dkist-processing-visp 5.0.0rc3__tar.gz → 5.1.1__tar.gz

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/CHANGELOG.rst

@@ -1,3 +1,55 @@
+v5.1.1 (2025-12-05)
+===================
+
+Misc
+----
+
+- Update dkist-processing-common to 11.9.0 to take advantage of globus account pools for inbound and outbound transfers. (`#252 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/252>`__)
+
+
+v5.1.0 (2025-12-03)
+===================
+
+Misc
+----
+
+- Update workflows to remove `InstrumentPolarizationCalibration`'s dependency on `SolarCalibration`. These two tasks can
+  now run in parallel. (`#248 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/248>`__)
+
+
+v5.0.0 (2025-12-02)
+===================
+
+Features
+--------
+
+- Only compute a single lamp gain for each beam. In the past a single map gain was also computed for each modulation state. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Add quality report metrics that show the quality of the vignette estimation in the Solar Gain tasks. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Update the Solar Gain task to measure vignetting signal, compute a single gain for each beam (as opposed to for each beam and modulator state),
+  and stop applying residual spectral shifts to the characteristic spectra before removing from the input gain array.
+  See the `Science Changelog <https://docs.dkist.nso.edu/projects/visp/en/stable/scientific_changelog.html>`_ and
+  `gain algorithm docs <https://docs.dkist.nso.edu/projects/visp/en/stable/gain_correction.html>`_ for more information. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Add Buds to parse the spectrograph setup into pipeline constants to be used when fitting a solar atlas. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+
+
+Misc
+----
+
+- Remove the `LineZonesMixin` and move its methods directly to the Geometric calibration task, which is now the only task that uses them. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Rename the ``solar_spectral_avg_window`` to ``solar_spatial_median_filter_width_px`` to more accurately capture what it does. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Rename all line-zone parameters to be "geo*" parameters instead of "solar*" parameters. These parameters are now only used in the
+  Geometric calibration task. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+
+
+Documentation
+-------------
+
+- Update the online doc page for `gain calibration <https://docs.dkist.nso.edu/projects/visp/en/stable/gain_correction.html>`_
+  to reflect the updates to the Solar Gain task. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+- Add intersphinx mappings for `lmfit <https://lmfit.github.io/lmfit-py/>`_ and `scikit-learn <https://scikit-learn.org/stable/>`_
+  for linking bliss. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+
+
 v4.0.0 (2025-11-12)
 ===================
 

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.0.0rc3
+Version: 5.1.1
 Summary: Science processing code for the ViSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
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@@ -347,6 +347,10 @@ Environment Variables
      - 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'
+   * - NOMAD_ALLOC_NAME
+     - annotation=str required=False default='unknown-allocation-name' alias='NOMAD_ALLOC_NAME' alias_priority=2 description='Allocation name for the deployed container the task is running on.'
+   * - NOMAD_GROUP_NAME
+     - annotation=str required=False default='unknown-allocation-group' alias='NOMAD_GROUP_NAME' alias_priority=2 description='Allocation group for the deployed container the task is running on'
    * - OTEL_EXPORTER_OTLP_TRACES_INSECURE
      - annotation=bool required=False default=True description='Use insecure connection for OTLP traces'
    * - OTEL_EXPORTER_OTLP_METRICS_INSECURE
@@ -387,12 +391,12 @@ Environment Variables
      - 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.'
+   * - GLOBUS_MAX_RETRIES
+     - annotation=int required=False default=5 description='Max retries for transient errors on calls to the globus api.'
+   * - GLOBUS_INBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for inbound transfers.' examples=[[{'client_id': 'id1', 'client_secret': 'secret1'}, {'client_id': 'id2', 'client_secret': 'secret2'}]]
+   * - GLOBUS_OUTBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for outbound transfers.' examples=[[{'client_id': 'id3', 'client_secret': 'secret3'}, {'client_id': 'id4', 'client_secret': 'secret4'}]]
    * - OBJECT_STORE_ENDPOINT
      - annotation=Union[str, NoneType] required=False default=None description='Object store Globus Endpoint ID.'
    * - SCRATCH_ENDPOINT

