setup pb with cython 0.15.1

[agramfort]

here is the backtrace:

fos(master)$ python setup.py install
running install
running build
running build_py
running build_ext
cythoning fos/core/collision.pyx to fos/core/collision.c
building 'fos.core.collision' extension
gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -DNDEBUG -g -O3 -arch i386 -I/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/7.1/include/python2.7 -c fos/core/collision.c -o build/temp.macosx-10.5-i386-2.7/fos/core/collision.o
gcc -bundle -undefined dynamic_lookup -g -arch i386 build/temp.macosx-10.5-i386-2.7/fos/core/collision.o -o build/lib.macosx-10.5-i386-2.7/fos/core/collision.so
cythoning fos/core/cython_gl.pyx to fos/core/cython_gl.c
warning: fos/core/cython_gl.pyx:22:15: Function signature does not match previous declaration

Error compiling Cython file:

...
cdef int i
cdef long summ=0
for i from 0<=i<lenind:
#print('st',strides[i],indices[i])
summ+=strides[i]*indices[i]
summ/=typesize

^

fos/core/cython_gl.pyx:77:8: Pythonic division not allowed without gil, consider using cython.cdivision(True)
building 'fos.core.cython_gl' extension
gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -DNDEBUG -g -O3 -arch i386 -I/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/7.1/include/python2.7 -c fos/core/cython_gl.c -o build/temp.macosx-10.5-i386-2.7/fos/core/cython_gl.o
fos/core/cython_gl.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1

[Garyfallidis]

Cool thx for this I am on it!

[Garyfallidis]

It should work again now.

[Garyfallidis]

Let me know if it works for you and then we can close this issue. On a further note cython_gl will most likely be removed in the future.

[agramfort]

the cythonizing work but I get:

fos/core/cython_gl.c:240:19: error: GL/gl.h: No such file or directory
error: command 'gcc' failed with exit status 1

FYI gl.h is at :

/usr/X11/include/GL/gl.h

on a mac

[Garyfallidis]

okay obviously it needs a switch to check if it is mac or win or linux etc. So, becauce currently we are not using this module I have disabled it from setup.py. Try again then. It should go smoothly this time and thank you for your feedback.

[agramfort]

ok better.

actor folder is not installed by setup.py install

we're getting there :)

On Thu, Nov 17, 2011 at 3:26 PM, Eleftherios Garyfallidis
[email protected]
wrote:

okay obviously it needs a switch to check if it is mac or win or linux etc. So, becauce currently we are not using this module I have disabled it from setup.py. Try again then. It should go smoothly this time and thank you for your feedback.

---

Reply to this email directly or view it on GitHub:
fos/fos#4 (comment)

[Garyfallidis]

Alex, Fos is not released yet and it will take some time to be released. For the moment you can have a look at it by locally installing it (using python setup.py build_ext --inplace) and adding it to your PYTHONPATH but I think you will mostly just spend your time because there is neither much documentation neither many utilities in Fos which are ready for general usage. Sorry, for that... we will do our best to deliver as soon as possible. Will definitely let you know.

[agramfort]

sure no pb. At least you're aware that this needs to be fixed :)

On Thu, Nov 17, 2011 at 5:16 PM, Eleftherios Garyfallidis
[email protected]
wrote:

Alex, Fos is not released yet and it will take some time to be released. For the moment you can have a look at it by locally installing it (using python setup.py build_ext --inplace) and adding it to your PYTHONPATH but I think you will mostly just spend your time because there is neither much documentation neither many utilities in Fos which are ready for general usage. Sorry, for that... we will do our best to deliver as soon as possible. Will definitely let you know.

---

Reply to this email directly or view it on GitHub:
fos/fos#4 (comment)

[Garyfallidis]

Yes I added the actor module too now. Many thanx!!! :-) Let me know if you want to get involved in Fos development. You should also have a look at the fos-pyglet which concentrates a lot on GLSL. I will try to release a Fos version where you can have slices together with tracks working interactively. This is implemented in spaghetti.py in Fos/applications but I am currently changing some bits and pieces. This should work fine with volumes and tracks registered in MNI space. It will need a bit more refinement to make it work with any space.

[Garyfallidis]

Also please remind me what kind of application would be useful for you. You never know you might get lucky.

[agramfort]

Yes I added the actor module too now. Many thanx!!! :-) Let me know if you want to get involved in Fos development.

not for now. Too much on my plate. I am just always happy to report bugs :)

You should also have a look at the fos-pyglet which concentrates a lot on GLSL. I will try to release a Fos version where you can have slices together with tracks working interactively. This is implemented in spaghetti.py in Fos/applications but I am currently changing some bits and pieces. This should work fine with volumes and tracks registered in MNI space. It will need a bit more refinement to make it work with any space.

sounds great. I'll investigate further when I have time.

Also please remind me what kind of application would be useful for you. You never know you might get lucky.

I do brain imaging, so I need to visualize surfaces with textures,
curvature, activations + volumes like in fslview or freeview. Also a
probably not so common feature is the ability
to scroll trough a temporal texture for M/EEG.