ngio 0.2.0b3__py3-none-any.whl → 0.2.2__py3-none-any.whl

ngio/images/__init__.py

@@ -2,12 +2,12 @@
 
 from ngio.images.image import Image, ImagesContainer
 from ngio.images.label import Label, LabelsContainer
-from ngio.images.omezarr_container import (
+from ngio.images.ome_zarr_container import (
     OmeZarrContainer,
-    create_empty_omezarr,
-    create_omezarr_from_array,
+    create_empty_ome_zarr,
+    create_ome_zarr_from_array,
     open_image,
-    open_omezarr_container,
+    open_ome_zarr_container,
 )
 
 __all__ = [
@@ -16,8 +16,8 @@ __all__ = [
     "Label",
     "LabelsContainer",
     "OmeZarrContainer",
-    "create_empty_omezarr",
-    "create_omezarr_from_array",
+    "create_empty_ome_zarr",
+    "create_ome_zarr_from_array",
     "open_image",
-    "open_omezarr_container",
+    "open_ome_zarr_container",
 ]

ngio/images/abstract_image.py

@@ -8,14 +8,15 @@ import zarr
 from ngio.common import (
     ArrayLike,
     Dimensions,
-    RasterCooROI,
-    WorldCooROI,
+    Roi,
+    RoiPixels,
     consolidate_pyramid,
     get_pipe,
     roi_to_slice_kwargs,
     set_pipe,
 )
 from ngio.ome_zarr_meta import (
+    AxesMapper,
     Dataset,
     ImageMetaHandler,
     LabelMetaHandler,
@@ -43,7 +44,7 @@ class AbstractImage(Generic[_image_handler]):
 
         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.
 
         """
@@ -63,7 +64,7 @@ class AbstractImage(Generic[_image_handler]):
             shape=self._zarr_array.shape, axes_mapper=self._dataset.axes_mapper
         )
 
-        self._axer_mapper = self._dataset.axes_mapper
+        self._axes_mapper = self._dataset.axes_mapper
 
     def __repr__(self) -> str:
         """Return a string representation of the image."""
@@ -99,6 +100,11 @@ class AbstractImage(Generic[_image_handler]):
         """Return the dimensions of the image."""
         return self._dimensions
 
+    @property
+    def axes_mapper(self) -> AxesMapper:
+        """Return the axes mapper of the image."""
+        return self._axes_mapper
+
     @property
     def is_3d(self) -> bool:
         """Return True if the image is 3D."""
@@ -129,6 +135,16 @@ class AbstractImage(Generic[_image_handler]):
         """Return True if the image is multichannel."""
         return self.dimensions.is_multi_channels
 
+    @property
+    def space_unit(self) -> str | None:
+        """Return the space unit of the image."""
+        return self.meta_handler.meta.space_unit
+
+    @property
+    def time_unit(self) -> str | None:
+        """Return the time unit of the image."""
+        return self.meta_handler.meta.time_unit
+
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel size of the image."""
@@ -144,6 +160,10 @@ class AbstractImage(Generic[_image_handler]):
         """Return the path of the image."""
         return self._dataset.path
 
+    def has_axis(self, axis: str) -> bool:
+        """Return True if the image has the given axis."""
+        return self.dimensions.has_axis(axis)
+
     def get_array(
         self,
         axes_order: Collection[str] | None = None,
@@ -170,7 +190,7 @@ class AbstractImage(Generic[_image_handler]):
 
     def get_roi(
         self,
-        roi: WorldCooROI,
+        roi: Roi,
         axes_order: Collection[str] | None = None,
         mode: Literal["numpy", "dask", "delayed"] = "numpy",
         **slice_kwargs: slice | int | Iterable[int],
@@ -214,7 +234,7 @@ class AbstractImage(Generic[_image_handler]):
 
     def set_roi(
         self,
-        roi: WorldCooROI,
+        roi: Roi,
         patch: ArrayLike,
         axes_order: Collection[str] | None = None,
         **slice_kwargs: slice | int | Iterable[int],
@@ -256,7 +276,7 @@ def consolidate_image(
 
 def get_roi_pipe(
     image: AbstractImage,
-    roi: WorldCooROI,
+    roi: Roi,
     axes_order: Collection[str] | None = None,
     mode: Literal["numpy", "dask", "delayed"] = "numpy",
     **slice_kwargs: slice | int | Iterable[int],
@@ -290,7 +310,7 @@ def get_roi_pipe(
 
