dkist-processing-dlnirsp 0.31.1__tar.gz → 0.32.1__tar.gz

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/CHANGELOG.rst

@@ -1,3 +1,21 @@
+v0.32.1 (2025-10-09)
+====================
+
+Misc
+----
+
+- Update `dkist-processing-common` to v11.7.0, which makes constants for the dataset extras. (`#113 <https://bitbucket.org/dkistdc/dkist-processing-dlnirsp/pull-requests/113>`__)
+
+
+v0.32.0 (2025-09-26)
+====================
+
+Misc
+----
+
+- Integrate dkist-processing-core 6.0.0 which brings a swap of Elastic APM to OpenTelemetry for metrics and tracing. (`#112 <https://bitbucket.org/dkistdc/dkist-processing-dlnirsp/pull-requests/112>`__)
+
+
 v0.31.1 (2025-09-17)
 ====================
 

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-dlnirsp
-Version: 0.31.1
+Version: 0.32.1
 Summary: Science processing code for the DLNIRSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -13,13 +13,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
-Requires-Dist: dkist-processing-common==11.5.1
+Requires-Dist: dkist-processing-common==11.7.0
 Requires-Dist: dkist-processing-math==2.2.1
 Requires-Dist: dkist-processing-pac==3.1.1
 Requires-Dist: dkist-header-validator==5.2.1
 Requires-Dist: dkist-fits-specifications==4.17.0
 Requires-Dist: dkist-spectral-lines==3.0.0
-Requires-Dist: dkist-service-configuration==2.2
+Requires-Dist: dkist-service-configuration==4.1.7
 Requires-Dist: astropy==7.0.2
 Requires-Dist: numpy==2.2.5
 Requires-Dist: numba==0.61.2
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 dkist-processing-dlnirsp
@@ -309,7 +326,83 @@ in their own package facilitates using the build_utils to test the integrity of
 
