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b/create_splits.py |
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import pdb |
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import os |
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import pandas as pd |
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from datasets.dataset_mtl_concat import Generic_WSI_MTL_Dataset, Generic_MIL_MTL_Dataset, save_splits |
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import argparse |
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import numpy as np |
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parser = argparse.ArgumentParser(description='Creating splits for whole slide classification') |
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parser.add_argument('--label_frac', type=float, default= -1, |
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help='fraction of labels (default: [1.0])') |
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parser.add_argument('--seed', type=int, default=1, |
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help='random seed (default: 1)') |
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parser.add_argument('--k', type=int, default=10, |
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help='number of splits (default: 10)') |
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parser.add_argument('--hold_out_test', action='store_true', default=False, |
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help='fraction to hold out (default: 0)') |
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parser.add_argument('--split_code', type=str, default=None) |
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parser.add_argument('--task', type=str, choices=['dummy_mtl_concat']) |
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args = parser.parse_args() |
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if args.task == 'dummy_mtl_concat': |
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args.n_classes=18 |
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dataset = Generic_WSI_MTL_Dataset(csv_path = 'dataset_csv/dummy_dataset.csv', |
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shuffle = False, |
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seed = args.seed, |
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print_info = True, |
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label_dicts = [{'Lung':0, 'Breast':1, 'Colorectal':2, 'Ovarian':3, |
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'Pancreatic':4, 'Adrenal':5, |
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'Skin':6, 'Prostate':7, 'Renal':8, 'Bladder':9, |
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'Esophagagostric':10, 'Thyroid':11, |
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'Head Neck':12, 'Glioma':13, |
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'Germ Cell':14, 'Endometrial': 15, 'Cervix': 16, 'Liver': 17}, |
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{'Primary':0, 'Metastatic':1}, |
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{'F':0, 'M':1}], |
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label_cols = ['label', 'site', 'sex'], |
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patient_strat= False) |
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else: |
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raise NotImplementedError |
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num_slides_cls = np.array([len(cls_ids) for cls_ids in dataset.patient_cls_ids]) |
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val_num = np.floor(num_slides_cls * 0.1).astype(int) |
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test_num = np.floor(num_slides_cls * 0.2).astype(int) |
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print(val_num) |
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print(test_num) |
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if __name__ == '__main__': |
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if args.label_frac > 0: |
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label_fracs = [args.label_frac] |
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else: |
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label_fracs = [1.0] |
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if args.hold_out_test: |
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custom_test_ids = dataset.sample_held_out(test_num=test_num) |
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else: |
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custom_test_ids = None |
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for lf in label_fracs: |
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if args.split_code is not None: |
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split_dir = 'splits/'+ str(args.split_code) + '_{}'.format(int(lf * 100)) |
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else: |
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split_dir = 'splits/'+ str(args.task) + '_{}'.format(int(lf * 100)) |
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dataset.create_splits(k = args.k, val_num = val_num, test_num = test_num, label_frac=lf, custom_test_ids=custom_test_ids) |
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os.makedirs(split_dir, exist_ok=True) |
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for i in range(args.k): |
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if dataset.split_gen is None: |
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ids = [] |
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for split in ['train', 'val', 'test']: |
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ids.append(dataset.get_split_from_df(pd.read_csv(os.path.join(split_dir, 'splits_{}.csv'.format(i))), split_key=split, return_ids_only=True)) |
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dataset.train_ids = ids[0] |
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dataset.val_ids = ids[1] |
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dataset.test_ids = ids[2] |
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else: |
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dataset.set_splits() |
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descriptor_df = dataset.test_split_gen(return_descriptor=True) |
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descriptor_df.to_csv(os.path.join(split_dir, 'splits_{}_descriptor.csv'.format(i))) |
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splits = dataset.return_splits(from_id=True) |
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save_splits(splits, ['train', 'val', 'test'], os.path.join(split_dir, 'splits_{}.csv'.format(i))) |
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save_splits(splits, ['train', 'val', 'test'], os.path.join(split_dir, 'splits_{}_bool.csv'.format(i)), boolean_style=True) |
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