def check(self, show_progress=False):
if show_progress:
pbar = util.progressbar('checking store', self.config.nrecords)
problems = 0
for i, args in enumerate(self.config.iter_nodes()):
tr = self.get(args)
if tr and not tr.is_zero:
if not tr.begin_value == tr.data[0]:
logger.warn('wrong begin value for trace at %s '
'(data corruption?)' % str(args))
problems += 1
if not tr.end_value == tr.data[-1]:
logger.warn('wrong end value for trace at %s '
'(data corruption?)' % str(args))
problems += 1
if not num.all(num.isfinite(tr.data)):
logger.warn('nans or infs in trace at %s' % str(args))
problems += 1
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
return problems
def check(self, show_progress=False):
if show_progress:
pbar = util.progressbar('checking store', self.config.nrecords)
problems = 0
for i, args in enumerate(self.config.iter_nodes()):
tr = self.get(args)
if tr and not tr.is_zero:
if not tr.begin_value == tr.data[0]:
logger.warn('wrong begin value for trace at %s '
'(data corruption?)' % str(args))
problems += 1
if not tr.end_value == tr.data[-1]:
logger.warn('wrong end value for trace at %s '
'(data corruption?)' % str(args))
problems += 1
if not num.all(num.isfinite(tr.data)):
logger.warn('nans or infs in trace at %s' % str(args))
problems += 1
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
return problems
def dump_waveforms(self,
engine,
sources,
path,
tmin=None,
tmax=None,
overwrite=False):
path_waveforms = op.join(path, 'waveforms')
# gf.store.remake_dir(path_waveforms, force=overwrite)
path_traces = op.join(
path_waveforms, '%(wmin_year)s', '%(wmin_month)s', '%(wmin_day)s',
'waveform_%(network)s_%(station)s_' +
'%(location)s_%(channel)s_%(tmin)s_%(tmax)s.mseed')
tmin_all, tmax_all = self.get_time_range(sources)
tmin = tmin if tmin is not None else tmin_all
tmax = tmax if tmax is not None else tmax_all
tts = util.time_to_str
tinc = self.tinc or self.get_useful_time_increment(engine, sources)
tmin = math.floor(tmin / tinc) * tinc
tmax = math.ceil(tmax / tinc) * tinc
nwin = int(round((tmax - tmin) / tinc))
pbar = util.progressbar('Generating waveforms', nwin)
for iwin in range(nwin):
pbar.update(iwin)
tmin_win = max(tmin, tmin + iwin * tinc)
tmax_win = min(tmax, tmin + (iwin + 1) * tinc)
if tmax_win <= tmin_win:
continue
trs = self.get_waveforms(engine, sources, tmin_win, tmax_win)
try:
io.save(trs,
path_traces,
additional=dict(wmin_year=tts(tmin_win, format='%Y'),
wmin_month=tts(tmin_win, format='%m'),
wmin_day=tts(tmin_win, format='%d'),
wmin=tts(tmin_win,
format='%Y-%m-%d_%H-%M-%S'),
wmax_year=tts(tmax_win, format='%Y'),
wmax_month=tts(tmax_win, format='%m'),
wmax_day=tts(tmax_win, format='%d'),
wmax=tts(tmax_win,
format='%Y-%m-%d_%H-%M-%S')),
overwrite=overwrite)
except FileSaveError as e:
logger.debug('Waveform exists %s' % e)
pbar.finish()
return [path_waveforms]
def __init__(self, label, n):
self._label = label
self._n = n
self._bar = None
if show_progress:
self._bar = util.progressbar(label, self._n)
if update_progress:
update_progress(label, 0, self._n)
def __init__(self, label, n):
self._label = label
self._n = n
self._bar = None
if show_progress:
self._bar = util.progressbar(label, self._n)
if update_progress:
update_progress(label, 0, self._n)
def dump_waveforms(self, engine, sources, path,
tmin=None, tmax=None, overwrite=False):
path_waveforms = op.join(path, 'waveforms')
gf.store.remake_dir(path_waveforms, force=overwrite)
path_traces = op.join(
path_waveforms,
'%(wmin_year)s',
'%(wmin_month)s',
'%(wmin_day)s',
'waveform_%(network)s_%(station)s_' +
