EQcorrscan v0.2.4

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release contain significant updates to the object-oriented API for matched-filter detection (while retaining the old API), alongside re-written, more efficient correlation internals, and a re-designed (more accurate and efficient) subspace detection module.

Note that 0.2.0-3 were released to PyPi as tests for conda installs - they have no functional difference to this version.

The change log for this release is as follows:

• Increase test coverage (edge-cases) in template_gen;
• Fix bug in template_gen.extract_from_stack for duplicate channels in
  template;
• Increase coverage somewhat in bright_lights, remove non-parallel
  option (previously only used for debugging in development);
• Increase test coverage in lag_calc;
• Speed-up tests for brightness;
• Increase test coverage for match_filter including testing io of
  detections;
• Increase subspace test coverage for edge cases;
• Speed-up catalog_to_dd_tests;
• Lag-calc will pick S-picks on channels ending E, N, 1 and 2, change
  from only picking on E and N before; warning added to docs;
• Add full tests for pre-processing;
• Run tests in parallel on ci, speed-up tests dramatically;
• Rename singular-value decomposition functions (with depreciation
  warnings);
• Rename SVD_moments to lower-case and add depreciation warning;
• Increase test coverage in utils.mag_calc;
• Add Template, Tribe, Family, Party objects and rename DETECTION to
  Detection;
  • Template objects maintain meta-data associated with their creation
    to stream-line processing of data (e.g. reduce chance of using the
    wrong filters).
  • Template events have a detect method which takes unprocessed data
    and does the correct processing using the Template meta-data, and
    computes the matched-filter detections.
  • Tribe objects are containers for multiple Templates.
  • Tribe objects have a detect method which groups Templates with
    similar meta-data (processing information) and runs these templates
    in parallel through the matched-filter routine. Tribe.detect outputs
    a Party of Family objects.
  • The Party object is a container for many Family objects.
  • Family objects are containers for detections from the same
    Template.
  • Family and Party objects have a lag_calc method which computes
    the cross-correlation pick-refinements.
  • The upshot of this is that it is possible to, in one line,
    generate a Tribe of templates, compute their matched-filter
    detections, and generate cross-correlation pick refinements, which
    output Event objects, which can be written to a catalog:
    Tribe.construct(method, **kwargs).detect(st, **kwargs).lag_calc(**kwargs).write()
  • Added 25 tests for these methods.
  • Add parameters threshold_type and threshold_input to Detection
    class. Add support for legacy Detection objects via NaN and unset
    values.
• Removed support for obspy < 1.0.0
• Update / correct doc-strings in template-gen functions when describing
  processing parameters.
• Add warning message when removing channels from continuous data in
  match_filter;
• Add min_snr option for template generation routines, if the
  signal-to-noise ratio is below a user-defined threshold, the channel
  will not be used.
• Stop enforcing two-channel template channel names.
• Fix bug in detection_multiplot which didn't allow streams with
  fewer traces than template;
• Update internals to custom C fftw-based correlation rather than openCV (Major change);
  • OpenCV has been removed as a dependancy;
  • eqcorrscan.core.match_filter.normxcorr2 now calls a compiled C routine;
  • Parallel workflows handled by openMP rather than Python Multiprocessing
    for matched-filter operations to allow better memory handling.
    • It is worth noting that we tried re-writing using SciPy internals
      which led to a significant speed-up, but with high memory costs,
      we ended up going with this option, which was the more difficult
      option, because it allows effective use on SLURM managed systems
      where python multiprocessing results in un-real memory spikes
      (issue #88).

EQcorrscan v0.1.6

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release represents a thorough bug-fix for a feature introduced in 0.1.4 (multiple templates from a single channel). This was not fixed in 0.1.5 and both 0.1.4 and 0.1.5 should be avoided.

EQcorrscan v0.1.5

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release represents a quick bug-fix for a feature introduced in 0.1.4 (multiple templates from a single channel). Otherwise it is as 0.1.4.

EQcorrscan v0.1.4

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release is mostly a feature release, with a few minor bug-fixes. For this release we add a subspace detector.

The following is the change-log for this release:

• Bug-fix in plot_repicked removed where data were not normalized
  properly;
• Bug-fix in lag_calc where data were missing in the continuous data
  fixed (this led to incorrect picks, major bug!);
• Output cross-channel correlation sum in lag-calc output;
• Add id to DETECTION objects, which is consistent with the events
  within DETECTION objects and catalog output, and used in lag_calc to
  allow linking of detections to catalog events;
• Add lots of logging and error messages to lag-calc to ensure user
  understands limits;
• Add error to day-proc to ensure user is aware of risks of padding;
• Change utils.pre_processing.process to accept different length of
  data enforcement, not just full day (allow for overlap in processing,
  which might be useful for reducing day start and end effects);
• Bug-fix in mag_calc.amp_pick_event, broke loop if data were missing;
• Lots of docs adjustment to sort order of doc-strings and hyper-links;
• Allow multiple uses of the same channel in templates (e.g. you can
  now use a template with two windows from the same channel, such as a P
  and an S);
• Add evaluation mode filter to utils.catalog_utils.filter_picks;
• Update subspace plot to work when detector is not partitioned;
• Make tests run a little faster;
• Add pep8 testing for all code.

