ngio 0.5.0a1__py3-none-any.whl → 0.5.0a3__py3-none-any.whl

ngio/__init__.py

@@ -9,7 +9,7 @@ except PackageNotFoundError:  # pragma: no cover
 __author__ = "Lorenzo Cerrone"
 __email__ = "lorenzo.cerrone@uzh.ch"
 
-from ngio.common import Dimensions, Roi, RoiPixels
+from ngio.common import Dimensions, Roi, RoiSlice
 from ngio.hcs import (
     OmeZarrPlate,
     OmeZarrWell,
@@ -52,7 +52,7 @@ __all__ = [
     "OmeZarrWell",
     "PixelSize",
     "Roi",
-    "RoiPixels",
+    "RoiSlice",
     "create_empty_ome_zarr",
     "create_empty_plate",
     "create_empty_well",

ngio/common/__init__.py

@@ -2,22 +2,27 @@
 
 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 (
-    Roi,
-    RoiPixels,
+from ngio.common._pyramid import (
+    ChunksLike,
+    ImagePyramidBuilder,
+    ShardsLike,
+    consolidate_pyramid,
+    on_disk_zoom,
 )
+from ngio.common._roi import Roi, RoiSlice
 from ngio.common._zoom import InterpolationOrder, dask_zoom, numpy_zoom
 
 __all__ = [
+    "ChunksLike",
     "Dimensions",
+    "ImagePyramidBuilder",
     "InterpolationOrder",
     "Roi",
-    "RoiPixels",
+    "RoiSlice",
+    "ShardsLike",
     "compute_masking_roi",
     "consolidate_pyramid",
     "dask_zoom",
-    "init_empty_pyramid",
     "numpy_zoom",
     "on_disk_zoom",
 ]

ngio/common/_masking_roi.py

@@ -7,7 +7,7 @@ import numpy as np
 import scipy.ndimage as ndi
 from dask.delayed import delayed
 
-from ngio.common._roi import Roi, RoiPixels
+from ngio.common._roi import Roi
 from ngio.ome_zarr_meta import PixelSize
 from ngio.utils import NgioValueError
 
@@ -135,52 +135,23 @@ def compute_masking_roi(
     rois = []
     for label, slice_ in slices.items():
         if len(slice_) == 2:
-            min_t, max_t = None, None
-            min_z, max_z = None, None
-            min_y, min_x = slice_[0].start, slice_[1].start
-            max_y, max_x = slice_[0].stop, slice_[1].stop
+            slices = {"y": slice_[0], "x": slice_[1]}
         elif len(slice_) == 3:
-            min_t, max_t = None, None
-            min_z, min_y, min_x = slice_[0].start, slice_[1].start, slice_[2].start
-            max_z, max_y, max_x = slice_[0].stop, slice_[1].stop, slice_[2].stop
+            slices = {"z": slice_[0], "y": slice_[1], "x": slice_[2]}
         elif len(slice_) == 4:
-            min_t, min_z, min_y, min_x = (
-                slice_[0].start,
-                slice_[1].start,
-                slice_[2].start,
-                slice_[3].start,
-            )
-            max_t, max_z, max_y, max_x = (
-                slice_[0].stop,
-                slice_[1].stop,
-                slice_[2].stop,
-                slice_[3].stop,
-            )
+            slices = {
+                "t": slice_[0],
+                "z": slice_[1],
+                "y": slice_[2],
+                "x": slice_[3],
+            }
         else:
             raise ValueError("Invalid slice length.")
 
