def run_as_update(self, options):
"""Updates data.
Parameters
----------
options: dictionary
The dictionary of all the command line arguments. Could in theory
contain other options passed in by the controller.
Notes
-----
Finds gaps in the target data, and if there's new data in the input
source, calls run with the start/end time of a given gap to fill
in.
It checks the start of the target data, and if it's missing, and
there's new data available, it backs up the starttime/endtime,
and recursively calls itself, to check the previous period, to see
if new data is available there as well. Calls run for each new
period, oldest to newest.
"""
algorithm = self._algorithm
input_channels = options.inchannels or \
algorithm.get_input_channels()
output_channels = options.outchannels or \
algorithm.get_output_channels()
# request output to see what has already been generated
output_timeseries = self._get_output_timeseries(
observatory=options.observatory,
starttime=options.starttime,
endtime=options.endtime,
channels=output_channels)
delta = output_timeseries[0].stats.delta
# find gaps in output, so they can be updated
output_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(output_timeseries))
for output_gap in output_gaps:
input_timeseries = self._get_input_timeseries(
observatory=options.observatory,
starttime=output_gap[0],
endtime=output_gap[1],
channels=input_channels)
if not algorithm.can_produce_data(
starttime=output_gap[0],
endtime=output_gap[1],
stream=input_timeseries):
continue
# check for fillable gap at start
if output_gap[0] == options.starttime:
# found fillable gap at start, recurse to previous interval
interval = options.endtime - options.starttime
starttime = options.starttime - interval - delta
endtime = options.starttime - delta
options.starttime = starttime
options.endtime = endtime
self.run_as_update(options)
# fill gap
options.starttime = output_gap[0]
options.endtime = output_gap[1]
self.run(options)
def run_as_update(self, options):
"""Updates data.
Parameters
----------
options: dictionary
The dictionary of all the command line arguments. Could in theory
contain other options passed in by the controller.
Notes
-----
Finds gaps in the target data, and if there's new data in the input
source, calls run with the start/end time of a given gap to fill
in.
It checks the start of the target data, and if it's missing, and
there's new data available, it backs up the starttime/endtime,
and recursively calls itself, to check the previous period, to see
if new data is available there as well. Calls run for each new
period, oldest to newest.
"""
algorithm = self._algorithm
input_channels = options.inchannels or \
algorithm.get_input_channels()
output_channels = options.outchannels or \
algorithm.get_output_channels()
# request output to see what has already been generated
output_timeseries = self._get_output_timeseries(
observatory=options.observatory,
starttime=options.starttime,
endtime=options.endtime,
channels=output_channels)
delta = output_timeseries[0].stats.delta
# find gaps in output, so they can be updated
output_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(output_timeseries))
for output_gap in output_gaps:
input_timeseries = self._get_input_timeseries(
observatory=options.observatory,
starttime=output_gap[0],
endtime=output_gap[1],
channels=input_channels)
if not algorithm.can_produce_data(starttime=output_gap[0],
endtime=output_gap[1],
stream=input_timeseries):
continue
# check for fillable gap at start
if output_gap[0] == options.starttime:
# found fillable gap at start, recurse to previous interval
interval = options.endtime - options.starttime
starttime = options.starttime - interval - delta
endtime = options.starttime - delta
options.starttime = starttime
