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Commit 0d8e2b83 authored by Marius Isken's avatar Marius Isken
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Merge branch 'master' of https://gitext.gfz-potsdam.de/heimann/grond

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README.md
View file @ 0d8e2b83
# Grond
*What do you want to bust today?!*
A bootstrap-based probabilistic battering ram to explore solution spaces in
earthquake source parameter estimation problems.
## Installation
First, install [Pyrocko](http://pyrocko.org/current/install.html),
then install Grond:
```bash
git clone https://gitext.gfz-potsdam.de/heimann/grond.git
cd grond
sudo python setup.py install
```
## Updating an existing installation
```bash
cd grond # change to the directory where you cloned grond to initially
git pull origin master
sudo python setup.py install
```
## Basic usage
Grond can be run as a command line tool or by calling Grond's library functions
from a Python script. To get a brief description on available options of
Grond's command line tool, run `grond --help` or `grond <subcommand> --help`.
Once dataset and configuration are ready, the command
`grond go <configfile> <eventname>` starts the optimization algorithm for a
selected event. Before running the optimization, to debug problems with the
dataset and configuration, use `grond check <configfile> <eventname>`. To get
a list of event names available in a configured setup, run
`grond events <configfile>`.
During the optimization, results are aggregated in a directory,
referred to in the configuration as `<rundir>`. To visualize the results run
`grond plot <plotnames> <rundir>`. The results can be exported in various way
by running the subcommand `grond export <what> <rundir>`.
## Example configuration file
......@@ -9,7 +49,7 @@
--- !grond.Config
# Path, where to store output (run-directories)
rundir_template: 'gruns/%(problem_name)s.run'
rundir_template: 'gruns/${problem_name}.run'
# -----------------------------------------------------------------------------
......@@ -19,20 +59,23 @@ rundir_template: 'gruns/%(problem_name)s.run'
dataset_config: !grond.DatasetConfig
# List of files with station coordinates
stations_stationxml_paths: [meta/gfz2015sfdd/responses.stationxml]
stations_stationxml_paths:
- 'events/${event_name}/responses.stationxml'
# File with hypocenter information and possibly reference solution
events_path: catalogs/gfz2015sfdd.txt
events_path: 'events/${event_name}/event.txt'
# List of directories with raw waveform data
waveform_paths: [data/gfz2015sfdd/raw]
waveform_paths:
- 'data/${event_name}/raw'
# List of files with instrument response information
responses_stationxml_paths: [meta/gfz2015sfdd/responses.stationxml]
responses_stationxml_paths:
- 'meta/${event_name}/responses.stationxml'
# List with station/channel codes to exclude
blacklist: [OTAV, RCBR, PTGA, AXAS2, SNAA, PAYG, RAR, SDV, VAL, XMAS, ODZ,
MSVF, SHEL, SUR, ROSA, 'IU.PTCN.00.T', 'C1.VA02..T', RPN]
Z51A, MSVF, SHEL, SUR, ROSA, 'IU.PTCN.00.T', 'C1.VA02..T', RPN]
# -----------------------------------------------------------------------------
......@@ -46,7 +89,8 @@ engine_config: !grond.EngineConfig
gf_stores_from_pyrocko_config: false
# List of directories with GF stores
gf_store_superdirs: ['gf_stores']
gf_store_superdirs:
- 'gf_stores'
# -----------------------------------------------------------------------------
......@@ -61,10 +105,10 @@ target_configs:
- !grond.TargetConfig
# Name of the super-group to which this contribution belongs
super_group: time_domain
super_group: 'time_domain'
# Name of the group to which this contribution belongs
group: rayleigh
group: 'rayleigh'
# Minimum distance of stations to be considered
distance_min: 1000e3
......@@ -73,7 +117,7 @@ target_configs:
distance_max: 10000e3
# List with names of channels to be considered
channels: [Z]
channels: ['Z']
# How to weight stations from this contribution in the global misfit
weight: 1.0
......@@ -82,49 +126,49 @@ target_configs:
