Initial ASDF extension and tests

.github/workflows/ci_tests.yml

@@ -144,3 +144,21 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
         verbose: true
+  asdf-schemas:
+    name: Test ASDF Schemas
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      with:
+        persist-credentials: false
+        fetch-depth: 0
+        path: photutils
+    - name: Set up Python 3.13
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6.2.0
+      with:
+        python-version: '3.13'
+    - name: Install dependencies
+      run: cd photutils && python -m pip install -e .[test]
+    - name: Validate ASDF schemas
+      run: cd photutils && pytest photutils/resources/schemas

photutils/converters/__init__.py

@@ -0,0 +1,7 @@
+from . functional_models import AiryDiskPSFConverter
+from . apertures import CircularApertureConverter
+
+__all__ = [
+    'AiryDiskPSFConverter',
+    'CircularApertureConverter',
+]

photutils/converters/apertures.py

@@ -0,0 +1,37 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+"""
+Converters to and from the ASDF data format for photutils apertures.
+"""
+
+from asdf.extension import Converter
+
+__all__ = ['CircularApertureConverter']
+
+
+class CircularApertureConverter(Converter):
+    """
+    ASDF converter for CircularAperture.
+    """
+
+    tags = ('tag:astropy.org:photutils/aperture/circular_aperture-*',)
+    types = ('photutils.aperture.circle.CircularAperture',)
+
+    def to_yaml_tree(self, obj, tag, ctx):  # noqa: ARG002
+        if obj.positions.shape == (2,):
+            pos = obj.positions.tolist()
+        else:
+            pos = obj.positions
+
+        return {
+            'positions': pos,
+            'r': obj.r,
+        }
+
+    def from_yaml_tree(self, node, tag, ctx):  # noqa: ARG002
+        from photutils.aperture.circle import CircularAperture
+
+        return CircularAperture(
+            positions=node['positions'],
+            r=node['r'],
+        )

photutils/converters/functional_models.py

@@ -0,0 +1,39 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+"""
+Converters to and from the ASDF format for photutils.psf.functional_models.
+"""
+
+from asdf_astropy.converters.transform.core import (TransformConverterBase,
+                                                    parameter_to_value)
+
+__all__ = ['AiryDiskPSFConverter']
+
+
+class AiryDiskPSFConverter(TransformConverterBase):
+    """
+    Converter for AiryDiskPSF.
+    """
+
+    tags = ('tag:astropy.org:photutils/psf/airy_disk_psf-*',)
+    types = ('photutils.psf.AiryDiskPSF',)
+
+    def to_yaml_tree_transform(self, model, tag, ctx):  # noqa: ARG002
+        return {
+            'flux': parameter_to_value(model.flux),
+            'x_0': parameter_to_value(model.x_0),
+            'y_0': parameter_to_value(model.y_0),
+            'radius': parameter_to_value(model.radius),
+            'bbox_factor': model.bbox_factor,
+        }
+
+    def from_yaml_tree_transform(self, node, tag, ctx):  # noqa: ARG002
+        from photutils.psf import AiryDiskPSF
+
+        return AiryDiskPSF(
+            flux=node['flux'],
+            x_0=node['x_0'],
+            y_0=node['y_0'],
+            radius=node['radius'],
+            bbox_factor=node['bbox_factor'],
+        )

photutils/converters/tests/test_apertures.py

@@ -0,0 +1,30 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+"""
+Tests for the photutils aperture converters.
+"""
+import asdf
+import numpy as np
+
+from photutils.aperture import CircularAperture
+
+apertures = [
+    CircularAperture(positions=[(1, 2), (3, 4)], r=5),
+    CircularAperture(positions=(5, 6), r=7),
+]
+
+
+def test_aperture_converters(tmp_path):
+    """
+    Test that the aperture converters can round-trip an aperture object.
+    """
+    for aperture in apertures:
+        with asdf.AsdfFile() as af:
+            af['aperture'] = aperture
+            af.write_to(tmp_path / 'aperture.asdf')
+
+        with asdf.open(tmp_path / 'aperture.asdf') as af:
+            aperture2 = af['aperture']
+
+            assert np.all(aperture.positions == aperture2.positions)
+            assert aperture.r == aperture2.r

