From d22e983b94ef988ed06e1a9c66af23da16aca4be Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Wed, 10 Mar 2021 10:34:10 -0700
Subject: [PATCH] Default algorithm's matrix to identity with no statefile
---
geomagio/adjusted/AdjustedMatrix.py | 2 +-
geomagio/algorithm/AdjustedAlgorithm.py | 7 +++--
test/algorithm_test/AdjustedAlgorithm_test.py | 28 +++++++++++++++----
3 files changed, 28 insertions(+), 9 deletions(-)
diff --git a/geomagio/adjusted/AdjustedMatrix.py b/geomagio/adjusted/AdjustedMatrix.py
index b5513877f..44ca88a77 100644
--- a/geomagio/adjusted/AdjustedMatrix.py
+++ b/geomagio/adjusted/AdjustedMatrix.py
@@ -23,7 +23,7 @@ class AdjustedMatrix(BaseModel):
"""
matrix: Optional[Any] = None
- pier_correction: Optional[float] = None
+ pier_correction: float = 0
metrics: Optional[List[Metric]] = None
starttime: Optional[UTCDateTime] = None
endtime: Optional[UTCDateTime] = None
diff --git a/geomagio/algorithm/AdjustedAlgorithm.py b/geomagio/algorithm/AdjustedAlgorithm.py
index 9782e9713..d103e2d22 100644
--- a/geomagio/algorithm/AdjustedAlgorithm.py
+++ b/geomagio/algorithm/AdjustedAlgorithm.py
@@ -43,7 +43,11 @@ class AdjustedAlgorithm(Algorithm):
"""Load algorithm state from a file.
File name is self.statefile.
"""
+ # Adjusted matrix defaults to identity matrix
+ matrix_size = len([c for c in self.get_input_channels() if c != "F"]) + 1
+ matrix = np.eye(matrix_size)
if self.statefile is None:
+ self.matrix = AdjustedMatrix(matrix=matrix)
return
try:
with open(self.statefile, "r") as f:
@@ -51,12 +55,9 @@ class AdjustedAlgorithm(Algorithm):
data = json.loads(data)
except IOError as err:
raise FileNotFoundError("statefile not found")
- # Adjusted matrix defaults to identity matrix
- matrix_size = len([c for c in self.get_input_channels() if c != "F"]) + 1
if "pier_correction" in data:
self.matrix = AdjustedMatrix(**data)
elif "PC" in data:
- matrix = np.eye(matrix_size)
# read data from legacy format
for row in range(matrix_size):
for col in range(matrix_size):
diff --git a/test/algorithm_test/AdjustedAlgorithm_test.py b/test/algorithm_test/AdjustedAlgorithm_test.py
index 98eba78b4..220d498c6 100644
--- a/test/algorithm_test/AdjustedAlgorithm_test.py
+++ b/test/algorithm_test/AdjustedAlgorithm_test.py
@@ -1,7 +1,7 @@
from geomagio.adjusted import AdjustedMatrix
from geomagio.algorithm import AdjustedAlgorithm
import geomagio.iaga2002 as i2
-from numpy.testing import assert_almost_equal, assert_equal
+from numpy.testing import assert_almost_equal, assert_array_equal, assert_equal
def test_construct():
@@ -24,7 +24,7 @@ def assert_streams_almost_equal(adjusted, expected, channels):
def test_process_XYZF_AdjustedMatrix():
- """algorithm_test.AdjustedAlgorithm_test.test_process()
+ """algorithm_test.AdjustedAlgorithm_test.test_process_XYZF_AdjustedMatrix()
Check adjusted data processing versus files generated from
original script
@@ -72,7 +72,7 @@ def test_process_XYZF_AdjustedMatrix():
def test_process_reverse_polarity_AdjustedMatrix():
- """algorithm_test.AdjustedAlgorithm_test.test_process()
+ """algorithm_test.AdjustedAlgorithm_test.test_process_reverse_polarity_AdjustedMatrix()
Check adjusted data processing versus files generated from
original script. Tests reverse polarity martix.
@@ -106,7 +106,7 @@ def test_process_reverse_polarity_AdjustedMatrix():
def test_process_XYZF_statefile():
- """algorithm_test.AdjustedAlgorithm_test.test_process()
+ """algorithm_test.AdjustedAlgorithm_test.test_process_XYZF_statefile()
Check adjusted data processing versus files generated from
original script
@@ -131,7 +131,7 @@ def test_process_XYZF_statefile():
def test_process_reverse_polarity_statefile():
- """algorithm_test.AdjustedAlgorithm_test.test_process()
+ """algorithm_test.AdjustedAlgorithm_test.test_process_reverse_polarity_statefile()
Check adjusted data processing versus files generated from
original script. Tests reverse polarity martix.
@@ -157,3 +157,21 @@ def test_process_reverse_polarity_statefile():
assert_streams_almost_equal(
adjusted=adjusted, expected=expected, channels=["H", "E"]
)
+
+
+def test_process_no_statefile():
+ """algorithm_test.AdjustedAlgorithm_test.test_process_no_statefile()
+
+ Check adjusted data processing versus raw data
+
+ Uses default AdjustedMatrix with identity transform
+ """
+ # initialize adjusted algorithm with no statefile
+ a = AdjustedAlgorithm()
+ # load boulder Jan 16 files from /etc/ directory
+ with open("etc/adjusted/BOU201601vmin.min") as f:
+ raw = i2.IAGA2002Factory().parse_string(f.read())
+ # process hezf (raw) channels with identity transform
+ adjusted = a.process(raw)
+ for i in range(len(adjusted)):
+ assert_array_equal(adjusted[i].data, raw[i].data)
--
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