Commit c18556d4 authored by Javier Quinteros's avatar Javier Quinteros

First very draft version of the documentation

parent 28a4a844
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# -*- coding: utf-8 -*-
#
# dasscripts documentation build configuration file, created by
# sphinx-quickstart on Dec 19 21:39:29 2019.
#
# 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.
import sys
import os
# 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.
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.todo',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
# source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'dasscripts'
copyright = u'2019-2020, Javier Quinteros - Deutsches GFZ Potsdam'
author = u'Javier Quinteros'
# 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 = '0.2'
# The full version, including alpha/beta/rc tags.
release = '0.2b1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ''
# Else, today_fmt is used as the format for a strftime call.
# today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['.build']
# The reST default role (used for this markup: `text`) to use for all
# documents.
# default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
# add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
# add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False
show_authors = True
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False
# -- 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 = 'default'
# 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 = {
'collapse_navigation': False,
'externalrefs': True,
'navigation_depth': 2,
'prev_next_buttons_location': 'both'
}
# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
html_title = 'Dasscripts Documentation'
# A shorter title for the navigation bar. Default is the same as html_title.
# html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
# html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
# html_favicon = None
# 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']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
# html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
# html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
# html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
# html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
# html_additional_pages = {}
# If false, no module index is generated.
# html_domain_indices = True
# If false, no index is generated.
# html_use_index = True
# If true, the index is split into individual pages for each letter.
# html_split_index = False
# If true, links to the reST sources are added to the pages.
# html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
# html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
# html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
# html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'Dasscripts-doc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
# 'papersize': 'letterpaper',
'papersize': 'a4paper',
# The font size ('10pt', '11pt' or '12pt').
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
# 'preamble': '',
}
# 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 = [
('index', 'Dasscripts-Documentation.tex', u'Dasscripts Documentation',
u'Javier Quinteros', 'manual')
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = 'GFZ-logo.jpg'
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
# latex_use_parts = False
# If true, show page references after internal links.
# latex_show_pagerefs = False
# If true, show URL addresses after external links.
# latex_show_urls = False
# Documents to append as an appendix to all manuals.
# latex_appendices = []
# If false, no module index is generated.
# latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'dasscripts', u'Dasscripts Documentation',
[u'Javier Quinteros'], 1)
]
# If true, show URL addresses after external links.
# man_show_urls = False
# -- 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 = [
('index', 'Dasscripts', u'Dasscripts Documentation',
u'Javier Quinteros', 'Dasscripts', 'Scripts to convert and manage data from DAS systems.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
# texinfo_appendices = []
# If false, no module index is generated.
# texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
# texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
# texinfo_no_detailmenu = False
dasconv package
===============
.. automodule:: dasconv
:members:
:undoc-members:
:show-inheritance:
Dasscripts documentation
########################
.. toctree::
:maxdepth: 2
:numbered:
:titlesonly:
userdoc.rst
modules.rst
Developer documentation
=======================
.. toctree::
:maxdepth: 4
dasconv
Dasscripts User documentation
#############################
Summary
=======
Dasscripts is basically a set of scripts to properly manage seismic
waveforms from DAS systems.
Installation
============
License
-------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Requirements
------------
* Python 3.6+
* Obspy
.. _installation:
Installation
------------
This software can be easily installed by means of pip with the following command ::
$ sudo pip install dasscripts
Optionally you could run it as a normal user (no sudo) and deploy it locally.
.. _installation_from_code:
Installation from source code
-----------------------------
You can always get the latest version of Dasscripts from its repository using git ::
$ git clone https://gitext.gfz-potsdam.de/javier/dasscripts.git
This will create a folder called dasscripts from which you can install the software ::
$ cd dasscripts
$ sudo python3 setup.py install
Running the code
================
To check if the software was properly installed you can run ::
$ dasconv -h
usage: dasconv [-h] [-l {CRITICAL,ERROR,WARNING,INFO,DEBUG}] [-d DIRECTORY]
[--start START] [--end END] [--chstart CHSTART]
[--chstop CHSTOP] [--chstep CHSTEP] [--decimate DECIMATE]
[--version]
filename
Read, manipulate and convert seismic waveforms generated by a DAS system.
positional arguments:
filename Experiment to read and process. It is usually the
first part of the filenames.
optional arguments:
-h, --help show this help message and exit
-l {CRITICAL,ERROR,WARNING,INFO,DEBUG}, --loglevel {CRITICAL,ERROR,WARNING,INFO,DEBUG}
Verbosity in the output.
-d DIRECTORY, --directory DIRECTORY
Directory where files are located.
--start START, --starttime START
Start of the selected time window. Format:
2019-02-01T00:01:02.123456Z
--end END, --endtime END
End of the selected time window. Format:
2019-02-01T00:01:02.123456Z
--chstart CHSTART First channel to export
--chstop CHSTOP Last channel to export
--chstep CHSTEP Step between channels in the selection
--decimate {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16}
Factor by which the sampling rate is lowered by
decimation.
--metadata Read and display the metadata from the TDMS files
--version show program's version number and exit
dasconv can be used to convert data from TDMS format into miniSEED. Below you will find some examples showing how to
use it to select subsets of the original data and export it. A complete list of its parameters and default values can
be found in the :ref:`Table of parameters<Table_Parameters>`
.. _Table_Parameters:
.. tabularcolumns:: |l|l|l|p{8cm}|c|
.. table:: Input parameters description
=================== ======== ========================================= ==========
Parameter Format Description Default
=================== ======== ========================================= ==========
filename str Experiment to read and process. It is
usually the first part of the filenames.
It is mandatory to provide it
--directory (-d) str Directory where the data is saved ``.``
--starttime (start) ISO 8601 Limit results to time series samples on
or after the specified start time. Any
--endtime (end) ISO 8601 Limit results to time series samples on
or before the specified end time. Any
--chstart int First channel to be read and exported ``0``
--chend int Last channel to be read and exported last one
--chstep int Step to calculate the index of the next
channel to export (1: next one; 2: skip
one, etc) ``1``
--decimate int Factor by which the sampling rate is
lowered by decimation. Exactly the factor
by which the number of samples will be
reduced ``5``
--metadata bool Read and display metadata information
instead of exporting data Disable
--version bool Print version information Disable
=================== ======== ========================================= ==========
Examples
--------
* Export waveforms from channels 800, 802 and 804 starting at 2019-05-08T09:37:35.409000 until 2019-05-08T09:38:05.400000.
The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
dasconv -d /home/user/test/ --start "2019-05-08T09:37:35.409000" --end "2019-05-08T09:38:05.400000" default --chstart 800 --chstop 805 --chstep 2
* Export waveforms from channels 0 and 1 from the beginning of the measurements until 2019-05-08T09:32:15.
The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
dasconv -d /home/user/test/ --endtime "2019-05-08T09:32:15" default --chstart 0 --chstop 1
* Export waveforms from channels 0 to 4 from the beginning of the measurements until 2019-05-08T09:32:15.
The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
dasconv -d /home/user/test/ --endtime "2019-05-08T09:32:15" default --chstart 0 --chstop 4 --decimate 2
Testing the service
-------------------
.. todo:: Provide a ``test`` directory with a tdms file and its miniSEED version. Use dasconv to convert the data and
check with the provided miniSEED file. The same for an ASCII format.
Two scripts are provided to test the functionality of the service at different
levels. These can be found in the ``test`` folder under the root directory of
your installation.
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