nixio.hdf5 package

Submodules

nixio.hdf5.h5dataset module

class nixio.hdf5.h5dataset.H5DataSet(parent, name, dtype=None, shape=None, compression=False)

Bases: object

classmethod create_from_h5obj(h5obj)
dtype
get_attr(name)
read_data(slc=None)
set_attr(name, value)
shape
write_data(data, slc=None)

nixio.hdf5.h5group module

class nixio.hdf5.h5group.H5Group(parent, name, create=False)

Bases: object

copy(source, dest, name=None, cls=None, shallow=False, keep_id=True)
create_dataset(name, shape, dtype, compression=False)

Creates a dataset object under the current group with a given name, shape, and type.

Parameters:
  • name – the name of the dataset
  • shape – tuple representing the shape of the dataset
  • dtype – the type of the data for this dataset (DataType)
  • compression – whether to compress the data (default: False)
Returns:

a new H5DataSet object
classmethod create_from_h5obj(h5obj)
delete(id_or_name, delete_if_empty=True)

Deletes the child HDF5 group that matches the given name or id.

delete_all(eid)

Deletes all references to a given list of objects, identified by their entity_id, below the current object.

find_children(filtr=None, limit=None)
get_attr(name)
get_by_id(id_)
get_by_id_or_name(id_or_name)
get_by_name(name)
get_by_pos(pos)
get_data(name)

Returns the data contained in the dataset identified by ‘name’, or an empty list if a dataset of that name does not exist in the Group.

Parameters:name – The name of the dataset
Returns:The data contained in the dataset as a numpy array or None
get_dataset(name)

Returns a contained H5DataSet object.

Parameters:name – name of the dataset
Returns:H5DataSet object
group
has_by_id(id_or_name)
has_data(name)

Return True if the Group contains a Dataset object with the given name.

Parameters:name – name of Dataset
Returns:True if Dataset exists in Group, False if it does not exist,

or exists and is not a Dataset

open_group(name, create=False)

Returns a new H5Group with the given name contained in the current group. If the current group does not exist in the file, it is automatically created.

Parameters:
  • name – the name of the group
  • create – creates the child group in the file if it does not exist
Returns:

a new H5Group object
parent
set_attr(name, value)
write_data(name, data, dtype=None, compression=False)

Writes the data to a Dataset contained in the group with the given name. Creates the Dataset if necessary.

Parameters:
  • name – name of the Dataset object
  • data – the data to write
  • dtype – optionally specify the data type, otherwise it will be

automatically determined by the data :param compression: whether to compress the data (default: False)

Module contents