From af8ea2e699fee3fee8c17707cd92095b6b6d765c Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Mon, 15 Mar 2021 14:33:01 -0600
Subject: [PATCH] Make algorithm an optional parameter for run methods
---
geomagio/Controller.py | 21 ++++++++---
geomagio/algorithm/FilterAlgorithm.py | 2 +-
geomagio/processing/obsrio.py | 53 ++++++++++++++++-----------
3 files changed, 47 insertions(+), 29 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 199ab64e4..e91ef4d25 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -7,7 +7,7 @@ from typing import List, Optional, Tuple, Union
from obspy.core import Stream, UTCDateTime
-from .algorithm import algorithms, AlgorithmException
+from .algorithm import Algorithm, algorithms, AlgorithmException
from .PlotTimeseriesFactory import PlotTimeseriesFactory
from .StreamTimeseriesFactory import StreamTimeseriesFactory
from . import TimeseriesUtility, Util
@@ -51,7 +51,7 @@ class Controller(object):
self,
inputFactory,
outputFactory,
- algorithm,
+ algorithm: Optional[Algorithm] = None,
inputInterval: Optional[str] = None,
outputInterval: Optional[str] = None,
):
@@ -61,7 +61,9 @@ class Controller(object):
self._outputFactory = outputFactory
self._outputInterval = outputInterval
- def _get_input_timeseries(self, observatory, channels, starttime, endtime):
+ def _get_input_timeseries(
+ self, observatory, channels, starttime, endtime, algorithm=None
+ ):
"""Get timeseries from the input factory for requested options.
Parameters
@@ -84,12 +86,13 @@ class Controller(object):
-------
timeseries : obspy.core.Stream
"""
+ algorithm = algorithm or self._algorithm
timeseries = Stream()
for obs in 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(
+ input_start, input_end = algorithm.get_input_interval(
start=starttime, end=endtime, observatory=obs, channels=channels
)
if input_start is None or input_end is None:
@@ -217,6 +220,7 @@ class Controller(object):
observatory: List[str],
starttime: UTCDateTime,
endtime: UTCDateTime,
+ algorithm: Optional[Algorithm] = None,
input_channels: Optional[List[str]] = None,
input_timeseries: Optional[Stream] = None,
output_channels: Optional[List[str]] = None,
@@ -243,13 +247,14 @@ class Controller(object):
# ensure realtime is a valid value:
if realtime <= 0:
realtime = False
- algorithm = self._algorithm
+ algorithm = algorithm or self._algorithm
input_channels = input_channels or algorithm.get_input_channels()
output_channels = output_channels or algorithm.get_output_channels()
next_starttime = algorithm.get_next_starttime()
starttime = next_starttime or starttime
# input
timeseries = input_timeseries or self._get_input_timeseries(
+ algorithm=algorithm,
observatory=observatory,
starttime=starttime,
endtime=endtime,
@@ -298,6 +303,7 @@ class Controller(object):
output_observatory: List[str],
starttime: UTCDateTime,
endtime: UTCDateTime,
+ algorithm: Optional[Algorithm] = None,
input_channels: Optional[List[str]] = None,
output_channels: Optional[List[str]] = None,
no_trim: bool = False,
@@ -337,7 +343,7 @@ class Controller(object):
# If an update_limit is set, make certain we don't step past it.
if update_limit > 0 and update_count >= update_limit:
return
- algorithm = self._algorithm
+ algorithm = algorithm or self._algorithm
if algorithm.get_next_starttime() is not None:
raise AlgorithmException("Stateful algorithms cannot use run_as_update")
input_channels = input_channels or algorithm.get_input_channels()
@@ -373,6 +379,7 @@ class Controller(object):
]
for output_gap in output_gaps:
input_timeseries = self._get_input_timeseries(
+ algorithm=algorithm,
observatory=observatory,
starttime=output_gap[0],
endtime=output_gap[1],
@@ -389,6 +396,7 @@ class Controller(object):
recurse_starttime = starttime - interval
recurse_endtime = starttime - 1
self.run_as_update(
+ algorithm=algorithm,
observatory=observatory,
output_observatory=output_observatory,
starttime=recurse_starttime,
@@ -414,6 +422,7 @@ class Controller(object):
file=sys.stderr,
)
self.run(
+ algorithm=algorithm,
observatory=observatory,
starttime=gap_starttime,
endtime=gap_endtime,
diff --git a/geomagio/algorithm/FilterAlgorithm.py b/geomagio/algorithm/FilterAlgorithm.py
index 50aa2f729..da0f2df18 100644
--- a/geomagio/algorithm/FilterAlgorithm.py
+++ b/geomagio/algorithm/FilterAlgorithm.py
@@ -123,7 +123,7 @@ class FilterAlgorithm(Algorithm):
outchannels=None,
):
- Algorithm.__init__(self, inchannels=None, outchannels=None)
+ Algorithm.__init__(self, inchannels=inchannels, outchannels=outchannels)
self.coeff_filename = coeff_filename
self.filtertype = filtertype
self.input_sample_period = input_sample_period
diff --git a/geomagio/processing/obsrio.py b/geomagio/processing/obsrio.py
index dc7c1b7f6..9a761e58c 100644
--- a/geomagio/processing/obsrio.py
+++ b/geomagio/processing/obsrio.py
@@ -140,9 +140,6 @@ def obsrio_day(
starttime, endtime = get_realtime_interval(realtime_interval)
# filter 10Hz U,V,W to H,E,Z
controller = Controller(
- algorithm=FilterAlgorithm(
