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create_stainings.py
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create_stainings.py
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import glob
from datasets.wsi_data import MultiFileMultiRegion
from single.restain import create_staining
if __name__ == '__main__':
schemes = ['datasets/staining_schemes/S01.tif',
'datasets/staining_schemes/S02.tif',
'datasets/staining_schemes/S03.tif',
'datasets/staining_schemes/S04.tif',
'datasets/staining_schemes/S05.tif',
'datasets/staining_schemes/S06.tif',
'datasets/staining_schemes/S07.tif',
'datasets/staining_schemes/S08.tif',
'datasets/staining_schemes/S09.tif']
img_files = sorted(glob.glob('../patho_data/peso/*_small.tif', recursive=True))
label_files = sorted(glob.glob('../patho_data/peso/*_labels.tif', recursive=True))
for p in zip(img_files, label_files):
print(p)
dataset = MultiFileMultiRegion(img_files=img_files, label_files=label_files, h=500,w=500, max_tries=100, min_non_white=0.7)
create_staining(schemes, n_out_schemes=484, out_schemes_folder='datasets/staining_schemes/', dataset_to_stain=dataset, verbose=0)