 Environment Variables
 ---------------------
-Only those specified by `dkist-processing-core <https://pypi.org/project/dkist-processing-core/>`_ and `dkist-processing-common <https://pypi.org/project/dkist-processing-common/>`_.
+
+.. list-table::
+   :widths: 10 90
+   :header-rows: 1
+
+   * - Variable
+     - Field Info
+   * - LOGURU_LEVEL
+     - annotation=str required=False default='INFO' alias_priority=2 validation_alias='LOGURU_LEVEL' description='Log level for the application'
+   * - MESH_CONFIG
+     - annotation=dict[str, MeshService] required=False default_factory=dict alias_priority=2 validation_alias='MESH_CONFIG' description='Service mesh configuration' examples=[{'upstream_service_name': {'mesh_address': 'localhost', 'mesh_port': 6742}}]
+   * - RETRY_CONFIG
+     - annotation=RetryConfig required=False default_factory=RetryConfig description='Retry configuration for the service'
+   * - OTEL_SERVICE_NAME
+     - annotation=str required=False default='unknown-service-name' alias_priority=2 validation_alias='OTEL_SERVICE_NAME' description='Service name for OpenTelemetry'
+   * - DKIST_SERVICE_VERSION
+     - annotation=str required=False default='unknown-service-version' alias_priority=2 validation_alias='DKIST_SERVICE_VERSION' description='Service version for OpenTelemetry'
+   * - NOMAD_ALLOC_ID
+     - annotation=str required=False default='unknown-allocation-id' alias_priority=2 validation_alias='NOMAD_ALLOC_ID' description='Nomad allocation ID for OpenTelemetry'
+   * - OTEL_EXPORTER_OTLP_TRACES_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP traces'
+   * - OTEL_EXPORTER_OTLP_METRICS_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP metrics'
+   * - OTEL_EXPORTER_OTLP_TRACES_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP traces endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_EXPORTER_OTLP_METRICS_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP metrics endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_PYTHON_DISABLED_INSTRUMENTATIONS
+     - annotation=list[str] required=False default_factory=list description='List of instrumentations to disable. https://opentelemetry.io/docs/zero-code/python/configuration/' examples=[['pika', 'requests']]
+   * - OTEL_PYTHON_FASTAPI_EXCLUDED_URLS
+     - annotation=str required=False default='health' description='Comma separated list of URLs to exclude from OpenTelemetry instrumentation in FastAPI.' examples=['client/.*/info,healthcheck']
+   * - SYSTEM_METRIC_INSTRUMENTATION_CONFIG
+     - annotation=Union[dict[str, bool], NoneType] required=False default=None description='Configuration for system metric instrumentation. https://opentelemetry-python-contrib.readthedocs.io/en/latest/instrumentation/system_metrics/system_metrics.html' examples=[{'system.memory.usage': ['used', 'free', 'cached'], 'system.cpu.time': ['idle', 'user', 'system', 'irq'], 'system.network.io': ['transmit', 'receive'], 'process.runtime.memory': ['rss', 'vms'], 'process.runtime.cpu.time': ['user', 'system'], 'process.runtime.context_switches': ['involuntary', 'voluntary']}]
+   * - ISB_USERNAME
+     - annotation=str required=False default='guest' description='Username for the interservice-bus.'
+   * - ISB_PASSWORD
+     - annotation=str required=False default='guest' description='Password for the interservice-bus.'
+   * - ISB_EXCHANGE
+     - annotation=str required=False default='master.direct.x' description='Exchange for the interservice-bus.'
+   * - ISB_QUEUE_TYPE
+     - annotation=str required=False default='classic' description='Queue type for the interservice-bus.' examples=['quorum', 'classic']
+   * - BUILD_VERSION
+     - annotation=str required=False default='dev' description='Fallback build version for workflow tasks.'
+   * - GQL_AUTH_TOKEN
+     - annotation=Union[str, NoneType] required=False default='dev' description='The auth token for the metadata-store-api.'
+   * - OBJECT_STORE_ACCESS_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The access key for the object store.'
+   * - OBJECT_STORE_SECRET_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The secret key for the object store.'
+   * - OBJECT_STORE_USE_SSL
+     - annotation=bool required=False default=False description='Whether to use SSL for the object store connection.'
+   * - MULTIPART_THRESHOLD
+     - annotation=Union[int, NoneType] required=False default=None description='Multipart threshold for the object store.'
+   * - S3_CLIENT_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 client configuration for the object store.'
+   * - S3_UPLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 upload configuration for the object store.'
+   * - S3_DOWNLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 download configuration for the object store.'
+   * - GLOBUS_TRANSPORT_PARAMS
+     - annotation=dict required=False default_factory=dict description='Globus transfer parameters.'
+   * - GLOBUS_CLIENT_ID
+     - annotation=Union[str, NoneType] required=False default=None description='Globus client ID for inbound/outbound transfers.'
+   * - GLOBUS_CLIENT_SECRET
+     - annotation=Union[str, NoneType] required=False default=None description='Globus client secret for inbound/outbound transfers.'
+   * - OBJECT_STORE_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Object store Globus Endpoint ID.'
+   * - SCRATCH_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Scratch Globus Endpoint ID.'
+   * - SCRATCH_BASE_PATH
+     - annotation=str required=False default='scratch/' description='Base path for scratch storage.'
+   * - SCRATCH_INVENTORY_DB_COUNT
+     - annotation=int required=False default=16 description='Number of databases in the scratch inventory (redis).'
+   * - DOCS_BASE_URL
+     - annotation=str required=False default='my_test_url' description='Base URL for the documentation site.'
+   * - FTS_ATLAS_DATA_DIR
+     - annotation=Union[str, NoneType] required=False default=None description='Common cached directory for downloaded FTS Atlas.'
 
 Development
 -----------

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/README.rst

@@ -14,7 +14,83 @@ in their own package facilitates using the build_utils to test the integrity of
 
