ngio 0.2.0b2__py3-none-any.whl → 0.2.1__py3-none-any.whl

ngio/images/label.py

@@ -13,7 +13,7 @@ from ngio.ome_zarr_meta import (
     PixelSize,
     find_label_meta_handler,
 )
-from ngio.tables import MaskingROITable
+from ngio.tables import MaskingRoiTable
 from ngio.utils import (
     NgioValidationError,
     NgioValueError,
@@ -35,7 +35,7 @@ class Label(AbstractImage[LabelMetaHandler]):
 
         Args:
             group_handler: The Zarr group handler.
-            path: The path to the image in the omezarr file.
+            path: The path to the image in the ome_zarr file.
             meta_handler: The image metadata handler.
 
         """
@@ -45,12 +45,16 @@ class Label(AbstractImage[LabelMetaHandler]):
             group_handler=group_handler, path=path, meta_handler=meta_handler
         )
 
+    def __repr__(self) -> str:
+        """Return the string representation of the label."""
+        return f"Label(path={self.path}, {self.dimensions})"
+
     @property
     def meta(self) -> NgioLabelMeta:
         """Return the metadata."""
         return self._meta_handler.meta
 
-    def build_masking_roi_table(self) -> MaskingROITable:
+    def build_masking_roi_table(self) -> MaskingRoiTable:
         """Compute the masking ROI table."""
         return build_masking_roi_table(self)
 
@@ -101,7 +105,7 @@ class LabelsContainer:
 
         Args:
             name (str): The name of the label.
-            path (str | None): The path to the image in the omezarr file.
+            path (str | None): The path to the image in the ome_zarr file.
             pixel_size (PixelSize | None): The pixel size of the image.
             strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -270,7 +274,7 @@ def _derive_label(
     return None
 
 
-def build_masking_roi_table(label: Label) -> MaskingROITable:
+def build_masking_roi_table(label: Label) -> MaskingRoiTable:
     """Compute the masking ROI table for a label."""
     if label.dimensions.is_time_series:
         raise NgioValueError("Time series labels are not supported.")
@@ -278,4 +282,4 @@ def build_masking_roi_table(label: Label) -> MaskingROITable:
     array = label.get_array(axes_order=["z", "y", "x"], mode="dask")
 
     rois = compute_masking_roi(array, label.pixel_size)
-    return MaskingROITable(rois, reference_label=label.meta.name)
+    return MaskingRoiTable(rois, reference_label=label.meta.name)

ngio/images/masked_image.py

@@ -7,7 +7,7 @@ from ngio.common import ArrayLike, get_masked_pipe, roi_to_slice_kwargs, set_mas
 from ngio.images.image import Image
 from ngio.images.label import Label
 from ngio.ome_zarr_meta import ImageMetaHandler, LabelMetaHandler
-from ngio.tables import MaskingROITable
+from ngio.tables import MaskingRoiTable
 from ngio.utils import (
     ZarrGroupHandler,
 )
@@ -22,13 +22,13 @@ class MaskedImage(Image):
         path: str,
         meta_handler: ImageMetaHandler | None,
         label: Label,
-        masking_roi_table: MaskingROITable,
+        masking_roi_table: MaskingRoiTable,
     ) -> None:
         """Initialize the Image at a single level.
 
         Args:
             group_handler: The Zarr group handler.
-            path: The path to the image in the omezarr file.
+            path: The path to the image in the ome_zarr file.
             meta_handler: The image metadata handler.
             label: The label image.
             masking_roi_table: The masking ROI table.
@@ -40,6 +40,13 @@ class MaskedImage(Image):
         self._label = label
         self._masking_roi_table = masking_roi_table
 
+    def __repr__(self) -> str:
+        """Return a string representation of the object."""
+        label_name = self._label.meta.name
+        if label_name is None:
+            label_name = self._masking_roi_table.reference_label
+        return f"MaskedImage(path={self.path}, {self.dimensions}, {label_name})"
+
     def get_roi(
         self,
         label: int,
@@ -116,13 +123,13 @@ class MaskedLabel(Label):
         path: str,
         meta_handler: LabelMetaHandler | None,
         label: Label,
-        masking_roi_table: MaskingROITable,
+        masking_roi_table: MaskingRoiTable,
     ) -> None:
         """Initialize the Image at a single level.
 
