diff --git a/Pipfile.lock b/Pipfile.lock
index b72106b8eefb519b47b17e3088014369cac845b3..abc664817d12d28756581fa6344ae0736cd1c1ff 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,1296 +1,982 @@
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+ ],
+ "version": "==1.4.1"
+ },
+ "virtualenv": {
+ "hashes": [
+ "sha256:a116629d4e7f4d03433b8afa27f43deba09d48bc48f5ecefa4f015a178efb6cf",
+ "sha256:a730548b27366c5e6cbdf6f97406d861cccece2e22275e8e1a757aeff5e00c70"
+ ],
+ "version": "==20.0.21"
+ },
+ "waitress": {
+ "hashes": [
+ "sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
+ "sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
+ ],
+ "version": "==1.4.4"
+ },
+ "wcwidth": {
+ "hashes": [
+ "sha256:79375666b9954d4a1a10739315816324c3e73110af9d0e102d906fdb0aec009f",
+ "sha256:8c6b5b6ee1360b842645f336d9e5d68c55817c26d3050f46b235ef2bc650e48f"
+ ],
+ "version": "==0.2.4"
+ },
+ "webob": {
+ "hashes": [
+ "sha256:a3c89a8e9ba0aeb17382836cdb73c516d0ecf6630ec40ec28288f3ed459ce87b",
+ "sha256:aa3a917ed752ba3e0b242234b2a373f9c4e2a75d35291dcbe977649bd21fd108"
+ ],
+ "version": "==1.8.6"
+ },
+ "webtest": {
+ "hashes": [
+ "sha256:44ddfe99b5eca4cf07675e7222c81dd624d22f9a26035d2b93dc8862dc1153c6",
+ "sha256:aac168b5b2b4f200af4e35867cf316712210e3d5db81c1cbdff38722647bb087"
+ ],
+ "index": "pypi",
+ "version": "==2.0.35"
+ },
+ "zipp": {
+ "hashes": [
+ "sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
+ "sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
+ ],
+ "version": "==3.1.0"
}
+ }
}
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index c95b517fd9b3ec3be101620380de40624e456edc..936aad858972e1fc41993f88b555b178c09aafd8 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -47,10 +47,19 @@ class Controller(object):
recursively backup so it can update all missing data.
"""
- def __init__(self, inputFactory, outputFactory, algorithm):
- self._inputFactory = inputFactory
+ def __init__(
+ self,
+ inputFactory,
+ outputFactory,
+ algorithm,
+ inputInterval: Optional[str] = None,
+ outputInterval: Optional[str] = None,
+ ):
self._algorithm = algorithm
+ self._inputFactory = inputFactory
+ self._inputInterval = inputInterval
self._outputFactory = outputFactory
+ self._outputInterval = outputInterval
def _get_input_timeseries(self, observatory, channels, starttime, endtime):
"""Get timeseries from the input factory for requested options.
