From 68cffbef4faab5bb89d7f9aeb89f72774739852f Mon Sep 17 00:00:00 2001
From: arigdon-usgs <arigdon@usgs.gov>
Date: Fri, 29 Jun 2018 11:52:29 -0600
Subject: [PATCH] Changes to fix missing channel specification issues in
XYZAlgorithm and StreamConverter, added a get_required_channels option
---
geomagio/StreamConverter.py | 35 +++++++++++++++---------------
geomagio/algorithm/Algorithm.py | 10 +++++++++
geomagio/algorithm/XYZAlgorithm.py | 24 +++++++++++++++++---
3 files changed, 49 insertions(+), 20 deletions(-)
diff --git a/geomagio/StreamConverter.py b/geomagio/StreamConverter.py
index d2e65e47b..bedc9dacb 100644
--- a/geomagio/StreamConverter.py
+++ b/geomagio/StreamConverter.py
@@ -28,15 +28,15 @@ def get_geo_from_mag(mag):
"""
h = mag.select(channel='H')[0]
d = mag.select(channel='D')[0]
- z = mag.select(channel='Z')[0]
- f = mag.select(channel='F')[0]
+ z = mag.select(channel='Z')
+ f = mag.select(channel='F')
mag_h = h.data
mag_d = d.data
(geo_x, geo_y) = ChannelConverter.get_geo_from_mag(mag_h, mag_d)
return obspy.core.Stream((
__get_trace('X', h.stats, geo_x),
__get_trace('Y', d.stats, geo_y),
- z, f))
+ )) + z + f
def get_geo_from_obs(obs):
@@ -116,15 +116,15 @@ def get_mag_from_geo(geo):
"""
x = geo.select(channel='X')[0]
y = geo.select(channel='Y')[0]
- z = geo.select(channel='Z')[0]
- f = geo.select(channel='F')[0]
+ z = geo.select(channel='Z')
+ f = geo.select(channel='F')
geo_x = x.data
geo_y = y.data
(mag_h, mag_d) = ChannelConverter.get_mag_from_geo(geo_x, geo_y)
return obspy.core.Stream((
__get_trace('H', x.stats, mag_h),
__get_trace('D', y.stats, mag_d),
- z, f))
+ )) + z + f
def get_mag_from_obs(obs):
@@ -142,8 +142,8 @@ def get_mag_from_obs(obs):
"""
h = obs.select(channel='H')[0]
e = __get_obs_e_from_obs(obs)
- z = obs.select(channel='Z')[0]
- f = obs.select(channel='F')[0]
+ z = obs.select(channel='Z')
+ f = obs.select(channel='F')
obs_h = h.data
obs_e = e.data
d0 = ChannelConverter.get_radians_from_minutes(
@@ -152,7 +152,7 @@ def get_mag_from_obs(obs):
return obspy.core.Stream((
__get_trace('H', h.stats, mag_h),
__get_trace('D', e.stats, mag_d),
- z, f))
+ )) + z + f
def get_obs_from_geo(geo, include_d=False):
@@ -189,8 +189,9 @@ def get_obs_from_mag(mag, include_d=False):
"""
h = mag.select(channel='H')[0]
d = mag.select(channel='D')[0]
- z = mag.select(channel='Z')[0]
- f = mag.select(channel='F')[0]
+ z = mag.select(channel='Z')
+ f = mag.select(channel='F')
+
mag_h = h.data
mag_d = d.data
d0 = ChannelConverter.get_radians_from_minutes(
@@ -200,11 +201,11 @@ def get_obs_from_mag(mag, include_d=False):
traces = (
__get_trace('H', h.stats, obs_h),
__get_trace('E', d.stats, obs_e),
- z, f)
+ )
if include_d:
obs_d = ChannelConverter.get_obs_d_from_obs(obs_h, obs_e)
traces = traces + (__get_trace('D', d.stats, obs_d),)
- return obspy.core.Stream(traces)
+ return obspy.core.Stream(traces) + z + f
def get_obs_from_obs(obs, include_e=False, include_d=False):
@@ -225,16 +226,16 @@ def get_obs_from_obs(obs, include_e=False, include_d=False):
new stream object containing observatory components H, D, E, Z, and F
"""
h = obs.select(channel='H')[0]
- z = obs.select(channel='Z')[0]
- f = obs.select(channel='F')[0]
- traces = (h, z, f)
+ z = obs.select(channel='Z')
+ f = obs.select(channel='F')
+ traces = (h, )
if include_d:
d = __get_obs_d_from_obs(obs)
traces = traces + (d, )
if include_e:
e = __get_obs_e_from_obs(obs)
traces = traces + (e, )
- return obspy.core.Stream(traces)
+ return obspy.core.Stream(traces) + z + f
def __get_trace(channel, stats, data):
diff --git a/geomagio/algorithm/Algorithm.py b/geomagio/algorithm/Algorithm.py
index 1aa1b7b6c..a3f264cb5 100644
--- a/geomagio/algorithm/Algorithm.py
+++ b/geomagio/algorithm/Algorithm.py
@@ -46,6 +46,16 @@ class Algorithm(object):
"""
return self._inchannels
+ def get_required_channels(self):
+ """Get only required channels
+
+ Returns
+ -------
+ array_like
+ list of channels essential to the algorithm
+ """
+ return self._inchannels
+
def get_output_channels(self):
"""Get output channels
diff --git a/geomagio/algorithm/XYZAlgorithm.py b/geomagio/algorithm/XYZAlgorithm.py
index 92aa4585c..b93f26a88 100644
--- a/geomagio/algorithm/XYZAlgorithm.py
+++ b/geomagio/algorithm/XYZAlgorithm.py
@@ -7,6 +7,7 @@ from __future__ import absolute_import
from .Algorithm import Algorithm
from .AlgorithmException import AlgorithmException
from .. import StreamConverter
+import numpy as np
# List of channels by geomagnetic observatory orientation.
# geo represents a geographic north/south orientation
@@ -51,11 +52,17 @@ class XYZAlgorithm(Algorithm):
channels: array_like
channels that are expected in stream.
"""
- for channel in self._inchannels:
+ for channel in self.get_required_channels():
if len(timeseries.select(channel=channel)) == 0:
raise AlgorithmException(
'Channel %s not found in input' % channel)
+ def get_required_channels(self):
+ """Only the first two channels are required
+ for the XYZAlgorithm
+ """
+ return self._inchannels[:2]
+
def process(self, timeseries):
"""converts a timeseries stream into a different coordinate system
@@ -104,6 +111,7 @@ class XYZAlgorithm(Algorithm):
elif informat == 'obs' or informat == 'obsd':
out_stream = StreamConverter.get_obs_from_obs(timeseries,
include_d=True)
+
return out_stream
@classmethod
@@ -134,5 +142,15 @@ class XYZAlgorithm(Algorithm):
"""
self._informat = arguments.xyz_from
self._outformat = arguments.xyz_to
- self._inchannels = CHANNELS[self._informat]
- self._outchannels = CHANNELS[self._outformat]
+ self._inchannels = arguments.inchannels or \
+ CHANNELS[self._informat]
+ # outchannels set according to specified outchannels or inchannel designation
+ # if the inchannels do not have 'Z' or 'F' neither will the outchannel
+ if arguments.outchannels:
+ self._outchannels = arguments.outchannels
+ else:
+ self._outchannels = CHANNELS[self._outformat]
+ if not 'Z' in self._inchannels:
+ del self._outchannels[self._outchannels.index('Z')]
+ if not 'F' in self._inchannels:
+ del self._outchannels[self._outchannels.index('F')]
--
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