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Commit 1f664871 authored by Hal Simpson's avatar Hal Simpson
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added empty channel in edge in, reordered routines in alphabetical order

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geomagio/edge/EdgeFactory.py
+ 168
− 115
View file @ 1f664871
......@@ -17,7 +17,6 @@ from geomagio import TimeseriesFactory, TimeseriesFactoryException
from obspy import earthworm
from ObservatoryMetadata import ObservatoryMetadata
import numpy.ma as ma
import sys
HOURSECONDS = 3600
DAYMINUTES = 1440
......@@ -129,6 +128,8 @@ class EdgeFactory(TimeseriesFactory):
self._post_process(timeseries, starttime, endtime, channels)
print timeseries
return timeseries
def put_timeseries(self, timeseries, observatory=None,
......@@ -161,71 +162,47 @@ class EdgeFactory(TimeseriesFactory):
for channel in channels:
if timeseries.select(channel=channel).count() == 0:
sys.stderr.write('Missing channel %s for output, continuing \n'
% channel)
continue
raise TimeseriesFactoryException(
'Missing channel "%s" for output' % channel)
for channel in channels:
self._convert_stream_to_masked(timeseries=timeseries,
channel=channel)
for trace in timeseries.select(channel=channel).split():
self._put_trace(trace, observatory, channel, type, interval)
def _put_trace(self, trace, observatory, channel, type, interval):
"""Put trace
def _clean_timeseries(self, timeseries, starttime, endtime):
"""Realigns timeseries data so the start and endtimes are the same
as what was originally asked for, even if the data was during
a gap.
Parameters
----------
trace: obspy.core.Stream.Trace
trace object with data to be written
observatory: str
observatory code.
channel: str
channel to be written
type: {'variation', 'quasi-definitive', 'definitive'}
data type.
interval: {'daily', 'hourly', 'minute', 'second'}
data interval.
"""
station = self._get_edge_station(observatory, channel,
type, interval)
location = self._get_edge_location(observatory, channel,
type, interval)
network = self._get_edge_network(observatory, channel,
type, interval)
edge_channel = self._get_edge_channel(observatory, channel,
type, interval)
self.ric = RawInputClient(self.tag, self.host, self.port,
self.cwbhost, self.cwbport)
timeseries: obspy.core.stream
The timeseries stream as returned by the call to getWaveform
starttime: obspy.core.UTCDateTime
the starttime of the requested data
endtime: obspy.core.UTCDateTime
the endtime of the requested data
totalsamps = len(trace.data)
starttime = trace.stats.starttime
if self.interval == 'second':
nsamp = HOURSECONDS
timeoffset = 1
samplerate = 1.
elif self.interval == 'minute':
nsamp = DAYMINUTES
timeoffset = 60
samplerate = 1. / 60
Notes: the original timeseries object is changed.
"""
for trace in timeseries:
trace_starttime = UTCDateTime(trace.stats.starttime)
trace_endtime = UTCDateTime(trace.stats.endtime)
for i in xrange(0, totalsamps, nsamp):
location = self.locationCode or location
seedname = self.ric.create_seedname(station,
edge_channel, location, network)
if totalsamps - i < nsamp:
endsample = totalsamps
else:
endsample = i + nsamp
nsamp = endsample - i
endtime = starttime + (nsamp - 1) * timeoffset
trace_send = trace.slice(starttime, endtime)
self._convert_trace_to_int(trace_send)
print 'send'
self.ric.send(seedname, nsamp, trace_send.data, starttime,
samplerate, 0, 0, 0, 0)
starttime += nsamp * timeoffset
self.ric.forceout(seedname)
self.ric.close()
if trace.stats.starttime > starttime:
cnt = int((trace_starttime - starttime) / trace.stats.delta)
trace.data = numpy.concatenate([
numpy.full(cnt, numpy.nan, dtype=numpy.float64),
trace.data])
trace.stats.starttime = starttime
if trace_endtime < endtime:
cnt = int((endtime - trace_endtime) / trace.stats.delta)
trace.data = numpy.concatenate([
trace.data,
numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
trace.stats.endttime = endtime
def _convert_trace_to_decimal(self, stream):
"""convert geomag edge traces stored as ints, to decimal by dividing
......@@ -268,11 +245,16 @@ class EdgeFactory(TimeseriesFactory):
for trace in timeseries.select(channel=channel):
trace.data = ma.masked_invalid(trace.data)
def _get_edge_network(self, observatory, channel, type, interval):
"""get edge network code.
def _create_missing_channel(self, starttime, endtime, observatory,
channel, type, interval, network, station, location):
"""fill a missing channel with nans.
Parameters
----------
starttime: obspy.core.UTCDateTime
the starttime of the requested data
endtime: obspy.core.UTCDateTime
the endtime of the requested data
observatory : str
observatory code
channel : str
......@@ -281,34 +263,36 @@ class EdgeFactory(TimeseriesFactory):
data type {definitive, quasi-definitive, variation}
interval : str
interval length {minute, second}
network: str
the network code
station: str
the observatory station code
location: str
the location code
Returns
-------
network
always NT
obspy.core.Stream
stream of the requested channel data
"""
return 'NT'
def _get_edge_station(self, observatory, channel, type, interval):
"""get edge station.
