dkist-processing-visp 5.0.0rc2__tar.gz → 5.1.0__tar.gz

{dkist_processing_visp-5.0.0rc2 → dkist_processing_visp-5.1.0}/CHANGELOG.rst

@@ -1,3 +1,46 @@
+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-5.0.0rc2 → dkist_processing_visp-5.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.0.0rc2
+Version: 5.1.0
 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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{dkist_processing_visp-5.0.0rc2 → dkist_processing_visp-5.1.0}/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-5.0.0rc2 → dkist_processing_visp-5.1.0}/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
@@ -186,10 +187,38 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
             "visp_solar_vignette_initial_continuum_poly_fit_order"
         )
 
+    @property
+    def solar_vignette_crval_bounds_px(self) -> float:
+        """
+        Define the bounds (in *pixels*) on crval when fitting the initial vignette signal.
+
+        The actual bounds on the value of crval are equal to ± the initial dispersion times this number. Note that the
+        total range searched by the fitting algorithm will be twice this number (in pixels).
+        """
+        return self._find_most_recent_past_value("visp_solar_vignette_crval_bounds_px") * u.pix
+
+    @property
+    def solar_vignette_dispersion_bounds_fraction(self) -> float:
+        """
+        Define the ± fraction away from the initial value for bounds on dispersion when fitting the initial vignette signal.
+
+        This value should be between 0 and 1. For example, the minimum bound is `init_value * (1 - solar_vignette_dispersion_bounds_fraction)`.
+        """
+        return self._find_most_recent_past_value("visp_solar_vignette_dispersion_bounds_fraction")
+
     @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:
@@ -228,6 +257,13 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
         config_dict = self._find_most_recent_past_value("visp_wavecal_atlas_download_config")
         return DownloadConfig.model_validate(config_dict)
 
+    @property
+    def wavecal_init_crval_guess_normalization_percentile(self) -> float | None:
+        """Define the CDF percentage used to normalize the Atlas to the input spectrum level when computing an initial CRVAL guess."""
+        return self._find_most_recent_past_value(
+            "visp_wavecal_init_crval_guess_normalization_percentile"
+        )
+
     @property
     def wavecal_init_resolving_power(self) -> int:
         """Define the initial guess for ViSP resolving power in wavecal fits."""

{dkist_processing_visp-5.0.0rc2 → dkist_processing_visp-5.1.0}/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-5.0.0rc2 → dkist_processing_visp-5.1.0}/dkist_processing_visp/tasks/solar.py

@@ -70,6 +70,7 @@ class WavelengthCalibrationParametersWithContinuum(WavelengthCalibrationParamete
 
     continuum_poly_fit_order: int
     normalized_abscissa: np.ndarray
+    zeroth_order_continuum_coefficient: float
 
     @property
     def continuum_function(self) -> Callable[[np.ndarray, Parameters], np.ndarray]:
@@ -93,16 +94,26 @@ class WavelengthCalibrationParametersWithContinuum(WavelengthCalibrationParamete
         #       dynamically create the required number of "poly_coeff_{o:02n}" fields. Sorry if this bites you!
         params = super().lmfit_parameters
         for o in range(self.continuum_poly_fit_order + 1):
+            # `np.polyval` uses its input coefficient list "backwards", so `poly_coeff_{self.continuum_poly_fit_order}`
+            # is the 0th order polynomial term.
             params.add(
                 f"poly_coeff_{o:02n}",
                 vary=True,
-                value=o // self.continuum_poly_fit_order,
+                value=(
+                    self.zeroth_order_continuum_coefficient
+                    if o == self.continuum_poly_fit_order
+                    else 0
+                ),
                 min=-1,
                 max=1,
             )
 
-        params[f"poly_coeff_{self.continuum_poly_fit_order:02n}"].min = 0.7
-        params[f"poly_coeff_{self.continuum_poly_fit_order:02n}"].max = 1.3
+        params[f"poly_coeff_{self.continuum_poly_fit_order:02n}"].min = (
+            self.zeroth_order_continuum_coefficient * 0.5
+        )
+        params[f"poly_coeff_{self.continuum_poly_fit_order:02n}"].max = (
+            self.zeroth_order_continuum_coefficient * 1.5
+        )
 
         # Remove the default continuum parameterization
         del params["continuum_level"]
@@ -551,9 +562,11 @@ class SolarCalibration(
 
         fitter = WavelengthCalibrationFitter(input_parameters=init_parameters, atlas=atlas)
         with self.telemetry_span("Fit atlas and continuum"):
+            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,
-                **self.parameters.solar_vignette_wavecal_fit_kwargs,
+                **extra_kwargs,
             )
 
         return fit_result
@@ -610,6 +623,7 @@ class SolarCalibration(
             negative_limit=-wavelength_range / 2,
             positive_limit=wavelength_range / 2,
             num_steps=500,
+            normalization_percentile=self.parameters.wavecal_init_crval_guess_normalization_percentile,
         )
 
         logger.info(f"{crval_init = !s}")
@@ -627,18 +641,22 @@ class SolarCalibration(
         resolving_power = self.parameters.wavecal_init_resolving_power
         opacity_factor = self.parameters.wavecal_init_opacity_factor
         straylight_faction = self.parameters.wavecal_init_straylight_fraction
+        relative_atlas_scaling = self.estimate_relative_continuum_level(
+            crval_init=crval_init,
+            wavelength_range=wavelength_range,
+            atlas=atlas,
+            representative_spectrum=representative_spectrum,
+        )
+        logger.info(f"0th order coefficient initial guess: {relative_atlas_scaling}")
 
