From 92cea08efedd785ff818bb1aaec5acec1340923e Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 20 Jan 2016 12:12:16 -0700
Subject: [PATCH] Move algorithms to separate package, abstract algorithm
arguments
---
geomagio/Controller.py | 33 +++------
geomagio/__init__.py | 5 --
geomagio/{ => algorithm}/Algorithm.py | 24 +++++-
.../{ => algorithm}/AlgorithmException.py | 0
geomagio/{ => algorithm}/DeltaFAlgorithm.py | 37 ++++++++--
geomagio/{ => algorithm}/XYZAlgorithm.py | 73 ++++++++++++++-----
geomagio/algorithm/__init__.py | 28 +++++++
test/Controller_test.py | 3 +-
test/__init__.py | 0
test/{ => algorithm_test}/Algorithm_test.py | 2 +-
.../{ => algorithm_test}/XYZAlgorithm_test.py | 4 +-
test/algorithm_test/__init__.py | 0
test/edge_test/__init__.py | 0
test/iaga2002_test/__init__.py | 0
test/imfv283_test/__init__.py | 0
test/pcdcp_test/__init__.py | 0
16 files changed, 149 insertions(+), 60 deletions(-)
rename geomagio/{ => algorithm}/Algorithm.py (79%)
rename geomagio/{ => algorithm}/AlgorithmException.py (100%)
rename geomagio/{ => algorithm}/DeltaFAlgorithm.py (66%)
rename geomagio/{ => algorithm}/XYZAlgorithm.py (62%)
create mode 100644 geomagio/algorithm/__init__.py
create mode 100644 test/__init__.py
rename test/{ => algorithm_test}/Algorithm_test.py (95%)
rename test/{ => algorithm_test}/XYZAlgorithm_test.py (92%)
create mode 100644 test/algorithm_test/__init__.py
create mode 100644 test/edge_test/__init__.py
create mode 100644 test/iaga2002_test/__init__.py
create mode 100644 test/imfv283_test/__init__.py
create mode 100644 test/pcdcp_test/__init__.py
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 60094a117..f6142619a 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -4,7 +4,7 @@
import argparse
import sys
from obspy.core import UTCDateTime
-from Algorithm import Algorithm
+from algorithm import algorithms
import TimeseriesUtility
from TimeseriesFactoryException import TimeseriesFactoryException
from Util import ObjectView
@@ -14,9 +14,6 @@ import iaga2002
import pcdcp
import imfv283
-from DeltaFAlgorithm import DeltaFAlgorithm
-from XYZAlgorithm import XYZAlgorithm
-
class Controller(object):
"""Controller for geomag algorithms.
@@ -301,17 +298,8 @@ def main(args):
else:
print >> sys.stderr, "Missing required output directive"
- if args.xyz is not None:
- algorithm = XYZAlgorithm(informat=args.xyz[0],
- outformat=args.xyz[1])
- elif args.deltaf is not None:
- algorithm = DeltaFAlgorithm(informat=args.deltaf)
- else:
- # TODO get smarter on inchannels/outchannels since input doesn't always
- # need to use the --inchannels argument, but might (as in iaga2002),
- # get it from the file.
- algorithm = Algorithm(inchannels=args.inchannels,
- outchannels=args.outchannels or args.inchannels)
+ algorithm = algorithms[args.algorithm]()
+ algorithm.configure(args)
# TODO check for unused arguments.
@@ -481,14 +469,11 @@ def parse_args(args):
help='Edge IP #. See --output-edge-* for other optional arguments')
# Algorithms group
- algorithm_group = parser.add_mutually_exclusive_group()
- algorithm_group.add_argument('--xyz',
- nargs=2,
- choices=['geo', 'mag', 'obs', 'obsd'],
- help='Enter the geomagnetic orientation(s) you want to read from' +
- ' and to respectfully.')
