bioptimus.data.tile_spec

Tile specification dataclass. Defines TileSpec, a pure data structure describing tile geometry (size, stride, resolution, measurement unit). This module lives in the data layer so it can be imported by both bioptimus.extraction and bioptimus.models without creating circular dependencies. For backward compatibility, TileSpec is re-exported from bioptimus.extraction.wsi.types.

TileSpec

@dataclass(frozen=True)
class TileSpec()

Defines the specifications of a tile within a WSI for extraction. Attributes:

size - The size of the tile as (width, height) or a single integer for both dimensions.
stride - The stride of the tile as (stride_width, stride_height) or a single integer for both dimensions.
resolution - The resolution at which the tile is defined.
unit - The unit of measurement for the tile dimensions.

Example:

>>> spec = TileSpec(
...     size=(256, 256), stride=(128, 128),
...     resolution=Resolution(level=0),
...     unit=MeasurementUnit.PIXELS,
... )
>>> print(spec.size)
(256, 256)

size

(width, height)

stride

(stride_width, stride_height)

width

@property
def width() -> int

Returns the tile width.

height

@property
def height() -> int

Returns the tile height.

stride_width

@property
def stride_width() -> int

Returns the horizontal stride.

stride_height

@property
def stride_height() -> int

Returns the vertical stride.

scale_to_reference

def scale_to_reference(downsample_ratio: float, mpp: MPP) -> TileSpec

Returns a new TileSpec scaled to reference-level pixels.

Ratio of the reference-level downsample to the target-resolution downsample.

Microns-per-pixel at the target resolution.

Returns: A new TileSpec in reference-level pixels. Raises:

ValueError - If unit is not PIXELS or UM, or if the scaled size or stride rounds to zero (the requested geometry is finer than one reference-level pixel).

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TileSpec

size

stride

width

height

stride_width

stride_height

scale_to_reference

​TileSpec

​size

​stride

​width

​height

​stride_width

​stride_height

​scale_to_reference

TileSpec

size

stride

width

height

stride_width

stride_height

scale_to_reference