# -*- coding: utf-8 -*-
# Support for Deep Zoom images.
#
# This module provides functionality for generating Deep Zoom images from
# CuImage objects
#
# References:
# CellViT: Vision Transformers for precise cell segmentation and classification
# Fabian Hörst et al., Medical Image Analysis, 2024
# DOI: https://doi.org/10.1016/j.media.2024.103143
import numpy as np
from cucim import CuImage # type: ignore
from cucim.clara.cache import preferred_memory_capacity # type: ignore
from openslide import OpenSlide
from openslide.deepzoom import DeepZoomGenerator
from PIL import Image
from typing import Any, cast
[docs]class DeepZoomGeneratorCucim(DeepZoomGenerator):
"""Create a DeepZoomGenerator, but instead of utilizing OpenSlide, use cucim to read regions.
Args:
osr (OpenSlide): OpenSlide Image. Needed for OS compatibility and for retrieving metadata.
cucim_slide (CuImage): CuImage slide. Used for retrieving image data.
tile_size (int, optional): the width and height of a single tile. For best viewer
performance, tile_size + 2 * overlap should be a power of two. Defaults to 254.
overlap (int, optional): the number of extra pixels to add to each interior edge
of a tile. Defaults to 1.
limit_bounds (bool, optional): True to render only the non-empty slide region.
Defaults to False.
"""
[docs] def __init__(
self,
osr: OpenSlide,
cucim_slide: Any,
tile_size: int = 254,
overlap: int = 1,
limit_bounds: bool = False,
):
super().__init__(osr, tile_size, overlap, limit_bounds)
self._cucim_slide = cucim_slide
self.memory_capacity = cast(
Any,
preferred_memory_capacity(
self._cucim_slide, patch_size=(tile_size, tile_size)
),
)
self.cache = CuImage.cache( # type: ignore
"per_process", memory_capacity=self.memory_capacity, record_stat=True
)
[docs] def get_tile(self, level: int, address: tuple[int, int]) -> Image.Image:
"""Return an RGB PIL.Image for a tile.
Args:
level (int): the Deep Zoom level
address (tuple[int, int]): the address of the tile within the level as a (col, row)
tuple
Returns:
Image.Image: PIL Image
"""
args, z_size = self._get_tile_info(level, address)
tile = self._cucim_slide.read_region(
location=args[0],
level=args[1],
size=args[2],
)
tile = Image.fromarray(np.array(tile), mode="RGB") # CuImage is RGB
# Scale to the correct size
if tile.size != z_size:
# Image.Resampling added in Pillow 9.1.0
# Image.LANCZOS removed in Pillow 10
tile.thumbnail(
z_size,
getattr(Image, "Resampling", Image).LANCZOS, # type: ignore
)
return tile