photutils/converters/tests/test_psf.py

@@ -0,0 +1,35 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+"""
+Tests for the photutils PSF converters.
+"""
+import asdf
+from astropy import units as u
+
+from photutils.psf import AiryDiskPSF
+
+psfs = [
+    AiryDiskPSF(flux=1 * u.Jy, x_0=0 * u.arcsec, y_0=0 * u.arcsec,
+                radius=1 * u.arcsec, bbox_factor=2),
+    AiryDiskPSF(flux=2 * u.Jy, x_0=1 * u.arcsec, y_0=1 * u.arcsec,
+                radius=2 * u.arcsec, bbox_factor=3),
+]
+
+
+def test_psf_converters(tmp_path):
+    """
+    Test that the PSF converters can round-trip a PSF object.
+    """
+    for psf in psfs:
+        with asdf.AsdfFile() as af:
+            af['psf'] = psf
+            af.write_to(tmp_path / 'psf.asdf')
+
+        with asdf.open(tmp_path / 'psf.asdf') as af:
+            psf2 = af['psf']
+
+            assert psf.flux == psf2.flux
+            assert psf.x_0 == psf2.x_0
+            assert psf.y_0 == psf2.y_0
+            assert psf.radius == psf2.radius
+            assert psf.bbox_factor == psf2.bbox_factor

photutils/extension.py

@@ -0,0 +1,78 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+ASDF extension for photutils.
+"""
+import importlib.resources as importlib_resources
+
+from asdf.extension import ManifestExtension
+from asdf.resource import DirectoryResourceMapping
+
+from .converters import apertures  # import CircularApertureConverter
+from .converters import functional_models  # import AiryDiskPSFConverter
+
+__all__ = [
+    'PHOTUTILS_APERTURE_CONVERTERS',
+    'PHOTUTILS_MANIFEST_URIS',
+    'PHOTUTILS_PSF_CONVERTERS',
+]
+
+PHOTUTILS_PSF_CONVERTERS = [
+    functional_models.AiryDiskPSFConverter(),
+]
+
+PHOTUTILS_APERTURE_CONVERTERS = [
+    apertures.CircularApertureConverter(),
+
+]
+
+PHOTUTILS_CONVERTERS = PHOTUTILS_PSF_CONVERTERS + PHOTUTILS_APERTURE_CONVERTERS
+
+
+# The order here is important; asdf will prefer to use extensions
+# that occur earlier in the list.
+PHOTUTILS_MANIFEST_URIS = [
+    'asdf://astropy.org/photutils/manifests/photutils-1.0.0',
+]
+
+
+def get_extensions():
+    """
+    Get the gwcs.converters extension.
+    This method is registered with the asdf.extensions entry point.
+
+    Returns
+    -------
+    list
+        A list of ASDF extensions.
+    """
+    return [
+        ManifestExtension.from_uri(
+            uri,
+            converters=PHOTUTILS_CONVERTERS,
+        )
+        for uri in PHOTUTILS_MANIFEST_URIS
+    ]
+
+
+def get_resource_mappings():
+    """
+    Get the resource mapping instances for the photutils schemas
+    and manifests.  This method is registered with the
+    asdf.resource_mappings entry point.
+
+    Returns
+    -------
+    list
+        A list of collections.abc.Mapping of ASDF resource mappings.
+    """
+    from . import resources
+
+    resources_root = importlib_resources.files(resources)
+
+    return [
+        DirectoryResourceMapping(resources_root / 'schemas',
+                                 'asdf://astropy.org/photutils/schemas',
+                                 recursive=True),
+        DirectoryResourceMapping(resources_root / 'manifests',
+                                 'asdf://astropy.org/photutils/manifests'),
+    ]

