What's New in ObsPy 1.0

Sebastien edited this page Feb 22, 2016 · 31 revisions

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ObsPy has been in development since 2008 and we now declare it stable enough to be called 1.0. It is a big release with significant internal changes, new features, stability enhancements, and much more to prepare ObsPy for future challenges and get rid of accumulated technical debt. This substantially increases the maturity and overall quality of ObsPy and also enhances it with quite a lot of new features.

This release contains contributions from 21 separate people. Thanks a bunch everyone! This would not have been possible without you!

We strongly encourage all users to update to the new version as it will effectively end support for the 0.10.x line (we will post a final source distribution-only 0.10.3 release soon). Please read at least the New Internal Structure section as it might necessitate changes on your side.

This document details significant new features and changes in ObsPy 1.0.0. It does not list all bug fixes and small improvements. The Full Changelog at the end is more comprehensive.

Documentation and resources for this version can (as always) be found at: https://docs.obspy.org


Aside from the occasional change and new feature, there never was any formal funding for ObsPy and it has been developed by enthusiastic volunteers. If you use ObsPy, please make sure to properly acknowledge us so we can justify investing time into it.


Index


Supported Systems

We officially support the following systems (meaning we test that they work with ObsPy; other versions - especially newer ones, might work, but we cannot guarantee that).

Python modules:

  • Python: 2.7, 3.3, 3.4, 3.5 (we dropped support for 2.6 but added support for 3.5)
  • NumPy: 1.6 - 1.10 (minimum NumPy is now 1.6)
  • SciPy: 0.9 - 0.17 (minimum SciPy is now 0.9)
  • matplotlib: 1.1 - 1.5
  • basemap: 1.0.2 - 1.0.7

Supported Operating Systems (mostly 32bit and 64bit):

  • Windows
  • OSX
  • Linux (tested with default packages on CentOS/RedHat 7, Debian 7 + 8, Fedora 22 + 23, openSUSE 13.2 + Leap 42.1, Ubuntu 12.04 + 14.04 + 15.10)
  • Raspberry Pi (Raspbian Wheezy + Jessie)

Updating ObsPy

Updating should be straight-forward. So depending on your installation do

# Anaconda Python Distribution
$ conda update -c obspy obspy
# Generic Python
$ pip install -U obspy
# Debian/Ubuntu
# add debs.obspy.org to your /etc/apt/sources.list first
$ apt-get update
$ apt-get upgrade python-obspy  # and/or python3-obspy

or whatever your package manager of choice needs to be told to update a package.

New Internal Structure

Over the years ObsPy has accumulated some cruft and technical debt. In this release we have massively restructured ObsPy to ease maintenance and to be able to tackle future challenges. A side effect of all these changes is that it might affect you - our users. We took great care to minimize these effects: Everything that worked with ObsPy 0.10.2 should still work with ObsPy 1.0.0 but you might get a lot of warnings. Please adjust your code until no more warnings are raised so it will work with future ObsPy versions..

ObsPy is now structured as follows:

  • obspy.clients: All modules retrieving data from the web or other resources.
  • obspy.core: Core classes which are also restructured to yield smaller and more maintainable files.
  • obspy.io: All modules reading and writing files in various formats.
  • obspy.geodetics: Geographic utilities.
  • obspy.realtime: Features for realtime seismogram analysis.
  • obspy.signal: All signal processing functions and classes.
  • obspy.taup: Theoretical arrival times using the tau-p method.

For example a script might yield the following output:

$ python some_obspy_script.py

/Users/lion/workspace/code/obspy/obspy/core/util/deprecation_helpers.py:57: ObsPyDeprecationWarning:
Function 'obspy.readEvents' is deprecated and will stop working with the next ObsPy version.
Please use 'obspy.read_events' instead.

/Users/lion/workspace/code/obspy/obspy/core/util/deprecation_helpers.py:68: ObsPyDeprecationWarning:
Module 'obspy.mseed' is deprecated and will stop working with the next ObsPy version.
Please import module 'obspy.io.mseed' instead.

Thus you should change

  1. obspy.readEvents() to obspy.read_events()
  2. obspy.mseed to obspy.io.mseed

and your code will continue to work with future ObsPy versions.

Support for New Data Formats

ObsPy gained support for a few new data formats. They can be read by just using the normal obspy.read(), obspy.read_events(), and obspy.read_inventory() functions.

