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ENH: ArrayProxy reshape #521

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Merged
matthew-brett merged 16 commits into from
Apr 6, 2017
Merged

ENH: ArrayProxy reshape #521

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4c4405b
Add ArrayProxy.reshape
effigies Mar 24, 2017
1eb6fbe
Typo
effigies Mar 24, 2017
8b41f55
Cifti2 arrayproxy tests should be negated or dropped...
effigies Mar 24, 2017
c6192ad
RF: Do not automatically load data CIFTI data
effigies Mar 25, 2017
d4e152a
Severely simplify _Cifti2AsNiftiImage
effigies Mar 25, 2017
49725c7
Permit tuple ArrayProxy spec in place of header
effigies Mar 28, 2017
0c62d74
ArrayProxy.reshape generates headerless ArrayProxy
effigies Mar 28, 2017
1626cfb
RF: Deprecate ArrayProxy.header to be removed in 3.0
effigies Mar 28, 2017
c6dfa6a
TEST: Test tuple specs and reshaped APs
effigies Mar 28, 2017
ad35340
Update Changelog
effigies Mar 28, 2017
c6950f5
DOC: Update ArrayProxy docstrings
effigies Mar 28, 2017
e35f327
RF: Update ArrayProxy.reshape to take -1 entries
effigies Mar 28, 2017
fbac7e4
FIX: Correct reshape method
effigies Mar 29, 2017
8ad9c32
TEST: Catch warning, test -1 reshaping
effigies Mar 29, 2017
f4f3894
TEST: Check for illegal specs
effigies Mar 29, 2017
37405c3
TEST: Check legal but incompatible shapes
effigies Mar 29, 2017
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11 changes: 11 additions & 0 deletions nibabel/arrayproxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -162,6 +162,17 @@ def __getitem__(self, slicer):
# Upcast as necessary for big slopes, intercepts
return apply_read_scaling(raw_data, self._slope, self._inter)

def reshape(self, shape):
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@matthew-brett matthew-brett Mar 28, 2017

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One-liner docstring?

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@matthew-brett matthew-brett Mar 28, 2017

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Would be good to allow -1 as element in shape, for compatibility with numpy array reshape.

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@effigies effigies Mar 28, 2017

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Done.

size = np.prod(self._shape)
if np.prod(shape) != size:
raise ValueError("cannot reshape array of size {:d} into shape "
"{!s}".format(size, shape))
new_ap = ArrayProxy(file_like=self.file_like,
header=self._header,
mmap=self._mmap)
new_ap._shape = shape
return new_ap


def is_proxy(obj):
""" Return True if `obj` is an array proxy
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1 change: 0 additions & 1 deletion nibabel/cifti2/parse_cifti2.py
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Expand Up @@ -147,7 +147,6 @@ def __init__(self, dataobj, affine, header=None,
if self.cifti_img is None:
raise ValueError('Nifti2 header does not contain a CIFTI2 '
'extension')
self.cifti_img.data = self.get_data()
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@matthew-brett matthew-brett Mar 25, 2017

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Or could be self.cifti_img.dataobj = self.dataobj. This doesn't load the data, but keeps it as an array proxy.

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@effigies effigies Mar 25, 2017

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I'm not sure the cifti_img attribute is doing any work at all. Even the check on the header is replicated here. I think it may be a refactoring hold-over that never got cleaned up. I'm pretty sure we could, without losing functionality, rewrite the entire class as:

class _Cifti2AsNiftiImage(Nifti2Image):
    header_class = _Cifti2AsNiftiHeader
    makeable = False



class Cifti2Parser(xml.XmlParser):
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6 changes: 3 additions & 3 deletions nibabel/cifti2/tests/test_cifti2io.py
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Expand Up @@ -63,12 +63,12 @@ def test_read_and_proxies():
assert_true(isinstance(img2.header, ci.Cifti2Header))
assert_equal(img2.shape, (1, 91282))
# While we cannot reshape arrayproxies, all images are in-memory
assert_true(img2.in_memory)
assert_true(not img2.in_memory)
data = img2.get_data()
assert_true(data is img2.dataobj)
assert_true(data is not img2.dataobj)
# Uncaching has no effect, images are always array images
img2.uncache()
assert_true(data is img2.get_data())
assert_true(data is not img2.get_data())


@needs_nibabel_data('nitest-cifti2')
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