dkist-processing-cryonirsp 3.0.0rc4__tar.gz → 3.1.0__tar.gz

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/.pre-commit-config.yaml

@@ -27,7 +27,13 @@ repos:
         args:
             - --convention=numpy
             - --add-ignore=D105
--   repo: https://bitbucket.org/dkistdc/pre-commit-hooks
-    rev: v1.0.2
+-   repo: https://bitbucket.org/dkistdc/pre-commit-hooks.git
+    rev: v1.1.0
     hooks:
     -   id: calibration-workflow-name
+    -   id: dkist-env-table
+        language_version: python3.13
+        require_serial: true
+        additional_dependencies:
+        - dkist-processing-common
+        - dkist-service-configuration

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/CHANGELOG.rst

@@ -1,3 +1,66 @@
+v3.1.0 (2026-10-09)
+===================
+
+Bugfixes
+--------
+
+- Lamp gain and CI solar gain calibrations now produce a single, correctly combined gain frame per beam even when the input spans more than one exposure condition, instead of one frame per exposure condition. (`#304 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/304>`__)
+
+
+v3.0.0 (2026-10-08)
+===================
+
+Features
+--------
+
+- Replace `BeamBoundariesCalibration` task with `SpatialBeamBoundaries`, which only computes the boundaries of the illuminated region along the spatial axis.
+  The spectral axis (or second spatial axis, for CI) boundaries are hard-coded as a pipeline parameter. (`#306 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/306>`__)
+- Save the full set of beam boundaries used to extract illuminated regions from the raw data as a dataset extra (called "BEAM_BOUNDARIES"). (`#306 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/306>`__)
+
+
+Misc
+----
+
+- Replace "y" and "x" language with "axis_0" and "axis_1", respectively, in the `BeamBoundaries` model. (`#306 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/306>`__)
+
+
+Documentation
+-------------
+
+- Update online documentation "Dataset Extras" page to include information about the beam boundaries extra. (`#306 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/306>`__)
+
+
+v2.1.5 (2026-10-08)
+===================
+
+Misc
+----
+
+- Integrated the ``dkist-env-table`` pre-commit hook and updated the README environment-variable table to match the current configuration. (`#303 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/303>`__)
+- Bump `dkist-fits-specifications` to v4.30.0, which adds support for the BEAM BOUNDARIES dataset extra. (`#308 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/308>`__)
+- Bump `dkist-processing-common` to v14.6.0. No major changes. (`#308 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/308>`__)
+
+
+v2.1.4 (2026-10-06)
+===================
+
+Misc
+----
+
+- Use the immutable Bitbucket reference atlas URLs in test configuration. (`#305 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/305>`__)
+- Bump `solar-wavelength-calibration` to v2.0.4, which uses git LFS for test atlas storage. (`#305 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/305>`__)
+
+
+v2.1.3 (2026-09-30)
+===================
+
+Misc
+----
+
+- Update dkist-processing-common to 14.5.2 to restore provenance recording for
+  manual parse tasks and trial dataset inventory, ASDF, and quality report tasks. (`#307 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/307>`__)
+
+
 v2.1.2 (2026-09-24)
 ===================
 

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-cryonirsp
-Version: 3.0.0rc4
+Version: 3.1.0
 Summary: Science processing code for the Cryo-NIRSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
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 Requires-Dist: universal_pathlib==0.3.10; extra == "frozen"
@@ -346,20 +346,20 @@ Requires-Dist: uri-template==1.3.0; extra == "frozen"
 Requires-Dist: urllib3==2.8.0; extra == "frozen"
 Requires-Dist: uuid6==2025.0.1; extra == "frozen"
 Requires-Dist: uvicorn==0.54.0; extra == "frozen"
-Requires-Dist: uvloop==0.22.1; extra == "frozen"
+Requires-Dist: uvloop==0.23.0; extra == "frozen"
 Requires-Dist: vine==5.1.0; extra == "frozen"
 Requires-Dist: voluptuous==0.16.0; extra == "frozen"
 Requires-Dist: watchfiles==1.3.0; extra == "frozen"
-Requires-Dist: wcwidth==0.9.1; extra == "frozen"
+Requires-Dist: wcwidth==0.9.2; extra == "frozen"
 Requires-Dist: webcolors==25.10.0; extra == "frozen"
 Requires-Dist: webencodings==0.6.1; extra == "frozen"
 Requires-Dist: websocket-client==1.9.2; extra == "frozen"
-Requires-Dist: websockets==17.1; extra == "frozen"
+Requires-Dist: websockets==17.2; extra == "frozen"
 Requires-Dist: wirerope==1.0.0; extra == "frozen"
 Requires-Dist: wrapt==2.5.0; extra == "frozen"
 Requires-Dist: yamale==6.1.0; extra == "frozen"
 Requires-Dist: yarl==1.25.1; extra == "frozen"
-Requires-Dist: zipp==4.1.0; extra == "frozen"
+Requires-Dist: zipp==4.1.1; extra == "frozen"
 
 dkist-processing-cryonirsp
 ==========================
@@ -378,6 +378,8 @@ in their own package facilitates using the build_utils to test the integrity of
 Environment Variables
 ---------------------
 
+.. dkist-env-table: start
+
 .. list-table::
    :widths: 10 90
    :header-rows: 1
@@ -469,6 +471,21 @@ Environment Variables
    * - FTS_ATLAS_DATA_DIR
      - annotation=Union[str, NoneType] required=False default=None description='Common cached directory for a downloaded FTS Atlas.'
 