'%(location)s_%(channel)s_%(tmin)s_%(tmax)s.mseed')
tmin_all, tmax_all = self.get_time_range(sources)
tmin = tmin if tmin is not None else tmin_all
tmax = tmax if tmax is not None else tmax_all
tts = util.time_to_str
tinc = self.tinc or self.get_useful_time_increment(engine, sources)
tmin = math.floor(tmin / tinc) * tinc
tmax = math.ceil(tmax / tinc) * tinc
nwin = int(round((tmax - tmin) / tinc))
pbar = util.progressbar('Generating waveforms', nwin)
for iwin in range(nwin):
pbar.update(iwin)
tmin_win = max(tmin, tmin + iwin*tinc)
tmax_win = min(tmax, tmin + (iwin+1)*tinc)
if tmax_win <= tmin_win:
continue
trs = self.get_waveforms(engine, sources, tmin_win, tmax_win)
try:
io.save(
trs, path_traces,
additional=dict(
wmin_year=tts(tmin_win, format='%Y'),
wmin_month=tts(tmin_win, format='%m'),
wmin_day=tts(tmin_win, format='%d'),
wmin=tts(tmin_win, format='%Y-%m-%d_%H-%M-%S'),
wmax_year=tts(tmax_win, format='%Y'),
wmax_month=tts(tmax_win, format='%m'),
wmax_day=tts(tmax_win, format='%d'),
wmax=tts(tmax_win, format='%Y-%m-%d_%H-%M-%S')),
overwrite=overwrite)
except FileSaveError as e:
logger.debug('Waveform exists %s' % e)
pbar.finish()
return [path_waveforms]
def command_redeploy(args):
parser, options, args = cl_parse('redeploy', args)
if not len(args) == 2:
parser.print_help()
sys.exit(1)
source_store_dir, dest_store_dir = args
try:
source = gf.Store(source_store_dir)
except gf.StoreError as e:
die(e)
try:
gf.store.Store.create_dependants(dest_store_dir)
except gf.StoreError:
pass
try:
dest = gf.Store(dest_store_dir, 'w')
except gf.StoreError as e:
die(e)
show_progress = True
if show_progress:
pbar = util.progressbar('redeploying', dest.config.nrecords)
for i, args in enumerate(dest.config.iter_nodes()):
try:
tr = source.get(args, interpolation='off')
dest.put(args, tr)
except (gf.meta.OutOfBounds, gf.store.NotAllowedToInterpolate) as e:
logger.debug('skipping %s, (%s)' % (sindex(args), e))
except gf.store.StoreError as e:
logger.warn('cannot insert %s, (%s)' % (sindex(args), e))
if show_progress:
pbar.update(i + 1)
if show_progress:
pbar.finish()
def command_redeploy(args):
parser, options, args = cl_parse('redeploy', args)
if not len(args) == 2:
parser.print_help()
sys.exit(1)
source_store_dir, dest_store_dir = args
try:
source = gf.Store(source_store_dir)
except gf.StoreError as e:
die(e)
try:
gf.store.Store.create_dependants(dest_store_dir)
except gf.StoreError:
pass
try:
dest = gf.Store(dest_store_dir, 'w')
except gf.StoreError as e:
die(e)
show_progress = True
if show_progress:
pbar = util.progressbar('redeploying', dest.config.nrecords)
for i, args in enumerate(dest.config.iter_nodes()):
try:
tr = source.get(args, interpolation='off')
dest.put(args, tr)
except (gf.meta.OutOfBounds, gf.store.NotAllowedToInterpolate) as e:
logger.debug('skipping %s, (%s)' % (sindex(args), e))
except gf.store.StoreError as e:
logger.warn('cannot insert %s, (%s)' % (sindex(args), e))
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
def chopper_grouped(self, gather, progress=None, *args, **kwargs):
keys = self.gather_keys(gather)
if len(keys) == 0:
return
outer_group_selector = None
if 'group_selector' in kwargs:
outer_group_selector = kwargs['group_selector']
outer_trace_selector = None
if 'trace_selector' in kwargs:
outer_trace_selector = kwargs['trace_selector']
# the use of this gather-cache makes it impossible to modify the pile
# during chopping
gather_cache = {}
pbar = None
if progress is not None:
pbar = util.progressbar(progress, len(keys))
for ikey, key in enumerate(keys):
def tsel(tr):
