import os import pickle import numpy as np import pandas as pd import torch import torch.nn.functional as F from PIL import Image from torch.utils.data import Dataset from utils import generate_click_prompt, random_box, random_click class Brat(Dataset): def __init__(self, args, data_path , transform = None, transform_msk = None, mode = 'Training',prompt = 'click', plane = False): self.args = args self.data_path = os.path.join(data_path,'Data') self.name_list = os.listdir(self.data_path) self.mode = mode self.prompt = prompt self.img_size = args.image_size self.transform = transform self.transform_msk = transform_msk def __len__(self): return len(self.name_list) def load_all_levels(self,path): import nibabel as nib data_dir = os.path.join(self.data_path) levels = ['t1','flair','t2','t1ce'] raw_image = [nib.load(os.path.join (data_dir,path,path+'_'+level+'.nii.gz')).get_fdata() for level in levels] raw_seg = nib.load(os.path.join(data_dir,path,path+'_seg.nii.gz')).get_fdata() return raw_image[0], raw_seg def __getitem__(self, index): # if self.mode == 'Training': # point_label = random.randint(0, 1) # inout = random.randint(0, 1) # else: # inout = 1 # point_label = 1 point_label = 1 label = 4 # the class to be segmented """Get the images""" name = self.name_list[index] img,mask = self.load_all_levels(name) mask[mask!=label] = 0 mask[mask==label] = 1 # if self.mode == 'Training': # label = 0 if self.label_list[index] == 'benign' else 1 # else: # label = int(self.label_list[index]) img = np.resize(img,(self.args.image_size, self.args.image_size,img.shape[-1])) mask = np.resize(mask,(self.args.out_size,self.args.out_size,mask.shape[-1])) img = torch.tensor(img).unsqueeze(0) mask = torch.tensor(mask).unsqueeze(0) mask = torch.clamp(mask,min=0,max=1).int() if self.prompt == 'click': point_label, pt = random_click(np.array(mask), point_label) # if self.transform: # state = torch.get_rng_state() # img = self.transform(img) # torch.set_rng_state(state) # if self.transform_msk: # mask = self.transform_msk(mask) # # if (inout == 0 and point_label == 1) or (inout == 1 and point_label == 0): # # mask = 1 - mask name = name.split('/')[-1].split(".jpg")[0] image_meta_dict = {'filename_or_obj':name} return { 'image':img, 'label': mask, 'p_label':point_label, 'pt':pt, 'image_meta_dict':image_meta_dict, }