+.. dkist-env-table: end
+
+Maintaining the generated table
+###############################
+
+The hook's additional dependencies are intentionally unpinned to avoid duplicating
+versions maintained in ``pyproject.toml``. Consequently, the generated table may
+temporarily reflect a newer published parent configuration than the version pinned
+by this project.
+
+When developing against an upstream release candidate that changes configuration
+fields, temporarily pin the relevant hook dependency in
+``.pre-commit-config.yaml`` to that RC. Remove the temporary pin after the final
+upstream release is available.
+
 Development
 -----------
 .. code-block:: bash

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/README.rst

@@ -15,6 +15,8 @@ in their own package facilitates using the build_utils to test the integrity of
 Environment Variables
 ---------------------
 
+.. dkist-env-table: start
+
 .. list-table::
    :widths: 10 90
    :header-rows: 1
@@ -106,6 +108,21 @@ Environment Variables
    * - FTS_ATLAS_DATA_DIR
      - annotation=Union[str, NoneType] required=False default=None description='Common cached directory for a downloaded FTS Atlas.'
 
+.. dkist-env-table: end
+
+Maintaining the generated table
+###############################
+
+The hook's additional dependencies are intentionally unpinned to avoid duplicating
+versions maintained in ``pyproject.toml``. Consequently, the generated table may
+temporarily reflect a newer published parent configuration than the version pinned
+by this project.
+
+When developing against an upstream release candidate that changes configuration
+fields, temporarily pin the relevant hook dependency in
+``.pre-commit-config.yaml`` to that RC. Remove the temporary pin after the final
+upstream release is available.
+
 Development
 -----------
 .. code-block:: bash

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/SCIENCE_CHANGELOG.rst

@@ -1,3 +1,13 @@
+v3.0.0 (2026-10-08)
+===================
+
+
+
+
+- The task that computes the boundaries of the useful, illuminated regions of the INPUT data has been simplified and made more robust to data with very high
+  dynamic range. This improvement will most affect data taken at 1430nm, but will slightly change the final array shape for all data. (`#306 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/306>`__)
+
+
 v2.0.0 (2026-07-17)
 ===================
 

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/dkist_processing_cryonirsp/models/parameters.py

@@ -140,7 +140,7 @@ class CryonirspParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmI
 
     @property
     def beam_boundaries_detector_margin_px(self) -> int:
-        """Return the distance away from a detector edge to hard-code boundaries that otherwise would run up to the edge."""
+        """Return the padding amount from the detector edge that sets a hard limit on the illumination regions."""
         return self._find_most_recent_past_value("cryonirsp_beam_boundaries_detector_margin_px")
 
     @property

{dkist_processing_cryonirsp-3.0.0rc4 → dkist_processing_cryonirsp-3.1.0}/dkist_processing_cryonirsp/tasks/beam_boundaries_base.py

@@ -6,6 +6,7 @@ import numpy as np
 from dkist_processing_common.codecs.fits import fits_array_encoder
 from dkist_processing_math.statistics import average_numpy_arrays
 from dkist_service_configuration.logging import logger
+from scipy import stats
 
 from dkist_processing_cryonirsp.codecs.fits import cryo_fits_array_decoder
 from dkist_processing_cryonirsp.models.beam_boundaries import BeamBoundaries
@@ -20,7 +21,10 @@ __all__ = ["SpatialBeamBoundariesBase"]
 
 class SpatialBeamBoundariesBase(CryonirspTaskBase):
     """
-    Task class for calculating the beam boundaries for later use during calibration.
+    Task class for calculating the illuminated beam boundaries in the spatial dimension for later use during calibration.
+
+    For CI data the term "spatial" here refers to the same chip dimension that corresponds to the spatial dimension in
+    SP data (numpy axis 0).
 
     Parameters
     ----------
@@ -49,7 +53,7 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
 
            i. Extract the beam's spectral extent
 
-           #. Collapse along the spectal dimension to form a 1D spatial signal
+           #. Collapse along the spectral dimension to form a 1D spatial signal
 
            #. Use a moving window comparison to construct a profile showing sharp changes in intensity
 
@@ -57,10 +61,10 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
 
         #. Adjust the regions so all beams have the same shape
 
-        #. Write the computed spatial bounds, and the spectral bounds from `parameters`, to scratch
+        #. Write the computed spatial bounds and the spectral bounds from `parameters` to scratch
 
-        NOTE: When this method referrs to the "spectral" dimension for CI data we really mean the spatial dimension that
-        corresponds to the chip axis that is the spectral dimensino in SP data.
+        NOTE: When this method refers to the "spectral" dimension for CI data we really mean the spatial dimension that
+        corresponds to the chip axis that is the spectral dimension in SP data (numpy axis 1).
 