@@ -90,6 +99,7 @@ class Controller(object):
starttime=input_start,
endtime=input_end,
channels=channels,
+ interval=self._inputInterval,
)
return timeseries
@@ -137,7 +147,11 @@ class Controller(object):
timeseries = Stream()
for obs in observatory:
timeseries += self._outputFactory.get_timeseries(
- observatory=obs, starttime=starttime, endtime=endtime, channels=channels
+ observatory=obs,
+ starttime=starttime,
+ endtime=endtime,
+ channels=channels,
+ interval=self._outputInterval,
)
return timeseries
diff --git a/geomagio/processing/__init__.py b/geomagio/processing/__init__.py
index 8bc3dc0a0ca0bf717c909d7466b7a4f986c77d84..21db616e01e5def35dd825bc59d243ecf2233851 100644
--- a/geomagio/processing/__init__.py
+++ b/geomagio/processing/__init__.py
@@ -1,3 +1,3 @@
-"""
-Required file for initializing entrypoints within processing workflow
-"""
+from .main import main
+
+__all__ = ["main"]
diff --git a/geomagio/processing/factory.py b/geomagio/processing/factory.py
new file mode 100644
index 0000000000000000000000000000000000000000..47576109e968ba65757a5f9427fe4972c12a902c
--- /dev/null
+++ b/geomagio/processing/factory.py
@@ -0,0 +1,28 @@
+import os
+from typing import Callable
+
+from ..TimeseriesFactory import TimeseriesFactory
+from ..edge import EdgeFactory, MiniSeedFactory
+
+
+def get_edge_factory(
+ data_type="variation", interval="second", **kwargs
+) -> TimeseriesFactory:
+ return EdgeFactory(
+ host=os.getenv("EDGE_HOST", "127.0.0.1"),
+ interval=interval,
+ type=data_type,
+ **kwargs
+ )
+
+
+def get_miniseed_factory(
+ data_type="variation", interval="second", **kwargs
+) -> TimeseriesFactory:
+ return MiniSeedFactory(
+ convert_channels=("U", "V", "W"),
+ host=os.getenv("EDGE_HOST", "127.0.0.1"),
+ interval=interval,
+ type=data_type,
+ **kwargs
+ )
diff --git a/geomagio/processing/main.py b/geomagio/processing/main.py
new file mode 100644
index 0000000000000000000000000000000000000000..8ecf32d16d55e410b5ef3a9603668aa296232cb4
--- /dev/null
+++ b/geomagio/processing/main.py
@@ -0,0 +1,180 @@
+import sys
+from typing import Optional
+
+import numpy
+import typer
+
+from ..TimeseriesFactory import TimeseriesFactory
+from .factory import get_edge_factory, get_miniseed_factory
+from .observatory import adjusted, deltaf, rotate, sqdist_minute
+from .obsrio import obsrio_minute, obsrio_second, obsrio_temperatures, obsrio_tenhertz
+
+
+def main():
+ typer.run(process)
+
+
+def process(
+ observatory: str,
+ is_obsrio: bool = False,
+ adjusted_statefile: Optional[str] = None,
+ sqdist_statefile_adjusted: Optional[str] = None,
+ sqdist_statefile_variation: Optional[str] = None,
+):
+ print(
+ f"Processing observatory {observatory} (is_obsrio={is_obsrio})", file=sys.stderr
+ )
+ if is_obsrio:
+ process_obsrio(observatory=observatory)
+ process_variation(observatory=observatory, interval="second")
+ process_variation(
+ interval="minute",
+ observatory=observatory,
+ sqdist_statefile=sqdist_statefile_variation,
+ )
+ if adjusted_statefile is not None:
+ process_adjusted(
+ adjusted_statefile=adjusted_statefile,
+ interval="second",
+ observatory=observatory,
+ )
+ process_adjusted(
+ adjusted_statefile=adjusted_statefile,
+ interval="minute",
+ observatory=observatory,
+ sqdist_statefile=sqdist_statefile_adjusted,
+ )
+
+
+def process_adjusted(
+ observatory: str,
+ adjusted_statefile: Optional[str] = None,
+ adjusted_matrix: Optional[numpy.ndarray] = None,
+ adjusted_pier_correction: Optional[float] = None,
+ input_factory: Optional[TimeseriesFactory] = None,
+ interval: str = "second",
+ output_factory: Optional[TimeseriesFactory] = None,
+ output_factory_extras: Optional[TimeseriesFactory] = None,
+ sqdist_statefile: Optional[str] = None,
+):
+ input_factory = input_factory or get_edge_factory(data_type="variation")
+ output_factory = output_factory or get_edge_factory(data_type="adjusted")
+ # optional separate output factory for G, H, D (for iaga2002...)
