update spatial data schema

CHANGELOG.rst

@@ -28,8 +28,14 @@ documentation
 ASDF
 ====
 
+-  update weldx extension and manifest version to ``0.1.1`` [:pull:`655`]
+
 -  removed legacy ``weldx`` tag and schema support [:pull:`600`]
 
+-  update `core/geometry/spatial_data` to version `0.1.1` with support for multidimensional data [:pull:`655`]
+
+-  add ``wx_shape`` validation support for ``core/data_array`` [:pull:`655`]
+
 deprecations
 ============
 

devtools/scripts/update_manifest.py

@@ -2,12 +2,17 @@
 
 import yaml
 
+from weldx.asdf.constants import (
+    WELDX_EXTENSION_URI,
+    WELDX_EXTENSION_VERSION,
+    WELDX_MANIFEST_URI,
+)
 from weldx.asdf.util import get_converter_for_tag
 
 
 def update_manifest(
     search_dir: str = "../../weldx/schemas",
-    out: str = "../../weldx/manifests/weldx-0.1.0.yaml",
+    out: str = f"../../weldx/manifests/weldx-{WELDX_EXTENSION_VERSION}.yaml",
 ):
     """Create manifest file from existing schemas."""
     # read existing manifest
@@ -16,6 +21,9 @@ def update_manifest(
         Loader=yaml.SafeLoader,
     )
 
+    manifest["id"] = WELDX_MANIFEST_URI
+    manifest["extension_uri"] = WELDX_EXTENSION_URI
+
     # keep only ASDF schema mappings
     manifest["tags"] = [
         mapping

weldx/asdf/constants.py

@@ -8,5 +8,7 @@
 WELDX_SCHEMA_URI_BASE = "asdf://weldx.bam.de/weldx/schemas/"
 WELDX_EXTENSION_URI_BASE = "asdf://weldx.bam.de/weldx/extensions/"
 
-WELDX_EXTENSION_VERSION = "0.1.0"
+WELDX_EXTENSION_VERSION = "0.1.1"
 WELDX_EXTENSION_URI = f"{WELDX_EXTENSION_URI_BASE}weldx-{WELDX_EXTENSION_VERSION}"
+
+WELDX_MANIFEST_URI = WELDX_URI_BASE + "manifests/weldx-" + WELDX_EXTENSION_VERSION

weldx/asdf/util.py

@@ -481,7 +481,7 @@ def get_converter_for_tag(tag: str) -> Union[WeldxConverter, None]:
 
 
 def get_highest_tag_version(
-    pattern: str, ctx: Union[SerializationContext, AsdfConfig] = None
+    pattern: Union[str, List[str]], ctx: Union[SerializationContext, AsdfConfig] = None
 ) -> Union[str, None]:
     """Get the highest available weldx extension tag version matching a pattern.
 

weldx/manifests/weldx-0.1.1.yaml

@@ -0,0 +1,128 @@
+%YAML 1.1
+---
+id: asdf://weldx.bam.de/weldx/manifests/weldx-0.1.1
+extension_uri: asdf://weldx.bam.de/weldx/extensions/weldx-0.1.1
+title: weldx extension manifest for tag mapping
+description: Manifest listing all tag URIs with schema URIs supported by weldx
+tags:
+- tag_uri: tag:stsci.edu:asdf/unit/quantity-1.1.0
+  schema_uri: http://stsci.edu/schemas/asdf/unit/quantity-1.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/uuid-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/uuid-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/base_metal-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/base_metal-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/connection-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/connection-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/joint_penetration-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/joint_penetration-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/sub_assembly-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/sub_assembly-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/weldment-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/weldment-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/weld_details-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/weld_details-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/design/workpiece-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/design/workpiece-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/process/arc_welding_process-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/process/arc_welding_process-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/process/gas_component-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/process/gas_component-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/process/shielding_gas_for_procedure-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/process/shielding_gas_for_procedure-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/aws/process/shielding_gas_type-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/aws/process/shielding_gas_type-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/dataset-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/dataset-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/data_array-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/data_array-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/dimension-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/dimension-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/file-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/file-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/mathematical_expression-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/mathematical_expression-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/time_series-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/time_series-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/variable-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/variable-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/geometry/spatial_data-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/geometry/spatial_data-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/geometry/spatial_data-0.1.1
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/geometry/spatial_data-0.1.1
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/graph/di_edge-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/graph/di_edge-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/graph/di_graph-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/graph/di_graph-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/graph/di_node-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/graph/di_node-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/transformations/coordinate_system_hierarchy-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/transformations/coordinate_system_hierarchy-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/transformations/local_coordinate_system-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/transformations/local_coordinate_system-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/core/transformations/rotation-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/core/transformations/rotation-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/debug/test_property_tag-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/debug/test_property_tag-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/debug/test_shape_validator-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/debug/test_shape_validator-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/debug/test_unit_validator-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/debug/test_unit_validator-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/equipment/measurement_equipment-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/equipment/measurement_equipment-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/DHUGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/DHUGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/DHVGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/DHVGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/DUGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/DUGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/DVGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/DVGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/FFGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/FFGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/HUGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/HUGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/HVGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/HVGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/IGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/IGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/UGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/UGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/UVGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/UVGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/VGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/VGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/groove/iso_9692_1_2013_12/VVGroove-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/groove/iso_9692_1_2013_12/VVGroove-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/error-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/error-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/measurement-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/measurement-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/measurement_chain-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/measurement_chain-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/signal-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/signal-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/signal_transformation-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/signal_transformation-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/measurement/source-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/measurement/source-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/process/GMAW-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/process/GMAW-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/process/CLOOS/pulse-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/process/CLOOS/pulse-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/process/CLOOS/spray_arc-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/process/CLOOS/spray_arc-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/time/datetimeindex-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/time/datetimeindex-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/time/time-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/time/time-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/time/timedelta-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/time/timedelta-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/time/timedeltaindex-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/time/timedeltaindex-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/time/timestamp-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/time/timestamp-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/units/quantity-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/units/quantity-0.1.0
+- tag_uri: asdf://weldx.bam.de/weldx/tags/units/units-0.1.0
+  schema_uri: asdf://weldx.bam.de/weldx/schemas/units/units-0.1.0
+...

