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docs: restructured to hierarchical file structure

new-parstack
Sebastian Heimann 6 years ago
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700d314487
  1. 132
      doc/Makefile
  2. 23
      doc/examples.rst
  3. 10
      doc/install.rst
  4. 17
      doc/install_quick.rst
  5. 33
      doc/reference.rst
  6. 2
      doc/source/apps/cake/index.rst
  7. 10
      doc/source/apps/cake/manual.rst
  8. 0
      doc/source/apps/fomosto/backends.rst
  9. 4
      doc/source/apps/fomosto/index.rst
  10. 6
      doc/source/apps/fomosto/tutorial.rst
  11. 6
      doc/source/apps/index.rst
  12. 2
      doc/source/apps/snuffler/extensions.rst
  13. 6
      doc/source/apps/snuffler/index.rst
  14. 0
      doc/source/apps/snuffler/manual.rst
  15. 20
      doc/source/apps/snuffler/tutorial.rst
  16. 2
      doc/source/conf.py
  17. 9
      doc/source/index.rst
  18. 2
      doc/source/install/details.rst
  19. 15
      doc/source/install/index.rst
  20. 4
      doc/source/install/system/anaconda2.rst
  21. 4
      doc/source/install/system/deb.rst
  22. 4
      doc/source/install/system/fedora.rst
  23. 17
      doc/source/install/system/index.rst
  24. 4
      doc/source/install/system/mac.rst
  25. 4
      doc/source/install/system/suse.rst
  26. 0
      doc/source/library/examples/cake_raytracing.rst
  27. 0
      doc/source/library/examples/catalog_search.rst
  28. 0
      doc/source/library/examples/dataset_management.rst
  29. 0
      doc/source/library/examples/fdsn_download.rst
  30. 12
      doc/source/library/examples/gf_forward.rst
  31. 0
      doc/source/library/examples/gf_store.rst
  32. 0
      doc/source/library/examples/guts.rst
  33. 21
      doc/source/library/examples/index.rst
  34. 0
      doc/source/library/examples/orthodrome.rst
  35. 6
      doc/source/library/examples/plotting.rst
  36. 20
      doc/source/library/examples/trace_handling.rst
  37. 6
      doc/source/library/examples/velocity_databases.rst
  38. 4
      doc/source/library/index.rst
  39. 0
      doc/source/library/reference/beachball.rst
  40. 0
      doc/source/library/reference/cake.rst
  41. 0
      doc/source/library/reference/catalog.rst
  42. 0
      doc/source/library/reference/crust2x2.rst
  43. 2
      doc/source/library/reference/crustdb.rst
  44. 0
      doc/source/library/reference/evalresp.rst
  45. 0
      doc/source/library/reference/fdsn.rst
  46. 0
      doc/source/library/reference/gf.rst
  47. 0
      doc/source/library/reference/gmtpy.rst
  48. 0
      doc/source/library/reference/gui_util.rst
  49. 0
      doc/source/library/reference/hamster_pile.rst
  50. 0
      doc/source/library/reference/ims.rst
  51. 33
      doc/source/library/reference/index.rst
  52. 0
      doc/source/library/reference/io.rst
  53. 0
      doc/source/library/reference/model.rst
  54. 0
      doc/source/library/reference/moment_tensor.rst
  55. 0
      doc/source/library/reference/orthodrome.rst
  56. 0
      doc/source/library/reference/pile.rst
  57. 0
      doc/source/library/reference/pile_viewer.rst
  58. 0
      doc/source/library/reference/plot.rst
  59. 0
      doc/source/library/reference/pz.rst
  60. 0
      doc/source/library/reference/rdseed.rst
  61. 0
      doc/source/library/reference/slink.rst
  62. 0
      doc/source/library/reference/snuffling.rst
  63. 0
      doc/source/library/reference/tectonics.rst
  64. 0
      doc/source/library/reference/trace.rst
  65. 0
      doc/source/library/reference/util.rst
  66. 0
      doc/source/overview.rst
  67. 0
      doc/source/static/STS2-Generic.polezero.txt
  68. 0
      doc/source/static/beachball-example01.png
  69. 0
      doc/source/static/beachball-example02.png
  70. 0
      doc/source/static/beachball-example03.png
  71. 0
      doc/source/static/cake_crust2.png
  72. 0
      doc/source/static/cake_plot_example.png
  73. 0
      doc/source/static/cake_plot_example_2.png
  74. 0
      doc/source/static/cake_plot_example_3.png
  75. 0
      doc/source/static/cake_plot_example_4.png
  76. 0
      doc/source/static/cake_plot_example_5.png
  77. 0
      doc/source/static/crustdb_plot.png
  78. 0
      doc/source/static/fomosto_report_displacement1.png
  79. 0
      doc/source/static/fomosto_view_1.png
  80. 0
      doc/source/static/fomosto_view_2.png
  81. 0
      doc/source/static/gf_static_displacement.png
  82. 0
      doc/source/static/gf_static_several.png
  83. 0
      doc/source/static/gf_static_wrapper.png
  84. 0
      doc/source/static/gf_synthetic.png
  85. 0
      doc/source/static/pyrocko_shadow.png
  86. 0
      doc/source/static/screenshot1.png
  87. 0
      doc/source/static/screenshot2.png
  88. 0
      doc/source/static/screenshot3.png
  89. 0
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  90. 0
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  91. 0
      doc/source/static/screenshot6.png
  92. 0
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  93. 0
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  94. 0
      doc/source/static/screenshot9.png
  95. 0
      doc/source/static/snuffler.png
  96. 0
      doc/source/static/test.mseed

