Add serialization logic for uncertainty objects

CHANGES.rst

@@ -10,6 +10,8 @@
 
 - require asdf 2.14.4 [#241]
 
+- Add support for astropy.nddata.uncertainty classes [#239]
+
 0.6.1 (2024-04-05)
 ------------------
 

asdf_astropy/converters/__init__.py

@@ -19,6 +19,7 @@
     "AstropyTableConverter",
     "AsdfTableConverter",
     "NdarrayMixinConverter",
+    "UncertaintyConverter",
     "TimeDeltaConverter",
     "TimeConverter",
     "CompoundConverter",
@@ -52,6 +53,7 @@
     SpectralCoordConverter,
 )
 from .fits import AsdfFitsConverter, AstropyFitsConverter, FitsConverter
+from .nddata import UncertaintyConverter
 from .table import AsdfTableConverter, AstropyTableConverter, ColumnConverter, NdarrayMixinConverter
 from .time import TimeConverter, TimeDeltaConverter
 from .transform import (

asdf_astropy/converters/nddata/__init__.py

@@ -0,0 +1,5 @@
+__all__ = [
+    "UncertaintyConverter",
+]
+
+from .uncertainty import UncertaintyConverter

asdf_astropy/converters/nddata/tests/test_uncertainty.py

@@ -0,0 +1,37 @@
+import asdf
+import numpy as np
+import pytest
+from astropy import units as u
+from astropy.nddata import StdDevUncertainty, UnknownUncertainty, VarianceUncertainty
+
+
+def create_uncertainty():
+    uncert = np.arange(100).reshape(10, 10)
+    uncertainty_stddev_1 = StdDevUncertainty(uncert, unit="m")
+    uncertainty_stddev_2 = StdDevUncertainty([2], unit="m")
+    uncertainty_unknown_1 = UnknownUncertainty(uncert, unit="m")
+    uncertainty_unknown_2 = UnknownUncertainty([0.4], unit=u.adu)
+    uncertainty_variance_1 = VarianceUncertainty(uncert, unit="m")
+    uncertainty_variance_2 = VarianceUncertainty([0.4], unit=u.adu)
+    return [
+        uncertainty_stddev_1,
+        uncertainty_stddev_2,
+        uncertainty_unknown_1,
+        uncertainty_unknown_2,
+        uncertainty_variance_1,
+        uncertainty_variance_2,
+    ]
+
+
+@pytest.mark.parametrize("uncertainty", create_uncertainty())
+def test_uncertainty_serialization(uncertainty, tmp_path):
+    file_path = tmp_path / "test_uncertainty.asdf"
+    with asdf.AsdfFile() as af:
+        af["uncertainty"] = uncertainty
+        af.write_to(file_path)
+
+    with asdf.open(file_path) as af:
+        loaded_uncert = af["uncertainty"]
+        assert type(loaded_uncert) == type(uncertainty)
+        assert (loaded_uncert._array == uncertainty._array).all()
+        assert loaded_uncert.unit == uncertainty.unit

asdf_astropy/converters/nddata/uncertainty.py

@@ -0,0 +1,35 @@
+class UncertaintyConverter:
+    tags = ("tag:astropy.org:astropy/nddata/uncertainty-*",)
+    types = (
+        "astropy.nddata.nduncertainty.StdDevUncertainty",
+        "astropy.nddata.nduncertainty.UnknownUncertainty",
+        "astropy.nddata.nduncertainty.VarianceUncertainty",
+    )
+
+    # Mapping of uncertainty class name (attribute of astropy.nddata)
+    # and code "name" stored in the data file.
+    # This will need to be separately versioned if the schema is updated.
+    _class_name_to_code = {
+        "StdDevUncertainty": "stddev",
+        "UnknownUncertainty": "unknown",
+        "VarianceUncertainty": "variance",
+    }
+    _class_code_to_name = {v: k for k, v in _class_name_to_code.items()}
+
+    def from_yaml_tree(self, node, tag, ctx):
+        import astropy.nddata
+
+        class_name = self._class_code_to_name[node["name"]]
+
+        return getattr(astropy.nddata, class_name)(node["array"], unit=node.get("unit"))
+
+    def to_yaml_tree(self, obj, tag, ctx):
+        node = {
+            "name": self._class_name_to_code[obj.__class__.__name__],
+            "array": obj.array,
+        }
+
+        if obj.unit is not None:
+            node["unit"] = obj.unit
+
+        return node