photutils/resources/manifests/photutils-1.0.0.yaml

@@ -0,0 +1,14 @@
+id: asdf://astropy.org/photutils/manifests/photutils-1.0.0
+extension_uri: asdf://astropy.org/photutils/extensions/photutils-1.0.0
+title: Photutils extension 1.0.0
+description: |-
+  A set of tags for serializing photutils objects.
+tags:
+- tag_uri: tag:astropy.org:photutils/aperture/circular_aperture-1.0.0
+  schema_uri: asdf://astropy.org/photutils/schemas/aperture/circular_aperture-1.0.0
+  title: CircularAperture
+  description: Circular aperture with one or more positions.
+- tag_uri: tag:astropy.org:photutils/psf/airy_disk_psf-1.0.0
+  schema_uri: asdf://astropy.org/photutils/schemas/psf/airy_disk_psf-1.0.0
+  title: AiryDiskPSF
+  description: A 2D Airy disk PSF model.

photutils/resources/schemas/aperture/circular_aperture-1.0.0.yaml

@@ -0,0 +1,38 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://astropy.org/photutils/schemas/aperture/circular_aperture-1.0.0"
+title: CircularAperture
+description: |
+  ASDF schema for serializing a CircularAperture with one or more positions.
+examples:
+  -
+    - A CircularAperture with a single position and radius of 5 pixels.
+    - |
+      !<tag:astropy.org:photutils/aperture/circular_aperture-1.0.0>
+        positions: [1.0, 2.0]
+        r: 5.0
+
+type: object
+properties:
+  positions:
+    title: Aperture position(s).
+    description: |
+      The pixel coordinates of the aperture center(s) in one of the following formats:
+
+        * single ``(x, y)`` pair as a tuple, list, or `~numpy.ndarray`
+        * tuple, list, or `~numpy.ndarray` of ``(x, y)`` pairs
+    anyOf:
+      - type: array
+        items:
+          type: number
+        maxItems: 2
+        minItems: 2
+      - tag: "tag:stsci.edu:asdf/core/ndarray-1.*"
+  r:
+    title: Aperture radius.
+    description: |
+      The radius of the circular aperture in pixels.
+    type: number
+required: [positions, r]
+...

photutils/resources/schemas/psf/airy_disk_psf-1.0.0.yaml

@@ -0,0 +1,56 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://astropy.org/photutils/schemas/psf/airy_disk_psf-1.0.0"
+title: AiryDiskPSF
+description: |
+  ASDF schema for serializing a 2D Airy disk PSF model.
+
+examples:
+  -
+    - An AiryDiskPSF with a flux of 71.4, centered at (24.3, 25.2) pixels, and a radius of 5 pixels.
+      psf.AiryDiskPSF(flux=71.4, x_0=24.3, y_0=25.2, radius=5)
+    - |
+      !<tag:astropy.org:photutils/psf/airy_disk_psf-1.0.0>
+        bbox_factor: 10.0
+        bounds:
+          radius: [1.1754943508222875e-38, null]
+        fixed: {radius: true}
+        flux: 71.4
+        inputs: [x, y]
+        outputs: [z]
+        radius: 5.0
+        x_0: 24.3
+        y_0: 25.2
+
+
+allOf:
+  - $ref: "http://stsci.edu/schemas/asdf/transform/transform-1.4.0"
+  - type: object
+    properties:
+      flux:
+        anyOf:
+          - tag: "tag:stsci.edu:asdf/unit/quantity-1.*"
+          - type: number
+        description: Total integrated flux of the PSF.
+      x_0:
+        anyOf:
+          - tag: "tag:stsci.edu:asdf/unit/quantity-1.*"
+          - type: number
+        description: "X coordinate of the PSF center (pixel coordinates)."
+      y_0:
+        anyOf:
+          - tag: "tag:stsci.edu:asdf/unit/quantity-1.*"
+          - type: number
+        description: "Y coordinate of the PSF center (pixel coordinates)."
+      radius:
+        anyOf:
+          - tag: "tag:stsci.edu:asdf/unit/quantity-1.*"
+          - type: number
+        description: "Characteristic radius of the Airy disk (e.g. first dark ring) in pixels."
+      bbox_factor:
+        type: number
+        description: Factor by which to multiply the radius to determine the size of the bounding box.
+
+    required: [flux, x_0, y_0, radius]
+...