ngio 0.5.0__py3-none-any.whl → 0.5.0a1__py3-none-any.whl

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

@@ -9,9 +9,6 @@ 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.coordinate_transformations 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 (
@@ -19,13 +16,14 @@ from ome_zarr_models.v04.coordinate_transformations import (
 )
 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 ImageLabelAttrsV04
-from ome_zarr_models.v04.labels import LabelsAttrs as LabelsAttrsV04
+from ome_zarr_models.v04.image_label import ImageLabelAttrs as LabelAttrsV04
 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,
@@ -39,7 +37,6 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
-    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     default_channel_name,
@@ -47,6 +44,37 @@ from ngio.ome_zarr_meta.ngio_specs import (
 from ngio.ome_zarr_meta.v04._custom_models import CustomWellAttrs as WellAttrsV04
 
 
+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")
+
+
 def _v04_omero_to_channels(v04_omero: OmeroV04 | None) -> ChannelsMeta | None:
     if v04_omero is None:
         return None
@@ -119,6 +147,8 @@ def _compute_scale_translation(
 def _v04_to_ngio_datasets(
     v04_multiscale: MultiscaleV04,
     axes_setup: AxesSetup,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
 ) -> list[Dataset]:
     """Convert a v04 multiscale to a list of ngio datasets."""
     datasets = []
@@ -149,6 +179,8 @@ def _v04_to_ngio_datasets(
     axes_handler = AxesHandler(
         axes=axes,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     for v04_dataset in v04_multiscale.datasets:
@@ -168,19 +200,25 @@ def _v04_to_ngio_datasets(
 
 def v04_to_ngio_image_meta(
     metadata: dict,
-    axes_setup: AxesSetup,
-) -> NgioImageMeta:
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> tuple[bool, NgioImageMeta | ValidationError]:
     """Convert a v04 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v04 image metadata.
         axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
+        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
+        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v04_image = ImageAttrsV04(**metadata)
+    v04_image = _is_v04_image_meta(metadata)
+    if isinstance(v04_image, ValidationError):
+        return False, v04_image
 
     if len(v04_image.multiscales) > 1:
         raise NotImplementedError(
@@ -190,15 +228,18 @@ def v04_to_ngio_image_meta(
     v04_muliscale = v04_image.multiscales[0]
 
     channels_meta = _v04_omero_to_channels(v04_image.omero)
+    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v04_to_ngio_datasets(
         v04_muliscale,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     name = v04_muliscale.name
     if name is not None and not isinstance(name, str):
         name = str(name)
-    return NgioImageMeta(
+    return True, NgioImageMeta(
         version="0.4",
         name=name,
         datasets=datasets,
@@ -208,19 +249,25 @@ def v04_to_ngio_image_meta(
 
 def v04_to_ngio_label_meta(
     metadata: dict,
-    axes_setup: AxesSetup,
-) -> NgioLabelMeta:
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> tuple[bool, NgioLabelMeta | ValidationError]:
     """Convert a v04 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v04 image metadata.
         axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
+        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
+        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v04_label = ImageLabelAttrsV04(**metadata)
+    v04_label = _is_v04_label_meta(metadata)
+    if isinstance(v04_label, ValidationError):
+        return False, v04_label
 
     if len(v04_label.multiscales) > 1:
         raise NotImplementedError(
@@ -228,9 +275,13 @@ def v04_to_ngio_label_meta(
         )
 
     v04_muliscale = v04_label.multiscales[0]
+
+    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v04_to_ngio_datasets(
         v04_muliscale,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     source = v04_label.image_label.source
@@ -250,7 +301,7 @@ def v04_to_ngio_label_meta(
     if name is not None and not isinstance(name, str):
         name = str(name)
 
-    return NgioLabelMeta(
+    return True, NgioLabelMeta(
         version="0.4",
         name=name,
         datasets=datasets,
@@ -366,55 +417,48 @@ def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
         "multiscales": [v04_muliscale],
         "image-label": metadata.image_label.model_dump(),
     }
-    v04_label = ImageLabelAttrsV04(**labels_meta)
+    v04_label = LabelAttrsV04(**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:
+) -> tuple[bool, NgioWellMeta | ValidationError]:
     """Convert a v04 well metadata to a ngio well metadata.
 
     Args:
         metadata (dict): The v04 well metadata.
 
