dkist-processing-visp 5.1.2rc2__tar.gz → 5.2.0rc1__tar.gz

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+v5.1.2 (2025-12-08)
+===================
+
+Features
+--------
+
+- Store quality data in object store and revise the workflow so that VispAssembleQualityData precedes the TransferL1Data task. (`#251 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/251>`__)
+
+
 v5.1.1 (2025-12-05)
 ===================
 

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.1.2rc2
+Version: 5.2.0rc1
 Summary: Science processing code for the ViSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -13,7 +13,7 @@ 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==11.9.1rc2
+Requires-Dist: dkist-processing-common==11.9.1
 Requires-Dist: dkist-processing-math==2.2.1
 Requires-Dist: dkist-processing-pac==3.1.1
 Requires-Dist: dkist-header-validator==5.2.1
@@ -30,6 +30,7 @@ Requires-Dist: scikit-learn==1.6.1
 Requires-Dist: peakutils==1.3.5
 Requires-Dist: Pillow==10.4.0
 Requires-Dist: moviepy==2.1.2
+Requires-Dist: solar-wavelength-calibration==2.0.0
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
@@ -125,8 +126,8 @@ Requires-Dist: attrs==25.4.0; extra == "frozen"
 Requires-Dist: babel==2.17.0; extra == "frozen"
 Requires-Dist: billiard==4.2.4; extra == "frozen"
 Requires-Dist: blinker==1.9.0; extra == "frozen"
-Requires-Dist: boto3==1.42.5; extra == "frozen"
-Requires-Dist: botocore==1.42.5; extra == "frozen"
+Requires-Dist: boto3==1.42.8; extra == "frozen"
+Requires-Dist: botocore==1.42.8; extra == "frozen"
 Requires-Dist: cachelib==0.13.0; extra == "frozen"
 Requires-Dist: celery==5.6.0; extra == "frozen"
 Requires-Dist: certifi==2025.11.12; extra == "frozen"
@@ -149,11 +150,11 @@ Requires-Dist: dacite==1.9.2; extra == "frozen"
 Requires-Dist: decorator==5.2.1; extra == "frozen"
 Requires-Dist: dill==0.4.0; extra == "frozen"
 Requires-Dist: dkist-header-validator==5.2.1; extra == "frozen"
-Requires-Dist: dkist-processing-common==11.9.1rc2; extra == "frozen"
+Requires-Dist: dkist-processing-common==11.9.1; extra == "frozen"
 Requires-Dist: dkist-processing-core==6.0.1; extra == "frozen"
 Requires-Dist: dkist-processing-math==2.2.1; extra == "frozen"
 Requires-Dist: dkist-processing-pac==3.1.1; extra == "frozen"
-Requires-Dist: dkist-processing-visp==5.1.2rc2; extra == "frozen"
+Requires-Dist: dkist-processing-visp==5.2.0rc1; extra == "frozen"
 Requires-Dist: dkist-service-configuration==4.1.13; extra == "frozen"
 Requires-Dist: dkist-spectral-lines==3.0.0; extra == "frozen"
 Requires-Dist: dkist_fits_specifications==4.17.0; extra == "frozen"
@@ -169,7 +170,6 @@ Requires-Dist: globus-sdk==4.2.0; extra == "frozen"
 Requires-Dist: google-re2==1.1.20251105; extra == "frozen"
 Requires-Dist: googleapis-common-protos==1.72.0; extra == "frozen"
 Requires-Dist: gqlclient==1.2.3; extra == "frozen"
-Requires-Dist: greenlet==3.3.0; extra == "frozen"
 Requires-Dist: grpcio==1.76.0; extra == "frozen"
 Requires-Dist: gunicorn==23.0.0; extra == "frozen"
 Requires-Dist: h11==0.16.0; extra == "frozen"
@@ -199,7 +199,7 @@ Requires-Dist: markdown-it-py==4.0.0; extra == "frozen"
 Requires-Dist: marshmallow==3.26.1; extra == "frozen"
 Requires-Dist: marshmallow-oneofschema==3.2.0; extra == "frozen"
 Requires-Dist: marshmallow-sqlalchemy==0.28.2; extra == "frozen"
-Requires-Dist: matplotlib==3.10.7; extra == "frozen"
+Requires-Dist: matplotlib==3.10.8; extra == "frozen"
