From 7c5440b6bcc105c03443882b50494681705bb731 Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Fri, 30 Apr 2021 14:31:22 -0600
Subject: [PATCH 1/6] add residual entrypoint, raise errors for missing
measurements
---
geomagio/api/ws/algorithms.py | 36 +++++++++++++++++++++++++++++++-
geomagio/residual/Calculation.py | 9 +++++---
geomagio/residual/Measurement.py | 3 ++-
3 files changed, 43 insertions(+), 5 deletions(-)
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index 572045ba8..af957ee43 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -1,8 +1,17 @@
-from fastapi import APIRouter, Depends
+from typing import List
+
+from fastapi import APIRouter, Depends, HTTPException
from starlette.responses import Response
from ... import TimeseriesFactory
from ...algorithm import DbDtAlgorithm
+from ...residual import (
+ calculate,
+ Reading,
+ MARK_TYPES,
+ INCLINATION_TYPES,
+ DECLINATION_TYPES,
+)
from .DataApiQuery import DataApiQuery
from .data import format_timeseries, get_data_factory, get_data_query, get_timeseries
@@ -25,3 +34,28 @@ def get_dbdt(
return format_timeseries(
timeseries=timeseries, format=query.format, elements=elements
)
+
+
+@router.post("/algorithms/residual", response_model=Reading)
+def calculate_residual(reading: Reading, adjust_reference: bool = True):
+ missing_types = get_missing_measurement_types(reading=reading)
+ if len(missing_types) != 0:
+ error_message = ", ".join(t.value for t in missing_types)
+ raise HTTPException(
+ status_code=400,
+ detail=f"Missing {error_message} measurements in input reading",
+ )
+ return calculate(reading=reading, adjust_reference=adjust_reference)
+
+
+def get_missing_measurement_types(reading: Reading) -> List[str]:
+ measurement_types = [m.measurement_type for m in reading.measurements]
+ missing_types = []
+ missing_types.extend(
+ [type for type in DECLINATION_TYPES if type not in measurement_types]
+ )
+ missing_types.extend(
+ [type for type in INCLINATION_TYPES if type not in measurement_types]
+ )
+ missing_types.extend([type for type in MARK_TYPES if type not in measurement_types])
+ return missing_types
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index ddc108a4d..c18fe228e 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -28,7 +28,10 @@ def calculate(reading: Reading, adjust_reference: bool = True) -> Reading:
NOTE: rest of reading object is shallow copy.
"""
# reference measurement, used to adjust absolutes
- reference = reading[mt.WEST_DOWN][0]
+ try:
+ reference = adjust_reference and reading[mt.WEST_DOWN][0] or None
+ except:
+ raise ValueError(f"Missing {mt.WEST_DOWN.value} measurement")
# calculate inclination
inclination, f, i_mean = calculate_I(
hemisphere=reading.hemisphere, measurements=reading.measurements
@@ -39,13 +42,13 @@ def calculate(reading: Reading, adjust_reference: bool = True) -> Reading:
corrected_f=corrected_f,
inclination=inclination,
mean=i_mean,
- reference=adjust_reference and reference or None,
+ reference=reference,
)
absoluteD, meridian = calculate_D_absolute(
azimuth=reading.azimuth,
h_baseline=absoluteH.baseline,
measurements=reading.measurements,
- reference=adjust_reference and reference or None,
+ reference=reference,
)
# populate diagnostics object with averaged measurements
diagnostics = Diagnostics(
diff --git a/geomagio/residual/Measurement.py b/geomagio/residual/Measurement.py
index f8be19437..bbf2f420a 100644
--- a/geomagio/residual/Measurement.py
+++ b/geomagio/residual/Measurement.py
@@ -54,7 +54,8 @@ def average_measurement(
measurements = [m for m in measurements if m.measurement_type in types]
if len(measurements) == 0:
# no measurements to average
- return None
+ error_message = ", ".join(t.value for t in types)
+ raise ValueError(f"Missing {error_message} measurements")
starttime = safe_min([m.time.timestamp for m in measurements if m.time])
endtime = safe_max([m.time.timestamp for m in measurements if m.time])
measurement = AverageMeasurement(
