Ome ngff

funlib/persistence/__init__.py

@@ -1,4 +1,4 @@
-from .arrays import Array, open_ds, prepare_ds  # noqa
+from .arrays import Array, open_ds, prepare_ds, open_ome_ds, prepare_ome_ds  # noqa
 
 __version__ = "0.5.3"
 __version_info__ = tuple(int(i) for i in __version__.split("."))

funlib/persistence/arrays/__init__.py

@@ -1,2 +1,3 @@
 from .array import Array  # noqa
 from .datasets import prepare_ds, open_ds  # noqa
+from .ome_datasets import prepare_ome_ds, open_ome_ds  # noqa

funlib/persistence/arrays/array.py

@@ -66,8 +66,10 @@ def __init__(
         voxel_size: Optional[Sequence[int]] = None,
         axis_names: Optional[Sequence[str]] = None,
         units: Optional[Sequence[str]] = None,
+        types: Optional[Sequence[str]] = None,
         chunks: Optional[Union[int, Sequence[int], str]] = "auto",
         lazy_op: Optional[LazyOp] = None,
+        strict_metadata: bool = True,
     ):
         if not isinstance(data, da.Array):
             self.data = da.from_array(data, chunks=chunks)
@@ -80,7 +82,9 @@ def __init__(
             voxel_size=Coordinate(voxel_size) if voxel_size is not None else None,
             axis_names=list(axis_names) if axis_names is not None else None,
             units=list(units) if units is not None else None,
+            types=list(types) if types is not None else None,
             shape=self._source_data.shape,
+            strict=strict_metadata,
         )
 
         if lazy_op is not None:
@@ -91,7 +95,7 @@ def __init__(
 
         self.freeze()
 
-        self.validate()
+        self.validate(strict_metadata)
 
     @property
     def chunk_shape(self) -> Coordinate:
@@ -101,8 +105,8 @@ def uncollapsed_dims(self, physical: bool = False) -> list[bool]:
         if physical:
             return [
                 x
-                for x, c in zip(self._uncollapsed_dims, self._metadata.axis_names)
-                if not c.endswith("^")
+                for x, t in zip(self._uncollapsed_dims, self._metadata.types)
+                if t == "space"
             ]
         else:
             return self._uncollapsed_dims
@@ -148,14 +152,22 @@ def axis_names(self) -> list[str]:
             if uncollapsed
         ]
 
+    @property
+    def types(self) -> list[str]:
+        return [
+            self._metadata.types[ii]
+            for ii, uncollapsed in enumerate(self.uncollapsed_dims(physical=False))
+            if uncollapsed
+        ]
+
     @property
     def physical_shape(self):
         return tuple(
             self._source_data.shape[ii]
-            for ii, (uncollapsed, name) in enumerate(
-                zip(self.uncollapsed_dims(physical=False), self._metadata.axis_names)
+            for ii, (uncollapsed, type) in enumerate(
+                zip(self.uncollapsed_dims(physical=False), self._metadata.types)
             )
-            if uncollapsed and not name.endswith("^")
+            if uncollapsed and type in ["space", "time"]
         )
 
     @property
@@ -414,8 +426,8 @@ def __index(self, coordinate):
             index = (Ellipsis,) + index
         return index
 
-    def validate(self):
-        self._metadata.validate()
+    def validate(self, strict: bool = False):
+        self._metadata.validate(strict)
         assert len(self.axis_names) == len(self._source_data.shape), (
             f"Axis names must be provided for every dimension. Got ({self.axis_names}) "
             f"but expected {len(self.shape)} to match the data shape: {self.shape}"

funlib/persistence/arrays/datasets.py

@@ -29,7 +29,9 @@ def open_ds(
     voxel_size: Optional[Sequence[int]] = None,
     axis_names: Optional[Sequence[str]] = None,
     units: Optional[Sequence[str]] = None,
+    types: Optional[Sequence[str]] = None,
     chunks: Optional[Union[int, Sequence[int], str]] = "strict",
+    strict_metadata: bool = False,
     **kwargs,
 ) -> Array:
     """
@@ -68,6 +70,11 @@ def open_ds(
 
             An override for the units of your dataset.
 
+        types (`str`, (optional)):
+
+            An override for the types of your axes. For more details see:
+            https://ngff.openmicroscopy.org/latest/#axes-md
+
         chunks (`Coordinate`, (optional)):
 
             An override for the size of the chunks in the dataset.
@@ -106,6 +113,7 @@ def open_ds(
         voxel_size=voxel_size,
         axis_names=axis_names,
         units=units,
+        types=types,
     )
 
     return Array(
@@ -114,6 +122,7 @@ def open_ds(
         metadata.voxel_size,
         metadata.axis_names,
         metadata.units,
+        metadata.types,
         data.chunks if chunks == "strict" else chunks,
     )
 
@@ -125,6 +134,7 @@ def prepare_ds(
     voxel_size: Optional[Coordinate] = None,
     axis_names: Optional[Sequence[str]] = None,
     units: Optional[Sequence[str]] = None,
+    types: Optional[Sequence[str]] = None,
     chunk_shape: Optional[Sequence[int]] = None,
     dtype: DTypeLike = np.float32,
     mode: str = "a",
@@ -155,8 +165,7 @@ def prepare_ds(
 
         axis_names:
 
-            The axis names of the dataset to create. The names of non-physical
-            dimensions should end with "^". e.g. ["samples^", "channels^", "z", "y", "x"]
+            The axis names of the dataset to create.
             Set to ["c{i}^", "d{j}"] by default. Where i, j are the index of the non-physical
             and physical dimensions respectively.
 
@@ -165,6 +174,11 @@ def prepare_ds(
             The units of the dataset to create. Only provide for physical dimensions.
             Set to all "" by default.
 
+        types:
+
+            The types of the axes of the dataset to create. For more details see:
+            https://ngff.openmicroscopy.org/latest/#axes-md
+
         chunk_shape:
 
             The shape of the chunks to use in the dataset. For all dimensions,
@@ -201,6 +215,7 @@ def prepare_ds(
         voxel_size=voxel_size,
         axis_names=axis_names,
         units=units,
+        types=types,
     )
 
     try:
@@ -250,6 +265,14 @@ def prepare_ds(
             )
             metadata_compatible = False
 
+        if given_metadata.types != existing_metadata.types:
+            logger.info(
+                "Types differ: given (%s) vs parsed (%s)",
+                given_metadata.types,
+                existing_metadata.types,
+            )
+            metadata_compatible = False
+
         if given_metadata.axis_names != existing_metadata.axis_names:
             logger.info(
                 "Axis names differ: given (%s) vs parsed (%s)",
@@ -292,6 +315,7 @@ def prepare_ds(
                     existing_metadata.voxel_size,
                     existing_metadata.axis_names,
                     existing_metadata.units,
+                    existing_metadata.types,
                     ds.chunks,
                 )
 
@@ -302,6 +326,7 @@ def prepare_ds(
         voxel_size=voxel_size,
         axis_names=axis_names,
         units=units,
+        types=types,
     )
 
     # create the dataset
@@ -325,10 +350,11 @@ def prepare_ds(
             default_metadata_format.units_attr: combined_metadata.units,
             default_metadata_format.voxel_size_attr: combined_metadata.voxel_size,
             default_metadata_format.offset_attr: combined_metadata.offset,
+            default_metadata_format.types_attr: combined_metadata.types,
         }
     )
 
     # open array
-    array = Array(ds, offset, voxel_size, axis_names, units)
+    array = Array(ds, offset, voxel_size, axis_names, units, types)
 
     return array