From 28f9dbe73134f71f6923e16d848afb617d799bba Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 26 Sep 2024 18:02:19 -0600
Subject: [PATCH] Fix _post_process() in FDSNFactory
The FDSNFactory was not working with input streams that contained multiple
segments. This was because FDSNFactory wasn't doing the full "_post_process"
like, for example, EdgeFactory. More specifically, FDSNFactory's `_post_process()`
method did not convert masked arrays (which is how obspy prefers to deal with
gappy data) into regular numpy arrays with NaNs for missing data, as expected
in all geomag-algorithms code.
This became quickly obvious once some of the less stable ASL variometers
were processed, like US-EYMN. This fix should allow us to now pull and plot
EYMN, DGMT, and other stations that were not working with the previous
release of FDSNFactory.
---
geomagio/edge/FDSNFactory.py | 25 ++++++++++++++++---------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/geomagio/edge/FDSNFactory.py b/geomagio/edge/FDSNFactory.py
index b4109d4d..c1112c92 100644
--- a/geomagio/edge/FDSNFactory.py
+++ b/geomagio/edge/FDSNFactory.py
@@ -285,11 +285,6 @@ class FDSNFactory(TimeseriesFactory):
if data.count() == 0:
return data
- if data.count() != 0:
- TimeseriesUtility.pad_and_trim_trace(
- trace=data[0], starttime=starttime, endtime=endtime
- )
-
self._set_metadata(data, observatory, channel, type, interval)
return data
@@ -302,10 +297,12 @@ class FDSNFactory(TimeseriesFactory):
channels: List[str],
):
"""Post process a timeseries stream after the raw data is
- is fetched from querymom. Specifically changes
- any MaskedArray to a ndarray with nans representing gaps.
- Then calls pad_timeseries to deal with gaps at the
- beggining or end of the streams.
+ is fetched from FDSN client. Specifically:
+ - adds USGS provisional data disclaimer
+ - changes any MaskedArray to ndarray with nans as gaps
+ - converts arcminutes to radians for any "D" channels
+ - calls pad_timeseries to deal with gaps at the
+ beggining or end of the streams.
Parameters
----------
@@ -335,6 +332,16 @@ class FDSNFactory(TimeseriesFactory):
if not any("DISCLAIMER" in comment for comment in trace.stats.comments):
trace.stats.comments.extend(disclaimer_texts)
+ if isinstance(trace.data, numpy.ma.MaskedArray):
+ trace.data.set_fill_value(numpy.nan)
+ trace.data = trace.data.filled()
+
+ if "D" in channels:
+ for trace in timeseries.select(channel="D"):
+ trace.data = ChannelConverter.get_radians_from_minutes(trace.data)
+
+ TimeseriesUtility.pad_timeseries(timeseries, starttime, endtime)
+
def _set_metadata(
self,
stream: Stream,
--
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