132
doc/Makefile

@ -1,130 +1,20 @@
# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
SPHINXPROJ = Pyrocko
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
-rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Pyrocko.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Pyrocko.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/Pyrocko"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Pyrocko"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
make -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
.PHONY: help Makefile
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
# 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)

23
doc/examples.rst

@ -1,23 +0,0 @@
Examples
=========
The pyrocko framework covers many aspects of seismological data handling and management. This section offers tutorials and real-world examples how to utilize the framework.
.. toctree::
:caption: Code and usage examples
:name: Examples
:numbered:
:maxdepth: 2
tutorials/trace_handling.rst
tutorials/dataset_management.rst
tutorials/fdsn_download.rst
tutorials/catalog_search.rst
tutorials/orthodrome.rst
tutorials/plotting.rst
tutorials/cake_raytracing.rst
tutorials/gf_store.rst
tutorials/gf_forward.rst
tutorials/velocity_databases.rst
tutorials/guts.rst

10
doc/install.rst

@ -1,10 +0,0 @@
Installation
============
Pyrocko can be installed on every operating system where its prerequisites are
available. This document describes how to install Pyrocko on Unix-like
operating systems, like Linux and MacOSX.
.. toctree::
install_quick
install_details

17
doc/install_quick.rst

@ -1,17 +0,0 @@
Quick system specific installation instructions
-----------------------------------------------
This section lists the commands needed to install Pyrocko and its prerequisites
on some popular systems.
.. toctree::
Debian based systems (Debian, Ubuntu, Mint) <install_deb>
Fedora <install_fedora>
OpenSuse <install_suse>
Mac OS X <install_mac>
Anaconda2 <install_anaconda2>
For instructions on how to install Pyrocko on other systems or if the
installation with any of the above procedures fails, see
:doc:`install_details`.