options.endtime = endtime
self.run_as_update(options)
# fill gap
options.starttime = output_gap[0]
options.endtime = output_gap[1]
self.run(options)
def test_get_stream_gaps():
"""geomag.TimeseriesUtility_test.test_get_stream_gaps
confirms that gaps are found in a stream
"""
stream = Stream([
__create_trace('H', [numpy.nan, 1, 1, numpy.nan, numpy.nan]),
__create_trace('Z', [0, 0, 0, 1, 1, 1])
])
for trace in stream:
# set time of first sample
trace.stats.starttime = UTCDateTime('2015-01-01T00:00:00Z')
# set sample rate to 1 second
trace.stats.delta = 1
# find gaps
gaps = TimeseriesUtility.get_stream_gaps(stream)
assert_equals(len(gaps['H']), 2)
# gap at start of H
gap = gaps['H'][0]
assert_equals(gap[0], UTCDateTime('2015-01-01T00:00:00Z'))
assert_equals(gap[1], UTCDateTime('2015-01-01T00:00:00Z'))
# gap at end of H
gap = gaps['H'][1]
assert_equals(gap[0], UTCDateTime('2015-01-01T00:00:03Z'))
assert_equals(gap[1], UTCDateTime('2015-01-01T00:00:04Z'))
# no gaps in Z channel
assert_equals(len(gaps['Z']), 0)
def can_produce_data(self, starttime, endtime, stream):
"""Can Product data
Parameters
----------
starttime: UTCDateTime
start time of requested output
end : UTCDateTime
end time of requested output
stream: obspy.core.Stream
The input stream we want to make certain has data for the algorithm
"""
input_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(stream))
for input_gap in input_gaps:
# Check for gaps that include the entire range
if (starttime >= input_gap[0] and
starttime <= input_gap[1] and
endtime < input_gap[2]):
return False
return True
def test_get_trace_gaps():
"""geomag.TimeseriesUtility_test.test_get_trace_gaps
confirm that gaps are found in a trace
"""
trace = __create_trace('H', [1, 1, numpy.nan, numpy.nan, 0, 1])
# set time of first sample
trace.stats.starttime = UTCDateTime('2015-01-01T00:00:00Z')
# set sample rate to 1 minute
trace.stats.delta = 60
# find gap
gaps = TimeseriesUtility.get_trace_gaps(trace)
assert_equals(len(gaps), 1)
gap = gaps[0]
assert_equals(gap[0], UTCDateTime('2015-01-01T00:02:00Z'))
assert_equals(gap[1], UTCDateTime('2015-01-01T00:03:00Z'))
def test_get_merged_gaps():
"""geomag.TimeseriesUtility_test.test_get_merged_gaps
confirm that gaps are merged
"""
merged = TimeseriesUtility.get_merged_gaps({
'H': [
# gap for 2 seconds, that starts after next gap
[
UTCDateTime('2015-01-01T00:00:01Z'),
UTCDateTime('2015-01-01T00:00:03Z'),
UTCDateTime('2015-01-01T00:00:04Z')
]
],
# gap for 1 second, that occurs before previous gap
'Z': [
[
UTCDateTime('2015-01-01T00:00:00Z'),
UTCDateTime('2015-01-01T00:00:00Z'),
UTCDateTime('2015-01-01T00:00:01Z')
],
[
UTCDateTime('2015-01-01T00:00:05Z'),
UTCDateTime('2015-01-01T00:00:07Z'),
UTCDateTime('2015-01-01T00:00:08Z')
],
]
})
assert_equals(len(merged), 2)
# first gap combines H and Z gaps
gap = merged[0]
assert_equals(gap[0], UTCDateTime('2015-01-01T00:00:00Z'))
assert_equals(gap[1], UTCDateTime('2015-01-01T00:00:03Z'))
# second gap is second Z gap
gap = merged[1]
assert_equals(gap[0], UTCDateTime('2015-01-01T00:00:05Z'))
assert_equals(gap[1], UTCDateTime('2015-01-01T00:00:07Z'))
def run_as_update(self, options, update_count=0):
"""Updates data.
Parameters
----------
options: dictionary
The dictionary of all the command line arguments. Could in theory
contain other options passed in by the controller.
Notes
-----
Finds gaps in the target data, and if there's new data in the input
source, calls run with the start/end time of a given gap to fill
in.
It checks the start of the target data, and if it's missing, and
there's new data available, it backs up the starttime/endtime,
and recursively calls itself, to check the previous period, to see
if new data is available there as well. Calls run for each new
period, oldest to newest.
