On Sat, 26 Jun 2010, McKell Carter wrote:
> Yes, 32K after masking. The full image size is 48X58X49.
cool -- I guess you've hit the bug in libnifti... damn you ;-)
here is my silly snippet to reproduce:
from nifti import NiftiImage
import numpy as np
def check(s, ni):
print "%s saving/loading" % s
fn1s = np.where(ni.data[:, 1,1,1] != 1)[0]
if len(fn1s):
fn1 = fn1s[0]
print [(i, ni.data[i, 1,1,1]) for i in (fn1-1, fn1)]
else:
print "everything 1s"
size=(48, 59,49, 15000)
print "Size ", size
ni = NiftiImage(np.ones(size[::-1]))
ni.save('/tmp/ones.nii.gz')
check('before', ni)
del ni
ni = NiftiImage('/tmp/ones.nii.gz')
check('after', ni)
nidr = ni.data.ravel()
# silly way but what a heck ;)
print "first non-1 ", np.where(nidr!=1)[0][0]
it outputs:
Size (48, 59, 49, 15000)
before saving/loading
everything 1s
after saving/loading
[(3393, 1.0), (3394, 0.0)]
first non-1 470907264
more fun came when I changed first dimension size to 25:
In [1]: ## working on region in file /home/yoh/.tmp/python-10698W9c.py...
Size (25, 59, 49, 15000)
** ERROR: NWAD: wrote only 83065408 of 83065408 bytes to file
before saving/loading
everything 1s
after saving/loading
++ WARNING: nifti_read_buffer(/tmp/ones.nii.gz):
data bytes needed = 83065408
data bytes input = 83065408
number missing = 0 (set to 0)
[(143, 1.0), (144, 0.0)]
first non-1 10383176
as to me it makes somewhat little sense ;)
in any case -- we will look into it. From a quick look I don't see where
we could be possibly hitting the limit here:
http://nifti.nimh.nih.gov/board/read.php?f=1&i=2357&t=2356
--
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