ngio 0.4.8__py3-none-any.whl → 0.5.0__py3-none-any.whl

ngio/ome_zarr_meta/v04/__init__.py

@@ -1,12 +1,14 @@
 """Utility to read/write OME-Zarr metadata v0.4."""
 
-from ngio.ome_zarr_meta.v04._v04_spec_utils import (
+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,
 )
@@ -14,10 +16,12 @@ from ngio.ome_zarr_meta.v04._v04_spec_utils import (
 __all__ = [
     "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/{_v04_spec_utils.py → _v04_spec.py}

@@ -9,7 +9,9 @@ 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.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 (
@@ -17,13 +19,13 @@ 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 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.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,
@@ -37,6 +39,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     default_channel_name,
@@ -44,37 +47,6 @@ 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
@@ -147,8 +119,6 @@ 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 = []
@@ -169,7 +139,7 @@ def _v04_to_ngio_datasets(
             unit = str(unit)
         axes.append(
             Axis(
-                name=v04_axis.name,
+                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)
@@ -179,8 +149,6 @@ 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:
@@ -200,25 +168,19 @@ def _v04_to_ngio_datasets(
 
 def v04_to_ngio_image_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
-) -> tuple[bool, NgioImageMeta | ValidationError]:
+    axes_setup: AxesSetup,
+) -> NgioImageMeta:
     """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 = _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(
@@ -228,18 +190,15 @@ 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 True, NgioImageMeta(
+    return NgioImageMeta(
         version="0.4",
         name=name,
         datasets=datasets,
@@ -249,25 +208,19 @@ def v04_to_ngio_image_meta(
 
 def v04_to_ngio_label_meta(
     metadata: dict,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = True,
-) -> tuple[bool, NgioLabelMeta | ValidationError]:
+    axes_setup: AxesSetup,
+) -> NgioLabelMeta:
     """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 = _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(
@@ -275,13 +228,9 @@ 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
@@ -301,7 +250,7 @@ def v04_to_ngio_label_meta(
     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,
@@ -417,48 +366,55 @@ def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
         "multiscales": [v04_muliscale],
         "image-label": metadata.image_label.model_dump(),
     }
-    v04_label = LabelAttrsV04(**labels_meta)
+    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,
-) -> tuple[bool, NgioWellMeta | ValidationError]:
+) -> NgioWellMeta:
     """Convert a v04 well metadata to a ngio well metadata.
 
     Args:
         metadata (dict): The v04 well metadata.
 
     Returns:
-        result (bool): True if the conversion was successful, False otherwise.
-        ngio_well_meta (NgioWellMeta): The ngio well metadata.
+        NgioWellMeta: The ngio well metadata.
     """
-    try:
-        v04_well = WellAttrsV04(**metadata)
-    except ValidationError as e:
-        return False, e
-
-    return True, NgioWellMeta(**v04_well.model_dump())
+    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,
-) -> tuple[bool, NgioPlateMeta | ValidationError]:
+) -> NgioPlateMeta:
     """Convert a v04 plate metadata to a ngio plate metadata.
 
     Args:
         metadata (dict): The v04 plate metadata.
 
     Returns:
-        result (bool): True if the conversion was successful, False otherwise.
-        ngio_plate_meta (NgioPlateMeta): The ngio plate metadata.
+        NgioPlateMeta: The ngio plate metadata.
     """
-    try:
-        v04_plate = HCSAttrsV04(**metadata)
-    except ValidationError as e:
-        return False, e
-
-    return True, NgioPlateMeta(**v04_plate.model_dump())
+    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:
@@ -470,7 +426,7 @@ def ngio_to_v04_well_meta(metadata: NgioWellMeta) -> dict:
     Returns:
         dict: The v04 well metadata.
     """
-    v04_well = WellAttrsV04(**metadata.model_dump())
+    v04_well = WellAttrsV04(well=metadata.model_dump())  # type: ignore
     return v04_well.model_dump(exclude_none=True, by_alias=True)
 
 
@@ -485,3 +441,16 @@ 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

@@ -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]