 Environment Variables
 ---------------------
-Only those specified by `dkist-processing-core <https://pypi.org/project/dkist-processing-core/>`_ and `dkist-processing-common <https://pypi.org/project/dkist-processing-common/>`_.
+
+.. list-table::
+   :widths: 10 90
+   :header-rows: 1
+
+   * - Variable
+     - Field Info
+   * - LOGURU_LEVEL
+     - annotation=str required=False default='INFO' alias_priority=2 validation_alias='LOGURU_LEVEL' description='Log level for the application'
+   * - MESH_CONFIG
+     - annotation=dict[str, MeshService] required=False default_factory=dict alias_priority=2 validation_alias='MESH_CONFIG' description='Service mesh configuration' examples=[{'upstream_service_name': {'mesh_address': 'localhost', 'mesh_port': 6742}}]
+   * - RETRY_CONFIG
+     - annotation=RetryConfig required=False default_factory=RetryConfig description='Retry configuration for the service'
+   * - OTEL_SERVICE_NAME
+     - annotation=str required=False default='unknown-service-name' alias_priority=2 validation_alias='OTEL_SERVICE_NAME' description='Service name for OpenTelemetry'
+   * - DKIST_SERVICE_VERSION
+     - annotation=str required=False default='unknown-service-version' alias_priority=2 validation_alias='DKIST_SERVICE_VERSION' description='Service version for OpenTelemetry'
+   * - NOMAD_ALLOC_ID
+     - annotation=str required=False default='unknown-allocation-id' alias_priority=2 validation_alias='NOMAD_ALLOC_ID' description='Nomad allocation ID for OpenTelemetry'
+   * - OTEL_EXPORTER_OTLP_TRACES_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP traces'
+   * - OTEL_EXPORTER_OTLP_METRICS_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP metrics'
+   * - OTEL_EXPORTER_OTLP_TRACES_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP traces endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_EXPORTER_OTLP_METRICS_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP metrics endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_PYTHON_DISABLED_INSTRUMENTATIONS
+     - annotation=list[str] required=False default_factory=list description='List of instrumentations to disable. https://opentelemetry.io/docs/zero-code/python/configuration/' examples=[['pika', 'requests']]
+   * - OTEL_PYTHON_FASTAPI_EXCLUDED_URLS
+     - annotation=str required=False default='health' description='Comma separated list of URLs to exclude from OpenTelemetry instrumentation in FastAPI.' examples=['client/.*/info,healthcheck']
+   * - SYSTEM_METRIC_INSTRUMENTATION_CONFIG
+     - annotation=Union[dict[str, bool], NoneType] required=False default=None description='Configuration for system metric instrumentation. https://opentelemetry-python-contrib.readthedocs.io/en/latest/instrumentation/system_metrics/system_metrics.html' examples=[{'system.memory.usage': ['used', 'free', 'cached'], 'system.cpu.time': ['idle', 'user', 'system', 'irq'], 'system.network.io': ['transmit', 'receive'], 'process.runtime.memory': ['rss', 'vms'], 'process.runtime.cpu.time': ['user', 'system'], 'process.runtime.context_switches': ['involuntary', 'voluntary']}]
+   * - ISB_USERNAME
+     - annotation=str required=False default='guest' description='Username for the interservice-bus.'
+   * - ISB_PASSWORD
+     - annotation=str required=False default='guest' description='Password for the interservice-bus.'
+   * - ISB_EXCHANGE
+     - annotation=str required=False default='master.direct.x' description='Exchange for the interservice-bus.'
+   * - ISB_QUEUE_TYPE
+     - annotation=str required=False default='classic' description='Queue type for the interservice-bus.' examples=['quorum', 'classic']
+   * - BUILD_VERSION
+     - annotation=str required=False default='dev' description='Fallback build version for workflow tasks.'
+   * - GQL_AUTH_TOKEN
+     - annotation=Union[str, NoneType] required=False default='dev' description='The auth token for the metadata-store-api.'
+   * - OBJECT_STORE_ACCESS_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The access key for the object store.'
+   * - OBJECT_STORE_SECRET_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The secret key for the object store.'
+   * - OBJECT_STORE_USE_SSL
+     - annotation=bool required=False default=False description='Whether to use SSL for the object store connection.'
+   * - MULTIPART_THRESHOLD
+     - annotation=Union[int, NoneType] required=False default=None description='Multipart threshold for the object store.'
+   * - S3_CLIENT_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 client configuration for the object store.'
+   * - S3_UPLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 upload configuration for the object store.'
+   * - S3_DOWNLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 download configuration for the object store.'
+   * - GLOBUS_TRANSPORT_PARAMS
+     - annotation=dict required=False default_factory=dict description='Globus transfer parameters.'
+   * - GLOBUS_CLIENT_ID
+     - annotation=Union[str, NoneType] required=False default=None description='Globus client ID for inbound/outbound transfers.'
+   * - GLOBUS_CLIENT_SECRET
+     - annotation=Union[str, NoneType] required=False default=None description='Globus client secret for inbound/outbound transfers.'
+   * - OBJECT_STORE_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Object store Globus Endpoint ID.'
+   * - SCRATCH_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Scratch Globus Endpoint ID.'
+   * - SCRATCH_BASE_PATH
+     - annotation=str required=False default='scratch/' description='Base path for scratch storage.'
+   * - SCRATCH_INVENTORY_DB_COUNT
+     - annotation=int required=False default=16 description='Number of databases in the scratch inventory (redis).'
+   * - DOCS_BASE_URL
+     - annotation=str required=False default='my_test_url' description='Base URL for the documentation site.'
+   * - FTS_ATLAS_DATA_DIR
+     - annotation=Union[str, NoneType] required=False default=None description='Common cached directory for downloaded FTS Atlas.'
 