weldx/schemas/weldx.bam.de/weldx/core/geometry/spatial_data-0.1.1.yaml

@@ -0,0 +1,90 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/yaml-schema/draft-01"
+id: "asdf://weldx.bam.de/weldx/schemas/core/geometry/spatial_data-0.1.1"
+
+title: |
+  Schema for a point cloud.
+description: |
+  This schema describes a collection of data points in 3d space.
+
+examples:
+  -
+    - A simple `SpatialData` with triangulation
+    - |
+      !<asdf://weldx.bam.de/weldx/tags/core/geometry/spatial_data-0.1.1>
+        coordinates: !core/ndarray-1.0.0
+          data:
+          - [0.0, 0.0, 0.0]
+          - [1.0, 0.0, 0.0]
+          - [1.0, 1.0, 0.0]
+          - [0.0, 1.0, 0.0]
+          datatype: float64
+          shape: [4, 3]
+        triangles: !core/ndarray-1.0.0
+          data:
+          - [0, 1, 2]
+          - [2, 3, 0]
+          datatype: uint32
+          shape: [2, 3]
+  -
+    - A `SpatialData` object with data in three dimensions
+    - |
+      !<asdf://weldx.bam.de/weldx/tags/core/geometry/spatial_data-0.1.1>
+        coordinates: !<asdf://weldx.bam.de/weldx/tags/core/data_array-0.1.0>
+          attributes: {}
+          coordinates:
+          - !<asdf://weldx.bam.de/weldx/tags/core/variable-0.1.0>
+            name: c
+            dimensions: [c]
+            dtype: <U1
+            data: !core/ndarray-1.0.0
+              data: [x, y, z]
+              datatype: [ucs4, 1]
+              shape: [3]
+          data: !<asdf://weldx.bam.de/weldx/tags/core/variable-0.1.0>
+            name: data
+            dimensions: [p, n, c]
+            dtype: <f8
+            data: !core/ndarray-1.0.0
+              data:
+              - - [0.0, 0.0, 0.0]
+                - [0.0, 1.0, 0.0]
+              - - [1.0, 0.0, 1.0]
+                - [0.0, 1.0, 1.0]
+              datatype: float64
+              shape: [2, 2, 3]
+
+type: object
+properties:
+  coordinates:
+    description: |
+      The coordinates of the data points.
+    oneOf:
+      - tag: "tag:stsci.edu:asdf/core/ndarray-1.*"
+        properties:
+          datatype:
+            type: string
+            enum: [float32, float64]
+        wx_shape: [(~), 3]
+      - tag: "asdf://weldx.bam.de/weldx/tags/core/data_array-0.1.*"
+        wx_shape: [..., 3]
+  attributes:
+    description: |
+      An arbitrary set of attributes. For example, normals, colors or measured point data can be stored using this
+      field. Each added attribute is an array with a number of data points equal to the number of points.
+    type: object
+  triangles:
+    description: |
+      An array of index triplets that specify which points form a triangle
+    tag: "tag:stsci.edu:asdf/core/ndarray-1.*"
+    properties:
+      datatype:
+        type: string
+        enum: [uint32, uint64]
+    wx_shape: [(~), 3]
+
+propertyOrder: [coordinates, attributes, triangles]
+required: [coordinates]
+flowStyle: block
+...