 Requires-Dist: mdit-py-plugins==0.5.0; extra == "frozen"
 Requires-Dist: mdurl==0.1.2; extra == "frozen"
 Requires-Dist: methodtools==0.4.7; extra == "frozen"
@@ -210,30 +210,30 @@ Requires-Dist: nbformat==5.10.4; extra == "frozen"
 Requires-Dist: networkx==3.6.1; extra == "frozen"
 Requires-Dist: numpy==2.2.5; extra == "frozen"
 Requires-Dist: object-clerk==1.0.0; extra == "frozen"
-Requires-Dist: opentelemetry-api==1.39.0; extra == "frozen"
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-Requires-Dist: opentelemetry-exporter-otlp-proto-http==1.39.0; extra == "frozen"
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-Requires-Dist: opentelemetry-instrumentation-system-metrics==0.60b0; extra == "frozen"
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+Requires-Dist: opentelemetry-exporter-otlp==1.39.1; extra == "frozen"
+Requires-Dist: opentelemetry-exporter-otlp-proto-common==1.39.1; extra == "frozen"
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc==1.39.1; extra == "frozen"
+Requires-Dist: opentelemetry-exporter-otlp-proto-http==1.39.1; extra == "frozen"
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+Requires-Dist: opentelemetry-instrumentation-psycopg2==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-instrumentation-pymongo==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-instrumentation-redis==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-instrumentation-requests==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-instrumentation-sqlalchemy==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-instrumentation-system-metrics==0.60b1; extra == "frozen"
 Requires-Dist: opentelemetry-propagator-aws-xray==1.0.2; extra == "frozen"
-Requires-Dist: opentelemetry-proto==1.39.0; extra == "frozen"
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-Requires-Dist: opentelemetry-semantic-conventions==0.60b0; extra == "frozen"
-Requires-Dist: opentelemetry-util-http==0.60b0; extra == "frozen"
+Requires-Dist: opentelemetry-proto==1.39.1; extra == "frozen"
+Requires-Dist: opentelemetry-sdk==1.39.1; extra == "frozen"
+Requires-Dist: opentelemetry-semantic-conventions==0.60b1; extra == "frozen"
+Requires-Dist: opentelemetry-util-http==0.60b1; extra == "frozen"
 Requires-Dist: ordered-set==4.1.0; extra == "frozen"
 Requires-Dist: packaging==25.0; extra == "frozen"
 Requires-Dist: pandas==2.3.3; extra == "frozen"
@@ -293,7 +293,7 @@ Requires-Dist: termcolor==3.2.0; extra == "frozen"
 Requires-Dist: text-unidecode==1.3; extra == "frozen"
 Requires-Dist: threadpoolctl==3.6.0; extra == "frozen"
 Requires-Dist: tifffile==2025.10.16; extra == "frozen"
-Requires-Dist: tornado==6.5.2; extra == "frozen"
+Requires-Dist: tornado==6.5.3; extra == "frozen"
 Requires-Dist: tqdm==4.67.1; extra == "frozen"
 Requires-Dist: traitlets==5.14.3; extra == "frozen"
 Requires-Dist: typing-inspection==0.4.2; extra == "frozen"
@@ -303,7 +303,7 @@ Requires-Dist: tzlocal==5.3.1; extra == "frozen"
 Requires-Dist: uc-micro-py==1.0.3; extra == "frozen"
 Requires-Dist: uncertainties==3.2.3; extra == "frozen"
 Requires-Dist: universal_pathlib==0.3.7; extra == "frozen"
-Requires-Dist: urllib3==2.6.1; extra == "frozen"
+Requires-Dist: urllib3==2.6.2; extra == "frozen"
 Requires-Dist: vine==5.1.0; extra == "frozen"
 Requires-Dist: voluptuous==0.15.2; extra == "frozen"
 Requires-Dist: wcwidth==0.2.14; extra == "frozen"

