ngio 0.5.0a1__py3-none-any.whl → 0.5.0a3__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_axes.py

@@ -352,6 +352,7 @@ class AxesHandler:
 
     @property
     def axes_names(self) -> tuple[str, ...]:
+        """On disk axes names."""
         return tuple(ax.name for ax in self._axes)
 
     @property

ngio/ome_zarr_meta/ngio_specs/_dataset.py

@@ -60,11 +60,20 @@ class Dataset:
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel size for the dataset."""
+        scale = self._scale
+        pix_size_dict = {}
+        # Mandatory axes: x, y
+        for ax in ["x", "y"]:
+            index = self.axes_handler.get_index(ax)
+            assert index is not None
+            pix_size_dict[ax] = scale[index]
+
+        for ax in ["z", "t"]:
+            index = self.axes_handler.get_index(ax)
+            pix_size_dict[ax] = scale[index] if index is not None else 1.0
+
         return PixelSize(
-            x=self.get_scale("x", default=1.0),
-            y=self.get_scale("y", default=1.0),
-            z=self.get_scale("z", default=1.0),
-            t=self.get_scale("t", default=1.0),
+            **pix_size_dict,
             space_unit=self.axes_handler.space_unit,
             time_unit=self.axes_handler.time_unit,
         )
@@ -78,21 +87,3 @@ class Dataset:
     def translation(self) -> tuple[float, ...]:
         """Return the translation as a tuple."""
         return tuple(self._translation)
-
-    def get_scale(self, axis_name: str, default: float | None = None) -> float:
-        """Return the scale for a given axis."""
-        idx = self.axes_handler.get_index(axis_name)
-        if idx is None:
-            if default is not None:
-                return default
-            raise ValueError(f"Axis {axis_name} not found in axes {self.axes_handler}.")
-        return self._scale[idx]
-
-    def get_translation(self, axis_name: str, default: float | None = None) -> float:
-        """Return the translation for a given axis."""
-        idx = self.axes_handler.get_index(axis_name)
-        if idx is None:
-            if default is not None:
-                return default
-            raise ValueError(f"Axis {axis_name} not found in axes {self.axes_handler}.")
-        return self._translation[idx]

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -1,32 +1,31 @@
 """HCS (High Content Screening) specific metadata classes for NGIO."""
 
+import warnings
 from typing import Annotated
 
-from ome_zarr_models.v04.hcs import HCSAttrs
-from ome_zarr_models.v04.plate import (
+from ome_zarr_models.common.plate import (
     Acquisition,
     Column,
-    Plate,
+    PlateBase,
     Row,
     WellInPlate,
 )
-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 ome_zarr_models.common.well_types import WellImage as WellImageCommon
 from pydantic import BaseModel, SkipValidation, field_serializer
 
 from ngio.ome_zarr_meta.ngio_specs._ngio_image import DefaultNgffVersion, NgffVersions
-from ngio.utils import NgioValueError, ngio_logger
+from ngio.utils import NgioValueError
 
 
 def path_in_well_validation(path: str) -> str:
     """Validate the path in the well."""
     # Check if the value contains only alphanumeric characters
     if not path.isalnum():
-        ngio_logger.warning(
+        warnings.warn(
             f"Path '{path}' contains non-alphanumeric characters. "
             "This may cause issues with some tools. "
-            "Consider using only alphanumeric characters in the path."
+            "Consider using only alphanumeric characters in the path.",
+            stacklevel=2,
         )
     return path
 
@@ -41,7 +40,7 @@ class ImageInWellPath(BaseModel):
     acquisition_name: str | None = None
 
 
-class CustomWellImage(WellImage04):
+class CustomWellImage(WellImageCommon):
     path: Annotated[str, SkipValidation]
 
     @field_serializer("path")
@@ -50,32 +49,29 @@ class CustomWellImage(WellImage04):
         return path_in_well_validation(value)
 
 
-class CustomWellMeta(WellMeta04):
-    images: list[CustomWellImage]  # type: ignore (override of WellMeta04.images)
-
-
-class CustomWellAttrs(WellAttrs04):
-    well: CustomWellMeta  # type: ignore (override of WellAttrs04.well)
+class PlateWithVersion(PlateBase):
+    version: NgffVersions
 
 
-class NgioWellMeta(CustomWellAttrs):
+class NgioWellMeta(BaseModel):
     """HCS well metadata."""
 
+    images: list[CustomWellImage]  # type: ignore (override of WellMeta04.images)
+    version: NgffVersions
+
     @classmethod
     def default_init(
         cls,
-        version: NgffVersions | None = None,
+        version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioWellMeta":
-        if version is None:
-            version = DefaultNgffVersion
-        well = cls(well=CustomWellMeta(images=[], version=version))
+        well = cls(images=[], version=version)
         return well
 
     @property
     def acquisition_ids(self) -> list[int]:
         """Return the acquisition ids in the well."""
         acquisitions = []
-        for images in self.well.images:
+        for images in self.images:
             if (
                 images.acquisition is not None
                 and images.acquisition not in acquisitions
@@ -85,7 +81,7 @@ class NgioWellMeta(CustomWellAttrs):
 
     def get_image_acquisition_id(self, image_path: str) -> int | None:
         """Return the acquisition id for the given image path."""
-        for images in self.well.images:
+        for images in self.images:
             if images.path == image_path:
                 return images.acquisition
         raise NgioValueError(f"Image at path {image_path} not found in the well.")
@@ -100,11 +96,9 @@ class NgioWellMeta(CustomWellAttrs):
             acquisition (int | None): The acquisition id to filter the images.
         """
         if acquisition is None:
-            return [images.path for images in self.well.images]
+            return [images.path for images in self.images]
         return [
-            images.path
-            for images in self.well.images
-            if images.acquisition == acquisition
+            images.path for images in self.images if images.acquisition == acquisition
         ]
 
     def add_image(
@@ -118,7 +112,7 @@ class NgioWellMeta(CustomWellAttrs):
             strict (bool): If True, check if the image already exists in the well.
                 If False, do not check if the image already exists in the well.
         """
-        list_of_images = self.well.images
+        list_of_images = self.images
         for image in list_of_images:
             if image.path == path:
                 raise NgioValueError(
@@ -137,9 +131,7 @@ class NgioWellMeta(CustomWellAttrs):
 
         new_image = CustomWellImage(path=path, acquisition=acquisition)
         list_of_images.append(new_image)
-        return NgioWellMeta(
-            well=CustomWellMeta(images=list_of_images, version=self.well.version)
-        )
+        return NgioWellMeta(images=list_of_images, version=self.version)
 
     def remove_image(self, path: str) -> "NgioWellMeta":
         """Remove an image from the well.
@@ -147,15 +139,11 @@ class NgioWellMeta(CustomWellAttrs):
         Args:
             path (str): The path of the image.
         """
-        list_of_images = self.well.images
+        list_of_images = self.images
         for image in list_of_images:
             if image.path == path:
                 list_of_images.remove(image)
-                return NgioWellMeta(
-                    well=CustomWellMeta(
-                        images=list_of_images, version=self.well.version
-                    )
-                )
+                return NgioWellMeta(images=list_of_images, version=self.version)
         raise NgioValueError(f"Image at path {path} not found in the well.")
 
 
@@ -218,26 +206,30 @@ def _relabel_wells(
     return new_wells
 
 
-class NgioPlateMeta(HCSAttrs):
+class NgioPlateMeta(BaseModel):
     """HCS plate metadata."""
 
+    plate: PlateWithVersion
+    version: NgffVersions
+
     @classmethod
     def default_init(
         cls,
         images: list[ImageInWellPath] | None = None,
         name: str | None = None,
-        version: NgffVersions | None = None,
+        version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioPlateMeta":
         plate = cls(
-            plate=Plate(
+            plate=PlateWithVersion(
                 rows=[],
                 columns=[],
                 acquisitions=None,
                 wells=[],
                 field_count=None,
-                version=version,
                 name=name,
-            )
+                version=version,
+            ),
+            version=version,
         )
 
         if images is None:
@@ -346,16 +338,16 @@ class NgioPlateMeta(HCSAttrs):
         else:
             wells = self.plate.wells
 
-        new_plate = Plate(
+        new_plate = PlateWithVersion(
             rows=rows,
             columns=self.plate.columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.plate.version,
+            version=self.version,
         )
-        return NgioPlateMeta(plate=new_plate), row_idx
+        return NgioPlateMeta(plate=new_plate, version=self.version), row_idx
 
     def add_column(self, column: str | int) -> "tuple[NgioPlateMeta, int]":
         """Add a column to the plate.
@@ -384,16 +376,16 @@ class NgioPlateMeta(HCSAttrs):
         else:
             wells = self.plate.wells
 
