grond 17 KB
Newer Older
Sebastian Heimann's avatar
Sebastian Heimann committed
1
2
3
4
5
6
7
#!/usr/bin/env python

import math
import sys
import logging
from optparse import OptionParser

8
from pyrocko import util, marker
Sebastian Heimann's avatar
Sebastian Heimann committed
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
from pyrocko.gf import Range

import grond

logger = logging.getLogger('main')

km = 1000.


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': 'print example configuration',
Sebastian Heimann's avatar
Sebastian Heimann committed
27
    'events': 'print available event names for given configuration',
Sebastian Heimann's avatar
Sebastian Heimann committed
28
    'check': 'check data and configuration',
Sebastian Heimann's avatar
Sebastian Heimann committed
29
30
31
32
33
    'go': 'run Grond optimization',
    'forward': 'run forward modelling',
    'harvest': 'manually run harvesting',
    'plot': 'plot optimization result',
    'export': 'export results',
34
    'qc-polarization': 'check sensor orientations with polarization analysis',
Sebastian Heimann's avatar
Sebastian Heimann committed
35
36
37
38
}

subcommand_usages = {
    'init': 'init [options]',
Sebastian Heimann's avatar
Sebastian Heimann committed
39
    'events': 'events <configfile>',
40
41
42
43
44
    'check': 'check <configfile> <eventnames> ... [options]',
    'go': 'go <configfile> <eventnames> ... [options]',
    'forward': (
        'forward <rundir> [options]',
        'forward <configfile> <eventnames> ... [options]'),
Sebastian Heimann's avatar
Sebastian Heimann committed
45
46
    'harvest': 'harvest <rundir> [options]',
    'plot': 'plot <plotnames> <rundir> [options]',
Sebastian Heimann's avatar
Sebastian Heimann committed
47
    'export': 'export (best|mean|ensemble|stats) <rundirs> ... [options]',
48
49
    'qc-polarization': 'qc-polarization <configfile> <eventname> '
                       '<targetconfigname> [options]',
Sebastian Heimann's avatar
Sebastian Heimann committed
50
51
52
53
54
55
56
57
58
59
60
61
62
}

subcommands = subcommand_descriptions.keys()

program_name = 'grond'

usage_tdata = d2u(subcommand_descriptions)
usage_tdata['program_name'] = program_name

usage = '''%(program_name)s <subcommand> [options] [--] <arguments> ...

Subcommands:

63
64
65
66
67
68
69
70
71
    init            %(init)s
    events          %(events)s
    check           %(check)s
    go              %(go)s
    forward         %(forward)s
    harvest         %(harvest)s
    plot            %(plot)s
    export          %(export)s
    qc-polarization %(qc_polarization)s
Sebastian Heimann's avatar
Sebastian Heimann committed
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87

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',
Sebastian Heimann's avatar
Sebastian Heimann committed
88
89
90
        help='set logger level to '
             '"critical", "error", "warning", "info", or "debug". '
             'Default is "%default".')
Sebastian Heimann's avatar
Sebastian Heimann committed
91
92
93
94
95
96


def process_common_options(options):
    util.setup_logging(program_name, options.loglevel)


97
def cl_parse(command, args, setup=None, details=None):
Sebastian Heimann's avatar
Sebastian Heimann committed
98
99
100
101
102
103
104
105
106
107
    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)

108
109
110
111
112
113
    description = descr[0].upper() + descr[1:] + '.'

    if details:
        description = description + '\n\n%s' % details

    parser = OptionParser(usage=susage, description=description)
Sebastian Heimann's avatar
Sebastian Heimann committed
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182

    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 command_init(args):

    dataset_config = grond.DatasetConfig(
        stations_path='stations.txt',
        events_path='events.txt',
        waveform_paths=['data'])

    target_configs = [grond.TargetConfig(
        distance_min=10*km,
        distance_max=1000*km,
        channels=['Z', 'R', 'T'],
        interpolation='multilinear',
        store_id='global_2s',
        inner_misfit_config=grond.InnerMisfitConfig(
            fmin=0.01,
            fmax=0.1))]

    s2 = math.sqrt(2.0)

    problem_config = grond.CMTProblemConfig(
        name_template='cmt_%(event_name)s',
        distance_min=2.*km,
        nbootstrap=100,
        mt_type='deviatoric',
        ranges=dict(
            time=Range(0, 10.0, relative='add'),
            north_shift=Range(-16*km, 16*km),
            east_shift=Range(-16*km, 16*km),
            depth=Range(1*km, 11*km),
            magnitude=Range(4.0, 6.0),
            rmnn=Range(-s2, s2),
            rmee=Range(-s2, s2),
            rmdd=Range(-s2, s2),
            rmne=Range(-1.0, 1.0),
            rmnd=Range(-1.0, 1.0),
            rmed=Range(-1.0, 1.0),
            duration=Range(1.0, 15.0)))