 def set_roi_pipe(
     image: AbstractImage,
-    roi: WorldCooROI,
+    roi: Roi,
     patch: ArrayLike,
     axes_order: Collection[str] | None = None,
     **slice_kwargs: slice | int | Iterable[int],
@@ -327,7 +347,7 @@ def build_image_roi_table(image: AbstractImage, name: str = "image") -> RoiTable
         image.dimensions.get("y"),
         image.dimensions.get("x"),
     )
-    image_roi = RasterCooROI(
+    image_roi = RoiPixels(
         name=name,
         x=0,
         y=0,
@@ -336,4 +356,4 @@ def build_image_roi_table(image: AbstractImage, name: str = "image") -> RoiTable
         y_length=dim_y,
         z_length=dim_z,
     )
-    return RoiTable(rois=[image_roi.to_world_coo_roi(pixel_size=image.pixel_size)])
+    return RoiTable(rois=[image_roi.to_roi(pixel_size=image.pixel_size)])

ngio/images/create.py

@@ -12,6 +12,10 @@ from ngio.ome_zarr_meta import (
     get_label_meta_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
+    DefaultNgffVersion,
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    NgffVersions,
     SpaceUnits,
     TimeUnits,
     canonical_axes_order,
@@ -31,10 +35,10 @@ def _init_generic_meta(
     levels: int | list[str] = 5,
     yx_scaling_factor: float | tuple[float, float] = 2.0,
     z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
+    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
+    time_unit: TimeUnits | str | None = DefaultTimeUnit,
     name: str | None = None,
-    version: str = "0.4",
+    version: NgffVersions = DefaultNgffVersion,
 ) -> tuple[_image_or_label_meta, list[float]]:
     """Initialize the metadata for an image or label."""
     scaling_factors = []
@@ -54,20 +58,6 @@ def _init_generic_meta(
         else:
             scaling_factors.append(1.0)
 
-    if space_unit is None:
-        space_unit = SpaceUnits.micrometer
-    elif isinstance(space_unit, str):
-        space_unit = SpaceUnits(space_unit)
-    elif not isinstance(space_unit, SpaceUnits):
-        raise NgioValueError(f"space_unit can not be {type(space_unit)}.")
-
-    if time_unit is None:
-        time_unit = TimeUnits.seconds
-    elif isinstance(time_unit, str):
-        time_unit = TimeUnits(time_unit)
-    elif not isinstance(time_unit, TimeUnits):
-        raise NgioValueError(f"time_units can not be {type(time_unit)}.")
-
     pixel_sizes = PixelSize(
         x=pixelsize,
         y=pixelsize,
@@ -88,7 +78,7 @@ def _init_generic_meta(
     return meta, scaling_factors
 
 
-def _create_empty_label(
+def create_empty_label_container(
     store: StoreOrGroup,
     shape: Collection[int],
     pixelsize: float,
@@ -97,14 +87,14 @@ def _create_empty_label(
     levels: int | list[str] = 5,
     yx_scaling_factor: float | tuple[float, float] = 2.0,
     z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
+    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
+    time_unit: TimeUnits | str | None = DefaultTimeUnit,
     axes_names: Collection[str] | None = None,
     name: str | None = None,
     chunks: Collection[int] | None = None,
     dtype: str = "uint16",
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty label with the given shape and metadata.
 
@@ -121,10 +111,10 @@ def _create_empty_label(
             dimensions. Defaults to 2.0.
         z_scaling_factor (float, optional): The down-scaling factor in z dimension.
             Defaults to 1.0.
-        space_unit (SpaceUnits | str | None, optional): The unit of space. Defaults to
-            None.
-        time_unit (TimeUnits | str | None, optional): The unit of time. Defaults to
-            None.
+        space_unit (SpaceUnits, optional): The unit of space. Defaults to
+            DefaultSpaceUnit.
+        time_unit (TimeUnits, optional): The unit of time. Defaults to
+            DefaultTimeUnit.
         axes_names (Collection[str] | None, optional): The names of the axes.
             If None the canonical names are used. Defaults to None.
         name (str | None, optional): The name of the image. Defaults to None.
@@ -134,7 +124,7 @@ def _create_empty_label(
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (str, optional): The version of the OME-Zarr specification.
-            Defaults to "0.4".
+            Defaults to DefaultVersion.
 
