dkist-processing-visp 5.8.5__tar.gz → 5.9.0__tar.gz

{dkist_processing_visp-5.8.5 → dkist_processing_visp-5.9.0}/.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_visp-5.8.5 → dkist_processing_visp-5.9.0}/CHANGELOG.rst

@@ -1,3 +1,23 @@
+v5.9.0 (2026-10-12)
+===================
+
+Misc
+----
+
+- Remove ``_geometry_inverse_transform`` and updated ``corrections_correct_geometry`` to delegate directly to ``dkist-processing-math``'s ``apply_affine_transform`` which handles array application, non-finite value replacement, and matrix caching. Corrected output is numerically unchanged. (`#331 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/331>`__)
+
+
+v5.8.6 (2026-10-08)
+===================
+
+Misc
+----
+
+- Integrated the ``dkist-env-table`` pre-commit hook and updated the README environment-variable table to match the current configuration. (`#337 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/337>`__)
+- Bump `dkist-processing-common` to v14.6.0. No major changes. (`#341 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/341>`__)
+- Bump `dkist-fits-specifications` to v4.30.0, which adds support for the BEAM BOUNDARIES dataset extra. (`#341 <https://bitbucket.org/dkistdc/dkist-processing-visp/pull-requests/341>`__)
+
+
 v5.8.5 (2026-10-06)
 ===================
 

{dkist_processing_visp-5.8.5 → dkist_processing_visp-5.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-visp
-Version: 5.8.5
+Version: 5.9.0
 Summary: Science processing code for the ViSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -13,11 +13,11 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.13
 Description-Content-Type: text/x-rst
-Requires-Dist: dkist-processing-common==14.5.2
-Requires-Dist: dkist-processing-math==2.2.3
+Requires-Dist: dkist-processing-common==14.6.0
+Requires-Dist: dkist-processing-math==3.0.0
 Requires-Dist: dkist-processing-pac==3.1.2
 Requires-Dist: dkist-header-validator==6.0.0
-Requires-Dist: dkist-fits-specifications==4.29.0
+Requires-Dist: dkist-fits-specifications==4.30.0
 Requires-Dist: solar-wavelength-calibration==2.0.4
 Requires-Dist: dkist-service-configuration==4.3.0
 Requires-Dist: dkist-spectral-lines==3.0.1
@@ -66,7 +66,7 @@ Requires-Dist: dkist-sphinx-theme; extra == "docs"
 Requires-Dist: packaging; extra == "docs"
 Provides-Extra: frozen
 Requires-Dist: Deprecated==3.0.0; extra == "frozen"
-Requires-Dist: ImageIO==2.38.0; extra == "frozen"
+Requires-Dist: ImageIO==2.38.1; extra == "frozen"
 Requires-Dist: Jinja2==3.1.6; extra == "frozen"
 Requires-Dist: Mako==1.4.3; extra == "frozen"
 Requires-Dist: MarkupSafe==3.0.4; extra == "frozen"
@@ -75,12 +75,12 @@ Requires-Dist: PyJWT==2.15.1; extra == "frozen"
 Requires-Dist: PyYAML==6.0.3; extra == "frozen"
 Requires-Dist: PyYAML-ft==8.0.0; extra == "frozen"
 Requires-Dist: Pygments==2.21.0; extra == "frozen"
-Requires-Dist: SQLAlchemy==2.1.3; extra == "frozen"
+Requires-Dist: SQLAlchemy==2.1.4; extra == "frozen"
 Requires-Dist: Send2Trash==2.1.0; extra == "frozen"
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 Requires-Dist: aiohappyeyeballs==2.7.1; extra == "frozen"
-Requires-Dist: aiohttp==3.14.4; extra == "frozen"
+Requires-Dist: aiohttp==3.14.5; extra == "frozen"
 Requires-Dist: aiosignal==1.4.0; extra == "frozen"
 Requires-Dist: aiosmtplib==5.1.3; extra == "frozen"
 Requires-Dist: aiosqlite==0.22.1; extra == "frozen"
@@ -99,6 +99,7 @@ Requires-Dist: apache-airflow-providers-postgres==7.1.0; extra == "frozen"
 Requires-Dist: apache-airflow-providers-smtp==3.1.0; extra == "frozen"
 Requires-Dist: apache-airflow-providers-standard==1.20.0; extra == "frozen"
 Requires-Dist: apache-airflow-task-sdk==1.3.1; extra == "frozen"
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 Requires-Dist: argon2-cffi==25.1.0; extra == "frozen"
 Requires-Dist: argon2-cffi-bindings==26.1.0; extra == "frozen"
@@ -108,17 +109,17 @@ Requires-Dist: asdf_standard==1.5.0; extra == "frozen"
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+Requires-Dist: botocore==1.43.112; extra == "frozen"
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 Requires-Dist: cadwyn==7.0.0; extra == "frozen"
 Requires-Dist: celery==5.6.3; extra == "frozen"
@@ -142,17 +143,17 @@ Requires-Dist: decorator==5.3.1; extra == "frozen"
 Requires-Dist: defusedxml==0.7.1; extra == "frozen"
 Requires-Dist: dill==0.4.1; extra == "frozen"
 Requires-Dist: dkist-header-validator==6.0.0; extra == "frozen"
-Requires-Dist: dkist-processing-common==14.5.2; extra == "frozen"
+Requires-Dist: dkist-processing-common==14.6.0; extra == "frozen"
 Requires-Dist: dkist-processing-core==7.5.0; extra == "frozen"
-Requires-Dist: dkist-processing-math==2.2.3; extra == "frozen"
+Requires-Dist: dkist-processing-math==3.0.0; extra == "frozen"
 Requires-Dist: dkist-processing-pac==3.1.2; extra == "frozen"
-Requires-Dist: dkist-processing-visp==5.8.5; extra == "frozen"
+Requires-Dist: dkist-processing-visp==5.9.0; 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==4.29.0; extra == "frozen"
-Requires-Dist: dnspython==2.8.0; extra == "frozen"
+Requires-Dist: dkist_fits_specifications==4.30.0; extra == "frozen"
+Requires-Dist: dnspython==2.9.0; extra == "frozen"
 Requires-Dist: email-validator==2.3.0; extra == "frozen"
-Requires-Dist: executing==2.2.1; extra == "frozen"
+Requires-Dist: executing==2.3.0; extra == "frozen"
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 Requires-Dist: fastapi-cli==0.0.32; extra == "frozen"
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@@ -169,7 +170,7 @@ Requires-Dist: greenlet==3.5.6; extra == "frozen"
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+Requires-Dist: httptools==0.9.0; extra == "frozen"
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 Requires-Dist: humanize==4.16.0; extra == "frozen"
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@@ -180,11 +181,11 @@ Requires-Dist: ipython==9.17.1; extra == "frozen"
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 Requires-Dist: itsdangerous==2.2.0; extra == "frozen"
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+Requires-Dist: jedi==0.20.1; extra == "frozen"
 Requires-Dist: jmespath==1.1.0; extra == "frozen"
 Requires-Dist: joblib==1.6.0; extra == "frozen"
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+Requires-Dist: json5==0.17.3; extra == "frozen"
+Requires-Dist: jsonpointer==3.2.1; extra == "frozen"
 Requires-Dist: jsonschema==4.26.0; extra == "frozen"
