Class TiffFileWSIReader

monai/data/wsi_reader.py:1291–1569

Read whole slide images and extract patches using TiffFile library. Args: level: the whole slide image level at which the patches are extracted. mpp: the resolution in micron per pixel at which the patches are extracted. mpp_rtol: the acceptable relative tolerance f

@require_pkg(pkg_name="tifffile")
class TiffFileWSIReader(BaseWSIReader):
    """
    Read whole slide images and extract patches using TiffFile library.

    Args:
        level: the whole slide image level at which the patches are extracted.
        mpp: the resolution in micron per pixel at which the patches are extracted.
        mpp_rtol: the acceptable relative tolerance for resolution in micro per pixel.
        mpp_atol: the acceptable absolute tolerance for resolution in micro per pixel.
        channel_dim: the desired dimension for color channel. Default to 0 (channel first).
        dtype: the data type of output image. Defaults to `np.uint8`.
        device: target device to put the extracted patch. Note that if device is "cuda"",
            the output will be converted to torch tenor and sent to the gpu even if the dtype is numpy.
        mode: the output image color mode, "RGB" or "RGBA". Defaults to "RGB".
        kwargs: additional args for `tifffile.TiffFile` module.

        Notes:
            - Objective power cannot be obtained via TiffFile backend.
            - Only one of resolution parameters, `level` or `mpp`, should be provided.
                If such parameters are provided in `get_data` method, those will override the values provided here.
                If none of them are provided here or in `get_data`, `level=0` will be used.

    """

    supported_suffixes = ["tif", "tiff", "svs"]
    backend = "tifffile"

    def __init__(self, **kwargs):
        super().__init__(**kwargs)

    @staticmethod
    def get_level_count(wsi) -> int:
        """
        Returns the number of levels in the whole slide image.

        Args:
            wsi: a whole slide image object loaded from a file.

        """
        return len(wsi.pages)

    def get_size(self, wsi, level: int) -> tuple[int, int]:
        """
        Returns the size (height, width) of the whole slide image at a given level.

        Args:
            wsi: a whole slide image object loaded from a file.
            level: the level number where the size is calculated.

        """
        return (wsi.pages[level].imagelength, wsi.pages[level].imagewidth)

    def get_downsample_ratio(self, wsi, level: int) -> float:
        """
        Returns the down-sampling ratio of the whole slide image at a given level.

        Args:
            wsi: a whole slide image object loaded from a file.