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

ngio/__init__.py

@@ -9,16 +9,16 @@ except PackageNotFoundError:  # pragma: no cover
 __author__ = "Lorenzo Cerrone"
 __email__ = "lorenzo.cerrone@uzh.ch"
 
-from ngio.common import ArrayLike, Dimensions
-from ngio.hcs import OmeZarrPlate, create_empty_plate, open_omezarr_plate
+from ngio.common import ArrayLike, Dimensions, Roi, RoiPixels
+from ngio.hcs import OmeZarrPlate, create_empty_plate, open_ome_zarr_plate
 from ngio.images import (
     Image,
     Label,
     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,
 )
 from ngio.ome_zarr_meta.ngio_specs import AxesSetup, ImageInWellPath, PixelSize
 
@@ -32,10 +32,12 @@ __all__ = [
     "OmeZarrContainer",
     "OmeZarrPlate",
     "PixelSize",
-    "create_empty_omezarr",
+    "Roi",
+    "RoiPixels",
+    "create_empty_ome_zarr",
     "create_empty_plate",
-    "create_omezarr_from_array",
+    "create_ome_zarr_from_array",
     "open_image",
-    "open_omezarr_container",
-    "open_omezarr_plate",
+    "open_ome_zarr_container",
+    "open_ome_zarr_plate",
 ]

ngio/common/__init__.py

@@ -15,7 +15,7 @@ from ngio.common._common_types import ArrayLike
 from ngio.common._dimensions import Dimensions
 from ngio.common._masking_roi import compute_masking_roi
 from ngio.common._pyramid import consolidate_pyramid, init_empty_pyramid, on_disk_zoom
-from ngio.common._roi import RasterCooROI, WorldCooROI, roi_to_slice_kwargs
+from ngio.common._roi import Roi, RoiPixels, roi_to_slice_kwargs
 from ngio.common._slicer import (
     SliceTransform,
     compute_and_slices,
@@ -29,9 +29,9 @@ from ngio.common._zoom import dask_zoom, numpy_zoom
 __all__ = [
     "ArrayLike",
     "Dimensions",
-    "RasterCooROI",
+    "Roi",
+    "RoiPixels",
     "SliceTransform",
-    "WorldCooROI",
     "compute_and_slices",
     "compute_masking_roi",
     "consolidate_pyramid",

ngio/common/_array_pipe.py

@@ -124,7 +124,7 @@ def get_pipe(
         case "dask":
             return _dask_get_pipe(array, slices, transformations)
 
-        case "delayed_numpy":
+        case "delayed":
             return _delayed_numpy_get_pipe(array, slices, transformations)
 
         case _:
@@ -179,12 +179,11 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
-    if "c" in slice_kwargs.keys():
-        # This makes the strong assumption that the
-        # user is passing the channel axis as "c"
-        # This will fail if the channel axis is queried
-        # with a different on-disk name
-        slice_kwargs.pop("c")
+    if not dimensions_label.has_axis("c"):
+        # Remove the 'c' from the slice_kwargs
+        # This will not work if the query uses non-default
+        # axes names for channel
+        slice_kwargs = {k: v for k, v in slice_kwargs.items() if k != "c"}
 
     label_patch = get_pipe(
         label_array,

ngio/common/_masking_roi.py

@@ -8,7 +8,7 @@ import dask.delayed
 import numpy as np
 import scipy.ndimage as ndi
 
-from ngio.common._roi import RasterCooROI, WorldCooROI
+from ngio.common._roi import Roi, RoiPixels
 from ngio.ome_zarr_meta import PixelSize
 from ngio.utils import NgioValueError
 
@@ -117,7 +117,7 @@ def lazy_compute_slices(segmentation: da.Array) -> dict[int, tuple[slice, ...]]:
 
 def compute_masking_roi(
     segmentation: np.ndarray | da.Array, pixel_size: PixelSize
-) -> list[WorldCooROI]:
+) -> list[Roi]:
     """Compute a ROIs for each label in a segmentation.
 
