[Pkg-exppsy-pynifti] Possible bug in header get/set methods on RedHat Linux

[Ryan Haynes]

I am trying to build pyNIFTI for use with pyMVPA on a Red Hat
Enterprise 5. I've tried three different versions of pynifti on both
Python 2.5 and 2.6. I'm running scipy-0.7.1 and numpy-1.4.0. The
problem seems to relate to reading the header (in
pynifti-0.20090303.1.tar.gz and pynifti-0.20090205.1) and writing the
header (pynifti-0.20081017.1). The following are the stack traces for
these two different (yet similar) errors:

with pynifti-0.20090303.1.tar.gz and pynifti-0.20090205.1:

  File "/s/data8/rhaynes/fmrianalyze-1.0/mvpa/Analysis/src/__init__.py",
line 482, in CreateDatasetFromBetas
    header = nim.asDict();
  File "/opt/lib/python2.5/site-packages/nifti/format.py", line 270, in asDict
    ret = nhdr2dict(nhdr, extensions=self.extensions)
  File "/opt/lib/python2.5/site-packages/nifti/utils.py", line 254, in nhdr2dict
    h['xyz_unit'] = ncl.xyzt2space(nhdr.xyzt_units)
TypeError: in method 'xyzt2space', argument 1 of type 'char'

----------------------

with pynifti-0.20081017.1:

  File "/s/data8/rhaynes/fmrianalyze-1.0/mvpa/Analysis/src/__init__.py",
line 496, in CreateDatasetFromBetas
    nim = NiftiImage(dataset,header);
  File "/opt/lib/python2.5/site-packages/nifti/niftiimage.py", line
57, in __init__
    NiftiFormat.__init__(self, source, header)
  File "/opt/lib/python2.5/site-packages/nifti/niftiformat.py", line
55, in __init__
    self.__newFromArray(source, header)
  File "/opt/lib/python2.5/site-packages/nifti/niftiformat.py", line
119, in __newFromArray
    updateNiftiHeaderFromDict(nhdr, hdic)
  File "/opt/lib/python2.5/site-packages/nifti/utils.py", line 259, in
updateNiftiHeaderFromDict
    nhdr.regular = hdrdict['regular']
  File "/opt/lib/python2.5/site-packages/nifti/nifticlib.py", line 94,
in <lambda>
    __setattr__ = lambda self, name, value: _swig_setattr(self,
nifti_1_header, name, value)
  File "/opt/lib/python2.5/site-packages/nifti/nifticlib.py", line 33,
in _swig_setattr
    return _swig_setattr_nondynamic(self,class_type,name,value,0)
  File "/opt/lib/python2.5/site-packages/nifti/nifticlib.py", line 26,
in _swig_setattr_nondynamic
    if method: return method(self,value)
TypeError: in method 'nifti_1_header_regular_set', argument 2 of type 'char'


As you can see, it appears to be a similar error with the 'char' type.
In pynifti-0.20081017.1 the error results from assigning the character
'r' to the field 'regular' which should be a valid value for this
field. I have also tried this exact code on my Windows XP system with
Python 2.5 and pynifti-0.20081017.1.win32-py2.5.exe and it runs
perfectly without errors. So, it appears that the error has to do with
something peculiar to the pyNIFTI code. My guess is that it has
something to do with the SWIG interface to the C++ libraries. I should
also note that I'm using the shared object library built from the 3rd
party folder in the pyNIFTI distributions and not the full version of
nifticlibs though I also had errors with a full build of nifticlibs.
Any suggestions would be greatly appreciated.

Thanks,
Ryan Haynes