WenjieDu
commented
10 months ago Hi there 👋,
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1. System Info
using : google colab need to install: tsdb>=0.2 pygrinder >=0.2 numpy pandas<2.0.0 torch torchvision -U python_utils nni torch>=1.10.0 scipy tensorboard h5py pypots==0.1.1 . need to import
import pypots from pypots.data.generating import gene_physionet2012 from pypots.utils.random import set_random_seed from pypots.data import load_specific_dataset # why sometimes return a erro of the directory of the document of from pypots.imputation import SAITS from pypots.data.load_preprocessing import preprocess_physionet2012 from pypots.utils.metrics import cal_mae from pypots.data import load_specific_dataset from pypots.optim import Adam from pypots.optim.base import Optimizer from pypots.utils.logging import logger import torch import torch.nn as nn import torch.nn.functional as F import torchvision import torchvision.transforms as transforms from torch.utils.data import DataLoader from torchvision import datasets from torchvision.transforms import ToTensor import tsdb import tsdb.data_processing from tsdb.utils.downloading import download_and_extract from tsdb.utils.file import purge_path, pickle_load, pickle_dump from tsdb.utils.logging import logger from tsdb.database import AVAILABLE_DATASETS, CACHED_DATASET_DIR import numpy as np from sklearn.preprocessing import StandardScaler from pygrinder import mcar, masked_fill from typing import Union, Optional, Callable import h5py import pandas as pd import os import shutil import sys import warnings import matplotlib.pyplot as plt %matplotlib inline from abc import abstractmethod from typing import Union, Optional from keras import models
2. Information
3. Reproduction
try to load the dataset physionet_2012 or 2019 will git erro of not found file of the outcame
4. Expected behavior
FILE NOT FOUND : /usr/local/lib/python3.10/dist-packages/tsdb/loading_funcs/physionet_2012.py in load_physionet2012(localpath) 50 for o in outcome_files: 51 outcome_file_path = os.path.join(localpath, o) ---> 52 with open(outcome_file_path, "r") as f: 53 outcome = pd.read_csv(f)[["In-hospital_death", "RecordID"]] 54 outcome["RecordID"] = outcome["RecordID"].astype(
FileNotFoundError: [Errno 2] No such file or directory: '/root/.tsdb_cached_datasets/physionet_2012/Outcomes-a.txt'