bioptimus.preprocess.wsi.provider.base

Abstract interface for tissue mask providers. Defines the TissueMaskProvider abstract base class that TileExtractor depends on for obtaining binary tissue masks.

TissueMaskProvider

class TissueMaskProvider(ABC)

Abstract base class for tissue mask providers. Every provider must implement generate, which receives an open WSIReader and returns a 2-D uint8 binary mask where 1 = tissue. TileExtractor depends only on this interface, so any concrete provider — algorithmic, model-based, or pre-computed — can be plugged in. Example:

class MyCustomMask(TissueMaskProvider):
    def generate(self, reader):
        return load_from_database(reader.path)

generate

@abstractmethod
def generate(reader: WSIReader, *, show_progress: bool = True) -> np.ndarray

Generates a binary tissue mask for the given slide.

An open WSI reader.

Whether to display a progress bar. Defaults to True.

Returns:

np.ndarray - A uint8 mask of shape (H, W) with values in {0, 1} where 1 = tissue.

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TissueMaskProvider

generate

​TissueMaskProvider

​generate

TissueMaskProvider

generate