33
doc/reference.rst

@ -1,33 +0,0 @@
Library Reference
=================
.. toctree::
:maxdepth: 1
reference_trace
reference_io
reference_pile
reference_util
reference_model
reference_hamster_pile
reference_crust2x2
reference_crustdb
reference_cake
reference_moment_tensor
reference_beachball
reference_evalresp
reference_pz
reference_orthodrome
reference_catalog
reference_rdseed
reference_snuffling
reference_pile_viewer
reference_gui_util
reference_slink
reference_gf
reference_fdsn
reference_ims
reference_plot
reference_gmtpy
reference_tectonics

2
doc/apps_cake.rst → doc/source/apps/cake/index.rst

@ -8,4 +8,4 @@ models).
.. toctree::
:maxdepth: 2
apps_cake_manual
manual

10
doc/apps_cake_manual.rst → doc/source/apps/cake/manual.rst

@ -258,7 +258,7 @@ Ten receiver distances ranging from 100 km to 1000 km and a source depth of 10km
cake plot-rays --crust2loc=45,10 --phases=P,p --sdepth=10 --distances=100:1000:10
.. figure:: _static/cake_plot_example.png
.. figure:: /static/cake_plot_example.png
:scale: 80%
The option ``--crust2loc`` refers to the :py:mod:`pyrocko.crust2x2` module and expects latitude and longitude of the source location.
@ -274,7 +274,7 @@ Receivers may be at any depth. Arbitrary reflection/conversion histories may be
cake plot-rays --sdepth=15 --distances=10 --rdepth=4.443 --crust2loc=0,0 \
--phase='pP\,pPv3pP\,pPv3pPv3pP\,p'
.. figure:: _static/cake_plot_example_2.png
.. figure:: /static/cake_plot_example_2.png
:scale: 80%
To print arrival times and other ray parameters, replace ``plot-rays`` with
@ -302,7 +302,7 @@ To use classic phase names, use the :option:`--classic` option::
cake plot-rays --classic=Pdiff,PKP,PKIKP --distances=110:150:5 --degrees
.. figure:: _static/cake_plot_example_3.png
.. figure:: /static/cake_plot_example_3.png
:scale: 80%
Model plots
@ -312,7 +312,7 @@ Model plots
cake plot-model --model=prem-no-ocean.m
.. figure:: _static/cake_plot_example_4.png
.. figure:: /static/cake_plot_example_4.png
:scale: 80%
Cake phases
@ -346,7 +346,7 @@ Here's another example to illustrate why cake needs its special phase definition
> cake plot-rays --phases='P,p,P\,p\' --sdepth=0.5 --rdepth=1.5 --distances=3,5 \
--model=waveguide.nd
.. figure:: _static/cake_plot_example_5.png
.. figure:: /static/cake_plot_example_5.png
:scale: 80%

0
doc/apps_fomosto_backends.rst → doc/source/apps/fomosto/backends.rst

4
doc/apps_fomosto.rst → doc/source/apps/fomosto/index.rst

@ -7,5 +7,5 @@ pre-calculated Green's function stores.
.. toctree::
:maxdepth: 2
apps_fomosto_tutorial
apps_fomosto_backends
tutorial
backends

6
doc/apps_fomosto_tutorial.rst → doc/source/apps/fomosto/tutorial.rst

@ -390,7 +390,7 @@ If we are not in the Green's function store's directory, we can equally use::
The extracted traces are shown in a Snuffler window, labeled as ``<counter>
(<source-depth>, <distance>) <component>``.
.. figure:: _static/fomosto_view_1.png
.. figure:: /static/fomosto_view_1.png
:align: center
It is also possible to directly compare the traces of two (or more) different
@ -405,7 +405,7 @@ their directory names to the view command::
Rearranging the view in Snuffler a bit, we can quickly spot some differences:
.. figure:: _static/fomosto_view_2.png
.. figure:: /static/fomosto_view_2.png
:align: center
Here we can see, that at the closest distance, the QSEIS trace (red) contains a
@ -578,7 +578,7 @@ and you will create a pdf file called ``iceland_reg_v2_0.25-0.5Hz.pdf`` in your
A example displacement seismogram.
.. figure:: _static/fomosto_report_displacement1.png
.. figure:: /static/fomosto_report_displacement1.png
:align: center
Creating decimated variants of a Green's function store