inner_misfit_config: !grond.InnerMisfitConfig
# Frequency band [Hz] of acausal filter (flat part of frequency taper)
fmin: 0.001
fmax: 0.005
fmin: 0.002
fmax: 0.008
# Factor defining fall-off of frequency taper
# (zero at fmin/ffactor, fmax*ffactor)
ffactor: 1.5
# Time window to include in the data fitting. Times can be defined offset
# to given phase arrivals. E.g. 'begin-600' would mean 600 s before arrival
# to given phase arrivals. E.g. 'begin-100' would mean 100 s before arrival
# of the phase named 'begin', which must be defined in the travel time
# tables in the GF store.
tmin: 'begin-600'
tmax: 'end+600'
tmin: '{stored:begin}-100'
tmax: '{stored:end}+100'
# How to fit the data (available choices: 'time_domain',
# 'frequency_domain', 'absolute', 'envelope', 'cc_max_norm')
domain: time_domain
domain: 'time_domain'
# How to interpolate the Green's functions (available choices:
# 'nearest_neighbor', 'multilinear')
interpolation: nearest_neighbor
interpolation: 'nearest_neighbor'
# Name of GF store to use
store_id: global_20s_shallow
store_id: 'global_20s_shallow'
# A second contribution to the misfit function (for descriptions, see above)
- !grond.TargetConfig
super_group: time_domain
group: love
super_group: 'time_domain'
group: 'love'
distance_min: 1000e3
distance_max: 10000e3
channels: [T]
channels: ['T']
weight: 1.0
inner_misfit_config: !grond.InnerMisfitConfig
fmin: 0.001
fmax: 0.005
fmin: 0.002
fmax: 0.008
ffactor: 1.5
tmin: 'begin-600'
tmax: 'end+600'
domain: time_domain
interpolation: nearest_neighbor
store_id: global_20s_shallow
tmin: '{stored:begin}-100'
tmax: '{stored:end}+100'
domain: 'time_domain'
interpolation: 'nearest_neighbor'
store_id: 'global_20s_shallow'
# -----------------------------------------------------------------------------
......@@ -135,7 +179,7 @@ target_configs:
problem_config: !grond.CMTProblemConfig
# Name used when creating output directory
name_template: cmt_surface_wave_%(event_name)s
name_template: 'cmt_surface_wave_${event_name}'
# Definition of model parameter space to be searched in the optimization
ranges:
......@@ -170,7 +214,7 @@ problem_config: !grond.CMTProblemConfig
nbootstrap: 100
# Type of moment tensor to restrict to (choices: 'full', 'deviatoric')
mt_type: deviatoric
mt_type: 'deviatoric'
# Whether to apply automatic weighting to balance the effects of geometric
# spreading etc.
......@@ -184,9 +228,9 @@ problem_config: !grond.CMTProblemConfig
solver_config: !grond.SolverConfig
# Distribution used when drawing new candidate models (choices: 'normal',
# 'multivariate_normal'). Used in 'transition', 'explorative', and
# 'non_explorative' phase
sampler_distribution: normal
# 'multivariate_normal') (used in 'transition', 'explorative', and
# 'non_explorative' phase)
sampler_distribution: 'normal'
# Number of iterations to operate in 'uniform' mode
niter_uniform: 1000
......