-        new_plate = Plate(
+        new_plate = PlateWithVersion(
             rows=self.plate.rows,
             columns=columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.plate.version,
+            version=self.version,
         )
-        return NgioPlateMeta(plate=new_plate), column_idx
+        return NgioPlateMeta(plate=new_plate, version=self.version), column_idx
 
     def add_well(
         self,
@@ -422,16 +414,16 @@ class NgioPlateMeta(HCSAttrs):
                 )
             )
 
-        new_plate = Plate(
+        new_plate = PlateWithVersion(
             rows=plate.plate.rows,
             columns=plate.plate.columns,
             acquisitions=plate.plate.acquisitions,
             wells=wells,
             field_count=plate.plate.field_count,
             name=plate.plate.name,
-            version=plate.plate.version,
+            version=plate.version,
         )
-        return NgioPlateMeta(plate=new_plate)
+        return NgioPlateMeta(plate=new_plate, version=plate.version)
 
     def add_acquisition(
         self,
@@ -461,16 +453,16 @@ class NgioPlateMeta(HCSAttrs):
             Acquisition(id=acquisition_id, name=acquisition_name, **acquisition_kwargs)
         )
 
-        new_plate = Plate(
+        new_plate = PlateWithVersion(
             rows=self.plate.rows,
             columns=self.plate.columns,
             acquisitions=acquisitions,
             wells=self.plate.wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.plate.version,
+            version=self.version,
         )
-        return NgioPlateMeta(plate=new_plate)
+        return NgioPlateMeta(plate=new_plate, version=self.version)
 
     def remove_well(self, row: str, column: str | int) -> "NgioPlateMeta":
         """Remove a well from the plate.
@@ -497,16 +489,16 @@ class NgioPlateMeta(HCSAttrs):
                 f"Well at row {row} and column {column} not found in the plate."
             )
 
-        new_plate = Plate(
+        new_plate = PlateWithVersion(
             rows=self.plate.rows,
             columns=self.plate.columns,
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
             name=self.plate.name,
-            version=self.plate.version,
+            version=self.version,
         )
-        return NgioPlateMeta(plate=new_plate)
+        return NgioPlateMeta(plate=new_plate, version=self.version)
 
     def derive(
         self,
@@ -531,16 +523,17 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions = None
 
         if version is None:
-            version = self.plate.version  # type: ignore (version is NgffVersions or None)
+            version = self.version
 
         return NgioPlateMeta(
-            plate=Plate(
+            plate=PlateWithVersion(
                 rows=rows,
                 columns=columns,
                 acquisitions=acquisitions,
                 wells=[],
                 field_count=self.plate.field_count,
-                version=version,
                 name=name,
-            )
+                version=version,
+            ),
+            version=version,
         )

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -13,11 +13,11 @@ import numpy as np
 from pydantic import BaseModel
 
 from ngio.ome_zarr_meta.ngio_specs._axes import (
+    AxesHandler,
     DefaultSpaceUnit,
     DefaultTimeUnit,
     SpaceUnits,
     TimeUnits,
-    build_canonical_axes_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs._channels import ChannelsMeta
 from ngio.ome_zarr_meta.ngio_specs._dataset import Dataset
@@ -66,42 +66,23 @@ class AbstractNgioImageMeta:
     @classmethod
     def default_init(
         cls,
-        levels: int | Sequence[str],
-        axes_names: Sequence[str],
-        pixel_size: PixelSize,
-        scaling_factors: Sequence[float] | None = None,
+        levels: Sequence[str],
+        axes_handler: AxesHandler,
+        scales: Sequence[tuple[float, ...]],
+        translations: Sequence[tuple[float, ...] | None],
         name: str | None = None,
         version: NgffVersions = DefaultNgffVersion,
     ):
         """Initialize the ImageMeta object."""
-        axes_handler = build_canonical_axes_handler(
-            axes_names,
-            space_units=pixel_size.space_unit,
-            time_units=pixel_size.time_unit,
-        )
-
-        px_size_dict = pixel_size.as_dict()
-        scale = [px_size_dict.get(name, 1.0) for name in axes_handler.axes_names]
-
-        if scaling_factors is None:
-            _default = {"x": 2.0, "y": 2.0}
-            scaling_factors = [
-                _default.get(name, 1.0) for name in axes_handler.axes_names
-            ]
-
-        if isinstance(levels, int):
-            levels = [str(i) for i in range(levels)]
-
         datasets = []
-        for level in levels:
+        for level, scale, translation in zip(levels, scales, translations, strict=True):
             dataset = Dataset(
                 path=level,
                 axes_handler=axes_handler,
                 scale=scale,
-                translation=None,
+                translation=translation,
             )
             datasets.append(dataset)
-            scale = [s * f for s, f in zip(scale, scaling_factors, strict=True)]
 