6
doc/apps.rst → doc/source/apps/index.rst

@ -13,6 +13,6 @@ practice.
.. toctree::
:maxdepth: 2
apps_snuffler
apps_cake
apps_fomosto
snuffler/index
cake/index
fomosto/index

2
doc/apps_snuffler_extensions.rst → doc/source/apps/snuffler/extensions.rst

@ -8,7 +8,7 @@ Snufflings can be reloaded at run-time using the menu entry 'Reload Snufflings'
in the main menu of Snuffler - no need to restart Snuffler when a snuffling is
modified or added.
Already existing snufflings can be downloaded from the `snuffling repository <https://github.com/pyrocko/contrib-snufflings >`_
Already existing snufflings can be downloaded from the `snuffling repository <https://github.com/pyrocko/contrib-snufflings>`_
Example Snuffling to show earthquake catalog information within Snuffler
------------------------------------------------------------------------

6
doc/apps_snuffler.rst → doc/source/apps/snuffler/index.rst

@ -6,6 +6,6 @@ Snuffler is a seismogram browser and workbench.
.. toctree::
:maxdepth: 2
apps_snuffler_manual
apps_snuffler_tutorial
apps_snuffler_extensions
manual
tutorial
extensions

0
doc/apps_snuffler_manual.rst → doc/source/apps/snuffler/manual.rst

20
doc/apps_snuffler_tutorial.rst → doc/source/apps/snuffler/tutorial.rst

@ -16,7 +16,7 @@ with Snuffler. Download the file, then run the command::
A window should open:
.. image:: _static/screenshot1.png
.. image:: /static/screenshot1.png
:align: center
Initially, no waveforms are shown. That is perfectly ok.
@ -27,7 +27,7 @@ in, respectively.
If you zoom in close enough, the trace data will appear:
.. image:: _static/screenshot2.png
.. image:: /static/screenshot2.png
:align: center
There are some more commands to navigate. The :kbd:`<space>` key brings you one
@ -47,7 +47,7 @@ How to get help:
* Press :kbd:`?` or select :guilabel:`Help` from the main menu.
* Use ``snuffler --help`` to see what command line options are available.
* There is a :doc:`apps_snuffler_manual`
* There is a :doc:`manual`
Before continuing, you should make yourself a bit familiar with basic
navigation in Snuffler.
@ -63,7 +63,7 @@ get an overview over tens of thousands of files without any problems.
Here's an example of just a few thousand files:
.. image:: _static/screenshot3.png
.. image:: /static/screenshot3.png
:align: center
If color is continuous, so is the trace (no gaps). If there is a gap in the
@ -112,7 +112,7 @@ Of course, you can also restrict it to use only specific files::
using quotes.
.. image:: _static/screenshot4.png
.. image:: /static/screenshot4.png
:align: center
Colored rectangles are shown for each file, so we can immediatly see that this
@ -122,7 +122,7 @@ at 2009-09-19 00:00. Zoom in until the traces appear, filter a bit.
Oh, there's an earthquake spanning the file boundaries!
.. image:: _static/screenshot5.png
.. image:: /static/screenshot5.png
:align: center
Notice, that the filtering works seamless across the file boundaries! By
@ -156,7 +156,7 @@ some small features. Normally the traces are clipped within the color boxes,
but you may choose to turn off display of the boxes and to disable the
clipping.
.. image:: _static/screenshot6.png
.. image:: /static/screenshot6.png
:align: center
The current scale range on each track is shown when :guilabel:`Show Scale
@ -181,7 +181,7 @@ Search (builtin)`. A panel opens in the bottom part of the Snuffler window.
Make sure you have internet access, select a minimum magnitude and hit
:guilabel:`Run`.
.. image:: _static/screenshot7.png
.. image:: /static/screenshot7.png
:align: center
Aha, so this one is coming in from Bali!
@ -202,7 +202,7 @@ around its name.
Now select :guilabel:`Sort by Distance` in the main menu.
.. image:: _static/screenshot8.png
.. image:: /static/screenshot8.png
:align: center
There's your traces sorted by distance to the event.
@ -219,7 +219,7 @@ network/station/location/channel ID) or may serve as time (span) markers only.
The latter can be created by clicking on the time axis rather than on the
traces. Here are some different normal markers:
.. image:: _static/screenshot9.png
.. image:: /static/screenshot9.png
:align: center
A color may be assigned to the selected markers using the number keys :kbd:`0`

