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vqdang avatar vqdang commented on June 2, 2024

Hi, in case you want to have more fine-grain control. You can use this approach rather than using the provided patch from the PatchExtractor, then you can control what type of padding you want.

from tiatoolbox.tools.patchextraction import \
    SlidingWindowPatchExtractor as Extractor
from tiatoolbox.wsicore.wsireader import VirtualWSIReader, get_wsireader

img_path = f'{root_dir}/imgs/{base_name}.thumb.png'
msk_path = f'{root_dir}/msks/{base_name}.png'
save_path = f'{SAVE_DIR}/{idx}'

img_reader = get_wsireader(img_path)
bounds = Extractor(
    img_reader,
    patch_size=patch_shape,
    stride=overlap_shape,
    within_bound=False,
    **resolution_kwargs
).coord_list

msk_reader = VirtualWSIReader(msk_path, mode='bool')
msk_reader.info = img_reader.info

for idx, bound in enumerate(bounds):
    img_patch = img_reader.read_bounds(
        bound,
        interpolation="optimise",
        coord_space='resolution',
        **resolution_kwargs,
    )
    msk_patch = msk_reader.read_bounds(
        bound,
        interpolation="nearest",
        coord_space='resolution',
        **resolution_kwargs,
    )

    base_name = f'{bound[0]:06d}-{bound[1]:06d}-{bound[2]:06d}-{bound[3]:06d}'
    imwrite(f'{save_path}.{base_name}.img.png', img_patch)
    imwrite(f'{save_path}.{base_name}.msk.png', msk_patch)

from tiatoolbox.

shaneahmed avatar shaneahmed commented on June 2, 2024

Closing this issue. Feel free to reopen if you still see any problems with the above solution.

from tiatoolbox.

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