def __init__(self, keys: KeysCollection, channel_dim: int = -1, allow_missing_keys: bool = False) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
channel_dim: which dimension of input image is the channel, default is the last dimension.
allow_missing_keys: don't raise exception if key is missing.
"""
super().__init__(keys, allow_missing_keys)
self.converter = AsChannelFirst(channel_dim=channel_dim)
def get_patch(self, wsi, location: Tuple[int, int], size: Tuple[int, int],
level: int, dtype: DtypeLike, mode: str) -> np.ndarray:
"""
Extracts and returns a patch image form the whole slide image.
Args:
wsi: a whole slide image object loaded from a file or a lis of such objects
location: (top, left) tuple giving the top left pixel in the level 0 reference frame. Defaults to (0, 0).
size: (height, width) tuple giving the patch size at the given level (`level`).
If None, it is set to the full image size at the given level.
level: the level number. Defaults to 0
dtype: the data type of output image
mode: the output image mode, 'RGB' or 'RGBA'
"""
# Extract a patch or the entire image
# (reverse the order of location and size to become WxH for OpenSlide)
pil_patch = wsi.read_region(location=location[::-1],
size=size[::-1],
level=level)
# convert to RGB/RGBA
pil_patch = pil_patch.convert(mode)
# Convert to numpy
patch = np.asarray(pil_patch, dtype=dtype)
# Make it channel first
patch = AsChannelFirst()(patch) # type: ignore
# Check if the color channel is 3 (RGB) or 4 (RGBA)
if mode == "RGBA" and patch.shape[0] != 4:
raise ValueError(
f"The image is expected to have four color channels in '{mode}' mode but has {patch.shape[0]}."
)
elif mode in "RGB" and patch.shape[0] != 3:
raise ValueError(
f"The image is expected to have three color channels in '{mode}' mode but has {patch.shape[0]}. "
)
return patch
