Merge branch 'op_replace_any' of github.com:BiomedSciAI/fuse-med-ml i…

…nto op_replace_any

fuse/utils/file_io/file_io.py

@@ -291,6 +291,7 @@ def save_dataframe(df: pd.DataFrame, filename: str, **kwargs: dict) -> None:
 
  assert file_type in [
  "csv",
+ "tsv",
  "hd5",
  "hdf5",
  "hdf",
@@ -304,6 +305,8 @@ def save_dataframe(df: pd.DataFrame, filename: str, **kwargs: dict) -> None:
  df.to_pickle(filename, **kwargs)
  elif file_type == "csv":
  df.to_csv(filename, **kwargs)
+ elif file_type == "tsv":
+ df.to_csv(filename, sep="\t" ** kwargs)
  elif file_type in ["hd5", "hdf5", "hdf"]:
  df.to_hdf(filename, **kwargs)
  elif file_type == "xslx":
@@ -322,6 +325,7 @@ def read_dataframe(filename: str) -> pd.DataFrame:
 
  assert file_type in [
  "csv",
+ "tsv",
  "hd5",
  "hdf5",
  "hdf",
@@ -334,6 +338,8 @@ def read_dataframe(filename: str) -> pd.DataFrame:
  df = pd.read_pickle(filename)
  elif file_type == "csv":
  df = pd.read_csv(filename)
+ elif file_type == "tsv":
+ df = pd.read_csv(filename, sep="\t")
  elif file_type in ["hd5", "hdf5", "hdf"]:
  df = pd.read_hdf(filename)
  elif file_type == "xslx":

fuse/utils/ndict.py

@@ -22,8 +22,8 @@
 
 import copy
 import types
-import numpy
-import torch
+from numpy import ndarray
+from torch import Tensor
 from typing import (
  Any,
  Callable,
@@ -273,7 +273,7 @@ def pop(self, key: str) -> Any:
  del self[key]
  return res
 
- def indices(self, indices: numpy.ndarray) -> dict:
+ def indices(self, indices: ndarray) -> dict:
  """
  Extract the specified indices from each element in the dictionary (if possible)
 
@@ -286,7 +286,7 @@ def indices(self, indices: numpy.ndarray) -> dict:
  for key in all_keys:
  try:
  value = self[key]
- if isinstance(value, (numpy.ndarray, torch.Tensor)):
+ if isinstance(value, (ndarray, Tensor)):
  new_value = value[indices]
  elif isinstance(value, Sequence):
  new_value = [item for i, item in enumerate(value) if indices[i]]