ngio 0.4.0a3__py3-none-any.whl → 0.4.0b1__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -17,7 +17,7 @@ from ngio.ome_zarr_meta.ngio_specs._axes import (
     DefaultTimeUnit,
     SpaceUnits,
     TimeUnits,
-    canonical_axes,
+    build_canonical_axes_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs._channels import ChannelsMeta
 from ngio.ome_zarr_meta.ngio_specs._dataset import Dataset
@@ -55,13 +55,13 @@ class AbstractNgioImageMeta:
             raise NgioValidationError("At least one dataset must be provided.")
 
         self._datasets = datasets
-        self._axes_mapper = datasets[0].axes_mapper
+        self._axes_handler = datasets[0].axes_handler
 
     def __repr__(self):
         class_name = type(self).__name__
         paths = [dataset.path for dataset in self.datasets]
-        on_disk_axes = self.axes_mapper.axes_names
-        return f"{class_name}(name={self.name}, datasets={paths}, axes={on_disk_axes})"
+        axes = self.axes_handler.axes_names
+        return f"{class_name}(name={self.name}, datasets={paths}, axes={axes})"
 
     @classmethod
     def default_init(
@@ -74,19 +74,20 @@ class AbstractNgioImageMeta:
         version: NgffVersions = DefaultNgffVersion,
     ):
         """Initialize the ImageMeta object."""
-        axes = canonical_axes(
+        axes_handler = build_canonical_axes_handler(
             axes_names,
             space_units=pixel_size.space_unit,
             time_units=pixel_size.time_unit,
         )
 
         px_size_dict = pixel_size.as_dict()
-        scale = [px_size_dict.get(ax.on_disk_name, 1.0) for ax in axes]
-        translation = [0.0] * len(scale)
+        scale = [px_size_dict.get(name, 1.0) for name in axes_handler.axes_names]
 
         if scaling_factors is None:
             _default = {"x": 2.0, "y": 2.0}
-            scaling_factors = [_default.get(ax.on_disk_name, 1.0) for ax in axes]
+            scaling_factors = [
+                _default.get(name, 1.0) for name in axes_handler.axes_names
+            ]
 
         if isinstance(levels, int):
             levels = [str(i) for i in range(levels)]
@@ -95,11 +96,9 @@ class AbstractNgioImageMeta:
         for level in levels:
             dataset = Dataset(
                 path=level,
-                on_disk_axes=axes,
-                on_disk_scale=scale,
-                on_disk_translation=translation,
-                allow_non_canonical_axes=False,
-                strict_canonical_order=True,
+                axes_handler=axes_handler,
+                scale=scale,
+                translation=None,
             )
             datasets.append(dataset)
             scale = [s * f for s, f in zip(scale, scaling_factors, strict=True)]
@@ -122,9 +121,18 @@ class AbstractNgioImageMeta:
             space_unit(str): The space unit to convert to.
             time_unit(str): The time unit to convert to.
         """
+        new_axes_handler = self.axes_handler.to_units(
+            space_unit=space_unit,
+            time_unit=time_unit,
+        )
         new_datasets = []
         for dataset in self.datasets:
-            new_dataset = dataset.to_units(space_unit=space_unit, time_unit=time_unit)
+            new_dataset = Dataset(
+                path=dataset.path,
+                axes_handler=new_axes_handler,
+                scale=dataset.scale,
+                translation=dataset.translation,
+            )
             new_datasets.append(new_dataset)
 
         return type(self)(
@@ -149,9 +157,9 @@ class AbstractNgioImageMeta:
         return self._datasets
 
     @property
-    def axes_mapper(self):
+    def axes_handler(self):
         """Return the axes mapper."""
-        return self._axes_mapper
+        return self._axes_handler
 
     @property
     def levels(self) -> int:
@@ -166,12 +174,12 @@ class AbstractNgioImageMeta:
     @property
     def space_unit(self) -> str | None:
         """Get the space unit of the pixel size."""
-        return self.datasets[0].pixel_size.space_unit
+        return self.axes_handler.space_unit
 
     @property
     def time_unit(self) -> str | None:
         """Get the time unit of the pixel size."""
-        return self.datasets[0].pixel_size.time_unit
+        return self.axes_handler.time_unit
 
     def _get_dataset_by_path(self, path: str) -> Dataset:
         """Get a dataset by its path."""
@@ -321,11 +329,11 @@ class AbstractNgioImageMeta:
     def scaling_factor(self, path: str | None = None) -> list[float]:
         """Get the scaling factors from a dataset to its lower resolution."""
         if self.levels == 1:
-            return [1.0] * len(self.axes_mapper.axes_names)
+            return [1.0] * len(self.axes_handler.axes_names)
         dataset, lr_dataset = self._get_closest_datasets(path=path)
 
         scaling_factors = []
-        for ax_name in self.axes_mapper.axes_names:
+        for ax_name in self.axes_handler.axes_names:
             s_d = dataset.get_scale(ax_name)
             s_lr_d = lr_dataset.get_scale(ax_name)
             scaling_factors.append(s_lr_d / s_d)
@@ -359,8 +367,8 @@ class AbstractNgioImageMeta:
             return 1.0
         dataset, lr_dataset = self._get_closest_datasets(path=path)
 