  • Support for additional waveform data formats:
    • Read support for the ASCII format for waveforms from the K-NET and KiK-net strong-motion seismograph networks. See documentation.
  • Support for additional event data formats:
  • Support for additional station data format:
    • The FDSN web service station text format can now be read. See documentation.
    • Read support for the NIED's moment tensor TEXT format. See documentation.
    • ESRI shapefile write support, useful in GIS applications. See documentation.
    • Google Earth KML output. See documentation.
    • Read support for SeisComP3 inventory files. See documentation.

New Clients

With 1.0.0 ObsPy gained support for a couple of new local and remote data sources.

  • SDS file system structure: The obspy.clients.filesystem module has a client to read data from SDS directory structure (or organize your own data in an SDS structure). Very useful for observatories. See documentation
  • Syngine: The obspy.clients.syngine modules grants access to the IRIS Syngine service. See documentation.
  • The old, deprecated obspy.neries client has been removed. The same data can be accessed with the obspy.clients.fdsn client.

Major improvements to PPSD class

The PPSD class has seen some major improvements and changes since the last stable release:

  • The Algorithm for power spectral density computation has been improved, affecting data especially at the long-period band (noise was generally overestimated at high periods)
  • PPSD now stores the psd for each individual time segment, so after processing all data, arbitrary stacks (e.g. by time span, day of time, day of year, ...) are possible now (see PPSD.calculate_histogram)
  • Metadata can now be provided to PPSD during initialization in any kind of format supported by ObsPy (StationXML, dataless SEED, RESP, ...)
  • Instrument response calculations now take into account the full response (i.e. not only poles and zeros and overall sensitivity)
  • Storing/loading data processed in a PPSD instance is now working without problems across dependency versions by using numpy's npz binary format, and saved PPSD data from multiple files can be combined (see PPSD.save_npz(), PPSD.load_npz() and PPSD.add_npz())
  • Default colormap for PPSD is now viridis, see PPSD.plot() documentation how to use PQLX style colormap, x-Axis can now be switched to frequency in the plot
  • Bin width and smoothing width in the histogram can now be controlled during PPSD initialization, also period limits for binning can be explicitly specified, so that computations across data on different sampling rates can share the same histogram layout

See full Changelog for all details and links to corresponding GitHub issues with full discussion.

Signal Processing Improvements

  • New Trace/Stream.slide() method to ease the implementation of windows algorithms. See documentation.
  • New Trace/Stream.remove_sensitivity() method to only apply a constant factor but not remove the full response. See documentation.
  • Much more stable Butterworth filters! Really worth a try - higher order and narrower filters are now stable. See here for some more details.
  • Sinc based reconstruction filter. This is essentially an almost optimal resampling filter and in many cases you should use it as it has the best results. See documentation and here for more details.
  • Higher order detrending methods. See documentation here and here.

Changes in the TauP Implementation

  • Now supports the nd velocity model files as an input.
  • Added geographic methods to calculate ray paths and pierce points on geographic bodies. See the documentation for more details: The get_travel_time_geo(), get_pierce_points_geo(), and get_ray_paths_geo() methods are new.
  • Support for buried receivers.
  • In general more accurate and faster calculations.
  • We now ship with a bunch more velocity models: 1066a, 1066b, ak135, ak135f, ak135f_no_mud, herrin, iasp91, jb, prem, pwdk, sp6

Other Notable Changes

  • obspy.clients.fdsn
    • Can now also download the text representations of stations and events, which are much smaller, though less flexible.
    • Downloads a gzipped response if possible.
  • obspy.imaging
    • Now also supports cartopy as an alternative to basemap. Will be used if installed and requested.

New Default Colormap

Where possible, ObsPy now uses a much superior default colormap. Long story short, the main features of the new colormap is being perceptually uniform, both in color and greyscale and being friendly to people with different kinds of color blindness. Fret not - you can always revert to the old colormaps if you want to, but first watch this very informative and entertaining video or read this blog post for the reasoning behind the change. Scientists should care about how their data are visualized, so it's well worth a watch/read!

Mass Downloader for FDSN Web Services

ObsPy now contains a module to download and integrate data from any number of FDSN web services at once. Users only have to describe the geographic domain and what they want to download and it does it for them. If you routinely download data - check it out: https://docs.obspy.org/packages/autogen/obspy.clients.fdsn.mass_downloader.html

The following picture shows a possible domain restriction to only download data from within Germany:

New Fancy Event Plots

If an event has moment tensors it can now be plotted in some fancy ways:

from obspy import read_events
cat = read_events("/path/to/CMTSOLUTION")
ev = cat[0]
ev.plot()

If you have mayavi installed you can even get interactive three dimensional radiation patterns:

ev.plot(kind="mayavi")

Rewritten SAC Module

The ObsPy SAC plugin has been rewritten, resulting in two changes in obspy.read and Stream/Trace.write using SAC files, and significant changes in the lower-level handling.

Changes in obspy.read, obspy.write

  1. The new SAC module will preserve the original iztype and reference time (if found in Trace.stats.sac) during writing, thus also preserving any existing relative time headers (e.g. travel-time picks). This better supports round-trip SAC file processing. The previous SAC module generally produced iztype = ib SAC files without checking the previous header iztype, which had the possibility of producing invalid relative time headers.
  2. obspy.read does not put unset SAC headers into trace.stats.sac unless debug_headers=True is set. This is a change in default behavior.

SACTrace replaces SacIO

The recommended way of reading and writing SAC files is still using obspy.read and obspy.write, but users of obspy.sac.SacIO will need to be aware of changes. The old obspy.sac.sacio has be rewritten and recycled into a new obspy.io.sac subpackage, and the old SacIO class is replaced by the SACTrace class, which provides a simplified I/O interface and more flexible reference time and relative-time header handling.

The previous SacIO I/O methods, ReadSacFile, ReadSacHeader, ReadSacXY, ReadSacXYHeader, WriteSacBinary, WriteSacHeader, and WriteSacXY are replaced by just two methods: SACTrace.read and SACTrace.write. Reading and writing of header-only vs. full-file, ASCII vs. binary, and big vs little-endian byte order are controlled by keywords in these two methods. Additionally, producing a SACTrace instance from a file does not require initializing an empty class instance first, as was required by SacIO.

from obspy.io.sac import SACTrace

# read from a binary file
sac = SACTrace.read(filename)

# read or write header only
sac = SACTrace.read(filename, headonly=True)
sac.write(filename, headonly=True)

# read from an ASCII file, write a big-endian binary SAC file
sac = SACTrace.read(filename, ascii=True)
sac.write(filename, byteorder='big')

The new SACTrace class also has more flexible reference time and relative time header handling. In SACTrace, the SAC reference time (a combination of nzyear, nzjday, nzhour, nzmin, nzsec, and nzmsec) can be accessed and manipulated through the SACTrace.reftime attribute (property), which is a UTCDateTime instance. The reference time (or any of the relative time headers) can be modified by adding/subtracting seconds, or by setting it to a new UTCDateTime instance entirely. Any changes to reftime will be reflected in the "nz" time headers, and will trigger corresponding changes in the relative time headers a, e, f, t0-t9 such that they stay correctly referenced in absolute time.

sac = SACTrace(nzyear=2000, nzjday=1, nzhour=0, nzmin=0, nzsec=0, nzmsec=0,
               t1=23.5, data=numpy.arange(100))
sac.reftime, sac.b, sac.e, sac.t1
# (2000-01-01T00:00:00.000000Z, 0.0, 99.0, 23.5)

# Move reference time by relative seconds, relative time headers are preserved.
sac.reftime -= 2.5
sac.reftime, sac.b, sac.e, sac.t1
# (1999-12-31T23:59:57.500000Z, 2.5, 101.5, 26.0)

# Set reference time to new absolute time, relative time headers are preserved.
sac.reftime = UTCDateTime(2000, 1, 1, 0, 2, 0, 0)
sac.reftime, sac.b, sac.e, sac.t1
# (2000-01-01T00:02:00.000000Z, -120.0, -21.0, -96.5)

Additionally, manually changing the iztype header will similarly preserve the absolute referencing of relative time headers.

Full Changelog

1.0.0 also contains all fixes from 0.10.3 which will be released right afterwards as a source distribution only (for special purposes; no binary packages provided).