"""
# If an update_limit is set, make certain we don't step past it.
if options.update_limit != 0:
if update_count >= options.update_limit:
return
print >> sys.stderr, 'checking gaps', \
options.starttime, options.endtime
algorithm = self._algorithm
input_channels = options.inchannels or \
algorithm.get_input_channels()
output_channels = options.outchannels or \
algorithm.get_output_channels()
# request output to see what has already been generated
output_timeseries = self._get_output_timeseries(
observatory=options.observatory,
starttime=options.starttime,
endtime=options.endtime,
channels=output_channels)
if len(output_timeseries) > 0:
# find gaps in output, so they can be updated
output_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(output_timeseries))
else:
output_gaps = [[
options.starttime,
options.endtime,
# next sample time not used
None
]]
for output_gap in output_gaps:
input_timeseries = self._get_input_timeseries(
observatory=options.observatory,
starttime=output_gap[0],
endtime=output_gap[1],
channels=input_channels)
if not algorithm.can_produce_data(starttime=output_gap[0],
endtime=output_gap[1],
stream=input_timeseries):
continue
# check for fillable gap at start
if output_gap[0] == options.starttime:
# found fillable gap at start, recurse to previous interval
interval = options.endtime - options.starttime
starttime = options.starttime - interval
endtime = options.starttime - 1
options.starttime = starttime
options.endtime = endtime
self.run_as_update(options, update_count + 1)
# fill gap
options.starttime = output_gap[0]
options.endtime = output_gap[1]
print >> sys.stderr, 'processing', \
options.starttime, options.endtime
self.run(options, input_timeseries)
def put_timeseries(self,
timeseries,
starttime=None,
endtime=None,
channels=None,
type=None,
interval=None):
"""Store timeseries data.
Parameters
----------
timeseries : obspy.core.Stream
stream containing traces to store.
starttime : UTCDateTime
time of first sample in timeseries to store.
uses first sample if unspecified.
endtime : UTCDateTime
time of last sample in timeseries to store.
uses last sample if unspecified.
channels : array_like
list of channels to store, optional.
uses default if unspecified.
type : {'definitive', 'provisional', 'quasi-definitive', 'variation'}
data type, optional.
uses default if unspecified.
interval : {'daily', 'hourly', 'minute', 'monthly', 'second'}
data interval, optional.
uses default if unspecified.
Raises
------
TimeseriesFactoryException
if any errors occur.
"""
if len(timeseries) == 0:
# no data to put
return
if not self.urlTemplate.startswith('file://'):
raise TimeseriesFactoryException('Only file urls are supported')
channels = channels or self.channels
type = type or self.type
interval = interval or self.interval
stats = timeseries[0].stats
delta = stats.delta
observatory = stats.station
starttime = starttime or stats.starttime
endtime = endtime or stats.endtime
urlIntervals = Util.get_intervals(starttime=starttime,
endtime=endtime,
size=self.urlInterval)
for urlInterval in urlIntervals:
url = self._get_url(observatory=observatory,
date=urlInterval['start'],
type=type,
interval=interval,
channels=channels)
url_data = timeseries.slice(
starttime=urlInterval['start'],
# subtract delta to omit the sample at end: `[start, end)`
endtime=(urlInterval['end'] - delta))
url_file = Util.get_file_from_url(url, createParentDirectory=True)
# existing data file, merge new data into existing
if os.path.isfile(url_file):
try:
existing_data = Util.read_file(url_file)
existing_data = self.parse_string(
existing_data,
observatory=url_data[0].stats.station,
type=type,
interval=interval,
channels=channels)
# TODO: make parse_string return the correct location code
for trace in existing_data:
# make location codes match, just in case
new_trace = url_data.select(
network=trace.stats.network,
station=trace.stats.station,
channel=trace.stats.channel)[0]
trace.stats.location = new_trace.stats.location
url_data = TimeseriesUtility.merge_streams(
existing_data, url_data)
except IOError:
# no data yet
pass
except NotImplementedError:
# factory only supports output
pass
with open(url_file, 'wb') as fh:
try:
self.write_file(fh, url_data, channels)
except NotImplementedError:
raise NotImplementedError(
'"put_timeseries" not implemented')
def run_as_update(self, options, update_count=0):
"""Updates data.
Parameters
----------
options: dictionary
The dictionary of all the command line arguments. Could in theory
contain other options passed in by the controller.
Notes
-----
Finds gaps in the target data, and if there's new data in the input
source, calls run with the start/end time of a given gap to fill
in.
It checks the start of the target data, and if it's missing, and
there's new data available, it backs up the starttime/endtime,
and recursively calls itself, to check the previous period, to see
if new data is available there as well. Calls run for each new
period, oldest to newest.