-        if max_t is None:
-            t_length = None
-        else:
-            t_length = max_t - min_t
-
-        if max_z is None:
-            z_length = None
-        else:
-            z_length = max_z - min_z
-
-        roi = RoiPixels(
-            name=str(label),
-            x_length=max_x - min_x,
-            y_length=max_y - min_y,
-            z_length=z_length,
-            t_length=t_length,
-            x=min_x,
-            y=min_y,
-            z=min_z,
-            label=label,
+        roi = Roi.from_values(
+            name=str(label), slices=slices, label=label, space="pixel"
         )
 
-        roi = roi.to_roi(pixel_size)
+        roi = roi.to_world(pixel_size=pixel_size)
         rois.append(roi)
     return rois

ngio/common/_pyramid.py

@@ -1,13 +1,11 @@
-import math
-from collections.abc import Callable, Sequence
-from typing import Literal
+from collections.abc import Callable, Mapping, Sequence
+from typing import Any, Literal
 
 import dask.array as da
 import numpy as np
 import zarr
-from zarr.core.array import CompressorLike
+from pydantic import BaseModel, ConfigDict, model_validator
 
-# from zarr.types import DIMENSION_SEPARATOR
 from ngio.common._zoom import (
     InterpolationOrder,
     _zoom_inputs_check,
@@ -15,10 +13,7 @@ from ngio.common._zoom import (
     numpy_zoom,
 )
 from ngio.utils import (
-    AccessModeLiteral,
     NgioValueError,
-    StoreOrGroup,
-    open_group_wrapper,
 )
 
 
@@ -41,9 +36,19 @@ def _on_disk_dask_zoom(
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
 
-    target_array = target_array.rechunk(target.chunks)  # type: ignore
-    target_array.compute_chunk_sizes()
+    # This is a potential fix for Dask 2025.11
+    # import dask.config
+    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
+    # current_chunk_size = dask.config.get("array.chunk-size")
+    # Increase the chunk size to avoid dask potentially creating
+    # corrupted chunks when writing chunks that are not multiple of the
+    # target chunk size
+    # dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
+    target_array = target_array.rechunk(target.chunks)
+    target_array = target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
+    # Restore previous chunk size
+    # dask.config.set({"array.chunk-size": current_chunk_size})
 
 
 def _on_disk_coarsen(
@@ -189,85 +194,220 @@ def consolidate_pyramid(
         processed.append(target_image)
 
 
-def _maybe_int(value: float | int) -> float | int:
-    """Convert a float to an int if it is an integer."""
-    if isinstance(value, int):
-        return value
-    if value.is_integer():
-        return int(value)
-    return value
-
-
-def init_empty_pyramid(
-    store: StoreOrGroup,
-    paths: list[str],
-    ref_shape: Sequence[int],
-    scaling_factors: Sequence[float],
-    axes: Sequence[str],
-    chunks: Sequence[int] | Literal["auto"] = "auto",
-    dtype: str = "uint16",
-    mode: AccessModeLiteral = "a",
-    dimension_separator: Literal[".", "/"] = "/",
-    compressors: CompressorLike = "auto",
-    zarr_format: Literal[2, 3] = 2,
-) -> None:
-    # Return the an Image object
-    if chunks != "auto" and len(chunks) != len(ref_shape):
-        raise NgioValueError(
-            "The shape and chunks must have the same number of dimensions."
-        )
+################################################
+#
+# Builders for image pyramids
+#
+################################################
+
+ChunksLike = tuple[int, ...] | Literal["auto"]
+ShardsLike = tuple[int, ...] | Literal["auto"]
 
-    if chunks != "auto":
-        chunks = tuple(min(c, s) for c, s in zip(chunks, ref_shape, strict=True))
-    else:
-        chunks = "auto"
 
-    if len(ref_shape) != len(scaling_factors):
-        raise NgioValueError(
-            "The shape and scaling factor must have the same number of dimensions."
+def shapes_from_scaling_factors(
+    base_shape: tuple[int, ...],
+    scaling_factors: tuple[float, ...],
+    num_levels: int,
+) -> list[tuple[int, ...]]:
+    """Compute the shapes of each level in the pyramid from scaling factors.
+
+    Args:
+        base_shape (tuple[int, ...]): The shape of the base level.
+        scaling_factors (tuple[float, ...]): The scaling factors between levels.
+        num_levels (int): The number of levels in the pyramid.
+
+    Returns:
+        list[tuple[int, ...]]: The shapes of each level in the pyramid.
+    """
+    shapes = []
+    current_shape = base_shape
+    for _ in range(num_levels):
+        shapes.append(current_shape)
+        current_shape = tuple(
+            max(1, int(s / f))
+            for s, f in zip(current_shape, scaling_factors, strict=True)
         )
+    return shapes
 