1.0.0: 
 - General:
   * Requirements have been increased to reflect latest distributions:
     * Removed support for Python 2.6.
     * Added support for Python 3.5.
     * matplotlib >= 1.1.0 is now required.
     * numpy >= 1.6.1 is now required
     * scipy >= 0.9.0 is now required
   * Reorganized the submodule structure. We provide a deprecation path so the
     old imports will continue to work for one ObsPy version.
   * Consistent naming scheme across the code base. This results in some
     functions having different names. Most things that worked with ObsPy 0.10
     will continue to work with this version, but starting with the next
     version they will fail. Pay attention to the deprecation warnings.
   * Support for additional waveform data formats:
     - Read support for the ASCII format for waveforms from the K-NET and
       KiK-net strong-motion seismograph networks.
   * Support for additional event data formats:
     - CMTSOLUTION files used by many waveform solvers.
     - ESRI shapefile write support, useful in GIS applications (see #1066)
     - Google Earth KML output.
   * Support for additional station data format:
     - The FDSN web service station text format can now be read.
     - Read support for the NIED's moment tensor TEXT format (see #1125)
     - Google Earth KML output.
     - Read support for SeisComP3 inventory files.
 - obspy.core:
   * New method for generating sliding windows from Stream/Trace windows.
     (see #860)
   * Stream/Trace.slice() now has the optional `nearest_sample` argument from
     Stream/Trace.trim().
   * Trace.remove_response() now has `plot` option to show/output a plot of all
     individual steps of instrument response removal in frequency domain
     (see #1116).
   * New method Stream/Trace.remove_sensitivity() to remove instrument
     sensitivity
   * Fix incorrect parsing of some non-ISO8601 date/time strings. (see #1215)
   * Added plotting method to Event (customizable subplots from a selection
     of map, beachball and farfield radiation plots, see #1192)
 - obspy.clients.fdsn:
   * Replace FDSN webservice shortcut `NERIES` with `EMSC` and deprecate the
     `NERIES` shortcut, will be removed in a future release (see #1146).
   * Now requests gzipped data for the XML files. Much smaller files!
   * The station service can now also be used to download files in the text
     format. This has limited information but is much faster.
   * New mass downloader to assist in downloading data across a large number
     of FDSN web services.
   * Catch invalid URLs when initialising Client and avoid confusing error
     messages (see #1162)
 - obspy.clients.filesystem.sds:
   * New client to read data from local SDS directory structure (see #1135).
   * Command line script `obspy-sds-report` to generate html page with
     information on latency, data availability percentage and number of gaps
     for a local SDS archive (see #1202)
 - obspy.clients.neries:
   * Removed the dedicated client. Data can still be accessed by using the FDSN
     client.
 - obspy.clients.syngine:
   * New client for the IRIS Syngine service to retrieve custom synthetic
     seismograms.
 - obspy.imaging:
   * Experimental support for Cartopy when plotting maps. Use the `method`
     argument to functions that plot maps to select between Basemap or Cartopy.
   * New default colormap for all plots. A backport of the new viridis colormap
     from matplotlib is available for those using older matplotlib releases.
   * Added plotting routines for farfield radiation patterns of moment tensors
 - obspy.io.kml:
   * New module for Google KML output of Inventory and Catalog objects
     (e.g. for use in Google Earth)
 - obspy.io.mseed:
   * Upgrade to libmseed 2.16
 - obspy.io.seiscomp.sc3ml:
   * New module reading SeisComP3 inventory files to ObsPy inventory objects
     (see #1182).
 - obspy.io.shapefile:
   * New module for ESRI shapefile write support (see #1066)
 - obspy.io.stationtxt:
   * New module reading the FDSN station files.
 - obspy.signal:
   * Switch to second-order sections for filters; backported from SciPy 0.16.0
     (see #1028)
   * New Lanczos interpolation/resampling (see #1101)
   * Higher order detrending methods (see #1173)
   * PPSD (see #931, #1108, #1130, #1187):
     - Algorithm for PSD computation was improved, especially affecting results
       at long periods (for detailed discussion see #931 and #1108).
     - Keywords `paz` and `parser` were removed in favor of new keyword
       `metadata`. PPSD now accepts `metadata` in a much wider range
       of formats:
          * Inventory objects (e.g. from StationXML or from FDSN webservice)
          * obspy.io.xseed Parser objects (e.g. from dataless SEED file)
          * filename of a RESP file
          * dictionary with poles and zeros information (like in
            prior versions)
       Most old codes should still work, issuing a deprecation warning, but
       old code that specifies *both* `paz` and `parser` keywords will raise
       an exception.
     - Whenever possible (i.e. when using for `metadata` an Inventory,
       a Parser or a RESP file), response calculation now takes into account
       the full response (all stages) as opposed to only using the poles and
       zeros response stage (as was done in previous versions when using a
       Parser object). When using a poles and zeros dictionary response
       calculation is unchanged (as no information on other stages is
       available, of course).
     - PPSD now stores the psd for each time segment that gets processed,
       instead of only storing the stacked histogram. That way, differing
       custom stacks with various selection criteria (e.g. time of day, by
       weekday, etc.) can now be made from the same processed data
       (see #1130).
     - New save/load mechanism using numpy .npz binary format that circumvents
       some problems with the old pickle mechanism:
       `PPSD.save_npz()` and `PPSD.load_npz()` (and `PPSD.add_npz()` to add
       data from additional npz files)
     - Change default colormap to new obspy default sequential colormap
       (matplotlibs new viridis colormap). The old PQLX colormap is provided by
       `obspy.imaging.cm.pqlx` and can be used with
       `PPSD.plot(..., cmap=...)`.
     - new option `PPSD.plot(..., cumulative=True)` for a cumulative plot of
       the histogram, i.e. a non-exceedence percentage visualization, similar
       to the `percentile` option.
     - x axis in `PPSD.plot()` can be switched to frequency in Hz with
       `PPSD.plot(..., xaxis_frequency=True)` (see #1130)
     - changes to special handling of rotational: now handled by kwarg
       `special_handling="ringlaser"` (kwarg `is_rotational_data` is
       deprecated, see #916)
     - special handling option for hydrophone data (no differentiation, see
       #916)
     - bin width on frequency axis can now be controlled using
       `PPSD(..., frequency_bin_width_octaves=...)` (in fractions of octaves,
       default is the old fixed setting of 1/8 octaves as in PQLX)
 - obspy.taup
   * Added support for nd file format for input velocity models. Allows for
     named discontinuities at arbitrary depths allowing for less Earth like
     models (see #1147).
   * Added three methods (`get_travel_times_geo()`, `get_pierce_points_geo()`
     and `get_ray_paths_geo()`) to `TauPyModel` to handle station and
     event location data as latitude and longitude, instead of the source to
     station distance in degrees. In addition `get_ray_paths_geo()` and
     `get_pierce_points_geo()` decorate the returned pierce points and ray
     paths with the latitude and longitude of each point. Some functionality
     needs the `geographiclib` module to be installed. (See #1164.)
   * ObsPy now ships with a bunch of new velocity models in addition to the
     existing ones: `prem`, `sp6`, `1066a,b`, `herrin` (See #1196).
   * Add support for buried receivers (see #1103.)
   * Port more accurate calculation of ray parameter from Java. The effect is
     stronger for longer phases, but also corrects issues with shorter body and
     surface waves (see #986.)
   * Fix incorrect branch splitting which also caused issues for extremely
     shallow phases (see #1057.)
   * Proper cache for model splits resulting in much faster calculations if
     the source depth is repeatedly the same (see #1248).

