ngio 0.5.0b6__py3-none-any.whl → 0.5.1__py3-none-any.whl

ngio/images/_label.py

@@ -18,12 +18,9 @@ from ngio.ome_zarr_meta import (
     update_ngio_labels_group_meta,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
-    DefaultSpaceUnit,
-    DefaultTimeUnit,
     NgffVersions,
-    SpaceUnits,
-    TimeUnits,
 )
+from ngio.ome_zarr_meta.ngio_specs._axes import AxesSetup
 from ngio.tables import MaskingRoiTable
 from ngio.utils import (
     NgioValidationError,
@@ -49,7 +46,7 @@ class Label(AbstractImage):
         self,
         group_handler: ZarrGroupHandler,
         path: str,
-        meta_handler: LabelMetaHandler | None,
+        meta_handler: LabelMetaHandler,
     ) -> None:
         """Initialize the Image at a single level.
 
@@ -59,8 +56,6 @@ class Label(AbstractImage):
             meta_handler: The image metadata handler.
 
         """
-        if meta_handler is None:
-            meta_handler = LabelMetaHandler(group_handler)
         super().__init__(
             group_handler=group_handler, path=path, meta_handler=meta_handler
         )
@@ -82,21 +77,6 @@ class Label(AbstractImage):
         assert isinstance(meta, NgioLabelMeta)
         return 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.update_meta(meta)
-
     def build_masking_roi_table(
         self, axes_order: Sequence[str] | None = None
     ) -> MaskingRoiTable:
@@ -120,10 +100,12 @@ class LabelsContainer:
     def __init__(
         self,
         group_handler: ZarrGroupHandler,
+        axes_setup: AxesSetup | None = None,
         ngff_version: NgffVersions | None = None,
     ) -> None:
         """Initialize the LabelGroupHandler."""
         self._group_handler = group_handler
+        self._axes_setup = axes_setup or AxesSetup()
         # If the group is empty, initialize the metadata
         try:
             self._meta_handler = LabelsGroupMetaHandler(group_handler)
@@ -147,8 +129,13 @@ class LabelsContainer:
         meta = self._meta_handler.get_meta()
         return meta
 
+    @property
+    def axes_setup(self) -> AxesSetup:
+        """Return the axes setup."""
+        return self._axes_setup
+
     def list(self) -> list[str]:
-        """Create the /labels group if it doesn't exist."""
+        """Return the list of label names in the group."""
         return self.meta.labels
 
     def get(
@@ -176,13 +163,17 @@ class LabelsContainer:
             )
 
         group_handler = self._group_handler.get_handler(name)
-        label_meta_handler = LabelMetaHandler(group_handler)
+        label_meta_handler = LabelMetaHandler(group_handler, axes_setup=self.axes_setup)
         path = (
             label_meta_handler.get_meta()
             .get_dataset(path=path, pixel_size=pixel_size, strict=strict)
             .path
         )
-        return Label(group_handler, path, label_meta_handler)
+        return Label(
+            group_handler=group_handler,
+            path=path,
+            meta_handler=label_meta_handler,
+        )
 
     def delete(self, name: str, missing_ok: bool = False) -> None:
         """Delete a label from the group.
@@ -218,6 +209,7 @@ class LabelsContainer:
         pixelsize: float | tuple[float, float] | None = None,
         z_spacing: float | None = None,
         time_spacing: float | None = None,
+        translation: Sequence[float] | None = None,
         channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
@@ -244,6 +236,8 @@ class LabelsContainer:
                 label.
             z_spacing (float | None): The z spacing of the new label.
             time_spacing (float | None): The time spacing of the new label.
+            translation (Sequence[float] | None): The translation for each axis
+                at the highest resolution level. Defaults to None.
             channels_policy (Literal["squeeze", "same", "singleton"] | int):
                 Possible policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
@@ -279,7 +273,6 @@ class LabelsContainer:
             )
 