     Returns:
-        NgioWellMeta: The ngio well metadata.
+        result (bool): True if the conversion was successful, False otherwise.
+        ngio_well_meta (NgioWellMeta): The ngio well metadata.
     """
-    v04_well = WellAttrsV04(**metadata).well.model_dump()
-    images = v04_well.get("images", [])
-    return NgioWellMeta(images=images, version="0.4")
+    try:
+        v04_well = WellAttrsV04(**metadata)
+    except ValidationError as e:
+        return False, e
+
+    return True, NgioWellMeta(**v04_well.model_dump())
 
 
 def v04_to_ngio_plate_meta(
     metadata: dict,
-) -> NgioPlateMeta:
+) -> tuple[bool, NgioPlateMeta | ValidationError]:
     """Convert a v04 plate metadata to a ngio plate metadata.
 
     Args:
         metadata (dict): The v04 plate metadata.
 
     Returns:
-        NgioPlateMeta: The ngio plate metadata.
+        result (bool): True if the conversion was successful, False otherwise.
+        ngio_plate_meta (NgioPlateMeta): The ngio plate metadata.
     """
-    v04_plate = HCSAttrsV04(**metadata).plate.model_dump()
-    return NgioPlateMeta(plate=v04_plate, version="0.4")  # type: ignore
+    try:
+        v04_plate = HCSAttrsV04(**metadata)
+    except ValidationError as e:
+        return False, e
+
+    return True, NgioPlateMeta(**v04_plate.model_dump())
 
 
 def ngio_to_v04_well_meta(metadata: NgioWellMeta) -> dict:
@@ -426,7 +470,7 @@ def ngio_to_v04_well_meta(metadata: NgioWellMeta) -> dict:
     Returns:
         dict: The v04 well metadata.
     """
-    v04_well = WellAttrsV04(well=metadata.model_dump())  # type: ignore
+    v04_well = WellAttrsV04(**metadata.model_dump())
     return v04_well.model_dump(exclude_none=True, by_alias=True)
 
 
@@ -441,16 +485,3 @@ def ngio_to_v04_plate_meta(metadata: NgioPlateMeta) -> dict:
     """
     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

@@ -1,14 +1,12 @@
 """Utility to read/write OME-Zarr metadata v0.4."""
 
-from ngio.ome_zarr_meta.v05._v05_spec import (
+from ngio.ome_zarr_meta.v05._v05_spec_utils 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,
 )
@@ -16,12 +14,10 @@ from ngio.ome_zarr_meta.v05._v05_spec import (
 __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/{_v05_spec.py → _v05_spec_utils.py}

@@ -9,9 +9,6 @@ For Images and Labels implements the following functionalities:
 - A function to convert a ngio image metadata to a v05 image metadata.
 """
 
-from ome_zarr_models.common.coordinate_transformations import (
-    ValidTransform as ValidTransformV05,
-)
 from ome_zarr_models.common.omero import Channel as ChannelV05
 from ome_zarr_models.common.omero import Omero as OmeroV05
 from ome_zarr_models.common.omero import Window as WindowV05
@@ -22,12 +19,11 @@ from ome_zarr_models.v05.coordinate_transformations import (
 )
 from ome_zarr_models.v05.hcs import HCSAttrs as HCSAttrsV05
 from ome_zarr_models.v05.image import ImageAttrs as ImageAttrsV05
-from ome_zarr_models.v05.image_label import ImageLabelAttrs as ImageLabelAttrsV05
-from ome_zarr_models.v05.labels import Labels as Labels
-from ome_zarr_models.v05.labels import LabelsAttrs as LabelsAttrsV05
+from ome_zarr_models.v05.image_label import ImageLabelAttrs as LabelAttrsV05
 from ome_zarr_models.v05.multiscales import Dataset as DatasetV05
 from ome_zarr_models.v05.multiscales import Multiscale as MultiscaleV05
-from pydantic import BaseModel
+from ome_zarr_models.v05.multiscales import ValidTransform as ValidTransformV05
+from pydantic import BaseModel, ValidationError
 
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
@@ -41,7 +37,6 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
-    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     default_channel_name,
@@ -58,7 +53,37 @@ class ImageV05WithOmero(BaseModel):
 
 
 class ImageLabelV05(BaseModel):
-    ome: ImageLabelAttrsV05
+    ome: LabelAttrsV05
+
+
+def _is_v05_image_meta(metadata: dict) -> ImageV05WithOmero | ValidationError:
+    """Check if the metadata is a valid OME-Zarr v05 metadata.
+
+    Args:
+        metadata (dict): The metadata to check.
+
+    Returns:
+        bool: True if the metadata is a valid OME-Zarr v05 metadata, False otherwise.
+    """
+    try:
+        return ImageV05WithOmero(**metadata)
+    except ValidationError as e:
+        return e
+
+
+def _is_v05_label_meta(metadata: dict) -> ImageLabelV05 | ValidationError:
+    """Check if the metadata is a valid OME-Zarr v05 metadata.
+
+    Args:
+        metadata (dict): The metadata to check.
+
+    Returns:
+        bool: True if the metadata is a valid OME-Zarr v05 metadata, False otherwise.
+    """
+    try:
+        return ImageLabelV05(**metadata)
+    except ValidationError as e:
+        return e
 
