dkist-processing-cryonirsp 2.0.0rc2__tar.gz → 2.0.1__tar.gz

dkist_processing_cryonirsp-2.0.1/.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-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/CHANGELOG.rst

@@ -1,3 +1,40 @@
+v2.0.1 (2026-07-22)
+===================
+
+Misc
+----
+
+- Update dkist-inventory to 1.11.9 which populates tile count for trial runs. (`#296 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/296>`__)
+
+
+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)
 =====================
 

{dkist_processing_cryonirsp-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-cryonirsp
-Version: 2.0.0rc2
+Version: 2.0.1
 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: structlog==26.1.0; extra == "frozen"
 Requires-Dist: sunpy==6.1.1; extra == "frozen"
-Requires-Dist: svcs==25.1.0; extra == "frozen"
+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"
@@ -326,36 +326,36 @@ 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: threadpoolctl==3.6.0; extra == "frozen"
-Requires-Dist: tifffile==2026.6.1; 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==4.69.0; 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==16.1.1; extra == "frozen"
 Requires-Dist: wirerope==1.0.0; 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: yarl==1.24.5; extra == "frozen"
 Requires-Dist: zipp==4.1.0; extra == "frozen"
 
 dkist-processing-cryonirsp

dkist_processing_cryonirsp-2.0.1/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-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/dkist_processing_cryonirsp/tasks/instrument_polarization.py

@@ -282,8 +282,20 @@ class InstrumentPolarizationCalibrationBase(CryonirspTaskBase, ABC):
                 self.parameters.polcal_num_spatial_bins,
                 self.parameters.polcal_num_spectral_bins,
             )
-            local_binned_array = next(resize_arrays_local_mean(gain_corrected_array, output_shape))
-            global_binned_array = next(resize_arrays_local_mean(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(

{dkist_processing_cryonirsp-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/dkist_processing_cryonirsp/tasks/sp_geometric.py

@@ -477,15 +477,18 @@ class SPGeometricCalibration(CryonirspTaskBase, ShiftMeasurementsMixin):
                 ref_spec=self.ref_spec, target_spec=target_spec, beam=beam, pos=i
             )
 
+            # Applying a negative `shift` is correct: `CorrectionsMixin.corrections_remove_spec_shifts` takes positive
+            # `shift` values, but ultimately shifts all rows by the negative shift. That behavior is recreated for a
+            # single spectral pixel on the following line.
             shifted_target = spnd.shift(target_spec, -shift, cval=np.nan)
             rms = np.nanstd(self.ref_spec - shifted_target)
 
             beam_shifts[i] = shift
             beam_rms[i] = rms
 
-        # Mask spatial positions with large residuals even after applying the measured shift
-        # Setting the threshold as 4 times the second quartile amount is a good way to estimate are large
-        # fraction of the CDF from a region that won't be polluted with outliers.
+        # Mask spatial positions with large residuals even after applying the measured shift.
+        # Setting the threshold as 4 times the second quartile amount is a good way to estimate what the 100% CDF level
+        # would be in the absence of outliers. This is then a good threshold to use to reject outliers.
         rms_median, rms_25_percentile = np.nanpercentile(beam_rms, [50, 25])
         rms_threshold = rms_median + 4 * (rms_median - rms_25_percentile)
         logger.info(f"Raw shift RMS threshold for beam {beam} is {rms_threshold}")
@@ -524,11 +527,11 @@ class SPGeometricCalibration(CryonirspTaskBase, ShiftMeasurementsMixin):
 
         The filtering steps are:
 
-        #. Normalize each spectral pixel by a fixed value of its CDF. This removes scaling differences between the reference and target spectra.
+        #. Normalize each spectral pixel by a fixed level of its CDF. This removes scaling differences between the reference and target spectra. The CDF level used is the `~dkist_processing_cryonirsp.models.parameters.CryonirspParameters.solar_characteristic_spatial_normalization_percentile`.
 
            a. At this stage we also clip values outside the range [0, 2]
 
-        #. Computed a smoothed spectral derivative for each spatial pixel. This step greatly increases the strength of the true spectral signal.
+        #. Compute a smoothed spectral derivative for each spatial pixel. This step greatly increases the strength of the true spectral signal.
 
