diff --git a/.travis.yml b/.travis.yml index 9040eb410..bf3abf771 100644 --- a/.travis.yml +++ b/.travis.yml @@ -75,6 +75,7 @@ install: pytest pytest-pep8 opencv + pyflakes=0.9.0 - source activate test-environment # install packages not available via conda # - pip install -r requirements.txt diff --git a/CHANGES.md b/CHANGES.md index 537f07be6..33eea1e66 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,27 @@ +## 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. + ## 0.1.0 * Implimented tests for synthetic generation and match-filter functions * Developed new tutorials that download from GeoNet and are much clearer diff --git a/MANIFEST.in b/MANIFEST.in index 74b64a4cf..d568d76be 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -18,5 +18,6 @@ prune eqcorrscan/doc/_build/latex prune eqcorrscan/plot prune eqcorrscan/detections prune eqcorrscan/grid +prune eqcorrscan/tests/test_data # prune eqcorrscan/stack_templates # prune eqcorrscan/templates diff --git a/README.md b/README.md index 4455fbe25..09a5bdeae 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Also within this package are: We are currently hovering around 9,000 lines of code (including doc-strings) - it is probably worth having a look at the docs to check what functions we have. We plan to write a series of tutorials to be -included on the EQcorrscan API to highlight key functions, currently our tutorial only shows +included on the EQcorrscan API to highlight key functions, currently our tutorials only show how to do the core matched-filter detection. # Licence @@ -108,3 +108,4 @@ will keep us all branching in the same way. * Thurber, C. H., Zeng, X., Thomas, A. M., & Audet, P. (2014). [Phase‐Weighted Stacking Applied to Low‐Frequency Earthquakes](http://www.bssaonline.org/content/early/2014/08/12/0120140077.abstract), __BSSA__, doi:10.1785/0120140077. * Frank, W. B., & Shapiro, N. M. (2014). [Automatic detection of low-frequency earthquakes (LFEs) based on a beamformed network response](http://gji.oxfordjournals.org/content/197/2/1215.short), __Geophysical Journal International__, 197(2), 1215-1223, doi:10.1093/gji/ggu058. * Rubinstein, J. L., & Ellsworth, W. L. (2010). [Precise estimation of repeating earthquake moment: Example from Parkfield, California](http://www.bssaonline.org/content/100/5A/1952.short), __BSSA__, doi:10.1785/0120100007 +fa66e06971b2dd1e4bf766 diff --git a/eqcorrscan/__init__.py b/eqcorrscan/__init__.py index 3d6f75ae9..a7996585c 100755 --- a/eqcorrscan/__init__.py +++ b/eqcorrscan/__init__.py @@ -30,10 +30,82 @@ You should have received a copy of the GNU General Public License along with EQcorrscan. If not, see . """ - +import sys +import importlib +import warnings __all__ = ['core', 'utils', 'par'] -__version__ = '0.1.0' + +__version__ = '0.1.1' + +# Cope with changes to name-space to remove most of the camel-case +_import_map = { + "eqcorrscan.utils.catalogue2DD": "eqcorrscan.utils.catalog_to_dd", + "eqcorrscan.utils.EQcorrscan_plotting": "eqcorrscan.utils.plotting" +} + + +class EQcorrscanDeprecationWarning(UserWarning): + """ + Force pop-up of warnings. + """ + pass + + +class EQcorrscanRestructureAndLoad(object): + """ + Path finder and module loader for transitioning + """ + def find_module(self, fullname, path=None): + # Compatibility with namespace paths. + if hasattr(path, "_path"): + path = path._path + + if not path or not path[0].startswith(__path__[0]): + return None + + for key in _import_map.keys(): + if fullname.startswith(key): + break + else: + return None + return self + + def load_module(self, name): + # Use cached modules. + if name in sys.modules: + return sys.modules[name] + # Otherwise check if the name is part of the import map. + elif name in _import_map: + new_name = _import_map[name] + else: + new_name = name + for old, new in _import_map.items(): + if not new_name.startswith(old): + continue + new_name = new_name.replace(old, new) + break + else: + return None + + # Don't load again if already loaded. + if new_name