"""
# If an update_limit is set, make certain we don't step past it.
if options.update_limit != 0:
if update_count >= options.update_limit:
return
print >> sys.stderr, 'checking gaps', \
options.starttime, options.endtime
algorithm = self._algorithm
input_channels = options.inchannels or \
algorithm.get_input_channels()
output_channels = options.outchannels or \
algorithm.get_output_channels()
# request output to see what has already been generated
output_timeseries = self._get_output_timeseries(
observatory=options.observatory,
starttime=options.starttime,
endtime=options.endtime,
channels=output_channels)
if len(output_timeseries) > 0:
# find gaps in output, so they can be updated
output_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(output_timeseries))
else:
output_gaps = [[
options.starttime,
options.endtime,
# next sample time not used
None
]]
for output_gap in output_gaps:
input_timeseries = self._get_input_timeseries(
observatory=options.observatory,
starttime=output_gap[0],
endtime=output_gap[1],
channels=input_channels)
if not algorithm.can_produce_data(
starttime=output_gap[0],
endtime=output_gap[1],
stream=input_timeseries):
continue
# check for fillable gap at start
if output_gap[0] == options.starttime:
# found fillable gap at start, recurse to previous interval
interval = options.endtime - options.starttime
starttime = options.starttime - interval
endtime = options.starttime - 1
options.starttime = starttime
options.endtime = endtime
self.run_as_update(options, update_count + 1)
# fill gap
options.starttime = output_gap[0]
options.endtime = output_gap[1]
print >> sys.stderr, 'processing', \
options.starttime, options.endtime
self.run(options)
def put_timeseries(self, timeseries, starttime=None, endtime=None,
channels=None, type=None, interval=None):
"""Store timeseries data.
Parameters
----------
timeseries : obspy.core.Stream
stream containing traces to store.
starttime : UTCDateTime
time of first sample in timeseries to store.
uses first sample if unspecified.
endtime : UTCDateTime
time of last sample in timeseries to store.
uses last sample if unspecified.
channels : array_like
list of channels to store, optional.
uses default if unspecified.
type : {'definitive', 'provisional', 'quasi-definitive', 'variation'}
data type, optional.
uses default if unspecified.
interval : {'daily', 'hourly', 'minute', 'monthly', 'second'}
data interval, optional.
uses default if unspecified.
Raises
------
TimeseriesFactoryException
if any errors occur.
"""
if len(timeseries) == 0:
# no data to put
return
if not self.urlTemplate.startswith('file://'):
raise TimeseriesFactoryException('Only file urls are supported')
channels = channels or self.channels
type = type or self.type
interval = interval or self.interval
stats = timeseries[0].stats
delta = stats.delta
observatory = stats.station
starttime = starttime or stats.starttime
endtime = endtime or stats.endtime
urlIntervals = Util.get_intervals(
starttime=starttime,
endtime=endtime,
size=self.urlInterval)
for urlInterval in urlIntervals:
url = self._get_url(
observatory=observatory,
date=urlInterval['start'],
type=type,
interval=interval,
channels=channels)
url_data = timeseries.slice(
starttime=urlInterval['start'],
# subtract delta to omit the sample at end: `[start, end)`
endtime=(urlInterval['end'] - delta))
url_file = Util.get_file_from_url(url, createParentDirectory=True)
# existing data file, merge new data into existing
if os.path.isfile(url_file):
try:
existing_data = Util.read_file(url_file)
existing_data = self.parse_string(existing_data,
observatory=url_data[0].stats.station,
type=type,
interval=interval,
channels=channels)
# TODO: make parse_string return the correct location code
for trace in existing_data:
# make location codes match, just in case
new_trace = url_data.select(
network=trace.stats.network,
station=trace.stats.station,
channel=trace.stats.channel)[0]
trace.stats.location = new_trace.stats.location
url_data = TimeseriesUtility.merge_streams(
existing_data, url_data)
except IOError:
# no data yet
pass
except NotImplementedError:
# factory only supports output
pass
with open(url_file, 'wb') as fh:
try:
self.write_file(fh, url_data, channels)
except NotImplementedError:
raise NotImplementedError(
'"put_timeseries" not implemented')