--
GitLab
From 81ee0797d69815f921754fc2f61cc02d7a7e1662 Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Fri, 30 Apr 2021 14:39:15 -0600
Subject: [PATCH 2/6] Order type imports, rename error message
---
geomagio/api/ws/algorithms.py | 8 ++++----
geomagio/residual/Measurement.py | 4 ++--
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index af957ee43..f904dd9a0 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -8,9 +8,9 @@ from ...algorithm import DbDtAlgorithm
from ...residual import (
calculate,
Reading,
- MARK_TYPES,
- INCLINATION_TYPES,
DECLINATION_TYPES,
+ INCLINATION_TYPES,
+ MARK_TYPES,
)
from .DataApiQuery import DataApiQuery
from .data import format_timeseries, get_data_factory, get_data_query, get_timeseries
@@ -40,10 +40,10 @@ def get_dbdt(
def calculate_residual(reading: Reading, adjust_reference: bool = True):
missing_types = get_missing_measurement_types(reading=reading)
if len(missing_types) != 0:
- error_message = ", ".join(t.value for t in missing_types)
+ missing_types = ", ".join(t.value for t in missing_types)
raise HTTPException(
status_code=400,
- detail=f"Missing {error_message} measurements in input reading",
+ detail=f"Missing {missing_types} measurements in input reading",
)
return calculate(reading=reading, adjust_reference=adjust_reference)
diff --git a/geomagio/residual/Measurement.py b/geomagio/residual/Measurement.py
index bbf2f420a..8b0fe6b3c 100644
--- a/geomagio/residual/Measurement.py
+++ b/geomagio/residual/Measurement.py
@@ -54,8 +54,8 @@ def average_measurement(
measurements = [m for m in measurements if m.measurement_type in types]
if len(measurements) == 0:
# no measurements to average
- error_message = ", ".join(t.value for t in types)
- raise ValueError(f"Missing {error_message} measurements")
+ missing_types = ", ".join(t.value for t in types)
+ raise ValueError(f"Missing {missing_types} measurements")
starttime = safe_min([m.time.timestamp for m in measurements if m.time])
endtime = safe_max([m.time.timestamp for m in measurements if m.time])
measurement = AverageMeasurement(
--
GitLab
From 0266b40715cb98f42f1e767b59905b22de8b1202 Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Fri, 30 Apr 2021 15:00:14 -0600
Subject: [PATCH 3/6] Use missing measurements method in calculation
---
geomagio/api/ws/algorithms.py | 17 +----------------
geomagio/residual/Calculation.py | 22 ++++++++++++++++++----
geomagio/residual/Measurement.py | 4 ----
geomagio/residual/__init__.py | 2 ++
4 files changed, 21 insertions(+), 24 deletions(-)
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index f904dd9a0..c67c463fe 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -8,9 +8,7 @@ from ...algorithm import DbDtAlgorithm
from ...residual import (
calculate,
Reading,
- DECLINATION_TYPES,
- INCLINATION_TYPES,
- MARK_TYPES,
+ get_missing_measurement_types,
)
from .DataApiQuery import DataApiQuery
from .data import format_timeseries, get_data_factory, get_data_query, get_timeseries
@@ -46,16 +44,3 @@ def calculate_residual(reading: Reading, adjust_reference: bool = True):
detail=f"Missing {missing_types} measurements in input reading",
)
return calculate(reading=reading, adjust_reference=adjust_reference)
-
-
-def get_missing_measurement_types(reading: Reading) -> List[str]:
- measurement_types = [m.measurement_type for m in reading.measurements]
- missing_types = []
- missing_types.extend(
- [type for type in DECLINATION_TYPES if type not in measurement_types]
- )
- missing_types.extend(
- [type for type in INCLINATION_TYPES if type not in measurement_types]
- )
- missing_types.extend([type for type in MARK_TYPES if type not in measurement_types])
- return missing_types
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index c18fe228e..6c44d4af3 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -28,10 +28,11 @@ def calculate(reading: Reading, adjust_reference: bool = True) -> Reading:
NOTE: rest of reading object is shallow copy.