- algorithm_group.add_argument('--deltaf',
- choices=['geo', 'obs', 'obsd'],
- help='Enter the geomagnetic orientation you want to read from')
+ parser.add_argument('--algorithm',
+ choices=[k for k in algorithms],
+ default='default')
+
+ for k in algorithms:
+ algorithms[k].add_arguments(parser)
return parser.parse_args(args)
diff --git a/geomagio/__init__.py b/geomagio/__init__.py
index 4b0f6a79f..9e086ee63 100644
--- a/geomagio/__init__.py
+++ b/geomagio/__init__.py
@@ -4,19 +4,14 @@ Geomag Algorithm Module
import ChannelConverter
import StreamConverter
-from Algorithm import Algorithm
-from AlgorithmException import AlgorithmException
from Controller import Controller
from ObservatoryMetadata import ObservatoryMetadata
from TimeseriesFactory import TimeseriesFactory
from TimeseriesFactoryException import TimeseriesFactoryException
import TimeseriesUtility
import Util
-from XYZAlgorithm import XYZAlgorithm
__all__ = [
- 'Algorithm',
- 'AlgorithmException',
'ChannelConverter',
'Controller',
'DeltaFAlgorithm',
diff --git a/geomagio/Algorithm.py b/geomagio/algorithm/Algorithm.py
similarity index 79%
rename from geomagio/Algorithm.py
rename to geomagio/algorithm/Algorithm.py
index bd7699089..fed7196b9 100644
--- a/geomagio/Algorithm.py
+++ b/geomagio/algorithm/Algorithm.py
@@ -1,6 +1,6 @@
"""Algorithm Interface."""
-import TimeseriesUtility
+from .. import TimeseriesUtility
class Algorithm(object):
@@ -91,3 +91,25 @@ class Algorithm(object):
endtime < input_gap[2]):
return False
return True
+
+ @classmethod
+ def add_arguments(cls, parser):
+ """Add command line arguments to argparse parser.
+
+ Parameters
+ ----------
+ parser: ArgumentParser
+ command line argument parser
+ """
+ pass
+
+ def configure(self, arguments):
+ """Configure algorithm using comand line arguments.
+
+ Parameters
+ ----------
+ arguments: Namespace
+ parsed command line arguments
+ """
+ self._inchannels = arguments.inchannels
+ self._outchannels = arguments.outchannels or arguments.inchannels
diff --git a/geomagio/AlgorithmException.py b/geomagio/algorithm/AlgorithmException.py
similarity index 100%
rename from geomagio/AlgorithmException.py
rename to geomagio/algorithm/AlgorithmException.py
diff --git a/geomagio/DeltaFAlgorithm.py b/geomagio/algorithm/DeltaFAlgorithm.py
similarity index 66%
rename from geomagio/DeltaFAlgorithm.py
rename to geomagio/algorithm/DeltaFAlgorithm.py
index d0619dee6..616c83d87 100644
--- a/geomagio/DeltaFAlgorithm.py
+++ b/geomagio/algorithm/DeltaFAlgorithm.py
@@ -4,7 +4,7 @@
from Algorithm import Algorithm
from AlgorithmException import AlgorithmException
-import StreamConverter as StreamConverter
+from .. import StreamConverter
# List of channels by geomagnetic observatory orientation.
# geo represents a geographic north/south orientation
@@ -27,10 +27,10 @@ class DeltaFAlgorithm(Algorithm):
will be converting from.
"""
- def __init__(self, informat=None):
+ def __init__(self, informat='obs'):
Algorithm.__init__(self, inchannels=CHANNELS[informat],
outchannels=['G'])
- self.informat = informat
+ self._informat = informat
def check_stream(self, timeseries):
"""checks a stream to make certain all the required channels
@@ -61,10 +61,35 @@ class DeltaFAlgorithm(Algorithm):
"""
self.check_stream(timeseries)
out_stream = None
-
- if self.informat == 'geo':
+ informat = self._informat
+ if informat == 'geo':
out_stream = StreamConverter.get_deltaf_from_geo(timeseries)
- elif self.informat == 'obs' or self.informat == 'obsd':
+ elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_deltaf_from_obs(timeseries)
return out_stream
+
+ @classmethod
+ def add_arguments(cls, parser):
+ """Add command line arguments to argparse parser.