2
doc/conf.py → doc/source/conf.py

@ -149,7 +149,7 @@ html_logo = 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']
html_static_path = ['static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.

9
doc/index.rst → doc/source/index.rst

@ -1,5 +1,5 @@
.. image:: _static/pyrocko_shadow.png
.. image:: /static/pyrocko_shadow.png
:align: left
Pyrocko Manual
@ -38,10 +38,9 @@ Contents
:maxdepth: 2
overview
install
apps
examples
library
install/index
apps/index
library/index
Indices and tables
------------------

2
doc/install_details.rst → doc/source/install/details.rst

@ -8,7 +8,7 @@ operating systems, like Linux and Mac OS X.
Concrete listings of the commands needed to install Pyrocko are given
in section
* :doc:`install_quick`
* :doc:`system/index`
Prerequisites
-------------

15
doc/source/install/index.rst

@ -0,0 +1,15 @@
Installation
============
Pyrocko can be installed on every operating system where its prerequisites are
available. This document describes how to install Pyrocko on Unix-like
operating systems, like Linux and MacOSX.
To install Pyrocko, first try to follow the instructions in
:doc:`system/index`. For additional information, refer to :doc:`details`. If
you run into problems during installation, `please let us know
<https://github.com/pyrocko/pyrocko/issues>`_.
.. toctree::
system/index
details

4
doc/install_anaconda2.rst → doc/source/install/system/anaconda2.rst

@ -14,5 +14,5 @@ Installation under Anaconda2
python setup.py install
For instructions on how to install Pyrocko on other systems or if the
installation with the above procedure fails, see :doc:`install_quick` or
:doc:`install_details`.
installation with the above procedure fails, see :doc:`index` or
:doc:`/install/details`.

4
doc/install_deb.rst → doc/source/install/system/deb.rst

@ -14,5 +14,5 @@ Installation on Debian based systems (Debian, Ubuntu, Mint)
sudo python setup.py install
For instructions on how to install Pyrocko on other systems or if the
installation with the above procedure fails, see :doc:`install_quick` or
:doc:`install_details`.
installation with the above procedure fails, see :doc:`index` or
:doc:`/install/details`.

4
doc/install_fedora.rst → doc/source/install/system/fedora.rst

@ -12,5 +12,5 @@ Installation on Fedora systems
sudo python setup.py install
For instructions on how to install Pyrocko on other systems or if the
installation with the above procedure fails, see :doc:`install_quick` or
:doc:`install_details`.
installation with the above procedure fails, see :doc:`index` or
:doc:`/install/details`.

17
doc/source/install/system/index.rst

@ -0,0 +1,17 @@
System specific installation instructions
-----------------------------------------
This section lists the commands needed to install Pyrocko and its prerequisites
on some popular systems.
.. toctree::
Debian based systems (Debian, Ubuntu, Mint) <deb>
Fedora <fedora>
OpenSuse <suse>
Mac OS X <mac>
Anaconda2 <anaconda2>
For instructions on how to install Pyrocko on other systems or if the
installation with any of the above procedures fails, see
:doc:`/install/details`.