 Requires-Dist: jsonschema-specifications==2025.9.1; extra == "frozen"
 Requires-Dist: jupyter-events==0.12.1; extra == "frozen"
@@ -216,43 +217,43 @@ Requires-Dist: mistune==3.3.4; extra == "frozen"
 Requires-Dist: more-itertools==11.1.0; extra == "frozen"
 Requires-Dist: moviepy==2.1.2; extra == "frozen"
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 Requires-Dist: natsort==8.4.0; extra == "frozen"
 Requires-Dist: nbclient==0.11.0; extra == "frozen"
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+Requires-Dist: nbconvert==7.17.2; extra == "frozen"
 Requires-Dist: nbformat==5.11.1; extra == "frozen"
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 Requires-Dist: networkx==3.7; extra == "frozen"
 Requires-Dist: notebook==7.6.3; extra == "frozen"
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 Requires-Dist: opentelemetry-propagator-aws-xray==1.0.2; extra == "frozen"
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-Requires-Dist: opentelemetry-semantic-conventions==0.66b0; extra == "frozen"
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 Requires-Dist: packaging==26.3; extra == "frozen"
 Requires-Dist: pandas==3.0.6; extra == "frozen"
@@ -261,12 +262,12 @@ Requires-Dist: parfive==2.3.1; extra == "frozen"
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 Requires-Dist: pathspec==1.1.1; extra == "frozen"
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+Requires-Dist: pendulum==3.3.0; extra == "frozen"
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 Requires-Dist: pip==26.2.1; extra == "frozen"
-Requires-Dist: platformdirs==4.12.3; extra == "frozen"
+Requires-Dist: platformdirs==4.13.0; extra == "frozen"
 Requires-Dist: pluggy==1.6.0; extra == "frozen"
 Requires-Dist: pooch==1.9.0; extra == "frozen"
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@@ -280,11 +281,11 @@ Requires-Dist: psycopg-binary==3.3.6; extra == "frozen"
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-Requires-Dist: pycparser==3.0; extra == "frozen"
-Requires-Dist: pydantic==2.13.5; extra == "frozen"
+Requires-Dist: pycparser==3.11; extra == "frozen"
+Requires-Dist: pydantic==2.14.1; extra == "frozen"
 Requires-Dist: pydantic-extra-types==2.11.1; extra == "frozen"
 Requires-Dist: pydantic-settings==2.15.0; extra == "frozen"
-Requires-Dist: pydantic_core==2.46.5; extra == "frozen"
+Requires-Dist: pydantic_core==2.50.1; extra == "frozen"
 Requires-Dist: pyerfa==2.0.1.5; extra == "frozen"
 Requires-Dist: pygtrie==2.6.2; extra == "frozen"
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@@ -293,7 +294,7 @@ Requires-Dist: python-dateutil==2.9.0.post0; extra == "frozen"
 Requires-Dist: python-dotenv==1.2.4; extra == "frozen"
 Requires-Dist: python-json-logger==4.2.0; extra == "frozen"
 Requires-Dist: python-multipart==0.0.32; extra == "frozen"
-Requires-Dist: python-slugify==9.1.2; extra == "frozen"
+Requires-Dist: python-slugify==9.1.3; extra == "frozen"
 Requires-Dist: pytz==2026.5; extra == "frozen"
 Requires-Dist: pyzmq==27.2.0; extra == "frozen"
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@@ -304,7 +305,7 @@ Requires-Dist: rfc3986-validator==0.1.1; extra == "frozen"
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 Requires-Dist: rich-argparse==1.8.0; extra == "frozen"
-Requires-Dist: rich-toolkit==0.20.5; extra == "frozen"
+Requires-Dist: rich-toolkit==0.20.6; extra == "frozen"
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 Requires-Dist: s3transfer==0.19.2; extra == "frozen"
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@@ -316,7 +317,7 @@ Requires-Dist: shellingham==1.5.4; extra == "frozen"
 Requires-Dist: six==1.17.0; extra == "frozen"
 Requires-Dist: sniffio==1.3.1; extra == "frozen"
 Requires-Dist: solar-wavelength-calibration==2.0.4; extra == "frozen"
-Requires-Dist: soupsieve==2.10; extra == "frozen"
+Requires-Dist: soupsieve==3.0.3; extra == "frozen"
 Requires-Dist: sqids==0.5.1; extra == "frozen"
 Requires-Dist: sqlparse==0.6.0; extra == "frozen"
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@@ -336,7 +337,7 @@ Requires-Dist: tinycss2==1.5.1; extra == "frozen"
 Requires-Dist: tornado==6.5.10; extra == "frozen"
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 Requires-Dist: traitlets==5.16.1; extra == "frozen"
-Requires-Dist: typer==0.27.2; extra == "frozen"
+Requires-Dist: typer==0.27.3; extra == "frozen"
 Requires-Dist: typing-inspection==0.4.4; extra == "frozen"
 Requires-Dist: typing_extensions==4.16.0; extra == "frozen"
 Requires-Dist: tzdata==2026.5; extra == "frozen"
@@ -379,6 +380,8 @@ 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
@@ -470,6 +473,21 @@ Environment Variables
    * - FTS_ATLAS_DATA_DIR
      - annotation=Union[str, NoneType] required=False default=None description='Common cached directory for 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_visp-5.8.5 → dkist_processing_visp-5.9.0}/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 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_visp-5.8.5 → dkist_processing_visp-5.9.0}/dkist_processing_visp/tasks/mixin/corrections.py

