3. What’s new¶
3.1. Version 0.3.2¶
- Implement reading Party objects from multiple files, including wildcard expansion. This will only read template information if it was not previously read in (which is a little more efficient).
- Allow reading of Party objects without reading the catalog files.
- Check quality of downloaded data in Tribe.client_detect() and remove it if it would otherwise result in errors.
- Add process_cores argument to Tribe.client_detect() and Tribe.detect() to provide a separate number of cores for processing and peak-finding - both functions are less memory efficient that fftw correlation and can result in memory errors if using lots of cores.
- Allow passing of cores_outer kwarg through to fftw correlate functions to control inner/outer thread numbers. If given, cores will define the number of inner-cores (used for parallel fft calculation) and cores_outer sets the number of channels to process in parallel (which results in increased memory usage).
- Allow Tribe and Party IO to use QUAKEML or SC3ML format for catalogs (NORDIC to come once obspy updates).
- Allow Party IO to not write detection catalogs if so desired, because writing and reading large catalogs can be slow.
- If detection-catalogs are not read in, then the detection events will be generated on the fly using Detection._calculate_event.
- BUG-FIX: When one template in a set of templates had a channel repeated, all detections had an extra, spurious pick in their event object. This should no-longer happen.
- Add select method to Party and Tribe to allow selection of a specific family/template.
- Add ability to “retry” downloading in Tribe.client_detect.
- Change behaviour of template_gen for data that are daylong, but do not start within 1 minute of a day-break - previous versions enforced padding to start and end at day-breaks, which led to zeros in the data and undesirable behaviour.
- BUG-FIX: Normalisation errors not properly passed back from internal fftw correlation functions, gaps not always properly handled during long-period trends - variance threshold is now raised, and Python checks for low-variance and applies gain to stabilise correlations if needed.
- Plotting functions are now tested and have a more consistent interface:
- All plotting functions accept the keyword arguments save, savefile, show, return_figure and title.
- All plotting functions return a figure.
- SVD_plot renamed to svd_plot
- Enforce pre-processing even when no filters or resampling is to be done to ensure gaps are properly processed (when called from Tribe.detect, Template.detect or Tribe.client_detect)
- BUG-FIX in Tribe.client_detect where data were processed from data
one sample too long resulting in minor differences in data processing
(due to difference in FFT length) and therefore minor differences
in resulting correlations (~0.07 per channel).
- Includes extra stability check in fftw_normxcorr which affects the last sample before a gap when that sample is near-zero.
- BUG-FIX: fftw correlation dot product was not thread-safe on some systems. The dot-product did not have the inner index protected as a private variable. This did not appear to cause issues for Linux with Python 3.x or Windows, but did cause issues for on Linux for Python 2.7 and Mac OS builds.
- KeyboardInterrupt (e.g. ctrl-c) should now be caught during python parallel processes.
- Stopped allowing outer-threading on OSX, clang openMP is not thread-safe for how we have this set-up. Inner threading is faster and more memory efficient anyway.
- Added testing script (test_eqcorrscan.py, which will be installed to your path on installation of EQcorrscan) that will download all the relevant data and run the tests on the installed package - no need to clone EQcorrscan to run tests!
3.2. Version 0.3.1¶
- Cleaned imports in utils modules
- Removed parallel checking loop in archive_read.
- Add better checks for timing in lag-calc functions (#207)
- Removed gap-threshold of twice the template length in Tribe.client_detect, see issue #224.
- Bug-fix: give multi_find_peaks a cores kwarg to limit thread usage.
- Check for the same value in a row in continuous data when computing correlations and zero resulting correlations where the whole window is the same value repeated (#224, #230).
- BUG-FIX: template generation from_client methods for swin=P_all or S_all now download all channels and return them (as they should). See #235 and #206
- Change from raising an error if data from a station are not long enough, to logging a critical warning and not using the station.
- Add ability to give multiple swin options as a list. Remains backwards compatible with single swin arguments.
- Add option to save_progress for long running Tribe methods. Files are written to temporary files local to the caller.
- Fix bug where if gaps overlapped the endtime set in pre_processing an error was raised - happened when downloading data with a deliberate pad at either end.
3.3. Version 0.3.0¶
- Compiled peak-finding routine written to speed-up peak-finding.
- Change default match-filter plotting to not decimate unless it has to.
- BUG-FIX: changed minimum variance for fftw correlation backend.
- Do not try to process when no processing needs to be done in core.match_filter._group_process.
- Length checking in core.match_filter._group_process done in samples rather than time.