+ output_factory_extras = output_factory_extras or output_factory
+ adjusted(
+ input_factory=input_factory,
+ interval=interval,
+ observatory=observatory,
+ output_factory=output_factory,
+ matrix=adjusted_matrix,
+ pier_correction=adjusted_pier_correction,
+ statefile=adjusted_statefile,
+ )
+ # compute delta f
+ deltaf(
+ deltaf_from="geo",
+ input_factory=output_factory,
+ interval=interval,
+ observatory=observatory,
+ output_factory=output_factory_extras,
+ )
+ # h,d based on adjusted
+ rotate(
+ observatory=observatory,
+ input_factory=output_factory,
+ interval=interval,
+ output_channels=("H", "D"),
+ output_factory=output_factory_extras,
+ xyz_from="geo",
+ xyz_to="mag",
+ )
+ if interval == "minute" and sqdist_statefile is not None:
+ sqdist_minute(
+ input_factory=output_factory,
+ observatory=observatory,
+ output_factory=output_factory,
+ statefile=sqdist_statefile,
+ )
+
+
+def process_obsrio(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+):
+ input_factory = input_factory or get_miniseed_factory(data_type="variation")
+ output_factory = output_factory or get_edge_factory(data_type="variation")
+ # filter to 1hz H,E,Z
+ obsrio_tenhertz(
+ observatory=observatory,
+ input_factory=input_factory,
+ output_factory=output_factory,
+ )
+ # copy 1hz f
+ obsrio_second(
+ observatory=observatory,
+ input_factory=input_factory,
+ output_factory=output_factory,
+ )
+ # filter to 1m (processes 1s in output_factory)
+ obsrio_minute(
+ observatory=observatory,
+ input_factory=output_factory,
+ output_factory=output_factory,
+ )
+ # filter temperatures to 1m
+ obsrio_temperatures(
+ observatory=observatory,
+ input_factory=input_factory,
+ output_factory=output_factory,
+ )
+
+
+def process_variation(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ interval: str = "second",
+ output_factory: Optional[TimeseriesFactory] = None,
+ sqdist_statefile: Optional[str] = None,
+):
+ input_factory = input_factory or get_edge_factory(data_type="variation")
+ output_factory = output_factory or get_edge_factory(data_type="variation")
+ # compute delta f
+ deltaf(
+ deltaf_from="obs",
+ input_factory=input_factory,
+ interval=interval,
+ observatory=observatory,
+ output_factory=output_factory,
+ )
+ # x,y based on declination baseline
+ rotate(
+ observatory=observatory,
+ input_factory=input_factory,
+ interval=interval,
+ output_channels=("X", "Y"),
+ output_factory=output_factory,
+ xyz_from="obs",
+ xyz_to="geo",
+ )
+ # d based on h,e
+ rotate(
+ input_factory=input_factory,
+ interval=interval,
+ observatory=observatory,
+ output_channels=("D",),
+ output_factory=output_factory,
+ xyz_from="obs",
+ xyz_to="obsd",
+ )
+ if interval == "minute" and sqdist_statefile is not None:
+ sqdist_minute(
+ input_factory=input_factory,
+ observatory=observatory,
+ output_factory=output_factory,
+ statefile=sqdist_statefile,
+ )
+
+
+if __name__ == "__main__":
+ main()
diff --git a/geomagio/processing/observatory.py b/geomagio/processing/observatory.py
new file mode 100644
index 0000000000000000000000000000000000000000..6032a9d47354e14b21285f223f4b6cc29e7a8cc1
--- /dev/null
+++ b/geomagio/processing/observatory.py
@@ -0,0 +1,201 @@
+import os
+from typing import Optional
+
+import numpy
+
+from ..algorithm import (
+ Algorithm,
+ AdjustedAlgorithm,
+ DeltaFAlgorithm,
+ SqDistAlgorithm,
+ XYZAlgorithm,
+)
+from ..edge import EdgeFactory, MiniSeedFactory
+from ..Controller import Controller, get_realtime_interval
+from ..TimeseriesFactory import TimeseriesFactory
+from .factory import get_edge_factory
+
+
+def adjusted(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ interval: str = "second",
+ output_factory: Optional[TimeseriesFactory] = None,
+ matrix: Optional[numpy.ndarray] = None,
+ pier_correction: Optional[float] = None,
+ statefile: Optional[str] = None,
+ realtime_interval: int = 600,
+):
+ """Run Adjusted algorithm.
+
+ Parameters
+ ----------
+ observatory: observatory to calculate
+ input_factory: where to read, should be configured with data_type
+ interval: data interval
+ output_factory: where to write, should be configured with data_type
+ matrix: adjusted matrix
+ pier_correction: adjusted pier correction
+ statefile: adjusted statefile
+ realtime_interval: window in seconds
+
+ Uses update_limit=10.
+ """
+ if not statefile and (not matrix or not pier_correction):
+ raise ValueError("Either statefile or matrix and pier_correction are required.")
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ algorithm=AdjustedAlgorithm(
+ matrix=matrix,
+ pier_correction=pier_correction,
+ statefile=statefile,
+ data_type="adjusted",
+ location="A0",
+ ),
+ inputFactory=input_factory or get_edge_factory(data_type="variation"),
+ inputInterval=interval,
+ outputFactory=output_factory or get_edge_factory(data_type="adjusted"),
+ outputInterval=interval,
+ )
+ controller.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=("H", "E", "Z", "F"),
+ output_channels=("X", "Y", "Z", "F"),
+ realtime=realtime_interval,
+ update_limit=10,
+ )
+
+
+def deltaf(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ interval: str = "second",
+ output_factory: Optional[TimeseriesFactory] = None,
+ deltaf_from="obs",
+ realtime_interval: int = 600,
+):
+ """Run Delta-F algorithm.
+
+ Parameters
+ ----------
+ observatory: observatory to calculate
+ input_factory: where to read, should be configured with data_type and interval
+ output_factory: where to write, should be configured with data_type and interval
+ deltaf_from: one of {"obs", "mag", "geo"}
+ realtime_interval: window in seconds
+
+ Uses update_limit=10.
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ algorithm=DeltaFAlgorithm(informat=deltaf_from),
+ inputFactory=input_factory or get_edge_factory(),
+ inputInterval=interval,
+ outputFactory=output_factory or get_edge_factory(),
+ outputInterval=interval,
+ )
+ controller.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ output_channels=("G",),
+ realtime=realtime_interval,
+ update_limit=10,
+ )
+
+
+def rotate(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ interval: str = "second",
+ output_channels=("X", "Y"),
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+ xyz_from="obs",
+ xyz_to="geo",
+):
+ """Run XYZ rotation algorithm.
+
+ Parameters
+ ----------
+ observatory: observatory to calculate
+ input_factory: where to read, should be configured with data_type and interval
+ output_channels: which channels to write
+ output_factory: where to write, should be configured with data_type and interval
+ realtime_interval: window in seconds
+ xyz_from: one of {"obs", "mag", "geo"}
+ xyz_to: one of {"obs", "obsd", "mag", "geo"}
+
+ Uses update_limit=10.
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ algorithm=XYZAlgorithm(informat=xyz_from, outformat=xyz_to),
+ inputFactory=input_factory or get_edge_factory(),
+ inputInterval=interval,
+ outputFactory=output_factory or get_edge_factory(),
+ outputInterval=interval,
+ )
+ controller.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ output_channels=output_channels,
+ realtime=realtime_interval,
+ update_limit=10,
+ )
+
+
+def sqdist_minute(
+ observatory: str,
+ statefile: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 1800,
+):
+ """Run SqDist algorithm.
+
+ Only supports "minute" interval.
+
+ Parameters
+ ----------
+ observatory: observatory to calculate
+ statefile: sqdist statefile must already exist
+ input_factory: where to read, should be configured with data_type and interval
+ output_factory: where to write, should be configured with data_type and interval
+ realtime_interval: window in seconds
+ """
+ if not statefile:
+ raise ValueError("Statefile is required.")
