HDF5 Wrapper

The hdf5_wrapper python package adds a wrapper to h5py that greatly simplifies reading/writing to/from hdf5-format files.

Usage

Once loaded, the contents of a file can be navigated in the same way as a native python dictionary.

import hdf5_wrapper

data = hdf5_wrapper.hdf5_wrapper('data.hdf5')

test = data['test']
for k, v in data.items():
  print('key: %s, value: %s' % (k, str(v)))

If the user indicates that a file should be opened in write-mode (w) or read/write-mode (a), then the file can be created or modified. Note: for these changes to be written to the disk, the wrapper may need to be closed or deleted.

import hdf5_wrapper
import numpy as np

data = hdf5_wrapper.hdf5_wrapper('data.hdf5', mode='w')
data['string'] = 'string'
data['integer'] = 123
data['array'] = np.random.randn(3, 4, 5)
data['child'] = {'float': 1.234}

Existing dictionaries can be placed on the current level:

existing_dict = {'some': 'value'}
data.insert(existing_dict)

And external hdf5 format files can be linked together:

for k in ['child_a', 'child_b']:
  data.link(k, '%s.hdf5' % (k))

API

class hdf5_wrapper.wrapper.hdf5_wrapper(fname: str = '', target: Optional[h5py._hl.files.File] = None, mode: str = 'r')

A class for reading/writing hdf5 files, which behaves similar to a native dict

close() → None

Closes the database

copy() → Dict[str, Any]

Copy the entire database into memory

Returns:a dictionary holding the database contents
Return type:dict
get_copy() → Dict[str, Any]

Copy the entire database into memory

Returns:a dictionary holding the database contents
Return type:dict
insert(x: Union[Dict[str, Any], hdf5_wrapper]) → None

Insert the contents of the target object to the current location

Parameters:x (dict, hdf5_wrapper) – the dictionary to insert
keys() → Iterable[str]

Get a list of groups and arrays located at the current level

Returns:a list of key names pointing to objects at the current level
Return type:list

Link an external hdf5 file to this location in the database

Parameters:
  • k (str) – the name of the new link in the database
  • target (str) – the path to the external database
values() → Iterable[Union[hdf5_wrapper.wrapper.hdf5_wrapper, Any]]

Get a list of values located on the current level