         Returns
         -------
@@ -92,8 +96,9 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
                 beam_boundaries.append((min_edge, max_edge))
 
         with self.telemetry_span("Matching beam sizes"):
+            spatial_size = beam_array.shape[0]
             matched_spatial_boundaries = self.match_beam_sizes(
-                beam_boundaries, full_spatial_size=beam_array.shape[0]
+                beam_boundaries, full_spatial_size=spatial_size
             )
 
         with self.telemetry_span("Writing beam boundaries"):
@@ -131,12 +136,13 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
         )
         averaged_gain_data = average_numpy_arrays(lin_corr_gain_arrays)
         spatial_edge_mask = self.parameters.beam_boundaries_detector_margin_px
-        averaged_gain_data[:spatial_edge_mask, :] = averaged_gain_data[spatial_edge_mask + 1, :][
-            None, :
-        ]
-        averaged_gain_data[-spatial_edge_mask:, :] = averaged_gain_data[
-            -(spatial_edge_mask + 1), :
-        ][None, :]
+
+        # Fill in the masked edge regions with a spatial constant copied from the first pixel past the masked region
+        start_edge_good_signal = averaged_gain_data[spatial_edge_mask + 1, :]
+        end_edge_good_signal = averaged_gain_data[-(spatial_edge_mask + 1), :]
+
+        averaged_gain_data[:spatial_edge_mask, :] = start_edge_good_signal[None, :]
+        averaged_gain_data[-spatial_edge_mask:, :] = end_edge_good_signal[None, :]
         return averaged_gain_data
 
     @staticmethod
@@ -152,19 +158,9 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
         moving_mean = np.convolve(spatial_signal, np.ones(window), "valid") / window
 
         profile = np.full_like(spatial_signal, np.nan)
-        profile[window : -window + 1] = moving_mean[window:] - moving_mean[:-window]
+        profile[window : len(profile) - (window - 1)] = moving_mean[window:] - moving_mean[:-window]
         return profile
 
-    @staticmethod
-    def robust_sigma(array: np.ndarray) -> float:
-        """
-        Robust estimation of the standard deviation based on the median absolute difference.
-
-        Assuming the values in array are roughly normally distributed.
-        """
-        median = np.nanmedian(array)
-        return 1.4826 * np.nanmedian(np.abs(array - median))
-
     @staticmethod
     def find_edges(
         edge_profile: np.ndarray, threshold_sigma: float, detector_margin: int
@@ -173,7 +169,7 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
         Identify peaks in an edge profile.
 
         The location of the maximum change in the profile is taken to be the minimum edge of the illuminated beam while
-        the location of the most negative change in the profile is taken to be the maximum edge illumintated beam.
+        the location of the most negative change in the profile is taken to be the maximum edge illuminated beam.
 
         Both edges are checked to ensure they are significant enough by comparing their value to a threshold controlled
         by ``threshold_sigma``. Edges that are below the threshold are interpreted as being essentially at the edge of
@@ -183,7 +179,9 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
         -------
         `[min_edge_idx, max_edge_idx]`
         """
-        threshold = threshold_sigma * SpatialBeamBoundariesBase.robust_sigma(edge_profile)
+        threshold = threshold_sigma * stats.median_abs_deviation(
+            edge_profile, nan_policy="omit", scale="normal"
+        )
         num_pix = len(edge_profile)
 
         bottom_candidate = np.nanargmax(edge_profile)
@@ -191,11 +189,11 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
 
         if bottom_candidate > top_candidate:
             # If the edges appear flipped around
-            # This could potentially happen if there is some sharp signal right at the edge of the otherwise-unillumintaed
-            # detector that gets interpreted as a spurious edge. In this case we make the assumption that the true begining
+            # This could potentially happen if there is some sharp signal right at the edge of the otherwise-unilluminated
+            # detector that gets interpreted as a spurious edge. In this case we make the assumption that the true beginning
             # of illumination is in the first half of the detector and the true end of illumination is in the second half.
             logger.info(
-                "Edge profile increasing/decreasing peaks appear to be swapped. This is likely due to spurious edges. Restricting seach to half the chip for each."
+                "Edge profile increasing/decreasing peaks appear to be swapped. This is likely due to spurious edges. Restricting search to half the chip for each."
             )
             half_idx = edge_profile.size // 2
             bottom_candidate = np.nanargmax(edge_profile[:half_idx])
@@ -218,9 +216,10 @@ class SpatialBeamBoundariesBase(CryonirspTaskBase):
 
         output_list = []
         for spatial_boundaries, spectral_slice in zip(spatial_boundary_list, spectral_slices):
+            spatial_min, spatial_max = spatial_boundaries
             boundary_obj = BeamBoundaries(
-                axis_0_min=spatial_boundaries[0],
-                axis_0_max=spatial_boundaries[1],
+                axis_0_min=spatial_min,
+                axis_0_max=spatial_max,
                 axis_1_min=spectral_slice.start,
                 axis_1_max=spectral_slice.stop,
             )