-        # The first time we have to change these ranges (which may never happen!) we should at least consider making
-        # them parameters.
-        wavelength_search_width = wavelength_range * 0.15
+        wavelength_search_width = dispersion * self.parameters.solar_vignette_crval_bounds_px
         bounds = BoundsModel(
-            # An alternative for the crval bounds would be `[input_wavelength_vector.min(), input_wavelength_vector.max()]`
             crval=LengthBoundRange(
                 min=crval_init - wavelength_search_width, max=crval_init + wavelength_search_width
             ),
             dispersion=DispersionBoundRange(
-                min=dispersion * 0.96,
-                max=dispersion * 1.04,
+                min=dispersion * (1 - self.parameters.solar_vignette_dispersion_bounds_fraction),
+                max=dispersion * (1 + self.parameters.solar_vignette_dispersion_bounds_fraction),
             ),
             incident_light_angle=AngleBoundRange(
                 min=incident_light_angle - 1 * u.deg, max=incident_light_angle + 1 * u.deg
@@ -646,7 +664,6 @@ class SolarCalibration(
             resolving_power=UnitlessBoundRange(min=1e5, max=5e5),
             opacity_factor=UnitlessBoundRange(min=1.0, max=10),
             straylight_fraction=UnitlessBoundRange(min=0.0, max=0.8),
-            continuum_level=UnitlessBoundRange(min=0.99, max=1.1),
         )
 
         init_params = WavelengthCalibrationParametersWithContinuum(
@@ -656,7 +673,7 @@ class SolarCalibration(
             grating_constant=grating_constant,
             doppler_velocity=doppler_velocity,
             order=spectral_order,
-            continuum_level=1.0,
+            continuum_level=1,
             resolving_power=resolving_power,
             opacity_factor=opacity_factor,
             straylight_fraction=straylight_faction,
@@ -664,10 +681,44 @@ class SolarCalibration(
             bounds=bounds,
             continuum_poly_fit_order=self.parameters.solar_vignette_initial_continuum_poly_fit_order,
             normalized_abscissa=normalized_abscissa,
+            zeroth_order_continuum_coefficient=relative_atlas_scaling,
         )
 
         return init_params
 
+    def estimate_relative_continuum_level(
+        self,
+        *,
+        crval_init: Quantity,
+        wavelength_range: Quantity,
+        atlas: Atlas,
+        representative_spectrum: np.ndarray,
+    ) -> float:
+        """
+        Estimate the multiplicative scaling between the representative spectrum and atlas solar transmission.
+
+        This scaling is used to set the initial guess of 0th-order polynomial fit coefficient. We estimate the scaling
+        factor by comparing the values of the two spectra at a given percent of the CDF. This percent is taken from
+        the `~dkist_processing_visp.models.parameters.VispParameters.wavecal_init_crval_guess_normalization_percentile`
+        pipeline parameter.
+        """
+        wave_min = crval_init - wavelength_range / 2
+        wave_max = crval_init + wavelength_range / 2
+
+        atlas_idx = np.where(
+            (atlas.solar_atlas_wavelength >= wave_min) & (atlas.solar_atlas_wavelength <= wave_max)
+        )
+        atlas_norm = np.nanpercentile(
+            atlas.solar_atlas_transmission[atlas_idx],
+            self.parameters.wavecal_init_crval_guess_normalization_percentile,
+        )
+        spec_norm = np.nanpercentile(
+            representative_spectrum,
+            self.parameters.wavecal_init_crval_guess_normalization_percentile,
+        )
+
+        return spec_norm / atlas_norm
+
     def compute_final_vignette_estimate(self, init_vignette_correction: np.ndarray) -> np.ndarray:
         """
         Fit the spectral shape of continuum residuals for each spatial pixel.

{dkist_processing_visp-5.0.0rc2 → dkist_processing_visp-5.1.0}/dkist_processing_visp/tests/conftest.py

@@ -149,6 +149,8 @@ class VispInputDatasetParameterValues:
     )
     visp_solar_characteristic_spatial_normalization_percentile: float = 90.0
     visp_solar_vignette_initial_continuum_poly_fit_order: int = 6
+    visp_solar_vignette_crval_bounds_px: float = 7
+    visp_solar_vignette_dispersion_bounds_fraction: float = 0.02
     visp_solar_vignette_wavecal_fit_kwargs: dict[str, Any] = field(
         default_factory=lambda: {
             "method": "differential_evolution",
@@ -184,6 +186,7 @@ class VispInputDatasetParameterValues:
             "solar_reference_atlas_hash_id": "md5:84ab4c50689ef235fe5ed4f7ee905ca0",
         }
     )
+    visp_wavecal_init_crval_guess_normalization_percentile: float = 95
     visp_wavecal_init_resolving_power: int = 150000
     visp_wavecal_init_straylight_fraction: float = 0.2
     visp_wavecal_init_opacity_factor: float = 5.0

{dkist_processing_visp-5.0.0rc2 → dkist_processing_visp-5.1.0}/dkist_processing_visp/tests/test_parameters.py

@@ -34,6 +34,7 @@ def arm_parameter_names() -> list[str]:
 @pytest.fixture(scope="session")
 def unit_parameter_names_and_units() -> dict[str, u.Unit | list[u.Unit]]:
     return {
+        "solar_vignette_crval_bounds_px": u.pix,
         "wavecal_camera_lens_parameters": [u.m, u.m / u.nm, u.m / u.nm**2],
         "wavecal_pixel_pitch_micron_per_pix": u.um / u.pix,
     }
@@ -102,7 +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)
@@ -170,3 +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]