diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index fcce9de087bf25a145d7fefea453a0202bc0322c..6cd3ae81d76c06c4fa73ad422f9aef2908a1d6e4 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -3,11 +3,9 @@
import argparse
import sys
-from obspy.core import UTCDateTime
+from obspy.core import Stream, UTCDateTime
from algorithm import algorithms
import TimeseriesUtility
-from TimeseriesFactoryException import TimeseriesFactoryException
-from Util import ObjectView
import edge
import iaga2002
@@ -43,6 +41,97 @@ class Controller(object):
self._algorithm = algorithm
self._outputFactory = outputFactory
+ def _get_input_timeseries(self, observatory, channels, starttime, endtime):
+ """Get timeseries from the input factory for requested options.
+
+ Parameters
+ ----------
+ observatory : array_like
+ observatories to request.
+ channels : array_like
+ channels to request.
+ starttime : obspy.core.UTCDateTime
+ time of first sample to request.
+ endtime : obspy.core.UTCDateTime
+ time of last sample to request.
+ renames : array_like
+ list of channels to rename
+ each list item should be array_like:
+ the first element is the channel to rename,
+ the last element is the new channel name
+
+ Returns
+ -------
+ timeseries : obspy.core.Stream
+ """
+ timeseries = Stream()
+ for obs in list(observatory):
+ # get input interval for observatory
+ # do this per observatory in case an
+ # algorithm needs different amounts of data
+ input_start, input_end = self._algorithm.get_input_interval(
+ start=starttime,
+ end=endtime,
+ observatory=obs,
+ channel=channels)
+ timeseries += self._inputFactory.get_timeseries(
+ observatory=obs,
+ starttime=input_start,
+ endtime=input_end,
+ channels=channels)
+ return timeseries
+
+ def _rename_channels(self, timeseries, renames):
+ """Rename trace channel names.
+
+ Parameters
+ ----------
+ timeseries : obspy.core.Stream
+ stream with channels to rename
+ renames : array_like
+ list of channels to rename
+ each list item should be array_like:
+ the first element is the channel to rename,
+ the last element is the new channel name
+
+ Returns
+ -------
+ timeseries : obspy.core.Stream
+ """
+ for r in renames:
+ from_name, to_name = r[0], r[-1]
+ for t in timeseries.select(channel=from_name):
+ t.stats.channel = to_name
+ return timeseries
+
+ def _get_output_timeseries(self, observatory, channels, starttime,
+ endtime):
+ """Get timeseries from the output factory for requested options.
+
+ Parameters
+ ----------
+ observatory : array_like
+ observatories to request.
+ channels : array_like
+ channels to request.
+ starttime : obspy.core.UTCDateTime
+ time of first sample to request.
+ endtime : obspy.core.UTCDateTime
+ time of last sample to request.
+
+ Returns
+ -------
+ timeseries : obspy.core.Stream
+ """
+ timeseries = Stream()
+ for obs in list(observatory):
+ timeseries += self._outputFactory.get_timeseries(
+ observatory=obs,
+ starttime=starttime,
+ endtime=endtime,
+ channels=channels)
+ return timeseries
+
def run(self, options):
"""run controller
Parameters
@@ -52,22 +141,28 @@ class Controller(object):
contain other options passed in by the controller.
"""
algorithm = self._algorithm
- input_channels = algorithm.get_input_channels()
- output_channels = self._get_output_channels(
- algorithm.get_output_channels(),
- options.outchannels)
- # get input
- start, end = self._algorithm.get_input_interval(
- start=options.starttime,
- end=options.endtime)
- timeseries = self._inputFactory.get_timeseries(
- starttime=start,
- endtime=end,
+ input_channels = options.inchannels or \
+ algorithm.get_input_channels()
+ output_channels = options.outchannels or \
+ algorithm.get_output_channels()
+ # input
+ timeseries = self._get_input_timeseries(
+ observatory=options.observatory,
+ starttime=options.starttime,
+ endtime=options.endtime,
channels=input_channels)
if timeseries.count() == 0:
return
# process
+ if options.rename_input_channel:
+ timeseries = self._rename_channels(
+ timeseries=timeseries,
+ renames=options.rename_input_channel)
processed = algorithm.process(timeseries)
+ if options.rename_output_channel:
+ processed = self._rename_channels(
+ timeseries=processed,
+ renames=options.rename_output_channel)
# output
self._outputFactory.put_timeseries(
timeseries=processed,
@@ -95,12 +190,13 @@ class Controller(object):
period, oldest to newest.
