implement hdf5 dataset reader op (#356)

fuse/data/ops/ops_read.py

@@ -20,6 +20,7 @@
 from typing import Hashable, List, Optional, Dict, Union
 from fuse.utils.file_io.file_io import read_dataframe
 import pandas as pd
+import h5py
 
 from fuse.data import OpBase
 from fuse.utils.ndict import NDict
@@ -113,3 +114,50 @@ def get_all_keys(self) -> List[Hashable]:
  :return: list of dataframe index values
  """
  return list(self.data.keys())
+
+
+class OpReadHDF5(OpBase):
+ """
+ Op reading data from hd5f based dataset
+ """
+
+ def __init__(
+ self,
+ data_filename: Optional[str] = None,
+ columns_to_extract: Optional[List[str]] = None,
+ rename_columns: Optional[Dict[str, str]] = None,
+ key_index: str = "data.sample_id",
+ key_column: str = "sample_id",
+ ):
+ """
+ :param data_filename: path to hdf5 file
+ :param columns_to_extract: list of columns to extract - dataset keys to extract. When None (default) all columns are extracted
+ :param rename_columns: rename columns
+ :param key_index: name of value in sample_dict which will be used as the key/index
+ :param key_column: name of the column which use as key/index. In case of None, the original dataframe index will be used to extract the values for a single sample.
+ """
+ # store input
+ self._data_filename = data_filename
+ self._columns_to_extract = columns_to_extract
+ self._rename_columns = rename_columns if rename_columns is not None else {}
+ self._key_index = key_index
+ self._key_column = key_column
+
+ self._h5 = h5py.File(self._data_filename, "r")
+
+ if self._columns_to_extract is None:
+ self._columns_to_extract = self._h5.keys()
+
+ self._num_samples = len(self._h5[self._columns_to_extract[0]])
+
+ def num_samples(self) -> int:
+ return self._num_samples
+
+ def __call__(self, sample_dict: NDict) -> Union[None, dict, List[dict]]:
+
+ index = sample_dict[self._key_index]
+ for column in self._columns_to_extract:
+ key_to_store = self._rename_columns.get(column, column)
+ sample_dict[key_to_store] = self._h5[column][index]
+
+ return sample_dict