         return cls(
             version=version,
@@ -337,50 +318,15 @@ class AbstractNgioImageMeta:
             )
         return dataset, lr_dataset
 
-    def scaling_factor(self, path: str | None = None) -> list[float]:
-        """Get the scaling factors from a dataset to its lower resolution."""
-        if self.levels == 1:
-            return [1.0] * len(self.axes_handler.axes_names)
-        dataset, lr_dataset = self._get_closest_datasets(path=path)
-
-        scaling_factors = []
-        for ax_name in self.axes_handler.axes_names:
-            s_d = dataset.get_scale(ax_name)
-            s_lr_d = lr_dataset.get_scale(ax_name)
-            scaling_factors.append(s_lr_d / s_d)
-        return scaling_factors
-
-    def yx_scaling(self, path: str | None = None) -> tuple[float, float]:
-        """Get the scaling factor from a dataset to its lower resolution."""
-        if self.levels == 1:
-            return 1.0, 1.0
-        dataset, lr_dataset = self._get_closest_datasets(path=path)
-
-        if lr_dataset is None:
-            raise NgioValueError(
-                "No lower resolution dataset found. "
-                "This is the lowest resolution dataset."
-            )
-
-        s_d = dataset.get_scale("y")
-        s_lr_d = lr_dataset.get_scale("y")
-        scale_y = s_lr_d / s_d
-
-        s_d = dataset.get_scale("x")
-        s_lr_d = lr_dataset.get_scale("x")
-        scale_x = s_lr_d / s_d
-
-        return scale_y, scale_x
-
-    def z_scaling(self, path: str | None = None) -> float:
-        """Get the scaling factor from a dataset to its lower resolution."""
+    def scaling_factor(self, path: str | None = None) -> tuple[float, ...]:
+        """Get the scaling factors to downscale to the next lower resolution dataset."""
         if self.levels == 1:
-            return 1.0
+            return (1.0,) * len(self.axes_handler.axes_names)
         dataset, lr_dataset = self._get_closest_datasets(path=path)
-
-        s_d = dataset.get_scale("z", default=1.0)
-        s_lr_d = lr_dataset.get_scale("z", default=1.0)
-        return s_lr_d / s_d
+        scale = dataset.scale
+        lr_scale = lr_dataset.scale
+        scaling_factors = [s / s_lr for s_lr, s in zip(scale, lr_scale, strict=True)]
+        return tuple(scaling_factors)
 
 
 class NgioLabelMeta(AbstractNgioImageMeta):

ngio/ome_zarr_meta/v04/__init__.py

@@ -1,6 +1,6 @@
 """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_plate_meta,

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

@@ -23,7 +23,6 @@ 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,
@@ -44,37 +43,6 @@ 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
@@ -203,7 +171,7 @@ 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:
@@ -216,9 +184,7 @@ 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(
@@ -239,7 +205,7 @@ 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,
@@ -252,7 +218,7 @@ 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:
@@ -265,9 +231,7 @@ 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 = LabelAttrsV04(**metadata)
 
     if len(v04_label.multiscales) > 1:
         raise NotImplementedError(
@@ -301,7 +265,7 @@ 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,
@@ -423,42 +387,33 @@ def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
 
 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 +425,7 @@ 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)
 
 

ngio/ome_zarr_meta/v05/__init__.py

@@ -1,6 +1,6 @@
 """Utility to read/write OME-Zarr metadata v0.4."""
 
-from ngio.ome_zarr_meta.v05._v05_spec_utils import (
+from ngio.ome_zarr_meta.v05._v05_spec import (
     ngio_to_v05_image_meta,
     ngio_to_v05_label_meta,
     ngio_to_v05_plate_meta,