"""
algorithm = self._algorithm
- input_channels = algorithm.get_input_channels()
- output_channels = self._get_output_channels(
- algorithm.get_output_channels(),
- options.outchannels)
+ 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._outputFactory.get_timeseries(
+ output_timeseries = self._get_output_timeseries(
+ observatory=options.observatory,
starttime=options.starttime,
endtime=options.endtime,
channels=output_channels)
@@ -109,12 +205,10 @@ class Controller(object):
output_gaps = TimeseriesUtility.get_merged_gaps(
TimeseriesUtility.get_stream_gaps(output_timeseries))
for output_gap in output_gaps:
- input_start, input_end = algorithm.get_input_interval(
- start=output_gap[0],
- end=output_gap[1])
- input_timeseries = self._inputFactory.get_timeseries(
- starttime=input_start,
- endtime=input_end,
+ 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],
@@ -125,40 +219,13 @@ class Controller(object):
if output_gap[0] == options.starttime:
# found fillable gap at start, recurse to previous interval
interval = options.endtime - options.starttime
- self.run_as_update(ObjectView({
- 'outchannels': options.outchannels,
- 'starttime': options.starttime - interval - delta,
- 'endtime': options.starttime - delta
- }))
+ options.starttime = options.starttime - interval - delta
+ options.endtime = options.starttime - delta
+ self.run_as_update(options)
# fill gap
- self.run(ObjectView({
- 'outchannels': options.outchannels,
- 'starttime': output_gap[0],
- 'endtime': output_gap[1]
- }))
-
- def _get_output_channels(self, algorithm_channels, commandline_channels):
- """get output channels
-
- Parameters
- ----------
- algorithm_channels: array_like
- list of channels required by the algorithm
- commandline_channels: array_like
- list of channels requested by the user
- Notes
- -----
- We want to return the channels requested by the user, but we require
- that they be in the list of channels for the algorithm.
- """
- if commandline_channels is not None:
- for channel in commandline_channels:
- if channel not in algorithm_channels:
- raise TimeseriesFactoryException(
- 'Output "%s" Channel not in Algorithm'
- % channel)
- return commandline_channels
- return algorithm_channels
+ options.starttime = output_gap[0]
+ options.endtime = output_gap[1]
+ self.run(options)
def main(args):
@@ -347,7 +414,11 @@ def parse_args(args):
help='UTC date YYYY-MM-DD HH:MM:SS')
parser.add_argument('--observatory',
- help='Observatory code ie BOU, CMO, etc')
+ help='Observatory code ie BOU, CMO, etc.' +
+ ' CAUTION: Using multiple observatories is not' +
+ ' recommended in most cases; especially with' +
+ ' single observatory formats like IAGA and PCDCP.',
+ nargs='*')
parser.add_argument('--inchannels',
nargs='*',
help='Channels H, E, Z, etc')
@@ -358,6 +429,16 @@ def parse_args(args):
parser.add_argument('--type',
default='variation',
choices=['variation', 'quasi-definitive', 'definitive'])
+ parser.add_argument('--rename-input-channel',
+ action='append',
+ help='Rename an input channel after it is read',
+ metavar=('FROM', 'TO'),
+ nargs=2)
+ parser.add_argument('--rename-output-channel',
+ action='append',
+ help='Rename an output channel before it is written',
+ metavar=('FROM', 'TO'),
+ nargs=2)
parser.add_argument('--locationcode',
choices=['R0', 'R1', 'RM', 'Q0', 'D0', 'C0'])
parser.add_argument('--outlocationcode',
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index 20aa4974bbb5d94db587a74030278a2ef063b20e..e547e63c9578b2ff053ad45ddb5e12841dddd3fa 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -110,3 +110,22 @@ def get_merged_gaps(gaps):
if merged_gap is not None:
merged_gaps.append(merged_gap)
return merged_gaps
+
+
+def get_channels(stream):
+ """Get a list of channels in a stream.
+
+ Parameters
+ ----------
+ stream : obspy.core.Stream
+
+ Returns
+ -------
+ channels : array_like
+ """
+ channels = {}
+ for trace in stream:
+ channel = trace.stats.channel
+ if channel:
+ channels[channel] = True
+ return [ch for ch in channels]
diff --git a/geomagio/algorithm/Algorithm.py b/geomagio/algorithm/Algorithm.py
index e3fdc3f471bd90e7160c21a70884d9504f33cea6..1aa1b7b6c2ea523fca1879e635088733402599f5 100644
--- a/geomagio/algorithm/Algorithm.py
+++ b/geomagio/algorithm/Algorithm.py
@@ -56,18 +56,24 @@ class Algorithm(object):
"""
return self._outchannels
- def get_input_interval(self, start, end):
+ def get_input_interval(self, start, end, observatory=None, channels=None):
"""Get Input Interval
start : UTCDateTime
- start time of requested output
+ start time of requested output.
end : UTCDateTime
- end time of requested output
+ end time of requested output.