in sys.modules: + module = sys.modules[new_name] + else: + module = importlib.import_module(new_name) + + # Warn here as at this point the module has already been imported. + warnings.warn("Module '%s' is deprecated and will stop working " + "with the next EQcorrscan version. Please import module " + "'%s' instead." % (name, new_name), + EQcorrscanDeprecationWarning) + sys.modules[new_name] = module + sys.modules[name] = module + return module + + +sys.meta_path.append(EQcorrscanRestructureAndLoad()) + if __name__ == '__main__': import doctest doctest.testmod(exclude_empty=True) diff --git a/eqcorrscan/core/bright_lights.py b/eqcorrscan/core/bright_lights.py index 2d2098566..384c2f130 100644 --- a/eqcorrscan/core/bright_lights.py +++ b/eqcorrscan/core/bright_lights.py @@ -573,7 +573,7 @@ def brightness(stations, nodes, lags, stream, threshold, thresh_type, from obspy.core.event import EventDescription, CreationInfo, Comment import obspy.Stream import matplotlib.pyplot as plt - from eqcorrscan.utils import EQcorrscan_plotting as plotting + from eqcorrscan.utils import plotting # Check that we actually have the correct stations realstations = [] for station in stations: @@ -659,7 +659,7 @@ def brightness(stations, nodes, lags, stream, threshold, thresh_type, del energy, indeces else: print('Reading the temp files and computing network response') - node_splits = len(nodes) // num_cores + node_splits = int(len(nodes) // num_cores) indeces = [range(node_splits)] for i in range(1, num_cores - 1): indeces.append(range(node_splits * i, node_splits * (i + 1))) diff --git a/eqcorrscan/core/match_filter.py b/eqcorrscan/core/match_filter.py index c217e8a90..e85842329 100644 --- a/eqcorrscan/core/match_filter.py +++ b/eqcorrscan/core/match_filter.py @@ -401,12 +401,12 @@ def match_filter(template_names, template_list, st, threshold, import matplotlib.pyplot as plt plt.ioff() import copy - from eqcorrscan.utils import EQcorrscan_plotting + from eqcorrscan.utils import plotting from eqcorrscan.utils import findpeaks from obspy import Trace import time - # Copy the stream here because we will fuck about with it + # Copy the stream here because we will muck about with it stream = st.copy() templates = copy.deepcopy(template_list) # Debug option to confirm that the channel names match those in the @@ -517,19 +517,19 @@ def match_filter(template_names, template_list, st, threshold, cccsum_hist = cccsum_plot.copy() cccsum_hist = cccsum_hist.decimate(int(stream[0].stats. sampling_rate / 10)).data - cccsum_plot = EQcorrscan_plotting.chunk_data(cccsum_plot, 10, - 'Maxabs').data + cccsum_plot = plotting.chunk_data(cccsum_plot, 10, + 'Maxabs').data # Enforce same length stream_plot.data = stream_plot.data[0:len(cccsum_plot)] cccsum_plot = cccsum_plot[0:len(stream_plot.data)] cccsum_hist = cccsum_hist[0:len(stream_plot.data)] - EQcorrscan_plotting.triple_plot(cccsum_plot, cccsum_hist, - stream_plot, rawthresh, True, - plotdir + '/cccsum_plot_' + - template_names[i] + '_' + - stream[0].stats.starttime. - datetime.strftime('%Y-%m-%d') + - '.' + plot_format) + plotting.triple_plot(cccsum_plot, cccsum_hist, + stream_plot, rawthresh, True, + plotdir + '/cccsum_plot_' + + template_names[i] + '_' + + stream[0].stats.starttime. + datetime.strftime('%Y-%m-%d') + + '.' + plot_format) if debug >= 4: print(' '.join(['Saved the cccsum to:', template_names[i], stream[0].stats.starttime.datetime. diff --git a/eqcorrscan/core/template_gen.py b/eqcorrscan/core/template_gen.py index 4e0d9f8c2..2b5ee3c13 100644 --- a/eqcorrscan/core/template_gen.py +++ b/eqcorrscan/core/template_gen.py @@ -3,6 +3,13 @@ for the application of cross-correlation of seismic data for the detection of \ repeating events. +.. note:: All of these functions work for a single template, however all of \ + them call _template_gen, which takes care of pick association and \ + cutting. If you have many templates in one day of data it would be \ + simple to write a wrapper that cuts multiple templates from one day \ + of processed data rather than re-processing the same day of data \ + for each template. + Code written by Calum John Chamberlain & Chet Hopp of \ Victoria University of Wellington, 2015. @@ -30,8 +37,72 @@ from __future__ import unicode_literals +def from_sac(sac_files, lowcut, highcut, samp_rate, filt_order, length, swin, + prepick=0.05, debug=0, plot=False): + """Function to read picks and waveforms from SAC data, and generate a \ + template from these. + + :type sac_files: list or stream + :param sac_files: List or stream of sac waveforms, or list of paths to \ + sac waveforms. + :type lowcut: float + :param lowcut: Low cut (Hz), if set to None will look in template \ + defaults file + :type highcut: float + :param highcut: High cut (Hz), if set to None will look in template \ + defaults file + :type samp_rate: float + :param samp_rate: New sampling rate in Hz, if set to None will look in \ + template defaults file + :type filt_order: int + :param filt_order: Filter level, if set to None will look in \ + template defaults file + :type swin: str + :param swin: Either 'all', 'P' or 'S', to select which phases to output. + :type length: float + :param length: Extract length in seconds, if None will look in template \ + defaults file. + :type prepick: float + :param prepick: Length to extract prior to the pick in seconds. + :type debug: int + :param debug: Debug level, higher number=more output. + :type plot: bool + :param plot: Turns template plotting on or off. + + :returns: obspy.Stream Newly cut template + + .. note:: This functionality is not supported for obspy versions below \ + 1.0.0 as references times are not read in by SACIO, which are needed \ + for defining pick times. + """ + from obspy import read, Stream + from eqcorrscan.utils.sac_util import sactoevent + from eqcorrscan.utils import pre_processing + # Check whether sac_files is a stream or a list + if isinstance(sac_files, list): + if isinstance(sac_files[0], str) or isinstance(sac_files[0], unicode): + sac_files = [read(sac_file)[0] for sac_file in sac_files] + if isinstance(sac_files[0], Stream): + # This is a list of streams... + st = sac_files[0] + for sac_file in sac_files[1:]: + st += sac_file + st = Stream(sac_files) + elif isinstance(sac_files, Stream): + st = sac_files + # Make an event object... + event = sactoevent(st) + # Process the data + st.merge(fill_value='interpolate') + st = pre_processing.shortproc(st, lowcut, highcut, filt_order, + samp_rate, debug) + template = _template_gen(picks=event.picks, st=st, length=length, + swin=swin, prepick=prepick, plot=plot) + return template + + def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin, - debug=0, plot=False): + prepick=0.05, debug=0, plot=False): r"""Function to read in picks from sfile then generate the template from \ the picks within this and the wavefile found in the pick file. @@ -56,12 +127,19 @@ def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin, :type length: float :param length: Extract length in seconds, if None will look in template \ defaults file. + :type prepick: float + :param prepick: Length to extract prior to the pick in seconds. :type debug: int :param debug: Debug level, higher number=more output. :type plot: bool :param plot: Turns template plotting on or off. :returns: obspy.Stream Newly cut template + + .. warning:: This will use whatever data is pointed to in the s-file, if \ + this is not the coninuous data, we recommend using other functions. \ + Differences in processing between short files and day-long files \ + (inherent to resampling) will produce lower cross-correlations. """ # Perform some checks first import os @@ -69,10 +147,10 @@ def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin, raise IOError('sfile does not exist') from eqcorrscan.utils import pre_processing - from eqcorrscan.utils import Sfile_util + from eqcorrscan.utils import sfile_util from obspy import read as obsread # Read in the header of the sfile - wavefiles = Sfile_util.readwavename(sfile) + wavefiles = sfile_util.readwavename(sfile) pathparts = sfile.split('/')[0:-1] new_path_parts = [] for part in pathparts: @@ -100,7 +178,7 @@ def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin, raise ValueError("Trace: " + tr.stats.station + " sampling rate: " + str(tr.stats.sampling_rate)) # Read in pick info - catalog = Sfile_util.readpicks(sfile) + catalog = sfile_util.readpicks(sfile) # Read the list of Picks for this event picks = catalog[0].picks print("I have found the following picks") @@ -113,7 +191,8 @@ def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin, st.merge(fill_value='interpolate') st = pre_processing.shortproc(st, lowcut, highcut, filt_order, samp_rate, debug) - st1 = _template_gen(picks, st, length, swin, plot=plot) + st1 = _template_gen(picks=picks, st=st, length=length, swin=swin, + prepick=prepick, plot=plot) return st1 @@ -170,16 +249,16 @@ def from_contbase(sfile, contbase_list, lowcut, highcut, samp_rate, filt_order, # import some things from eqcorrscan.utils import pre_processing - from eqcorrscan.utils import Sfile_util + from eqcorrscan.utils import sfile_util import glob from obspy import read as obsread # Read in the header of the sfile - event = Sfile_util.readheader(sfile) + event = sfile_util.readheader(sfile) day = event.origins[0].time # Read in pick info - catalog = Sfile_util.readpicks(sfile) + catalog = sfile_util.readpicks(sfile) picks = catalog[0].picks print("I have found the following picks") pick_chans = [] @@ -249,7 +328,10 @@ def from_quakeml(quakeml, st, lowcut, highcut, samp_rate, filt_order, :param quakeml: QuakeML file containing pick information, can contain \ multiple events. :type st: class: obspy.Stream - :param st: Stream containing waveform data for template (hopefully) + :param st: Stream containing waveform data for template (hopefully). \ + Note that this should be the same length of stream as you will use \ + for the continuous detection, e.g. if you detect in day-long files, \ + give this a day-long file! :type lowcut: float :param lowcut: Low cut (Hz), if set to None will look in template \ defaults file @@ -275,6 +357,11 @@ def from_quakeml(quakeml, st, lowcut, highcut, samp_rate, filt_order, :param plot: Display template plots or not :returns: list of obspy.Stream Newly cut templates + + .. warning:: We suggest giving this function a full day of data, to \ + ensure templates are generated with **exactly** the same processing \ + as the continuous data. Not doing this will result in slightly \ + reduced cross-correlation values. """ # Perform some checks first import os @@ -295,8 +382,9 @@ def from_quakeml(quakeml, st, lowcut, highcut, samp_rate, filt_order, st.merge(fill_value='interpolate') for tr in st: tr = pre_processing.dayproc(tr, lowcut, highcut, filt_order, - samp_rate, debug, - UTCDateTime(tr.stats.starttime.date)) + samp_rate, debug=debug, + starttime=UTCDateTime(tr.stats. + starttime.date)) # Read QuakeML file into Catalog class catalog = read_events(quakeml) templates = [] @@ -368,6 +456,7 @@ def from_seishub(catalog, url, lowcut, highcut, samp_rate, filt_order, else: from obspy.seishub import Client from eqcorrscan.utils import pre_processing + from obspy import UTCDateTime client = Client(url) temp_list = [] for event in catalog: @@ -380,9 +469,12 @@ def from_seishub(catalog, url, lowcut, highcut, samp_rate, filt_order, sta = pick.waveform_id.station_code chan = pick.waveform_id.channel_code loc = pick.waveform_id.location_code - starttime = pick.time - (prepick + 600) - # Enforce some pad, 10min either side, to reduce filter effects - endtime = pick.time + length + 600 - prepick + starttime = UTCDateTime(pick.time.date) + endtime = starttime + 86400 + # Here we download a full day of data. We do this so that minor + # differences in processing during processing due to the effect + # of resampling do not impinge on our cross-correaltions. + if debug > 0: print('start-time: ' + str(starttime)) print('end-time: ' + str(endtime)) @@ -401,8 +493,9 @@ def from_seishub(catalog, url, lowcut, highcut, samp_rate, filt_order, st.plot() print('Preprocessing data for event: '+str(event.resource_id)) st.merge(fill_value='interpolate') - st1 = pre_processing.shortproc(st, lowcut, highcut, filt_order, - samp_rate, debug) + st1 = pre_processing.dayproc(st, lowcut, highcut, filt_order, + samp_rate, starttime=starttime, + debug=debug) template = _template_gen(event.picks, st1, length, swin, prepick, plot=plot) del st, st1 @@ -456,6 +549,7 @@ def from_client(catalog, client_id, lowcut, highcut, samp_rate, filt_order, from obspy.fdsn import Client from obspy.fdsn.header import FDSNException from eqcorrscan.utils import pre_processing + from obspy import UTCDateTime import warnings client = Client(client_id) @@ -469,13 +563,16 @@ def from_client(catalog, client_id, lowcut, highcut, samp_rate, filt_order, sta = pick.waveform_id.station_code chan = pick.waveform_id.channel_code loc = pick.waveform_id.location_code - starttime = pick.time - (prepick + 600) - # Enforce some pad, 10min either side, to reduce filter effects - endtime = pick.time + length + 600 - prepick + starttime = UTCDateTime(pick.time.date) + endtime = starttime + 86400 + # Here we download a full day of data. We do this so that minor + # differences in processing during processing due to the effect + # of resampling do not impinge on our cross-correaltions. if debug > 0: print('start-time: ' + str(starttime)) print('end-time: ' + str(endtime)) print('pick-time: ' + str(pick.time)) + print('pick phase: ' + pick.phase_hint) print('.'.join([net, sta, loc, chan])) if 'st' not in locals(): try: @@ -493,8 +590,9 @@ def from_client(catalog, client_id, lowcut, highcut, samp_rate, filt_order, st.plot() print('Pre-processing data for event: '+str(event.resource_id)) st.merge(fill_value='interpolate') - st1 = pre_processing.shortproc(st, lowcut, highcut, filt_order, - samp_rate, debug) + st1 = pre_processing.dayproc(st, lowcut, highcut, filt_order, + samp_rate, starttime=starttime, + debug=debug, parallel=True) if debug > 0: st1.plot() template = _template_gen(event.picks, st1, length, swin, prepick, @@ -537,7 +635,7 @@ def _template_gen(picks, st, length, swin='all', prepick=0.05, plot=False): all channels with picks will be used. """ import copy - from eqcorrscan.utils.EQcorrscan_plotting import pretty_template_plot as\ + from eqcorrscan.utils.plotting import pretty_template_plot as\ tplot from obspy import Stream import warnings @@ -648,7 +746,9 @@ def _template_gen(picks, st, length, swin='all', prepick=0.05, plot=False): 10, st1.sort(['starttime'])[-1].stats.endtime + 10) - tplot(st1, background=background) + tplot(st1, background=background, + title='Template for '+str(st1[0].stats.starttime), + picks=picks) del stplot del st # st1.plot(size=(800,600)) diff --git a/eqcorrscan/core/thresholding.py b/eqcorrscan/core/thresholding.py index 6ae2e0590..deacfcf6f 100755 --- a/eqcorrscan/core/thresholding.py +++ b/eqcorrscan/core/thresholding.py @@ -88,7 +88,7 @@ def coherence_test(stream, stations, nodes, lags, wlen): # path = os.path.dirname(os.path.abspath(__file__)) # sys.path.insert(0, path[0:len(path)-5]) # from core import bright_lights -# from utils import EQcorrscan_plotting as plotting +# from utils 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When it is not found, a full rebuild will be done. -config: 66c486cd85f32812f89c64141c06ce4c +config: e9ef4141a04a343e14d396aa0126b14f tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/eqcorrscan/doc/_build/html/_modules/EQcorrscan_plotting.html b/eqcorrscan/doc/_build/html/_modules/EQcorrscan_plotting.html index d005d9076..bedc00f4e 100644 --- a/eqcorrscan/doc/_build/html/_modules/EQcorrscan_plotting.html +++ b/eqcorrscan/doc/_build/html/_modules/EQcorrscan_plotting.html @@ -7,7 +7,7 @@ - EQcorrscan_plotting — EQcorrscan 0.1.0 documentation + EQcorrscan_plotting — EQcorrscan 0.1.1 documentation @@ -32,7 +32,7 @@ - + @@ -72,31 +72,37 @@
  • 1.4. Functions
    • -
  • 2. EQcorrscan tutorial