initial import

apps/lassie

+#!/usr/bin/env python
+
+import sys
+import logging
+from optparse import OptionParser
+
+from pyrocko import util
+
+import lassie
+
+logger = logging.getLogger('main')
+
+
+def d2u(d):
+    if isinstance(d, dict):
+        return dict((k.replace('-', '_'), v) for (k, v) in d.iteritems())
+    else:
+        return d.replace('-', '_')
+
+
+subcommand_descriptions = {
+    'init': 'create initial configuration file',
+    'scan': 'detect seismic events',
+    'map-geometry': 'make station map'
+}
+
+subcommand_usages = {
+    'init': 'init',
+    'scan': 'scan [options]',
+    'map-geometry': 'map-geometry <configfile> [options]',
+}
+
+subcommands = subcommand_descriptions.keys()
+
+program_name = 'lassie'
+
+usage_tdata = d2u(subcommand_descriptions)
+usage_tdata['program_name'] = program_name
+
+usage = program_name + ''' <subcommand> [options] [--] <arguments> ...
+
+Subcommands:
+
+    init          %(init)s
+    scan          %(scan)s
+    map-geometry  %(map_geometry)s
+
+To get further help and a list of available options for any subcommand run:
+
+    %(program_name)s <subcommand> --help
+
+''' % usage_tdata
+
+
+def add_common_options(parser):
+    parser.add_option(
+        '--loglevel',
+        action='store',
+        dest='loglevel',
+        type='choice',
+        choices=('critical', 'error', 'warning', 'info', 'debug'),
+        default='info',
+        help ='set logger level to '
+              '"critical", "error", "warning", "info", or "debug". '
+              'Default is "%default".')
+
+
+def process_common_options(options):
+    util.setup_logging(program_name, options.loglevel)
+
+
+def cl_parse(command, args, setup=None):
+    usage = subcommand_usages[command]
+    descr = subcommand_descriptions[command]
+
+    if isinstance(usage, basestring):
+        usage = [usage]
+
+    susage = '%s %s' % (program_name, usage[0])
+    for s in usage[1:]:
+        susage += '\n%s%s %s' % (' '*7, program_name, s)
+
+    parser = OptionParser(
+        usage=susage,
+        description=descr[0].upper() + descr[1:] + '.')
+
+    if setup:
+        setup(parser)
+
+    add_common_options(parser)
+    (options, args) = parser.parse_args(args)
+    process_common_options(options)
+    return parser, options, args
+
+
+def die(message, err=''):
+    if err:
+        sys.exit('%s: error: %s \n %s' % (program_name, message, err))
+    else:
+        sys.exit('%s: error: %s' % (program_name, message))
+
+
+def help_and_die(parser, message):
+    parser.print_help(sys.stderr)
+    sys.stderr.write('\n')
+    die(message)
+
+
+def escape(s):
+    return s.replace("'", "\\'")
+
+def command_init(args):
+    def setup(parser):
+        parser.add_option(
+            '--stations', dest='stations_path',
+            help='stations file')
+
+    parser, options, args = cl_parse('init', args, setup=setup)
+
+    if args:
+        data_path = '\n'.join("- '%s'" % escape(x) for x in args)
+    else:
+        data_path = "- 'DATA'"
+
+    if options.stations_path:
+        stations_path = options.stations_path
+    else:
+        stations_path = 'STATIONS_PATH'
+
+    print '''%%YAML 1.1
+--- !lassie.Config
+
+## Configuration file for Lassie, your friendly earthquake detector
+## 
+## Receiver coordinates can be read from a stations file in Pyrocko format:
+stations_path: '%(stations_path)s'
+
+## Receivers can also be listed in the config file, lat/lon and carthesian 
+## (x/y/z) = (North/East/Down) coordinates are supported and may be combined 
+## (interpreted as reference + offset). Omitted values are treated as zero.
+# receivers:
+# - !lassie.Receiver
+#   codes: ['', 'ACC13', '']
+#   lat: 10.
+#   lon: 12.
+#   x: 2397.56
+#   y: 7331.94
+#   z: -404.1
+
+## List of data directories. Lassie will recurse into subdirectories to find
+## all contained waveform files.
+data_paths:
+%(data_path)s
+
+## Processing time interval (default: use time interval of available data)
+# tmin: '2016-02-05 16:00:00'
+# tmax: '2016-02-05 17:40:00'
+
+## Search grid, if not given here, a default grid will be chosen
+
+# grid: 
+# !coarse.Carthesian3DGrid
+#   lat: 10.
+#   lon: 12.
+#   xmin: 2360.0
+#   xmax: 2450.0
+#   ymin: 7270.0
+#   ymax: 7360.0
+#   zmin: -415.0
+#   zmax: -400.0
+#   dx: 2.0
+#   dy: 2.0
+#   dz: 2.0
+
+## Size factor to use when automatically choosing a grid size
+autogrid_radius_factor: 1.5
+
+## Grid density factor used when automatically choosing a grid
+autogrid_density_factor: 10.0
+
+## Image function contributions
+ifcs:
+- !lassie.WavePacketIFC
+  name: 'P'
+  weight: 1.0
+  fmin: 1.0
+  fmax: 50.0
+  fsmooth_factor: 0.1
+  shifter: !lassie.VelocityShifter
+    velocity: 3600.
+- !lassie.WavePacketIFC
+  name: 'S'
+  weight: 1.0
+  fmin: 1.0
+  fmax: 10.0
+  fsmooth_factor: 0.1
+  shifter: !lassie.VelocityShifter
+    velocity: 2500.
+
+## Whether to divide image function frames by their mean value
+sharpness_normalization: true
+
+## Threshold on detector function
+detector_threshold: 200.0
+
+## Output filename for detections
+detections_path: 'detections.txt'
+''' % dict(
+    stations_path=stations_path,
+    data_path=data_path)
+
+
+def command_scan(args):
+    def setup(parser):
+        parser.add_option(
+            '--force', dest='force', action='store_true',
+            help='overwrite existing files')
+
+        parser.add_option(
+            '--show-detections', dest='show_detections', action='store_true',
+            help='show plot for every detection found')
+
+        parser.add_option(
+            '--show-movie', dest='show_movie', action='store_true',
+            help='show movie when showing detections')
+
+        parser.add_option(
+            '--stop-after-first', dest='stop_after_first', action='store_true',
+            help='show plot for every detection found')
+
+    parser, options, args = cl_parse('scan', args, setup=setup)
+    if len(args) != 1:
+        help_and_die(parser, 'missing argument')
+
+    config_path = args[0]
+    config = lassie.read_config(config_path)
+    print config
+    try:
+        lassie.scan(
+            config,
+            force=options.force,
+            show_detections=options.show_detections,
+            show_movie=options.show_movie,
+            stop_after_first=options.stop_after_first)
+
+    except lassie.LassieError, e:
+        die(str(e))
+
+
+def command_map_geometry(args):
+    parser, options, args = cl_parse('map-geometry', args)
+    if len(args) != 2:
+        help_and_die(parser, 'missing arguments')
+
+    config_path = args[0]
+    output_path = args[1]
+    config = lassie.read_config(config_path)
+    lassie.map_geometry(config, output_path)
+
+
+if __name__ == '__main__':
+
+    usage_sub = 'fomosto %s [options]'
+    if len(sys.argv) < 2:
+        sys.exit('Usage: %s' % usage)
+
+    args = list(sys.argv)
+    args.pop(0)
+    command = args.pop(0)
+
+    if command in subcommands:
+        globals()['command_' + d2u(command)](args)
+
+    elif command in ('--help', '-h', 'help'):
+        if command == 'help' and args:
+            acommand = args[0]
+            if acommand in subcommands:
+                globals()['command_' + acommand](['--help'])
+
+        sys.exit('Usage: %s' % usage)
+
+    else:
+        die('no such subcommand: %s' % command)

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+       style="color:#000000;fill:none;stroke:#1f1a17;stroke-width:2;marker:none;visibility:visible;display:inline;overflow:visible;enable-background:accumulate"
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+       transform="translate(70.535714,-71.964286)" />
+  </g>
+</svg>

setup.py

+#!/usr/bin/env python
+
+from distutils.core import setup
+
+setup(
+    name='lassie',
+    packages=['lassie'],
+    package_dir={'lassie': 'src'},
+    scripts=['apps/lassie'],
+    package_data={'lassie': []})

src/__init__.py

+from lassie.common import *  # noqa
+from lassie.receiver import *  # noqa
+from lassie.grid import *  # noqa
+from lassie.shifter import *  # noqa
+from lassie.ifc import *  # noqa
+from lassie.core import *  # noqa
+from lassie.plot import *  # noqa
+from lassie.config import *  # noqa

src/common.py

+from collections import defaultdict
+
+guts_prefix = 'lassie'
+
+
+class LassieError(Exception):
+    pass
+
+
+def grouped_by(l, key):
+    d = defaultdict(list)
+    for x in l:
+        d[key(x)].append(x)
+
+    return d
+
+__all__ = [
+    'LassieError',
+]

src/config.py

+import logging
+
+from pyrocko.guts import Object, String, Float, Timestamp, List, Bool, load
+from pyrocko import model
+
+from lassie import receiver, ifc, grid, geo
+
+guts_prefix = 'lassie'
+
+logger = logging.getLogger('lassie.config')
+
+
+class Config(Object):
+
+    stations_path = String.T(
+        optional=True,
+        help='stations file in Pyrocko format')
+
+    receivers = List.T(
+        receiver.Receiver.T(),
+        help='receiver coordinates if not read from file')
+
+    data_paths = List.T(
+        String.T(),
+        help='list of directories paths to search for data')
+
+    blacklist = List.T(
+        String.T(),
+        help='codes in the form NET.STA.LOC of receivers to be excluded')
+
+    tmin = Timestamp.T(
+        optional=True,
+        help='beginning of time interval to be processed')
+
+    tmax = Timestamp.T(
+        optional=True,
+        help='end of time interval to be processed')
+
+    detections_path = String.T(
+        optional=True,
+        help='output file name for for detections')
+
+    grid = grid.Grid.T(
+        optional=True,
+        help='definition of search grid, if not given, a default grid is '
+             'chosen')
+
+    autogrid_radius_factor = Float.T(
+        default=1.5,
+        help='size factor to use when automatically choosing a grid size')
+
+    autogrid_density_factor = Float.T(
+        default=10.0,
+        help='grid density factor used when automatically choosing a grid '
+             'spacing')
+
+    ifcs = List.T(
+        ifc.IFC.T(),
+        help='image function contributions')
+
+    sharpness_normalization = Bool.T(
+        default=True,
+        help='whether to divide image function frames by their mean value')
+
+    detector_threshold = Float.T(
+        default=200.,
+        help='threshold on detector function')
+
+    def __init__(self, *args, **kwargs):
+        Object.__init__(self, *args, **kwargs)
+        self._receivers = None
+        self._grid = None
+
+    def get_receivers(self):
+        '''Aggregate receivers from different sources.'''
+
+        if self._receivers is None:
+            self._receivers = list(self.receivers)
+            if self.stations_path:
+                for station in model.load_stations(self.stations_path):
+                    self._receivers.append(
+                        receiver.Receiver(
+                            codes=station.nsl(),
+                            lat=station.lat,
+                            lon=station.lon))
+
+        return self._receivers
+
+    def get_grid(self):
+        '''Get grid or make default grid.'''
+
+        if self._grid is None:
+
+            if not self.grid:
+                receivers = self.get_receivers()
+
+                fsmooth_max = max(
+                    ifc.get_fsmooth() for ifc in self.ifcs)
+
+                vmin = min(ifc.shifter.get_vmin() for ifc in self.ifcs)
+
+                spacing = vmin / fsmooth_max / self.autogrid_density_factor
+
+                lat0, lon0, north, east, depth = geo.bounding_box_square(
+                    *receiver.receivers_coords(receivers),
+                    scale=self.autogrid_radius_factor)
+
+                self._grid = grid.Carthesian3DGrid(
+                    lat=lat0,
+                    lon=lon0,
+                    xmin=north[0],
+                    xmax=north[1],
+                    dx=spacing,
+                    ymin=east[0],
+                    ymax=east[1],
+                    dy=spacing,
+                    zmin=depth[0],
+                    zmax=depth[1],
+                    dz=spacing)
+
+                logger.info('automatic grid:\n%s' % self._grid)
+
+            else:
+                self._grid = self.grid
+
+            self._grid.update()
+
+        return self._grid
+
+
+def read_config(file_path):
+    conf = load(filename=file_path)
+    return conf
+
+__all__ = [
+    'Config',
+    'read_config',
+]

src/core.py

+import sys
+import os
+import logging
+import os.path as op
+
+import numpy as num
+
+from pyrocko import pile, trace, util, io
+from pyrocko.parstack import parstack
+
+from lassie import common, plot, grid as gridmod
+
+logger = logging.getLogger('lassie.core')
+
+
+def scan(
+        config,
+        show_detections=False,
+        show_movie=False,
+        force=False,