return gather(tr) == key and (outer_trace_selector is None
or outer_trace_selector(tr))
def gsel(gr):
if gr not in gather_cache:
gather_cache[gr] = gr.gather_keys(gather)
return key in gather_cache[gr] and (
outer_group_selector is None or outer_group_selector(gr))
kwargs['trace_selector'] = tsel
kwargs['group_selector'] = gsel
for traces in self.chopper(*args, **kwargs):
yield traces
if pbar:
pbar.update(ikey + 1)
if pbar:
pbar.finish()
def chopper_grouped(self, gather, progress=None, *args, **kwargs):
keys = self.gather_keys(gather)
if len(keys) == 0:
return
outer_group_selector = None
if 'group_selector' in kwargs:
outer_group_selector = kwargs['group_selector']
outer_trace_selector = None
if 'trace_selector' in kwargs:
outer_trace_selector = kwargs['trace_selector']
# the use of this gather-cache makes it impossible to modify the pile
# during chopping
gather_cache = {}
pbar = None
if progress is not None:
pbar = util.progressbar(progress, len(keys))
for ikey, key in enumerate(keys):
def tsel(tr):
return gather(tr) == key and (outer_trace_selector is None or
outer_trace_selector(tr))
def gsel(gr):
if gr not in gather_cache:
gather_cache[gr] = gr.gather_keys(gather)
return key in gather_cache[gr] and (
outer_group_selector is None or outer_group_selector(gr))
kwargs['trace_selector'] = tsel
kwargs['group_selector'] = gsel
for traces in self.chopper(*args, **kwargs):
yield traces
if pbar:
pbar.update(ikey+1)
if pbar:
pbar.finish()
def make_decimated(self, decimate, config=None, force=False,
show_progress=False):
'''Create decimated version of GF store.
Create a downsampled version of the GF store. Downsampling is done for
the integer factor `decimate` which should be in the range [2,8]. If
`config` is ``None``, all traces of the GF store are decimated and held
available (i.e. the index mapping of the original store is used),
otherwise, a different spacial stepping can be specified by giving a
modified GF store configuration in `config` (see :py:meth:`create`).
Decimated GF sub-stores are created under the `decimated` subdirectory
within the GF store directory. Holding available decimated versions of
the GF store can save computation time, IO bandwidth, or decrease
memory footprint at the cost of increased disk space usage, when
computation are done for lower frequency signals.
'''
if not self._f_index:
self.open()
if not (2 <= decimate <= 8):
raise StoreError('decimate argument must be in the range [2,8]')
assert self.mode == 'r'
if config is None:
config = self.config
config = copy.deepcopy(config)
config.sample_rate = self.config.sample_rate / decimate
if decimate in self._decimated:
del self._decimated[decimate]
store_dir = self._decimated_store_dir(decimate)
if os.path.exists(store_dir):
if force:
shutil.rmtree(store_dir)
else:
raise CannotCreate('store already exists at %s' % store_dir)
store_dir_incomplete = store_dir + '-incomplete'
Store.create(store_dir_incomplete, config, force=force)
decimated = Store(store_dir_incomplete, 'w')
if show_progress:
pbar = util.progressbar('decimating store', self.config.nrecords)
for i, args in enumerate(decimated.config.iter_nodes()):
tr = self.get(args, decimate=decimate)
decimated.put(args, tr)
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
decimated.close()
shutil.move(store_dir_incomplete, store_dir)
self._decimated[decimate] = None
def command_export(args):
from subprocess import Popen, PIPE
try:
from tunguska import gfdb
except ImportError as err:
die('the kiwi tools must be installed to use this feature', err)
def setup(parser):
parser.add_option('--nchunks',
