dkist-processing-cryonirsp 1.19.18__tar.gz → 2.0.0__tar.gz

dkist_processing_cryonirsp-2.0.0/.snyk

@@ -0,0 +1,13 @@
+# Snyk (https://snyk.io) policy file, patches or ignores known vulnerabilities
+# https://docs.snyk.io/manage-risk/policies/the-.snyk-file#syntax-of-the-.snyk-file
+version: v1.25.0
+ignore:
+  SNYK-PYTHON-APACHEAIRFLOWCORE-17879182:
+    - "*" :
+        reason: 'Patched in Airflow 3.3.0, but we are not ready to upgrade till 3.3.1 or later'
+        expires: '2027-07-07T00:00:00.000Z'
+  SNYK-PYTHON-APACHEAIRFLOWCORE-17933331:
+    - '*':
+        reason: 'Ignored by bulk CI/CD Snyk policy update'
+        expires: '2099-12-31T23:59:59.999Z'
+        created: '2026-07-10T15:53:27.931Z'

{dkist_processing_cryonirsp-1.19.18 → dkist_processing_cryonirsp-2.0.0}/CHANGELOG.rst

@@ -1,3 +1,40 @@
+v2.0.0 (2026-07-17)
+===================
+
+Features
+--------
+
+- Compute spectral shift calculations on smoothed/filtered spectral derivatives of the reference and target spectra. This
+  amplifies the spectral signal and greatly improves the accuracy of the individual shift measurements. (`#292 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/292>`__)
+- The calculation of a single spectral shift is now *only* via interpolation of the correlation signal between the reference
+  and target spectra. Previously a second refinement of this value was done via a chi-squared minimization, but this was shown
+  to increase noise with no increase in accuracy. (`#292 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/292>`__)
+
+
+Bugfixes
+--------
+
+- Filter out non-finite values and use `resize_arrays_local_mean` to average arrays in the instrument polarization
+  task instead of `resize_arrays`. With an output shape of `(1,1)`, `resize_arrays` returns the center pixel. (`#290 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/290>`__)
+
+
+Misc
+----
+
+- Add option to all local trial workflows (``--parameter-doc``) that uses an existing input dataset parameter-part document
+  to populate the parameters during a local run. This is an easy way for a user to run a pipeline locally using the exact
+  parameters used in production. (`#292 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/292>`__)
+
+
+v1.19.19 (2026-06-22)
+=====================
+
+Bugfixes
+--------
+
+- Harden writing statistics headers in the case where the data is very similar causing the kurtosis or skew calculations to return NaN. (`#294 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/294>`__)
+
+
 v1.19.18 (2026-06-18)
 =====================
 

