dkist-processing-visp 5.7.15__tar.gz → 5.7.16__tar.gz

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+v5.7.16 (2026-05-28)
+====================
+
+Misc
+----
+
+- Combine the translation and rotation steps of the geometric correction into a single interpolation. This preserves the existing science calibration behavior while simplifying the transform math and reducing repeated processing during geometry correction. (`#317 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/317>`__)
+
+
 v5.7.15 (2026-05-27)
 ====================
 

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.7.15
+Version: 5.7.16
 Summary: Science processing code for the ViSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -118,8 +118,8 @@ Requires-Dist: babel==2.18.0; extra == "frozen"
 Requires-Dist: beautifulsoup4==4.14.3; extra == "frozen"
 Requires-Dist: billiard==4.2.4; extra == "frozen"
 Requires-Dist: bleach==6.3.0; extra == "frozen"
-Requires-Dist: boto3==1.43.15; extra == "frozen"
-Requires-Dist: botocore==1.43.15; extra == "frozen"
+Requires-Dist: boto3==1.43.16; extra == "frozen"
+Requires-Dist: botocore==1.43.16; extra == "frozen"
 Requires-Dist: cadwyn==6.2.2; extra == "frozen"
 Requires-Dist: celery==5.6.3; extra == "frozen"
 Requires-Dist: certifi==2026.5.20; extra == "frozen"
@@ -145,7 +145,7 @@ Requires-Dist: dkist-processing-common==14.3.2; extra == "frozen"
 Requires-Dist: dkist-processing-core==7.3.0; extra == "frozen"
 Requires-Dist: dkist-processing-math==2.2.2; extra == "frozen"
 Requires-Dist: dkist-processing-pac==3.1.2; extra == "frozen"
-Requires-Dist: dkist-processing-visp==5.7.15; extra == "frozen"
+Requires-Dist: dkist-processing-visp==5.7.16; extra == "frozen"
 Requires-Dist: dkist-service-configuration==4.3.0; extra == "frozen"
 Requires-Dist: dkist-spectral-lines==3.0.1; extra == "frozen"
 Requires-Dist: dkist_fits_specifications==4.26.0; extra == "frozen"
@@ -171,7 +171,7 @@ Requires-Dist: httpcore==1.0.9; extra == "frozen"
 Requires-Dist: httptools==0.8.0; extra == "frozen"
 Requires-Dist: httpx==0.28.1; extra == "frozen"
 Requires-Dist: humanize==4.15.0; extra == "frozen"
-Requires-Dist: idna==3.16; extra == "frozen"
+Requires-Dist: idna==3.17; extra == "frozen"
 Requires-Dist: imageio-ffmpeg==0.6.0; extra == "frozen"
 Requires-Dist: importlib_metadata==9.0.0; extra == "frozen"
 Requires-Dist: ipykernel==7.2.0; extra == "frozen"
@@ -262,7 +262,7 @@ Requires-Dist: pexpect==4.9.0; extra == "frozen"
 Requires-Dist: pika==1.4.1; extra == "frozen"
 Requires-Dist: pillow==10.4.0; extra == "frozen"
 Requires-Dist: pip==26.1.1; extra == "frozen"
-Requires-Dist: platformdirs==4.9.6; extra == "frozen"
+Requires-Dist: platformdirs==4.10.0; extra == "frozen"
 Requires-Dist: pluggy==1.6.0; extra == "frozen"
 Requires-Dist: pooch==1.9.0; extra == "frozen"
 Requires-Dist: proglog==0.1.12; extra == "frozen"
@@ -299,7 +299,7 @@ Requires-Dist: rfc3987-syntax==1.1.0; extra == "frozen"
 Requires-Dist: rich==15.0.0; extra == "frozen"
 Requires-Dist: rich-argparse==1.8.0; extra == "frozen"
 Requires-Dist: rich-toolkit==0.19.10; extra == "frozen"
-Requires-Dist: rpds-py==0.30.0; extra == "frozen"
+Requires-Dist: rpds-py==2026.5.1; extra == "frozen"
 Requires-Dist: s3transfer==0.17.1; extra == "frozen"
 Requires-Dist: scikit-image==0.25.2; extra == "frozen"
 Requires-Dist: scikit-learn==1.6.1; extra == "frozen"
@@ -328,7 +328,7 @@ Requires-Dist: text-unidecode==1.3; extra == "frozen"
 Requires-Dist: threadpoolctl==3.6.0; extra == "frozen"
 Requires-Dist: tifffile==2026.5.15; extra == "frozen"
 Requires-Dist: tinycss2==1.4.0; extra == "frozen"
-Requires-Dist: tornado==6.5.5; extra == "frozen"
+Requires-Dist: tornado==6.5.6; extra == "frozen"
 Requires-Dist: tqdm==4.67.3; extra == "frozen"
 Requires-Dist: traitlets==5.15.0; extra == "frozen"
 Requires-Dist: typer==0.26.2; extra == "frozen"