4
doc/install_mac.rst → doc/source/install/system/mac.rst

@ -20,5 +20,5 @@ Installation on Mac OS X systems
sudo python setup.py install --install-scripts=/usr/local/bin
For instructions on how to install Pyrocko on other systems or if the
installation with the above procedure fails, see :doc:`install_quick` or
:doc:`install_details`.
installation with the above procedure fails, see :doc:`index` or
:doc:`/install/details`.

4
doc/install_suse.rst → doc/source/install/system/suse.rst

@ -14,5 +14,5 @@ Installation on OpenSuse systems
sudo python setup.py install
For instructions on how to install Pyrocko on other systems or if the
installation with the above procedure fails, see :doc:`install_quick` or
:doc:`install_details`.
installation with the above procedure fails, see :doc:`index` or
:doc:`/install/details`.

0
doc/tutorials/cake_raytracing.rst → doc/source/library/examples/cake_raytracing.rst

0
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0
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0
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12
doc/tutorials/gf_forward.rst → doc/source/library/examples/gf_forward.rst

@ -75,11 +75,11 @@ Further API documentation for the utilized objects can be found at :class:`~pyro
trace.snuffle(synthetic_traces, markers=markers)
.. figure :: ../_static/gf_synthetic.png
.. figure :: /static/gf_synthetic.png
:align: center
:alt: Synthetic seismograms calculated through pyrocko.gf
Synthetic seismograms calculated through :class:`pyrocko.gf` displayed in :doc:`../apps_snuffler`. The three traces show the east, north and vertical synthetical displacement stimulated by a double-couple source at 155 km distance.
Synthetic seismograms calculated through :class:`pyrocko.gf` displayed in :doc:`/apps/snuffler/index`. The three traces show the east, north and vertical synthetical displacement stimulated by a double-couple source at 155 km distance.
Calculate spatial surface displacement from a local store
@ -89,7 +89,7 @@ In this example we create a :class:`~pyrocko.gf.seismosizer.RectangularSource` a
We will utilize :class:`~pyrocko.gf.seismosizer.LocalEngine`, :class:`~pyrocko.gf.targets.StaticTarget` and :class:`~pyrocko.gf.targets.SatelliteTarget`.
.. figure:: ../_static/gf_static_displacement.png
.. figure:: /static/gf_static_displacement.png
:align: center
:alt: Static displacement from a strike-slip fault calculated through pyrocko
@ -187,7 +187,7 @@ Calculate forward model of thrust event and display wrapped phase
In this example we compare the synthetic unwappred and wrapped LOS displacements caused by a thrust rupture.
.. figure:: ../_static/gf_static_wrapper.png
.. figure:: /static/gf_static_wrapper.png
:align: center
:alt: Static displacement from a thrust fault calculated through pyrocko
@ -325,7 +325,7 @@ Combining severals sources
---------------------------
In this example we combine two rectangular sources and plot the forward model in profile.
.. figure:: ../_static/gf_static_several.png
.. figure:: /static/gf_static_several.png
:align: center
Synthetic LOS displacements from a flower-structure made of one strike-slip fault and one thrust fault. LOS as for Sentinel-1 satellite (Look Angle: 36., Heading:-76). Positive motion toward the satellite.
@ -513,4 +513,4 @@ In this example we combine two rectangular sources and plot the forward model in
plt.show()
plot_static_los_profile(result,110,15*km,5*km,0,0)
plot_static_los_profile(result,110,15*km,5*km,0,0)

0
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0
doc/tutorials/guts.rst → doc/source/library/examples/guts.rst

21
doc/source/library/examples/index.rst

@ -0,0 +1,21 @@
Examples
=========
The pyrocko framework covers many aspects of seismological data handling and management. This section offers tutorials and real-world examples how to utilize the framework.
.. toctree::
:caption: Code and usage examples
:name: Examples
:maxdepth: 2
trace_handling.rst
dataset_management.rst
fdsn_download.rst
catalog_search.rst
orthodrome.rst
plotting.rst
cake_raytracing.rst
gf_store.rst
gf_forward.rst
velocity_databases.rst
guts.rst