         Args:
             group_handler: The Zarr group handler.
-            path: The path to the image in the omezarr file.
+            path: The path to the image in the ome_zarr file.
             meta_handler: The image metadata handler.
             label: The label image.
             masking_roi_table: The masking ROI table.
@@ -134,6 +141,13 @@ class MaskedLabel(Label):
         self._label = label
         self._masking_roi_table = masking_roi_table
 
+    def __repr__(self) -> str:
+        """Return a string representation of the object."""
+        label_name = self._label.meta.name
+        if label_name is None:
+            label_name = self._masking_roi_table.reference_label
+        return f"MaskedLabel(path={self.path}, {self.dimensions}, {label_name})"
+
     def get_roi(
         self,
         label: int,

ngio/images/{omezarr_container.py → ome_zarr_container.py}

@@ -13,14 +13,11 @@ from ngio.ome_zarr_meta import (
     NgioImageMeta,
     PixelSize,
 )
-from ngio.ome_zarr_meta.ngio_specs import (
-    SpaceUnits,
-    TimeUnits,
-)
+from ngio.ome_zarr_meta.ngio_specs import NgffVersion, SpaceUnits, TimeUnits
 from ngio.tables import (
     FeatureTable,
     GenericRoiTable,
-    MaskingROITable,
+    MaskingRoiTable,
     RoiTable,
     Table,
     TablesContainer,
@@ -125,6 +122,36 @@ class OmeZarrContainer:
         """Return the paths of the levels in the image."""
         return self._images_container.levels_paths
 
+    @property
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.get_image().is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.get_image().is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.get_image().is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.get_image().is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.get_image().is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.get_image().is_multi_channels
+
     def initialize_channel_meta(
         self,
         labels: Collection[str] | int | None = None,
@@ -163,7 +190,7 @@ class OmeZarrContainer:
         """Get an image at a specific level.
 
         Args:
-            path (str | None): The path to the image in the omezarr file.
+            path (str | None): The path to the image in the ome_zarr file.
             pixel_size (PixelSize | None): The pixel size of the image.
             strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -187,7 +214,7 @@ class OmeZarrContainer:
         Args:
             masking_label_name (str): The name of the label.
             masking_table_name (str | None): The name of the masking table.
-            path (str | None): The path to the image in the omezarr file.
+            path (str | None): The path to the image in the ome_zarr file.
             pixel_size (PixelSize | None): The pixel size of the image.
             strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -262,21 +289,21 @@ class OmeZarrContainer:
             store, cache=self._group_handler.use_cache, mode=self._group_handler.mode
         )
 
-        new_omezarr = OmeZarrContainer(
+        new_ome_zarr = OmeZarrContainer(
             group_handler=handler,
             validate_arrays=False,
         )
 
         if copy_labels:
             self.labels_container._group_handler.copy_handler(
-                new_omezarr.labels_container._group_handler
+                new_ome_zarr.labels_container._group_handler
             )
 
         if copy_tables:
             self.tables_container._group_handler.copy_handler(
-                new_omezarr.tables_container._group_handler
+                new_ome_zarr.tables_container._group_handler
             )
-        return new_omezarr
+        return new_ome_zarr
 
     def list_tables(self) -> list[str]:
         """List all tables in the image."""
@@ -295,7 +322,7 @@ class OmeZarrContainer:
     @overload
     def get_table(
         self, name: str, check_type: Literal["masking_roi_table"]
-    ) -> MaskingROITable: ...
+    ) -> MaskingRoiTable: ...
 
     @overload
     def get_table(
@@ -318,7 +345,7 @@ class OmeZarrContainer:
                     )
                 return table
             case "masking_roi_table":
-                if not isinstance(table, MaskingROITable):
+                if not isinstance(table, MaskingRoiTable):
                     raise NgioValueError(
                         f"Table '{name}' is not a masking ROI table. "
                         f"Found type: {table.type()}"
@@ -349,7 +376,7 @@ class OmeZarrContainer:
         """Compute the ROI table for an image."""
         return self.get_image().build_image_roi_table(name=name)
 
-    def build_masking_roi_table(self, label: str) -> MaskingROITable:
+    def build_masking_roi_table(self, label: str) -> MaskingRoiTable:
         """Compute the masking ROI table for a label."""
         return self.get_label(label).build_masking_roi_table()
 
@@ -380,7 +407,7 @@ class OmeZarrContainer:
 
