#!/usr/bin/env python # -*- coding: utf-8 -*- import numpy as np import torch import torchvision.transforms as transforms from torch.utils.data.dataset import Dataset from torch.utils.data.dataloader import DataLoader from torch.utils.data.sampler import WeightedRandomSampler from PIL import Image from sklearn.preprocessing import MinMaxScaler import pickle from .logger import BaseLogger from typing import List, Dict, Union import pandas as pd logger = BaseLogger.get_logger(__name__) class PrivateAugment(torch.nn.Module): """ Augmentation defined privately. Variety of augmentation can be written in this class if necessary. """ # For X-ray photo. xray_augs_list = [ transforms.RandomAffine(degrees=(-3, 3), translate=(0.02, 0.02)), transforms.RandomAdjustSharpness(sharpness_factor=2), transforms.RandomAutocontrast() ] class InputDataMixin: """ Class to normalizes input data. """ def _make_scaler(self) -> MinMaxScaler: """ Make scaler to normalize input data by min-max normalization with train data. Returns: MinMaxScaler: scaler """ scaler = MinMaxScaler() _df_train = self.df_source[self.df_source['split'] == 'train'] # should be normalized with min and max of training data _ = scaler.fit(_df_train[self.input_list]) # fit only return scaler def save_scaler(self, save_path :str) -> None: """ Save scaler Args: save_path (str): path for saving scaler. """ #save_scaler_path = Path(save_datetime_dir, 'scaler.pkl') with open(save_path, 'wb') as f: pickle.dump(self.scaler, f) def load_scaler(self, scaler_path :str) -> None: """ Load scaler. Args: scaler_path (str): path to scaler """ with open(scaler_path, 'rb') as f: scaler = pickle.load(f) return scaler def _normalize_inputs(self, df_inputs: pd.DataFrame) -> torch.FloatTensor: """ Normalize inputs. Args: df_inputs (pd.DataFrame): DataFrame of inputs Returns: torch.FloatTensor: normalized inputs Note: After iloc[[idx], index_input_list], pd.DataFrame is obtained. DataFrame fits the input type of self.scaler.transform. However, after normalizing, the shape of inputs_value is (1, N), where N is the number of input values. Since the shape (1, N) is not acceptable when forwarding, convert (1, N) -> (N,) is needed. """ inputs_value = self.scaler.transform(df_inputs).reshape(-1) # np.float64 inputs_value = np.array(inputs_value, dtype=np.float32) # -> np.float32 inputs_value = torch.from_numpy(inputs_value).clone() # -> torch.float32 return inputs_value def _load_input_value_if_mlp(self, idx: int) -> Union[torch.FloatTensor, str]: """ Load input values after converting them into tensor if MLP is used. Args: idx (int): index Returns: Union[torch.Tensor[float], str]: tensor of input values, or empty string """ inputs_value = '' if self.params.mlp is None: return inputs_value index_input_list = [self.col_index_dict[input] for input in self.input_list] _df_inputs = self.df_split.iloc[[idx], index_input_list] inputs_value = self._normalize_inputs( _df_inputs) return inputs_value class ImageMixin: """ Class to normalize and transform image. """ def _make_augmentations(self) -> List: """ Define which augmentation is applied. When training, augmentation is needed for train data only. When test, no need of augmentation. """ _augmentation = [] if (self.params.isTrain) and (self.split == 'train'): if self.params.augmentation == 'xrayaug': _augmentation = PrivateAugment.xray_augs_list elif self.params.augmentation == 'trivialaugwide': _augmentation.append(transforms.TrivialAugmentWide()) elif self.params.augmentation == 'randaug': _augmentation.append(transforms.RandAugment()) else: # ie. self.params.augmentation == 'no': pass _augmentation = transforms.Compose(_augmentation) return _augmentation def _make_transforms(self) -> List: """ Make list of transforms. Returns: list of transforms: image normalization """ _transforms = [] _transforms.append(transforms.ToTensor()) if self.params.normalize_image == 'yes': # transforms.Normalize accepts only Tensor. if self.params.in_channel == 1: _transforms.append(transforms.Normalize(mean=(0.5, ), std=(0.5, ))) else: # ie. self.params.in_channel == 3 _transforms.append(transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])) _transforms = transforms.Compose(_transforms) return _transforms def _open_image_in_channel(self, imgpath: str, in_channel: int) -> Image: """ Open image in channel. Args: imgpath (str): path to image in_channel (int): channel, or 1 or 3 Returns: Image: PIL image """ if in_channel == 1: image = Image.open(imgpath).convert('L') # eg. np.array(image).shape = (64, 64) return image else: # ie. self.params.in_channel == 3 image = Image.open(imgpath).convert('RGB') # eg. np.array(image).shape = (64, 64, 3) return image def _load_image_if_cnn(self, idx: int) -> Union[torch.Tensor, str]: """ Load image and convert it to tensor if any of CNN or ViT is used. Args: idx (int): index Returns: Union[torch.Tensor[float], str]: tensor converted from image, or empty string """ image = '' if self.params.net