types

Tile and mega-tile specification types for WSI extraction. Defines the TileSpec and MegaTileSpec dataclasses as well as the GridLayout enum and the MegaTileRegion container. TileSpec Encapsulates tile size, stride, target resolution, and measurement unit. Used by TileExtractor. GridLayout Enum for rectangular vs. hexagonal tiling grids. MegaTileSpec Describes a mega tile — a grid of smaller tiles — including grid dimensions, per-tile specification, layout, stride, and valid-tile-ratio bounds. Used by MegaTileExtractor. MegaTileRegion Immutable container returned by the mega-tile extractor. Holds the top-left location, grid shape, per-tile RegionSpec list, tile-availability mask, and aggregate tissue statistics. Example:

>>> from bioptimus.extraction.wsi.types import TileSpec, MegaTileSpec, GridLayout
>>> from bioptimus.io.wsi.types import Level, MeasurementUnit
>>> tile = TileSpec(
...     size=(256, 256), stride=(256, 256),
...     resolution=Level(0), unit=MeasurementUnit.PIXELS,
... )
>>> mega = MegaTileSpec(
...     megatile_shape=(5, 5), tile_spec=tile,
...     grid_layout=GridLayout.RECTANGULAR,
... )
>>> mega.num_tiles
25

GridLayout

class GridLayout(str, Enum)

Layout strategy for arranging tiles within a mega tile.

Standard row-major rectangular grid.

Offset hex grid — odd rows are shifted right by half a tile width, producing a honeycomb pattern.

Example:

>>> GridLayout.RECTANGULAR.value
'RECTANGULAR'

MegaTileSpec

@dataclass(frozen=True)
class MegaTileSpec()

Defines the specification of a mega tile — a grid of smaller tiles. A mega tile groups rows × cols individual tiles into a single logical region that can be extracted from a WSI. The per-tile geometry is delegated to TileSpec.

tuple[int, int]

Number of tiles as (rows, cols).

TileSpec

Size, stride, resolution, and unit for each individual tile.

GridLayout

Rectangular or hexagonal arrangement. Defaults to RECTANGULAR.

tuple[int, int] | None

Stride expressed in number of tiles as (stride_rows, stride_cols). None defaults to megatile_shape (no overlap).

float

Minimum fraction of tiles that must pass the tissue-mask threshold for the mega tile to be kept. Defaults to 0.5.

float | None

Optional upper bound on the valid-tile fraction. None means no upper limit.

Example:

>>> tile = TileSpec(
...     size=(256, 256), stride=(256, 256),
...     resolution=Level(0), unit=MeasurementUnit.PIXELS,
... )
>>> mega = MegaTileSpec(megatile_shape=(5, 5), tile_spec=tile)
>>> mega.rows, mega.cols
(5, 5)
>>> mega.num_tiles
25

megatile_shape

(rows, cols) in number of tiles

megatile_stride

(stride_rows, stride_cols)

rows

@property
def rows() -> int

Number of tile rows in the mega tile.

cols

@property
def cols() -> int

Number of tile columns in the mega tile.

num_tiles

@property
def num_tiles() -> int

Total number of tiles in the mega tile grid.

effective_stride

@property
def effective_stride() -> tuple[int, int]

Returns the stride, defaulting to megatile_shape when not set.

tuple[int, int]

tuple[int, int]: (stride_rows, stride_cols) in tiles.

MegaTileRegion

@dataclass(frozen=True)
class MegaTileRegion()

A group of tiles forming one extracted mega tile. Returned by MegaTileExtractor.

RegionLocation

Absolute slide coordinates of the top-left corner of the mega tile.

MegaTileSpec

The specification that produced this mega tile (grid shape, tile spec, layout, stride, and valid-ratio bounds).

List[RegionSpec]

Per-tile region specifications, ordered row-major (tile_specs[row * cols + col]).

np.ndarray

Boolean array of shape (rows, cols) indicating which tiles passed the tissue threshold.

float

Fraction of tiles that are valid (tissue).

Example:

>>> mega.grid_shape
(5, 5)
>>> mega.valid_ratio
0.72
>>> mega.tile_availability.sum()
18

grid_shape

@property
def grid_shape() -> tuple[int, int]

(rows, cols) — number of tiles in each direction.

grid_layout

@property
def grid_layout() -> GridLayout

Layout used during extraction.

rows

@property
def rows() -> int

Number of tile rows.

cols

@property
def cols() -> int

Number of tile columns.

num_valid_tiles

@property
def num_valid_tiles() -> int

Count of tiles that passed the tissue threshold.

num_tiles

@property
def num_tiles() -> int

Total tile slots in the grid.

Overview

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Reference

GridLayout

MegaTileSpec

megatile_shape

megatile_stride

rows

cols

num_tiles

effective_stride

MegaTileRegion

grid_shape

grid_layout

rows

cols

num_valid_tiles

num_tiles

​GridLayout

​MegaTileSpec

​megatile_shape

​megatile_stride

​rows

​cols

​num_tiles

​effective_stride

​MegaTileRegion

​grid_shape

​grid_layout

​rows

​cols

​num_valid_tiles

​num_tiles

GridLayout

MegaTileSpec

megatile_shape

megatile_stride

rows

cols

num_tiles

effective_stride

MegaTileRegion

grid_shape

grid_layout

rows

cols

num_valid_tiles

num_tiles