From b94c90b4f2beb977d27c1cc67d4d28fdcf4ae051 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 11 Dec 2024 16:32:18 -0700
Subject: [PATCH] Added mode for managing existing spikes. Added logic to
create_spike_metadata to allow empty arrays.
---
geomagio/algorithm/SpikesAlgorithm.py | 49 +++++++++++++++++++++++----
1 file changed, 42 insertions(+), 7 deletions(-)
diff --git a/geomagio/algorithm/SpikesAlgorithm.py b/geomagio/algorithm/SpikesAlgorithm.py
index 185b5023..b73a9013 100644
--- a/geomagio/algorithm/SpikesAlgorithm.py
+++ b/geomagio/algorithm/SpikesAlgorithm.py
@@ -4,6 +4,7 @@ import numpy as np
from obspy.core.utcdatetime import UTCDateTime
from obspy import Trace
from typing import List, Optional
+from enum import Enum
from .MetadataAlgorithm import MetadataAlgorithm
from ..metadata import Metadata
@@ -11,6 +12,12 @@ from ..metadata.flag.Flag import ArtificialDisturbance, ArtificialDisturbanceTyp
from ..metadata import MetadataCategory
+class SpikesMode(str, Enum):
+ MERGE = "merge"
+ OVERWRITE = "overwrite"
+
+
+# TODO: Add option to choose _despike method(s) and add more methods
class SpikesAlgorithm(MetadataAlgorithm):
"""
Algorithm that identifies spikes in data and generates metadata flags.
@@ -21,10 +28,14 @@ class SpikesAlgorithm(MetadataAlgorithm):
Size of the rolling window for dynamic alignment (no shrinking or padding). Defaults to 1000.
threshold: int
Threshold for spike detection (threshold * sigma). Defaults to 6.
+ mode:SpikesMode
+ Merge will automatically merge new spikes with preexisting spikes from requested period (if they exist), overwrite will automatically overwrite preexisting spikes with
+ new spikes from requested period (if they exist). Default is overwrite, meaning only new spikes are saved.
"""
window_size: Optional[int] = 1000
threshold: Optional[int] = 6
+ mode: Optional[SpikesMode] = SpikesMode.OVERWRITE
def _despike(
self, signal: Trace, timestamps: List[UTCDateTime]
@@ -114,14 +125,30 @@ class SpikesAlgorithm(MetadataAlgorithm):
if len(spike_timestamps) > 0:
spike_metadata = self.create_spike_metadata(spike_timestamps, trace)
if existing_metadata:
- # update ID to preexisting one
- spike_metadata.id = existing_metadata[0].id
+ if self.mode == SpikesMode.OVERWRITE:
+ # only use new metadata by updating ID to preexisting one
+ spike_metadata.id = existing_metadata[0].id
+ if self.mode == SpikesMode.MERGE:
+ # concatenate existing timestamps with new timestamps
+ existing_timestamps = existing_metadata[0].metadata["spikes"]
+ merged_timestamps = np.unique(
+ np.concatenate((spike_timestamps, existing_timestamps))
+ )
+ spike_metadata = self.create_spike_metadata(
+ merged_timestamps, trace
+ )
+ spike_metadata.id = existing_metadata[0].id
return spike_metadata
if len(spike_timestamps) == 0 and existing_metadata is not None:
- # TODO:change existing spike metadata to rejected or data_valid to false? Update array?
- # convert existing_metadata back into Metadata
- pass
+ if self.mode == SpikesMode.OVERWRITE:
+ # update ID to preexisting one with empty spike array
+ spike_metadata = self.create_spike_metadata(spike_timestamps, trace)
+ spike_metadata.id = existing_metadata[0].id
+ if self.mode == SpikesMode.MERGE:
+ # simply return preexisting metadata because you are adding zero spikes
+ spike_metadata = existing_metadata
+ return spike_metadata
return None
@@ -164,6 +191,14 @@ class SpikesAlgorithm(MetadataAlgorithm):
ArtificialDisturbance
Metadata object for the detected spikes.
"""
+ # use trace starttime and endtime if spike_timestamps is empty
+ if len(spike_timestamps) >= 1:
+ starttime = spike_timestamps[0]
+ endtime = spike_timestamps[-1]
+ else:
+ starttime = trace.stats.starttime
+ endtime = trace.stats.endtime
+
metadata_dict = {
"description": f"Spikes detected using a window of {self.window_size} and a threshold of {self.threshold}*sigma",
"artificial_disturbance_type": ArtificialDisturbanceType.SPIKES,
@@ -171,8 +206,8 @@ class SpikesAlgorithm(MetadataAlgorithm):
}
return self.create_metadata(
- starttime=spike_timestamps[0],
- endtime=spike_timestamps[-1],
+ starttime=starttime,
+ endtime=endtime,
metadata_class=ArtificialDisturbance,
metadata_dict=metadata_dict,
category=MetadataCategory.FLAG,
--
GitLab