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ algorithm=SqDistAlgorithm(
+ alpha=2.3148e-5,
+ gamma=3.3333e-2,
+ m=1440,
+ mag=True,
+ smooth=180,
+ statefile=statefile,
+ ),
+ inputFactory=input_factory or get_edge_factory(interval="minute"),
+ inputInterval="minute",
+ outputFactory=output_factory or get_edge_factory(interval="minute"),
+ outputInterval="minute",
+ )
+ # sqdist is stateful, use run
+ controller.run(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=("X", "Y", "Z", "F"),
+ output_channels=("MDT", "MSQ", "MSV"),
+ realtime=realtime_interval,
+ rename_output_channel=(("H_Dist", "MDT"), ("H_SQ", "MSQ"), ("H_SV", "MSV")),
+ update_limit=10,
+ )
diff --git a/geomagio/processing/obsrio.py b/geomagio/processing/obsrio.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd93e8d27af8632eb08b0c5fe426de3c5a2d6d5d
--- /dev/null
+++ b/geomagio/processing/obsrio.py
@@ -0,0 +1,133 @@
+import os
+from typing import Optional
+
+from ..algorithm import Algorithm, FilterAlgorithm
+from ..edge import EdgeFactory, MiniSeedFactory
+from ..Controller import Controller, get_realtime_interval
+from ..TimeseriesFactory import TimeseriesFactory
+from .factory import get_edge_factory, get_miniseed_factory
+
+
+def obsrio_minute(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+):
+ """Filter 1Hz legacy H,E,Z,F to 1 minute legacy.
+
+ Should be called after obsrio_second() and obsrio_tenhertz(),
+ which populate 1Hz legacy H,E,Z,F.
+ """
+ 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.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(channel,),
+ output_channels=(channel,),
+ realtime=realtime_interval,
+ update_limit=10,
+ )
+
+
+def obsrio_second(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+):
+ """Copy 1Hz miniseed F to 1Hz legacy F.
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ algorithm=Algorithm(),
+ 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.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=("F",),
+ output_channels=("F",),
+ realtime=realtime_interval,
+ update_limit=10,
+ )
+
+
+def obsrio_temperatures(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+):
+ """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"),
+ outputInterval="minute",
+ )
+ renames = {"LK1": "UK1", "LK2": "UK2", "LK3": "UK3", "LK4": "UK4"}
+ for input_channel in renames.keys():
+ output_channel = renames[input_channel]
+ controller.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(input_channel,),
+ output_channels=(output_channel,),
+ realtime=realtime_interval,
+ rename_output_channel=((input_channel, output_channel),),
+ update_limit=10,
+ )
+
+
+def obsrio_tenhertz(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+):
+ """Filter 10Hz miniseed U,V,W to 1Hz legacy H,E,Z.
+ """
+ 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"),
+ outputInterval="second",
+ )
+ renames = {"U": "H", "V": "E", "W": "Z"}
+ for input_channel in renames.keys():
+ output_channel = renames[input_channel]
+ controller.run_as_update(
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(input_channel,),
+ output_channels=(output_channel,),
+ realtime=realtime_interval,
+ rename_output_channel=((input_channel, output_channel),),
+ update_limit=10,
+ )
diff --git a/setup.py b/setup.py
index 06ea10308c9893f04cbecc6f165e951112f31341..b5f576dde7349632ebf562881a472162d55ad747 100644
--- a/setup.py
+++ b/setup.py
@@ -18,6 +18,7 @@ setuptools.setup(
"Source": "https://github.com/usgs/geomag-algorithms",
},
python_requires=">=3.6, <4",
+ console_scripts=["geomagio-process=geomagio.processing:main"],
scripts=["bin/geomag.py", "bin/geomag_webservice.py", "bin/make_cal.py"],
setup_requires=[
"setuptools-pipfile",