import os import torch import torch.utils.data as data import numpy as np from PIL import Image import logging from .data_path import get_dataset_path class NIH(data.Dataset): pathologies = [ 'Atelectasis', 'Cardiomegaly', 'Effusion', 'Infiltration', 'Mass', 'Nodule', 'Pneumonia', 'Pneumothorax', 'Consolidation', 'Edema', 'Emphysema', 'Fibrosis', 'Pleural_Thickening', 'Hernia'] def __init__(self, split="train", data_pct=1.0, transform=None, return_label=False): super().__init__() self.root = get_dataset_path('NIH') self.return_label = return_label self.num_classes = len(self.pathologies) self.split = split self.transform = transform # if os.path.exists(os.path.join(self.root, 'NIH_proc')): # logging.info('NIH Proc') # self.nih_proc = True # else: # logging.info('NIH Original') # self.nih_proc = False self.nih_proc = False if not return_label: logging.info('NIH for Pretrain on train_val') with open(os.path.join(self.root, 'train_val_list.txt'), 'r') as f: lines = f.readlines() if self.nih_proc: self.data = [os.path.join(self.root, 'NIH_proc', l.strip()) for l in lines if l.strip() != ''] else: self.data = [os.path.join(self.root, 'NIH_512_jpg', l.strip()) for l in lines if l.strip() != ''] logging.info(f'NIH Num Pretrain: {len(self.data)}') else: assert split in ('train', 'val', 'test') self.data = [] self.img_label = [] img_root = os.path.join(self.root, 'NIH_512') if not os.path.exists(img_root): img_root = img_root.replace('NIH_512', 'NIH_512_jpg') with open(f'annotations/nih/Xray14_{split}_official.txt', "r") as fileDescriptor: line = True while line: line = fileDescriptor.readline() if line: lineItems = line.split() imagePath = os.path.join(img_root, lineItems[0]) imageLabel = lineItems[1:self.num_classes + 1] imageLabel = [int(i) for i in imageLabel] self.data.append(imagePath) self.img_label.append(imageLabel) if data_pct < 1.0 and split == 'train': state = np.random.RandomState(seed=42) num_data = len(self.data) indices = state.choice(np.arange(num_data), size=int(data_pct * num_data), replace=False) self.data = [self.data[idx] for idx in indices] self.img_label = [self.img_label[idx] for idx in indices] logging.info(f'NIH Downstream {split} set: {len(self.data)}') def __getitem__(self, index): if not self.return_label: img_path = self.data[index] else: img_path = self.data[index] label = self.img_label[index] # if self.nih_proc: # img = Image.open(img_path.replace('.png', '.jpg')).convert('RGB') # else: # img = Image.open(img_path).convert('RGB') if 'jpg' in img_path: img = Image.open(img_path.replace('.png', '.jpg')).convert('RGB') else: img = Image.open(img_path).convert('RGB') if self.transform != None: img = self.transform(img) if not self.return_label: return img else: return img, torch.FloatTensor(label) def __len__(self): return len(self.data)