ngio 0.2.0a2__py3-none-any.whl → 0.5.0b4__py3-none-any.whl

ngio/ome_zarr_meta/v04/__init__.py

@@ -1,11 +1,27 @@
 """Utility to read/write OME-Zarr metadata v0.4."""
 
-from ngio.ome_zarr_meta.v04._meta_handlers import (
-    V04ImageMetaHandler,
-    V04LabelMetaHandler,
+from ngio.ome_zarr_meta.v04._v04_spec import (
+    ngio_to_v04_image_meta,
+    ngio_to_v04_label_meta,
+    ngio_to_v04_labels_group_meta,
+    ngio_to_v04_plate_meta,
+    ngio_to_v04_well_meta,
+    v04_to_ngio_image_meta,
+    v04_to_ngio_label_meta,
+    v04_to_ngio_labels_group_meta,
+    v04_to_ngio_plate_meta,
+    v04_to_ngio_well_meta,
 )
 
 __all__ = [
-    "V04ImageMetaHandler",
-    "V04LabelMetaHandler",
+    "ngio_to_v04_image_meta",
+    "ngio_to_v04_label_meta",
+    "ngio_to_v04_labels_group_meta",
+    "ngio_to_v04_plate_meta",
+    "ngio_to_v04_well_meta",
+    "v04_to_ngio_image_meta",
+    "v04_to_ngio_label_meta",
+    "v04_to_ngio_labels_group_meta",
+    "v04_to_ngio_plate_meta",
+    "v04_to_ngio_well_meta",
 ]

ngio/ome_zarr_meta/v04/_custom_models.py

@@ -0,0 +1,18 @@
+from typing import Annotated
+
+from ome_zarr_models.v04.well import WellAttrs as WellAttrs04
+from ome_zarr_models.v04.well_types import WellImage as WellImage04
+from ome_zarr_models.v04.well_types import WellMeta as WellMeta04
+from pydantic import SkipValidation
+
+
+class CustomWellImage(WellImage04):
+    path: Annotated[str, SkipValidation]
+
+
+class CustomWellMeta(WellMeta04):
+    images: list[CustomWellImage]  # type: ignore[valid-type]
+
+
+class CustomWellAttrs(WellAttrs04):
+    well: CustomWellMeta  # type: ignore[valid-type]

ngio/ome_zarr_meta/v04/{_v04_spec_utils.py → _v04_spec.py}

@@ -9,22 +9,24 @@ For Images and Labels implements the following functionalities:
 - A function to convert a ngio image metadata to a v04 image metadata.
 """
 
-from ome_zarr_models.common.multiscales import ValidTransform as ValidTransformV04
 from ome_zarr_models.v04.axes import Axis as AxisV04
 from ome_zarr_models.v04.coordinate_transformations import VectorScale as VectorScaleV04
 from ome_zarr_models.v04.coordinate_transformations import (
     VectorTranslation as VectorTranslationV04,
 )
+from ome_zarr_models.v04.hcs import HCSAttrs as HCSAttrsV04
 from ome_zarr_models.v04.image import ImageAttrs as ImageAttrsV04
-from ome_zarr_models.v04.image_label import ImageLabelAttrs as LabelAttrsV04
+from ome_zarr_models.v04.image_label import ImageLabelAttrs as ImageLabelAttrsV04
+from ome_zarr_models.v04.labels import LabelsAttrs as LabelsAttrsV04
 from ome_zarr_models.v04.multiscales import Dataset as DatasetV04
 from ome_zarr_models.v04.multiscales import Multiscale as MultiscaleV04
+from ome_zarr_models.v04.multiscales import ValidTransform as ValidTransformV04
 from ome_zarr_models.v04.omero import Channel as ChannelV04
 from ome_zarr_models.v04.omero import Omero as OmeroV04
 from ome_zarr_models.v04.omero import Window as WindowV04
-from pydantic import ValidationError
 
 from ngio.ome_zarr_meta.ngio_specs import (
+    AxesHandler,
     AxesSetup,
     Axis,
     AxisType,
@@ -35,40 +37,12 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
+    NgioPlateMeta,
+    NgioWellMeta,
     default_channel_name,
 )
-from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersion
-
-
-def _is_v04_image_meta(metadata: dict) -> ImageAttrsV04 | ValidationError:
-    """Check if the metadata is a valid OME-Zarr v04 metadata.
-
-    Args:
-        metadata (dict): The metadata to check.
-
-    Returns:
-        bool: True if the metadata is a valid OME-Zarr v04 metadata, False otherwise.
-    """
-    try:
-        return ImageAttrsV04(**metadata)
-    except ValidationError as e:
-        return e
-
-
-def _is_v04_label_meta(metadata: dict) -> LabelAttrsV04 | ValidationError:
-    """Check if the metadata is a valid OME-Zarr v04 metadata.
-
-    Args:
-        metadata (dict): The metadata to check.
-
-    Returns:
-        bool: True if the metadata is a valid OME-Zarr v04 metadata, False otherwise.
-    """
-    try:
-        return LabelAttrsV04(**metadata)
-    except ValidationError as e:
-        return e
-    raise RuntimeError("Unreachable code")
+from ngio.ome_zarr_meta.v04._custom_models import CustomWellAttrs as WellAttrsV04
 
