Tiling patches or generate patches of whole slide image based on Openslide
- Tiling patches and saving them to local disk
- Generate patch generator for testing of WSIs
- First assign the slide_folder(will findslides in subfolder(s)) and save_folder.
slide_folder = os.path.join(os.curdir, 'data', 'slide')
save_folder = os.path.join(os.curdir, 'data', 'patch')- For tiling patches and saving them to disks
TileSaving(slide_folder, save_folder, n_procs=4, target_size=512, ds_rate=0, black_thresh=50).tiling()- For get patch generation (using in the inference code)
loader_sequence = TestDataGenerator(slide_folder).get_patch_generator(mode='sequence')
for patch_gen, idx in loader_sequence:
for patch, c, r in patch_gen:
if patch == -1:
# patch is black
pass
elif patch == -2:
# patch is blank
pass
else:
# patch is valid
pass
loader_randomly = TestDataGenerator(slide_folder).get_patch_generator(mode='random')
for patch_gen, idx in loader_randomly:
for patch, c, r in patch_gen:
if patch == -1:
# patch is black
pass
elif patch == -2:
# patch is blank
pass
else:
# patch is valid
pass