Bamboost
bamboostcorehdf5filemap

bamboost.core.hdf5.filemap

Source: https://github.com/smec-ethz/bamboost/tree/main/bamboost/core/hdf5/filemap.py

Attributes

  • _VT_filemap=typing.Type[h5py.h5py.Group | h5py.h5py.Dataset]

Classes

KeysViewHDF5

Attributes:
  • __repr__=bamboost.core.hdf5.filemap.KeysViewHDF5.__str__
KeysViewHDF5.__str__(self) -> str

_FileMapMixin

_FileMapMixin.__repr__(self)
_FileMapMixin.keys(self) -> KeysViewHDF5
_FileMapMixin.datasets(self) -> tuple[str, ...]
_FileMapMixin.groups(self) -> tuple[str, ...]
_FileMapMixin._ipython_key_completions_(self)
_FileMapMixin._repr_pretty_(self, p, _cycle)
Arguments:
  • p
  • _cycle

FileMap

FileMap(self, file)
Arguments:
Attributes:
  • _file=bamboost.core.hdf5.filemap.FileMap(file)
  • _dict:dict[HDF5Path, bamboost.core.hdf5.filemap._VT_filemap]={bamboost.core.hdf5.hdf5path.HDF5Path('/'): h5py.h5py.Group}

    A cache of all known paths in the file and their types (Group or Dataset). Paths are absolute.

  • _children:dict[HDF5Path, set[str]]={}

    A cache of immediate children names for each group path.

  • _expanded_groups:set[HDF5Path]=set()

    A set of group paths that have been expanded (i.e., their children have been fetched from the file).

FileMap.__len__(self) -> int
FileMap.__iter__(self) -> Iterator[HDF5Path]
FileMap.__delitem__(self, key) -> None
Arguments:
  • key:str
FileMap.__setitem__(self, key, value) -> None
Arguments:
FileMap.__getitem__(self, key) -> _VT_filemap
Arguments:
  • key:str
FileMap.expand_group(self, path) -> None

Fetch immediate children of the given path from the HDF5 file and cache them.

Arguments:
FileMap.populate(self, *, exclude_numeric=False) -> None

Eagerly visit all groups and datasets to cache them. Assumes the file is open.

Arguments:
  • exclude_numeric:bool=False
FileMap.invalidate(self) -> None

FilteredFileMap

FilteredFileMap(self, file_map, parent) -> None
Arguments:
Attributes:
  • parent=HDF5Path(parent)
  • file_map=bamboost.core.hdf5.filemap.FilteredFileMap(file_map)
FilteredFileMap.__len__(self)
FilteredFileMap.__iter__(self)
FilteredFileMap.__delitem__(self, key)
Arguments:
  • key
FilteredFileMap.__setitem__(self, key, value)
Arguments:
  • key:str
  • value
FilteredFileMap.__getitem__(self, key)
Arguments:
  • key:str
FilteredFileMap.children(self) -> Iterator[HDF5Path]
FilteredFileMap.children_groups(self) -> Iterator[HDF5Path]
FilteredFileMap.children_datasets(self) -> Iterator[HDF5Path]

file

This module provides an enhanced interface for working with HDF5 files. Its main goal is to provide automatic file management with heavy caching to limit file access to a minimum.

hdf5path

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Attributes
Classes
KeysViewHDF5
__str__
_FileMapMixin
__repr__
keys
datasets
groups
_ipython_key_completions_
_repr_pretty_
FileMap
__len__
__iter__
__delitem__
__setitem__
__getitem__
expand_group
populate
invalidate
FilteredFileMap
__len__
__iter__
__delitem__
__setitem__
__getitem__
children
children_groups
children_datasets