No such file or directory: 'Camelyon16/pt_files/normal_024.pt'

[jieruyao49]

The directory of the camelyon16 dataset I downloaded is as follows. Where should I download the .pt files?

CAMELYON16
  -training
     -normal
        -normal_xxx.tif
     -turmor
        -turmor_xxx.tif
     -lesion_annotation
        -turmor_xxx.xml
  -testing
     -images
        -test_xxx.tif
     -evaluation
        -evaluation_masks.zip
        -evaluation_matlab.zip
        -evaluation_python.zip

[hans0809]

pt文件就是一些存储下来的特征向量，类似.npy这种，供参考：

import os
import glob
import cv2
import timm
import torch
import numpy as np
import tqdm
import gc

model = timm.create_model('resnet50', pretrained=True)
model.fc=torch.nn.Identity()

model.cuda()
model.eval()

def extract_feas(model,bag_path,save_dir=''):
    print(bag_path)
    noraml_or_abnormal=bag_path.split('\\')[-3]
    st_name=bag_path.split('\\')[-2]
    bag_name=bag_path.split('\\')[-1]
    all_instances=os.listdir(bag_path)
    embed=[]
    for instance in tqdm.tqdm(all_instances):
        instance_path=os.path.join(bag_path,instance)
        patch=cv2.imread(instance_path)
        cv2.cvtColor(patch,cv2.COLOR_BGR2RGB)
        patch=torch.tensor(np.transpose(patch,(2,0,1)))
        patch=patch.cuda().float().unsqueeze(0)

        f=model(patch)
        f_np=f.detach().cpu().numpy().squeeze(0)
        embed.append(f_np)
        gc.collect()

    feas=np.array(embed)
    print(feas.shape)
    save_path=os.path.join(save_dir,noraml_or_abnormal,st_name,bag_name)
    if not os.path.exists(save_path):
        os.makedirs(save_path)
    print(save_path)
    np.save(os.path.join(save_path,bag_name+'.npy'),feas)

if __name__ == "__main__":
    all_bags=glob.glob(r'Patch\img\*\*\*')
    for bag_path in all_bags:
        extract_feas(model,bag_path)

[szc19990412]

We use the CLAM method to process WSI, and we can acquire the matching pt file, which corresponds to all patches in each WSI's features.