    config = grond.Config(
        dataset_config=dataset_config,
        target_configs=target_configs,
        problem_config=problem_config)

    print config


Sebastian Heimann's avatar
Sebastian Heimann committed
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
def command_events(args):
    def setup(parser):
        pass

    parser, options, args = cl_parse('events', args, setup)
    if len(args) != 1:
        help_and_die(parser, 'missing arguments')

    config_path = args[0]
    config = grond.read_config(config_path)

    for event_name in grond.get_event_names(config):
        print event_name


Sebastian Heimann's avatar
Sebastian Heimann committed
198
199
def command_check(args):
    def setup(parser):
200
201
202
203
204
        parser.add_option(
            '--target-ids', dest='target_string_ids', metavar='TARGET_IDS',
            help='process only selected targets. TARGET_IDS is a '
                 'comma-separated list of target IDs. Target IDs have the '
                 'form SUPERGROUP.GROUP.NETWORK.STATION.LOCATION.CHANNEL.')
Sebastian Heimann's avatar
Sebastian Heimann committed
205

Sebastian Heimann's avatar
Sebastian Heimann committed
206
207
        parser.add_option(
            '--plot', dest='show_plot', action='store_true',
208
209
            help='plot sample synthetics and data.')

210
211
212
213
        parser.add_option(
            '--waveforms', dest='show_waveforms', action='store_true',
            help='show raw, restituted, projected, and processed waveforms')

214
215
216
217
218
219
        parser.add_option(
            '--nrandom', dest='n_random_synthetics', metavar='N', type='int',
            default=10,
            help='set number of random synthetics to forward model (default: '
                 '10). If set to zero, create synthetics for the reference '
                 'solution.')
Sebastian Heimann's avatar
Sebastian Heimann committed
220

Sebastian Heimann's avatar
Sebastian Heimann committed
221
    parser, options, args = cl_parse('check', args, setup)
222
223
    if len(args) < 2:
        help_and_die(parser, 'missing arguments')
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
224

Sebastian Heimann's avatar
Sebastian Heimann committed
225
    config_path = args[0]
226
227
    event_names = args[1:]

Sebastian Heimann's avatar
Sebastian Heimann committed
228
229
    config = grond.read_config(config_path)

230
231
232
233
    target_string_ids = None
    if options.target_string_ids:
        target_string_ids = options.target_string_ids.split(',')

Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
234
235
    grond.check(
        config,
236
        event_names=event_names,
Sebastian Heimann's avatar
Sebastian Heimann committed
237
        target_string_ids=target_string_ids,
238
        show_plot=options.show_plot,
239
        show_waveforms=options.show_waveforms,
240
        n_random_synthetics=options.n_random_synthetics)
Sebastian Heimann's avatar
Sebastian Heimann committed
241
242


Sebastian Heimann's avatar
Sebastian Heimann committed
243
244
245
246
247
248
249
250
def command_go(args):
    def setup(parser):
        parser.add_option(
            '--force', dest='force', action='store_true',
            help='overwrite existing run directory')
        parser.add_option(
            '--status', dest='status', default='state',
            help='status output selection (choices: state, matrix)')
Sebastian Heimann's avatar
Sebastian Heimann committed
251
252
253
        parser.add_option(
            '--parallel', dest='nparallel', type='int', default=1,
            help='set number of events to process in parallel')
Sebastian Heimann's avatar
Sebastian Heimann committed
254
255

    parser, options, args = cl_parse('go', args, setup)
256
257
    if len(args) < 2:
        help_and_die(parser, 'missing arguments')
Sebastian Heimann's avatar
Sebastian Heimann committed
258
259

    config_path = args[0]
260
261
    event_names = args[1:]

Sebastian Heimann's avatar
Sebastian Heimann committed
262
263
264
265
266
267
    config = grond.read_config(config_path)
    if options.status == 'quiet':
        status = ()
    else:
        status = tuple(options.status.split(','))

Sebastian Heimann's avatar
Sebastian Heimann committed
268
269
    grond.go(
        config,
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
270
        event_names=event_names,
Sebastian Heimann's avatar
Sebastian Heimann committed
271
272
273
        force=options.force,
        status=status,
        nparallel=options.nparallel)
Sebastian Heimann's avatar
Sebastian Heimann committed
274
275
276


def command_forward(args):
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
277
    def setup(parser):
278
        pass
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
279
280

    parser, options, args = cl_parse('forward', args, setup)
281
282
    if len(args) < 1:
        help_and_die(parser, 'missing arguments')
Sebastian Heimann's avatar
Sebastian Heimann committed
283

284
    event_names = args[1:]
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
285

