Package: python-nifti
Version: 0.20070425.1-1~etch.apsy0
Severity: normal
Hi Michael,
while you are asleep here is a food for thought for the early morning...
well -- subject describes it all. here is the code sample to give more
information (read till the end since another issue there as well)
import numpy, nifti
z = numpy.zeros([3,4,5,6])
ni1 = nifti.NiftiImage(z)
ni2 = nifti.NiftiImage(z)
ni1.save('/tmp/1.nii.gz')
hdr1 = ni1.header
hdr2 = ni2.header
for item in hdr1.keys():
if not hdr2.has_key(item):
print "hdr2 has no " + key
else:
if `hdr1[item]` != `hdr2[item]`: print "Differ: ", item,
hdr1[item], hdr2[item]
ni2.updateHeader(hdr2)
output of it is
$> python showbug.py
Differ: vox_offset 352.0 348.0
** ERROR (nifti_set_filename): failed to set prefix for ''
** ERROR: nifti_convert_nhdr2nim: bad filename
Traceback (most recent call last):
File "showbug.py", line 58, in ?
ni2.updateHeader(hdr2)
File "/usr/lib/python2.4/site-packages/nifti/niftiimage.py", line 766, in
updateHeader
raise RuntimeError, \
RuntimeError: Could not recreate NIfTI image struct from updated header.
so we have absent filename and also vox_offset differs in saved and
not-saved versions.
another issue I encountered is that other nifti files I saw they have 1
in higher dimensions (in dim I mean) and I believe dim[5]==1 has some
meaning for something in nifti header format.
I could not adjust it via modifying header's dim list -- after saving
they all remained 0s. So I guess they simply better be set to 1 whenever
we create niftiimage out of numpy array.
cheers... sleep well... see you in few weeks ;-)
-- System Information:
Debian Release: 4.0
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Shell: /bin/sh linked to /bin/bash
Kernel: Linux 2.6.18-4-amd64
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Versions of packages python-nifti depends on:
ii libc6 2.3.6.ds1-13 GNU C Library: Shared libraries
ii libniftiio0 0.5-3~etch.apsy0 IO libraries for the NIfTI-1 data
ii python 2.4.4-2 An interactive high-level object-o
ii python-central 0.5.12 register and build utility for Pyt
ii python-numpy [python-nu 1:1.0.1-1 Numerical Python adds a fast array
ii python-numpy-ext 1:1.0.1-1 Numerical Python adds a fast array
ii python-scipy 0.5.2-0.1 scientific tools for Python
ii python2.4 2.4.4-3 An interactive high-level object-o
python-nifti recommends no packages.
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