hdf_pointer

BasePointer

Pointer to a location in an hdf5 file. The constructor takes a :class:`~.file_handler.FileHandler` and the in-file path to the object. The base class represents a generic group in the file

BasePointer (
    file_handler: bamboost.common.file_handler.FileHandler,
    path_to_data: str
)

Parameters:

• file_handler : bamboost.common.file_handler.FileHandler

  file this belongs to

• path_to_data : <class 'str'>

  infile path to object

Variables:

• path_to_data :

• obj :

  The object this BasePointer points to. File needs to be open for access.

• attrs :

new_pointer

new_pointer (
    cls,
    file_handler: bamboost.common.file_handler.FileHandler,
    path_to_data: str
) -> bamboost.common.hdf_pointer.BasePointer

Returns a new pointer object.

Parameters:

• cls : Any

• file_handler : <class 'bamboost.common.file_handler.FileHandler'>

• path_to_data : <class 'str'>

Returns:

bamboost.common.hdf_pointer.BasePointer

BasePointer[key]

__getitem__ (self, key)

None

Parameters:

• self : Any

• key : Any

Returns:

<class 'inspect._empty'>

Group

Pointer to a location in an hdf5 file. The constructor takes a :class:`~.file_handler.FileHandler` and the in-file path to the object. The base class represents a generic group in the file

Group (
    file_handler: bamboost.common.file_handler.FileHandler,
    path_to_data: str
)

Parameters:

• file_handler : bamboost.common.file_handler.FileHandler

  file this belongs to

• path_to_data : <class 'str'>

  infile path to object

Inherits from:

• bamboost.common.hdf_pointer.BasePointer
  new_pointerpath_to_dataobj__getitem__attrs

Variables:

iter(Group)

__iter__ (self)

None

Parameters:

• self : Any

Returns:

<class 'inspect._empty'>

keys

keys (self) -> set

None

Parameters:

• self : Any

Returns:

<class 'set'>

groups

groups (self) -> set

None

Parameters:

• self : Any

Returns:

<class 'set'>

datasets

datasets (self) -> set

None

Parameters:

• self : Any

Returns:

<class 'set'>

MutableGroup

Used for the `userdata` group.

MutableGroup (
    file_handler: bamboost.common.file_handler.FileHandler,
    path_to_data: str
)

Parameters:

• file_handler : bamboost.common.file_handler.FileHandler

• path_to_data : <class 'str'>

Inherits from:

• bamboost.common.hdf_pointer.Group
  __iter__keysgroupsdatasets
• bamboost.common.hdf_pointer.BasePointer
  new_pointerpath_to_dataobjattrs

Variables:

MutableGroup[key]

__getitem__ (self, key) -> Any

Used to access datasets (:class:`~bamboost.common.hdf_pointer.Dataset`) or groups inside this group (:class:`~bamboost.common.hdf_pointer.MutableGroup`)

Parameters:

• self : Any

• key : Any

Returns:

typing.Any

MutableGroup[key] = ...

__setitem__ (self, key, newvalue)

Used to set an attribute. Will be written as an attribute to the group.

Parameters:

• self : Any

• key : Any

• newvalue : Any

Returns:

<class 'inspect._empty'>

update_attrs

update_attrs (self, attrs: dict) -> None

Update the attributes of the group.

Parameters:

• self : Any

• attrs : <class 'dict'>

  the dictionary to write as attributes

Returns:

None

add_dataset

add_dataset (
    self,
    name: str,
    vector: numpy.ndarray,
    attrs: dict = None,
    dtype: str = None
) -> None

Add a dataset to the group. Error is thrown if attempting to overwrite with different shape than before. If same shape, data is overwritten (this is inherited from h5py -> require_dataset)

Parameters:

• self : Any

• name : <class 'str'>

  Name for the dataset

• vector : <class 'numpy.ndarray'>

  Data to write (max 2d)

• attrs : <class 'dict'>

  Optional. Attributes of dataset.

• dtype : <class 'str'>

  Optional. dtype of dataset. If not specified, uses dtype of inpyt array

Returns:

None

require_group

require_group (self, name: str) -> bamboost.common.hdf_pointer.Group

Add a new group to the current group. If exists, return existing.

Parameters:

• self : Any

• name : <class 'str'>

Returns:

bamboost.common.hdf_pointer.Group

bamboost.hdf_pointer.Group

Dataset

Pointer to a location in an hdf5 file. The constructor takes a :class:`~.file_handler.FileHandler` and the in-file path to the object. The base class represents a generic group in the file

Dataset (
    file_handler: bamboost.common.file_handler.FileHandler,
    path_to_data: str
)

Parameters:

• file_handler : bamboost.common.file_handler.FileHandler

  file this belongs to

• path_to_data : <class 'str'>

  infile path to object

Inherits from:

• bamboost.common.hdf_pointer.BasePointer
  new_pointerpath_to_dataobj

Variables:

• attrs :

• shape :

• dtype :

Dataset[key]

__getitem__ (self, slice)

None

Parameters:

• self : Any

• slice : Any

Returns:

<class 'inspect._empty'>