apps/grond
View file @ 0d8e2b83
......@@ -24,22 +24,24 @@ def d2u(d):
subcommand_descriptions = {
'init': 'print example configuration',
'events': 'print available event names for given configuration',
'check': 'check data and configuration',
'go': 'run Grond optimization',
'forward': 'run forward modelling',
'harvest': 'manually run harvesting',
'map-geometry': 'make station map',
'plot': 'plot optimization result',
'export': 'export results',
}
subcommand_usages = {
'init': 'init [options]',
'check': 'check <configfile> [options]',
'go': 'go <configfile> [options]',
'forward': 'forward <rundir> [options]',
'events': 'events <configfile>',
'check': 'check <configfile> <eventnames> ... [options]',
'go': 'go <configfile> <eventnames> ... [options]',
'forward': (
'forward <rundir> [options]',
'forward <configfile> <eventnames> ... [options]'),
'harvest': 'harvest <rundir> [options]',
'map-geometry': 'map-geometry <configfile> [options]',
'plot': 'plot <plotnames> <rundir> [options]',
'export': 'export (best|mean|ensemble|stats) <rundirs> ... [options]',
}
......@@ -56,11 +58,11 @@ usage = '''%(program_name)s <subcommand> [options] [--] <arguments> ...
Subcommands:
init %(init)s
events %(events)s
check %(check)s
go %(go)s
forward %(forward)s
harvest %(harvest)s
map-geometry %(map_geometry)s
plot %(plot)s
export %(export)s
......@@ -79,9 +81,9 @@ def add_common_options(parser):
type='choice',
choices=('critical', 'error', 'warning', 'info', 'debug'),
default='info',
help ='set logger level to '
'"critical", "error", "warning", "info", or "debug". '
'Default is "%default".')
help='set logger level to '
'"critical", "error", "warning", "info", or "debug". '
'Default is "%default".')
def process_common_options(options):
......@@ -174,33 +176,68 @@ def command_init(args):
print config
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
def command_check(args):
def setup(parser):
parser.add_option(
'--event', dest='event_name', metavar='EVENTNAME',
help='process only event EVENTNAME')
'--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.')
parser, options, args = cl_parse('check', args, setup)
if len(args) != 1:
help_and_die(parser, 'no config file given')
parser.add_option(
'--plot', dest='show_plot', action='store_true',
help='plot sample synthetics and data.')
parser.add_option(
'--waveforms', dest='show_waveforms', action='store_true',
help='show raw, restituted, projected, and processed waveforms')
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.')
event_names = None
if options.event_name:
event_names = [options.event_name]
parser, options, args = cl_parse('check', args, setup)
if len(args) < 2:
help_and_die(parser, 'missing arguments')
config_path = args[0]
event_names = args[1:]
config = grond.read_config(config_path)
target_string_ids = None
if options.target_string_ids:
target_string_ids = options.target_string_ids.split(',')
grond.check(
config,
event_names=event_names)
event_names=event_names,
target_string_ids=target_string_ids,
show_plot=options.show_plot,
show_waveforms=options.show_waveforms,
n_random_synthetics=options.n_random_synthetics)
def command_go(args):
def setup(parser):
parser.add_option(
'--event', dest='event_name', metavar='EVENTNAME',
help='process only event EVENTNAME')
parser.add_option(
'--force', dest='force', action='store_true',
help='overwrite existing run directory')
......@@ -212,20 +249,18 @@ def command_go(args):
help='set number of events to process in parallel')
parser, options, args = cl_parse('go', args, setup)
if len(args) != 1:
help_and_die(parser, 'no config file given')
if len(args) < 2:
help_and_die(parser, 'missing arguments')
config_path = args[0]
event_names = args[1:]
config = grond.read_config(config_path)
if options.status == 'quiet':
status = ()
else:
status = tuple(options.status.split(','))
event_names = None
if options.event_name:
event_names = [options.event_name]
grond.go(
config,
event_names=event_names,
......@@ -236,19 +271,18 @@ def command_go(args):
def command_forward(args):
def setup(parser):
parser.add_option(
'--event', dest='event_name', metavar='EVENTNAME',
help='process only event EVENTNAME')
pass
parser, options, args = cl_parse('forward', args, setup)
if len(args) != 1:
help_and_die(parser, 'incorrect number of arguments')
if len(args) < 1:
help_and_die(parser, 'missing arguments')
event_names = None
if options.event_name:
event_names = [options.event_name]
event_names = args[1:]
run_path, = args
if not event_names:
help_and_die(parser, 'no event names given')
run_path = args[0]
grond.forward(
run_path,
event_names=event_names)
......@@ -278,19 +312,6 @@ def command_harvest(args):
weed=options.weed)
def command_map_geometry(args):
from grond import plot
parser, options, args = cl_parse('map-geometry', args)
if len(args) != 2:
help_and_die(parser, 'two arguments required')
config_path = args[0]
output_path = args[1]
config = grond.read_config(config_path)
plot.map_geometry(config, output_path)
def command_plot(args):
from grond import plot
......@@ -304,8 +325,8 @@ def command_plot(args):
help='comma-separated list of ouptut formats (default: pdf)')
parser.add_option(
'--dpi', '--dpi', dest='dpi', type=float, default=72.,
help='DPI setting for raster formats (default=72)')
'--dpi', '--dpi', dest='dpi', type=float, default=120.,
help='DPI setting for raster formats (default=120)')
plotnames_avail = plot.available_plotnames()
......