- input_sample_period=60.0, output_sample_period=86400.0
- ),
inputFactory=input_factory or get_edge_factory(data_type="variation"),
inputInterval="minute",
outputFactory=output_factory or get_miniseed_factory(data_type="variation"),
@@ -151,9 +148,13 @@ def obsrio_day(
renames = {"H": "U", "E": "V", "Z": "W", "F": "F"}
for input_channel in renames.keys():
output_channel = renames[input_channel]
- controller._algorithm._inchannels = (input_channel,)
- controller._algorithm._outchannels = (output_channel,)
controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=60.0,
+ output_sample_period=86400.0,
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
observatory=(observatory,),
output_observatory=(observatory,),
starttime=starttime,
@@ -177,9 +178,6 @@ def obsrio_hour(
starttime, endtime = get_realtime_interval(realtime_interval)
# filter 10Hz U,V,W to H,E,Z
controller = Controller(
- algorithm=FilterAlgorithm(
- input_sample_period=60.0, output_sample_period=3600.0
- ),
inputFactory=input_factory or get_edge_factory(data_type="variation"),
inputInterval="minute",
outputFactory=output_factory or get_miniseed_factory(data_type="variation"),
@@ -188,9 +186,13 @@ def obsrio_hour(
renames = {"H": "U", "E": "V", "Z": "W", "F": "F"}
for input_channel in renames.keys():
output_channel = renames[input_channel]
- controller._algorithm._inchannels = (input_channel,)
- controller._algorithm._outchannels = (output_channel,)
controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=60.0,
+ output_sample_period=3600.0,
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
observatory=(observatory,),
output_observatory=(observatory,),
starttime=starttime,
@@ -217,16 +219,19 @@ def obsrio_minute(
"""
starttime, endtime = get_realtime_interval(realtime_interval)
controller = Controller(
- algorithm=FilterAlgorithm(input_sample_period=1, output_sample_period=60),
inputFactory=input_factory or get_edge_factory(data_type="variation"),
inputInterval="second",
outputFactory=output_factory or get_edge_factory(data_type="variation"),
outputInterval="minute",
)
for channel in ["H", "E", "Z", "F"]:
- controller._algorithm._inchannels = (channel,)
- controller._algorithm._outchannels = (channel,)
controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=1,
+ output_sample_period=60,
+ inchannels=(channel,),
+ outchannels=(channel,),
+ ),
observatory=(observatory,),
output_observatory=(observatory,),
starttime=starttime,
@@ -248,14 +253,12 @@ def obsrio_second(
"""Copy 1Hz miniseed F to 1Hz legacy F."""
starttime, endtime = get_realtime_interval(realtime_interval)
controller = Controller(
- algorithm=Algorithm(),
+ algorithm=Algorithm(inchannels=("F",), outchannels=("F",)),
inputFactory=input_factory or get_miniseed_factory(data_type="variation"),
inputInterval="second",
outputFactory=output_factory or get_edge_factory(data_type="variation"),
outputInterval="second",
)
- controller._algorithm._inchannels = ("F",)
- controller._algorithm._outchannels = ("F",)
controller.run_as_update(
observatory=(observatory,),
output_observatory=(observatory,),
@@ -278,7 +281,6 @@ def obsrio_temperatures(
"""Filter temperatures 1Hz miniseed (LK1-4) to 1 minute legacy (UK1-4)."""
starttime, endtime = get_realtime_interval(realtime_interval)
controller = Controller(
- algorithm=FilterAlgorithm(input_sample_period=1, output_sample_period=60),
inputFactory=input_factory or get_miniseed_factory(data_type="variation"),
inputInterval="second",
outputFactory=output_factory or get_edge_factory(data_type="variation"),
@@ -287,9 +289,13 @@ def obsrio_temperatures(
renames = {"LK1": "UK1", "LK2": "UK2", "LK3": "UK3", "LK4": "UK4"}
for input_channel in renames.keys():
output_channel = renames[input_channel]
- controller._algorithm._inchannels = (input_channel,)
- controller._algorithm._outchannels = (output_channel,)
controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=1,
+ output_sample_period=60,
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
observatory=(observatory,),
output_observatory=(observatory,),
starttime=starttime,
@@ -313,7 +319,6 @@ def obsrio_tenhertz(
starttime, endtime = get_realtime_interval(realtime_interval)
# filter 10Hz U,V,W to H,E,Z
controller = Controller(
- algorithm=FilterAlgorithm(input_sample_period=0.1, output_sample_period=1),
inputFactory=input_factory or get_miniseed_factory(data_type="variation"),
inputInterval="tenhertz",
outputFactory=output_factory or get_edge_factory(data_type="variation"),
@@ -322,9 +327,13 @@ def obsrio_tenhertz(
renames = {"U": "H", "V": "E", "W": "Z"}
for input_channel in renames.keys():
output_channel = renames[input_channel]
- controller._algorithm._inchannels = (input_channel,)
- controller._algorithm._outchannels = (output_channel,)
controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=0.1,
+ output_sample_period=1,
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
observatory=(observatory,),
output_observatory=(observatory,),
starttime=starttime,
--
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