EQcorrscan v0.1.3

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release is mostly a feature release, with a few minor bug-fixes. For this release we add a subspace detector.

The following is the change-log for this release:

• Now testing on OSX (python 2.7 and 3.5) - also added linux python 3.4;
• Add lag-calculation and tests for it;
• Change how lag-calc does the trace splitting to reduce memory usage;
• Added pick-filtering utility to clean up tutorials;
• Change template generation function names for clarity (wrappers for
  depreciated names);
• Add more useful error messages when picks are not associated with
  waveforms;
• Add example plots for more plotting functions;
• Add subspace detector including docs and tutorial.
• Add delayed option to all template_gen functions, set to True by
  default which retains old behaviour.

EQcorrscan v0.1.2

A Python package for the detection and analysis of repeating and near-repeating seismicity.

This release mostly introduces extensive testing to the package. We now support and test on Windows and Linux, we also support OS X, but we don't currently have continuous integration testing for OS X. This release also marks the support for Python 3.5 as well as 2.7.

The following is the change-log for this release:

0.1.2

• Add handling for empty location information in sfiles.
• Added project setup script which creates a useful directory structure and copies a default match-filter script to the directory.
• Add archive reader helper for default script, and parameter classes and definitions for default script.
• Re-write history to make repository smaller, removed trash files that had been added carelessly.
• Now tested on appveyor, so able to be run on Windows.
• Added ability to read hypoDD/tomoDD phase files to obspy events.
• Added simple despiking algorithm - not ideal for correlation as spikes are interpolated around when found: eqcorrscan.utils.despike.
• Option to output catalog object from match_filter - this will become the default once we introduce meta-data to templates - currently the picks for events are the template trace start-times, which will be before the phase-pick by the lag defined in the template creation - also added event into detection class, so you can access the event info from the detections, or create a catalog from a list of detections.
• Add option to extract detections at run-time in match_filter.match_filter.
• Edited multi_event_singlechan to take a catalog with multiple picks, but requires you to specify the station and channel to plot.
• Add normalize option to stacking routines.
• Add tests for stacking - PWS test needs more checks.
• Add many examples to doc-strings, not complete though.
• Change docs to have one page per function.
• Python 3.5 testing underway, all tests pass, testing about 74% of codebase.
• Add io functions to match_filter to simplify detection handling including writing detections to catalog and to text file.
• Stricter match_filter testing to enforce exactly the same result with a variety of systems.
• Add hack to template_gen tutorial to fix differences in sorting between python 3.x and python 2.
• Added advanced network triggering routine from Konstantinos, allows different parameters for individual stations - note only uses recursive sta-lta triggering at the moment. Useful for template generations alongside pickers.
• Added magnitude of completeness and b-value calculators to utils.mag_calc

EQcorrscan v0.1.1

A python package to conduct match-filter earthquake detections.

This package contains routines to enable the user to conduct match-filter earthquake detections using obspy bindings when reading and writing seismic data, and the correlation routine in openCV. Neither of these packages are installed by this software, due to a range of licenses being implemented. However, both are open-source and should be installed before using this package. This package was written to implement the Matlab routines used by Chamberlain et al. (2014) for the detection of low-frequency earthquakes.

The changes in this version have been substantial enough to warrant an end to the 0.0.x line, we have removed the PICK and EVENTINFO classes and are now using Obspy's obspy.core.event classes. This allows us more flexibility with event and pick information, and provides a means for writing and reading many other forms of data. This does mean that scripts dependent on the PICK and EVENTINFO classes will no longer work, however, in this release we have provided functions to map between the two class sets.

The change-log for this version is as follows:

0.1.1

• Cope with events not always having time_errors in them in eventtoSfile;
• Convert Quakeml depths from m to km;
• Multiple little fixes to make Sfile conversion play well with GeoNet QuakeML files;
• Add function to convert from obspy.core.inventory.station.Station to string format
  for Seisan STATION0.HYP file;
• Merged feature branch - hypoDD into develop, this provides mappings for the
  hypoDD location program, including generation of dt.cc files;
• Added tests for functions in catalog_to_dd;
• Implemented unittest tests;
• Changed name of EQcorrscan_plotting to plotting;
• Added depreciation warnings;
• Changed internal structure of pre-processing to aid long-term upkeep;
• Added warnings in docs for template_gen relating to template generation from
  set length files;
• Updated template_creation tutorial to use day-long data;
• Renamed Sfile_util to sfile_util, and functions there-in: will warn about name changes;
• Updated template plotting to include pick labels;
• Updated template_creation tutorial to download S-picks as well as P-picks;
• Update sfile_util to cope with many possible unfilled objects;
• Added sac_util to convert from sac headers to useful event information - note,
  does not convert all things, just origin and pick times;
• Added from_sac function to template_gen.

EQcorrscan v0.1.0

A python package to conduct match-filter earthquake detections.