0
doc/tutorials/orthodrome.rst → doc/source/library/examples/orthodrome.rst

6
doc/tutorials/plotting.rst → doc/source/library/examples/plotting.rst

@ -65,7 +65,7 @@ This example demonstrates how to create beachballs from (random) moment tensors.
plt.show()
.. figure :: ../_static/beachball-example01.png
.. figure :: /static/beachball-example01.png
:align: center
:alt: Beachballs (focal mechanisms) created by moment tensors.
@ -102,7 +102,7 @@ for a moment tensor.
fig.savefig('beachball-example03.pdf')
plt.show()
.. figure :: ../_static/beachball-example03.png
.. figure :: /static/beachball-example03.png
:align: center
:alt: Beachballs (focal mechanisms) options created from moment tensor
@ -251,7 +251,7 @@ if the axis are not 1:1.
fig.savefig('beachball-example02.pdf')
plt.show()
.. figure :: ../_static/beachball-example02.png
.. figure :: /static/beachball-example02.png
:align: center
:alt: Beachballs (focal mechanisms) created in corners of graph.

20
doc/tutorials/trace_handling.rst → doc/source/library/examples/trace_handling.rst

@ -1,5 +1,5 @@
Seismic traces
===============
==============
Pyrocko brings everything to seismic waveform data conviniently and reliable. The following examples describe the object and syntax of a basic pyrocko feature.
@ -35,9 +35,9 @@ SUDS suds some
information will be lost.
Load, filter and save
----------------------
---------------------
Read a test file :download:`test.mseed <../_static/test.mseed>` with :meth:`pyrocko.io.load`, containing a three component seismogram, apply Butterworth lowpass filter to the seismograms and dump the results to a new file with :meth:`pyrocko.io.save`.
Read a test file :download:`test.mseed </static/test.mseed>` with :meth:`pyrocko.io.load`, containing a three component seismogram, apply Butterworth lowpass filter to the seismograms and dump the results to a new file with :meth:`pyrocko.io.save`.
::
@ -78,7 +78,7 @@ ie. ``station``.
Quickly inspect a trace
-----------------------
To visualize a single trace from a file, use the :meth:`pyrocko.trace.Trace.snuffle` method. To look at a list of traces, use the :func:`pyrocko.trace.snuffle` function. If you want to see the contents of a pile, the :meth:`~pyrocko.pile.Pile.snuffle` method is your friend. Alternatively, you could of course save the traces to file and use the standalone :doc:`../apps_snuffler` to look at them.
To visualize a single trace from a file, use the :meth:`pyrocko.trace.Trace.snuffle` method. To look at a list of traces, use the :func:`pyrocko.trace.snuffle` function. If you want to see the contents of a pile, the :meth:`~pyrocko.pile.Pile.snuffle` method is your friend. Alternatively, you could of course save the traces to file and use the standalone :doc:`/apps/snuffler/index` to look at them.
::
@ -128,7 +128,7 @@ For each traceobject the name of the station is defined, the channel, the sampli
Extracting part of a trace (trimming)
-------------------------------------
Trimming is archived with :func:`pyrocko.io.chop`. Here we cut 10 s from the beginning and the end of the example trace (:download:`test.mseed <../_static/test.mseed>`).
Trimming is archived with :func:`pyrocko.io.chop`. Here we cut 10 s from the beginning and the end of the example trace (:download:`test.mseed </static/test.mseed>`).
::
@ -149,7 +149,7 @@ Trimming is archived with :func:`pyrocko.io.chop`. Here we cut 10 s from the beg
Time shift a trace
--------------------------
------------------
This shifts a trace to a specified time with :meth:`pyrocko.trace.Trace.shift`
::
@ -168,7 +168,7 @@ This shifts a trace to a specified time with :meth:`pyrocko.trace.Trace.shift`
Resampling a trace
--------------------------
------------------
Example for downsampling a trace in a file to a sampling rate with :meth:`pyrocko.trace.Trace.downsample_to`.
@ -228,7 +228,7 @@ An inefficient, non-portable, non-header-preserving, but simple, method to conve
Finding the comparative misfits of mulitple traces
---------------------------------------------
--------------------------------------------------
Three traces will be created, where one will be the used as a reference trace
(``rt``). Using :meth:`pyrocko.trace.Trace.misfit`, we can find the misfits
@ -298,7 +298,7 @@ that purpose:
Restitute to displacement using poles and zeros
--------------------------------------------------
-----------------------------------------------
Often we want to deconvolve instrument responses from seismograms. The method
:meth:`pyrocko.trace.Trace.transfer` implements a convolution with a
@ -310,7 +310,7 @@ function. For a transfer function given as poles and zeros, we can use
instances of the class :class:`pyrocko.trace.PoleZeroResponse`. There is
also a class :class:`pyrocko.trace.InverseEvalrespResponse`, which uses the common ``RESP`` files through the ``evalresp`` library.
Here is a complete example using a SAC pole-zero file (:download:`STS2-Generic.polezero.txt <../_static/STS2-Generic.polezero.txt>`) to deconvolve the transfer function from an example seismogram
Here is a complete example using a SAC pole-zero file (:download:`STS2-Generic.polezero.txt </static/STS2-Generic.polezero.txt>`) to deconvolve the transfer function from an example seismogram
::