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/dkist_processing_visp/tasks/mixin/corrections.py

@@ -5,19 +5,42 @@ from typing import Iterable
 
 import numpy as np
 import scipy.ndimage as spnd
-from dkist_processing_math.transform import affine_transform_arrays
-from dkist_processing_math.transform import rotate_arrays_about_point
+from scipy.ndimage import affine_transform
 
 
 class CorrectionsMixin:
     """Mixin to provide support for various array corrections used by the workflow tasks."""
 
+    @staticmethod
+    def _geometry_inverse_transform(
+        array_shape: tuple[int, ...], shift: np.ndarray, angle: float
+    ) -> tuple[np.ndarray, np.ndarray]:
+        """
+        Build the inverse transform used by `scipy.ndimage.affine_transform`.
+
+        The forward correction translates by `-shift` and then rotates by `-angle`
+        about the array center. `affine_transform` instead wants the mapping from
+        output coordinates back to input coordinates, so we supply the inverse
+        rotation matrix and the corresponding center-preserving offset here.
+        """
+        cosine_angle = np.cos(angle)
+        sine_angle = np.sin(angle)
+        inverse_rotation_matrix = np.array(
+            [[cosine_angle, -sine_angle], [sine_angle, cosine_angle]],
+            dtype=np.float64,
+        )
+
+        rotation_center = 0.5 * (np.asarray(array_shape, dtype=np.float64) - 1.0)
+        transform_offset = rotation_center + shift - inverse_rotation_matrix @ rotation_center
+
+        return inverse_rotation_matrix, transform_offset
+
     @staticmethod
     def corrections_correct_geometry(
         arrays: Iterable[np.ndarray] | np.ndarray,
         shift: np.ndarray = np.zeros(2),
         angle: float = 0.0,
-        mode: str = "edge",
+        mode: str = "nearest",
         order: int = 5,
         cval: float = np.nan,
     ) -> Generator[np.ndarray, None, None]:
@@ -38,7 +61,7 @@ class CorrectionsMixin:
         angle : float
             The angle (in radians) between slit hairlines and pixel axes.
 
-        mode : {'constant', 'edge', 'symmetric', 'reflect', 'wrap'}
+        mode : {'constant', 'nearest', 'symmetric', 'reflect', 'wrap'}
             Points outside the boundaries of the input are filled according
             to the given mode.  Modes match the behaviour of `numpy.pad`.
 