         label_group = self._group_handler.get_group(name, create_mode=True)
-
         derive_label(
             ref_image=ref_image,
             store=label_group,
@@ -288,6 +281,7 @@ class LabelsContainer:
             z_spacing=z_spacing,
             time_spacing=time_spacing,
             name=name,
+            translation=translation,
             channels_policy=channels_policy,
             ngff_version=ngff_version,
             chunks=chunks,
@@ -321,6 +315,7 @@ def derive_label(
     z_spacing: float | None = None,
     time_spacing: float | None = None,
     name: str | None = None,
+    translation: Sequence[float] | None = None,
     channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
@@ -334,7 +329,7 @@ def derive_label(
     # Deprecated arguments
     labels: Sequence[str] | None = None,
     pixel_size: PixelSize | None = None,
-) -> ZarrGroupHandler:
+) -> tuple[ZarrGroupHandler, AxesSetup]:
     """Derive a new OME-Zarr label from an existing image or label.
 
     If a kwarg is not provided, the value from the reference image will be used.
@@ -347,6 +342,8 @@ def derive_label(
         z_spacing (float | None): The z spacing of the new label.
         time_spacing (float | None): The time spacing of the new label.
         name (str | None): The name of the new label.
+        translation (Sequence[float] | None): The translation for each axis
+            at the highest resolution level. Defaults to None.
         channels_policy (Literal["squeeze", "same", "singleton"] | int): Possible
             policies:
             - If "squeeze", the channels axis will be removed (no matter its size).
@@ -371,12 +368,13 @@ def derive_label(
             and time_spacing instead.
 
     Returns:
-        ZarrGroupHandler: The group handler of the new label.
+        tuple[ZarrGroupHandler, AxesSetup]: The group handler of the new label
+            and the axes setup.
 
     """
     if dtype is None and isinstance(ref_image, Image):
         dtype = "uint32"
-    group_handler = abstract_derive(
+    group_handler, axes_setup = abstract_derive(
         ref_image=ref_image,
         meta_type=NgioLabelMeta,
         store=store,
@@ -385,6 +383,7 @@ def derive_label(
         z_spacing=z_spacing,
         time_spacing=time_spacing,
         name=name,
+        translation=translation,
         channels_meta=None,
         channels_policy=channels_policy,
         ngff_version=ngff_version,
@@ -398,13 +397,22 @@ def derive_label(
         labels=labels,
         pixel_size=pixel_size,
     )
-    return group_handler
+    return group_handler, axes_setup
 
 
 def build_masking_roi_table(
     label: Label, axes_order: Sequence[str] | None = None
 ) -> MaskingRoiTable:
-    """Compute the masking ROI table for a label."""
+    """Compute the masking ROI table for a label.
+
+    Args:
+        label: The label to compute the masking ROI table for.
+        axes_order: The order of axes for the computation. If None,
+            uses the label's default axes order.
+
+    Returns:
+        A MaskingRoiTable containing ROIs for each label in the segmentation.
+    """
     axes_order = axes_order or label.axes
     array = label.get_as_dask(axes_order=axes_order)
     rois = compute_masking_roi(array, label.pixel_size, axes_order=axes_order)

ngio/images/_masked_image.py

@@ -34,7 +34,7 @@ class MaskedImage(Image):
         self,
         group_handler: ZarrGroupHandler,
         path: str,
-        meta_handler: ImageMetaHandler | None,
+        meta_handler: ImageMetaHandler,
         label: Label,
         masking_roi_table: MaskingRoiTable,
     ) -> None:
@@ -299,7 +299,7 @@ class MaskedLabel(Label):
         self,
         group_handler: ZarrGroupHandler,
         path: str,
-        meta_handler: LabelMetaHandler | None,
+        meta_handler: LabelMetaHandler,
         label: Label,
         masking_roi_table: MaskingRoiTable,
     ) -> None: