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.
- 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:
- 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:
- 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.
- 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
, andEllipsis
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.