reader always returns axes as list of dicts

ome_zarr/reader.py

@@ -11,6 +11,7 @@
 
 from .io import ZarrLocation
 from .types import JSONDict
+from .writer import axes_to_dicts
 
 LOGGER = logging.getLogger("ome_zarr.reader")
 
@@ -281,8 +282,10 @@ def __init__(self, node: Node) -> None:
                 "version", "0.1"
             )  # should this be matched with Format.version?
             datasets = multiscales[0]["datasets"]
-            axes = multiscales[0].get("axes")
-            # TODO - convert each axis to dictionary (if str or None)?
+            # axes field introduced in 0.3. If missing (v0.1 or v0.2) data will be 5d
+            axes = multiscales[0].get("axes", ["t", "c", "z", "y", "x"])
+            # if axis is list of strings, convert to v0.4+ format, as a list of dicts
+            axes = axes_to_dicts(axes)
             node.metadata["axes"] = axes
             datasets = [d["path"] for d in datasets]
             self.datasets: List[str] = datasets
@@ -298,11 +301,8 @@ def __init__(self, node: Node) -> None:
                 for c in data.chunks
             ]
             LOGGER.info("resolution: %s", resolution)
-            if axes is not None:
-                axes = tuple(
-                    axis if isinstance(axis, str) else axis.get("name") for axis in axes
-                )
-            LOGGER.info(" - shape %s = %s", axes, data.shape)
+            axis_names = tuple(axis.get("name") for axis in axes)
+            LOGGER.info(" - shape %s = %s", axis_names, data.shape)
             LOGGER.info(" - chunks =  %s", chunk_sizes)
             LOGGER.info(" - dtype = %s", data.dtype)
             node.data.append(data)

ome_zarr/writer.py

@@ -17,9 +17,7 @@
 KNOWN_AXES = {"x": "space", "y": "space", "z": "space", "c": "channel", "t": "time"}
 
 
-def _axes_to_dicts(
-    axes: Union[List[str], List[Dict[str, str]]]
-) -> List[Dict[str, str]]:
+def axes_to_dicts(axes: Union[List[str], List[Dict[str, str]]]) -> List[Dict[str, str]]:
     """Returns a list of axis dicts with name and type"""
     axes_dicts = []
     for axis in axes:
@@ -139,7 +137,7 @@ def _validate_axes(
         axes = list(axes)
 
     # axes may be list of 'x', 'y' or list of {'name': 'x'}
-    axes_dicts = _axes_to_dicts(axes)
+    axes_dicts = axes_to_dicts(axes)
     axes_names = _axes_to_names(axes_dicts)
 
     # check names (only enforced for version 0.3)