alphabase.io.tempmmap¶

This module allows to create temporary memory-mapped arrays.

Functions:

`array`(shape, dtype[, tmp_dir_abs_path])	Create a writable temporary memory-mapped array.
`clear`()	Reset the temporary folder containing temp memory-mapped arrays and create a new one.
`create_empty_mmap`(shape, dtype[, file_path, ...])	Initialize a new HDF5 file compatible with mmap.
`mmap_array_from_path`(hdf_file)	reconnect to an exisiting HDF5 file to generate a writable temporary memory-mapped array.
`ones`(shape, dtype)	Create a writable temporary memory-mapped array filled with ones.
`redefine_temp_location`(path)	Redefine the location where the temp arrays are written to.
`zeros`(shape, dtype)	Create a writable temporary memory-mapped array filled with zeros.

alphabase.io.tempmmap.array(shape: tuple, dtype: dtype, tmp_dir_abs_path: str = None) → ndarray[source][source]¶

Create a writable temporary memory-mapped array.

Parameters:

shape (tuple) – A tuple with the shape of the array.
dtype (type) – The np.dtype of the array.
tmp_dir_abs_path (str, optional) – If specified the memory mapped array will be created in this directory. An absolute path is expected. Defaults to None. If not specified the global TEMP_DIR_NAME location will be used.

Returns:

A writable temporary memory-mapped array.

Return type:

type

alphabase.io.tempmmap.clear() → str[source][source]¶

Reset the temporary folder containing temp memory-mapped arrays and create a new one.

WARNING: All existing temp mmapp arrays will be unusable!

Returns:: The name of the new temporary folder.
Return type:: str

alphabase.io.tempmmap.create_empty_mmap(shape: tuple, dtype: dtype, file_path: str = None, overwrite: bool = False, tmp_dir_abs_path: str = None)[source][source]¶

Initialize a new HDF5 file compatible with mmap. Returns the path to the initialized file. File can be mapped using the mmap_array_from_path function.

Parameters:

shape (tuple) – A tuple with the shape of the array.
dtype (type) – The np.dtype of the array.
file_path (str, optional) – The absolute path to the file that should be created. This includes the file name. Defaults to None. If None a random file name will be generated in the default tempdir location.
overwrite (bool , optional) – If True the file will be overwritten if it already exists. Defaults to False.
tmp_dir_abs_path (str, optional) – If specified the default tempdir location will be updated to this path. Defaults to None. An absolute path to a directory is expected.

Returns:

path to the newly created file.

Return type:

str

alphabase.io.tempmmap.mmap_array_from_path(hdf_file: str) → ndarray[source][source]¶

reconnect to an exisiting HDF5 file to generate a writable temporary memory-mapped array.

Parameters:: hdf_file (str) – path to the array that should be reconnected to.
Returns:: A writable temporary memory-mapped array.
Return type:: type

alphabase.io.tempmmap.ones(shape: tuple, dtype: dtype) → ndarray[source][source]¶

Create a writable temporary memory-mapped array filled with ones.

Parameters:

shape (tuple) – A tuple with the shape of the array.
dtype (type) – The np.dtype of the array.

Returns:

A writable temporary memory-mapped array filled with ones.

Return type:

type

alphabase.io.tempmmap.redefine_temp_location(path: str) → str[source][source]¶

Redefine the location where the temp arrays are written to.

Parameters:: path (string)
Returns:: the location of the new temporary directory.
Return type:: str

alphabase.io.tempmmap.zeros(shape: tuple, dtype: dtype) → ndarray[source][source]¶

Create a writable temporary memory-mapped array filled with zeros.

Parameters:

shape (tuple) – A tuple with the shape of the array.
dtype (type) – The np.dtype of the array.

Returns:

A writable temporary memory-mapped array filled with zeros.

Return type:

type