6
doc/tutorials/velocity_databases.rst → doc/source/library/examples/velocity_databases.rst

@ -49,7 +49,7 @@ We can use :mod:`pyrocko.cake` to access the data and handle the velocity model
>>> cake_plot.my_model_plot(model)
.. image:: ../_static/cake_crust2.png
.. image:: /static/cake_crust2.png
:align: center
:alt: pyrocko.crust2 plotting
@ -74,7 +74,7 @@ The `Global Crustal Database <https://earthquake.usgs.gov/data/crust/>`_ gathers
europe.plot(plot_median=False, plot_mode=False, vrange=(2000, 6000), phase='s')
.. image:: ../_static/crustdb_plot.png
.. image:: /static/crustdb_plot.png
:align: center
:alt: pyrocko.crustdb.CrustDB.plot
@ -82,4 +82,4 @@ The `Global Crustal Database <https://earthquake.usgs.gov/data/crust/>`_ gathers
Other selection methods are :func:`~pyrocko.crustdb.CrustDB.selectPolygon` and
:func:`~pyrocko.crustdb.CrustDB.selectRegion`.
See :doc:`../reference_crustdb` for more information on the API.
See :doc:`/library/reference/crustdb` for more information on the API.

4
doc/library.rst → doc/source/library/index.rst

@ -6,5 +6,5 @@ The Pyrocko library can be used as a framework for own developments.
.. toctree::
:maxdepth: 2
examples
reference
examples/index
reference/index

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2
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@ -3,7 +3,7 @@ The :mod:`crustdb` Module
The `Global Crustal Database <https://earthquake.usgs.gov/data/crust/>`_ gathers empirical 1D velocity models from seismic reflection and refraction profiles. As of 2013 there are 138939 profiles, mainly P and fewer S wave records in the database.
See the tutorial for usage example, :doc:`tutorials/velocity_databases`.
See the tutorial for usage example, :doc:`/library/examples/velocity_databases`.
.. note ::

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33
doc/source/library/reference/index.rst

@ -0,0 +1,33 @@
Library Reference
=================
.. toctree::
:maxdepth: 1
beachball
cake
catalog
crust2x2
crustdb
evalresp
fdsn
gf
gmtpy
gui_util
hamster_pile
ims
io
model
moment_tensor
orthodrome
pile
pile_viewer
plot
pz
rdseed
slink
snuffling
tectonics
trace
util

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