plotting for spectral-temporal surfaces
+* export temporal profiles
+* export spectral libraries
+* show location of selected spectra
+
+Your feedback (wishes, comments, bugs, ...) is always welcome. Add it to the `issue section <https://bitbucket.org/jakimowb/sensecarbontsviewer/issues>`_
+or send me an email `benjamin.jakimow@geo.hu-berlin.de <benjamin.jakimow@geo.hu-berlin.de>`_.
+
+
+
+License and Use
+---------------
+
+This program is free software; you can redistribute it and/or modify it under the terms of the `GNU General Public License Version 3 (GNU GPL-3) <https://www.gnu.org/licenses/gpl-3.0.en.html>`_ , as published by the Free Software Foundation.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/source/installation.md

+# Installation #
+## A. Standard QGIS Plugin Installation ##
+1. Download the most recent zip archive of the HUB TimeSeriesViewer QGIS Plugin from https://bitbucket.org/jakimowb/hub-timeseriesviewer/downloads
+2. Extract the ``timeseriesviewerplugin`` folder and copy it to the user' QGIS python plugin directory
+``~/.qgis2/python/plugins/timeseriesviewerplugin``
+
+    Alternatively, you can choose any other folder ``my/qgis/plugins/timeseriesviewerplugin`` if your ensure that it is known to the QGIS_PLUGINPATH:
+
+    * In QGIS, got to Settings >> Options >> System.
+    * Enable the Environment group box.
+    * Create a new entry that append ``my/qgis/plugins`` to the variable ``QGIS_PLUGINPATH``.
+
+3. Finally restart QGIS, open the Plugin Manager and enable the HUB-TimeSeriesViewer.
+
+
+## B. Developers ##
+You really want to use [git](https://en.wikipedia.org/wiki/Git_%28software%29) to install and update the viewer.
+
+If git is not available in your shell, you can download it from [https://git-scm.com/downloads](https://git-scm.com/downloads). You can install git without admin rights.
+
+Larger binary files, e.g. for exemplary data, will are distributed via the Git Large File Storage (lfs) extension [https://git-lfs.github.com](https://git-lfs.github.com).
+
+
+1. Open your shell and clone the repository into a local QGIS Python Plugin Folder
+
+        cd %USERPROFILE%\.qgis2\python\plugins
+        git clone https://bitbucket.org/jakimowb/hub-timeseriesviewer.git
+
+2. Checkout the development branch (this might change with the fist stable master version)
+        git checkout development
+        git lfs checkout
+
+3. Start QGIS, go to Plugins -> Manage and Install and enable the "HUB TimeSeriesViewer" Plugin
+4. Download updates if available
+
+        cd %USERPROFILE%\.qgis2\python\plugins\hub-timeseriesviewer
+        git pull
\ No newline at end of file

doc/source/news.md

+# News #
+2017-06-27: [Poster](https://bitbucket.org/jakimowb/hub-timeseriesviewer/downloads/Jakimow.et.al.TimeSeriesViewer.pdf) & demo presentation at [Multitemp 2017](https://multitemp2017.vito.be)
+
+2017-05-21: many changes, done in development branch "develop", e.g:
+            QGIS MapCanvases for interactive maps, temporal profiles, ...
+            Feel free to test it if you like, but please note that it is still not stable.
+
+2017-02-14: first setup for test users in the recent development branch qgis_apo
+
+2016-12-02: Work on this project continued. During the last months I focused on
+the [EnMAP-Box](https://bitbucket.org/hu-geomatics/enmap-box) where I gained a lot of experience in using Qt and QGIS API.
+Referring to this, I created the [qgis_api](/branch/qgis_api) which contains the most recent developments.

make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=HUBTimeSeriesViewer
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

source/conf.py

+# -*- coding: utf-8 -*-
+#
+# HUB TimeSeriesViewer documentation build configuration file, created by
+# sphinx-quickstart on Fri Jan 19 11:54:14 2018.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'HUB TimeSeriesViewer'
+copyright = u'2018, Benjamin Jakimow, Sebastian van der Linden, Patrick Hostert'
+author = u'Benjamin Jakimow, Sebastian van der Linden, Patrick Hostert'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0'
+# The full version, including alpha/beta/rc tags.
+release = u'0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'HUBTimeSeriesViewerdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'HUBTimeSeriesViewer.tex', u'HUB TimeSeriesViewer Documentation',
+     u'Benjamin Jakimow, Sebastian van der Linden, Patrick Hostert', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'hubtimeseriesviewer', u'HUB TimeSeriesViewer Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'HUBTimeSeriesViewer', u'HUB TimeSeriesViewer Documentation',
+     author, 'HUBTimeSeriesViewer', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

source/index.rst

+.. HUB TimeSeriesViewer documentation master file, created by
+   sphinx-quickstart on Fri Jan 19 11:54:14 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to HUB TimeSeriesViewer's documentation!
+================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`