diff --git a/etc/adjusted/BOU_expected.json b/etc/adjusted/BOU_expected.json
index ebe0a6c9bab156e2e39fc6ca9f158ee514421096..70ba3f81b1eaa396998d7c6f1a4ecc2375fde8e9 100644
--- a/etc/adjusted/BOU_expected.json
+++ b/etc/adjusted/BOU_expected.json
@@ -2,1126 +2,1126 @@
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diff --git a/etc/adjusted/CMO_expected.json b/etc/adjusted/CMO_expected.json
index 4b53c32650c9a31e7e10969db32890a2b64d7c34..660d162d6541f4e006af220067862647a542675b 100644
--- a/etc/adjusted/CMO_expected.json
+++ b/etc/adjusted/CMO_expected.json
@@ -2,3388 +2,3388 @@
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- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
],
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
]
],
"inf_one_interval": [
[
[
- 0.9530416740423117,
- -0.30283917768120405,
- 0,
- 86.51389127230165
+ 0.953054851299307,
+ -0.30279770543195383,
+ 0.0,
+ 86.35089806216253
],
[
- 0.3028391776812039,
- 0.9530416740423118,
- 0,
- 297.5848898679969
+ 0.302797705431954,
+ 0.9530548512993069,
+ 0.0,
+ 298.0973733623943
],
[
- 0,
- 0,
- 1,
+ 0.0,
+ 0.0,
+ 1.0,
-53.71111111111132
],
[
- 0,
- 0,
- 0,
- 1
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
]
]
]
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index 72708859b8382b38829db4c34d3cc926417ac739..7eb1ca1f0685ffa6fbee89342c53ff40f90313ce 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -355,7 +355,7 @@ def calculate_scale_value(
/ corrected_f
) + (m2.angle - m1.angle)
residual_change = m2.residual - m1.residual
- scale_value = corrected_f * field_change / np.abs(residual_change)
+ scale_value = np.radians(corrected_f * field_change / np.abs(residual_change))
return scale_value
diff --git a/geomagio/residual/Reading.py b/geomagio/residual/Reading.py
index 752ffc4b0c4d778072584b2de468785444f61f52..75648d9b4882f96bb22cf5ac4f2c9c708a884787 100644
--- a/geomagio/residual/Reading.py
+++ b/geomagio/residual/Reading.py
@@ -182,11 +182,10 @@ def get_ordinates(
h_abs, d_abs, z_abs = get_absolutes(readings)
h_bas, d_bas, z_bas = get_baselines(readings)
# recreate ordinate variometer measurements from absolutes and baselines
- h_ord = h_abs - h_bas
d_ord = d_abs - d_bas
z_ord = z_abs - z_bas
- e_ord = h_abs * np.radians(d_ord)
- h_ord = np.sqrt(h_ord**2 - e_ord**2)
+ e_ord = h_abs * np.sin(np.radians(d_ord)) # this is right, but breaks tests
+ h_ord = np.sqrt(h_abs**2 - e_ord**2) - h_bas # this is right, but breaks tests
return (h_ord, e_ord, z_ord)
diff --git a/geomagio/residual/SpreadsheetAbsolutesFactory.py b/geomagio/residual/SpreadsheetAbsolutesFactory.py
index 27c5be9ef4e27c32300af13eac015a9865133ea0..fc22cae1f6cf914ab585210bfe48ed4b03cd239c 100644
--- a/geomagio/residual/SpreadsheetAbsolutesFactory.py
+++ b/geomagio/residual/SpreadsheetAbsolutesFactory.py
@@ -287,7 +287,8 @@ class SpreadsheetAbsolutesFactory(object):
"""
def __init__(self, base_directory="/Volumes/geomag/pub/observatories"):
- self.base_directory = base_directory
+ # trim filename off base_directory
+ self.base_directory = os.path.dirname(base_directory)
def get_readings(
self,
@@ -300,23 +301,26 @@ class SpreadsheetAbsolutesFactory(object):
readings = []
start_filename = f"{observatory}-{starttime.datetime:%Y%j%H%M}.xlsm"
end_filename = f"{observatory}-{endtime.datetime:%Y%j%H%M}.xlsm"
- for year in range(starttime.year, endtime.year + 1):
- # start in observatory year directory to scan fewer files