dkist_processing_visp-5.2.0rc1/changelog/234.bugfix.rst

@@ -0,0 +1,2 @@
+The modification of CRPIX1 and CRPIX2 to account for beam-overlap trimming is now correct for some early (OCP1) ViSP
+data that had their WCS axes switched in the headers.

dkist_processing_visp-5.2.0rc1/changelog/234.doc.rst

@@ -0,0 +1 @@
+Add online documentation page for new WavelengthCalibration task.

dkist_processing_visp-5.2.0rc1/changelog/234.feature.rst

@@ -0,0 +1 @@
+Add the WavelengthCalibration task, which computes an absolute wavelength solution that is encoded in L1 headers.

dkist_processing_visp-5.2.0rc1/changelog/234.science.rst

@@ -0,0 +1,2 @@
+L1 data now have a correct wavelength solution encoded in their headers. See :doc:`here </wavelength_calibration>`
+  for more information.

dkist_processing_visp-5.2.0rc1/changelog/253.misc.rst

@@ -0,0 +1 @@
+Update logging lines to print `np.int*` types as plain ints instead of the `__repr__`, which shows the full type.

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/dkist_processing_visp/models/parameters.py

@@ -5,6 +5,7 @@ from random import randint
 from typing import Any
 
 import astropy.units as u
+from astropy.units import Quantity
 from dkist_processing_common.models.parameters import ParameterArmIdMixin
 from dkist_processing_common.models.parameters import ParameterBase
 from dkist_processing_common.models.parameters import ParameterWavelengthMixin
@@ -200,7 +201,7 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
     @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.
+        Define the ± fraction 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)`.
         """
@@ -230,6 +231,33 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
         """Return fractional number of samples required for the RANSAC regressor used to fit the 2D vignette signal."""
         return self._find_most_recent_past_value("visp_solar_vignette_min_samples")
 
+    @property
+    def wavecal_crval_bounds_px(self) -> Quantity:
+        """
+        Define the bounds (in *pix*) on crval when performing wavecal fitting.
+
+        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_wavecal_crval_bounds_px") * u.pix
+
+    @property
+    def wavecal_dispersion_bounds_fraction(self) -> Quantity:
+        """
+        Define the ± fraction from the initial value for bounds on dispersion when performing wavecal fitting.
+
+        This value should be between 0 and 1. For example, the minimum bound is `init_value * (1 - wavecal_dispersion_bounds_fraction)`.
+        """
+        return self._find_most_recent_past_value("visp_wavecal_dispersion_bounds_fraction")
+
+    @property
+    def wavecal_incident_light_angle_bounds_deg(self) -> Quantity:
+        """Define the bounds (in *deg*) on incident_light_angle when performing wavecal fitting."""
+        return (
+            self._find_most_recent_past_value("visp_wavecal_incident_light_angle_bounds_deg")
+            * u.deg
+        )
+
     @property
     def wavecal_camera_lens_parameters(self) -> list[u.Quantity]:
         r"""
@@ -279,6 +307,20 @@ class VispParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmIdMixi
         """Define the initial guess for opacity factor in wavecal fits."""
         return self._find_most_recent_past_value("visp_wavecal_init_opacity_factor")
 
+    @property
+    def wavecal_fit_kwargs(self) -> dict[str, Any]:
+        """Define extra keyword arguments to pass to the wavelength calibration fitter."""
+        doc_dict = self._find_most_recent_past_value("visp_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 polcal_spatial_median_filter_width_px(self) -> int:
         """Return the size of the median filter to apply in the spatial dimension to polcal data."""

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/dkist_processing_visp/models/tags.py

@@ -2,6 +2,7 @@
 
 from enum import Enum
 
+from dkist_processing_common.models.tags import StemName
 from dkist_processing_common.models.tags import Tag
 
 from dkist_processing_visp.models.task_name import VispTaskName
@@ -63,6 +64,16 @@ class VispTag(Tag):
         """
         return cls.format_tag(VispStemName.map_scan, map_scan_num)
 
+    @classmethod
+    def task_characteristic_spectra(cls) -> str:
+        """Tags intermediate characteristic spectra."""
+        return cls.format_tag(StemName.task, VispTaskName.solar_char_spec.value)
+
+    @classmethod
+    def task_wavelength_calibration(cls) -> str:
+        """Tags wavelength calibration."""
+        return cls.format_tag(StemName.task, VispTaskName.wavelength_calibration.value)
+
     ##################
     # Composite tags #
     ##################

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/dkist_processing_visp/models/task_name.py

@@ -7,3 +7,5 @@ class VispTaskName(str, Enum):
     """Controlled list of task tag names."""
 
     background = "BACKGROUND"
+    solar_char_spec = "SOLAR_CHAR_SPEC"
+    wavelength_calibration = "WAVELENGTH_CALIBRATION"