     """
     if axes_names is None:
@@ -179,7 +169,7 @@ def _create_empty_label(
     return group_handler
 
 
-def _create_empty_image(
+def create_empty_image_container(
     store: StoreOrGroup,
     shape: Collection[int],
     pixelsize: float,
@@ -188,14 +178,14 @@ def _create_empty_image(
     levels: int | list[str] = 5,
     yx_scaling_factor: float | tuple[float, float] = 2,
     z_scaling_factor: float = 1.0,
-    space_unit: SpaceUnits | str | None = None,
-    time_unit: TimeUnits | str | None = None,
+    space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
+    time_unit: TimeUnits | str | None = DefaultTimeUnit,
     axes_names: Collection[str] | None = None,
     name: str | None = None,
     chunks: Collection[int] | None = None,
     dtype: str = "uint16",
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -212,10 +202,10 @@ def _create_empty_image(
             dimensions. Defaults to 2.0.
         z_scaling_factor (float, optional): The down-scaling factor in z dimension.
             Defaults to 1.0.
-        space_unit (SpaceUnits | str | None, optional): The unit of space. Defaults to
-            None.
-        time_unit (TimeUnits | str | None, optional): The unit of time. Defaults to
-            None.
+        space_unit (SpaceUnits, optional): The unit of space. Defaults to
+            DefaultSpaceUnit.
+        time_unit (TimeUnits, optional): The unit of time. Defaults to
+            DefaultTimeUnit.
         axes_names (Collection[str] | None, optional): The names of the axes.
             If None the canonical names are used. Defaults to None.
         name (str | None, optional): The name of the image. Defaults to None.
@@ -225,7 +215,7 @@ def _create_empty_image(
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (str, optional): The version of the OME-Zarr specification.
-            Defaults to "0.4".
+            Defaults to DefaultVersion.
 
     """
     if axes_names is None:

ngio/images/image.py

@@ -7,14 +7,22 @@ from dask import array as da
 
 from ngio.common import Dimensions
 from ngio.images.abstract_image import AbstractImage, consolidate_image
-from ngio.images.create import _create_empty_image
+from ngio.images.create import create_empty_image_container
 from ngio.ome_zarr_meta import (
     ImageMetaHandler,
     NgioImageMeta,
     PixelSize,
     find_image_meta_handler,
 )
-from ngio.ome_zarr_meta.ngio_specs import Channel, ChannelsMeta, ChannelVisualisation
+from ngio.ome_zarr_meta.ngio_specs import (
+    Channel,
+    ChannelsMeta,
+    ChannelVisualisation,
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    SpaceUnits,
+    TimeUnits,
+)
 from ngio.utils import (
     NgioValidationError,
     StoreOrGroup,
@@ -55,7 +63,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
         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.
 
         """
@@ -142,7 +150,7 @@ class ImagesContainer:
         image = self.get()
         return image.wavelength_ids
 
-    def initialize_channel_meta(
+    def set_channel_meta(
         self,
         labels: Collection[str] | int | None = None,
         wavelength_id: Collection[str] | None = None,
@@ -196,7 +204,7 @@ class ImagesContainer:
         meta.set_channels_meta(channel_meta)
         self._meta_handler.write_meta(meta)
 
-    def update_percentiles(
+    def set_channel_percentiles(
         self,
         start_percentile: float = 0.1,
         end_percentile: float = 99.9,
@@ -230,6 +238,21 @@ class ImagesContainer:
         meta.set_channels_meta(new_meta)
         self._meta_handler.write_meta(meta)
 
