A Python Toolbox for Retrieving, Processing and Management of Seismological Datasets
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README.md

obspyDMT: A Python Toolbox for Retrieving, Processing and Management of Seismological Datasets

DOI

obspyDMT (obspy Data Management Tool) is a command line tool for retrieving, processing and management of seismological datasets in a fully automatic way.

Table of contents

Gallery

Quick tour Earthquake meta-data
Seismicity map Event-based mode
Update of an existing waveform data set Time-continuous mode
Processing and instrument correction Synthetic seismograms
Explore station meta-data (StationXML files, filterstages) Speeding up data retrieval and processing by parallelization
KML format (e.g., Google-Earth) VTK format (e.g., Paraview)

Quick tour

Run a quick tour:

obspyDMT --tour

dmt_tour_dir directory will be created in the current path, and retrieved/processed waveforms as well as meta-data will be organized there (refer to Directory structure section for more information).

The retrieved waveforms can be plotted by:

obspyDMT --datapath dmt_tour_dir --local --plot_waveform

To plot the processed/corrected waveforms, --plot_dir_name processed can be added to the previous command line:

obspyDMT --datapath dmt_tour_dir --local --plot_waveform --plot_dir_name processed

obspyDMT has many tools to plot the contents of a data set. As an example, the following command line plots the ray coverage (ray path between each source-receiver pair) of dmt_tour_dir directory:

obspyDMT --datapath dmt_tour_dir --local --plot_ev --plot_sta --plot_ray

Earthquake meta-data

First, we request event information from one of several supported seismicity catalogs, without downloading any waveforms yet:

obspyDMT --datapath neic_event_metadata --min_mag 5.5 --min_date 2014-01-01 --max_date 2015-01-01 --event_catalog NEIC_USGS --event_info

neic_event_metadata/ directory - created with the above command - can be updated for events that occured in 2015 of magnitude more than 5.5: (no waveform retrieval)

obspyDMT --datapath neic_event_metadata --min_mag 5.5 --min_date 2015-01-01 --max_date 2016-01-01 --event_catalog NEIC_USGS --event_info

To plot the content of local data set (neic_event_metadata/):

obspyDMT --datapath neic_event_metadata --local --plot_ev --plot_focal

Seismicity map

Seismicity map (--plot_seismicity option flag) of Japan region based on earthquakes of magnitude more than 5.0 that occured from 2000-01-01 until 2017-01-01 from NEIC event catalog. Note --event_rect option flag to define a region around Japan:

obspyDMT --datapath japan_seismicity --min_mag 5.0 --min_date 2000-01-01 --max_date 2017-01-01 --event_catalog NEIC_USGS --event_rect 110./175./15/60 --plot_seismicity --event_info

Global seismicity map of archived earthquakes in NEIC catalogue with magnitude more than 5.0 that occurred between 1990 and 2016. One command queried the NEIC catalogue, stored and organised the retrieved information and generated the seismicity map. (No actual waveform data were queried in this example):

obspyDMT --datapath neic_event_dir --min_date 1990-01-01 --max_date 2017-01-01 --min_mag 5.0 --event_catalog NEIC_USGS --event_info --plot_seismicity

The results of some basic statistics (magnitude and depth histograms) are also generated and plotted automatically (top-left panel). Note the rendering of coloured beach balls in the map inset (deepest seismicity in the foreground). The global map also contains beach balls rather than just simple black dots, but they do not become apparent at this zoom level.

ISC catalog

The International Seismological Centre (ISC) provides two catalogs:  

  • COMPREHENSIVE bulletin contains all events collected by the ISC, including most recent events, which are awaiting review.
  • REVIEWED bulletin includes all events that have been reviewed and relocated by an ISC analyst.

--isc_catalog option specifies the ISC bulletin type (default: COMPREHENSIVE). Example:

obspyDMT --datapath test_isc_comprehensive --min_date 2013-01-01 --max_date 2015-01-01 --min_mag 6.5 --event_catalog ISC --isc_catalog COMPREHENSIVE --event_info --plot_seismicity

Retrieval result for the same request using --isc_catalog REVIEWED:

Event-based mode

Here, we retrieve actual BHZ seismograms from II network that recorded earthquakes of magnitude more than 7.5 that occured from 2014-01-01 until 2015-01-01 (NEIC catalog). For this example, only stations with network code II, location code 00 and channel codes BHZ are retrieved:

obspyDMT --datapath event_based_dir --min_date 2014-01-01 --max_date 2015-01-01 --min_mag 7.5 --event_catalog NEIC_USGS --data_source IRIS --net "II" --loc "00" --cha "BHZ" --preset 100 --offset 1800

--data_source specifies that the waveform data center of IRIS should be contacted for seismograms. Omitting this flag would trigger the default --data_source IRIS. --preset 100 and --offset 1800 specify the retrieval of waveform time windows of 100 s before to 1800 s after the reference time. Since we are downloading in event-based mode, i.e., centered around earthquake occurrences, the reference time defaults to the event origin time. This could be changed to the time of P-wave arrival by invoking --cut_time_phase, in which case each seismogram would have a different absolute start time.

To plot the stations/events/rays:

obspyDMT --datapath event_based_dir --local --plot_ev --plot_focal --plot_sta --plot_ray

Update an existing data set

In the course of working with a waveform data set, it often becomes necessary to update. This could mean requesting the same data again (because part of the earlier request failed for some reason), or expanding the number of earthquakes, stations, or seismograms. The following command updates the data-set that we created in the previous Event-based mode section with BHZ channels of AW and E* networks (E*: all stations that their network codes start with E) from the GFZ data center:

obspyDMT --datapath event_based_dir --data_source "GFZ" --net "AW,E*" --cha "BHZ" --preset 100 --offset 1800

Additionally, we can update the data set with BHZ channels of G* networks (i.e., all stations that their network codes start with G) from the IPGP data center:

obspyDMT --datapath event_based_dir --data_source "IPGP" --net "G*" --cha "BHZ" --preset 100 --offset 1800

To plot the stations/events/rays:

obspyDMT --datapath event_based_dir --local --plot_ev --plot_focal --plot_sta --plot_ray

Time-continuous mode

In contrast to the examples of Event-based mode section and Update of an existing waveform data set, some usage cases require waveforms that are not relative to or centered on specific earthquake occurances. We refer to this usage mode as "time-continuous" --continuous.

For example, the following command retrieves one-month long time series (from 2011-03-03 until 2011-04-03) recorded by two stations (--sta "BFO,RER" --loc "00" --cha "BHZ") from the IRIS data center:

obspyDMT --continuous --datapath continuous_example --min_date 2011-03-03 --max_date 2011-04-03 --sta "BFO,RER" --loc '00' --cha "BHZ" --data_source IRIS

Processing and instrument correction

obspyDMT can process the waveforms directly after retrieving the data, or it can process an existing data set in a separate step (local mode). By default, obspyDMT follows processing instructions described in the process_unit.py located at /path/to/my/obspyDMT/obspyDMT directory. Although this file is fully customizable, several common processing steps can be done via options flags (without changing/writing new processing instructions).

The following command retrieves all BHZ channels from the IRIS data center that:

  • 50 <= Azimuth <= 55 (specified by --min_azi and --max_azi)
  • 94 <= Distance <= 100 (specified by --min_epi and max_epi)
  • recorded events of magnitude more than 6.8 that occured on 2014-07-21.
obspyDMT --datapath data_fiji_island --min_mag 6.8 --min_date 2014-07-21 --max_date 2014-07-22 --event_catalog NEIC_USGS --data_source IRIS --min_azi 50 --max_azi 55 --min_epi 94 --max_epi 100 --cha BHZ --instrument_correction

To plot the processed/corrected waveforms (Note --plot_dir_name processed, omitting this option would result in plotting raw counts, i.e., --plot_dir_name raw):

obspyDMT --datapath data_fiji_island --local --plot_waveform --plot_dir processed

Synthetic seismograms

obspyDMT can retrieve synthetic waveforms matching the real data using Syngine webservice. The following example command retrieves not only observed waveforms but also their synthetic counterparts, computed on an IASP91 background model (note --syngine --syngine_bg_model iasp91_2s):

obspyDMT --datapath data_fiji_island --min_mag 6.8 --min_date 2014-07-21 --max_date 2014-07-22 --event_catalog NEIC_USGS --data_source IRIS --min_azi 50 --max_azi 55 --min_epi 94 --max_epi 100 --cha BHZ --instrument_correction --syngine --syngine_bg_model iasp91_2s

To plot the synthetic waveforms (note --plot_dir_name syngine_iasp91_2s):

obspyDMT --datapath data_fiji_island --local --plot_waveform --plot_dir_name syngine_iasp91_2s

Explore station meta-data (StationXML files, filterstages)

obspyDMT implements several plotting options to explore station meta-data. For example, the following command generates a visual representation of transfer function spectra (amplitude and phase) of IC.XAN station in China. Blue lines show transfer function components computed for all filter stages in the StationXML file; red lines are for the analogue part.

obspyDMT --datapath /path/to/STXML.IC.XAN.00.BHZ --plot_stationxml --plotxml_paz --plotxml_min_freq 0.0001

To plot transfer function spectra (amplitude and phase) of GT.LBTB station in Botswana:

obspyDMT --datapath /path/to/STXML.GT.LBTB.00.BHZ --plot_stationxml --plotxml_paz --plotxml_min_freq 0.0001

Transfer function spectra (amplitude and phase) of each stage in the StationXML file can be also plotted by (note --plotxml_allstages):

obspyDMT --datapath /path/to/STXML.GT.LBTB.00.BHZ --plot_stationxml --plotxml_min_freq 0.0001 --plotxml_allstages

In the phase response, two stages (1 and 5) have non-zero values.

Speeding up data retrieval and processing by parallelization

To increase the efficiency in retrieving waveform data, a functionality for parallelized data retrieval can be enabled as follows:

--req_parallel --req_np 4

The second flag (--req_np 4) specifies the number of parallel requests.

A further speed-up can be achieved by specifying a bulk request. Instead of requesting individual items, this will send a list of items (time series or meta data) to the data center:

--bulk

To enable parallel processing with, for example, 10 threads:

--parallel_process --process_np 10

KML

Take the example of Event-based mode section. To create a KML file (readable by Google-Earth) based on that data set:

obspyDMT --datapath event_based_dir --local --plot_ev --plot_sta --plot_focal --plot_ray --create_kml

or to plot events of magnitude more than 7.0 in the global example of Seismicity map section:

obspyDMT --datapath neic_event_dir --local --plot_ev --plot_focal --min_mag 7.0 --create_kml

VTK

Take the global example of Seismicity map section. To create a VTK file (readable by Paraview) for all events in that data set:

obspyDMT --datapath neic_event_dir --local --create_event_vtk

Supported event catalogs and data centers

Print supported data centers that can be passed as arguments to --data_source:

obspyDMT --print_data_sources

Print supported earthquake catalogs that can be passed as arguments to --event_catalog:

obspyDMT --print_event_catalogs

Read an existing local event catalog

--read_catalog <PATH> option flag reads in an existing event catalog located at <PATH> and proceeds. Currently supported catalog metadata formats: "CSV", "QUAKEML", "NDK", "ZMAP" (Refer to obspy documentation for details on QuakeML, NDK and ZMAP formats).

CSV format: obspyDMT can read a CSV file as an event catalog. This must be a list of comma-separated values containing some or all of the fields below, one event per line:

event_number,event_id,datetime,latitude,longitude,depth,magnitude,magnitude_type,author,flynn_region,mrr,mtt,mpp,mrt,mrp,mtp,stf_func,stf_duration

File catalog.txt, generated by obspyDMT in EVENTS-INFO subdirectory provides an example of such a file.

Example:

#number,event_id,datetime,latitude,longitude,depth,magnitude,magnitude_type,author,flynn_region,mrr,mtt,mpp,mrt,mrp,mtp,stf_func,stf_duration
1,20110311_054623.a,2011-03-11T05:46:23.200000Z,38.2963,142.498,19.7,9.1,MW,None,NAN,None,None,None,None,None,None,triangle,164.914

datetime, latitude, longitude, depth and magnitude are mandatory. Optional fields may be set to None, as in the following example where only datetime, latitude, longitude, depth and magnitude are set:

#number,event_id,datetime,latitude,longitude,depth,magnitude,magnitude_type,author,flynn_region,mrr,mtt,mpp,mrt,mrp,mtp,stf_func,stf_duration
1,None,2011-03-11T05:46:23.200000Z,38.2963,142.498,19.7,9.1,None,None,None,None,None,None,None,None,None,None,None

Directory structure

For each request, obspyDMT creates the depicted directory tree inside the user-specified directory datapath/, and arranges the retrieved data either in different event directories (for event-based requests) or in chronologically named directories (for continuous requests). It also creates a directory in which a catalog of all requested events/time spans is stored. Raw waveforms, StationXML/response files and corrected waveforms are collected in sub-directories. While retrieving the data, obspyDMT creates metadata files such as station/event location files, stored in the info/ directory of each event.

How to cite obspyDMT

Please consider acknowledging obspyDMT if it helps you to obtain results and figures for publication or presentation, by citing:

Hosseini, K. and Sigloch, K.: ObspyDMT: a Python toolbox for retrieving and processing large seismological data sets, Solid Earth, 8, 1047-1070, https://doi.org/10.5194/se-8-1047-2017, 2017.

Installation

Once working Python and ObsPy environments are available, obspyDMT can be installed in different ways:

1. install obspyDMT package locally (using PyPi): which tends to be the most user-friendly option:

pip install obspyDMT

2. install obspyDMT from the source code: The latest version of obspyDMT is available on GitHub. After installing git:

git clone https://github.com/kasra-hosseini/obspyDMT.git /path/to/my/obspyDMT

obspyDMT can be installed by:

cd /path/to/my/obspyDMT
pip install -e .

or

cd /path/to/my/obspyDMT
python setup.py install

obspyDMT can be used from a system shell without explicitly calling the Python interpreter. The following command checks the dependencies required for running the code properly:

obspyDMT --check

obspyDMT contains various option flags for customizing the request. Each option has a reasonable default value, which the user can change to adjust obspyDMT option flags to a specific request. The following command displays all available options with their default values:

obspyDMT --help

The options are grouped by topics. To display only a list of these topic headings, use

obspyDMT --options

and to see the full help text for only one topic (e.g., group 2), use

obspyDMT --list_option 2