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/dkist_processing_visp/tasks/geometric.py

@@ -1086,7 +1086,7 @@ class GeometricCalibration(
             "rel_height": self.parameters.geo_zone_rel_height,
         }
         zones = self.compute_line_zones(array, **zone_kwargs)
-        logger.info(f"Found {zones = }")
+        logger.info(f"Found zones = {[tuple(int(i) for i in z) for z in zones]}")
         mask = np.zeros(array.shape).astype(bool)
         for z in zones:
             mask[z[0] : z[1], :] = True

{dkist_processing_visp-5.1.2rc2 → dkist_processing_visp-5.2.0rc1}/dkist_processing_visp/tasks/science.py

@@ -12,6 +12,7 @@ from astropy.time import TimeDelta
 from dkist_processing_common.codecs.fits import fits_access_decoder
 from dkist_processing_common.codecs.fits import fits_array_decoder
 from dkist_processing_common.codecs.fits import fits_hdulist_encoder
+from dkist_processing_common.codecs.json import json_decoder
 from dkist_processing_common.models.fits_access import MetadataKey
 from dkist_processing_common.models.task_name import TaskName
 from dkist_processing_common.tasks.mixin.quality import QualityMixin
@@ -42,6 +43,7 @@ class CalibrationCollection:
     angle: dict
     state_offset: dict
     spec_shift: dict
+    wavelength_calibration_header: dict
     demod_matrices: dict | None
 
     @cached_property
@@ -176,6 +178,15 @@ class ScienceCalibration(
         spec_shift_dict = dict()
         demod_dict = dict() if self.constants.correct_for_polarization else None
 
+        # WaveCal
+        #########
+        wavecal_header = next(
+            self.read(
+                tags=[VispTag.intermediate(), VispTag.task_wavelength_calibration()],
+                decoder=json_decoder,
+            )
+        )
+
         for beam in range(1, self.constants.num_beams + 1):
             for readout_exp_time in self.constants.observe_readout_exp_times:
                 # Dark
@@ -270,6 +281,7 @@ class ScienceCalibration(
             angle=angle_dict,
             state_offset=state_offset_dict,
             spec_shift=spec_shift_dict,
+            wavelength_calibration_header=wavecal_header,
             demod_matrices=demod_dict,
         )
 
@@ -761,22 +773,31 @@ class ScienceCalibration(
         """
         Update calibrated headers with any information gleaned during science calibration.
 
-        Right now all this does is put map scan values in the header.
+        #. Apply the wavelength calibration header values
+        #. Add map scan keywords
+        #. Adjust CRPIX values based on any chopping needed to return only regions where the beams overlap
 
         Parameters
         ----------
-        header : fits.Header
+        header
             The header to update
 
-        map_scan : int
+        map_scan
             Current map scan
 
+        calibrations
+            Container of intermediate calibration objects. Used to figure out how much to adjust CRPIX values.
+
         Returns
         -------
         fits.Header
             Updated header
 
         """
+        # Apply the wavelength calibration
+        # This needs to be done prior to adjusting CRPIX values below
+        header.update(calibrations.wavelength_calibration_header)
+
         # Update the map scan number
         header["VSPNMAPS"] = self.constants.num_map_scans
         header["VSPMAP"] = map_scan
@@ -784,27 +805,51 @@ class ScienceCalibration(
         # Adjust the CRPIX values if the beam overlap slicing chopped from the start of the array
         x_slice, y_slice = calibrations.beams_overlap_slice
 