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/README.rst

@@ -33,6 +33,10 @@ Environment Variables
      - 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'
+   * - NOMAD_ALLOC_NAME
+     - annotation=str required=False default='unknown-allocation-name' alias='NOMAD_ALLOC_NAME' alias_priority=2 description='Allocation name for the deployed container the task is running on.'
+   * - NOMAD_GROUP_NAME
+     - annotation=str required=False default='unknown-allocation-group' alias='NOMAD_GROUP_NAME' alias_priority=2 description='Allocation group for the deployed container the task is running on'
    * - OTEL_EXPORTER_OTLP_TRACES_INSECURE
      - annotation=bool required=False default=True description='Use insecure connection for OTLP traces'
    * - OTEL_EXPORTER_OTLP_METRICS_INSECURE
@@ -73,12 +77,12 @@ Environment Variables
      - 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.'
+   * - GLOBUS_MAX_RETRIES
+     - annotation=int required=False default=5 description='Max retries for transient errors on calls to the globus api.'
+   * - GLOBUS_INBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for inbound transfers.' examples=[[{'client_id': 'id1', 'client_secret': 'secret1'}, {'client_id': 'id2', 'client_secret': 'secret2'}]]
+   * - GLOBUS_OUTBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for outbound transfers.' examples=[[{'client_id': 'id3', 'client_secret': 'secret3'}, {'client_id': 'id4', 'client_secret': 'secret4'}]]
    * - OBJECT_STORE_ENDPOINT
      - annotation=Union[str, NoneType] required=False default=None description='Object store Globus Endpoint ID.'
    * - SCRATCH_ENDPOINT

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/SCIENCE_CHANGELOG.rst

@@ -1,3 +1,22 @@
+v5.0.0 (2025-12-02)
+===================
+
+
+
+
+- Major update to the gain algorithm to mitigate polarization artifacts in L1 science frames. This change can be split into
+  three parts. See the `gain correction <https://docs.dkist.nso.edu/projects/visp/en/stable/gain_correction.html>`_ page for more information.
+
+  #. Compute a single gain correction image for each beam. In the past we had computed a separate gain image for each modstate as well, but this was found to couple residual polarization structure into the final science frames.
+
+  #. Stop "refining" (i.e., applying small spectral offsets to) the characteristic solar spectrum on a per-spatial-pixel basis. This was initially done to minimize line residuals in Telluric lines but was found to have a more-negative on polarimetric residuals.
+
+  #. Separate vignetting caused by aperture masks from the solar signal used to remove spectral lines in the final gain image. This is done by fitting a solar atlas and taking the deviation in continuum to be the vignetting signal.
+
+  Computing a single gain per beam will greatly reduce the polarization artifacts in L1 data. Measuring the vignette
+  signal directly will further reduce these artifacts and improve flatness across the array. (`#246 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/246>`__)
+
+
 v4.0.0 (2025-11-12)
 ===================
 

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/bitbucket-pipelines.yml

@@ -42,6 +42,7 @@ definitions:
         caches:
           - pip
         name: Test
+        size: 2x
         script:
           - pip install -U pip wheel build setuptools_scm setuptools
           - pip install .[test]

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/models/parameters.py

@@ -1,6 +1,7 @@
 """Visp calibration pipeline parameters."""
 
 from datetime import datetime
+from random import randint
 from typing import Any
 
 import astropy.units as u
@@ -208,7 +209,16 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
     @property
     def solar_vignette_wavecal_fit_kwargs(self) -> dict[str, Any]:
         """Define extra keyword arguments to pass to the wavelength calibration fitter."""
-        return self._find_most_recent_past_value("visp_solar_vignette_wavecal_fit_kwargs")
+        doc_dict = self._find_most_recent_past_value("visp_solar_vignette_wavecal_fit_kwargs")
+        rng_kwarg = dict()
+        fitting_method = doc_dict.get("method", False)
+        if fitting_method in ["basinhopping", "differential_evolution", "dual_annealing"]:
+            rng = randint(1, 1_000_000)
+            rng_kwarg["rng"] = rng
+
+        # The order here allows us to override `rng` in a parameter value
+        fit_kwargs = rng_kwarg | doc_dict
+        return fit_kwargs
 
     @property
     def solar_vignette_spectral_poly_fit_order(self) -> int:

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/tasks/geometric.py

@@ -274,7 +274,12 @@ class GeometricCalibration(
         self.prep_input_solar_gain()
 
     def prep_lamp_gain(self):
-        """Apply dark corrections fo INPUT lamp frames."""
+        """
+        Create average, dark-corrected lamp gain images for each modstate from INPUT lamp gains.
+
+        This is different from the results of the `~dkist_processing_visp.tasks.lamp.LampCalibration` task because in
+        that task the hairlines are masked out, but here we *need* the hairlines to compute the rotation angle.
+        """
         for readout_exp_time in self.constants.lamp_readout_exp_times:
             for beam in range(1, self.constants.num_beams + 1):
                 logger.info(

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/tasks/solar.py

@@ -562,15 +562,7 @@ class SolarCalibration(
 
         fitter = WavelengthCalibrationFitter(input_parameters=init_parameters, atlas=atlas)
         with self.telemetry_span("Fit atlas and continuum"):
-            rng_kwarg = dict()
-            fitting_method = self.parameters.solar_vignette_wavecal_fit_kwargs.get("method", False)
-            if fitting_method in ["basinhopping", "differential_evolution", "dual_annealing"]:
-                # For methods that support the `rng` kwarg we use the recipe run id as the rng seed
-                rng = self.recipe_run_id
-                rng_kwarg["rng"] = rng
-
-            # The order here allows us to override the default `rng` (above) in a parameter value
-            extra_kwargs = rng_kwarg | self.parameters.solar_vignette_wavecal_fit_kwargs
+            extra_kwargs = self.parameters.solar_vignette_wavecal_fit_kwargs
             logger.info(f"Calling fitter with extra kwargs: {extra_kwargs}")
             fit_result = fitter(
                 input_spectrum=representative_spectrum,

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/tests/test_parameters.py

@@ -103,7 +103,11 @@ def test_non_wave_parameters(
             pn = f"{pn}_{arm_id}"
         pv = expected[pn]
         is_wavelength_param = isinstance(pv, dict) and "wavelength" in pv
-        if parameter_name not in parse_parameter_names and not is_wavelength_param:
+        if (
+            parameter_name not in parse_parameter_names
+            and not is_wavelength_param
+            and parameter_name != "solar_vignette_wavecal_fit_kwargs"
+        ):
             param_obj_value = getattr(task_param_attr, parameter_name)
             if isinstance(pv, tuple):
                 pv = list(pv)
@@ -171,3 +175,47 @@ def test_wave_parameters(
         is_wavelength_param = isinstance(pv, dict) and "wavelength" in pv
         if is_wavelength_param and property_name not in parse_parameter_names + arm_parameter_names:
             assert getattr(task_param_attr, property_name) == pv["values"][idx]
+
+
+class AnyInt:
+    pass
+
+
+@pytest.mark.parametrize("arm_id", [pytest.param("1")])
+@pytest.mark.parametrize(
+    "db_value, expected",
+    [
+        pytest.param({"method": "nelder"}, {"method": "nelder"}, id="non_rng_method"),
+        pytest.param(
+            {"method": "basinhopping"}, {"method": "basinhopping", "rng": AnyInt}, id="random_rng"
+        ),
+        pytest.param(
+            {"method": "differential_evolution", "rng": 6.28},
+            {"method": "differential_evolution", "rng": 6.28},
+            id="override_rng",
+        ),
+        pytest.param(dict(), dict(), id="no_kwargs"),
+    ],
+)
+def test_fit_kwarg_parameters(
+    basic_science_task_with_parameter_mixin,
+    db_value,
+    expected,
+):
+    """
+    Given: A Science task with the parameter mixin
+    When: Accessing properties for parameters that do not depend on wavelength
+    Then: The correct value is returned
+    """
+    task, _ = next(
+        basic_science_task_with_parameter_mixin(
+            VispInputDatasetParameterValues(visp_solar_vignette_wavecal_fit_kwargs=db_value)
+        )
+    )
+    kwarg_dict = task.parameters.solar_vignette_wavecal_fit_kwargs
+    assert kwarg_dict.keys() == expected.keys()
+    for k in expected.keys():
+        if expected[k] is AnyInt:
+            assert type(kwarg_dict[k]) is int
+        else:
+            assert expected[k] == kwarg_dict[k]