+    def set_axes_unit(
+        self,
+        space_unit: SpaceUnits = DefaultSpaceUnit,
+        time_unit: TimeUnits = DefaultTimeUnit,
+    ) -> None:
+        """Set the axes unit of the image.
+
+        Args:
+            space_unit (SpaceUnits): The space unit of the image.
+            time_unit (TimeUnits): The time unit of the image.
+        """
+        meta = self.meta
+        meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
+        self._meta_handler.write_meta(meta)
+
     def derive(
         self,
         store: StoreOrGroup,
@@ -238,6 +261,7 @@ class ImagesContainer:
         labels: Collection[str] | None = None,
         pixel_size: PixelSize | None = None,
         axes_names: Collection[str] | None = None,
+        name: str | None = None,
         chunks: Collection[int] | None = None,
         dtype: str | None = None,
         overwrite: bool = False,
@@ -252,6 +276,7 @@ class ImagesContainer:
             labels (Collection[str] | None): The labels of the new image.
             pixel_size (PixelSize | None): The pixel size of the new image.
             axes_names (Collection[str] | None): The axes names of the new image.
+            name (str | None): The name of the new image.
             chunks (Collection[int] | None): The chunk shape of the new image.
             dtype (str | None): The data type of the new image.
             overwrite (bool): Whether to overwrite an existing image.
@@ -267,6 +292,7 @@ class ImagesContainer:
             labels=labels,
             pixel_size=pixel_size,
             axes_names=axes_names,
+            name=name,
             chunks=chunks,
             dtype=dtype,
             overwrite=overwrite,
@@ -281,7 +307,7 @@ class ImagesContainer:
         """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
@@ -346,6 +372,7 @@ def derive_image_container(
     labels: Collection[str] | None = None,
     pixel_size: PixelSize | None = None,
     axes_names: Collection[str] | None = None,
+    name: str | None = None,
     chunks: Collection[int] | None = None,
     dtype: str | None = None,
     overwrite: bool = False,
@@ -360,6 +387,7 @@ def derive_image_container(
         labels (Collection[str] | None): The labels of the new image.
         pixel_size (PixelSize | None): The pixel size of the new image.
         axes_names (Collection[str] | None): The axes names of the new image.
+        name (str | None): The name of the new image.
         chunks (Collection[int] | None): The chunk shape of the new image.
         dtype (str | None): The data type of the new image.
         overwrite (bool): Whether to overwrite an existing image.
@@ -399,9 +427,12 @@ def derive_image_container(
             f"Got {chunks} for shape {shape}."
         )
 
+    if name is None:
+        name = ref_meta.name
+
     if dtype is None:
         dtype = ref_image.dtype
-    handler = _create_empty_image(
+    handler = create_empty_image_container(
         store=store,
         shape=shape,
         pixelsize=pixel_size.x,
@@ -413,6 +444,7 @@ def derive_image_container(
         time_unit=pixel_size.time_unit,
         space_unit=pixel_size.space_unit,
         axes_names=axes_names,
+        name=name,
         chunks=chunks,
         dtype=dtype,
         overwrite=overwrite,
@@ -443,7 +475,7 @@ def derive_image_container(
             )
         _labels = labels
 
-    image_container.initialize_channel_meta(
+    image_container.set_channel_meta(
         labels=_labels,
         wavelength_id=wavelength_id,
         percentiles=None,

ngio/images/label.py

@@ -5,7 +5,7 @@ from typing import Literal
 
 from ngio.common import compute_masking_roi
 from ngio.images.abstract_image import AbstractImage, consolidate_image
-from ngio.images.create import _create_empty_label
+from ngio.images.create import create_empty_label_container
 from ngio.images.image import Image
 from ngio.ome_zarr_meta import (
     LabelMetaHandler,
@@ -13,7 +13,13 @@ from ngio.ome_zarr_meta import (
     PixelSize,
     find_label_meta_handler,
 )
-from ngio.tables import MaskingROITable
+from ngio.ome_zarr_meta.ngio_specs import (
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    SpaceUnits,
+    TimeUnits,
+)
+from ngio.tables import MaskingRoiTable
 from ngio.utils import (
     NgioValidationError,
     NgioValueError,
@@ -35,7 +41,7 @@ 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 +51,31 @@ 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 set_axes_unit(
+        self,
+        space_unit: SpaceUnits = DefaultSpaceUnit,
+        time_unit: TimeUnits = DefaultTimeUnit,
+    ) -> None:
+        """Set the axes unit of the image.
+
+        Args:
+            space_unit (SpaceUnits): The space unit of the image.
+            time_unit (TimeUnits): The time unit of the image.
+        """
+        meta = self.meta
+        meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
+        self._meta_handler.write_meta(meta)
+
+    def build_masking_roi_table(self) -> MaskingRoiTable:
         """Compute the masking ROI table."""
         return build_masking_roi_table(self)
 
@@ -101,7 +126,7 @@ 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
@@ -249,7 +274,7 @@ def _derive_label(
         axes_names = list(axes_names)
         axes_names = axes_names[:c_axis] + axes_names[c_axis + 1 :]
 
-    _ = _create_empty_label(
+    _ = create_empty_label_container(
         store=store,
         shape=shape,
         pixelsize=ref_image.pixel_size.x,
@@ -270,7 +295,7 @@ 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 +303,4 @@ 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,