From c251b8e02c111f6c32b3b6c031964873ad37335c Mon Sep 17 00:00:00 2001
From: arigdon-usgs <arigdon@usgs.gov>
Date: Wed, 25 Jul 2018 11:17:35 -0600
Subject: [PATCH] Clean Timeseries fix to make sure start and end times are
valid sample times
---
geomagio/edge/EdgeFactory.py | 26 +++++++++++++--------
test/edge_test/EdgeFactory_test.py | 37 +++++++++++++++++++++++++++---
2 files changed, 50 insertions(+), 13 deletions(-)
diff --git a/geomagio/edge/EdgeFactory.py b/geomagio/edge/EdgeFactory.py
index a26993d47..ef6d210c4 100644
--- a/geomagio/edge/EdgeFactory.py
+++ b/geomagio/edge/EdgeFactory.py
@@ -220,19 +220,25 @@ class EdgeFactory(TimeseriesFactory):
for trace in timeseries:
trace_starttime = obspy.core.UTCDateTime(trace.stats.starttime)
trace_endtime = obspy.core.UTCDateTime(trace.stats.endtime)
+ trace_delta = trace.stats.delta
+
+ if trace_starttime > starttime:
+ cnt = int((trace_starttime - starttime) / trace_delta)
+ if cnt > 0:
+ trace.data = numpy.concatenate([
+ numpy.full(cnt, numpy.nan, dtype=numpy.float64),
+ trace.data])
+ trace_starttime = trace_starttime - trace_delta * cnt
+ trace.stats.starttime = trace_starttime
- if trace.stats.starttime > starttime:
- cnt = int((trace_starttime - starttime) / trace.stats.delta)
- trace.data = numpy.concatenate([
- numpy.full(cnt, numpy.nan, dtype=numpy.float64),
- trace.data])
- trace.stats.starttime = starttime
if trace_endtime < endtime:
cnt = int((endtime - trace_endtime) / trace.stats.delta)
- trace.data = numpy.concatenate([
- trace.data,
- numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
- trace.stats.endttime = endtime
+ if cnt > 0:
+ trace.data = numpy.concatenate([
+ trace.data,
+ numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
+ trace_endtime = trace_endtime + trace_delta * cnt
+ trace.stats.endttime = trace_endtime
def _convert_timeseries_to_decimal(self, stream):
"""convert geomag edge timeseries data stored as ints, to decimal by
diff --git a/test/edge_test/EdgeFactory_test.py b/test/edge_test/EdgeFactory_test.py
index e43055b50..4b583878f 100644
--- a/test/edge_test/EdgeFactory_test.py
+++ b/test/edge_test/EdgeFactory_test.py
@@ -1,10 +1,9 @@
"""Tests for EdgeFactory.py"""
-from obspy.core.utcdatetime import UTCDateTime
-from obspy.core.stream import Stream
-from obspy.core.trace import Trace
+from obspy.core import Stats, Stream, Trace, UTCDateTime
from geomagio.edge import EdgeFactory
from nose.tools import assert_equals
+import numpy as np
def test__get_edge_network():
@@ -93,3 +92,35 @@ def dont_get_timeseries():
'BOU', 'Expect timeseries to have stats')
assert_equals(timeseries.select(channel='H')[0].stats.channel,
'H', 'Expect timeseries stats channel to be equal to H')
+
+
+def test_clean_timeseries():
+ """edge_test.EdgeFactory_test.test_clean_timeseries()
+ """
+ edge_factory = EdgeFactory()
+ trace1 = _create_trace([1, 1, 1, 1, 1], 'H', UTCDateTime("2018-01-01"))
+ trace2 = _create_trace([2, 2],'E',UTCDateTime("2018-01-01"))
+ timeseries = Stream(traces=[trace1, trace2])
+ edge_factory._clean_timeseries(timeseries,trace1.stats.starttime,trace1.stats.endtime)
+ assert_equals(len(trace1.data),len(trace2.data))
+ assert_equals(trace1.stats.starttime,trace2.stats.starttime)
+ assert_equals(trace1.stats.endtime,trace2.stats.endtime)
+ # change starttime by less than 1 delta
+ starttime = trace1.stats.starttime
+ endtime = trace1.stats.endtime
+ edge_factory._clean_timeseries(timeseries,starttime-30,endtime+30)
+ assert_equals(trace1.stats.starttime,starttime)
+ # Change starttime by more than 1 delta
+ edge_factory._clean_timeseries(timeseries,starttime-90,endtime+90)
+ assert_equals(trace1.stats.starttime,starttime-60)
+ assert_equals(np.isnan(trace1.data[0]),np.isnan(np.NaN))
+
+
+def _create_trace(data,channel,starttime,delta=60.):
+ stats = Stats()
+ stats.channel = channel
+ stats.delta = delta
+ stats.starttime = starttime
+ stats.npts = len(data)
+ data = np.array(data,dtype=np.float64)
+ return Trace(data,stats)
--
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