This package contains routines to enable the user to conduct match-filter earthquake detections using obspy bindings when reading and writing seismic data, and the correlation routine in openCV. Neither of these packages are installed by this software, due to a range of licenses being implemented. However, both are open-source and should be installed before using this package. This package was written to implement the Matlab routines used by Chamberlain et al. (2014) for the detection of low-frequency earthquakes.

The changes in this version have been substantial enough to warrant an end to the 0.0.x line, we have removed the PICK and EVENTINFO classes and are now using Obspy's obspy.core.event classes. This allows us more flexibility with event and pick information, and provides a means for writing and reading many other forms of data. This does mean that scripts dependent on the PICK and EVENTINFO classes will no longer work, however, in this release we have provided functions to map between the two class sets.

The change-log for this version is as follows:

0.1.0 Changes

• Implimented tests for synthetic generation and match-filter functions
• Developed new tutorials that download from GeoNet and are much clearer
• Changed from PICK and EVENTINFO classes to obspy.core.event classes, note
  this will break some previous scripts, however wrappers are included for this,
  this ended up being the biggy, and is the reason for ceasing the 0.0.x line.
• Added synthetic seismogram generation, very basic seismograms, but they work
  as templates for the detection of some seismicity.
• Added compatibility with Obspy v.1.0.0.
• All files now follow pep8.
• Removed parameter files completely, and redundant scripts.

EQcorrscan v0.0.9

A python package to conduct match-filter earthquake detections.

This package contains routines to enable the user to conduct match-filter earthquake detections using obspy bindings when reading and writing seismic data, and the correlation routine in openCV. Neither of these packages are installed by this software, due to a range of licenses being implemented. However, both are open-source and should be installed before using this package. This package was written to implement the Matlab routines used by Chamberlain et al. (2014) for the detection of low-frequency earthquakes.

This release works towards pep8 compatibility and fixes bugs from previous releases. Of note is a major bug-fix in match_filter - arguments were the wrong way round when calling the _template_loop internal function.

Again, update your version using:

pip install -U --no-deps EQcorrscan

For a full description of the changes from previous versions see the CHANGES.md file. The change-log for this version is as follows:

0.0.9

• Working towards following pep8
• Change how match_filter handles missing data - now remove template traces (which have been copied)
  rather than adding null traces to the data stream - more memory efficient, and faster
• Change float handling for large amplitudes in Sfile_utils
• Change distance decimal handling in Sfile_utils
• Add magnitude-frequency plotting to EQcorrscan_plotting
• Update tutorial and docs for tutorial
• Major bug-fix Change in match_filter - debug and index were the wrong way
  round from version 0.0.5 onwards, hence for multiple templates, cross-correlation
  vectors were not matched for templates. Will push a release because of this.

EQcorrscan v0.0.8

A python package to conduct match-filter earthquake detections.

This package contains routines to enable the user to conduct match-filter earthquake detections using obspy bindings when reading and writing seismic data, and the correlation routine in openCV. Neither of these packages are installed by this software, due to a range of licenses being implemented. However, both are open-source and should be installed before using this package. This package was written to implement the Matlab routines used by Chamberlain et al. (2014) for the detection of low-frequency earthquakes.

This latest update implements a lot of changes, including better incorporation of synthetic seismogram generation, SVD magnitude calculations, hierarchical clustering based on average cross-correlation values between detections, clustering in space and time, and multiple bug-fixes. There is one major bug-fix, which applies to the match_filter routine in core. This does not change the operation and outcome, but will apply to users who want to run multiple groups of templates serially, say if you run out of memory running all templates in parallel.

Again, update your version using:

pip install -U --no-deps EQcorrscan

For a full description of the changes from previous versions see the CHANGES.md file. The change-log for this version is as follows:

0.0.8:

• Added SVD magnitude inversion to utils.mag_calc,
  tested for multi-channel;
• Bug-fix in s-file printing when printing AIN,
  convert to int now before print;
• Add master option to stacking.align_traces,
  alignment can be forced to this;
• Add plot directory output option to match_filter;
• Change plot downsampling to 10 Hz in match_filter;
• Clustering.cluster
  now output groups properly when
  computing clustering by cross-correlation;
• Add plot_synth_real
  function to EQcorrscan_plotting -
  use for plotting a synthetic template on top of a real template;
• Add space-time
  clustering fucntion to clustering,
  use to group repeating events;
• Add re_thresh_csv
  to clustering, can be used to increase
  the detection threshold after detection run;
• Add mock modules to conf.py for ReadTheDocs, also removed
  requirements.txt file as it was unused;
• Added parallel options to distance_matrix computation in clustering.
• Change matplotlib import location in match_filter to allow
  other functions to be called without turning off interactive plots.
• Add both option to utils.synth_seis to allow individual creation
  of both P and S phases.
• Add sanity check for nyquist frequency to utils.pre_processing, now
  breaks if highcut >= samp_rate
• Add plot_format option to core.match_filter
• Add multiple phase capability to utils.synth_seis
• BUG-FIX Change match-filter data stream handling to copy the stream and
  keep it safe before adding null-traces or removing excess traces. Match_filter
  will now remove excess, un-needed traces from the copied stream. This is specifically
  necessary when splitting a large template set, with a range of channels, into smaller
  groups to be run serially.

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