 
 def _v04_omero_to_channels(v04_omero: OmeroV04 | None) -> ChannelsMeta | None:
@@ -157,34 +131,38 @@ def _v04_to_ngio_datasets(
             v04_multiscale.coordinateTransformations, global_scale, global_translation
         )
 
-    for v04_dataset in v04_multiscale.datasets:
-        axes = []
-        for v04_axis in v04_multiscale.axes:
-            unit = v04_axis.unit
-            if unit is not None and not isinstance(unit, str):
-                unit = str(unit)
-            axes.append(
-                Axis(
-                    on_disk_name=v04_axis.name,
-                    axis_type=AxisType(v04_axis.type),
-                    # (for some reason the type is a generic JsonValue,
-                    # but it should be a string or None)
-                    unit=v04_axis.unit,  # type: ignore
-                )
+    # Prepare axes handler
+    axes = []
+    for v04_axis in v04_multiscale.axes:
+        unit = v04_axis.unit
+        if unit is not None and not isinstance(unit, str):
+            unit = str(unit)
+        axes.append(
+            Axis(
+                name=str(v04_axis.name),
+                axis_type=AxisType(v04_axis.type),
+                # (for some reason the type is a generic JsonValue,
+                # but it should be a string or None)
+                unit=v04_axis.unit,  # type: ignore
             )
+        )
+    axes_handler = AxesHandler(
+        axes=axes,
+        axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
+    )
 
-        _on_disk_scale, _on_disk_translation = _compute_scale_translation(
+    for v04_dataset in v04_multiscale.datasets:
+        _scale, _translation = _compute_scale_translation(
             v04_dataset.coordinateTransformations, global_scale, global_translation
         )
         datasets.append(
             Dataset(
                 path=v04_dataset.path,
-                on_disk_axes=axes,
-                on_disk_scale=_on_disk_scale,
-                on_disk_translation=_on_disk_translation,
-                axes_setup=axes_setup,
-                allow_non_canonical_axes=allow_non_canonical_axes,
-                strict_canonical_order=strict_canonical_order,
+                axes_handler=axes_handler,
+                scale=_scale,
+                translation=_translation,
             )
         )
     return datasets
@@ -195,7 +173,7 @@ def v04_to_ngio_image_meta(
     axes_setup: AxesSetup | None = None,
     allow_non_canonical_axes: bool = False,
     strict_canonical_order: bool = True,
-) -> tuple[bool, NgioImageMeta | ValidationError]:
+) -> NgioImageMeta:
     """Convert a v04 image metadata to a ngio image metadata.
 
     Args:
@@ -208,9 +186,7 @@ def v04_to_ngio_image_meta(
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v04_image = _is_v04_image_meta(metadata)
-    if isinstance(v04_image, ValidationError):
-        return False, v04_image
+    v04_image = ImageAttrsV04(**metadata)
 
     if len(v04_image.multiscales) > 1:
         raise NotImplementedError(
@@ -231,7 +207,7 @@ def v04_to_ngio_image_meta(
     name = v04_muliscale.name
     if name is not None and not isinstance(name, str):
         name = str(name)
-    return True, NgioImageMeta(
+    return NgioImageMeta(
         version="0.4",
         name=name,
         datasets=datasets,
@@ -244,7 +220,7 @@ def v04_to_ngio_label_meta(
     axes_setup: AxesSetup | None = None,
     allow_non_canonical_axes: bool = False,
     strict_canonical_order: bool = True,
-) -> tuple[bool, NgioLabelMeta | ValidationError]:
+) -> NgioLabelMeta:
     """Convert a v04 image metadata to a ngio image metadata.
 
