wassname/scikit-image
1
0
Fork 0
mirror of https://github.com/wassname/scikit-image.git synced 2026-09-09 11:33:41 +08:00
Code Issues Packages Projects Releases Wiki Activity

ENH: move 'util.array_views' to 'util.shape'

Browse Source
This commit is contained in:
Nicolas Pinto
2012-02-12 14:59:06 -05:00
parent 93cd71553e
commit 1108bd892e
4 changed files with 252 additions and 263 deletions
Download Patch File Download Diff File Expand all files Collapse all files
skimage/util/shape.py
+221
View File
@@ -0,0 +1,221 @@
# Authors: Nicolas Poilvert <nicolas.poilvert@gmail.com>
# Nicolas Pinto <nicolas.pinto@gmail.com>
# License: BSD 3-clause
__all__ = ['view_as_blocks', 'view_as_windows']
import numpy as np
from numpy.lib.stride_tricks import as_strided
def view_as_blocks(arr_in, block_shape):
"""Block view of the input n-dimensionaly array (using re-striding).
Parameters
----------
arr: ndarray
The n-dimensional input array.
block_shape: tuple
The shape of the block.
Returns
-------
arr_out: ndarray
Block view of the input array.
Examples
--------
>>> import numpy as np
>>> from skimage.util.shape import view_as_blocks
>>> A = np.arange(4*4).reshape(4,4)
>>> A
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11],
[12, 13, 14, 15]])
>>> B = view_as_blocks(A, block_shape=(2, 2))
>>> B[0, 1]
array([[2, 3],
[6, 7]])
>>> B[1, 0, 1, 1]
13
>>> A = np.arange(4*4*6).reshape(4,4,6)
>>> A
array([[[ 0, 1, 2, 3, 4, 5],
[ 6, 7, 8, 9, 10, 11],
[12, 13, 14, 15, 16, 17],
[18, 19, 20, 21, 22, 23]],
<BLANKLINE>
[[24, 25, 26, 27, 28, 29],
[30, 31, 32, 33, 34, 35],
[36, 37, 38, 39, 40, 41],
[42, 43, 44, 45, 46, 47]],
<BLANKLINE>
[[48, 49, 50, 51, 52, 53],
[54, 55, 56, 57, 58, 59],
[60, 61, 62, 63, 64, 65],
[66, 67, 68, 69, 70, 71]],
<BLANKLINE>
[[72, 73, 74, 75, 76, 77],
[78, 79, 80, 81, 82, 83],
[84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95]]])
>>> B = view_as_blocks(A, block_shape=(1, 2, 2))
>>> B.shape
(4, 2, 3, 1, 2, 2)
>>> B[2:, 0, 2]
array([[[[52, 53],
[58, 59]]],
<BLANKLINE>
<BLANKLINE>
[[[76, 77],
[82, 83]]]])
"""
# -- basic checks on arguments
if not isinstance(block_shape, tuple):
raise TypeError('block needs to be a tuple')
block_shape = np.array(block_shape)
if (block_shape <= 0).any():
raise ValueError("'block_shape' elements must be strictly positive")
if block_shape.size != arr_in.ndim:
raise ValueError("'block_shape' must have the same length "
"as 'arr_in.shape'")
arr_shape = np.array(arr_in.shape)
if (arr_shape % block_shape).sum() != 0:
raise ValueError("'block_shape' is not compatible with 'arr_in'")
# -- restride the array to build the block view
arr_in = np.ascontiguousarray(arr_in)
new_shape = tuple(arr_shape / block_shape) + tuple(block_shape)
new_strides = tuple(arr_in.strides * block_shape) + arr_in.strides
arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides)
return arr_out
def view_as_windows(arr_in, window_shape):
"""Rolling window view of the input n-dimensionaly array (using
re-striding).
Parameters
----------
arr_in: ndarray
The n-dimensional input array.
window_shape: tuple
Defines the shape of the elementary n-dimensional orthotope
(better know as hyperrectangle [1]) of the rolling window view.
Returns
-------
arr_out: ndarray
(rolling) window view of the input array.
Notes
-----
One should be very careful with rolling views when it comes to
memory usage. Indeed, although a 'view' has the same memory
footprint as its base array, the actual array that emerges when this
'view' is used in a computation is generally a (much) larger array
than the original, especially for 2-dimensional arrays and above.
For example, let us consider a 3 dimensional array of size (100,
100, 100) of ``float64``. This array takes about 8*100**3 Bytes for
storage which is just 8 MB. If one decides to build a rolling view
on this array with a window of (3, 3, 3) the hypothetical size of
the rolling view (if one was to reshape the view for example) would
be 8*(100-3+1)**3*3**3 which is about 203 MB! The scaling becomes
even worse as the dimension of the input array becomes larger.
References
----------
.. [1] http://en.wikipedia.org/wiki/Hyperrectangle
Examples
--------
>>> import numpy as np
>>> from skimage.util.shape import view_as_windows
>>> A = np.arange(10)
>>> A
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> window_shape = (3,)
>>> B = view_as_windows(A, window_shape)
>>> B.shape
(8, 3)
>>> B
array([[0, 1, 2],
[1, 2, 3],
[2, 3, 4],
[3, 4, 5],
[4, 5, 6],
[5, 6, 7],
[6, 7, 8],
[7, 8, 9]])
>>> A = np.arange(5*4).reshape(5, 4)
>>> A
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11],
[12, 13, 14, 15],
[16, 17, 18, 19]])
>>> window_shape = (4, 3)
>>> B = view_as_windows(A, window_shape)
>>> B.shape
(2, 2, 4, 3)
>>> B
array([[[[ 0, 1, 2],
[ 4, 5, 6],
[ 8, 9, 10],
[12, 13, 14]],
<BLANKLINE>
[[ 1, 2, 3],
[ 5, 6, 7],
[ 9, 10, 11],
[13, 14, 15]]],
<BLANKLINE>
<BLANKLINE>
[[[ 4, 5, 6],
[ 8, 9, 10],
[12, 13, 14],
[16, 17, 18]],
<BLANKLINE>
[[ 5, 6, 7],
[ 9, 10, 11],
[13, 14, 15],
[17, 18, 19]]]])
"""
# -- basic checks on arguments
if not isinstance(arr_in, np.ndarray):
raise TypeError("'arr_in' must be a numpy ndarray")
if not isinstance(window_shape, tuple):
raise TypeError("'window_shape' must be a tuple")
if not (len(window_shape) == arr_in.ndim):
raise ValueError("'window_shape' is incompatible with 'arr_in.shape'")
arr_shape = np.array(arr_in.shape)
window_shape = np.array(window_shape, dtype=arr_shape.dtype)
if ((arr_shape - window_shape) < 0).any():
raise ValueError("'window_shape' is too large")
if ((window_shape - 1) < 0).any():
raise ValueError("'window_shape' is too small")
# -- build rolling window view
arr_in = np.ascontiguousarray(arr_in)
new_shape = tuple(arr_shape - window_shape + 1) + tuple(window_shape)
new_strides = arr_in.strides + arr_in.strides
arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides)
return arr_out