@@ -61,19 +84,58 @@ class CorrectionsMixin:
         Generator
             2D array(s) containing the data of the rotated and shifted beam
         """
-        arrays = [arrays] if isinstance(arrays, np.ndarray) else arrays
-        for array in arrays:
-            array = array.astype(np.float64)
-            array[np.where(array == np.inf)] = np.max(array[np.isfinite(array)])
-            array[np.where(array == -np.inf)] = np.min(array[np.isfinite(array)])
-            array[np.isnan(array)] = np.nanmedian(array)
-            translated = affine_transform_arrays(
-                array, translation=-shift, mode=mode, order=order, cval=cval
-            )
-            yield next(
-                rotate_arrays_about_point(
-                    translated, angle=-angle, mode=mode, order=order, cval=cval
+        uncorrected_arrays = (arrays,) if isinstance(arrays, np.ndarray) else arrays
+        shift = np.asarray(shift, dtype=np.float64)
+
+        previous_array_shape = None
+        inverse_transform_matrix = None
+        transform_offset = None
+
+        for array in uncorrected_arrays:
+            input_array = np.asarray(array, dtype=np.float64)
+
+            # `affine_transform` does not handle NaN and inf values well, so normalize them
+            # before interpolation. We identify the finite pixels once and reuse those
+            # results instead of rescanning the full array for each replacement case.
+            finite_pixel_mask = np.isfinite(input_array)
+            if not finite_pixel_mask.all():
+                finite_pixel_values = input_array[finite_pixel_mask]
+
+                if finite_pixel_values.size == 0:
+                    input_array.fill(cval if np.isfinite(cval) else np.nan)
+                else:
+                    # Replace +inf, -inf, and NaN using the finite pixels we already
+                    # collected, and only computing the replacement values if necessary.
+                    positive_infinity_mask = np.isposinf(input_array)
+                    if positive_infinity_mask.any():
+                        input_array[positive_infinity_mask] = finite_pixel_values.max()
+
+                    negative_infinity_mask = np.isneginf(input_array)
+                    if negative_infinity_mask.any():
+                        input_array[negative_infinity_mask] = finite_pixel_values.min()
+
+                    nan_pixel_mask = np.isnan(input_array)
+                    if nan_pixel_mask.any():
+                        input_array[nan_pixel_mask] = np.nanmedian(input_array)
+
+            if input_array.shape != previous_array_shape:
+                inverse_transform_matrix, transform_offset = (
+                    CorrectionsMixin._geometry_inverse_transform(
+                        array_shape=input_array.shape,
+                        shift=shift,
+                        angle=angle,
+                    )
                 )
+                previous_array_shape = input_array.shape
+
+            yield affine_transform(
+                input_array,
+                matrix=inverse_transform_matrix,
+                offset=transform_offset,
+                order=order,
+                mode=mode,
+                cval=cval,
+                prefilter=(order > 1),
             )
 
     @staticmethod

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/dkist_processing_visp/tasks/science.py

@@ -1,5 +1,6 @@
 """ViSP science calibration task. See :doc:`this page </science_calibration>` for more information."""
 
+import time
 from collections import defaultdict
 from dataclasses import dataclass
 from functools import cached_property
@@ -140,6 +141,7 @@ class ScienceCalibration(
         None
 
         """
+        start = time.perf_counter()
         with self.telemetry_span("Loading calibration objects"):
             calibrations = self.collect_calibration_objects()
 
@@ -162,6 +164,8 @@ class ScienceCalibration(
             self.quality_write_intermediate_task_type_counts(
                 task_type=TaskName.observe.value, total_frames=no_of_raw_science_frames
             )
+        elapsed = time.perf_counter() - start
+        logger.info(f"Science task completed in {elapsed:.2f} s")
 
     def collect_calibration_objects(self) -> CalibrationCollection:
         """

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/dkist_processing_visp/tests/test_science.py

@@ -683,9 +683,9 @@ def test_generate_nan_mask(science_calibration_task, dummy_calibration_collectio
     solar_gain_array = calibration_collection.solar_gain[VispTag.beam(beam)]
     angle = calibration_collection.angle[VispTag.beam(beam)]
     spec_shift = calibration_collection.spec_shift[VispTag.beam(beam)]
-    state_offset = calibration_collection.state_offset[VispTag.beam(beam)][
-        VispTag.modstate(modstate)
-    ]
+    # Use a non-zero shift so the geometric correction creates edge pixels that
+    # should be masked in the final binary NaN mask.
+    state_offset = np.array([1.0, 0.0])
     nan_mask = task.generate_nan_mask(
         solar_corrected_array=np.random.random(size=solar_gain_array.shape),
         state_offset=state_offset,