         #. Apply a spectral windowing function to protect the correlation of the reference and target spectra from weird and wild edge-effects.
         """
@@ -635,7 +638,7 @@ class SPGeometricCalibration(CryonirspTaskBase, ShiftMeasurementsMixin):
             )
             peak_interp = peak_idx[0]
 
-        shift = 1 * (peak_interp - truncated_corr.size // 2)
+        shift = peak_interp - truncated_corr.size // 2
 
         return shift.item(0)
 

{dkist_processing_cryonirsp-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/dkist_processing_cryonirsp/tests/conftest.py

@@ -441,13 +441,42 @@ def cryonirsp_testing_parameters_factory(
         )
         cryonirsp_linearization_max_memory_gb: float = 4.0
         cryonirsp_linearization_optical_density_filter_attenuation_g278: WavelengthParameter = (
-            WavelengthParameter(values=(-1.64, -1.64, -1.64, -1.64))
+            WavelengthParameter(
+                # fmt: off
+                values=(-0.998, -0.892, -0.838, -0.843, -1.066, -1.200, -1.224, -1.362,
+                        -1.452, -1.640, -1.655, -1.657, -1.658, -1.706, -1.708, -1.715,
+                        -1.721, -1.790, -1.920, -2.020, -2.130, -2.330, -2.490, -2.640,
+                        -2.830),
+                wavelength=(530.0, 600.0, 630.0, 673.0, 750.0, 792.0, 800.0, 854.0,
+                            900.0, 1049.5, 1074.7, 1079.0, 1083.0, 1251.0, 1282.0, 1430.0,
+                            1695.0, 1950.0, 2218.0, 2400.0, 2600.0, 3028.0, 3445.0, 3936.0,
+                            4662.5)
+            )
+            # fmt: on
         )
         cryonirsp_linearization_optical_density_filter_attenuation_g358: WavelengthParameter = (
-            WavelengthParameter(values=(-3.75, -3.75, -3.75, -3.75))
+            WavelengthParameter(
+                # fmt: off
+                values=(-2.498, -2.730, -2.937, -3.027, -3.056, -3.015, -3.018, -3.020,
+                        -3.114, -3.204, -3.422, -3.580, -3.626, -3.633, -3.640, -3.749,
+                        -3.839, -3.862, -3.940, -3.983, -4.167),
+                wavelength=(530.0, 560.0, 600.0, 630.0, 673.0, 750.0, 792.0, 800.0,
+                            854.0, 890.0, 980.0, 1049.5, 1074.7, 1079.0, 1083.0, 1160.0,
+                            1251.0, 1282.0, 1430.0, 1565.0, 2200.0)
+            )
+            # fmt: on
         )
         cryonirsp_linearization_optical_density_filter_attenuation_g408: WavelengthParameter = (
-            WavelengthParameter(values=(-4.26, -4.26, -4.26, -4.26))
+            WavelengthParameter(
+                # fmt: off
+                values=(-2.968, -3.224, -3.447, -3.532, -3.571, -3.543, -3.561, -3.571,
+                        -3.658, -3.848, -4.066, -4.225, -4.279, -4.285, -4.290, -4.394,
+                        -4.462, -4.496, -4.554, -4.598, -4.810),
+                wavelength=(530.0, 560.0, 600.0, 630.0, 673.0, 750.0, 792.0, 800.0,
+                            843.0, 900.0, 973.0, 1049.5, 1074.7, 1079.0, 1083.0, 1160.0,
+                            1231.0, 1282.0, 1430.0, 1565.0, 2200.0)
+            )
+            # fmt: on
         )
         cryonirsp_camera_mirror_focal_length_mm: float = 932.0
         cryonirsp_pixel_pitch_micron: float = 18.0