is None: return image imgpath = self.df_split.iat[idx, self.col_index_dict['imgpath']] image = self._open_image_in_channel(imgpath, self.params.in_channel) image = self.augmentation(image) image = self.transform(image) return image class DeepSurvMixin: """ Class to handle required data for deepsurv. """ def _load_periods_if_deepsurv(self, idx: int) -> Union[torch.FloatTensor, str]: """ Return period if deepsurv. Args: idx (int): index Returns: Union[torch.FloatTensor, str]: period, or empty string """ periods = '' if self.params.task != 'deepsurv': return periods assert (self.params.task == 'deepsurv') and (len(self.label_list) == 1), 'Deepsurv cannot work in multi-label.' periods = self.df_split.iat[idx, self.col_index_dict[self.period_name]] # int64 periods = np.array(periods, dtype=np.float32) # -> np.float32 periods = torch.from_numpy(periods).clone() # -> torch.float32 return periods class DataSetWidget(InputDataMixin, ImageMixin, DeepSurvMixin): """ Class for a widget to inherit multiple classes simultaneously. """ pass class LoadDataSet(Dataset, DataSetWidget): """ Dataset for split. """ def __init__( self, params, split: str ) -> None: """ Args: params (ParamSet): parameter for model split (str): split """ self.params = params self.df_source = self.params.df_source self.split = split self.input_list = self.params.input_list self.label_list = self.params.label_list if self.params.task == 'deepsurv': self.period_name = self.params.period_name self.df_split = self.df_source[self.df_source['split'] == self.split] self.col_index_dict = {col_name: self.df_split.columns.get_loc(col_name) for col_name in self.df_split.columns} # For input data if self.params.mlp is not None: assert (self.input_list != []), f"input list is empty." if params.isTrain: self.scaler = self._make_scaler() else: # load scaler used at training. self.scaler = self.load_scaler(self.params.scaler_path) # For image if self.params.net is not None: self.augmentation = self._make_augmentations() self.transform = self._make_transforms() def __len__(self) -> int: """ Return length of DataFrame. Returns: int: length of DataFrame """ return len(self.df_split) def _load_label(self, idx: int) -> Dict[str, Union[int, float]]: """ Return labels. If no column of label when csv of external dataset is used, empty dictionary is returned. Args: idx (int): index Returns: Dict[str, Union[int, float]]: dictionary of label name and its value """ # For checking if columns of labels exist when used csv for external dataset. label_list_in_split = list(self.df_split.columns[self.df_split.columns.str.startswith('label')]) label_dict = dict() if label_list_in_split != []: for label_name in self.label_list: label_dict[label_name] = self.df_split.iat[idx, self.col_index_dict[label_name]] else: # no label pass return label_dict def __getitem__(self, idx: int) -> Dict: """ Return data row specified by index. Args: idx (int): index Returns: Dict: dictionary of data to be passed model """ uniqID = self.df_split.iat[idx, self.col_index_dict['uniqID']] group = self.df_split.iat[idx, self.col_index_dict['group']] imgpath = self.df_split.iat[idx, self.col_index_dict['imgpath']] split = self.df_split.iat[idx, self.col_index_dict['split']] inputs_value = self._load_input_value_if_mlp(idx) image = self._load_image_if_cnn(idx) label_dict = self._load_label(idx) periods = self._load_periods_if_deepsurv(idx) _data = { 'uniqID': uniqID, 'group': group, 'imgpath': imgpath, 'split': split, 'inputs': inputs_value, 'image': image, 'labels': label_dict, 'periods': periods } return _data def _make_sampler(split_data: LoadDataSet) -> WeightedRandomSampler: """ Make sampler. Args: split_data (LoadDataSet): dataset Returns: WeightedRandomSampler: sampler """ _target = [] for _, data in enumerate(split_data): _target.append(list(data['labels'].values())[0]) class_sample_count = np.array([len(np.where(_target == t)[0]) for t in np.unique(_target)]) weight = 1. / class_sample_count samples_weight = np.array([weight[t] for t in _target]) sampler = WeightedRandomSampler(samples_weight, len(samples_weight)) return sampler def create_dataloader( params, split: str = None ) -> DataLoader: """ Create data loader ofr split. Args: params (ParamSet): parameter for dataloader split (str): split. Defaults to None. Returns: DataLoader: data loader """ split_data = LoadDataSet(params, split) if params.isTrain: batch_size = params.batch_size shuffle = True else: batch_size = params.test_batch_size shuffle = False if params.sampler == 'yes': assert ((params.task == 'classification') or (params.task == 'deepsurv')), 'Cannot make sampler in regression.' assert (len(params.label_list) == 1), 'Cannot make sampler for multi-label.' shuffle = False sampler = _make_sampler(split_data) else: # When params.sampler == 'no' sampler = None split_loader = DataLoader( dataset=split_data, batch_size=batch_size, shuffle=shuffle, num_workers=0, sampler=sampler ) return split_loader