0.10.3: 
  - obspy.core:
    * Fix reading of multiple catalog files using globs (see #1065).
    * Fixed a bug when using
      `Trace.remove_response(..., water_level=None)`.
      With that setting that is supposed to not use any water level
      stabilization in the inversion of the instrument response
      spectrum actually the instrument response was never inverted and
      thus instead of a deconvolution a convolution was performed
      (see #1104).
    * Fixing floating point precision/rounding issue with UTCDateTime when
      initializing with floating point seconds, i.e. with microseconds,
      that could lead to microseconds being off by 1 microsecond
      (see #1096)
    * Correct gap/overlap time returned by Stream.get_gaps() and printed
      by Stream.print_gaps() which was incorrect by one time the sampling
      interval (see #1151)
    * Stream.get_gaps(): return overlaps specified in units of samples
      as negative integers (see #1151)
  - obspy.fdsn:
    * More detailed error messages on failing requests (see #1079)
    * Follows redirects for POST requests (see #1143)
  - obspy.imaging:
    * fix some bugs in `obspy-scan` (see #1138)
  - obspy.mseed:
    * Blockette 100 is now only written for Traces that need it. Previously
      it was written or not for all Traces, depending on whether the last
      Trace needed it or not. (see #1069)
    * Fixed a bug that prevented microsecond accuracy for times before 1970
      (see #1102).
    * Updated to libmseed 2.17.
  - obspy.signal:
    * Bug fixed within rotate.rotate2zne(). Additionally it can now also
      perform the inverse rotation (see #1061).
    * Bug fixed in triggering. When using option `max_len_delete` and a trigger
      occurred right before the end of data, one trigger was potentially lost
      (see #1145 for details).
  - obspy.station:
    * Plotting responses across multiple channels is more robust now in
      presence of some strange channels (e.g. with zero sampling rate,
      happens e.g. for state of health channels, see #1115)
    * ObsPy no longer assumes that the StationXML namespace is the default
      namespace (see #1060).
    * Checking if a file is a StationXML file is less rigorous (and much
      faster) now (not checking strict validity against xsd schema but
      only looking for a FDSNStationXML root element, see #1114).
      This means that `read_inventory()` without explicitly specified
      format will correctly detect more files as StationXML that have very
      slight breaches of the schema but still can be interpreted as
      StationXML.
    * fix saving `xcorrPickCorrection()` results to an image file (see #1154)
  - obspy.taup:
    * Calculating arrival times for surface waves now works (see #1055)
    * Calculating arrivals for underside reflections now works (see #1089)
  - obspy.y:
    * correct misspelled name of a Y specific header field (see #1127)
  - obspy.zmap
    * Add support for time values with sub-second precision (see #1093)