 Development
 -----------

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/dkist_processing_dlnirsp/tasks/bad_pixel_map.py

@@ -70,7 +70,7 @@ class BadPixelCalibration(DlnirspTaskBase):
             logger.info("VIS data detected. Setting dynamic bad pixel map to empty.")
             dynamic_bad_pixel_map = np.zeros_like(static_bad_pixel_map)
 
-        with self.apm_writing_step("Combine dynamic and static maps and write"):
+        with self.telemetry_span("Combine dynamic and static maps and write"):
             logger.info("Combining dynamic and static bad pixel maps")
             logger.info(f"Static map has {int(np.sum(static_bad_pixel_map))} bad pixels")
             logger.info(f"Dynamic map has {int(np.sum(dynamic_bad_pixel_map))} bad pixels")
@@ -99,7 +99,7 @@ class BadPixelCalibration(DlnirspTaskBase):
         (a settable pipeline parameter) are flagged as bad pixels. Prior to computing the standard deviation of the
         difference image the illuminated array mask is applied so non-illuminated regions don't impact the results.
         """
-        with self.apm_processing_step("Smooth average lamp gain image"):
+        with self.telemetry_span("Smooth average lamp gain image"):
             avg_lamp_gain = next(
                 self.read(
                     tags=[
@@ -117,7 +117,7 @@ class BadPixelCalibration(DlnirspTaskBase):
                 mode="constant",
                 cval=np.nanmedian(avg_lamp_gain),
             )
-        with self.apm_processing_step("Compute gain dynamic bad pixel map"):
+        with self.telemetry_span("Compute gain dynamic bad pixel map"):
             logger.info("Finding bad pixel locations in lamp gain")
             diff = smoothed_array - avg_lamp_gain
             diff[~self.group_id_illuminated_idx] = np.nan
@@ -146,7 +146,7 @@ class BadPixelCalibration(DlnirspTaskBase):
         is then subtracted from the original array. Pixels in this difference array that are deviant by a large amount
         (a settable pipeline parameter) are flagged as bad pixels.
         """
-        with self.apm_processing_step("Compute lamp dark sigma image"):
+        with self.telemetry_span("Compute lamp dark sigma image"):
             smallest_lamp_exp_time = sorted(self.constants.lamp_gain_exposure_times)[0]
             logger.info(f"Using darks from exposure time = {smallest_lamp_exp_time}")
             lamp_darks = self.read(
@@ -159,7 +159,7 @@ class BadPixelCalibration(DlnirspTaskBase):
             )
             dark_sigma = stddev_numpy_arrays(lamp_darks)
 
-        with self.apm_processing_step("Smooth dark sigma array"):
+        with self.telemetry_span("Smooth dark sigma array"):
             logger.info("Smoothing dark sigma array")
             smoothed_array = spnd.median_filter(
                 dark_sigma,
@@ -168,7 +168,7 @@ class BadPixelCalibration(DlnirspTaskBase):
                 cval=np.nanmedian(dark_sigma),
             )
 
-        with self.apm_processing_step("Compute dark dynamic bad pixel map"):
+        with self.telemetry_span("Compute dark dynamic bad pixel map"):
             logger.info("Finding bad pixel locations in dark sigma")
             diff = smoothed_array - dark_sigma
 

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/dkist_processing_dlnirsp/tasks/dark.py

@@ -45,7 +45,7 @@ class DarkCalibration(DlnirspTaskBase, QualityMixin):
         """
         target_exp_times = self.constants.non_dark_task_exposure_times
         logger.info(f"{target_exp_times = }")
-        with self.apm_task_step(
+        with self.telemetry_span(
             f"Calculating dark frames for {self.constants.num_beams} beams and {len(target_exp_times)} exp times"
         ):
             total_dark_frames_used = 0
@@ -62,11 +62,11 @@ class DarkCalibration(DlnirspTaskBase, QualityMixin):
                 total_dark_frames_used += current_exp_dark_count
                 input_dark_arrays = self.read(tags=dark_tags, decoder=fits_array_decoder)
 
-                with self.apm_processing_step(f"Calculating dark for {exp_time = }"):
+                with self.telemetry_span(f"Calculating dark for {exp_time = }"):
                     logger.info(f"Calculating dark for {exp_time = }")
                     averaged_dark_array = average_numpy_arrays(input_dark_arrays)
 