{dkist_processing_cryonirsp-1.19.18 → dkist_processing_cryonirsp-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-cryonirsp
-Version: 1.19.18
+Version: 2.0.0
 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: svcs==26.1.0; extra == "frozen"
 Requires-Dist: tabulate==0.10.0; extra == "frozen"
 Requires-Dist: talus==1.3.4; extra == "frozen"
 Requires-Dist: tenacity==8.5.0; extra == "frozen"
 Requires-Dist: termcolor==3.3.0; extra == "frozen"
 Requires-Dist: terminado==0.18.1; extra == "frozen"
 Requires-Dist: text-unidecode==1.3; extra == "frozen"
-Requires-Dist: tifffile==2026.6.1; extra == "frozen"
+Requires-Dist: threadpoolctl==3.6.0; extra == "frozen"
+Requires-Dist: tifffile==2026.7.14; extra == "frozen"
 Requires-Dist: tinycss2==1.5.1; extra == "frozen"
 Requires-Dist: tornado==6.5.7; extra == "frozen"
-Requires-Dist: tqdm==4.68.3; extra == "frozen"
+Requires-Dist: tqdm==4.68.4; extra == "frozen"
 Requires-Dist: traitlets==5.15.1; extra == "frozen"
-Requires-Dist: typer==0.26.7; extra == "frozen"
+Requires-Dist: typer==0.27.0; extra == "frozen"
 Requires-Dist: typing-inspection==0.4.2; extra == "frozen"
-Requires-Dist: typing_extensions==4.15.0; extra == "frozen"
-Requires-Dist: tzdata==2026.2; extra == "frozen"
-Requires-Dist: tzlocal==5.4.3; extra == "frozen"
+Requires-Dist: typing_extensions==4.16.0; extra == "frozen"
+Requires-Dist: tzdata==2026.3; extra == "frozen"
+Requires-Dist: tzlocal==5.4.4; extra == "frozen"
 Requires-Dist: uc-micro-py==2.0.0; extra == "frozen"
 Requires-Dist: uncertainties==3.2.3; extra == "frozen"
 Requires-Dist: universal_pathlib==0.3.10; extra == "frozen"
 Requires-Dist: uri-template==1.3.0; extra == "frozen"
 Requires-Dist: urllib3==2.7.0; extra == "frozen"
 Requires-Dist: uuid6==2025.0.1; extra == "frozen"
-Requires-Dist: uvicorn==0.49.0; extra == "frozen"
+Requires-Dist: uvicorn==0.51.0; extra == "frozen"
 Requires-Dist: uvloop==0.22.1; extra == "frozen"
 Requires-Dist: vine==5.1.0; extra == "frozen"
 Requires-Dist: voluptuous==0.16.0; extra == "frozen"
 Requires-Dist: watchfiles==1.2.0; extra == "frozen"
-Requires-Dist: wcwidth==0.8.1; extra == "frozen"
+Requires-Dist: wcwidth==0.8.2; extra == "frozen"
 Requires-Dist: webcolors==25.10.0; extra == "frozen"
 Requires-Dist: webencodings==0.5.1; extra == "frozen"
 Requires-Dist: websocket-client==1.9.0; extra == "frozen"
-Requires-Dist: websockets==16.0; extra == "frozen"
+Requires-Dist: websockets==16.1; extra == "frozen"
 Requires-Dist: wirerope==1.0.0; extra == "frozen"
-Requires-Dist: wrapt==2.2.1; extra == "frozen"
+Requires-Dist: wrapt==2.2.2; extra == "frozen"
 Requires-Dist: yamale==6.1.0; extra == "frozen"
 Requires-Dist: yarl==1.24.2; extra == "frozen"
 Requires-Dist: zipp==4.1.0; extra == "frozen"

dkist_processing_cryonirsp-2.0.0/SCIENCE_CHANGELOG.rst

@@ -0,0 +1,39 @@
+v2.0.0 (2026-07-17)
+===================
+
+
+
+
+- Improvements to the calculation of the spectral curvature to make them more robust against noisy input data. This change
+  only affects science data for datasets where the spectral curvature was previously mis-identified. For these datasets this
+  change will correct un-aligned spectral axes in L1 data and improve the quality of gain correction because the solar gain
+  frames will have better removal of solar absorption lines. (`#292 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/292>`__)
+- Demodulation matrices are now derived from a correctly computed average over the full array. Previously, a bug had resulted
+  in the "average" actually just being the value of the central pixel. This change does result in small changes to the derived
+  demodulation matrices, but has been shown to not change L1 data in a substantial way. (`#290 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/290>`__)
+
+v1.8.0 (2025-06-16)
+===================
+
+Misc
+----
+
+- Update the beam alignment code to handle edge effects in determining the shift required to align beams one and two. The final spectra passed to the cross correlation method are now cropped by removing the outside 10% of pixels on each edge. (`#195 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/195>`__)
+
+
+v1.0.0 (2024-08-21)
+===================
+
+Misc
+----
+
+- CRYO-NIRSP processing pipeline data accepted for release to the community.
+
+
+v0.0.1 (2023-08-25)
+===================
+
+Misc
+----
+
+- Initial release of pipeline for science review