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/dkist_processing_visp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.7.15
+Version: 5.7.16
 Summary: Science processing code for the ViSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -118,8 +118,8 @@ Requires-Dist: babel==2.18.0; extra == "frozen"
 Requires-Dist: beautifulsoup4==4.14.3; extra == "frozen"
 Requires-Dist: billiard==4.2.4; extra == "frozen"
 Requires-Dist: bleach==6.3.0; extra == "frozen"
-Requires-Dist: boto3==1.43.15; extra == "frozen"
-Requires-Dist: botocore==1.43.15; extra == "frozen"
+Requires-Dist: boto3==1.43.16; extra == "frozen"
+Requires-Dist: botocore==1.43.16; extra == "frozen"
 Requires-Dist: cadwyn==6.2.2; extra == "frozen"
 Requires-Dist: celery==5.6.3; extra == "frozen"
 Requires-Dist: certifi==2026.5.20; extra == "frozen"
@@ -145,7 +145,7 @@ Requires-Dist: dkist-processing-common==14.3.2; extra == "frozen"
 Requires-Dist: dkist-processing-core==7.3.0; extra == "frozen"
 Requires-Dist: dkist-processing-math==2.2.2; extra == "frozen"
 Requires-Dist: dkist-processing-pac==3.1.2; extra == "frozen"
-Requires-Dist: dkist-processing-visp==5.7.15; extra == "frozen"
+Requires-Dist: dkist-processing-visp==5.7.16; extra == "frozen"
 Requires-Dist: dkist-service-configuration==4.3.0; extra == "frozen"
 Requires-Dist: dkist-spectral-lines==3.0.1; extra == "frozen"
 Requires-Dist: dkist_fits_specifications==4.26.0; extra == "frozen"
@@ -171,7 +171,7 @@ Requires-Dist: httpcore==1.0.9; extra == "frozen"
 Requires-Dist: httptools==0.8.0; extra == "frozen"
 Requires-Dist: httpx==0.28.1; extra == "frozen"
 Requires-Dist: humanize==4.15.0; extra == "frozen"
-Requires-Dist: idna==3.16; extra == "frozen"
+Requires-Dist: idna==3.17; extra == "frozen"
 Requires-Dist: imageio-ffmpeg==0.6.0; extra == "frozen"
 Requires-Dist: importlib_metadata==9.0.0; extra == "frozen"
 Requires-Dist: ipykernel==7.2.0; extra == "frozen"
@@ -262,7 +262,7 @@ Requires-Dist: pexpect==4.9.0; extra == "frozen"
 Requires-Dist: pika==1.4.1; extra == "frozen"
 Requires-Dist: pillow==10.4.0; extra == "frozen"
 Requires-Dist: pip==26.1.1; extra == "frozen"
-Requires-Dist: platformdirs==4.9.6; extra == "frozen"
+Requires-Dist: platformdirs==4.10.0; extra == "frozen"
 Requires-Dist: pluggy==1.6.0; extra == "frozen"
 Requires-Dist: pooch==1.9.0; extra == "frozen"
 Requires-Dist: proglog==0.1.12; extra == "frozen"
@@ -299,7 +299,7 @@ Requires-Dist: rfc3987-syntax==1.1.0; extra == "frozen"
 Requires-Dist: rich==15.0.0; extra == "frozen"
 Requires-Dist: rich-argparse==1.8.0; extra == "frozen"
 Requires-Dist: rich-toolkit==0.19.10; extra == "frozen"
-Requires-Dist: rpds-py==0.30.0; extra == "frozen"
+Requires-Dist: rpds-py==2026.5.1; extra == "frozen"
 Requires-Dist: s3transfer==0.17.1; extra == "frozen"
 Requires-Dist: scikit-image==0.25.2; extra == "frozen"
 Requires-Dist: scikit-learn==1.6.1; extra == "frozen"
@@ -328,7 +328,7 @@ Requires-Dist: text-unidecode==1.3; extra == "frozen"
 Requires-Dist: threadpoolctl==3.6.0; extra == "frozen"
 Requires-Dist: tifffile==2026.5.15; extra == "frozen"
 Requires-Dist: tinycss2==1.4.0; extra == "frozen"
-Requires-Dist: tornado==6.5.5; extra == "frozen"
+Requires-Dist: tornado==6.5.6; extra == "frozen"
 Requires-Dist: tqdm==4.67.3; extra == "frozen"
 Requires-Dist: traitlets==5.15.0; extra == "frozen"
 Requires-Dist: typer==0.26.2; extra == "frozen"

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/dkist_processing_visp.egg-info/requires.txt

