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SeisIO v0.4.0: Respocalypse Now
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@jpjones76 jpjones76 released this 23 Sep 21:17
v0.4.0
db224e9

Instrument Response Improvements

SeisIO can now use full (multi-stage) instrument responses or simplified
(pole-zero) instrument responses.

  • Added two new Instrument Response (:resp) types: CoeffResp and
    MultiStageResp. These allow full descriptions of multi-stage instrument
    responses in FDSN station XML.

    • Full multi-stage instrument responses can be requested by passing keyword
      msr=true to appropriate funcitons.

  • Instrument response Types PZResp and PZResp64 have changed in two ways:

    • Field :c renamed to :a0 for consistency with FDSN and SEED
    • Field :f0 added as a container for the frequency at which :a0 is applied.

New/Changed

  • fctoresp(f,c): generate a new instrument response from lower corner
    frequency f and damping constant c. If no damping constant is specified,
    assumes c = 1/√2.
  • remove_resp!(S) remove (flatten to DC) the frequency responses of seismic
    channels in a GphysData object.
  • resptofc(R): attempt to guess critical frequency :f0 from poles and zeros
    of a PZResp or PZResp64 object.
  • translate_resp!(S, R): translate response of seismic data channels
    in GphysData object S to response R.
    • translate_resp works on channels with MultiStageResp responses, with
      two caveats:
      1. Only the first stage of the response changes.
      2. The first stage must be a PZResp or PZResp64 object for the response to
        be translated.

Removed

  • equalize_resp! (replaced by translate_resp!)
  • fctopz (replaced by fctoresp)
  • SeisIO.resp_f (deprecated)

Expanded Read Support

With the addition of the readers below, SeisIO read support now covers many
data formats with a handful of simple wrapper functions:

read_data, read_data!

Wrapper for reading entire data files into memory.

Format String
AH-1 ah1
AH-2 ah2
Bottle bottle
GeoCSV, time-sample pair geocsv
GeoCSV, sample list geocsv.slist
Lennartz ASCII lennartzascii
Mini-SEED mseed
PASSCAL SEG Y passcal
PC-SUDS suds
SAC sac
SEG Y (rev 0 or rev 1) segy
UW datafile uw
Win32 win32

Improvements

  • read_data("passcal", ..., swap=true) reads big-endian PASSCAL SEG Y.
  • read_data method extended to take either one or two Strings as arguments.
    • If one String is passed to read_data, the string is treated as a file pattern; guess is called to determine the file format.
    • If two Strings are passed, the first is treated as a file format String; the second is treated as a file pattern string.
      • Note: read_data is much faster when the file format String is supplied.

read_meta, read_meta!

Wrapper for reading instrument metadata files into memory.

Format String
Dataless SEED dataless
FDSN Station XML sxml
SACPZ sacpz
SEED RESP resp

read_hdf5, read_hdf5!

Extract data from an HDF5 archive that uses a recognized seismic data format.
This works differently from read_data in that HDF5 archives are generally
large and contain data from multiple channels; they are scanned selectively
for data in a user-defined time window matching a user-specified ID pattern.

Format String
ASDF asdf

read_quake

A wrapper to read discrete event data into a SeisEvent structure. Because
seismic event files are typically self-contained, this does not accept
wildcard file strings and has no "in-place" version.

Format String
QuakeML qml
PC-SUDS event suds
UW event uw

Other Changes

Documentation Improvements

  • Public documentation of low-level file formats has been copied into docs/desc.
  • CLI information on supported file formats can now be found in SeisIO.formats,
    a dictionary accessed by format name (as given above).

Processing on Download

get_data can now process requests after download by specifying keywords:
demean, detrend, rr (remove instrument response), taper, ungap, unscale.

  • There are no keywords in get_data to filter data or translate seismometer
    responses to a non-flat curve; too many additional keywords would be needed.

New Functionality

  • ?RESP_wont_read shows some common SEED RESP issues for problem files.
  • convert_seis! converts seismograms in S to other units (m, m/s, m/s²) by differentiation or integration.
  • env! efficiently computes the signal envelope by segment within each (regularly-sampled) channel.
  • get_file_ver gets the version of a SeisIO native format file.
  • get_seis_channels(S) returns numeric indices of channels in S whose instrument codes indicate seismic data.
  • guess guesses data file format and endianness.
  • inst_code(C) returns the instrument code of GphysChannel object C.
  • inst_code(S,i) returns the instrument code of channel i.
  • inst_codes(S) returns the instrument code of every channel in S.
  • resp_a0!(S) updates the sensitivity :a0 of PZResp/PZResp64 responses in GphysData object S, including PZResp/PZResp64 stages of type MultiStageResp responses. It can also be called on individual InstrumentResponse objects.
  • scan_hdf5 scans supported Seismic HDF5 formats and returns a list of strings describing the waveform contents.
  • set_file_ver sets the version of a SeisIO native format file.
  • using SeisIO.SUDS; suds_support() lists current SUDS support.
  • validate_units(S) validates strings in :units to ensure UCUM compliance.
  • vucum(str) validates UCUM units for str.
  • writesacpz(S) writes instrument responses to SACPZ files.

Consistency, Performance, Bug Fixes

  • Adjusted user agent settings when connecting to FDSN servers in California.
  • get_data now warns when requesting a (non-miniseed) format from FDSN
    dataselect servers that don't implement the format keyword.
  • Fixed a bug that could cause buffer size to degrade performance with some
    file readers after reading long files.
  • FDSN_sta_xml and functions that call it (e.g. get_data) now only spam
    "overwrite" warnings at (user-specified verbosity) v > 0.
  • Meta-data readers and parsers now strictly use A0 from file, rather than
    recalculating it under certain circumstances.
  • Rewrote SL_info; performance should be greatly improved and it should no
    longer cause timeout errors in automated tests.
  • Fixed issue #20
  • Fixed issue #19
  • tx_float now always uses Float64 precision; Float32 lacks the resolution
    to handle long time series.
  • detrend! has seen many improvements:
    • now uses linear regression on gapless channels with :fs > 0.0 && n=1,
      yielding a ~12x speedup and >99% less memory use.
    • detrend!(..., n=N) now allows degree n=0, equivalent to demean!.
    • greatly increased accuracy at single precision.
  • Most processing functions now accept a numeric channel list using keyword
    chans= to restrict processing to certain channels.
    • The only exception to the above is sync!; sync! with channel restrictions
      makes no sense.
  • All functions that accept a numeric channel list as a keyword now call this
    keyword chans; chans can be an Integer, UnitRange, or Array{Int64, 1}.
  • Added resample as a "safe" (out-of-place) version of resample!
  • Station XML handling has been rewritten, yielding 97% reduced memory use, 5.1x
    speedup, and a workaround for the GeoNet server-side StationXML error (fixes issue #15)
  • FDSNEvq now returns full event catalogs by default (fixes issue #16)
  • Documentation updated (fixes issue #17)
  • writesac() with a GphysChannel object now accepts keyword fname to set
    the file name (issue #18)
    • When specifying fname=FSTR, if FSTR doesn't end with (case-insensitive)
      ".sac", the suffix ".sac" is appended to FSTR automatically.
  • New PZResp/PZResp64 objects should now always have :a0 = 1.0, :f0 = 1.0,
    regardless of initialization method.
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