-    # Ensure scaling factors are int if possible
-    # To reduce the risk of floating point issues
-    scaling_factors = [_maybe_int(s) for s in scaling_factors]
 
-    root_group = open_group_wrapper(store, mode=mode, zarr_format=zarr_format)
+def _check_order(shapes: Sequence[tuple[int, ...]]):
+    """Check if the shapes are in decreasing order."""
+    num_pixels = [np.prod(shape) for shape in shapes]
+    for i in range(1, len(num_pixels)):
+        if num_pixels[i] >= num_pixels[i - 1]:
+            raise NgioValueError("Shapes are not in decreasing order.")
 
-    array_static_kwargs = {
-        "dtype": dtype,
-        "overwrite": True,
-        "compressors": compressors,
-    }
 
-    if zarr_format == 2:
-        array_static_kwargs["chunk_key_encoding"] = {
-            "name": "v2",
-            "separator": dimension_separator,
-        }
-    else:
-        array_static_kwargs["chunk_key_encoding"] = {
-            "name": "default",
-            "separator": dimension_separator,
-        }
-        array_static_kwargs["dimension_names"] = axes
+class PyramidLevel(BaseModel):
+    path: str
+    shape: tuple[int, ...]
+    scale: tuple[float, ...]
+    chunks: ChunksLike = "auto"
+    shards: ShardsLike | None = None
 
-    for path in paths:
-        if any(s < 1 for s in ref_shape):
+    @model_validator(mode="after")
+    def _model_validation(self) -> "PyramidLevel":
+        # Same length as shape
+        if len(self.scale) != len(self.shape):
             raise NgioValueError(
-                "Level shape must be at least 1 on all dimensions. "
-                f"Calculated shape: {ref_shape} at level {path}."
+                "Scale must have the same length as shape "
+                f"({len(self.shape)}), got {len(self.scale)}"
             )
-        new_arr = root_group.create_array(
-            name=path,
-            shape=tuple(ref_shape),
+        if any(isinstance(s, float) and s < 0 for s in self.scale):
+            raise NgioValueError("Scale values must be positive.")
+
+        if isinstance(self.chunks, tuple):
+            if len(self.chunks) != len(self.shape):
+                raise NgioValueError(
+                    "Chunks must have the same length as shape "
+                    f"({len(self.shape)}), got {len(self.chunks)}"
+                )
+            normalized_chunks = []
+            for dim_size, chunk_size in zip(self.shape, self.chunks, strict=True):
+                normalized_chunks.append(min(dim_size, chunk_size))
+            self.chunks = tuple(normalized_chunks)
+
+        if isinstance(self.shards, tuple):
+            if len(self.shards) != len(self.shape):
+                raise NgioValueError(
+                    "Shards must have the same length as shape "
+                    f"({len(self.shape)}), got {len(self.shards)}"
+                )
+        return self
+
+
+class ImagePyramidBuilder(BaseModel):
+    levels: list[PyramidLevel]
+    axes: tuple[str, ...]
+    data_type: str = "uint16"
+    dimension_separator: Literal[".", "/"] = "/"
+    compressors: Any = "auto"
+    zarr_format: Literal[2, 3] = 2
+    other_array_kwargs: Mapping[str, Any] = {}
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+
+    @classmethod
+    def from_scaling_factors(
+        cls,
+        levels_paths: tuple[str, ...],
+        scaling_factors: tuple[float, ...],
+        base_shape: tuple[int, ...],
+        base_scale: tuple[float, ...],
+        axes: tuple[str, ...],
+        chunks: ChunksLike = "auto",
+        shards: ShardsLike | None = None,
+        data_type: str = "uint16",
+        dimension_separator: Literal[".", "/"] = "/",
+        compressors: Any = "auto",
+        zarr_format: Literal[2, 3] = 2,
+        other_array_kwargs: Mapping[str, Any] | None = None,
+    ) -> "ImagePyramidBuilder":
+        shapes = shapes_from_scaling_factors(
+            base_shape=base_shape,
+            scaling_factors=scaling_factors,
+            num_levels=len(levels_paths),
+        )
+        return cls.from_shapes(
+            shapes=shapes,
+            base_scale=base_scale,
+            axes=axes,
+            levels_paths=levels_paths,
             chunks=chunks,
-            **array_static_kwargs,
+            shards=shards,
+            data_type=data_type,
+            dimension_separator=dimension_separator,
+            compressors=compressors,
+            zarr_format=zarr_format,
+            other_array_kwargs=other_array_kwargs,
         )
 
