import torch
import pandas as pd
import numpy as np
from bert_tokenizer import load_list
from torch.utils.data import Dataset, DataLoader
class ImpressionsDataset(Dataset):
"""The dataset to contain report impressions and their labels."""
def __init__(self, csv_path, list_path):
""" Initialize the dataset object
@param csv_path (string): path to the csv file containing labels
@param list_path (string): path to the list of encoded impressions
"""
self.df = pd.read_csv(csv_path)
self.df = self.df[['Enlarged Cardiomediastinum', 'Cardiomegaly', 'Lung Opacity',
'Lung Lesion', 'Edema', 'Consolidation', 'Pneumonia', 'Atelectasis',
'Pneumothorax', 'Pleural Effusion', 'Pleural Other', 'Fracture',
'Support Devices', 'No Finding']]
self.df.replace(0, 2, inplace=True) #negative label is 2
self.df.replace(-1, 3, inplace=True) #uncertain label is 3
self.df.fillna(0, inplace=True) #blank label is 0
self.encoded_imp = load_list(path=list_path)
def __len__(self):
"""Compute the length of the dataset
@return (int): size of the dataframe
"""
return self.df.shape[0]
def __getitem__(self, idx):
""" Functionality to index into the dataset
@param idx (int): Integer index into the dataset
@return (dictionary): Has keys 'imp', 'label' and 'len'. The value of 'imp' is
a LongTensor of an encoded impression. The value of 'label'
is a LongTensor containing the labels and 'the value of
'len' is an integer representing the length of imp's value
"""
if torch.is_tensor(idx):
idx = idx.tolist()
label = self.df.iloc[idx].to_numpy()
label = torch.LongTensor(label)
imp = self.encoded_imp[idx]
imp = torch.LongTensor(imp)
return {"imp": imp, "label": label, "len": imp.shape[0]}