 
 def _v05_omero_to_channels(v05_omero: OmeroV05 | None) -> ChannelsMeta | None:
@@ -133,6 +158,8 @@ def _compute_scale_translation(
 def _v05_to_ngio_datasets(
     v05_multiscale: MultiscaleV05,
     axes_setup: AxesSetup,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
 ) -> list[Dataset]:
     """Convert a v05 multiscale to a list of ngio datasets."""
     datasets = []
@@ -163,6 +190,8 @@ def _v05_to_ngio_datasets(
     axes_handler = AxesHandler(
         axes=axes,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     for v05_dataset in v05_multiscale.datasets:
@@ -182,19 +211,25 @@ def _v05_to_ngio_datasets(
 
 def v05_to_ngio_image_meta(
     metadata: dict,
-    axes_setup: AxesSetup,
-) -> NgioImageMeta:
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> tuple[bool, NgioImageMeta | ValidationError]:
     """Convert a v05 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v05 image metadata.
-        axes_setup (AxesSetup): The axes setup. This is
+        axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
+        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
+        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v05_image = ImageV05WithOmero(**metadata)
+    v05_image = _is_v05_image_meta(metadata)
+    if isinstance(v05_image, ValidationError):
+        return False, v05_image
     v05_image = v05_image.ome
     if len(v05_image.multiscales) > 1:
         raise NotImplementedError(
@@ -204,15 +239,18 @@ def v05_to_ngio_image_meta(
     v05_multiscale = v05_image.multiscales[0]
 
     channels_meta = _v05_omero_to_channels(v05_image.omero)
+    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v05_to_ngio_datasets(
         v05_multiscale,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     name = v05_multiscale.name
     if name is not None and not isinstance(name, str):
         name = str(name)
-    return NgioImageMeta(
+    return True, NgioImageMeta(
         version="0.5",
         name=name,
         datasets=datasets,
@@ -222,19 +260,25 @@ def v05_to_ngio_image_meta(
 
 def v05_to_ngio_label_meta(
     metadata: dict,
-    axes_setup: AxesSetup,
-) -> NgioLabelMeta:
+    axes_setup: AxesSetup | None = None,
+    allow_non_canonical_axes: bool = False,
+    strict_canonical_order: bool = True,
+) -> tuple[bool, NgioLabelMeta | ValidationError]:
     """Convert a v05 image metadata to a ngio image metadata.
 
     Args:
         metadata (dict): The v05 image metadata.
-        axes_setup (AxesSetup): The axes setup. This is
+        axes_setup (AxesSetup, optional): The axes setup. This is
             required to convert image with non-canonical axes names.
+        allow_non_canonical_axes (bool, optional): Allow non-canonical axes.
+        strict_canonical_order (bool, optional): Strict canonical order.
 
     Returns:
-        NgioLabelMeta: The ngio label metadata.
+        NgioImageMeta: The ngio image metadata.
     """
-    v05_label = ImageLabelV05(**metadata)
+    v05_label = _is_v05_label_meta(metadata)
+    if isinstance(v05_label, ValidationError):
+        return False, v05_label
     v05_label = v05_label.ome
 
     if len(v05_label.multiscales) > 1:
@@ -244,9 +288,12 @@ def v05_to_ngio_label_meta(
 
     v05_multiscale = v05_label.multiscales[0]
 
+    axes_setup = axes_setup if axes_setup is not None else AxesSetup()
     datasets = _v05_to_ngio_datasets(
         v05_multiscale,
         axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
     )
 
     if v05_label.image_label is not None:
@@ -269,7 +316,7 @@ def v05_to_ngio_label_meta(
     if name is not None and not isinstance(name, str):
         name = str(name)
 
-    return NgioLabelMeta(
+    return True, NgioLabelMeta(
         version="0.5",
         name=name,
         datasets=datasets,
@@ -388,7 +435,7 @@ def ngio_to_v05_label_meta(metadata: NgioLabelMeta) -> dict:
         "multiscales": [v05_muliscale],
         "image-label": metadata.image_label.model_dump(),
     }
-    v05_label = ImageLabelAttrsV05(**labels_meta, version="0.5")
+    v05_label = LabelAttrsV05(**labels_meta, version="0.5")
     v05_label = ImageLabelV05(
         ome=v05_label,
     )
@@ -405,33 +452,42 @@ class HCSV05(BaseModel):
 
 def v05_to_ngio_well_meta(
     metadata: dict,
-) -> NgioWellMeta:
+) -> tuple[bool, NgioWellMeta | ValidationError]:
     """Convert a v05 well metadata to a ngio well metadata.
 