@@ -84,8 +84,8 @@ babel==2.18.0
 beautifulsoup4==4.14.3
 billiard==4.2.4
 bleach==6.3.0
-boto3==1.43.15
-botocore==1.43.15
+boto3==1.43.16
+botocore==1.43.16
 cadwyn==6.2.2
 celery==5.6.3
 certifi==2026.5.20
@@ -111,7 +111,7 @@ dkist-processing-common==14.3.2
 dkist-processing-core==7.3.0
 dkist-processing-math==2.2.2
 dkist-processing-pac==3.1.2
-dkist-processing-visp==5.7.15
+dkist-processing-visp==5.7.16
 dkist-service-configuration==4.3.0
 dkist-spectral-lines==3.0.1
 dkist_fits_specifications==4.26.0
@@ -137,7 +137,7 @@ httpcore==1.0.9
 httptools==0.8.0
 httpx==0.28.1
 humanize==4.15.0
-idna==3.16
+idna==3.17
 imageio-ffmpeg==0.6.0
 importlib_metadata==9.0.0
 ipykernel==7.2.0
@@ -228,7 +228,7 @@ pexpect==4.9.0
 pika==1.4.1
 pillow==10.4.0
 pip==26.1.1
-platformdirs==4.9.6
+platformdirs==4.10.0
 pluggy==1.6.0
 pooch==1.9.0
 proglog==0.1.12
@@ -265,7 +265,7 @@ rfc3987-syntax==1.1.0
 rich==15.0.0
 rich-argparse==1.8.0
 rich-toolkit==0.19.10
-rpds-py==0.30.0
+rpds-py==2026.5.1
 s3transfer==0.17.1
 scikit-image==0.25.2
 scikit-learn==1.6.1
@@ -294,7 +294,7 @@ text-unidecode==1.3
 threadpoolctl==3.6.0
 tifffile==2026.5.15
 tinycss2==1.4.0
-tornado==6.5.5
+tornado==6.5.6
 tqdm==4.67.3
 traitlets==5.15.0
 typer==0.26.2

{dkist_processing_visp-5.7.15 → dkist_processing_visp-5.7.16}/pyproject.toml

@@ -9,8 +9,8 @@ exclude = ["build*"]
 
 [tool.dkist-dev-tools]
 # Most recently frozen version by dkist-dev-tools
-version = "5.7.15"
-date = 2026-05-27T06:45:45.578458
+version = "5.7.16"
+date = 2026-05-28T12:17:45.447074
 
 [project]
 dynamic = ["version"]
@@ -146,8 +146,8 @@ frozen = [
     "beautifulsoup4 == 4.14.3",
     "billiard == 4.2.4",
     "bleach == 6.3.0",
-    "boto3 == 1.43.15",
-    "botocore == 1.43.15",
+    "boto3 == 1.43.16",
+    "botocore == 1.43.16",
     "cadwyn == 6.2.2",
     "celery == 5.6.3",
     "certifi == 2026.5.20",
@@ -173,7 +173,7 @@ frozen = [
     "dkist-processing-core == 7.3.0",
     "dkist-processing-math == 2.2.2",
     "dkist-processing-pac == 3.1.2",
-    "dkist-processing-visp == 5.7.15",
+    "dkist-processing-visp == 5.7.16",
     "dkist-service-configuration == 4.3.0",
     "dkist-spectral-lines == 3.0.1",
     "dkist_fits_specifications == 4.26.0",
@@ -199,7 +199,7 @@ frozen = [
     "httptools == 0.8.0",
     "httpx == 0.28.1",
     "humanize == 4.15.0",
-    "idna == 3.16",
+    "idna == 3.17",
     "imageio-ffmpeg == 0.6.0",
     "importlib_metadata == 9.0.0",
     "ipykernel == 7.2.0",
@@ -290,7 +290,7 @@ frozen = [
     "pika == 1.4.1",
     "pillow == 10.4.0",
     "pip == 26.1.1",
-    "platformdirs == 4.9.6",
+    "platformdirs == 4.10.0",
     "pluggy == 1.6.0",
     "pooch == 1.9.0",
     "proglog == 0.1.12",
@@ -327,7 +327,7 @@ frozen = [
     "rich == 15.0.0",
     "rich-argparse == 1.8.0",
     "rich-toolkit == 0.19.10",
-    "rpds-py == 0.30.0",
+    "rpds-py == 2026.5.1",
     "s3transfer == 0.17.1",
     "scikit-image == 0.25.2",
     "scikit-learn == 1.6.1",
@@ -356,7 +356,7 @@ frozen = [
     "threadpoolctl == 3.6.0",
     "tifffile == 2026.5.15",
     "tinycss2 == 1.4.0",
-    "tornado == 6.5.5",
+    "tornado == 6.5.6",
     "tqdm == 4.67.3",
     "traitlets == 5.15.0",
     "typer == 0.26.2",