From a44be2eb891062fb885a9db6aea4ee3a01e91c83 Mon Sep 17 00:00:00 2001
From: arigdon-usgs <arigdon@usgs.gov>
Date: Mon, 30 Jul 2018 12:54:16 -0600
Subject: [PATCH] Cleaned up merge_stream(), takes empty channels out at the
beginning and adds them in before the merge() function
---
geomagio/TimeseriesUtility.py | 27 +++++++++++----------------
test/TimeseriesUtility_test.py | 24 ++++++++++++++++++------
2 files changed, 29 insertions(+), 22 deletions(-)
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index 89ad4ff9..4fc34689 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -195,36 +195,31 @@ def merge_streams(*streams):
stream with contiguous traces merged, and gaps filled with numpy.nan
"""
merged = obspy.core.Stream()
- masked_trace = None
+ masked = obspy.core.Stream()
- # add unmasked, split traces to be merged
+ # sort out empty
for stream in streams:
- merged += mask_stream(stream)
-
- # if trace is completely masked separate out to be added back in later
- for trace in merged:
- if trace.data.mask.all():
- if not masked_trace:
- masked_trace = trace
+ for trace in stream:
+ if numpy.isnan(trace.data).all():
+ masked += trace
else:
- masked_trace += trace
+ merged += trace
+
+ merged = mask_stream(merged)
# split traces that contain gaps
merged = merged.split()
+ merged += masked
+
# merge data
merged.merge(
# 1 = do not interpolate
interpolation_samples=1,
+ fill_value=numpy.NaN,
# 1 = when there is overlap, use data from trace with last endtime
method=1)
- # trim masked trace to the same size as other traces (not done in merge())
- # and add back to merged stream
- if masked_trace:
- masked_trace.trim(merged[0].stats.starttime, merged[0].stats.endtime)
- merged += masked_trace
-
# convert back to NaN filled array
merged = unmask_stream(merged)
return merged
diff --git a/test/TimeseriesUtility_test.py b/test/TimeseriesUtility_test.py
index 644c7f76..4a7a2587 100644
--- a/test/TimeseriesUtility_test.py
+++ b/test/TimeseriesUtility_test.py
@@ -136,12 +136,24 @@ def test_merge_streams():
for trace in timeseries2:
trace.stats.starttime = UTCDateTime('2018-01-01T00:02:00Z')
trace.stats.npts = npts2
- Merged_streams1 = TimeseriesUtility.merge_streams(timeseries1)
+ merged_streams1 = TimeseriesUtility.merge_streams(timeseries1)
# Make sure the empty 'F' was not removed from stream
- assert_equals(len(timeseries1), len(Merged_streams1))
+ assert_equals(1, len(merged_streams1.select(channel = 'F')))
# Merge multiple streams with overlapping timestamps
timeseries = timeseries1 + timeseries2
- Merged_streams = TimeseriesUtility.merge_streams(timeseries)
- assert_equals(len(Merged_streams), len(timeseries1))
- assert_equals(len(Merged_streams[0].data), 6)
- assert_equals(len(Merged_streams[2]), 6)
+ merged_streams = TimeseriesUtility.merge_streams(timeseries)
+ assert_equals(len(merged_streams), len(timeseries1))
+ assert_equals(len(merged_streams[0].data), 6)
+ assert_equals(len(merged_streams[2]), 6)
+
+ trace7 = __create_trace('H', [1,1,1,1])
+ trace8 = __create_trace('E', [numpy.nan, numpy.nan, numpy.nan, numpy.nan])
+ trace9 = __create_trace('F', [numpy.nan, numpy.nan, numpy.nan, numpy.nan])
+ timeseries3 = Stream(traces=[trace7,trace8,trace9])
+ npts3 = len(trace7.data)
+ for trace in timeseries3:
+ trace.stats.starttime = UTCDateTime('2018-01-01T00:00:00Z')
+ trace.stats.npts = npts3
+ merged_streams3 = TimeseriesUtility.merge_streams(timeseries3)
+ assert_equals(len(timeseries3),len(merged_streams3))
+
--
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