--- a +++ b/dataLoader/NextXVisit.py @@ -0,0 +1,65 @@ +import numpy as np +from torch.utils.data.dataset import Dataset +from dataLoader.utils import seq_padding,code2index, position_idx, index_seg +import torch + + +class NextVisit(Dataset): + def __init__(self, token2idx, label2idx, age2idx, dataframe, max_len, code='code', age='age', label='label'): + # dataframe preproecssing + # filter out the patient with number of visits less than min_visit + self.vocab = token2idx + self.label_vocab = label2idx + self.max_len = max_len + self.code = dataframe[code] + self.age = dataframe[age] + self.label = dataframe[label] + self.patid = dataframe.patid + + self.age2idx = age2idx + + def __getitem__(self, index): + """ + return: age, code, position, segmentation, mask, label + """ + # cut data + age = self.age[index] + code = self.code[index] + label = self.label[index] + patid = self.patid[index] + + # extract data + age = age[(-self.max_len+1):] + code = code[(-self.max_len+1):] + + # avoid data cut with first element to be 'SEP' + if code[0] != 'SEP': + code = np.append(np.array(['CLS']), code) + age = np.append(np.array(age[0]), age) + else: + code[0] = 'CLS' + + # mask 0:len(code) to 1, padding to be 0 + mask = np.ones(self.max_len) + mask[len(code):] = 0 + + # pad age sequence and code sequence + age = seq_padding(age, self.max_len, token2idx=self.age2idx) + + tokens, code = code2index(code, self.vocab) + _, label = code2index(label, self.label_vocab) + + # get position code and segment code + tokens = seq_padding(tokens, self.max_len) + position = position_idx(tokens) + segment = index_seg(tokens) + + # pad code and label + code = seq_padding(code, self.max_len, symbol=self.vocab['PAD']) + label = seq_padding(label, self.max_len, symbol=-1) + + return torch.LongTensor(age), torch.LongTensor(code), torch.LongTensor(position), torch.LongTensor(segment), \ + torch.LongTensor(mask), torch.LongTensor(label), torch.LongTensor([int(patid)]) + + def __len__(self): + return len(self.code) \ No newline at end of file