Asdf-Support

ndcube/asdf/converters/extracoords_converter.py

@@ -0,0 +1,29 @@
+from asdf.extension import Converter
+
+
+class ExtraCoordsConverter(Converter):
+    tags = ["tag:sunpy.org:ndcube/extra_coords/extra_coords/ExtraCoords-*"]
+    types = ["ndcube.extra_coords.extra_coords.ExtraCoords"]
+
+    def from_yaml_tree(self, node, tag, ctx):
+        from ndcube.extra_coords.extra_coords import ExtraCoords
+        extra_coords = ExtraCoords()
+        extra_coords._wcs = node.get("wcs")
+        extra_coords._mapping = node.get("mapping")
+        if "lookup_tables" in node:
+            extra_coords._lookup_tables = node.get("lookup_tables")
+        extra_coords._dropped_tables = node.get("dropped_tables")
+        extra_coords._ndcube = node.get("ndcube")
+        return extra_coords
+
+    def to_yaml_tree(self, extracoords, tag, ctx):
+        node = {}
+        if extracoords._wcs is not None:
+            node["wcs"] = extracoords._wcs
+        if extracoords._mapping is not None:
+            node["mapping"] = extracoords._mapping
+        if extracoords._lookup_tables:
+            node["lookup_tables"] = extracoords._lookup_tables
+        node["dropped_tables"] = extracoords._dropped_tables
+        node["ndcube"] = extracoords._ndcube
+        return node

ndcube/asdf/converters/ndcube_converter.py

@@ -0,0 +1,26 @@
+import numpy as np
+
+from asdf.extension import Converter
+
+
+class NDCubeConverter(Converter):
+    tags = ["tag:sunpy.org:ndcube/ndcube/NDCube-*"]
+    types = ["ndcube.ndcube.NDCube"]
+
+    def from_yaml_tree(self, node, tag, ctx):
+        from ndcube.ndcube import NDCube
+
+        data = np.asanyarray(node["data"])
+        wcs = node["wcs"]
+        ndcube = NDCube(data, wcs)
+        ndcube._extra_coords = node["extra_coords"]
+
+        return ndcube
+
+    def to_yaml_tree(self, ndcube, tag, ctx):
+        node = {}
+        node["data"] = np.asarray(ndcube.data)
+        node["wcs"] = ndcube.wcs
+        node["extra_coords"] = ndcube.extra_coords
+
+        return node

ndcube/asdf/converters/tablecoord_converter.py

@@ -0,0 +1,85 @@
+from asdf.extension import Converter
+
+
+class TimeTableCoordConverter(Converter):
+    tags = ["tag:sunpy.org:ndcube/extra_coords/table_coord/TimeTableCoordinate-*"]
+    types = ["ndcube.extra_coords.table_coord.TimeTableCoordinate"]
+
+    def from_yaml_tree(self, node, tag, ctx):
+        from ndcube.extra_coords.table_coord import TimeTableCoordinate
+
+        table = node.get("table")
+        names = node.get("names")
+        physical_types = node.get("physical_types")
+        reference_time = node.get("reference_time")
+        timetablecoordinate = TimeTableCoordinate(
+            table, names=names, physical_types=physical_types, reference_time=reference_time)
+
+        return timetablecoordinate
+
+    def to_yaml_tree(self, timetablecoordinate, tag, ctx):
+        node = {}
+        node["table"] = timetablecoordinate.table
+        node["names"] = timetablecoordinate.names
+        node["mesh"] = timetablecoordinate.mesh
+        if timetablecoordinate.physical_types is not None:
+            node["physical_types"] = timetablecoordinate.physical_types
+        node["reference_time"] = timetablecoordinate.reference_time
+
+        return node
+
+
+class QuantityTableCoordinateConverter(Converter):
+    tags = ["tag:sunpy.org:ndcube/extra_coords/table_coord/QuantityTableCoordinate-*"]
+    types = ["ndcube.extra_coords.table_coord.QuantityTableCoordinate"]
+
+    def from_yaml_tree(self, node, tag, ctx):
+        from ndcube.extra_coords.table_coord import QuantityTableCoordinate
+
+        unit = node.get("unit")
+        table = node.get("table")
+        names = node.get("names")
+        mesh = node.get("mesh")
+        physical_types = node.get("physical_types")
+        quantitytablecoordinate = QuantityTableCoordinate(*table,
+                                                          names=names, physical_types=physical_types,)
+        quantitytablecoordinate.unit = unit
+        quantitytablecoordinate.mesh = mesh
+        return quantitytablecoordinate
+
+    def to_yaml_tree(self, quantitytablecoordinate, tag, ctx):
+        node = {}
+        node["unit"] = quantitytablecoordinate.unit
+        node["table"] = quantitytablecoordinate.table
+        node["names"] = quantitytablecoordinate.names
+        node["mesh"] = quantitytablecoordinate.mesh
+        if quantitytablecoordinate.physical_types is not None:
+            node["physical_types"] = quantitytablecoordinate.physical_types
+
+        return node
+
+
+class SkyCoordTableCoordinateConverter(Converter):
+    tags = ["tag:sunpy.org:ndcube/extra_coords/table_coord/SkyCoordTableCoordinate-*"]
+    types = ["ndcube.extra_coords.table_coord.SkyCoordTableCoordinate"]
+
+    def from_yaml_tree(self, node, tag, ctx):
+        from ndcube.extra_coords.table_coord import SkyCoordTableCoordinate
+
+        table = node.get("table")
+        names = node.get("names")
+        mesh = node.get("mesh")
+        physical_types = node.get("physical_types")
+        skycoordinatetablecoordinate = SkyCoordTableCoordinate(table, mesh=mesh,
+                                                               names=names, physical_types=physical_types)
+        return skycoordinatetablecoordinate
+
+    def to_yaml_tree(self, skycoordinatetablecoordinate, tag, ctx):
+        node = {}
+        node["table"] = skycoordinatetablecoordinate.table
+        node["names"] = skycoordinatetablecoordinate.names
+        node["mesh"] = skycoordinatetablecoordinate.mesh
+        if skycoordinatetablecoordinate.physical_types is not None:
+            node["physical_types"] = skycoordinatetablecoordinate.physical_types
+
+        return node