src/__init__.py
View file @ 0d8e2b83
from core import * # noqa
from cmt import * # noqa
from double_dc import * # noqa
from dataset import * # noqa
src/cmt.py
View file @ 0d8e2b83
......@@ -37,7 +37,6 @@ class CMTProblem(core.Problem):
core.Parameter('rel_moment_iso', label='$M_{0}^{ISO}/M_{0}$'),
core.Parameter('rel_moment_clvd', label='$M_{0}^{CLVD}/M_{0}$')]
base_source = gf.Source.T()
targets = List.T(core.MisfitTarget.T())
ranges = Dict.T(String.T(), gf.Range.T())
......@@ -164,28 +163,45 @@ class CMTProblem(core.Problem):
return out
def evaluate(self, x, result_mode='sparse'):
def evaluate(self, x, result_mode='sparse', mask=None):
source = self.unpack(x)
engine = self.get_engine()
for target in self.targets:
target.set_result_mode(result_mode)
resp = engine.process(source, self.targets)
if mask is not None:
assert len(mask) == len(self.targets)
targets_ok = [
target for (target, ok) in zip(self.targets, mask) if ok]
else:
targets_ok = self.targets
data = []
results = []
for target, result in zip(self.targets, resp.results_list[0]):
resp = engine.process(source, targets_ok)
if mask is not None:
ires_ok = 0
results = []
for target, ok in zip(self.targets, mask):
if ok:
results.append(resp.results_list[0][ires_ok])
ires_ok += 1
else:
results.append(
gf.SeismosizerError(
'skipped because of previous failure'))
else:
results = list(resp.results_list[0])
data = []
for target, result in zip(self.targets, results):
if isinstance(result, gf.SeismosizerError):
logger.debug(
'%s.%s.%s.%s: %s' % (target.codes + (str(result),)))
data.append((None, None))
results.append(None)
else:
data.append((result.misfit_value, result.misfit_norm))
results.append(result)
ms, ns = num.array(data, dtype=num.float).T
if result_mode == 'full':
......@@ -200,7 +216,7 @@ class CMTProblem(core.Problem):
resp = engine.process(source, plain_targets)
results = []
for target, result in zip(self.targets, resp.result_list[0]):
for target, result in zip(self.targets, resp.results_list[0]):
if isinstance(result, gf.SeismosizerError):
logger.debug(
'%s.%s.%s.%s: %s' % (target.codes + (str(result),)))
......@@ -232,7 +248,6 @@ class CMTProblem(core.Problem):
def inter_group_weights2(self, ns):
group, ngroups = self.get_group_mask()
ws = num.zeros(ns.shape)
for igroup in xrange(ngroups):
mask = group == igroup
......@@ -269,7 +284,6 @@ class CMTProblem(core.Problem):
def global_misfits(self, misfits):
ws = self.get_target_weights()[num.newaxis, :] * \
self.inter_group_weights2(misfits[:, :, 1])
gms = num.sqrt(num.nansum((ws*misfits[:, :, 0])**2, axis=1) /
num.nansum((ws*misfits[:, :, 1])**2, axis=1))
return gms
......@@ -303,7 +317,7 @@ class CMTProblemConfig(core.ProblemConfig):
event_time=util.time_to_str(event.time))
problem = CMTProblem(
name=self.name_template % subs,
name=core.expand_template(self.name_template, subs),
apply_balancing_weights=self.apply_balancing_weights,
base_source=base_source,
targets=targets,
......