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/tests/test_solar.py

@@ -310,16 +310,10 @@ def solar_gain_task(
 
 
 @pytest.mark.parametrize(
-    "background_on, fit_kwargs",
+    "background_on",
     [
-        pytest.param(True, {"method": "nelder"}, id="background_on-non_rng_method"),
-        pytest.param(False, "conftest", id="background_off-conftest_fit_kwargs"),
-        pytest.param(
-            False,
-            {"method": "differential_evolution", "rng": 6.28},
-            id="background_off-override_rng",
-        ),
-        pytest.param(False, dict(), id="background_off-no_fit_kwargs"),
+        pytest.param(True, id="background_on"),
+        pytest.param(False, id="background_off"),
     ],
 )
 def test_solar_gain_task(
@@ -335,7 +329,6 @@ def test_solar_gain_task(
     assign_input_dataset_doc_to_task,
     mocker,
     fake_gql_client,
-    fit_kwargs,
 ):
     """
     Given: A set of raw solar gain images and necessary intermediate calibrations
@@ -351,7 +344,6 @@ def test_solar_gain_task(
     input_shape = (num_wave_pix * 2, 100)
     intermediate_shape = (num_wave_pix, 100)
     beam_border = input_shape[0] // 2
-    conftest_fit_kwargs = VispInputDatasetParameterValues().visp_solar_vignette_wavecal_fit_kwargs
     assign_input_dataset_doc_to_task(
         task,
         VispInputDatasetParameterValues(
@@ -361,9 +353,6 @@ def test_solar_gain_task(
             visp_wavecal_init_resolving_power=resolving_power,
             visp_wavecal_camera_lens_parameters_1=lens_parameters_no_units,
             visp_solar_vignette_initial_continuum_poly_fit_order=1,
-            visp_solar_vignette_wavecal_fit_kwargs=(
-                conftest_fit_kwargs if fit_kwargs == "conftest" else fit_kwargs
-            ),
         ),
         arm_id=1,
     )

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/workflows/l0_processing.py

@@ -41,8 +41,13 @@ l0_pipeline.add_node(
     task=SolarCalibration,
     upstreams=[LampCalibration, GeometricCalibration, BackgroundLightCalibration],
 )
-l0_pipeline.add_node(task=InstrumentPolarizationCalibration, upstreams=SolarCalibration)
-l0_pipeline.add_node(task=ScienceCalibration, upstreams=InstrumentPolarizationCalibration)
+l0_pipeline.add_node(
+    task=InstrumentPolarizationCalibration,
+    upstreams=[BackgroundLightCalibration, GeometricCalibration],
+)
+l0_pipeline.add_node(
+    task=ScienceCalibration, upstreams=[SolarCalibration, InstrumentPolarizationCalibration]
+)
 l0_pipeline.add_node(task=VispWriteL1Frame, upstreams=ScienceCalibration)
 
 # Movie flow

{dkist_processing_visp-5.0.0rc3 → dkist_processing_visp-5.1.1}/dkist_processing_visp/workflows/trial_workflows.py

@@ -43,8 +43,13 @@ full_trial_pipeline.add_node(
     task=SolarCalibration,
     upstreams=[LampCalibration, GeometricCalibration, BackgroundLightCalibration],
 )
-full_trial_pipeline.add_node(task=InstrumentPolarizationCalibration, upstreams=SolarCalibration)
-full_trial_pipeline.add_node(task=ScienceCalibration, upstreams=InstrumentPolarizationCalibration)
+full_trial_pipeline.add_node(
+    task=InstrumentPolarizationCalibration,
+    upstreams=[BackgroundLightCalibration, GeometricCalibration],
+)
+full_trial_pipeline.add_node(
+    task=ScienceCalibration, upstreams=[SolarCalibration, InstrumentPolarizationCalibration]
+)
 full_trial_pipeline.add_node(task=VispWriteL1Frame, upstreams=ScienceCalibration)
 
 # Movie flow