dest='nchunks',
type='int',
default=1,
metavar='N',
help='split output gfdb into N chunks')
parser, options, args = cl_parse('export', args, setup=setup)
show_progress = True
if len(args) not in (1, 2):
parser.print_help()
sys.exit(1)
target_path = args.pop()
if os.path.isdir(target_path):
target_path = os.path.join(target_path, 'kiwi_gfdb')
logger.warn('exported gfdb will be named as "%s.*"' % target_path)
source_store_dir = get_store_dir(args)
source = gf.Store(source_store_dir, 'r')
config = source.config
if not isinstance(config, gf.meta.ConfigTypeA):
die('only stores of type A can be exported to Kiwi format')
if os.path.isfile(target_path + '.index'):
die('destation already exists')
cmd = [
str(x) for x in [
'gfdb_build', target_path, options.nchunks, config.ndistances,
config.nsource_depths, config.ncomponents, config.deltat,
config.distance_delta, config.source_depth_delta,
config.distance_min, config.source_depth_min
]
]
p = Popen(cmd, stdin=PIPE)
p.communicate()
out_db = gfdb.Gfdb(target_path)
if show_progress:
pbar = util.progressbar('exporting',
config.nrecords / config.ncomponents)
for i, (z, x) in enumerate(config.iter_nodes(level=-1)):
data_out = []
for ig in range(config.ncomponents):
try:
tr = source.get((z, x, ig), interpolation='off')
data_out.append((tr.t, tr.data * config.factor))
except gf.store.StoreError as e:
logger.warn('cannot get %s, (%s)' % (sindex((z, x, ig)), e))
data_out.append(None)
# put a zero valued sample to no-data zero-traces at a compatible time
tmins = [
entry[0][0] for entry in data_out
if entry is not None and entry[0].size != 0
]
if tmins:
tmin = min(tmins)
for entry in data_out:
if entry is not None and entry[0].size == 0:
entry[0].resize(1)
entry[1].resize(1)
entry[0][0] = tmin
entry[1][0] = 0.0
out_db.put_traces_slow(x, z, data_out)
if show_progress:
pbar.update(i + 1)
if show_progress:
pbar.finish()
source.close()
def command_import(args):
try:
from tunguska import gfdb
except ImportError:
die('the kiwi tools must be installed to use this feature')
parser, options, args = cl_parse('import', args)
show_progress = True
if not len(args) == 2:
parser.print_help()
sys.exit(1)
source_path, dest_store_dir = args
if os.path.isdir(source_path):
source_path = pjoin(source_path, 'db')
source_path = re.sub(r'(\.\d+\.chunk|\.index)$', '', source_path)
db = gfdb.Gfdb(source_path)
config = gf.meta.ConfigTypeA(id='imported_gfs',
distance_min=db.firstx,
distance_max=db.firstx + (db.nx - 1) * db.dx,
distance_delta=db.dx,
source_depth_min=db.firstz,
source_depth_max=db.firstz +
(db.nz - 1) * db.dz,
source_depth_delta=db.dz,
sample_rate=1.0 / db.dt,
ncomponents=db.ng)
try:
gf.store.Store.create(dest_store_dir, config=config)
dest = gf.Store(dest_store_dir, 'w')
if show_progress:
pbar = util.progressbar(
'importing', dest.config.nrecords / dest.config.ncomponents)
for i, args in enumerate(dest.config.iter_nodes(level=-1)):
source_depth, distance = [float(x) for x in args]
traces = db.get_traces_pyrocko(distance, source_depth)
ig_to_trace = dict((tr.meta['ig'] - 1, tr) for tr in traces)
for ig in range(db.ng):
if ig in ig_to_trace:
tr = ig_to_trace[ig]
gf_tr = gf.store.GFTrace(tr.get_ydata(),
int(round(tr.tmin / tr.deltat)),
tr.deltat)
else:
gf_tr = gf.store.Zero
dest.put((source_depth, distance, ig), gf_tr)
if show_progress:
pbar.update(i + 1)
if show_progress:
pbar.finish()
dest.close()
except gf.StoreError as e:
die(e)
def command_export(args):
from subprocess import Popen, PIPE
try:
from tunguska import gfdb
except ImportError as err:
die('the kiwi tools must be installed to use this feature', err)
def setup(parser):
parser.add_option(
'--nchunks', dest='nchunks', type='int', default=1, metavar='N',
help='split output gfdb into N chunks')
parser, options, args = cl_parse('export', args, setup=setup)
show_progress = True
if len(args) not in (1, 2):
parser.print_help()
sys.exit(1)
target_path = args.pop()
if op.isdir(target_path):
target_path = op.join(target_path, 'kiwi_gfdb')
logger.warn('exported gfdb will be named as "%s.*"' % target_path)
source_store_dir = get_store_dir(args)
source = gf.Store(source_store_dir, 'r')
config = source.config
if not isinstance(config, gf.meta.ConfigTypeA):
die('only stores of type A can be exported to Kiwi format')
if op.isfile(target_path + '.index'):
die('destation already exists')
cmd = [str(x) for x in [
'gfdb_build',
target_path,
options.nchunks,
config.ndistances,
config.nsource_depths,
config.ncomponents,
config.deltat,
config.distance_delta,
config.source_depth_delta,
config.distance_min,
config.source_depth_min]]
p = Popen(cmd, stdin=PIPE)
p.communicate()
out_db = gfdb.Gfdb(target_path)
if show_progress:
pbar = util.progressbar(
'exporting', config.nrecords/config.ncomponents)
for i, (z, x) in enumerate(config.iter_nodes(level=-1)):
data_out = []
for ig in range(config.ncomponents):
try:
tr = source.get((z, x, ig), interpolation='off')
data_out.append((tr.t, tr.data * config.factor))
except gf.store.StoreError as e:
logger.warn('cannot get %s, (%s)' % (sindex((z, x, ig)), e))
data_out.append(None)
# put a zero valued sample to no-data zero-traces at a compatible time
tmins = [
entry[0][0]
for entry in data_out
if entry is not None and entry[0].size != 0]
if tmins:
tmin = min(tmins)
for entry in data_out:
if entry is not None and entry[0].size == 0:
entry[0].resize(1)
entry[1].resize(1)
entry[0][0] = tmin
entry[1][0] = 0.0
out_db.put_traces_slow(x, z, data_out)
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
source.close()
def command_import(args):
try:
from tunguska import gfdb
except ImportError:
die('the kiwi tools must be installed to use this feature')
parser, options, args = cl_parse('import', args)
show_progress = True
if not len(args) == 2:
parser.print_help()
sys.exit(1)
source_path, dest_store_dir = args
if op.isdir(source_path):
source_path = op.join(source_path, 'db')
source_path = re.sub(r'(\.\d+\.chunk|\.index)$', '', source_path)
db = gfdb.Gfdb(source_path)
config = gf.meta.ConfigTypeA(
id='imported_gfs',
distance_min=db.firstx,
distance_max=db.firstx + (db.nx-1) * db.dx,
distance_delta=db.dx,
source_depth_min=db.firstz,
source_depth_max=db.firstz + (db.nz-1) * db.dz,
source_depth_delta=db.dz,
sample_rate=1.0/db.dt,
ncomponents=db.ng
)
try:
gf.store.Store.create(dest_store_dir, config=config)
dest = gf.Store(dest_store_dir, 'w')
if show_progress:
pbar = util.progressbar(
'importing', dest.config.nrecords/dest.config.ncomponents)
for i, args in enumerate(dest.config.iter_nodes(level=-1)):
source_depth, distance = [float(x) for x in args]
traces = db.get_traces_pyrocko(distance, source_depth)
ig_to_trace = dict((tr.meta['ig']-1, tr) for tr in traces)
for ig in range(db.ng):
if ig in ig_to_trace:
tr = ig_to_trace[ig]
gf_tr = gf.store.GFTrace(
tr.get_ydata(),
int(round(tr.tmin / tr.deltat)),
tr.deltat)
else:
gf_tr = gf.store.Zero
dest.put((source_depth, distance, ig), gf_tr)
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
dest.close()
except gf.StoreError as e:
die(e)
def make_decimated(self, decimate, config=None, force=False,
show_progress=False):
'''Create decimated version of GF store.
