Merge pull request #297 from scverse/fix/generic

Small fixes generic reader and cli

Author: LucaMarconato

src/spatialdata_io/__main__.py

@@ -621,8 +621,8 @@ def macsima_wrapper(
 @click.option("--name", "-n", type=str, help="name of the element to be stored")
 @click.option(
     "--data-axes",
-    type=click.Choice(["cyx", "czyx"], case_sensitive=False),
-    help="Axes of the data for image files. Valid values are 'cyx' and 'czyx'.",
+    type=str,
+    help="Axes of the data for image files. Valid values are permutations of 'cyx' and 'czyx'.",
 )
 @click.option(
     "--coordinate-system",
@@ -638,6 +638,8 @@ def read_generic_wrapper(
     coordinate_system: str | None = None,
 ) -> None:
     """Read generic data to SpatialData"""
+    if data_axes is not None and "".join(sorted(data_axes)) not in ["cxy", "cxyz"]:
+        raise ValueError("data_axes must be a permutation of 'cyx' or 'czyx'.")
     generic_to_zarr(input=input, output=output, name=name, data_axes=data_axes, coordinate_system=coordinate_system)
 
 

src/spatialdata_io/converters/generic_to_zarr.py

@@ -69,14 +69,14 @@ def generic_to_zarr(
     )
 
     if output.exists():
-        sdata = SpatialData.read_zarr(output)
+        sdata = SpatialData.read(output)
         if name in sdata:
             raise ValueError(
                 f"Name {name} already exists in {output}; please provide a different name or delete the "
                 f"existing element."
             )
         sdata[name] = element
-        sdata.write_element(name, element_name=name)
+        sdata.write_element(element_name=name)
         print(f"Element {name} written to {output}")
     else:
         sdata = SpatialData.init_from_elements(elements={name: element})

src/spatialdata_io/readers/generic.py

@@ -49,6 +49,8 @@ def generic(
     -------
     Parsed spatial element.
     """
+    if isinstance(input, str):
+        input = Path(input)
     if coordinate_system is None:
         coordinate_system = DEFAULT_COORDINATE_SYSTEM
     if input.suffix in VALID_SHAPE_TYPES: