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

ngio/__init__.py

@@ -9,33 +9,53 @@ 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,
+    OmeZarrWell,
+    create_empty_plate,
+    create_empty_well,
+    open_ome_zarr_plate,
+    open_ome_zarr_well,
+)
 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,
+    DefaultNgffVersion,
+    ImageInWellPath,
+    NgffVersions,
+    PixelSize,
 )
-from ngio.ome_zarr_meta.ngio_specs import AxesSetup, ImageInWellPath, PixelSize
 
 __all__ = [
     "ArrayLike",
     "AxesSetup",
+    "DefaultNgffVersion",
     "Dimensions",
     "Image",
     "ImageInWellPath",
     "Label",
+    "NgffVersions",
     "OmeZarrContainer",
     "OmeZarrPlate",
+    "OmeZarrWell",
     "PixelSize",
-    "create_empty_omezarr",
+    "Roi",
+    "RoiPixels",
+    "create_empty_ome_zarr",
     "create_empty_plate",
-    "create_omezarr_from_array",
+    "create_empty_well",
+    "create_ome_zarr_from_array",
     "open_image",
-    "open_omezarr_container",
-    "open_omezarr_plate",
+    "open_ome_zarr_container",
+    "open_ome_zarr_plate",
+    "open_ome_zarr_well",
 ]

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 _:
@@ -179,6 +179,12 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
+    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,
         dimensions=dimensions_label,

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

@@ -10,7 +10,7 @@ import numpy as np
 from pydantic import BaseModel, ConfigDict, Field
 
 from ngio.common._dimensions import Dimensions
-from ngio.ome_zarr_meta.ngio_specs import PixelSize, SpaceUnits
+from ngio.ome_zarr_meta.ngio_specs import DefaultSpaceUnit, PixelSize, SpaceUnits
 from ngio.utils import NgioValueError
 
 
@@ -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
@@ -36,20 +36,20 @@ class WorldCooROI(BaseModel):
     x: float = 0.0
     y: float = 0.0
     z: float = 0.0
-    unit: SpaceUnits = Field(SpaceUnits.micrometer, repr=False)
+    unit: SpaceUnits | str | None = Field(DefaultSpaceUnit, repr=False)
 
     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 +1,19 @@
 """OME-Zarr HCS objects models."""
 
-from ngio.hcs.plate import OmeZarrPlate, create_empty_plate, open_omezarr_plate
+from ngio.hcs.plate import (
+    OmeZarrPlate,
+    OmeZarrWell,
+    create_empty_plate,
+    create_empty_well,
+    open_ome_zarr_plate,
+    open_ome_zarr_well,
+)
 
-__all__ = ["OmeZarrPlate", "create_empty_plate", "open_omezarr_plate"]
+__all__ = [
+    "OmeZarrPlate",
+    "OmeZarrWell",
+    "create_empty_plate",
+    "create_empty_well",
+    "open_ome_zarr_plate",
+    "open_ome_zarr_well",
+]