slycat.hdf5

class slycat.hdf5.ArraySet(file)[source]

Bases: object

Wraps an instance of h5py.File to implement a Slycat arrayset.

array_count()[source]: Note: this assumes that array indices are contiguous, which we don’t explicitly enforce.

keys()[source]

start_array(array_index, dimensions, attributes)[source]

Add an uninitialized darray to the arrayset.

An existing array with the same index will be overwritten.

Parameters:

array_index (integer, required.) – Zero-based index of the array to create.
dimensions (list of dicts, required.) – Description of the new array dimensions.
attributes (list of dicts, required.) – Description of the new array attributes.

Returns:

array

Return type:

slycat.hdf5.DArray

store_array(array_index, array)[source]

Store a slycat.darray.Prototype in the arrayset.

An existing array with the same index will be overwritten.

Parameters:

array_index (integer, required.) – The index of the array to be created / overwritten.
array (slycat.darray.Prototype, required.) – Existing darray to be stored.

Returns:

array

Return type:

slycat.hdf5.DArray

class slycat.hdf5.DArray(storage)[source]

Bases: Prototype

Slycat darray implementation that stores data in an HDF5 file.

property attributes

Return metadata describing the darray attributes.

Returns:: attributes
Return type:: list of dicts

property dimensions

Return metadata describing the darray dimensions.

Returns:: dimensions
Return type:: list of dicts

get_data(attribute)[source]

Return a reference to the data storage for a darray attribute.

Parameters:: attribute (integer, optional) – The integer index of the attribute data to retrieve.
Returns:: data – An object implementing a subset of the numpy.ndarray interface that contains the attribute data. Note that the returned object only references the underlying data - data is not retrieved from the file until you access it using the [] operator.
Return type:: reference to a numpy-array-like object.

get_statistics(attribute)[source]: Return statistics describing one attribute.

get_unique(attribute, hyperslice)[source]

property ndim

Return the number of dimensions in the darray.

Returns:: ndim – The number of dimensions in the darray.
Return type:: integer

set_data(attribute, hyperslice, data)[source]

Overwrite the contents of a darray attribute.

Parameters:

attribute (integer) – The zero-based integer index of the attribute to be overwritten.
hyperslice (integer, slice, Ellipsis, or tuple containing one or more integer, slice, and Ellipsis instances.) – Defines the attribute region to be overwritten.
data (numpy.ndarray) – Data to be written to the attribute.

property shape

Return the darray shape (its size along each dimension).

Returns:: shape – The size of the darray along each dimension.
Return type:: tuple of integers

property size

Return the darray size (total number of elements stored in the darray).

Returns:: size – The total number of elements stored in the darray.
Return type:: integer

slycat.hdf5.dtype(input_type)[source]: Convert a string attribute type into a dtype suitable for use with h5py.

slycat.hdf5.path(array, directory)[source]

slycat.hdf5.start_arrayset(file)[source]

Create a new array set using an open hdf5 file.

Parameters:: file (h5py.File, required.) – An hdf5 file open for writing.
Returns:: arrayset
Return type:: slycat.hdf5.ArraySet