+        # Note: We KNOW that `x_slice` and `y_slice` correspond to the *array* dimensions corresponding to spectral and
+        # spatial directions, respectively. Some early ViSP data swap the *WCS* dimensions so that CRPIX1 contains
+        # information about the spectral axis, even though the spectral axis is always in the 0th array axis (and thus
+        # the second WCS axis because FITS and numpy are backwards; are we confused yet?).
+        #
+        # We want the adjustment of the CRPIX values to produce accurate WCS information, even if they're associated
+        # with the wrong array axes. For this reason we dynamically associate the WCS axis number with `x_slice` and
+        # `y_slice` via the `*_wcs_axis_num` properties.
+        #
+        # To say it differently, we KNOW that `x_slice` always refers to chopping in the spectral dimension, so we need
+        # to update the CRPIX associate with the spectral WCS, no matter which WCS axis that is.
+
         # This if catches 0's and Nones
         if x_slice.start:
             # .start will only be non-None or 0 if the slice is from the start. In this case we need to update the WCS
             logger.info(
-                f"Adjusting CRPIX2 from {header['CRPIX2']} to {header['CRPIX2'] - x_slice.start}"
+                f"Adjusting spectral CRPIX{self.spectral_wcs_axis_num} from "
+                f"{header[f'CRPIX{self.spectral_wcs_axis_num}']} to {header[f'CRPIX{self.spectral_wcs_axis_num}'] - x_slice.start}"
+            )
+            header[f"CRPIX{self.spectral_wcs_axis_num}"] = (
+                header[f"CRPIX{self.spectral_wcs_axis_num}"] - x_slice.start
             )
-            header["CRPIX2"] = header["CRPIX2"] - x_slice.start
             logger.info(
-                f"Adjusting CRPIX2A from {header['CRPIX2A']} to {header['CRPIX2A'] - x_slice.start}"
+                f"Adjusting spectral CRPIX{self.spectral_wcs_axis_num}A from "
+                f"{header[f'CRPIX{self.spectral_wcs_axis_num}A']} to {header[f'CRPIX{self.spectral_wcs_axis_num}A'] - x_slice.start}"
+            )
+            header[f"CRPIX{self.spectral_wcs_axis_num}A"] = (
+                header[f"CRPIX{self.spectral_wcs_axis_num}A"] - x_slice.start
             )
-            header["CRPIX2A"] = header["CRPIX2A"] - x_slice.start
 
         if y_slice.start:
             logger.info(
-                f"Adjusting CRPIX1 from {header['CRPIX1']} to {header['CRPIX1'] - y_slice.start}"
+                f"Adjusting spatial CRPIX{self.spatial_wcs_axis_num} from "
+                f"{header[f'CRPIX{self.spatial_wcs_axis_num}']} to {header[f'CRPIX{self.spatial_wcs_axis_num}'] - y_slice.start}"
+            )
+            header[f"CRPIX{self.spatial_wcs_axis_num}"] = (
+                header[f"CRPIX{self.spatial_wcs_axis_num}"] - y_slice.start
             )
-            header["CRPIX1"] = header["CRPIX1"] - y_slice.start
             logger.info(
-                f"Adjusting CRPIX1A from {header['CRPIX1A']} to {header['CRPIX1A'] - y_slice.start}"
+                f"Adjusting spatial CRPIX{self.spatial_wcs_axis_num}A from "
+                f"{header[f'CRPIX{self.spatial_wcs_axis_num}A']} to {header[f'CRPIX{self.spatial_wcs_axis_num}A'] - y_slice.start}"
+            )
+            header[f"CRPIX{self.spatial_wcs_axis_num}A"] = (
+                header[f"CRPIX{self.spatial_wcs_axis_num}A"] - y_slice.start
             )
-            header["CRPIX1A"] = header["CRPIX1A"] - y_slice.start
 
         return header
 
@@ -900,3 +945,35 @@ class ScienceCalibration(
 
         filename = next(self.read(tags=tags))
         logger.info(f"Wrote intermediate file for {tags = } to {filename}")
+
+    @cached_property
+    def spectral_wcs_axis_num(self) -> int:
+        """
+        Return the WCS axis number corresponding to wavelength.
+
+        We need to check this dynamically because some early ViSP data got the WCS backward w.r.t. the array dimensions.
+        """
+        try:
+            spectral_axis_num = next(
+                (i for i in range(1, 4) if getattr(self.constants, f"axis_{i}_type") == "AWAV")
+            )
+        except StopIteration as e:
+            raise ValueError("Could not find WCS axis with type AWAV") from e
+
+        return spectral_axis_num
+
+    @cached_property
+    def spatial_wcs_axis_num(self) -> int:
+        """
+        Return the WCS axis number corresponding to Helioprojective latitude.
+
+        We need to check this dynamically because some early ViSP data got the WCS backward w.r.t. the array dimensions.
+        """
+        try:
+            spatial_axis_num = next(
+                (i for i in range(1, 4) if getattr(self.constants, f"axis_{i}_type") == "HPLT-TAN")
+            )
+        except StopIteration as e:
+            raise ValueError("Cound not find WCS axis with type HPLT-TAN") from e
+
+        return spatial_axis_num