     This function expects a 2D or 3D segmentation array.
@@ -143,7 +143,7 @@ def compute_masking_roi(
             max_z, max_y, max_x = slice_[0].stop, slice_[1].stop, slice_[2].stop
         else:
             raise ValueError("Invalid slice length.")
-        roi = RasterCooROI(
+        roi = RoiPixels(
             name=str(label),
             x_length=max_x - min_x,
             y_length=max_y - min_y,
@@ -153,6 +153,6 @@ def compute_masking_roi(
             z=min_z,
         )
 
-        roi = roi.to_world_coo_roi(pixel_size)
+        roi = roi.to_roi(pixel_size)
         rois.append(roi)
     return rois

ngio/common/_roi.py

@@ -26,7 +26,7 @@ def _to_world(value: int, pixel_size: float) -> float:
     return value * pixel_size
 
 
-class WorldCooROI(BaseModel):
+class Roi(BaseModel):
     """Region of interest (ROI) metadata."""
 
     name: str
@@ -40,16 +40,16 @@ class WorldCooROI(BaseModel):
 
     model_config = ConfigDict(extra="allow")
 
-    def to_raster_coo(
+    def to_pixel_roi(
         self, pixel_size: PixelSize, dimensions: Dimensions
-    ) -> "RasterCooROI":
+    ) -> "RoiPixels":
         """Convert to raster coordinates."""
         dim_x = dimensions.get("x")
         dim_y = dimensions.get("y")
         # Will default to 1 if z does not exist
         dim_z = dimensions.get("z", strict=False)
 
-        return RasterCooROI(
+        return RoiPixels(
             name=self.name,
             x=_to_raster(self.x, pixel_size.x, dim_x),
             y=_to_raster(self.y, pixel_size.y, dim_y),
@@ -59,7 +59,7 @@ class WorldCooROI(BaseModel):
             z_length=_to_raster(self.z_length, pixel_size.z, dim_z),
         )
 
-    def zoom(self, zoom_factor: float = 1) -> "WorldCooROI":
+    def zoom(self, zoom_factor: float = 1) -> "Roi":
         """Zoom the ROI by a factor.
 
         Args:
@@ -71,7 +71,7 @@ class WorldCooROI(BaseModel):
         return zoom_roi(self, zoom_factor)
 
 
-class RasterCooROI(BaseModel):
+class RoiPixels(BaseModel):
     """Region of interest (ROI) metadata."""
 
     name: str
@@ -83,9 +83,9 @@ class RasterCooROI(BaseModel):
     z_length: int
     model_config = ConfigDict(extra="allow")
 
-    def to_world_coo_roi(self, pixel_size: PixelSize) -> WorldCooROI:
+    def to_roi(self, pixel_size: PixelSize) -> Roi:
         """Convert to world coordinates."""
-        return WorldCooROI(
+        return Roi(
             name=self.name,
             x=_to_world(self.x, pixel_size.x),
             y=_to_world(self.y, pixel_size.y),
@@ -105,7 +105,7 @@ class RasterCooROI(BaseModel):
         }
 
 
-def zoom_roi(roi: WorldCooROI, zoom_factor: float = 1) -> WorldCooROI:
+def zoom_roi(roi: Roi, zoom_factor: float = 1) -> Roi:
     """Zoom the ROI by a factor.
 
     Args:
@@ -127,7 +127,7 @@ def zoom_roi(roi: WorldCooROI, zoom_factor: float = 1) -> WorldCooROI:
     new_x = max(roi.x - diff_x / 2, 0)
     new_y = max(roi.y - diff_y / 2, 0)
 
-    new_roi = WorldCooROI(
+    new_roi = Roi(
         name=roi.name,
         x=new_x,
         y=new_y,
@@ -142,13 +142,13 @@ def zoom_roi(roi: WorldCooROI, zoom_factor: float = 1) -> WorldCooROI:
 
 
 def roi_to_slice_kwargs(
-    roi: WorldCooROI,
+    roi: Roi,
     pixel_size: PixelSize,
     dimensions: Dimensions,
     **slice_kwargs: slice | int | Iterable[int],
 ) -> dict[str, slice | int | Iterable[int]]:
     """Convert a WorldCooROI to slice_kwargs."""
-    raster_roi = roi.to_raster_coo(
+    raster_roi = roi.to_pixel_roi(
         pixel_size=pixel_size, dimensions=dimensions
     ).to_slices()
 

ngio/hcs/__init__.py

@@ -1,5 +1,5 @@
 """OME-Zarr HCS objects models."""
 