+
+ Parameters
+ ----------
+ parser: ArgumentParser
+ command line argument parser
+ """
+ parser.add_argument('--deltaf-from',
+ choices=['geo', 'obs', 'obsd'],
+ default='obs',
+ help='Geomagnetic orientation to read from')
+
+ def configure(self, arguments):
+ """Configure algorithm using comand line arguments.
+
+ Parameters
+ ----------
+ arguments: Namespace
+ parsed command line arguments
+ """
+ self._informat = arguments.deltaf_from
+ self._inchannels = CHANNELS[self._informat]
diff --git a/geomagio/XYZAlgorithm.py b/geomagio/algorithm/XYZAlgorithm.py
similarity index 62%
rename from geomagio/XYZAlgorithm.py
rename to geomagio/algorithm/XYZAlgorithm.py
index 12c3a1e0c..64d1e9158 100644
--- a/geomagio/XYZAlgorithm.py
+++ b/geomagio/algorithm/XYZAlgorithm.py
@@ -5,7 +5,7 @@
from Algorithm import Algorithm
from AlgorithmException import AlgorithmException
-import StreamConverter as StreamConverter
+from .. import StreamConverter
# List of channels by geomagnetic observatory orientation.
# geo represents a geographic north/south orientation
@@ -33,11 +33,11 @@ class XYZAlgorithm(Algorithm):
be converting to.
"""
- def __init__(self, informat=None, outformat=None):
+ def __init__(self, informat='obs', outformat='geo'):
Algorithm.__init__(self, inchannels=CHANNELS[informat],
outchannels=CHANNELS[outformat])
- self.informat = informat
- self.outformat = outformat
+ self._informat = informat
+ self._outformat = outformat
def check_stream(self, timeseries):
"""checks an stream to make certain all the required channels
@@ -69,36 +69,69 @@ class XYZAlgorithm(Algorithm):
"""
self.check_stream(timeseries)
out_stream = None
- if self.outformat == 'geo':
- if self.informat == 'geo':
+ informat = self._informat
+ outformat = self._outformat
+ if outformat == 'geo':
+ if informat == 'geo':
out_stream = timeseries
- elif self.informat == 'mag':
+ elif informat == 'mag':
out_stream = StreamConverter.get_geo_from_mag(timeseries)
- elif self.informat == 'obs' or self.informat == 'obsd':
+ elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_geo_from_obs(timeseries)
- elif self.outformat == 'mag':
- if self.informat == 'geo':
+ elif outformat == 'mag':
+ if informat == 'geo':
out_stream = StreamConverter.get_mag_from_geo(timeseries)
- elif self.informat == 'mag':
+ elif informat == 'mag':
out_stream = timeseries
- elif self.informat == 'obs' or self.informat == 'obsd':
+ elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_mag_from_obs(timeseries)
- elif self.outformat == 'obs':
- if self.informat == 'geo':
+ elif outformat == 'obs':
+ if informat == 'geo':
out_stream = StreamConverter.get_obs_from_geo(timeseries)
- elif self.informat == 'mag':
+ elif informat == 'mag':
out_stream = StreamConverter.get_obs_from_mag(timeseries)
- elif self.informat == 'obs' or self.informat == 'obsd':
+ elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_obs_from_obs(timeseries,
include_e=True)
- elif self.outformat == 'obsd':
- if self.informat == 'geo':
+ elif outformat == 'obsd':
+ if informat == 'geo':
out_stream = StreamConverter.get_obs_from_geo(timeseries,
include_d=True)
- elif self.informat == 'mag':
+ elif informat == 'mag':
out_stream = StreamConverter.get_obs_from_mag(timeseries,
include_d=True)
- elif self.informat == 'obs' or self.informat == 'obsd':
+ elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_obs_from_obs(timeseries,
include_d=True)
return out_stream
+
+ @classmethod
+ def add_arguments(cls, parser):
+ """Add command line arguments to argparse parser.