"""
# reference measurement, used to adjust absolutes
- try:
- reference = adjust_reference and reading[mt.WEST_DOWN][0] or None
- except:
- raise ValueError(f"Missing {mt.WEST_DOWN.value} measurement")
+ missing_types = get_missing_measurement_types(reading=reading)
+ if len(missing_types) != 0:
+ missing_types = ", ".join(t.value for t in missing_types)
+ raise ValueError(f"Missing {missing_types} measurements in input reading")
+ reference = adjust_reference and reading[mt.WEST_DOWN][0] or None
# calculate inclination
inclination, f, i_mean = calculate_I(
hemisphere=reading.hemisphere, measurements=reading.measurements
@@ -281,3 +282,16 @@ def calculate_scale_value(
residual_change = m2.residual - m1.residual
scale_value = corrected_f * field_change / np.abs(residual_change)
return scale_value
+
+
+def get_missing_measurement_types(reading: Reading) -> List[str]:
+ measurement_types = [m.measurement_type for m in reading.measurements]
+ missing_types = []
+ missing_types.extend(
+ [type for type in DECLINATION_TYPES if type not in measurement_types]
+ )
+ missing_types.extend(
+ [type for type in INCLINATION_TYPES if type not in measurement_types]
+ )
+ missing_types.extend([type for type in MARK_TYPES if type not in measurement_types])
+ return missing_types
diff --git a/geomagio/residual/Measurement.py b/geomagio/residual/Measurement.py
index 8b0fe6b3c..e052f53bc 100644
--- a/geomagio/residual/Measurement.py
+++ b/geomagio/residual/Measurement.py
@@ -52,10 +52,6 @@ def average_measurement(
"""
if types:
measurements = [m for m in measurements if m.measurement_type in types]
- if len(measurements) == 0:
- # no measurements to average
- missing_types = ", ".join(t.value for t in types)
- raise ValueError(f"Missing {missing_types} measurements")
starttime = safe_min([m.time.timestamp for m in measurements if m.time])
endtime = safe_max([m.time.timestamp for m in measurements if m.time])
measurement = AverageMeasurement(
diff --git a/geomagio/residual/__init__.py b/geomagio/residual/__init__.py
index ec2de5e8a..352c66b32 100644
--- a/geomagio/residual/__init__.py
+++ b/geomagio/residual/__init__.py
@@ -9,6 +9,7 @@ from .Calculation import (
calculate_HZ_absolutes,
calculate_I,
calculate_scale_value,
+ get_missing_measurement_types,
)
from .CalFileFactory import CalFileFactory
from .Measurement import Measurement, AverageMeasurement, average_measurement
@@ -35,6 +36,7 @@ __all__ = [
"calculate_I",
"calculate_scale_value",
"DECLINATION_TYPES",
+ "get_missing_measurement_types",
"INCLINATION_TYPES",
"MARK_TYPES",
"Measurement",
--
GitLab
From 39606901d475826d1e31161add2f7cbc622574f3 Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Fri, 30 Apr 2021 16:21:25 -0600
Subject: [PATCH 4/6] Move missing type method to residual
---
geomagio/api/ws/algorithms.py | 5 +----
geomagio/residual/Calculation.py | 15 +--------------
geomagio/residual/Reading.py | 7 +++++++
geomagio/residual/__init__.py | 2 --
4 files changed, 9 insertions(+), 20 deletions(-)
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index c67c463fe..f2eeee314 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -1,5 +1,3 @@
-from typing import List
-
from fastapi import APIRouter, Depends, HTTPException
from starlette.responses import Response
@@ -8,7 +6,6 @@ from ...algorithm import DbDtAlgorithm
from ...residual import (
calculate,
Reading,
- get_missing_measurement_types,
)
from .DataApiQuery import DataApiQuery
from .data import format_timeseries, get_data_factory, get_data_query, get_timeseries
@@ -36,7 +33,7 @@ def get_dbdt(
@router.post("/algorithms/residual", response_model=Reading)
def calculate_residual(reading: Reading, adjust_reference: bool = True):
- missing_types = get_missing_measurement_types(reading=reading)
+ missing_types = reading.get_missing_measurement_types()
if len(missing_types) != 0:
missing_types = ", ".join(t.value for t in missing_types)
raise HTTPException(
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index 6c44d4af3..fe1ab1c1e 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -28,7 +28,7 @@ def calculate(reading: Reading, adjust_reference: bool = True) -> Reading:
NOTE: rest of reading object is shallow copy.
