Can you describe what went wrong when you did "sage -i pynifti-p0"? Had you downloaded the package? It won't get into the repository until someone reviews my ticket.
Did you try installing nifticlib when you did it by hand? Thanks, Marshall On Aug 7, 1:23 am, Arvid <[email protected]> wrote: > Thanks for the effort of bringing pynifti (and pymvpa) avaliable. > For me (on Ubuntu 9,04, or Mac Leopard) > > $ sage -i pynifti-p0 > > unfortunately did not work directly. However, > downloading the sources 'pynifti_0.20090303.1.tar.gz' and > 'pymvpa_0.4.2.tar.gz', then > > $ sage -sh and $ make all and $ python setup.py install > > in the unpacked directories of pynifti_... and pymvpa_... , > respectively, > works OK, i.e. > > sage: import nifti > sage: import mvpa > > On the Mac (Leopard) I have problems with the nifticlib 1.1 library > (i.e. $SAGE_HOME/local/lib/python2.6/site-packages/ > nifti/_clib.so, 2): Symbol not found: _Xznzclose ) > that must be installed before the punifti or pymvpa packages. > > - Arvid Lundervold > > On Aug 6, 4:28 pm, Marshall Hampton <[email protected]> wrote: > > > I have a proposed experimental pynifti package, tracked as ticket > > #6678: > > >http://trac.sagemath.org/sage_trac/ticket/6678 > > > -Marshall > > > On Aug 5, 10:23 pm, Marshall Hampton <[email protected]> wrote: > > > > Maybe this was some sort of path issue I don't understand, but when I > > > tried things again it seemed to work, i.e. if I go into my SAGE_ROOT > > > folder and use either sage or the sage python, the "import nifti" > > > works. So what I described above seems to be sufficient, and this > > > could be made into an spkg. I will give that a try tomorrow if I can > > > find the time. > > > > -Marshall Hampton > > > > On Aug 5, 10:12 pm, William Stein <[email protected]> wrote: > > > > > On Wed, Aug 5, 2009 at 8:09 PM, Marshall Hampton > > > > <[email protected]>wrote: > > > > > > I gave this a shot but it seems its not trivial to install. > > > > > > 1) I installed pymvpa with: > > > > > > pymvpa-0.4.2: sage -python setup.py build_ext > > > > > > 2) I installed the nifti c libraries with: > > > > > > nifticlib-1.1.0: make all > > > > > > 2b) then I copied everything in the bin, lib, and include directories > > > > > into the corresponding SAGE_LOCAL places. > > > > > > 3) Then I tried to install pynifti but had trouble. Going into a sage > > > > > shell: > > > > > > pynifti-0.20090303.1: sage -sh > > > > > > building with: > > > > > > pynifti-0.20090303.1: python setup.py build > > > > > > and installing with: > > > > > > pynifti-0.20090303.1: python setup.py install > > > > > > seems to go OK but when I try to test I get an error: > > > > > > pynifti-0.20090303.1: sage -python > > > > > Python 2.6.2 (r262:71600, Jul 16 2009, 10:01:32) > > > > > [GCC 4.0.1 (Apple Inc. build 5465)] on darwin > > > > > Type "help", "copyright", "credits" or "license" for more information. > > > > > >>> import nifti > > > > > Traceback (most recent call last): > > > > > File "<stdin>", line 1, in <module> > > > > > File "nifti/__init__.py", line 21, in <module> > > > > > from nifti.image import NiftiImage, MemMappedNiftiImage > > > > > File "nifti/image.py", line 27, in <module> > > > > > import nifti.clib as ncl > > > > > ImportError: No module named clib > > > > > > ...I'm not sure how to proceed. > > > > > I recommend emailing the developers of pynifti and see if they care > > > > about > > > > getting it to install into Sage. If so, obviously they could install > > > > Sage > > > > and try the above, but with their added knowledge of pynifti, they might > > > > succeed... > > > > > -- William > > > > > > This looks like a nice opportunity for Sage to become more relevant in > > > > > biomedical imaging. > > > > > > -Marshall Hampton > > > > > > On Aug 5, 1:46 pm, Harald Schilly <[email protected]> wrote: > > > > > > On Aug 5, 8:36 pm, Arvid <[email protected]> wrote: > > > > > > > > Will it be possible to incorporate access to NIfTI and ANALYZE > > > > > > > files > > > > > > > in SAGE through PyNIfTI > > > > > > > (http://niftilib.sourceforge.net/pynifti/)? > > > > > > > Hi, I can't access the sourceforge website right now, but it is > > > > > > "easy" > > > > > > to install additional python packages in sage. They don't need to be > > > > > > included or packaged. Just go into the "sage environment" with > > > > > > "sage - > > > > > > sh" and install the package there. Background: Sage has it's own > > > > > > python and you have to install it there, not system wide python > > > > > > installation. > > > > > > Your actual problem seems to be that additional C/C++ software is > > > > > > missing, it can be installed in the same way. > > > > > > And, I don't think this will be included in sage, soon. The general > > > > > > process is, to first create an experimental or optional package, > > > > > > that > > > > > > can be downloaded and installed. Once many users need it and after a > > > > > > voting it is included as a standard package. > > > > > > > H > > > > > -- > > > > William Stein > > > > Associate Professor of Mathematics > > > > University of Washingtonhttp://wstein.org --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