-                with self.apm_writing_step(f"Writing dark for {exp_time = }"):
+                with self.telemetry_span(f"Writing dark for {exp_time = }"):
                     logger.info(f"Writing dark for {exp_time = }")
                     self.write(
                         data=averaged_dark_array,
@@ -74,7 +74,7 @@ class DarkCalibration(DlnirspTaskBase, QualityMixin):
                         encoder=fits_array_encoder,
                     )
 
-        with self.apm_processing_step("Computing and logger quality metrics"):
+        with self.telemetry_span("Computing and logger quality metrics"):
             no_of_raw_dark_frames: int = self.scratch.count_all(
                 tags=[
                     DlnirspTag.linearized_frame(),

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/dkist_processing_dlnirsp/tasks/geometric.py

@@ -57,25 +57,25 @@ class GeometricCalibration(DlnirspTaskBase, CorrectionsMixin, QualityMixin):
 
         6. Write shifts, scales, and reference wavelength axis to a file
         """
-        with self.apm_task_step("Apply dark and lamp corrections"):
+        with self.telemetry_span("Apply dark and lamp corrections"):
             logger.info("Computing average dark/lamp corrected gain image")
             self.compute_average_corrected_gain()
 
-        with self.apm_task_step("Compute spectral curvature"):
+        with self.telemetry_span("Compute spectral curvature"):
             logger.info("Computing spectral curvature")
             shift_dict, scale_dict = self.compute_spectral_curvature_and_dispersion()
 
-        with self.apm_task_step("Compute reference wavelength grid"):
+        with self.telemetry_span("Compute reference wavelength grid"):
             logger.info("Computing reference wavelength grid")
             reference_wavelength_axis = self.compute_reference_wavelength_axis(
                 shift_dict, scale_dict
             )
 
-        with self.apm_writing_step("Write geometric calibration calibration"):
+        with self.telemetry_span("Write geometric calibration calibration"):
             logger.info("Writing geometric calibration")
             self.write_geometric_calibration(shift_dict, scale_dict, reference_wavelength_axis)
 
-        with self.apm_processing_step("Computing and logging quality metrics"):
+        with self.telemetry_span("Computing and logging quality metrics"):
             no_of_raw_solar_frames: int = self.scratch.count_all(
                 tags=[DlnirspTag.linearized_frame(), DlnirspTag.task_solar_gain()],
             )

{dkist_processing_dlnirsp-0.31.1 → dkist_processing_dlnirsp-0.32.1}/dkist_processing_dlnirsp/tasks/ifu_drift.py

@@ -50,7 +50,7 @@ class IfuDriftCalibration(DlnirspTaskBase):
 
         4. Apply this shift to the IFU metrology files and save for use in the downstream pipeline.
         """
-        with self.apm_processing_step("Average solar gain images"):
+        with self.telemetry_span("Average solar gain images"):
             logger.info("Computing average solar gain array")
             solar_gain_data = self.get_avg_solar_gain()
 
@@ -60,7 +60,7 @@ class IfuDriftCalibration(DlnirspTaskBase):
                 encoder=fits_array_encoder,
             )
 
-        with self.apm_processing_step("Compute binary arrays"):
+        with self.telemetry_span("Compute binary arrays"):
             logger.info("Computing solar binary image")
             solar_binary = self.compute_solar_binary(solar_gain_data)
 
@@ -79,12 +79,12 @@ class IfuDriftCalibration(DlnirspTaskBase):
                 encoder=fits_array_encoder,
             )
 
-        with self.apm_processing_step("Compute IFU drift"):
+        with self.telemetry_span("Compute IFU drift"):
             logger.info("Computing IFU drift amount")
             drift = self.compute_ifu_drift(solar_binary, ifu_binary)
             logger.info(f"IFU drift = {drift}")
 
-        with self.apm_processing_step("Drift IFU metrology arrays"):
+        with self.telemetry_span("Drift IFU metrology arrays"):
             logger.info("Drifting IFU group ID array")
             drifted_ifu_id_array = self.apply_drift_to_array(raw_ifu_id_array, drift)
 
@@ -121,7 +121,7 @@ class IfuDriftCalibration(DlnirspTaskBase):
                 )
                 drifted_arrays_dict[tag] = drifted_array * beam_correction_array
 
-        with self.apm_writing_step("Write drifted IFU metrology arrays"):
+        with self.telemetry_span("Write drifted IFU metrology arrays"):
             logger.info("Writing drifted IFU metrology arrays")
             self.write_drifted_metrology_arrays(drifted_arrays_dict)