-        s_d = dataset.get_scale("z")
-        s_lr_d = lr_dataset.get_scale("z")
+        s_d = dataset.get_scale("z", default=1.0)
+        s_lr_d = lr_dataset.get_scale("z", default=1.0)
         return s_lr_d / s_d
 
 

ngio/ome_zarr_meta/ngio_specs/_pixel_size.py

@@ -2,6 +2,7 @@
 
 import math
 from functools import total_ordering
+from typing import overload
 
 import numpy as np
 
@@ -84,10 +85,25 @@ class PixelSize:
         )
         return self.distance(ref) < other.distance(ref)
 
-    def as_dict(self) -> dict:
+    def as_dict(self) -> dict[str, float]:
         """Return the pixel size as a dictionary."""
         return {"t": self.t, "z": self.z, "y": self.y, "x": self.x}
 
+    @overload
+    def get(self, axis: str, default: float) -> float: ...
+
+    @overload
+    def get(self, axis: str, default: None = None) -> float | None: ...
+
+    def get(self, axis: str, default: float | None = None) -> float | None:
+        """Get the pixel size for a given axis (in canonical name)."""
+        px_size = self.as_dict().get(axis, default)
+        if px_size is None:
+            raise ValueError(
+                f"Invalid axis name: {axis}, must be one of 'x', 'y', 'z', 't'."
+            )
+        return px_size
+
     @property
     def space_unit(self) -> SpaceUnits | str | None:
         """Return the space unit."""

ngio/ome_zarr_meta/v04/_v04_spec_utils.py

@@ -26,6 +26,7 @@ from ome_zarr_models.v04.omero import Window as WindowV04
 from pydantic import ValidationError
 
 from ngio.ome_zarr_meta.ngio_specs import (
+    AxesHandler,
     AxesSetup,
     Axis,
     AxisType,
@@ -160,34 +161,38 @@ def _v04_to_ngio_datasets(
             v04_multiscale.coordinateTransformations, global_scale, global_translation
         )
 
-    for v04_dataset in v04_multiscale.datasets:
-        axes = []
-        for v04_axis in v04_multiscale.axes:
-            unit = v04_axis.unit
-            if unit is not None and not isinstance(unit, str):
-                unit = str(unit)
-            axes.append(
-                Axis(
-                    on_disk_name=v04_axis.name,
-                    axis_type=AxisType(v04_axis.type),
-                    # (for some reason the type is a generic JsonValue,
-                    # but it should be a string or None)
-                    unit=v04_axis.unit,  # type: ignore
-                )
+    # Prepare axes handler
+    axes = []
+    for v04_axis in v04_multiscale.axes:
+        unit = v04_axis.unit
+        if unit is not None and not isinstance(unit, str):
+            unit = str(unit)
+        axes.append(
+            Axis(
+                name=v04_axis.name,
+                axis_type=AxisType(v04_axis.type),
+                # (for some reason the type is a generic JsonValue,
+                # but it should be a string or None)
+                unit=v04_axis.unit,  # type: ignore
             )
+        )
+    axes_handler = AxesHandler(
+        axes=axes,
+        axes_setup=axes_setup,
+        allow_non_canonical_axes=allow_non_canonical_axes,
+        strict_canonical_order=strict_canonical_order,
+    )
 
-        _on_disk_scale, _on_disk_translation = _compute_scale_translation(
+    for v04_dataset in v04_multiscale.datasets:
+        _scale, _translation = _compute_scale_translation(
             v04_dataset.coordinateTransformations, global_scale, global_translation
         )
         datasets.append(
             Dataset(
                 path=v04_dataset.path,
-                on_disk_axes=axes,
-                on_disk_scale=_on_disk_scale,
-                on_disk_translation=_on_disk_translation,
-                axes_setup=axes_setup,
-                allow_non_canonical_axes=allow_non_canonical_axes,
-                strict_canonical_order=strict_canonical_order,
+                axes_handler=axes_handler,
+                scale=_scale,
+                translation=_translation,
             )
         )
     return datasets
@@ -314,12 +319,12 @@ def _ngio_to_v04_multiscale(name: str | None, datasets: list[Dataset]) -> Multis
     Returns:
         MultiscaleV04: The v04 multiscale.
     """
-    ax_mapper = datasets[0].axes_mapper
+    ax_mapper = datasets[0].axes_handler
     v04_axes = []
     for axis in ax_mapper.axes:
         v04_axes.append(
             AxisV04(
-                name=axis.on_disk_name,
+                name=axis.name,
                 type=axis.axis_type.value if axis.axis_type is not None else None,
                 unit=axis.unit if axis.unit is not None else None,
             )
@@ -327,18 +332,16 @@ def _ngio_to_v04_multiscale(name: str | None, datasets: list[Dataset]) -> Multis
 