ndcube/asdf/entry_points.py

@@ -0,0 +1,47 @@
+"""
+This file contains the entry points for asdf.
+"""
+import importlib.resources as importlib_resources
+
+from asdf.extension import ManifestExtension
+from asdf.resource import DirectoryResourceMapping
+
+
+def get_resource_mappings():
+    """
+    Get the resource mapping instances for myschemas
+    and manifests.  This method is registered with the
+    asdf.resource_mappings entry point.
+
+    Returns
+    -------
+    list of collections.abc.Mapping
+    """
+    from ndcube.asdf import resources
+    resources_root = importlib_resources.files(resources)
+    return [
+        DirectoryResourceMapping(
+            resources_root / "schemas", "asdf://sunpy.org/ndcube/schemas/"),
+        DirectoryResourceMapping(
+            resources_root / "manifests", "asdf://sunpy.org/ndcube/manifests/"),
+    ]
+
+
+def get_extensions():
+    """
+    Get the list of extensions.
+    """
+    from ndcube.asdf.converters.extracoords_converter import ExtraCoordsConverter
+    from ndcube.asdf.converters.ndcube_converter import NDCubeConverter
+    from ndcube.asdf.converters.tablecoord_converter import (
+        QuantityTableCoordinateConverter,
+        SkyCoordTableCoordinateConverter,
+        TimeTableCoordConverter,
+    )
+
+    ndcube_converters = [NDCubeConverter(),ExtraCoordsConverter(),TimeTableCoordConverter(),QuantityTableCoordinateConverter(),SkyCoordTableCoordinateConverter()]
+    _manifest_uri = "asdf://sunpy.org/ndcube/manifests/ndcube-0.1.0"
+
+    return [
+        ManifestExtension.from_uri(_manifest_uri, converters=ndcube_converters)
+    ]

ndcube/asdf/resources/manifests/ndcube-0.1.0.yaml

@@ -0,0 +1,22 @@
+%YAML 1.1
+---
+id: asdf://sunpy.org/ndcube/manifests/ndcube-0.1.0
+extension_uri: asdf://sunpy.org/extensions/ndcube-0.1.0
+title: NDCube ASDF Manifest
+description: ASDF schemas and tags for NDCube classes.
+
+tags:
+  - tag_uri: "tag:sunpy.org:ndcube/ndcube/NDCube-0.1.0"
+    schema_uri: "asdf://sunpy.org/ndcube/schemas/NDCube-0.1.0"
+
+  - tag_uri:  "tag:sunpy.org:ndcube/extra_coords/extra_coords/ExtraCoords-0.1.0"
+    schema_uri: "asdf://sunpy.org/ndcube/schemas/ExtraCoords-0.1.0"
+
+  - tag_uri:  "tag:sunpy.org:ndcube/extra_coords/table_coord/TimeTableCoordinate-0.1.0"
+    schema_uri: "asdf://sunpy.org/ndcube/schemas/TimeTableCoordinate-0.1.0"
+
+  - tag_uri:  "tag:sunpy.org:ndcube/extra_coords/table_coord/QuantityTableCoordinate-0.1.0"
+    schema_uri: "asdf://sunpy.org/ndcube/schemas/QuantityTableCoordinate-0.1.0"
+
+  - tag_uri:  "tag:sunpy.org:ndcube/extra_coords/table_coord/SkyCoordTableCoordinate-0.1.0"
+    schema_uri: "asdf://sunpy.org/ndcube/schemas/SkyCoordTableCoordinate-0.1.0"

ndcube/asdf/resources/schemas/ExtraCoords-0.1.0.yaml

@@ -0,0 +1,34 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://sunpy.org/ndcube/schemas/ExtraCoords-0.1.0"
+
+title:
+  Represents the ndcube ExtraCoords object
+
+description:
+  Represents the ndcube ExtraCoords object
+
+type: object
+properties:
+  wcs:
+    tag: "tag:stsci.edu:gwcs/wcs-1.*"
+  mapping:
+    type: array
+  lookup_tables:
+    type: array
+    items:
+      type: array
+      properties:
+        index:
+          type: array
+        table:
+          $ref: "asdf://sunpy.org/ndcube/schemas/TimeTableCoordinate-0.1.0"
+  dropped_tables:
+    type: array
+  ndcube:
+    $ref: "asdf://sunpy.org/ndcube/schemas/NDCube-0.1.0"
+
+required: [ndcube]
+allowAdditionalProperties: False
+...