     Args:
@@ -257,9 +233,7 @@ def v04_to_ngio_label_meta(
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v04_label = _is_v04_label_meta(metadata)
-    if isinstance(v04_label, ValidationError):
-        return False, v04_label
+    v04_label = ImageLabelAttrsV04(**metadata)
 
     if len(v04_label.multiscales) > 1:
         raise NotImplementedError(
@@ -286,14 +260,14 @@ def v04_to_ngio_label_meta(
         else:
             image_label_source = source.image
         image_label_source = ImageLabelSource(
-            version=NgffVersion.v04,
+            version="0.4",
             source={"image": image_label_source},
         )
     name = v04_muliscale.name
     if name is not None and not isinstance(name, str):
         name = str(name)
 
-    return True, NgioLabelMeta(
+    return NgioLabelMeta(
         version="0.4",
         name=name,
         datasets=datasets,
@@ -301,48 +275,45 @@ def v04_to_ngio_label_meta(
     )
 
 
-def _ngio_to_v04_multiscale(datasets: list[Dataset]) -> MultiscaleV04:
+def _ngio_to_v04_multiscale(name: str | None, datasets: list[Dataset]) -> MultiscaleV04:
     """Convert a ngio multiscale to a v04 multiscale.
 
     Args:
+        name (str | None): The name of the multiscale.
         datasets (list[Dataset]): The ngio datasets.
 
     Returns:
         MultiscaleV04: The v04 multiscale.
     """
-    ax_mapper = datasets[0].axes_mapper
+    ax_mapper = datasets[0].axes_handler
     v04_axes = []
-    for axis in ax_mapper.on_disk_axes:
+    for axis in ax_mapper.axes:
         v04_axes.append(
             AxisV04(
-                name=axis.on_disk_name,
+                name=axis.name,
                 type=axis.axis_type.value if axis.axis_type is not None else None,
-                unit=axis.unit.value if axis.unit is not None else None,
+                unit=axis.unit if axis.unit is not None else None,
             )
         )
 
     v04_datasets = []
     for dataset in datasets:
-        transform = [VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale))]
-        if sum(dataset._on_disk_translation) > 0:
+        transform = [VectorScaleV04(type="scale", scale=list(dataset._scale))]
+        if sum(dataset._translation) > 0:
             transform = (
-                VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale)),
+                VectorScaleV04(type="scale", scale=list(dataset._scale)),
                 VectorTranslationV04(
-                    type="translation", translation=list(dataset._on_disk_translation)
+                    type="translation", translation=list(dataset._translation)
                 ),
             )
         else:
-            transform = (
-                VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale)),
-            )
+            transform = (VectorScaleV04(type="scale", scale=list(dataset._scale)),)
 
         v04_datasets.append(
             DatasetV04(path=dataset.path, coordinateTransformations=transform)
         )
     return MultiscaleV04(
-        axes=v04_axes,
-        datasets=tuple(v04_datasets),
-        version="0.4",
+        axes=v04_axes, datasets=tuple(v04_datasets), version="0.4", name=name
     )
 
 
@@ -387,11 +358,13 @@ def ngio_to_v04_image_meta(metadata: NgioImageMeta) -> dict:
     Returns:
         dict: The v04 image metadata.
     """
-    v04_muliscale = _ngio_to_v04_multiscale(metadata.datasets)
+    v04_muliscale = _ngio_to_v04_multiscale(
+        name=metadata.name, datasets=metadata.datasets
+    )
     v04_omero = _ngio_to_v04_omero(metadata._channels_meta)
 
     v04_image = ImageAttrsV04(multiscales=[v04_muliscale], omero=v04_omero)
-    return v04_image.model_dump(exclude_none=True)
+    return v04_image.model_dump(exclude_none=True, by_alias=True)
 