     Args:
         metadata (dict): The v05 well metadata.
 
     Returns:
-        NgioWellMeta: The ngio well metadata.
+        result (bool): True if the conversion was successful, False otherwise.
+        ngio_well_meta (NgioWellMeta): The ngio well metadata.
     """
-    v05_well = WellV05(**metadata).ome.well.model_dump()
-    images = v05_well.get("images", [])
-    return NgioWellMeta(images=images, version="0.5")
+    try:
+        v05_well = WellV05(**metadata)
+    except ValidationError as e:
+        return False, e
+
+    return True, NgioWellMeta(**v05_well.ome.model_dump())
 
 
 def v05_to_ngio_plate_meta(
     metadata: dict,
-) -> NgioPlateMeta:
+) -> tuple[bool, NgioPlateMeta | ValidationError]:
     """Convert a v05 plate metadata to a ngio plate metadata.
 
     Args:
         metadata (dict): The v05 plate metadata.
 
     Returns:
-        NgioPlateMeta: The ngio plate metadata.
+        result (bool): True if the conversion was successful, False otherwise.
+        ngio_plate_meta (NgioPlateMeta): The ngio plate metadata.
     """
-    v05_plate = HCSV05(**metadata).ome.plate.model_dump()
-    return NgioPlateMeta(plate=v05_plate, version="0.5")  # type: ignore
+    try:
+        v05_plate = HCSV05(**metadata)
+    except ValidationError as e:
+        return False, e
+
+    return True, NgioPlateMeta(**v05_plate.ome.model_dump())
 
 
 def ngio_to_v05_well_meta(metadata: NgioWellMeta) -> dict:
@@ -443,7 +499,7 @@ def ngio_to_v05_well_meta(metadata: NgioWellMeta) -> dict:
     Returns:
         dict: The v05 well metadata.
     """
-    v05_well = WellAttrsV05(well=metadata.model_dump())  # type: ignore
+    v05_well = WellAttrsV05(**metadata.model_dump())
     v05_well = WellV05(ome=v05_well)
     return v05_well.model_dump(exclude_none=True, by_alias=True)
 
@@ -460,36 +516,3 @@ def ngio_to_v05_plate_meta(metadata: NgioPlateMeta) -> dict:
     v05_plate = HCSAttrsV05(**metadata.model_dump())
     v05_plate = HCSV05(ome=v05_plate)
     return v05_plate.model_dump(exclude_none=True, by_alias=True)
-
-
-class LabelsV05(BaseModel):
-    ome: LabelsAttrsV05
-
-
-def v05_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.
-    """
-    v05_label_group = LabelsV05(**metadata)
-    return NgioLabelsGroupMeta(labels=v05_label_group.ome.labels, version="0.5")
-
-
-def ngio_to_v05_labels_group_meta(metadata: NgioLabelsGroupMeta) -> dict:
-    """Convert a ngio label group metadata to a v05 label group metadata.
-
-    Args:
-        metadata (NgioLabelsGroupMeta): The ngio label group metadata.
-
-    Returns:
-        dict: The v05 label group metadata.
-    """
-    v05_labels_attrs = LabelsAttrsV05(labels=metadata.labels, version="0.5")
-    v05_labels_group = LabelsV05(ome=v05_labels_attrs)
-    return v05_labels_group.model_dump(exclude_none=True, by_alias=True)

ngio/resources/__init__.py

@@ -31,7 +31,7 @@ _resources = {
                 dtype="uint8",
             ),
         ],
-        pixelsize=0.325,
+        xy_pixelsize=0.325,
         z_spacing=1.0,
         time_spacing=1.0,
         name="Cardiomyocyte Differentiation",

ngio/resources/resource_model.py

@@ -27,7 +27,7 @@ class SampleInfo(BaseModel):
 
     img_path: Path
     labels: list[LabelsInfo] = Field(default_factory=list)
-    pixelsize: float
+    xy_pixelsize: float
     z_spacing: float = 1.0
     time_spacing: float = 1.0
     space_unit: SpaceUnits = DefaultSpaceUnit