ndcube/asdf/resources/schemas/NDCube-0.1.0.yaml

@@ -0,0 +1,23 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://sunpy.org/ndcube/schemas/NDCube-0.1.0"
+
+title:
+  Represents the ndcube NDCube object
+
+description:
+  Represents the ndcube NDCube object
+
+type: object
+properties:
+  data:
+    tag: "tag:stsci.edu:asdf/core/ndarray-1.*"
+  wcs:
+    tag: "tag:stsci.edu:gwcs/wcs-1.*"
+  extra_coords:
+    $ref: "asdf://sunpy.org/ndcube/schemas/ExtraCoords-0.1.0"
+
+required: [data , wcs]
+allowAdditionalProperties: False
+...

ndcube/asdf/resources/schemas/QuantityTableCoordinate-0.1.0.yaml

@@ -0,0 +1,29 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://sunpy.org/ndcube/schemas/QuantityTableCoordinate-0.1.0"
+
+title:
+  Represents the QuantityTableCoords class
+
+description:
+  Represents the QuantityTableCoords class
+
+type: object
+properties:
+  unit:
+    tag: "tag:stsci.edu:asdf/unit/unit-*"
+  table:
+    type: array
+    properties:
+      tag: "tag:stsci.edu:asdf/unit/quantity-*"
+  names:
+    type: array
+  mesh:
+    type: boolean
+  physical_types:
+    type: array
+
+required: ["table"]
+additionalProperties: False
+...

ndcube/asdf/resources/schemas/SkyCoordTableCoordinate-0.1.0.yaml

@@ -0,0 +1,25 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://sunpy.org/ndcube/schemas/SkyCoordTableCoordinate-0.1.0"
+
+title:
+  Represents the SkyCoordTableCoordinate class
+
+description:
+  Represents the SkyCoordTableCoordinate class
+
+type: object
+properties:
+  table:
+    tag: "tag:astropy.org:astropy/coordinates/skycoord-*"
+  names:
+    type: array
+  mesh:
+    type: boolean
+  physical_types:
+    type: array
+
+required: ["table"]
+additionalProperties: False
+...

ndcube/asdf/resources/schemas/TimeTableCoordinate-0.1.0.yaml

@@ -0,0 +1,27 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://sunpy.org/ndcube/schemas/TimeTableCoordinate-0.1.0"
+
+title:
+  Represents the TimeTableCoords class
+
+description:
+  Represents the TimeTableCoords class
+
+type: object
+properties:
+  table:
+    tag: "tag:stsci.edu:asdf/time/time-1*"
+  names:
+    type: array
+  mesh:
+    type: boolean
+  physical_types:
+    type: array
+  reference_time:
+    tag: "tag:stsci.edu:asdf/time/time-1*"
+
+required: ["table"]
+additionalProperties: False
+...

pyproject.toml

@@ -72,6 +72,16 @@ exclude = ["ndcube._dev*"]
 [tool.setuptools_scm]
 write_to = "ndcube/_version.py"
 
+[tool.pytest.ini_options]
+asdf_schema_root = 'ndcube/asdf/resources/schemas'
+asdf_schema_tests_enabled = true
+
+[project.entry-points."asdf.resource_mappings"]
+ndcube = "ndcube.asdf.entry_points:get_resource_mappings"
+
+[project.entry-points."asdf.extensions"]
+ndcube = "ndcube.asdf.entry_points:get_extensions"
+
 [tool.towncrier]
     package = "ndcube"
     filename = "CHANGELOG.rst"

pytest.ini

@@ -25,6 +25,9 @@ addopts =
     -p no:threadexception
     -m "not mpl_image_compare"
     --doctest-ignore-import-errors
+asdf_schema_tests_enabled = true
+asdf_schema_root = ndcube/asdf/resources
+remote_data_strict = True
 filterwarnings =
     # Turn all warnings into errors so they do not pass silently.
     error
@@ -48,4 +51,3 @@ filterwarnings =
     ignore:Animating a NDCube does not support transposing the array. The world axes may not display as expected because the array will not be transposed:UserWarning
     # This is raised by the Windows and mac os build for visualization.rst
     ignore:FigureCanvasAgg is non-interactive, and thus cannot be shown:UserWarning
-remote_data_strict = True