         Args:
             name (str): The name of the label.
-            path (str | None): The path to the image in the omezarr file.
+            path (str | None): The path to the image in the ome_zarr file.
             pixel_size (PixelSize | None): The pixel size of the image.
             strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -405,7 +432,7 @@ class OmeZarrContainer:
             label_name (str): The name of the label.
             masking_label_name (str): The name of the masking label.
             masking_table_name (str | None): The name of the masking table.
-            path (str | None): The path to the image in the omezarr file.
+            path (str | None): The path to the image in the ome_zarr file.
             pixel_size (PixelSize | None): The pixel size of the image.
             strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -477,7 +504,7 @@ class OmeZarrContainer:
         )
 
 
-def open_omezarr_container(
+def open_ome_zarr_container(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
@@ -503,7 +530,7 @@ def open_image(
 
     Args:
         store (StoreOrGroup): The Zarr store or group to create the image in.
-        path (str | None): The path to the image in the omezarr file.
+        path (str | None): The path to the image in the ome_zarr file.
         pixel_size (PixelSize | None): The pixel size of the image.
         strict (bool): Only used if the pixel size is provided. If True, the
                 pixel size must match the image pixel size exactly. If False, the
@@ -521,7 +548,7 @@ def open_image(
     )
 
 
-def create_empty_omezarr(
+def create_empty_ome_zarr(
     store: StoreOrGroup,
     shape: Collection[int],
     xy_pixelsize: float,
@@ -542,7 +569,7 @@ def create_empty_omezarr(
     channel_colors: Collection[str] | None = None,
     channel_active: Collection[bool] | None = None,
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
 ) -> OmeZarrContainer:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -581,7 +608,7 @@ def create_empty_omezarr(
             active. Defaults to None.
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        version (NgffVersion, optional): The version of the OME-Zarr specification.
             Defaults to "0.4".
     """
     handler = _create_empty_image(
@@ -603,18 +630,18 @@ def create_empty_omezarr(
         version=version,
     )
 
-    omezarr = OmeZarrContainer(group_handler=handler)
-    omezarr.initialize_channel_meta(
+    ome_zarr = OmeZarrContainer(group_handler=handler)
+    ome_zarr.initialize_channel_meta(
         labels=channel_labels,
         wavelength_id=channel_wavelengths,
         percentiles=percentiles,
         colors=channel_colors,
         active=channel_active,
     )
-    return omezarr
+    return ome_zarr
 
 
-def create_omezarr_from_array(
+def create_ome_zarr_from_array(
     store: StoreOrGroup,
     array: np.ndarray,
     xy_pixelsize: float,
@@ -634,7 +661,7 @@ def create_omezarr_from_array(
     name: str | None = None,
     chunks: Collection[int] | None = None,
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
 ) -> OmeZarrContainer:
     """Create an OME-Zarr image from a numpy array.
 
@@ -694,15 +721,15 @@ def create_omezarr_from_array(
         version=version,
     )
 
-    omezarr = OmeZarrContainer(group_handler=handler)
-    image = omezarr.get_image()
+    ome_zarr = OmeZarrContainer(group_handler=handler)
+    image = ome_zarr.get_image()
     image.set_array(array)
     image.consolidate()
-    omezarr.initialize_channel_meta(
+    ome_zarr.initialize_channel_meta(
         labels=channel_labels,
         wavelength_id=channel_wavelengths,
         percentiles=percentiles,
         colors=channel_colors,
         active=channel_active,
     )
-    return omezarr
+    return ome_zarr

ngio/ome_zarr_meta/__init__.py

@@ -16,6 +16,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     AxesMapper,
     Dataset,
     ImageInWellPath,
+    NgffVersion,
     NgioImageMeta,
     NgioLabelMeta,
     NgioPlateMeta,
@@ -31,6 +32,8 @@ __all__ = [
     "ImageMetaHandler",
     "LabelMetaHandler",
     "LabelMetaHandler",
+    "NgffVersion",
+    "NgffVersion",
     "NgioImageMeta",
     "NgioLabelMeta",
     "NgioPlateMeta",

ngio/ome_zarr_meta/ngio_specs/__init__.py

@@ -35,6 +35,7 @@ from ngio.ome_zarr_meta.ngio_specs._ngio_hcs import (
 )
 from ngio.ome_zarr_meta.ngio_specs._ngio_image import (
     ImageLabelSource,
+    NgffVersion,
     NgioImageLabelMeta,
     NgioImageMeta,
     NgioLabelMeta,
@@ -56,6 +57,7 @@ __all__ = [
     "Dataset",
     "ImageInWellPath",
     "ImageLabelSource",
+    "NgffVersion",
     "NgioColors",
     "NgioImageLabelMeta",
     "NgioImageMeta",

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -1,7 +1,5 @@
 """HCS (High Content Screening) specific metadata classes for NGIO."""
 