 
 def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
@@ -403,10 +376,98 @@ def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
     Returns:
         dict: The v04 image metadata.
     """
-    v04_muliscale = _ngio_to_v04_multiscale(metadata.datasets)
-    v04_label = LabelAttrsV04(
-        multiscales=[v04_muliscale],
-        # image_label is aliased as 'imae-label'
-        image_label=metadata.image_label.model_dump(),  # type: ignore
+    v04_muliscale = _ngio_to_v04_multiscale(
+        name=metadata.name, datasets=metadata.datasets
     )
-    return v04_label.model_dump(exclude_none=True)
+    labels_meta = {
+        "multiscales": [v04_muliscale],
+        "image-label": metadata.image_label.model_dump(),
+    }
+    v04_label = ImageLabelAttrsV04(**labels_meta)
+    return v04_label.model_dump(exclude_none=True, by_alias=True)
+
+
+def v04_to_ngio_labels_group_meta(
+    metadata: dict,
+) -> NgioLabelsGroupMeta:
+    """Convert a v04 label group metadata to a ngio label group metadata.
+
+    Args:
+        metadata (dict): The v04 label group metadata.
+
+    Returns:
+        NgioLabelGroupMeta: The ngio label group metadata.
+    """
+    v04_label_group = LabelsAttrsV04(**metadata).model_dump()
+    labels = v04_label_group.get("labels", [])
+    return NgioLabelsGroupMeta(labels=labels, version="0.4")
+
+
+def v04_to_ngio_well_meta(
+    metadata: dict,
+) -> NgioWellMeta:
+    """Convert a v04 well metadata to a ngio well metadata.
+
+    Args:
+        metadata (dict): The v04 well metadata.
+
+    Returns:
+        NgioWellMeta: The ngio well metadata.
+    """
+    v04_well = WellAttrsV04(**metadata).well.model_dump()
+    images = v04_well.get("images", [])
+    return NgioWellMeta(images=images, version="0.4")
+
+
+def v04_to_ngio_plate_meta(
+    metadata: dict,
+) -> NgioPlateMeta:
+    """Convert a v04 plate metadata to a ngio plate metadata.
+
+    Args:
+        metadata (dict): The v04 plate metadata.
+
+    Returns:
+        NgioPlateMeta: The ngio plate metadata.
+    """
+    v04_plate = HCSAttrsV04(**metadata).plate.model_dump()
+    return NgioPlateMeta(plate=v04_plate, version="0.4")  # type: ignore
+
+
+def ngio_to_v04_well_meta(metadata: NgioWellMeta) -> dict:
+    """Convert a ngio well metadata to a v04 well metadata.
+
+    Args:
+        metadata (NgioWellMeta): The ngio well metadata.
+
+    Returns:
+        dict: The v04 well metadata.
+    """
+    v04_well = WellAttrsV04(well=metadata.model_dump())  # type: ignore
+    return v04_well.model_dump(exclude_none=True, by_alias=True)
+
+
+def ngio_to_v04_plate_meta(metadata: NgioPlateMeta) -> dict:
+    """Convert a ngio plate metadata to a v04 plate metadata.
+
+    Args:
+        metadata (NgioPlateMeta): The ngio plate metadata.
+
+    Returns:
+        dict: The v04 plate metadata.
+    """
+    v04_plate = HCSAttrsV04(**metadata.model_dump())
+    return v04_plate.model_dump(exclude_none=True, by_alias=True)
+
+
+def ngio_to_v04_labels_group_meta(metadata: NgioLabelsGroupMeta) -> dict:
+    """Convert a ngio label group metadata to a v04 label group metadata.
+
+    Args:
+        metadata (NgioLabelsGroupMeta): The ngio label group metadata.
+
+    Returns:
+        dict: The v04 label group metadata.
+    """
+    v04_label_group = LabelsAttrsV04(labels=metadata.labels)
+    return v04_label_group.model_dump(exclude_none=True, by_alias=True)

ngio/ome_zarr_meta/v05/__init__.py

@@ -0,0 +1,27 @@
+"""Utility to read/write OME-Zarr metadata v0.4."""
+
+from ngio.ome_zarr_meta.v05._v05_spec import (
+    ngio_to_v05_image_meta,
+    ngio_to_v05_label_meta,
+    ngio_to_v05_labels_group_meta,
+    ngio_to_v05_plate_meta,
+    ngio_to_v05_well_meta,
+    v05_to_ngio_image_meta,
+    v05_to_ngio_label_meta,
+    v05_to_ngio_labels_group_meta,
+    v05_to_ngio_plate_meta,
+    v05_to_ngio_well_meta,
+)
+
+__all__ = [
+    "ngio_to_v05_image_meta",
+    "ngio_to_v05_label_meta",
+    "ngio_to_v05_labels_group_meta",
+    "ngio_to_v05_plate_meta",
+    "ngio_to_v05_well_meta",
+    "v05_to_ngio_image_meta",
+    "v05_to_ngio_label_meta",
+    "v05_to_ngio_labels_group_meta",
+    "v05_to_ngio_plate_meta",
+    "v05_to_ngio_well_meta",
+]

ngio/ome_zarr_meta/v05/_custom_models.py

@@ -0,0 +1,18 @@
+from typing import Annotated
+
+from ome_zarr_models.v05.well import WellAttrs as WellAttrs05
+from ome_zarr_models.v05.well_types import WellImage as WellImage05
+from ome_zarr_models.v05.well_types import WellMeta as WellMeta05
+from pydantic import SkipValidation
+
+
+class CustomWellImage(WellImage05):
+    path: Annotated[str, SkipValidation]
+
+
+class CustomWellMeta(WellMeta05):
+    images: list[CustomWellImage]  # type: ignore[valid-type]
+
+
+class CustomWellAttrs(WellAttrs05):
+    well: CustomWellMeta  # type: ignore[valid-type]