After installing swig, ie. "sudo apt-get install swig"
and amd64 build of nifticlib 1.1.0-2 in ubuntu jaunty from https://launchpad.net/ubuntu/jaunty/amd64/libnifti1-dev/1.1.0-2 and "sage -i pynifti-p0" I get: ... gcc -pthread -shared build/temp.linux-x86_64-2.6/build/src.linux- x86_64-2.6/nifti/clib_wrap.o -Lbuild/nifticlibs -lniftiio -lznz -lz -o build/lib.linux-x86_64-2.6/nifti/_clib.so --Wl,--no-undefined build/nifticlibs/libniftiio.a: could not read symbols: Archive has no index; run ranlib to add one collect2: ld returned 1 exit status build/nifticlibs/libniftiio.a: could not read symbols: Archive has no index; run ranlib to add one collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.6/build/ src.linux-x86_64-2.6/nifti/clib_wrap.o -Lbuild/nifticlibs -lniftiio - lznz -lz -o build/lib.linux-x86_64-2.6/nifti/_clib.so --Wl,--no- undefined" failed with exit status 1 ... However, (again) downloading the "pymvpa_0.4.2.tar.gz" and "pynifti_0.20090303.1.tar.gz" sources from http://alioth.debian.org/frs/?group_id=30954 and within a sage shell ("sage -sh") running "make all" and "python setup.py install", both packages can be imported in sage ("sage: import nifti" and "sage: import mvpa") without error messages. A nifticlib-problem with "pynifti-p0.spkg" ? - Arvid Lundervold ... On Aug 7, 3:02 pm, Marshall Hampton <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
