From 241b724ff195ed1a146856234f477a7b23d4238e Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 6 Nov 2018 17:57:29 -0700
Subject: [PATCH] Add "without_gaps" option to get_stream_start_end_times, add
"pad_and_trim_trace" method and update pad_timeseries to use it
---
geomagio/TimeseriesUtility.py | 89 ++++++++++++++++++++++++++---------
1 file changed, 68 insertions(+), 21 deletions(-)
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index 385bb0b2..cc6ef041 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -59,7 +59,7 @@ def create_empty_trace(starttime, endtime, observatory,
return obspy.core.Trace(data, stats)
-def get_stream_start_end_times(timeseries):
+def get_stream_start_end_times(timeseries, without_gaps=False):
"""get start and end times from a stream.
Traverses all traces, and find the earliest starttime, and
the latest endtime.
@@ -73,6 +73,9 @@ def get_stream_start_end_times(timeseries):
tuple: (starttime, endtime)
starttime: obspy.core.UTCDateTime
endtime: obspy.core.UTCDateTime
+
+ NOTE: when the entire timeseries is a gap, and without_gaps is True,
+ the returned endtime will be one delta earlier than starttime.
"""
starttime = obspy.core.UTCDateTime(datetime.now())
endtime = obspy.core.UTCDateTime(0)
@@ -81,6 +84,15 @@ def get_stream_start_end_times(timeseries):
starttime = trace.stats.starttime
if trace.stats.endtime > endtime:
endtime = trace.stats.endtime
+ if without_gaps:
+ gaps = get_merged_gaps(get_stream_gaps(timeseries))
+ for gap in gaps:
+ if gap[0] == starttime and gap[1] != endtime:
+ # gap at start of timeseries, move to first data point
+ starttime = gap[2]
+ elif gap[1] == endtime:
+ # gap at end of timeseries
+ endtime = gap[0] - timeseries[0].stats.delta
return (starttime, endtime)
@@ -313,9 +325,9 @@ def merge_streams(*streams):
def pad_timeseries(timeseries, starttime, endtime):
- """Realigns timeseries data so the start and endtimes are the same
- as what was originally asked for, even if the data was during
- a gap.
+ """Calls pad_and_trim_trace for each trace in a stream.
+
+ Traces should be merged before calling this method.
Parameters
----------
@@ -329,20 +341,55 @@ def pad_timeseries(timeseries, starttime, endtime):
Notes: the original timeseries object is changed.
"""
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_endtime < endtime:
- cnt = int((endtime - trace_endtime) / trace.stats.delta)
- if cnt > 0:
- trace.data = numpy.concatenate([
- trace.data,
- numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
+ pad_and_trim_trace(trace, starttime, endtime)
+
+
+def pad_and_trim_trace(trace, starttime, endtime):
+ """Pads and trims trace data so it is in the range [starttime, endtime].
+
+ Uses trace stats to compute start/end times that are consistent with
+ other trace data. (starttime and endtime are not checked).
+
+ Parameters
+ ----------
+ trace: obspy.core.Trace
+ One trace to be processed
+ starttime: obspy.core.UTCDateTime
+ the starttime of the requested data
+ endtime: obspy.core.UTCDateTime
+ the endtime of the requested data
+
+ Notes: the original timeseries object is changed.
+ """
+ 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:
+ # trim to starttime
+ cnt = int((starttime - trace_starttime) / trace_delta) + 1
+ if cnt > 0:
+ trace.data = trace.data[cnt + 1:]
+ trace_starttime = trace_starttime + trace_delta * cnt
+ trace.stats.starttime = trace_starttime
+ elif trace_starttime > starttime:
+ # pad to 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_endtime > endtime:
+ # trim to endtime
+ cnt = int((trace_endtime - endtime) / trace_delta)
+ if cnt > 0:
+ trace.data = trace.data[:-cnt]
+ trace.stats.npts = len(trace.data)
+ elif trace_endtime < endtime:
+ # pad to endtime
+ cnt = int((endtime - trace_endtime) / trace.stats.delta)
+ if cnt > 0:
+ trace.data = numpy.concatenate([
+ trace.data,
+ numpy.full(cnt, numpy.nan, dtype=numpy.float64)])
--
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