{dkist_processing_cryonirsp-1.19.18 → dkist_processing_cryonirsp-2.0.0}/dkist_processing_cryonirsp/models/parameters.py

@@ -37,11 +37,36 @@ class CryonirspParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmI
         """Pixel precision (1/upsample_factor) to use during phase matching of beam/modulator images."""
         return self._find_most_recent_past_value("cryonirsp_geo_upsample_factor")
 
+    @property
+    def geo_savgol_window_length_px(self) -> int:
+        """Size of the window for the SavGol filter used to smooth the spectral derivative during prep for spectral shift measurements."""
+        return self._find_most_recent_past_value("cryonirsp_geo_savgol_window_length_px")
+
+    @property
+    def geo_savgol_polyorder(self) -> int:
+        """Order of the polynomial fit in the SavGol filter used to smooth the spectral derivative during prep for the spectral shift measurements."""
+        return self._find_most_recent_past_value("cryonirsp_geo_savgol_polyorder")
+
+    @property
+    def geo_derivative_cutoff_threshold(self) -> float:
+        """Threshold value for the spectral derivative above which pixels will be set to NaN."""
+        return self._find_most_recent_past_value("cryonirsp_geo_derivative_cutoff_threshold")
+
     @property
     def geo_max_shift(self) -> int:
         """Max allowed pixel shift when computing spectral curvature."""
         return self._find_most_recent_past_value("cryonirsp_geo_max_shift")
 
+    @property
+    def geo_shift_peak_interpolation_width_px(self) -> int:
+        """Return the ± pixel width used to interpolate the correlation peaks when computing spectral curvature."""
+        return self._find_most_recent_past_value("cryonirsp_geo_shift_peak_interpolation_width_px")
+
+    @property
+    def geo_poly_fit_min_samples(self) -> float:
+        """Return fractional number of samples required for the RANSAC regressor used to fit spectral shifts along the slit."""
+        return self._find_most_recent_past_value("cryonirsp_geo_poly_fit_min_samples")
+
     @property
     def geo_poly_fit_order(self) -> int:
         """Order of polynomial used to fit spectral shift as a function of slit position."""

{dkist_processing_cryonirsp-1.19.18 → dkist_processing_cryonirsp-2.0.0}/dkist_processing_cryonirsp/tasks/instrument_polarization.py

@@ -12,6 +12,7 @@ from dkist_processing_math.arithmetic import divide_arrays_by_array
 from dkist_processing_math.arithmetic import subtract_array_from_arrays
 from dkist_processing_math.statistics import average_numpy_arrays
 from dkist_processing_math.transform.binning import resize_arrays
+from dkist_processing_math.transform.binning import resize_arrays_local_mean
 from dkist_processing_pac.fitter.polcal_fitter import PolcalFitter
 from dkist_processing_pac.input_data.drawer import Drawer
 from dkist_processing_pac.input_data.dresser import Dresser
@@ -281,8 +282,20 @@ class InstrumentPolarizationCalibrationBase(CryonirspTaskBase, ABC):
                 self.parameters.polcal_num_spatial_bins,
                 self.parameters.polcal_num_spectral_bins,
             )
-            local_binned_array = next(resize_arrays(gain_corrected_array, output_shape))
-            global_binned_array = next(resize_arrays(gain_corrected_array, (1, 1)))
+            finite_gain_corrected_array_mean = np.mean(
+                gain_corrected_array[np.isfinite(gain_corrected_array)]
+            )
+            finite_gain_corrected_array = np.where(
+                np.isfinite(gain_corrected_array),
+                gain_corrected_array,
+                finite_gain_corrected_array_mean,
+            )
+            local_binned_array = next(
+                resize_arrays_local_mean(finite_gain_corrected_array, output_shape)
+            )
+            global_binned_array = next(
+                resize_arrays_local_mean(finite_gain_corrected_array, (1, 1))
+            )
 
         with self.telemetry_span(f"Create reduced CryonirspL0FitsAccess for {apm_str}"):
             local_result = CryonirspL0FitsAccess(