asdf_astropy/extensions.py

@@ -12,6 +12,7 @@
 from .converters.coordinates.sky_coord import SkyCoordConverter
 from .converters.coordinates.spectral_coord import SpectralCoordConverter
 from .converters.fits.fits import AsdfFitsConverter, AstropyFitsConverter
+from .converters.nddata.uncertainty import UncertaintyConverter
 from .converters.table.table import AsdfTableConverter, AstropyTableConverter, ColumnConverter, NdarrayMixinConverter
 from .converters.time.time import TimeConverter
 from .converters.time.time_delta import TimeDeltaConverter
@@ -476,6 +477,7 @@
     AstropyTableConverter(),
     AstropyFitsConverter(),
     NdarrayMixinConverter(),
+    UncertaintyConverter(),
 ]
 
 _COORDINATES_MANIFEST_URIS = [
@@ -493,6 +495,7 @@
 
 
 _ASTROPY_EXTENSION_MANIFEST_URIS = [
+    "asdf://astropy.org/astropy/manifests/astropy-1.3.0",
     "asdf://astropy.org/astropy/manifests/astropy-1.2.0",
     "asdf://astropy.org/astropy/manifests/astropy-1.1.0",
     "asdf://astropy.org/astropy/manifests/astropy-1.0.0",

asdf_astropy/resources/manifests/astropy-1.2.0.yaml

@@ -6,15 +6,15 @@ description: |-
   model classes, which are handled by an implementation of the ASDF
   transform extension.
 asdf_standard_requirement:
-  gte: 1.6.0
+  gte: 1.1.0
 tags:
-- tag_uri: tag:astropy.org:astropy/time/timedelta-1.1.0
-  schema_uri: http://astropy.org/schemas/astropy/time/timedelta-1.1.0
+- tag_uri: tag:astropy.org:astropy/time/timedelta-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/time/timedelta-1.0.0
   title: Represents an instance of TimeDelta from astropy
   description: |-
     Represents the time difference between two times.
-- tag_uri: tag:astropy.org:astropy/fits/fits-1.1.0
-  schema_uri: http://astropy.org/schemas/astropy/fits/fits-1.1.0
+- tag_uri: tag:astropy.org:astropy/fits/fits-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/fits/fits-1.0.0
   title: A FITS file inside of an ASDF file.
   description: |-
     This schema is useful for distributing ASDF files that can
@@ -28,12 +28,12 @@ tags:
     be accessible in its proper form in the ASDF file.
 
     Only image and binary table extensions are supported.
-- tag_uri: tag:astropy.org:astropy/table/table-1.2.0
-  schema_uri: http://astropy.org/schemas/astropy/table/table-1.2.0
+- tag_uri: tag:astropy.org:astropy/table/table-1.1.0
+  schema_uri: http://astropy.org/schemas/astropy/table/table-1.1.0
   title: A table.
   description: |-
     A table is represented as a list of columns, where each entry is a
-    [column](ref:http://stsci.edu/schemas/asdf/table/column-1.1.0)
+    [column](ref:http://stsci.edu/schemas/asdf/core/column-1.0.0)
     object, containing the data and some additional information.
 
     The data itself may be stored inline as text, or in binary in either
@@ -42,8 +42,8 @@ tags:
 
     Each column in the table must have the same first (slowest moving)
     dimension.
-- tag_uri: tag:astropy.org:astropy/transform/units_mapping-1.1.0
-  schema_uri: http://astropy.org/schemas/astropy/transform/units_mapping-1.1.0
+- tag_uri: tag:astropy.org:astropy/transform/units_mapping-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/transform/units_mapping-1.0.0
   title: Mapper that operates on the units of the input.
   description: |-
     This transform operates on the units of the input, first converting to
@@ -54,3 +54,8 @@ tags:
   title: NdarrayMixin column.
   description: |-
     Represents an astropy.table.NdarrayMixin instance.
+- tag_uri: tag:astropy.org:astropy/nddata/uncertainty-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/nddata/uncertainty-1.0.0
+  title: Represent an astropy.nddata uncertainty
+  description: |-
+    Represents an instance of an astropy.nddata uncertainty