src/core.py
View file @ 0d8e2b83
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src/dataset.py
View file @ 0d8e2b83
import copy
import logging
from collections import defaultdict
import numpy as num
from pyrocko import util, pile, model, config, trace, snuffling, gui_util
from pyrocko import util, pile, model, config, trace, \
marker as pmarker
from pyrocko.fdsn import enhanced_sacpz, station as fs
from pyrocko.guts import Object, Tuple, String, Float, dump_all, load_all
......@@ -16,11 +18,22 @@ class InvalidObject(Exception):
class NotFound(Exception):
def __init__(self, *value):
self.value = value
def __init__(self, reason, codes=None, time_range=None):
self.reason = reason
self.time_range = time_range
self.codes = codes
def __str__(self):
return ' '.join([str(v) for v in self.value])
s = self.reason
if self.codes:
s += ' (%s)' % '.'.join(self.codes)
if self.time_range:
s += ' (%s - %s)' % (
util.time_to_str(self.time_range[0]),
util.time_to_str(self.time_range[1]))
return s
class DatasetError(Exception):
......@@ -47,7 +60,7 @@ def dump_station_corrections(station_corrections, filename):
class Dataset(object):
def __init__(self):
def __init__(self, event_name=None):
self.events = []
self.pile = pile.Pile()
self.stations = {}
......@@ -66,6 +79,7 @@ class Dataset(object):
self.synthetic_test = None
self._picks = None
self._cache = {}
self._event_name = event_name
def empty_cache(self):
self._cache = {}
......@@ -84,15 +98,20 @@ class Dataset(object):
self.stations[station.nsl()] = station
if pyrocko_stations_filename is not None:
logger.debug('Loading stations from file %s'
% pyrocko_stations_filename)
logger.debug(
'Loading stations from file %s' %
pyrocko_stations_filename)
for station in model.load_stations(pyrocko_stations_filename):
self.stations[station.nsl()] = station
if stationxml_filenames is not None and len(stationxml_filenames) > 0:
logger.debug('Loading stations from StationXML file %s'
% stationxml_filenames)
for stationxml_filename in stationxml_filenames:
logger.debug(
'Loading stations from StationXML file %s' %
stationxml_filename)
sx = fs.load_xml(filename=stationxml_filename)
for station in sx.get_pyrocko_stations():
self.stations[station.nsl()] = station
......@@ -116,7 +135,7 @@ class Dataset(object):
fileformat=fileformat,
show_progress=show_progress)
def add_responses(self, sacpz_dirname=None, stationxml_filenames=None):
def add_responses(self, sacpz_dirname=None, stationxml_filenames=None):
if sacpz_dirname:
logger.debug('Loading SAC PZ responses from %s' % sacpz_dirname)
for x in enhanced_sacpz.iload_dirname(sacpz_dirname):
......@@ -124,13 +143,15 @@ class Dataset(object):
if stationxml_filenames:
for stationxml_filename in stationxml_filenames:
logger.debug('Loading StationXML responses from %s' %
logger.debug(
'Loading StationXML responses from %s' %
stationxml_filename)
self.responses_stationxml.append(
fs.load_xml(filename=stationxml_filename))
def add_clippings(self, markers_filename):
markers = snuffling.load_markers(markers_filename)
markers = pmarker.load_markers(markers_filename)
clippings = {}
for marker in markers:
nslc = marker.one_nslc()
......@@ -151,15 +172,27 @@ class Dataset(object):