slycat.hdf5¶
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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.
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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:
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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:
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class
slycat.hdf5.
DArray
(storage)[source]¶ Bases:
slycat.darray.Prototype
Slycat darray implementation that stores data in an HDF5 file.
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attributes
¶ Return metadata describing the darray attributes.
Returns: attributes Return type: list of dicts
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dimensions
¶ Return metadata describing the darray dimensions.
Returns: dimensions Return type: list of dicts
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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.
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ndim
¶ Return the number of dimensions in the darray.
Returns: ndim – The number of dimensions in the darray. Return type: integer
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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.
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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
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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
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slycat.hdf5.
dtype
(type)[source]¶ Convert a string attribute type into a dtype suitable for use with h5py.
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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