asdf_astropy/resources/manifests/astropy-1.3.0.yaml

@@ -0,0 +1,61 @@
+id: asdf://astropy.org/astropy/manifests/astropy-1.3.0
+extension_uri: asdf://astropy.org/astropy/extensions/astropy-1.3.0
+title: Astropy extension 1.3.0
+description: |-
+  A set of tags for serializing astropy objects.  This does not include most
+  model classes, which are handled by an implementation of the ASDF
+  transform extension.
+asdf_standard_requirement:
+  gte: 1.6.0
+tags:
+- tag_uri: tag:astropy.org:astropy/time/timedelta-1.1.0
+  schema_uri: http://astropy.org/schemas/astropy/time/timedelta-1.1.0
+  title: Represents an instance of TimeDelta from astropy
+  description: |-
+    Represents the time difference between two times.
+- tag_uri: tag:astropy.org:astropy/fits/fits-1.1.0
+  schema_uri: http://astropy.org/schemas/astropy/fits/fits-1.1.0
+  title: A FITS file inside of an ASDF file.
+  description: |-
+    This schema is useful for distributing ASDF files that can
+    automatically be converted to FITS files by specifying the exact
+    content of the resulting FITS file.
+
+    Not all kinds of data in FITS are directly representable in ASDF.
+    For example, applying an offset and scale to the data using the
+    `BZERO` and `BSCALE` keywords.  In these cases, it will not be
+    possible to store the data in the native format from FITS and also
+    be accessible in its proper form in the ASDF file.
+
+    Only image and binary table extensions are supported.
+- tag_uri: tag:astropy.org:astropy/table/table-1.2.0
+  schema_uri: http://astropy.org/schemas/astropy/table/table-1.2.0
+  title: A table.
+  description: |-
+    A table is represented as a list of columns, where each entry is a
+    [column](ref:http://stsci.edu/schemas/asdf/table/column-1.1.0)
+    object, containing the data and some additional information.
+
+    The data itself may be stored inline as text, or in binary in either
+    row- or column-major order by use of the `strides` property on the
+    individual column arrays.
+
+    Each column in the table must have the same first (slowest moving)
+    dimension.
+- tag_uri: tag:astropy.org:astropy/transform/units_mapping-1.1.0
+  schema_uri: http://astropy.org/schemas/astropy/transform/units_mapping-1.1.0
+  title: Mapper that operates on the units of the input.
+  description: |-
+    This transform operates on the units of the input, first converting to
+    the expected input units, then assigning replacement output units without
+    further conversion.
+- tag_uri: tag:astropy.org:astropy/table/ndarraymixin-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/table/ndarraymixin-1.0.0
+  title: NdarrayMixin column.
+  description: |-
+    Represents an astropy.table.NdarrayMixin instance.
+- tag_uri: tag:astropy.org:astropy/nddata/uncertainty-1.0.0
+  schema_uri: http://astropy.org/schemas/astropy/nddata/uncertainty-1.0.0
+  title: Represent an astropy.nddata uncertainty
+  description: |-
+    Represents an instance of an astropy.nddata uncertainty

asdf_astropy/resources/schemas/nddata/uncertainty-1.0.0.yaml

@@ -0,0 +1,22 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "http://astropy.org/schemas/astropy/nddata/uncertainty-1.0.0"
+
+title: Represents an astropy.nddata uncertainty class
+
+description: >-
+  This object represents an uncertainty.
+
+allOf:
+  - type: object
+    properties:
+      name:
+        enum: ["stddev", "unknown", "variance"]
+      array:
+        type: object
+      unit:
+        anyOf:
+          - tag: "tag:stsci.edu:asdf/unit/unit-*"
+          - tag: "tag:astropy.org:astropy/units/unit-1.*"
+    required: [name, array]

docs/asdf-astropy/schemas.rst

@@ -30,6 +30,19 @@ fits/fits-1.0.0
 
     fits/fits-1.0.0
 
+NDData
+------
+
+The following schemas are associated with **astropy** objects from the
+:ref:`astropy_nddata` submodule:
+
+nddata/uncertainty-1.0.0
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. asdf-autoschemas::
+
+    nddata/uncertainty-1.0.0
+
 Table
 -----
 

pyproject.toml

@@ -96,6 +96,7 @@ extend-ignore = [
     # Individually ignored checks
     "SLF001", # private-member-access
     "FBT001", # boolean positional arguments in function definition
+    "RUF012", # mutable class attributes should be annotated with typing.ClassVar
 ]
 extend-exclude = ["docs/*"]