@@ -1,40 +1,16 @@
 """Helper for ViSP array corrections."""
 
-from typing import Generator
-from typing import Iterable
+from collections.abc import Generator
+from collections.abc import Iterable
 
 import numpy as np
 import scipy.ndimage as spnd
-from scipy.ndimage import affine_transform
+from dkist_processing_math.transform import apply_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,
@@ -47,7 +23,8 @@ class CorrectionsMixin:
         """
         Shift and then rotate data.
 
-        This method applies the inverse of the given shift and angle.
+        This method applies the inverse of the given shift and angle in a single interpolation
+        pass via `dkist_processing_math.transform.apply_affine_transform`.
 
         Parameters
         ----------
@@ -55,8 +32,8 @@ class CorrectionsMixin:
             2D array(s) containing the data for the un-shifted beam
 
         shift : np.ndarray
-            The shift in the spectral dimension needed to "straighten" the spectra
-            so a single wavelength is at the same pixel for all slit positions.
+            The (row, col) shift, in pixels, needed to bring this array into alignment with the
+            other modstates and beams.
 
         angle : float
             The angle (in radians) between slit hairlines and pixel axes.
@@ -78,65 +55,23 @@ class CorrectionsMixin:
             Used in conjunction with mode 'constant', the value outside
             the image boundaries.
 
-
         Returns
         -------
         Generator
             2D array(s) containing the data of the rotated and shifted beam
         """
-        uncorrected_arrays = (arrays,) if isinstance(arrays, np.ndarray) else arrays
+        # `-shift` and `-angle` because the pipeline defines shift/angle as the distortion to
+        # correct for; the forward correction moves content in the opposite direction.
         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),
-            )
+        yield from apply_affine_transform(
+            arrays,
+            shift=-shift,
+            angle=-angle,
+            order="shift_then_rotate",
+            interp_order=order,
+            mode=mode,
+            cval=cval,
+        )
 
     @staticmethod
     def corrections_remove_spec_geometry(

{dkist_processing_visp-5.8.5 → dkist_processing_visp-5.9.0}/dkist_processing_visp/tests/test_geometric.py

@@ -7,7 +7,7 @@ from dkist_processing_common._util.scratch import WorkflowFileSystem
 from dkist_processing_common.codecs.basemodel import basemodel_decoder
 from dkist_processing_common.codecs.fits import fits_array_decoder
 from dkist_processing_common.models.quality import TaskCount
-from dkist_processing_math import transform
+from dkist_processing_math.transform import apply_affine_transform
 
 from dkist_processing_visp.models.tags import VispTag
 from dkist_processing_visp.tasks.geometric import GeometricCalibration
@@ -33,9 +33,13 @@ def make_solar_array_data(
     beam_list = []
     for beam in [1, 2]:
         true_solar = 10 * (np.ones(intermediate_shape) + modstate + beam)
+
         translated_solar = next(
-            transform.translate_arrays(
-                arrays=true_solar, translation=offsets[beam - 1][modstate - 1]
+            apply_affine_transform(
+                true_solar,
+                shift=np.asarray(offsets[beam - 1][modstate - 1]),
+                angle=0.0,
+                order="shift_then_rotate",
             )
         )
         translated_solar[translated_solar == 0] = 10 * (modstate + beam + 1)
@@ -44,7 +48,12 @@ def make_solar_array_data(
         translated_solar[:, 30] = 5.0
         translated_solar[:, 70] = 5.0
         distorted_solar = next(
-            transform.rotate_arrays_about_point(arrays=translated_solar, angle=angles[beam - 1])
+            apply_affine_transform(
+                translated_solar,
+                shift=np.zeros(2),
+                angle=angles[beam - 1],
+                order="shift_then_rotate",
+            )
         )
         beam_list.append((distorted_solar + dark_signal) * num_raw_per_fpa)
 
@@ -111,9 +120,13 @@ def make_lamp_array_data(
     beam_list = []
     for beam in [1, 2]:
         true_lamp = 10 * (np.ones(intermediate_shape) + modstate + beam)
+
         translated_lamp = next(
-            transform.translate_arrays(
-                arrays=true_lamp, translation=offsets[beam - 1][modstate - 1]
+            apply_affine_transform(
+                true_lamp,
+                shift=np.asarray(offsets[beam - 1][modstate - 1]),
+                angle=0.0,
+                order="shift_then_rotate",
             )
         )
         translated_lamp[translated_lamp == 0] = 10 * (modstate + beam + 1)
@@ -124,7 +137,12 @@ def make_lamp_array_data(
         # Chop out part of the second hairline so the fitter has to skip over these pixels
         translated_lamp[5:9, 70] = 10 * (modstate + beam + 1)
         distorted_lamp = next(
-            transform.rotate_arrays_about_point(arrays=translated_lamp, angle=angles[beam - 1])
+            apply_affine_transform(
+                translated_lamp,
+                shift=np.zeros(2),
+                angle=angles[beam - 1],
+                order="shift_then_rotate",
+            )
         )
         beam_list.append((distorted_lamp + dark_signal) * num_raw_per_fpa)