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 <wst...@gmail.com> wrote: > On Wed, Aug 5, 2009 at 8:09 PM, Marshall Hampton <hampto...@gmail.com>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 <harald.schi...@gmail.com> wrote: > > > On Aug 5, 8:36 pm, Arvid <arvid.lunderv...@gmail.com> 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 sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
