From fd55e855147964e5518d05fa24144bb073fb76c8 Mon Sep 17 00:00:00 2001
From: Hal Simpson <hasimpson@usgs.gov>
Date: Mon, 8 Jun 2015 13:16:59 -0600
Subject: [PATCH] broke out update vs. normal timeseries, added functions to
help analyze gaps. Still need to complete update
---
geomagio/Controller.py | 101 +++++++++++++++++++++++++++++++++++++++--
1 file changed, 98 insertions(+), 3 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 7a336a80..4ae42842 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -1,4 +1,8 @@
-"""Conrtoller class for geomag algorithms"""
+"""Controller class for geomag algorithms"""
+
+import obspy.core
+import numpy.ma as ma
+import sys
class Controller(object):
@@ -13,10 +17,11 @@ class Controller(object):
algorithm: the algorithm(s) that will take procees the timeseries data
"""
- def __init__(self, inputFactory, outputFactory, algorithm):
+ def __init__(self, inputFactory, outputFactory, algorithm, update=False):
self._inputFactory = inputFactory
self._algorithm = algorithm
self._outputFactory = outputFactory
+ self._update = update
def run(self, starttime, endtime):
"""run an algorithm as setup up by the main script.
@@ -28,10 +33,100 @@ class Controller(object):
endtime : UTCDateTime
time of last sample to be worked on.
"""
+ if (self._update):
+ self.run_as_update(starttime, endtime)
+ else:
+ self.run_as_timeseries(starttime, endtime)
+
+ def run_as_update(self, starttime, endtime):
+ input_channels = self._algorithm.get_input_channels()
+ output_channels = self._algorithm.get_output_channels()
+
+ timeseries_in = self._inputFactory.get_timeseries(starttime,
+ endtime, channels=input_channels)
+ timeseries_out = self._inputFactory.get_timeseries(starttime,
+ endtime, channels=output_channels)
+
+ full_gaps, gaps = self._create_gap_stream(timeseries_out,
+ output_channels)
+
+ #self.get_gap_times(timeseries_out, output_channels)
+
+ #starttime, endtime = self._algorithm.get_data_time_extent(channels, )
+
+ #for each gap in start/end array
+ # get corresponding input timeseries
+ # processed = self._algorithm.process(timeseries)
+ # self._outputFactory.put_timeseries(timeseries=processed,
+ # channels=output_channels)
+
+ def run_as_timeseries(self, starttime, endtime):
input_channels = self._algorithm.get_input_channels()
+
timeseries = self._inputFactory.get_timeseries(starttime, endtime,
- channels=input_channels)
+ channels=input_channels)
+
processed = self._algorithm.process(timeseries)
output_channels = self._algorithm.get_output_channels()
self._outputFactory.put_timeseries(timeseries=processed,
channels=output_channels)
+
+ def _convert_stream_to_masked(self, timeseries, channel):
+ """convert geomag edge traces in a timeseries stream to a MaskedArray
+ This allows for gaps and splitting.
+ Parameters
+ ----------
+ stream : obspy.core.stream
+ a stream retrieved from a geomag edge representing one channel.
+ channel: string
+ the channel to be masked.
+ """
+ for trace in timeseries.select(channel=channel):
+ trace.data = ma.masked_invalid(trace.data)
+
+ def _create_gap_stream(self, timeseries, channels):
+ gap_stream = obspy.core.Stream()
+ for channel in channels:
+ for trace in timeseries.select(channel=channel):
+ trace.data = ma.masked_invalid(trace.data)
+ for data in trace.split():
+ gap_stream += data
+
+ gaps = gap_stream.getGaps()
+ for gap in gaps:
+ gap[4] = gap[4] + 60
+ gap[5] = gap[5] - 60
+ print gaps
+
+ # sync gaps across channels
+
+ full_gaps = []
+ gap_cnt = len(gaps)
+ for i in range(0, gap_cnt):
+ gap = gaps[i]
+ if self._contained_in_gap(gap, full_gaps):
+ continue
+
+ starttime = gap[4]
+ endtime = gap[5]
+ for x in range(i+1, gap_cnt):
+ nxtgap = gaps[x]
+ if ((nxtgap[4] >= starttime and nxtgap[4] <= endtime)
+ or (nxtgap[5] >= starttime and nxtgap[5] <= endtime)):
+ if nxtgap[4] < starttime:
+ starttime = nxtgap[4]
+ if nxtgap[5] > endtime:
+ endtime = nxtgap[5]
+
+ full_gaps.append([starttime, endtime])
+
+ print full_gaps
+ return (full_gaps, gaps)
+
+ def _contained_in_gap(self, gap, gaps):
+ starttime = gap[4]
+ endtime = gap[5]
+ for gap in gaps:
+ if starttime >= gap[0] and endtime <= gap[1]:
+ return True
+ return False
--
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