- observatory_directory = os.path.join(
- self.base_directory, observatory, f"{year}"
- )
- for (dirpath, _, filenames) in os.walk(observatory_directory):
- for filename in filenames:
- if start_filename <= filename < end_filename:
- readings.append(
- self.parse_spreadsheet(
- path=os.path.join(dirpath, filename),
- observatory=observatory,
- starttime=starttime,
- endtime=endtime,
- include_measurements=include_measurements,
- )
- )
+ all_dirs = []
+ all_files = []
+ for (dirpath, _, filenames) in os.walk(self.base_directory):
+ # accumulate dirpaths and filenames before sorting on filenames
+ all_dirs += len(filenames) * [dirpath]
+ all_files += filenames
+ # unique and sorted filenames
+ filenames, idxs = numpy.unique(all_files, return_index=True)
+ dirpaths = numpy.array(all_dirs)[idxs]
+ for dirpath, filename in zip(dirpaths, filenames):
+ if start_filename <= filename < end_filename:
+ readings.append(
+ self.parse_spreadsheet(
+ path=os.path.join(dirpath, filename),
+ observatory=observatory,
+ starttime=starttime,
+ endtime=endtime,
+ include_measurements=include_measurements,
+ )
+ )
return readings
def parse_spreadsheet(
@@ -356,7 +360,7 @@ class SpreadsheetAbsolutesFactory(object):
measurements=measurements,
metadata=metadata,
pier_correction=metadata["pier_correction"],
- scale_value=numpy.degrees(metadata["scale_value"]),
+ scale_value=metadata["scale_value"],
diagnostics=self._parse_diagnostics(calculation_sheet),
)
diff --git a/geomagio/residual/SpreadsheetSummaryFactory.py b/geomagio/residual/SpreadsheetSummaryFactory.py
index 98ee84d4724b42b88ce59bd42bc0836ee2572a13..ba3b6c981421e06ce9797f597b7bb408515ab6f5 100644
--- a/geomagio/residual/SpreadsheetSummaryFactory.py
+++ b/geomagio/residual/SpreadsheetSummaryFactory.py
@@ -1,5 +1,6 @@
import os
+import numpy
from obspy import UTCDateTime
import openpyxl
from typing import List
@@ -39,7 +40,7 @@ class SpreadsheetSummaryFactory(object):
"""Read absolutes from summary spreadsheets"""
def __init__(self, base_directory: str):
- self.base_directory = base_directory
+ self.base_directory = os.path.dirname(base_directory)
def get_readings(
self, observatory: str, starttime: UTCDateTime, endtime: UTCDateTime
@@ -55,19 +56,23 @@ class SpreadsheetSummaryFactory(object):
readings = []
start_filename = f"{observatory}{starttime.datetime:%Y%j%H%M}.xlsm"
end_filename = f"{observatory}{endtime.datetime:%Y%j%H%M}.xlsm"
- for year in range(starttime.year, endtime.year + 1):
- observatory_directory = os.path.join(
- self.base_directory, observatory, f"{year}"
- )
- for (dirpath, _, filenames) in os.walk(observatory_directory):
- filenames.sort()
- for filename in filenames:
- if start_filename <= filename < end_filename:
- rs = self.parse_spreadsheet(
- os.path.join(dirpath, filename),
- )
- for r in rs:
- readings.append(r)
+ all_dirs = []
+ all_files = []
+ for (dirpath, _, filenames) in os.walk(self.base_directory):
+ # accumulate dirpaths and filenames before sorting on filenames
+ all_dirs += len(filenames) * [dirpath]
+ all_files += filenames
+ # unique and sorted filenames
+ filenames, idxs = numpy.unique(all_files, return_index=True)
+ dirpaths = numpy.array(all_dirs)[idxs]
+
+ for dirpath, filename in zip(dirpaths, filenames):
+ if start_filename <= filename < end_filename:
+ rs = self.parse_spreadsheet(
+ os.path.join(dirpath, filename),
+ )
+ for r in rs:
+ readings.append(r)
return readings
def parse_spreadsheet(self, path: str) -> List[Reading]:
diff --git a/test/adjusted_test/adjusted_test.py b/test/adjusted_test/adjusted_test.py
index 7d81f9cbb308b914f5db2dc7620a1ccfc3754bbb..1395e2c61ed6c9803bc42716586af08cb2dbbe80 100644
--- a/test/adjusted_test/adjusted_test.py
+++ b/test/adjusted_test/adjusted_test.py
@@ -36,7 +36,7 @@ def format_result(result) -> dict:
return Ms
-def get_excpected_matrices(observatory, key):
+def get_expected_matrices(observatory, key):
with open(f"etc/adjusted/{observatory}_expected.json", "r") as file:
expected = json.load(file)
return expected[key]
@@ -74,7 +74,7 @@ def test_BOU201911202001_infinite_one_interval():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("BOU", "inf_one_interval")
+ expected_matrices = get_expected_matrices("BOU", "inf_one_interval")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -107,7 +107,7 @@ def test_BOU201911202001_infinite_weekly():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("BOU", "inf_weekly")
+ expected_matrices = get_expected_matrices("BOU", "inf_weekly")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -160,7 +160,7 @@ def test_BOU201911202001_short_acausal():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("BOU", "short_acausal")
+ expected_matrices = get_expected_matrices("BOU", "short_acausal")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -191,7 +191,7 @@ def test_BOU201911202001_short_causal():
).calculate(readings=readings)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("BOU", "short_causal")
+ expected_matrices = get_expected_matrices("BOU", "short_causal")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -227,7 +227,7 @@ def test_CMO2015_infinite_one_interval():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("CMO", "inf_one_interval")
+ expected_matrices = get_expected_matrices("CMO", "inf_one_interval")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -268,7 +268,7 @@ def test_CMO2015_infinite_weekly():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("CMO", "inf_weekly")
+ expected_matrices = get_expected_matrices("CMO", "inf_weekly")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -307,7 +307,7 @@ def test_CMO2015_short_acausal():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("CMO", "short_acausal")
+ expected_matrices = get_expected_matrices("CMO", "short_acausal")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
@@ -346,7 +346,7 @@ def test_CMO2015_short_causal():
)
matrices = format_result([adjusted_matrix.matrix for adjusted_matrix in result])
- expected_matrices = get_excpected_matrices("CMO", "short_causal")
+ expected_matrices = get_expected_matrices("CMO", "short_causal")
for i in range(len(matrices)):
assert_array_almost_equal(
matrices[i],
diff --git a/test/residual_test/residual_test.py b/test/residual_test/residual_test.py
index 8b156125bd3696e86b1a2dd60df4674ddff6ab62..5f70ff83f9768739861b8e8d6f4687c4a43acf67 100644
--- a/test/residual_test/residual_test.py
+++ b/test/residual_test/residual_test.py
@@ -19,8 +19,6 @@ def assert_readings_equal(expected: Reading, actual: Reading, decimal: int):
"""
Compares calculation actuals to expected absolutes from spreadsheet
"""
- print(expected.json(exclude={"measurements", "metadata"}, indent=2))
- print(actual.json(exclude={"measurements", "metadata"}, indent=2))
expected_absolutes = {a.element: a for a in expected.absolutes}
actual_absolutes = {a.element: a for a in actual.absolutes}
assert_almost_equal(