Create a downsampled version of the GF store. Downsampling is done for
the integer factor `decimate` which should be in the range [2,8]. If
`config` is ``None``, all traces of the GF store are decimated and held
available (i.e. the index mapping of the original store is used),
otherwise, a different spacial stepping can be specified by giving a
modified GF store configuration in `config` (see :py:meth:`create`).
Decimated GF sub-stores are created under the `decimated` subdirectory
within the GF store directory. Holding available decimated versions of
the GF store can save computation time, IO bandwidth, or decrease
memory footprint at the cost of increased disk space usage, when
computation are done for lower frequency signals.
'''
if not self._f_index:
self.open()
if not (2 <= decimate <= 8):
raise StoreError('decimate argument must be in the range [2,8]')
assert self.mode == 'r'
if config is None:
config = self.config
config = copy.deepcopy(config)
config.sample_rate = self.config.sample_rate / decimate
if decimate in self._decimated:
del self._decimated[decimate]
store_dir = self._decimated_store_dir(decimate)
if os.path.exists(store_dir):
if force:
shutil.rmtree(store_dir)
else:
raise CannotCreate('store already exists at %s' % store_dir)
store_dir_incomplete = store_dir + '-incomplete'
Store.create(store_dir_incomplete, config, force=force)
decimated = Store(store_dir_incomplete, 'w')
if show_progress:
pbar = util.progressbar('decimating store', self.config.nrecords)
for i, args in enumerate(decimated.config.iter_nodes()):
tr = self.get(args, decimate=decimate)
decimated.put(args, tr)
if show_progress:
pbar.update(i+1)
if show_progress:
pbar.finish()
decimated.close()
shutil.move(store_dir_incomplete, store_dir)
self._decimated[decimate] = None
def ensure_waveforms(self, engine, sources, path, tmin=None, tmax=None):
path_waveforms = op.join(path, 'waveforms')
util.ensuredir(path_waveforms)
p = self._get_pile(path_waveforms)
nslc_ids = set(target.codes for target in self.get_targets())
def have_waveforms(tmin, tmax):
trs_have = p.all(
tmin=tmin, tmax=tmax,
load_data=False, degap=False,
trace_selector=lambda tr: tr.nslc_id in nslc_ids)
return any(tr.data_len() > 0 for tr in trs_have)
def add_files(paths):
p.load_files(paths, fileformat='mseed', show_progress=False)
path_traces = op.join(
path_waveforms,
'%(wmin_year)s',
'%(wmin_month)s',
'%(wmin_day)s',
'waveform_%(network)s_%(station)s_' +
'%(location)s_%(channel)s_%(tmin)s_%(tmax)s.mseed')
tmin_all, tmax_all = self.get_time_range(sources)
tmin = tmin if tmin is not None else tmin_all
tmax = tmax if tmax is not None else tmax_all
tts = util.time_to_str
tinc = self.tinc or self.get_useful_time_increment(engine, sources)
tmin = math.floor(tmin / tinc) * tinc
tmax = math.ceil(tmax / tinc) * tinc
nwin = int(round((tmax - tmin) / tinc))
pbar = None
for iwin in range(nwin):
tmin_win = tmin + iwin*tinc
tmax_win = tmin + (iwin+1)*tinc
if have_waveforms(tmin_win, tmax_win):
continue
if pbar is None:
pbar = util.progressbar('Generating waveforms', (nwin-iwin))
pbar.update(iwin)
trs = self.get_waveforms(engine, sources, tmin_win, tmax_win)
try:
wpaths = io.save(
trs, path_traces,
additional=dict(
wmin_year=tts(tmin_win, format='%Y'),
wmin_month=tts(tmin_win, format='%m'),
wmin_day=tts(tmin_win, format='%d'),
wmin=tts(tmin_win, format='%Y-%m-%d_%H-%M-%S'),
wmax_year=tts(tmax_win, format='%Y'),
wmax_month=tts(tmax_win, format='%m'),
wmax_day=tts(tmax_win, format='%d'),
wmax=tts(tmax_win, format='%Y-%m-%d_%H-%M-%S')))
for wpath in wpaths:
logger.debug('Generated file: %s' % wpath)
add_files(wpaths)
except FileSaveError as e:
raise ScenarioError(str(e))
if pbar is not None:
pbar.finish()