- BUG-FIX: Fix bug where data lengths were not correct in match_filter.Tribe.detect when sampling time-stamps were inconsistent between channels, which previously resulted in error.
- BUG-FIX: Fix memory-leak in tribe.construct
- Add plotting options for plotting rate to Party.plot
- Add filtering detections by date as Party.filter
- BUG-FIX: Change method for Party.rethreshold: list.remove was not reliable.
- Add option full_peaks to detect methods to map to find_peaks.
- pre-processing (and match-filter object methods) are now gap-aware and will accept gappy traces and can return gappy traces. By default gaps are filled to maintain backwards compatibility. Note that the fftw correlation backend requires gaps to be padded with zeros.
- Removed sfile_utils This support for Nordic IO has been upgraded and moved to obspy for obspy version 1.1.0. All functions are there and many bugs have been fixed. This also means the removal of nordic-specific functions in EQcorrscan - the following functions have been removed: * template_gen.from_sfile * template_gen.from_contbase * mag_calc.amp_pick_sfile * mag_calc.pick_db All removed functions will error and tell you to use obspy.io.nordic.core. This now means that you can use obspy’s read_events to read in sfiles.
- Added P_all and S_all options to template generation functions to allow creation of multi-channel templates starting at the P and S times respectively.
- Refactored template_gen, all options are available via template_gen(method=…), and depreciation warnings are in place.
- Added some docs for converting older templates and detections into Template and Party objects.
3.4. Version 0.2.7¶
- Patch multi_corr.c to work with more versions of MSVC;
- Revert to using single-precision floats for correlations (as in previous, < 0.2.x versions) for memory efficiency.
3.5. Version 0.2.6¶
Added the ability to change the correlation functions used in detection methods through the parameter xcorr_func of match_filter, Template.detect and Tribe.detect, or using the set_xcorr context manager in the utils.correlate module. Supported options are:
- or passing a function that implements the xcorr interface.
Added the ability to change the concurrency strategy of xcorr functions using the paramter concurrency of match_filter, Template.detect and Tribe.detect. Supported options are:
- None - for single-threaded execution in a single process
- multithread - for multi-threaded execution
- multiprocess- for multiprocess execution
- concurrent - allows functions to describe their own preferred currency
methods, defaults to multithread
Change debug printing output, it should be a little quieter;
Speed-up time-domain using a threaded C-routine - separate from frequency domain C-routines;
Expose useful parallel options for all correlation routines;
Expose cores argument for match-filter objects to allow limits to be placed on how much of your machine is used;
Limit number of workers created during pre-processing to never be more than the number of traces in the stream being processed;
Implement openMP parallelisation of cross-correlation sum routines - memory consumption reduced by using shared memory, and by computing the cross-correlation sums rather than individual channel cross-correlations. This also leads to a speed-up. This routine is the default concurrent correlation routine;
Test examples in rst doc files to ensure they are up-to-date;
Tests that were prone to timeout issues have been migrated to run on circleci to allow quick re-starting of fails not due to code errors
3.6. Version 0.2.5¶
- Fix bug with _group_process that resulted in stalled processes.
- Force NumPy version
- Support indexing of Tribe and Party objects by template-name.
- Add tests for lag-calc issue with preparing data
- Change internals of eqcorrscan.core.lag_calc._prepare_data to use a dictionary for delays, and to work correctly! Issues arose from not checking for masked data properly and not checking length properly.
- Fix bug in match_filter.match_filter when checking for equal length traces, length count was one sample too short.
3.7. Version 0.2.4¶
- 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:
- 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).
3.8. Version 0.2.0-0.2.3¶
- See 0.2.4: these versions were not fully released while trying to get anaconda packages to build properly.
3.9. Version 0.1.6¶
- Fix bug introduced in version 0.1.5 for match_filter where looping
through multiple templates did not correctly match image and template data: 0.1.5 fix did not work; * Bug-fix in catalog_to_dd for events without magnitudes; * Amend match-filter to not edit the list of template names in place. Previously, if a template was not used (due to no matching continuous data) then the name of the template was removed: this now copies the list of template_names internally and does not change the external list.
3.10. Version 0.1.5¶
- Migrate coverage to codecov;
- Fix bug introduced in version 0.1.5 for match_filter where looping
through multiple templates did not correctly match image and template data.
3.11. Version 0.1.4¶
- 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.
3.12. Version 0.1.3¶
- 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.
3.13. Version 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, but only testing about 65% 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
3.14. Version 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.