{dkist_processing_cryonirsp-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/dkist_processing_cryonirsp/tests/test_instrument_polarization.py

@@ -386,7 +386,7 @@ def test_single_step(
     fake_gql_client,
 ):
     """
-    Given: An InstrumentPolarizationCalibration task with all ancillary files
+    Given: An InstrumentPolarizationCalibration task with all ancillary files including nans
     When: Calling just the reduce_single_step method of the task
     Then: The output of the method is the average of the corrected array (not the center)
     """
@@ -420,6 +420,7 @@ def test_single_step(
             decoder=cryo_fits_array_decoder,
         )
     )
+    polcal_gain_array[0, 0] = np.nan  # replace value
     local_result, global_result = task.reduce_single_step(
         beam=beam,
         exposure_conditions=exposure_conditions,
@@ -451,19 +452,18 @@ def test_single_step(
             beam_boundary=beam_boundary,
         )
     )
-    pol_cal_arrays = (obj.data for obj in polcal_list)
-    avg_inst_pol_cal_array = average_numpy_arrays(pol_cal_arrays)
-    corrected_polcal_array = (avg_inst_pol_cal_array - polcal_dark_array) / polcal_gain_array
+    polcal_arrays = (obj.data for obj in polcal_list)
+    avg_inst_polcal_array = average_numpy_arrays(polcal_arrays)
+    corrected_polcal_array = (avg_inst_polcal_array - polcal_dark_array) / polcal_gain_array
 
     assert local_result.data.shape == (
         task.parameters.polcal_num_spatial_bins,
         task.parameters.polcal_num_spectral_bins,
     )
+    if local_result.data.shape == (1, 1):
+        np.testing.assert_allclose(local_result.data, np.nanmean(corrected_polcal_array))
     assert global_result.data.shape == (1, 1, 1)
-    center = tuple(s // 2 for s in corrected_polcal_array.shape)
-    for result in [local_result, global_result]:
-        assert not np.allclose(result.data, corrected_polcal_array[center], rtol=1e-08)  # BUG FIX
-        np.testing.assert_allclose(result.data, corrected_polcal_array.mean())
+    np.testing.assert_allclose(global_result.data, np.nanmean(corrected_polcal_array))
 
 
 def test_ci_instrument_polarization_calibration_task(

{dkist_processing_cryonirsp-2.0.0rc2 → dkist_processing_cryonirsp-2.0.1}/dkist_processing_cryonirsp/tests/test_parameters.py

@@ -87,15 +87,29 @@ def test_filter_parameters(basic_science_task_with_parameter_mixin, wave):
     task_params = task.parameters
     task_params._wavelength = wave
     expected = {
-        "_linearization_optical_density_filter_attenuation_g278": -1.64,
-        "_linearization_optical_density_filter_attenuation_g358": -3.75,
-        "_linearization_optical_density_filter_attenuation_g408": -4.26,
+        "_linearization_optical_density_filter_attenuation_g278": closest_value_to_wave(
+            task_params, "cryonirsp_linearization_optical_density_filter_attenuation_g278", wave
+        ),
+        "_linearization_optical_density_filter_attenuation_g358": closest_value_to_wave(
+            task_params, "cryonirsp_linearization_optical_density_filter_attenuation_g358", wave
+        ),
+        "_linearization_optical_density_filter_attenuation_g408": closest_value_to_wave(
+            task_params, "cryonirsp_linearization_optical_density_filter_attenuation_g408", wave
+        ),
     }
     for param in expected:
         assert getattr(task_params, param) == expected[param]
     task._purge()
 
 
+def closest_value_to_wave(
+    parameter_obj: CryonirspParsingParameters, paramter_name: str, wave: float
+):
+    value_dict = parameter_obj.input_dataset_parameters[paramter_name][0].parameter_value
+    idx = np.argmin(np.abs(np.array(value_dict["wavelength"]) - wave))
+    return value_dict["values"][idx]
+
+
 def _is_file_param(param_value: Any) -> bool:
     return isinstance(param_value, InputDatasetFilePointer)