     v04_datasets = []
     for dataset in datasets:
-        transform = [VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale))]
-        if sum(dataset._on_disk_translation) > 0:
+        transform = [VectorScaleV04(type="scale", scale=list(dataset._scale))]
+        if sum(dataset._translation) > 0:
             transform = (
-                VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale)),
+                VectorScaleV04(type="scale", scale=list(dataset._scale)),
                 VectorTranslationV04(
-                    type="translation", translation=list(dataset._on_disk_translation)
+                    type="translation", translation=list(dataset._translation)
                 ),
             )
         else:
-            transform = (
-                VectorScaleV04(type="scale", scale=list(dataset._on_disk_scale)),
-            )
+            transform = (VectorScaleV04(type="scale", scale=list(dataset._scale)),)
 
         v04_datasets.append(
             DatasetV04(path=dataset.path, coordinateTransformations=transform)

ngio/resources/__init__.py

@@ -28,6 +28,7 @@ _resources = {
                 / "mask.png",
                 create_masking_table=True,
                 ensure_unique_labels=False,
+                dtype="uint8",
             ),
         ],
         xy_pixelsize=0.325,

ngio/resources/resource_model.py

@@ -19,6 +19,7 @@ class LabelsInfo(BaseModel):
     label_path: Path
     ensure_unique_labels: bool = True
     create_masking_table: bool = False
+    dtype: str = "uint32"
 
 
 class SampleInfo(BaseModel):

ngio/{common/transforms → transforms}/__init__.py

@@ -1,5 +1,5 @@
 """Concrete IO transformations."""
 
-from ngio.common.transforms._zoom import ZoomTransform
+from ngio.transforms._zoom import ZoomTransform
 
 __all__ = ["ZoomTransform"]

ngio/transforms/_zoom.py

@@ -0,0 +1,19 @@
+from ngio.common._zoom import (
+    InterpolationOrder,
+)
+from ngio.images._abstract_image import AbstractImage
+from ngio.io_pipes._zoom_transform import BaseZoomTransform
+
+
+class ZoomTransform(BaseZoomTransform):
+    def __init__(
+        self,
+        input_image: AbstractImage,
+        target_image: AbstractImage,
+        order: InterpolationOrder = "nearest",
+    ) -> None:
+        super().__init__(
+            input_dimensions=input_image.dimensions,
+            target_dimensions=target_image.dimensions,
+            order=order,
+        )

ngio/utils/_datasets.py

@@ -38,6 +38,11 @@ class UnzipAndRename(pooch.Unzip):
             return None
 
         tmp_dir = Path(extract_dir) / "tmp"
+        # If tmp_dir exists, remove it
+        if tmp_dir.exists():
+            shutil.rmtree(tmp_dir, ignore_errors=True)
+        tmp_dir.mkdir(parents=True, exist_ok=True)
+
         super()._extract_file(fname, tmp_dir)
 
         list_extracted_dirs = tmp_dir.iterdir()

ngio/utils/_zarr_utils.py

@@ -8,6 +8,7 @@ import zarr
 from filelock import BaseFileLock, FileLock
 from zarr.errors import ContainsGroupError, GroupNotFoundError
 from zarr.storage import DirectoryStore, FSStore, MemoryStore, Store, StoreLike
+from zarr.types import DIMENSION_SEPARATOR
 
 from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
 from ngio.utils._errors import NgioError
@@ -342,6 +343,8 @@ class ZarrGroupHandler:
         shape: tuple[int, ...],
         dtype: str,
         chunks: tuple[int, ...] | None = None,
+        dimension_separator: DIMENSION_SEPARATOR = "/",
+        compressor: str = "default",
         overwrite: bool = False,
     ) -> zarr.Array:
         if self.mode == "r":
@@ -353,7 +356,8 @@ class ZarrGroupHandler:
                 shape=shape,
                 dtype=dtype,
                 chunks=chunks,
-                dimension_separator="/",
+                dimension_separator=dimension_separator,
+                compressor=compressor,
                 overwrite=overwrite,
             )
         except ContainsGroupError as e:

{ngio-0.4.0a3.dist-info → ngio-0.4.0b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.0a3
+Version: 0.4.0b1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

ngio-0.4.0b1.dist-info/RECORD

@@ -0,0 +1,85 @@
+ngio/__init__.py,sha256=rEgnXuU6TCejUUGsxt4eKmjMhxjYh0fYBxWF4o5YjbE,1435
+ngio/common/__init__.py,sha256=aPSuUbdGryrxbnlWrsVNe3LZoBAWC4GijR1BNH1UwuU,612
+ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
+ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
+ngio/common/_pyramid.py,sha256=F5OI_mULxzMTpMeihC4Y22cjuB5GKN2jRdpwfMXJHiE,8018
+ngio/common/_roi.py,sha256=DFI2BJdJ-JNC5uZARxlvL25ZYHb9HJhCP-sOID_Db20,10196
+ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
+ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
+ngio/experimental/__init__.py,sha256=3pmBtHi-i8bKjTsvrOJM56ZyRX3Pv_dceCdt88-8COQ,147
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