+
+ Parameters
+ ----------
+ parser: ArgumentParser
+ command line argument parser
+ """
+ parser.add_argument('--xyz-from',
+ choices=['geo', 'mag', 'obs', 'obsd'],
+ default='obs',
+ help='Geomagnetic orientation to read from')
+ parser.add_argument('--xyz-to',
+ choices=['geo', 'mag', 'obs', 'obsd'],
+ default='geo',
+ help='Geomagnetic orientation to convert to')
+
+ def configure(self, arguments):
+ """Configure algorithm using comand line arguments.
+
+ Parameters
+ ----------
+ arguments: Namespace
+ parsed command line arguments
+ """
+ self._informat = arguments.xyz_from
+ self._outformat = arguments.xyz_to
+ self._inchannels = CHANNELS[self._informat]
+ self._outchannels = CHANNELS[self._outformat]
diff --git a/geomagio/algorithm/__init__.py b/geomagio/algorithm/__init__.py
new file mode 100644
index 000000000..caaabb0c7
--- /dev/null
+++ b/geomagio/algorithm/__init__.py
@@ -0,0 +1,28 @@
+"""
+Geomag Algorithms module
+"""
+
+# base classes
+from Algorithm import Algorithm
+from AlgorithmException import AlgorithmException
+# algorithms
+from DeltaFAlgorithm import DeltaFAlgorithm
+from XYZAlgorithm import XYZAlgorithm
+
+
+# algorithms is used by Controller to auto generate arguments
+algorithms = {
+ 'identity': Algorithm,
+ 'deltaf': DeltaFAlgorithm,
+ 'xyz': XYZAlgorithm
+}
+
+
+__all__ = [
+ # base classes
+ 'Algorithm',
+ 'AlgorithmException',
+ # algorithms
+ 'DeltaFAlgorithm',
+ 'XYZAlgorithm'
+]
diff --git a/test/Controller_test.py b/test/Controller_test.py
index e407a9eca..4b1992c98 100644
--- a/test/Controller_test.py
+++ b/test/Controller_test.py
@@ -1,5 +1,6 @@
#! /usr/bin/env python
-from geomagio import Algorithm, Controller, TimeseriesFactory
+from geomagio import Controller, TimeseriesFactory
+from geomagio.algorithm import Algorithm
from nose.tools import assert_is_instance
diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/Algorithm_test.py b/test/algorithm_test/Algorithm_test.py
similarity index 95%
rename from test/Algorithm_test.py
rename to test/algorithm_test/Algorithm_test.py
index cf4d2e3cb..8ce878f1d 100644
--- a/test/Algorithm_test.py
+++ b/test/algorithm_test/Algorithm_test.py
@@ -2,7 +2,7 @@
from obspy.core.stream import Stream
from nose.tools import assert_equals
from nose.tools import assert_is_instance
-from geomagio import Algorithm
+from geomagio.algorithm import Algorithm
def test_algorithm_process():
diff --git a/test/XYZAlgorithm_test.py b/test/algorithm_test/XYZAlgorithm_test.py
similarity index 92%
rename from test/XYZAlgorithm_test.py
rename to test/algorithm_test/XYZAlgorithm_test.py
index b84f87198..0ffcfb3ec 100644
--- a/test/XYZAlgorithm_test.py
+++ b/test/algorithm_test/XYZAlgorithm_test.py
@@ -2,8 +2,8 @@
from obspy.core.stream import Stream
from nose.tools import assert_equals
from nose.tools import assert_is
-from geomagio import XYZAlgorithm
-from StreamConverter_test import __create_trace
+from geomagio.algorithm import XYZAlgorithm
+from ..StreamConverter_test import __create_trace
def test_xyzalgorithm_process():
diff --git a/test/algorithm_test/__init__.py b/test/algorithm_test/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/edge_test/__init__.py b/test/edge_test/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/iaga2002_test/__init__.py b/test/iaga2002_test/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/imfv283_test/__init__.py b/test/imfv283_test/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/pcdcp_test/__init__.py b/test/pcdcp_test/__init__.py
new file mode 100644
index 000000000..e69de29bb
--
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