Parameters
----------
observatory : str
observatory code
channel : str
single character channel {H, E, D, Z, F}
type : str
data type {definitive, quasi-definitive, variation}
interval : str
interval length {minute, second}
stats = obspy.core.Stats()
stats.channel = channel
stats.starttime = starttime
stats.network = network
stats.station = station
stats.location = location
if interval == 'second':
stats.sampling_rate = 1.
elif interval == 'minute':
stats.sampling_rate = 1 / 60.
elif interval == 'hourly':
stats.sampling_rate = 1 / 3600
elif interval == 'daily':
stats.sampling_rate = 1 / 86400
length = int((endtime - starttime) * stats.sampling_rate)
stats.npts = length + 1
Returns
-------
station
the observatory is returned as the station
"""
return observatory
data = numpy.full(length, numpy.nan, dtype=numpy.float64)
return obspy.core.Stream(obspy.core.Trace(data, stats))
def _get_edge_channel(self, observatory, channel, type, interval):
"""get edge channel.
......@@ -380,6 +364,48 @@ class EdgeFactory(TimeseriesFactory):
location = 'D0'
return location
def _get_edge_network(self, observatory, channel, type, interval):
"""get edge network code.
Parameters
----------
observatory : str
observatory code
channel : str
single character channel {H, E, D, Z, F}
type : str
data type {definitive, quasi-definitive, variation}
interval : str
interval length {minute, second}
Returns
-------
network
always NT
"""
return 'NT'
def _get_edge_station(self, observatory, channel, type, interval):
"""get edge station.
Parameters
----------
observatory : str
observatory code
channel : str
single character channel {H, E, D, Z, F}
type : str
data type {definitive, quasi-definitive, variation}
interval : str
interval length {minute, second}
Returns
-------
station
the observatory is returned as the station
"""
return observatory
def _get_interval_code(self, interval):
"""get edge interval code.
......@@ -450,43 +476,13 @@ class EdgeFactory(TimeseriesFactory):
data = self.client.getWaveform(network, station, location,
edge_channel, starttime, endtime)
data.merge()
if data.count() == 0:
data = self._create_missing_channel(starttime, endtime, observatory,
channel, type, interval, network, station, location)
self._set_metadata(data,
observatory, channel, type, interval)
return data
def _clean_timeseries(self, timeseries, starttime, endtime):
"""Realigns timeseries data so the start and endtimes are the same
as what was originally asked for, even if the data was during
a gap.
Parameters
----------
timeseries: obspy.core.stream
The timeseries stream as returned by the call to getWaveform
starttime: obspy.core.UTCDateTime
the starttime of the requested data
endtime: obspy.core.UTCDateTime
the endtime of the requested data
Notes: the original timeseries object is changed.
"""
for trace in timeseries:
trace_starttime = UTCDateTime(trace.stats.starttime)
trace_endtime = UTCDateTime(trace.stats.endtime)
if trace.stats.starttime > starttime:
cnt = int((trace_starttime - starttime) / trace.stats.delta)
trace.data = numpy.concatenate([
numpy.full(cnt, numpy.nan, dtype=numpy.float64),
trace.data])
trace.stats.starttime = starttime
if trace_endtime < endtime:
cnt = int((endtime - trace_endtime) / trace.stats.delta)
trace.data = numpy.concatenate([
trace.data,
numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
trace.stats.endttime = endtime
def _post_process(self, timeseries, starttime, endtime, channels):
"""Post process a timeseries stream after the raw data is
is fetched from a waveserver. Specifically changes
......@@ -515,6 +511,63 @@ class EdgeFactory(TimeseriesFactory):
self._clean_timeseries(timeseries, starttime, endtime)
def _put_trace(self, trace, observatory, channel, type, interval):
"""Put trace
Parameters
----------
trace: obspy.core.Stream.Trace
trace object with data to be written
observatory: str
observatory code.
channel: str
channel to be written
type: {'variation', 'quasi-definitive', 'definitive'}
data type.
interval: {'daily', 'hourly', 'minute', 'second'}
data interval.
"""
station = self._get_edge_station(observatory, channel,
type, interval)
location = self._get_edge_location(observatory, channel,
type, interval)
network = self._get_edge_network(observatory, channel,
type, interval)
edge_channel = self._get_edge_channel(observatory, channel,
type, interval)
self.ric = RawInputClient(self.tag, self.host, self.port,
self.cwbhost, self.cwbport)
totalsamps = len(trace.data)
starttime = trace.stats.starttime
if self.interval == 'second':
nsamp = HOURSECONDS
timeoffset = 1
samplerate = 1.
elif self.interval == 'minute':
nsamp = DAYMINUTES
timeoffset = 60
samplerate = 1. / 60
for i in xrange(0, totalsamps, nsamp):
location = self.locationCode or location
seedname = self.ric.create_seedname(station,
edge_channel, location, network)
if totalsamps - i < nsamp:
endsample = totalsamps
else:
endsample = i + nsamp
nsamp = endsample - i
endtime = starttime + (nsamp - 1) * timeoffset
trace_send = trace.slice(starttime, endtime)
self._convert_trace_to_int(trace_send)
self.ric.send(seedname, nsamp, trace_send.data, starttime,
samplerate, 0, 0, 0, 0)
starttime += nsamp * timeoffset
self.ric.forceout(seedname)
self.ric.close()
def _set_metadata(self, stream, observatory, channel, type, interval):
"""set metadata for a given stream/channel
Parameters
......
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