Sebastian Heimann's avatar
Sebastian Heimann committed
286
287
288
    if not event_names:
        help_and_die(parser, 'no event names given')

289
    run_path = args[0]
Sebastian Heimann's avatar
wip    
Sebastian Heimann committed
290
291
292
    grond.forward(
        run_path,
        event_names=event_names)
Sebastian Heimann's avatar
Sebastian Heimann committed
293
294
295
296
297
298
299
300
301
302


def command_harvest(args):
    def setup(parser):
        parser.add_option(
            '--force', dest='force', action='store_true',
            help='overwrite existing harvest directory')
        parser.add_option(
            '--neach', dest='neach', type=int, default=10,
            help='take NEACH best samples from each chain (default: 10)')
Sebastian Heimann's avatar
Sebastian Heimann committed
303
304
        parser.add_option(
            '--weed', dest='weed', type=int, default=0,
305
306
307
308
309
310
311
312
313
314
315
            help='weed out bootstrap samples with bad global performance. '
                 '0: no weeding (default), '
                 '1: only bootstrap chains where all NEACH best samples '
                 'global misfit is less than the global average misfit of all '
                 'NEACH best in all chains plus one standard deviation are '
                 'included in the harvest ensemble, '
                 '2: same as 1 but additionally individual samples are '
                 'removed if their global misfit is greater than the global '
                 'average misfit of all NEACH best in all chains, '
                 '3: harvesting is done on the global chain only, bootstrap '
                 'chains are excluded')
Sebastian Heimann's avatar
Sebastian Heimann committed
316
317
318
319
320
321

    parser, options, args = cl_parse('harvest', args, setup)
    if len(args) != 1:
        help_and_die(parser, 'no rundir')

    run_path, = args
Sebastian Heimann's avatar
Sebastian Heimann committed
322
323
324
325
326
    grond.harvest(
        run_path,
        force=options.force,
        nbest=options.neach,
        weed=options.weed)
Sebastian Heimann's avatar
Sebastian Heimann committed
327
328
329


def command_plot(args):
330
331
332
333
334
335
336
337
338
339
340

    def setup(parser):
        parser.add_option(
            '--save', dest='save', action='store_true', default=False,
            help='save figures to files')

        parser.add_option(
            '--format', '--formats', dest='formats', default='pdf',
            help='comma-separated list of ouptut formats (default: pdf)')

        parser.add_option(
341
342
            '--dpi', '--dpi', dest='dpi', type=float, default=120.,
            help='DPI setting for raster formats (default=120)')
343

344
345
346
347
348
349
350
351
352
353
354
    # plotnames_avail = plot.available_plotnames()
    # made explicit to avoid import of pyplot before backend can be chosen
    plotnames_avail = [
        'bootstrap',
        'sequence',
        'contributions',
        'jointpar',
        'hudson',
        'fits',
        'solution',
        'location']
355
356
357
358
359
360
361

    details = '''Available <plotnames> are: %s, or "all". Multiple plots are
selected by specifying a comma-separated list.''' % (
        ', '.join('"%s"' % x for x in plotnames_avail))

    parser, options, args = cl_parse('plot', args, setup, details)

Sebastian Heimann's avatar
Sebastian Heimann committed
362
363
364
    if len(args) != 2:
        help_and_die(parser, 'two arguments required')

365
366
367
368
369
370
    if args[0] == 'all':
        plotnames = plotnames_avail
    else:
        plotnames = args[0].split(',')

    formats = options.formats.split(',')
Sebastian Heimann's avatar
Sebastian Heimann committed
371
    dirname = args[1]
372

373
374
375
376
377
378
    if options.save:
        import matplotlib
        matplotlib.use('Agg')

    from grond import plot

379
380
381
382
383
384
385
    try:
        plot.plot_result(
            dirname, plotnames,
            save=options.save, formats=formats, dpi=options.dpi)

    except grond.GrondError, e:
        die(str(e))
Sebastian Heimann's avatar
Sebastian Heimann committed
386
387
388
389


def command_export(args):

Sebastian Heimann's avatar
Sebastian Heimann committed
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
    def setup(parser):
        parser.add_option(
            '--type', dest='type', metavar='TYPE',
            choices=('event', 'source', 'vector'),
            help='select type of objects to be exported. Choices: '
                 '"event" (default), "source", "vector".')

        parser.add_option(
            '--parameters', dest='parameters', metavar='PLIST',
            help='select parameters to be exported. PLIST is a '
                 'comma-separated list where each entry has the form '
                 '"<parameter>[.<measure>]". Available measures: "best", '
                 '"mean", "std", "minimum", "percentile16", "median", '
                 '"percentile84", "maximum".')