weldx/tags/core/data_array.py

@@ -1,8 +1,12 @@
 """Serialization for xarray.DataArray."""
+from typing import List
+
+from asdf.tagged import TaggedDict
 from xarray import DataArray
 
 import weldx.tags.core.common_types as ct
 from weldx.asdf.types import WeldxConverter
+from weldx.asdf.util import _get_instance_shape
 
 
 class XarrayDataArrayConverter(WeldxConverter):
@@ -41,3 +45,8 @@ def from_yaml_tree(self, node: dict, tag: str, ctx):
         # (but since it gets automatically derived if not set, we define it now.
 
         return da
+
+    @staticmethod
+    def shape_from_tagged(node: TaggedDict) -> List[int]:
+        """Calculate the shape from static tagged tree instance."""
+        return _get_instance_shape(node["data"]["data"])

weldx/tags/core/geometry/spatial_data.py

@@ -1,27 +1,29 @@
-from copy import deepcopy
+from copy import copy
 
-import numpy as np
-
-from weldx.asdf.util import dataclass_serialization_class
+from weldx.asdf.types import WeldxConverter
+from weldx.asdf.util import get_highest_tag_version
 from weldx.geometry import SpatialData
 
+__all__ = ["SpatialDataConverter"]
+
 
-def _to_yaml_tree_mod(tree):
-    tree = deepcopy(tree)
-    tree["coordinates"] = tree["coordinates"].data
-    return tree
+class SpatialDataConverter(WeldxConverter):
+    """Converter for SpatialData."""
 
+    tags = ["asdf://weldx.bam.de/weldx/tags/core/geometry/spatial_data-0.1.*"]
+    types = [SpatialData]
 
-def _from_yaml_tree_mod(tree):
-    if "coordinates" in tree:
-        tree["coordinates"] = np.asarray(tree["coordinates"])
-    return tree
+    def to_yaml_tree(self, obj: SpatialData, tag: str, ctx) -> dict:
+        """Serialize into tree."""
+        tree = copy(obj.__dict__)  # shallow copy so we dont change original object
+        if tree["coordinates"].ndim <= 2:
+            tree["coordinates"] = tree["coordinates"].values
+        return tree
 
+    def from_yaml_tree(self, node: dict, tag: str, ctx) -> SpatialData:
+        """Reconstruct from yaml node."""
+        return SpatialData(**node)
 
-SpatialDataConverter = dataclass_serialization_class(
-    class_type=SpatialData,
-    class_name="core/geometry/spatial_data",
-    version="0.1.0",
-    to_yaml_tree_mod=_to_yaml_tree_mod,
-    from_yaml_tree_mod=_from_yaml_tree_mod,
-)
+    def select_tag(self, obj, tags, ctx) -> str:
+        """Determine the output tag for serialization."""
+        return get_highest_tag_version(self.tags)

weldx/tests/asdf_tests/test_asdf_core.py

@@ -720,23 +720,28 @@ class TestPointCloud:
     @staticmethod
     @pytest.mark.parametrize("copy_arrays", [True, False])
     @pytest.mark.parametrize("lazy_load", [True, False])
-    def test_asdf_serialization(copy_arrays, lazy_load):
+    @pytest.mark.parametrize("reshape", [True, False])
+    def test_asdf_serialization(copy_arrays, lazy_load, reshape):
+        time = None
         coordinates = [
             [0.0, 0.0, 0.0],
             [1.0, 0.0, 0.0],
             [1.0, 1.0, 0.0],
             [0.0, 1.0, 0.0],
         ]
-
         triangles = [[0, 1, 2], [2, 3, 0]]
 
-        pc = SpatialData(coordinates=coordinates, triangles=triangles)
+        if reshape:
+            coordinates = np.array(coordinates).reshape((2, 2, 3))
+            time = ["0s", "1s"]
+
+        pc = SpatialData(coordinates=coordinates, triangles=triangles, time=time)
         tree = {"point_cloud": pc}
         pc_file = write_read_buffer(
             tree, open_kwargs={"copy_arrays": copy_arrays, "lazy_load": lazy_load}
         )["point_cloud"]
 
-        assert np.all(pc_file.coordinates == pc.coordinates)
+        assert pc_file == pc
 
 
 # --------------------------------------------------------------------------------------