-from ngio.hcs.plate import OmeZarrPlate, create_empty_plate, open_omezarr_plate
+from ngio.hcs.plate import OmeZarrPlate, create_empty_plate, open_ome_zarr_plate
 
-__all__ = ["OmeZarrPlate", "create_empty_plate", "open_omezarr_plate"]
+__all__ = ["OmeZarrPlate", "create_empty_plate", "open_ome_zarr_plate"]

ngio/hcs/plate.py

@@ -3,6 +3,7 @@
 from ngio.images import OmeZarrContainer
 from ngio.ome_zarr_meta import (
     ImageInWellPath,
+    NgffVersion,
     NgioPlateMeta,
     NgioWellMeta,
     find_plate_meta_handler,
@@ -78,7 +79,7 @@ class OmeZarrPlate:
 
     def __repr__(self) -> str:
         """Return a string representation of the plate."""
-        return f"Plate([rows x columns] ({len(self.rows)} x {len(self.columns)})"
+        return f"Plate([rows x columns] ({len(self.rows)} x {len(self.columns)}))"
 
     @property
     def meta_handler(self):
@@ -110,21 +111,54 @@ class OmeZarrPlate:
         """Return the acquisitions ids in the plate."""
         return self.meta.acquisitions_ids
 
-    @property
-    def wells_paths(self) -> list[str]:
-        """Return the wells paths in the plate."""
-        return self.meta.wells_paths
-
-    def get_well_path(self, row: str, column: int | str) -> str:
+    def _well_path(self, row: str, column: int | str) -> str:
         """Return the well path in the plate."""
         return self.meta.get_well_path(row=row, column=column)
 
-    def get_image_path(self, row: str, column: int | str, path: str) -> str:
+    def _image_path(self, row: str, column: int | str, path: str) -> str:
         """Return the image path in the plate."""
         well = self.get_well(row, column)
         if path not in well.paths():
             raise ValueError(f"Image {path} does not exist in well {row}{column}")
-        return f"{self.get_well_path(row, column)}/{path}"
+        return f"{self._well_path(row, column)}/{path}"
+
+    def wells_paths(self) -> list[str]:
+        """Return the wells paths in the plate."""
+        return self.meta.wells_paths
+
+    def images_paths(self, acquisition: int | None = None) -> list[str]:
+        """Return the images paths in the plate.
+
+        If acquisition is None, return all images paths in the plate.
+        Else, return the images paths in the plate for the given acquisition.
+
+        Args:
+            acquisition (int | None): The acquisition id to filter the images.
+        """
+        images = []
+        for well_path, wells in self.get_wells().items():
+            for img_path in wells.paths(acquisition):
+                images.append(f"{well_path}/{img_path}")
+        return images
+
+    def well_images_paths(
+        self, row: str, column: int | str, acquisition: int | None = None
+    ) -> list[str]:
+        """Return the images paths in a well.
+
+        If acquisition is None, return all images paths in the well.
+        Else, return the images paths in the well for the given acquisition.
+
+        Args:
+            row (str): The row of the well.
+            column (int | str): The column of the well.
+            acquisition (int | None): The acquisition id to filter the images.
+        """
+        images = []
+        well = self.get_well(row=row, column=column)
+        for path in well.paths(acquisition):
+            images.append(self._image_path(row=row, column=column, path=path))
+        return images
 
     def get_well(self, row: str, column: int | str) -> OmeZarrWell:
         """Get a well from the plate.
@@ -136,36 +170,56 @@ class OmeZarrPlate:
         Returns:
             OmeZarrWell: The well.
         """
-        well_path = self.meta.get_well_path(row=row, column=column)
+        well_path = self._well_path(row=row, column=column)
         group_handler = self._group_handler.derive_handler(well_path)
         return OmeZarrWell(group_handler)
 
     def get_wells(self) -> dict[str, OmeZarrWell]:
-        """Get all wells in the plate."""
+        """Get all wells in the plate.
+
+        Returns:
+            dict[str, OmeZarrWell]: A dictionary of wells, where the key is the well
+                path and the value is the well object.
+        """
         wells = {}
-        for well_path in self.wells_paths:
+        for well_path in self.wells_paths():
             group_handler = self._group_handler.derive_handler(well_path)
             well = OmeZarrWell(group_handler)
             wells[well_path] = well
         return wells
 
-    def get_images(self, acquisition: int | None = None) -> list[OmeZarrContainer]:
+    def get_images(self, acquisition: int | None = None) -> dict[str, OmeZarrContainer]:
         """Get all images in the plate.
 