-from typing import Literal
-
 from ome_zarr_models.v04.hcs import HCSAttrs
 from ome_zarr_models.v04.plate import (
     Acquisition,
@@ -14,6 +12,7 @@ from ome_zarr_models.v04.well import WellAttrs
 from ome_zarr_models.v04.well_types import WellImage, WellMeta
 from pydantic import BaseModel
 
+from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersion
 from ngio.utils import NgioValueError
 
 
@@ -34,8 +33,10 @@ class NgioWellMeta(WellAttrs):
     def default_init(
         cls,
         images: list[ImageInWellPath] | None = None,
-        version: Literal["0.4"] | None = None,
+        version: NgffVersion | None = None,
     ) -> "NgioWellMeta":
+        if version is None:
+            version = "0.4"
         well = cls(well=WellMeta(images=[], version=version))
         if images is None:
             return well
@@ -164,7 +165,7 @@ class NgioPlateMeta(HCSAttrs):
         cls,
         images: list[ImageInWellPath] | None = None,
         name: str | None = None,
-        version: str | None = None,
+        version: NgffVersion | None = None,
     ) -> "NgioPlateMeta":
         plate = cls(
             plate=Plate(

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -7,8 +7,7 @@ can be converted to the OME standard.
 """
 
 from collections.abc import Collection
-from enum import Enum
-from typing import Any, TypeVar
+from typing import Any, Literal, TypeVar
 
 import numpy as np
 from pydantic import BaseModel
@@ -22,12 +21,7 @@ from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
 from ngio.utils import NgioValidationError, NgioValueError
 
 T = TypeVar("T")
-
-
-class NgffVersion(str, Enum):
-    """Allowed NGFF versions."""
-
-    v04 = "0.4"
+NgffVersion = Literal["0.4"]
 
 
 class ImageLabelSource(BaseModel):
@@ -45,9 +39,11 @@ class ImageLabelSource(BaseModel):
 class AbstractNgioImageMeta:
     """Base class for ImageMeta and LabelMeta."""
 
-    def __init__(self, version: str, name: str | None, datasets: list[Dataset]) -> None:
+    def __init__(
+        self, version: NgffVersion, name: str | None, datasets: list[Dataset]
+    ) -> None:
         """Initialize the ImageMeta object."""
-        self._version = NgffVersion(version)
+        self._version = version
         self._name = name
 
         if len(datasets) == 0:
@@ -70,7 +66,7 @@ class AbstractNgioImageMeta:
         pixel_size: PixelSize,
         scaling_factors: Collection[float] | None = None,
         name: str | None = None,
-        version: str = "0.4",
+        version: NgffVersion = "0.4",
     ):
         """Initialize the ImageMeta object."""
         axes = canonical_axes(
@@ -335,19 +331,13 @@ class NgioLabelMeta(AbstractNgioImageMeta):
 
     def __init__(
         self,
-        version: str,
+        version: NgffVersion,
         name: str | None,
         datasets: list[Dataset],
         image_label: ImageLabelSource | None = None,
     ) -> None:
         """Initialize the ImageMeta object."""
         super().__init__(version, name, datasets)
-
-        # Make sure that there are no channel axes
-        channel_axis = self.axes_mapper.get_axis("c")
-        if channel_axis is not None:
-            raise NgioValidationError("Label metadata must not have channel axes.")
-
         image_label = (
             ImageLabelSource.default_init(self.version)
             if image_label is None
@@ -380,7 +370,7 @@ class NgioImageMeta(AbstractNgioImageMeta):
 
     def __init__(
         self,
-        version: str,
+        version: NgffVersion,
         name: str | None,
         datasets: list[Dataset],
         channels: ChannelsMeta | None = None,

ngio/ome_zarr_meta/v04/_v04_spec_utils.py

@@ -41,7 +41,6 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgioWellMeta,
     default_channel_name,
 )
-from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersion
 
 
 def _is_v04_image_meta(metadata: dict) -> ImageAttrsV04 | ValidationError:
@@ -290,7 +289,7 @@ 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

ngio/tables/__init__.py

@@ -4,7 +4,7 @@ from ngio.tables.backends import ImplementedTableBackends
 from ngio.tables.tables_container import (
     FeatureTable,
     GenericRoiTable,
-    MaskingROITable,
+    MaskingRoiTable,
     RoiTable,
     Table,
     TablesContainer,
@@ -19,7 +19,7 @@ __all__ = [
     "GenericRoiTable",
     "GenericTable",
     "ImplementedTableBackends",
-    "MaskingROITable",
+    "MaskingRoiTable",
     "RoiTable",
     "Table",
     "TablesContainer",

ngio/tables/tables_container.py

@@ -2,7 +2,7 @@
 
 from typing import Literal, Protocol
 
-from ngio.tables.v1 import FeatureTableV1, MaskingROITableV1, RoiTableV1
+from ngio.tables.v1 import FeatureTableV1, MaskingRoiTableV1, RoiTableV1
 from ngio.tables.v1._generic_table import GenericTable
 from ngio.tables.v1._roi_table import _GenericRoiTableV1
 from ngio.utils import (
@@ -15,7 +15,7 @@ from ngio.utils import (
 
 GenericRoiTable = _GenericRoiTableV1
 RoiTable = RoiTableV1
-MaskingROITable = MaskingROITableV1
+MaskingRoiTable = MaskingRoiTableV1
 FeatureTable = FeatureTableV1
 
 
@@ -253,7 +253,7 @@ class TablesContainer:
 
 
 ImplementedTables().add_implementation(RoiTableV1)
-ImplementedTables().add_implementation(MaskingROITableV1)
+ImplementedTables().add_implementation(MaskingRoiTableV1)
 ImplementedTables().add_implementation(FeatureTableV1)
 
 ###################################################################################

ngio/tables/v1/__init__.py

@@ -2,6 +2,6 @@
 
 from ngio.tables.v1._feature_table import FeatureTableV1
 from ngio.tables.v1._generic_table import GenericTable
-from ngio.tables.v1._roi_table import MaskingROITableV1, RoiTableV1
+from ngio.tables.v1._roi_table import MaskingRoiTableV1, RoiTableV1
 
-__all__ = ["FeatureTableV1", "GenericTable", "MaskingROITableV1", "RoiTableV1"]
+__all__ = ["FeatureTableV1", "GenericTable", "MaskingRoiTableV1", "RoiTableV1"]

ngio/tables/v1/_feature_table.py

@@ -49,7 +49,6 @@ class FeatureTableV1:
             path = f"../labels/{reference_label}"
             self._meta = FeatureTableMeta(region=RegionMeta(path=path))
 
-        self._reference_label = reference_label
         self._instance_key = "label"
         if dataframe is None:
             self._dataframe = None
@@ -59,6 +58,15 @@ class FeatureTableV1:
             )
         self._table_backend = None
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        num_rows = len(self.dataframe) if self.dataframe is not None else 0
+        num_columns = len(self.dataframe.columns) if self.dataframe is not None else 0
+        properties = f"num_rows={num_rows}, num_columns={num_columns}"
+        if self.reference_label is not None:
+            properties += f", reference_label={self.reference_label}"
+        return f"FeatureTableV1({properties})"
+
     @staticmethod
     def type() -> str:
         """Return the type of the table."""
@@ -79,6 +87,17 @@ class FeatureTableV1:
             return None
         return self._table_backend.backend_name()
 
+    @property
+    def reference_label(self) -> str | None:
+        """Return the reference label."""
+        path = self._meta.region
+        if path is None:
+            return None
+
+        path = path.path
+        path = path.split("/")[-1]
+        return path
+
     @property
     def dataframe(self) -> pd.DataFrame:
         """Return the table as a DataFrame."""

ngio/tables/v1/_generic_table.py

@@ -51,6 +51,16 @@ class GenericTable:
 
         self._table_backend = None
 
+    def __repr__(self) -> str:
+        """Return a string representation of the table."""
+        if self._dataframe is not None:
+            num_rows = len(self.dataframe)
+            num_columns = len(self.dataframe.columns)
+            prop = f"num_rows={num_rows}, num_columns={num_columns}, mode=dataframe"
+        else:
+            prop = "mode=anndata"
+        return f"GenericTable({prop})"
+
     @staticmethod
     def type() -> str:
         """Return the type of the table."""