+ observatory : string
+ observatory code.
+ channels : string
+ input channels.
Returns
-------
- tuple : (input_start, input_end)
- start and end of required input to generate requested output.
+ input_start : UTCDateTime
+ start of input required to generate requested output
+ input_end : UTCDateTime
+ end of input required to generate requested output.
"""
return (start, end)
diff --git a/geomagio/edge/EdgeFactory.py b/geomagio/edge/EdgeFactory.py
index 7b92a33ea51715e3a2702c0acf8d1d00995c82e8..307275a9cd826e1a22b8d876030a89419ee31341 100644
--- a/geomagio/edge/EdgeFactory.py
+++ b/geomagio/edge/EdgeFactory.py
@@ -17,7 +17,7 @@ import obspy.core
from datetime import datetime
from obspy import earthworm
from obspy.core import UTCDateTime
-from .. import ChannelConverter
+from .. import ChannelConverter, TimeseriesUtility
from ..TimeseriesFactory import TimeseriesFactory
from ..TimeseriesFactoryException import TimeseriesFactoryException
from ..ObservatoryMetadata import ObservatoryMetadata
@@ -183,12 +183,11 @@ class EdgeFactory(TimeseriesFactory):
if (starttime is None or endtime is None):
starttime, endtime = self._get_stream_start_end_times(timeseries)
-
for channel in channels:
if timeseries.select(channel=channel).count() == 0:
raise TimeseriesFactoryException(
- 'Missing channel "%s" for output' % channel)
-
+ 'Missing channel "%s" for output, available channels %s' %
+ (channel, str(TimeseriesUtility.get_channels(timeseries))))
for channel in channels:
self._put_channel(timeseries, observatory, channel, type,
interval, starttime, endtime)
diff --git a/geomagio/iaga2002/IAGA2002Writer.py b/geomagio/iaga2002/IAGA2002Writer.py
index 56c510f3d0dbc273eea1dc9e06cb8723fb5da909..cd070075a3c5e046044ea54586301c142d857793 100644
--- a/geomagio/iaga2002/IAGA2002Writer.py
+++ b/geomagio/iaga2002/IAGA2002Writer.py
@@ -3,7 +3,7 @@ from cStringIO import StringIO
from datetime import datetime
import numpy
import textwrap
-from .. import ChannelConverter
+from .. import ChannelConverter, TimeseriesUtility
from ..TimeseriesFactoryException import TimeseriesFactoryException
from ..Util import create_empty_trace
import IAGA2002Parser
@@ -30,6 +30,11 @@ class IAGA2002Writer(object):
channels: array_like
channels to be written from timeseries object
"""
+ for channel in channels:
+ if timeseries.select(channel=channel).count() == 0:
+ raise TimeseriesFactoryException(
+ 'Missing channel "%s" for output, available channels %s' %
+ (channel, str(TimeseriesUtility.get_channels(timeseries))))
stats = timeseries[0].stats
if len(channels) != 4:
self._pad_to_four_channels(timeseries, channels)
diff --git a/geomagio/pcdcp/PCDCPWriter.py b/geomagio/pcdcp/PCDCPWriter.py
index e26c29075ae4b3320619ac617ce5190babe4f767..3042df76e476185449be5b5cf288cc8aa20fa280 100644
--- a/geomagio/pcdcp/PCDCPWriter.py
+++ b/geomagio/pcdcp/PCDCPWriter.py
@@ -3,7 +3,8 @@ import numpy
import PCDCPParser
from cStringIO import StringIO
from datetime import datetime
-from geomagio import ChannelConverter
+from .. import ChannelConverter, TimeseriesUtility
+from ..TimeseriesFactoryException import TimeseriesFactoryException
from obspy.core import Stream
@@ -26,6 +27,11 @@ class PCDCPWriter(object):
channels : array_like
Channels to be written from timeseries object.
"""
+ for channel in channels:
+ if timeseries.select(channel=channel).count() == 0:
+ raise TimeseriesFactoryException(
+ 'Missing channel "%s" for output, available channels %s' %
+ (channel, str(TimeseriesUtility.get_channels(timeseries))))
stats = timeseries[0].stats
out.write(self._format_header(stats))
out.write(self._format_data(timeseries, channels))