-        ref_shape = [
-            math.floor(s / sc) for s, sc in zip(ref_shape, scaling_factors, strict=True)
-        ]
-        chunks = tuple(
-            min(c, s) for c, s in zip(new_arr.chunks, ref_shape, strict=True)
+    @classmethod
+    def from_shapes(
+        cls,
+        shapes: Sequence[tuple[int, ...]],
+        base_scale: tuple[float, ...],
+        axes: tuple[str, ...],
+        levels_paths: Sequence[str] | None = None,
+        chunks: ChunksLike = "auto",
+        shards: ShardsLike | None = None,
+        data_type: str = "uint16",
+        dimension_separator: Literal[".", "/"] = "/",
+        compressors: Any = "auto",
+        zarr_format: Literal[2, 3] = 2,
+        other_array_kwargs: Mapping[str, Any] | None = None,
+    ) -> "ImagePyramidBuilder":
+        levels = []
+        if levels_paths is None:
+            levels_paths = tuple(str(i) for i in range(len(shapes)))
+        _check_order(shapes)
+        scale_ = base_scale
+        for i, (path, shape) in enumerate(zip(levels_paths, shapes, strict=True)):
+            levels.append(
+                PyramidLevel(
+                    path=path,
+                    shape=shape,
+                    scale=scale_,
+                    chunks=chunks,
+                    shards=shards,
+                )
+            )
+            if i + 1 < len(shapes):
+                # This only works for downsampling pyramids
+                # The _check_order function ensures that
+                # shapes are decreasing
+                next_shape = shapes[i + 1]
+                scaling_factor = tuple(
+                    s1 / s2
+                    for s1, s2 in zip(
+                        shape,
+                        next_shape,
+                        strict=True,
+                    )
+                )
+                scale_ = tuple(
+                    s * f for s, f in zip(scale_, scaling_factor, strict=True)
+                )
+        other_array_kwargs = other_array_kwargs or {}
+        return cls(
+            levels=levels,
+            axes=axes,
+            data_type=data_type,
+            dimension_separator=dimension_separator,
+            compressors=compressors,
+            zarr_format=zarr_format,
+            other_array_kwargs=other_array_kwargs,
         )
-    return None
+
+    def to_zarr(self, group: zarr.Group) -> None:
+        """Save the pyramid specification to a Zarr group.
+
+        Args:
+            group (zarr.Group): The Zarr group to save the pyramid specification to.
+        """
+        array_static_kwargs = {
+            "dtype": self.data_type,
+            "overwrite": True,
+            "compressors": self.compressors,
+            **self.other_array_kwargs,
+        }
+
+        if self.zarr_format == 2:
+            array_static_kwargs["chunk_key_encoding"] = {
+                "name": "v2",
+                "separator": self.dimension_separator,
+            }
+        else:
+            array_static_kwargs["chunk_key_encoding"] = {
+                "name": "default",
+                "separator": self.dimension_separator,
+            }
+            array_static_kwargs["dimension_names"] = self.axes
+        for p_level in self.levels:
+            group.create_array(
+                name=p_level.path,
+                shape=tuple(p_level.shape),
+                chunks=p_level.chunks,
+                shards=p_level.shards,
+                **array_static_kwargs,
+            )