"""
# reference measurement, used to adjust absolutes
- missing_types = get_missing_measurement_types(reading=reading)
+ missing_types = reading.get_missing_measurement_types()
if len(missing_types) != 0:
missing_types = ", ".join(t.value for t in missing_types)
raise ValueError(f"Missing {missing_types} measurements in input reading")
@@ -282,16 +282,3 @@ def calculate_scale_value(
residual_change = m2.residual - m1.residual
scale_value = corrected_f * field_change / np.abs(residual_change)
return scale_value
-
-
-def get_missing_measurement_types(reading: Reading) -> List[str]:
- measurement_types = [m.measurement_type for m in reading.measurements]
- missing_types = []
- missing_types.extend(
- [type for type in DECLINATION_TYPES if type not in measurement_types]
- )
- missing_types.extend(
- [type for type in INCLINATION_TYPES if type not in measurement_types]
- )
- missing_types.extend([type for type in MARK_TYPES if type not in measurement_types])
- return missing_types
diff --git a/geomagio/residual/Reading.py b/geomagio/residual/Reading.py
index 06c8efb97..519245b69 100644
--- a/geomagio/residual/Reading.py
+++ b/geomagio/residual/Reading.py
@@ -8,6 +8,7 @@ from pydantic import BaseModel
from .. import TimeseriesUtility
from ..TimeseriesFactory import TimeseriesFactory
from .Absolute import Absolute
+from .Calculation import DECLINATION_TYPES, INCLINATION_TYPES, MARK_TYPES
from .Measurement import Measurement, average_measurement
from .Diagnostics import Diagnostics
from .MeasurementType import MeasurementType
@@ -52,6 +53,12 @@ class Reading(BaseModel):
return absolute
return None
+ def get_missing_measurement_types(self) -> List[str]:
+ measurement_types = [m.measurement_type for m in self.measurements]
+ all_types = DECLINATION_TYPES + INCLINATION_TYPES + MARK_TYPES
+ missing = [t for t in all_types if t not in measurement_types]
+ return missing
+
def load_ordinates(
self,
observatory: str,
diff --git a/geomagio/residual/__init__.py b/geomagio/residual/__init__.py
index 352c66b32..ec2de5e8a 100644
--- a/geomagio/residual/__init__.py
+++ b/geomagio/residual/__init__.py
@@ -9,7 +9,6 @@ from .Calculation import (
calculate_HZ_absolutes,
calculate_I,
calculate_scale_value,
- get_missing_measurement_types,
)
from .CalFileFactory import CalFileFactory
from .Measurement import Measurement, AverageMeasurement, average_measurement
@@ -36,7 +35,6 @@ __all__ = [
"calculate_I",
"calculate_scale_value",
"DECLINATION_TYPES",
- "get_missing_measurement_types",
"INCLINATION_TYPES",
"MARK_TYPES",
"Measurement",
--
GitLab
From 3a9d06c984aa5fa785956e91af5db32bf99d611a Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Fri, 30 Apr 2021 16:26:13 -0600
Subject: [PATCH 5/6] return None if no types are found to average
---
geomagio/residual/Measurement.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/geomagio/residual/Measurement.py b/geomagio/residual/Measurement.py
index e052f53bc..f8be19437 100644
--- a/geomagio/residual/Measurement.py
+++ b/geomagio/residual/Measurement.py
@@ -52,6 +52,9 @@ def average_measurement(
"""
if types:
measurements = [m for m in measurements if m.measurement_type in types]
+ if len(measurements) == 0:
+ # no measurements to average
+ return None
starttime = safe_min([m.time.timestamp for m in measurements if m.time])
endtime = safe_max([m.time.timestamp for m in measurements if m.time])
measurement = AverageMeasurement(
--
GitLab
From 1f85191863c7a31da0173a22f0d9cdf618b70586 Mon Sep 17 00:00:00 2001
From: pcain-usgs <pcain@usgs.gov>
Date: Tue, 4 May 2021 09:30:22 -0600
Subject: [PATCH 6/6] Raise value error with HTTPException
---
geomagio/api/ws/algorithms.py | 12 ++++--------
geomagio/residual/Reading.py | 8 ++++++--
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index f2eeee314..bcc42a359 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -33,11 +33,7 @@ def get_dbdt(
@router.post("/algorithms/residual", response_model=Reading)
def calculate_residual(reading: Reading, adjust_reference: bool = True):
- missing_types = reading.get_missing_measurement_types()
- if len(missing_types) != 0:
- missing_types = ", ".join(t.value for t in missing_types)
- raise HTTPException(
- status_code=400,
- detail=f"Missing {missing_types} measurements in input reading",
- )
- return calculate(reading=reading, adjust_reference=adjust_reference)
+ try:
+ return calculate(reading=reading, adjust_reference=adjust_reference)
+ except ValueError as e:
+ raise HTTPException(status_code=400, detail=str(e))
diff --git a/geomagio/residual/Reading.py b/geomagio/residual/Reading.py
index 519245b69..437da4992 100644
--- a/geomagio/residual/Reading.py
+++ b/geomagio/residual/Reading.py
@@ -8,10 +8,14 @@ from pydantic import BaseModel
from .. import TimeseriesUtility
from ..TimeseriesFactory import TimeseriesFactory
from .Absolute import Absolute
-from .Calculation import DECLINATION_TYPES, INCLINATION_TYPES, MARK_TYPES
from .Measurement import Measurement, average_measurement
from .Diagnostics import Diagnostics
-from .MeasurementType import MeasurementType
+from .MeasurementType import (
+ MeasurementType,
+ DECLINATION_TYPES,
+ INCLINATION_TYPES,
+ MARK_TYPES,
+)
class Reading(BaseModel):
--
GitLab