         Args:
             acquisition: The acquisition id to filter the images.
         """
-        images = []
-        for well_path, well in self.get_wells().items():
-            for img_path in well.paths(acquisition):
-                full_path = f"{well_path}/{img_path}"
-                img_group_handler = self._group_handler.derive_handler(full_path)
-                images.append(OmeZarrContainer(img_group_handler))
+        images = {}
+        for image_path in self.images_paths(acquisition):
+            img_group_handler = self._group_handler.derive_handler(image_path)
+            images[image_path] = OmeZarrContainer(img_group_handler)
         return images
 
+    def get_image(
+        self, row: str, column: int | str, image_path: str
+    ) -> OmeZarrContainer:
+        """Get an image from the plate.
+
+        Args:
+            row (str): The row of the well.
+            column (int | str): The column of the well.
+            image_path (str): The path of the image.
+
+        Returns:
+            OmeZarrContainer: The image.
+        """
+        image_path = self._image_path(row=row, column=column, path=image_path)
+        group_handler = self._group_handler.derive_handler(image_path)
+        return OmeZarrContainer(group_handler)
+
     def get_well_images(
         self, row: str, column: str | int, acquisition: int | None = None
-    ) -> list[OmeZarrContainer]:
+    ) -> dict[str, OmeZarrContainer]:
         """Get all images in a well.
 
         Args:
@@ -173,16 +227,12 @@ class OmeZarrPlate:
             column: The column of the well.
             acquisition: The acquisition id to filter the images.
         """
-        well_path = self.meta.get_well_path(row=row, column=column)
-        group_handler = self._group_handler.derive_handler(well_path)
-        well = OmeZarrWell(group_handler)
-
-        images = []
-        for path in well.paths(acquisition):
-            image_path = f"{well_path}/{path}"
-            group_handler = self._group_handler.derive_handler(image_path)
-            images.append(OmeZarrContainer(group_handler))
-
+        images = {}
+        for image_paths in self.well_images_paths(
+            row=row, column=column, acquisition=acquisition
+        ):
+            group_handler = self._group_handler.derive_handler(image_paths)
+            images[image_paths] = OmeZarrContainer(group_handler)
         return images
 
     def _add_image(
@@ -220,7 +270,9 @@ class OmeZarrPlate:
                 # Initialize the well metadata
                 # if the group is empty
                 well_meta = NgioWellMeta.default_init()
-                meta_handler = get_well_meta_handler(group_handler, version="0.4")
+                version = self.meta.plate.version
+                version = version if version is not None else "0.4"
+                meta_handler = get_well_meta_handler(group_handler, version=version)
             else:
                 meta_handler = find_well_meta_handler(group_handler)
                 well_meta = meta_handler.meta
@@ -339,7 +391,7 @@ class OmeZarrPlate:
         )
 
 
-def open_omezarr_plate(
+def open_ome_zarr_plate(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
@@ -364,7 +416,7 @@ def create_empty_plate(
     store: StoreOrGroup,
     name: str,
     images: list[ImageInWellPath] | None = None,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
     cache: bool = False,
     overwrite: bool = False,
     parallel_safe: bool = True,
@@ -391,7 +443,7 @@ def create_empty_plate(
                 acquisition_id=image.acquisition_id,
                 acquisition_name=image.acquisition_name,
             )
-    return open_omezarr_plate(
+    return open_ome_zarr_plate(
         store=store,
         cache=cache,
         mode="r+",

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 +100,41 @@ 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."""
+        return self.dimensions.is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.dimensions.is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.dimensions.is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.dimensions.is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.dimensions.is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.dimensions.is_multi_channels
+
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel size of the image."""
@@ -114,6 +150,10 @@ 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,
@@ -140,7 +180,7 @@ 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],
@@ -184,7 +224,7 @@ 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],
@@ -226,7 +266,7 @@ 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],
@@ -260,7 +300,7 @@ 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],
@@ -297,7 +337,7 @@ 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,
@@ -306,4 +346,4 @@ 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 +12,7 @@ from ngio.ome_zarr_meta import (
     get_label_meta_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
+    NgffVersion,
     SpaceUnits,
     TimeUnits,
     canonical_axes_order,
@@ -34,7 +35,7 @@ def _init_generic_meta(
     space_unit: SpaceUnits | str | None = None,
     time_unit: TimeUnits | str | None = None,
     name: str | None = None,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
 ) -> tuple[_image_or_label_meta, list[float]]:
     """Initialize the metadata for an image or label."""
     scaling_factors = []
@@ -104,7 +105,7 @@ def _create_empty_label(
     chunks: Collection[int] | None = None,
     dtype: str = "uint16",
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
 ) -> ZarrGroupHandler:
     """Create an empty label with the given shape and metadata.
 
@@ -195,7 +196,7 @@ def _create_empty_image(
     chunks: Collection[int] | None = None,
     dtype: str = "uint16",
     overwrite: bool = False,
-    version: str = "0.4",
+    version: NgffVersion = "0.4",
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr image with the given shape and metadata.
 

ngio/images/image.py

@@ -55,7 +55,7 @@ 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.
 
         """
@@ -281,7 +281,7 @@ 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