        parser.add_option(
            '--output', dest='filename', metavar='FILE',
            help='write output to FILE')

    parser, options, args = cl_parse('export', args, setup)
    if len(args) < 2:
        help_and_die(parser, 'arguments required')

    what = args[0]

    dirnames = args[1:]

    what_choices = ('best', 'mean', 'ensemble', 'stats')

    if what not in what_choices:
        help_and_die(
            parser,
            'invalid choice: %s (choose from %s)' % (
                repr(what), ', '.join(repr(x) for x in what_choices)))

    if options.parameters:
        pnames = options.parameters.split(',')
Sebastian Heimann's avatar
Sebastian Heimann committed
427
    else:
Sebastian Heimann's avatar
Sebastian Heimann committed
428
429
430
431
432
433
434
435
436
437
438
439
        pnames = None

    try:
        grond.export(
            what,
            dirnames,
            filename=options.filename,
            type=options.type,
            pnames=pnames)

    except grond.GrondError, e:
        die(str(e))
Sebastian Heimann's avatar
Sebastian Heimann committed
440
441


442
443
444
def command_qc_polarization(args):

    def setup(parser):
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
        parser.add_option(
            '--time-factor', dest='time_factor', type=float,
            metavar='NUMBER',
            default=0.5,
            help='set duration to extract before and after synthetic P phase '
                 'arrival, relative to 1/fmin. fmin is taken from the '
                 'selected target group in the config file (default=%default)')
        parser.add_option(
            '--distance-min', dest='distance_min', type=float,
            metavar='NUMBER',
            help='minimum event-station distance [m]')
        parser.add_option(
            '--distance-max', dest='distance_max', type=float,
            metavar='NUMBER',
            help='maximum event-station distance [m]')
        parser.add_option(
            '--depth-min', dest='depth_min', type=float,
            metavar='NUMBER',
            help='minimum station depth [m]')
        parser.add_option(
            '--depth-max', dest='depth_max', type=float,
            metavar='NUMBER',
            help='maximum station depth [m]')
        parser.add_option(
            '--picks', dest='picks_filename',
            metavar='FILENAME',
            help='add file with P picks in Snuffler marker format')
        parser.add_option(
            '--save', dest='output_filename',
            metavar='FILENAME.FORMAT',
            help='save output to file FILENAME.FORMAT')
        parser.add_option(
            '--dpi', dest='output_dpi', type=float, default=120.,
            metavar='NUMBER',
            help='DPI setting for raster formats (default=120)')
480
481
482
483
484

    parser, options, args = cl_parse('qc-polarization', args, setup)
    if len(args) != 3:
        help_and_die(parser, 'missing arguments')

485
486
487
488
489
490
    if options.output_filename:
        import matplotlib
        matplotlib.use('Agg')

    import grond.qc

491
492
493
494
495
496
497
498
    config_path, event_name, target_config_name = args

    config = grond.read_config(config_path)

    ds = config.get_dataset(event_name)

    engine = config.engine_config.get_engine()

499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
    nsl_to_time = None
    if options.picks_filename:
        markers = marker.load_markers(options.picks_filename)
        marker.associate_phases_to_events(markers)

        nsl_to_time = {}
        for m in markers:
            if isinstance(m, marker.PhaseMarker):
                ev = m.get_event()
                if ev is not None and ev.name == event_name:
                    nsl_to_time[m.one_nslc()[:3]] = m.tmin

        if not nsl_to_time:
            help_and_die(
                parser,
                'no markers associated with event "%s" found in file "%s"' % (
                    event_name, options.picks_filename))

517
518
519
520
521
522
523
524
525
526
527
528
529
    target_config_names_avail = []
    for target_config in config.target_configs:
        name = '%s.%s' % (target_config.super_group, target_config.group or '')
        if name == target_config_name:
            imc = target_config.inner_misfit_config
            fmin = imc.fmin
            fmax = imc.fmax
            ffactor = imc.ffactor

            store = engine.get_store(target_config.store_id)
            timing = '{cake:P|cake:p|cake:P\\|cake:p\\}'

            grond.qc.polarization(
530
531
532
533
534
535
536
537
538
                ds, store, timing, fmin=fmin, fmax=fmax, ffactor=ffactor,
                time_factor=options.time_factor,
                distance_min=options.distance_min,
                distance_max=options.distance_max,
                depth_min=options.depth_min,
                depth_max=options.depth_max,
                nsl_to_time=nsl_to_time,
                output_filename=options.output_filename,
                output_dpi=options.output_dpi)
539
540
541
542
543
544
545
546
547

            return

        target_config_names_avail.append(name)

        die('no target_config named "%s" found. Available: %s' % (
            target_config_name, ', '.join(target_config_names_avail)))


Sebastian Heimann's avatar
Sebastian Heimann committed
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
if __name__ == '__main__':

    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)