arrayproxy

Array proxy base class

The proxy API is - at minimum:

• The object has a read-only attribute shape
• read only is_proxy attribute / property set to True
• the object returns the data array from np.asarray(prox)
• returns array slice from prox[<slice_spec>] where <slice_spec> is any ndarray slice specification that does not use numpy ‘advanced indexing’.
• modifying no object outside obj will affect the result of np.asarray(obj). Specifically:
  • Changes in position (obj.tell()) of passed file-like objects will not affect the output of from np.asarray(proxy).
  • if you pass a header into the __init__, then modifying the original header will not affect the result of the array return.

See nibabel.tests.test_proxy_api for proxy API conformance checks.

ArrayProxy(*args, **kwargs)	Class to act as proxy for the array that can be read from a file
is_proxy(obj)	Return True if obj is an array proxy

ArrayProxy

class nibabel.arrayproxy.ArrayProxy(*args, **kwargs)

Bases: object

Class to act as proxy for the array that can be read from a file

The array proxy allows us to freeze the passed fileobj and header such that it returns the expected data array.

This implementation assumes a contiguous array in the file object, with one of the numpy dtypes, starting at a given file position offset with single slope and intercept scaling to produce output values.

The class __init__ requires a header object with methods:

• get_data_shape
• get_data_dtype
• get_data_offset
• get_slope_inter

The header should also have a ‘copy’ method. This requirement will go away when the deprecated ‘header’ propoerty goes away.

This implementation allows us to deal with Analyze and its variants, including Nifti1, and with the MGH format.

Other image types might need more specific classes to implement the API. See nibabel.minc1, nibabel.ecat and nibabel.parrec for examples.

Initialize array proxy instance

Parameters:

file_like : object

File-like object or filename. If file-like object, should implement at least read and seek.

header : object

Header object implementing get_data_shape, get_data_dtype, get_data_offset, get_slope_inter

mmap : {True, False, ‘c’, ‘r’}, optional, keyword only

mmap controls the use of numpy memory mapping for reading data. If False, do not try numpy memmap for data array. If one of {‘c’, ‘r’}, try numpy memmap with mode=mmap. A mmap value of True gives the same behavior as mmap='c'. If file_like cannot be memory-mapped, ignore mmap value and read array from file.

scaling : {‘fp’, ‘dv’}, optional, keyword only

Type of scaling to use - see header get_data_scaling method.

__init__(*args, **kwargs)

Initialize array proxy instance

Parameters:

file_like : object

File-like object or filename. If file-like object, should implement at least read and seek.

header : object

Header object implementing get_data_shape, get_data_dtype, get_data_offset, get_slope_inter

mmap : {True, False, ‘c’, ‘r’}, optional, keyword only

mmap controls the use of numpy memory mapping for reading data. If False, do not try numpy memmap for data array. If one of {‘c’, ‘r’}, try numpy memmap with mode=mmap. A mmap value of True gives the same behavior as mmap='c'. If file_like cannot be memory-mapped, ignore mmap value and read array from file.

scaling : {‘fp’, ‘dv’}, optional, keyword only

Type of scaling to use - see header get_data_scaling method.

get_unscaled()

Read of data from file

This is an optional part of the proxy API

header

inter

is_proxy

offset

order = 'F'

shape

slope

is_proxy

nibabel.arrayproxy.is_proxy(obj)

Return True if obj is an array proxy