Points class metadata

[giovp]

Following #12 and #16 we should find a consensus on how to store points "metadata".

Visium points

• centroid coordinates as array in adata.obsm["spatial"]
• radius/diameter as attribute in Points class and stored in .zattr following closely how current metadata is store ome-ngff
• radius/diameter transform (one scalar value for scaling), following closely ome-zarr metadata (see

  spatialdata/spatialdata/_io/write.py

  Lines 20 to 62 in ea5dae6

  	def _write_metadata(
  	group: zarr.Group,
  	group_type: str,
  	shape: Tuple[int, ...],
  	attr: Optional[Mapping[str, Optional[str]]] = MappingProxyType({"attr": "X", "key": None}),
  	fmt: Format = SpatialDataFormat(),
  	axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
  	coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
  	**metadata: Union[str, JSONDict, List[JSONDict]],
  	) -> None:
  	"""Write metdata to a group."""
  	dims = len(shape)
  	axes = _get_valid_axes(dims, axes, fmt)
  	datasets: List[Dict[str, Any]] = []
  	datasets.append({"path": attr})
  	if coordinate_transformations is None:
  	shape = [shape] # type: ignore[assignment]
  	coordinate_transformations = fmt.generate_coordinate_transformations(shape)
  	fmt.validate_coordinate_transformations(dims, 1, coordinate_transformations)
  	if coordinate_transformations is not None:
  	for dataset, transform in zip(datasets, coordinate_transformations):
  	dataset["coordinateTransformations"] = transform
  	if axes is not None:
  	axes = _get_valid_axes(axes=axes, fmt=fmt)
  	if axes is not None:
  	ndim = len(axes)
  	multiscales = [
  	dict(
  	version=fmt.version,
  	datasets=_validate_datasets(datasets, ndim, fmt),
  	**metadata,
  	)
  	]
  	if axes is not None:
  	multiscales[0]["axes"] = axes
  	group.attrs["@type"] = group_type
  	group.attrs["multiscales"] = multiscales

  )

Transcript points

• would start by just pickling the kdtree (possibly within anndata) and store path in .zattr

[LucaMarconato]

As I explained here #12 (comment) at the moment I am storing the points metadata in a slightly different way due to practical coding convenience since I want to finish implementing a fully functional io and interactive viz. Then we should explore the alternatives, set a convention a refactor the code (will be quick).