Mailman 3 October 2013 - scikit-image

Re: Build error
by Stéfan van der Walt Oct. 14, 2013

Oct. 14, 2013

On Mon, Oct 14, 2013 at 5:21 PM, Jean K <jean.kossaifi(a)gmail.com> wrote: > You are absolutely right, thanks! > I had already installed Cython locally but didn't add it properly to the > PATH. > > However after I fixed it I got another error: Do you have Cython v0.19 installed? If so, then perhaps try a clean build. Stéfan

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Re: Build error
by Jean K Oct. 14, 2013

Oct. 14, 2013

You are absolutely right, thanks! I had already installed Cython locally but didn't add it properly to the PATH. However after I fixed it I got another error: > [...] building extension "skimage.segmentation._felzenszwalb_cy" sources > building extension "skimage.segmentation._quickshift" sources > building extension "skimage.segmentation._slic" sources > building data_files sources > build_src: building npy-pkg config files > customize UnixCCompiler > customize UnixCCompiler using build_ext > building 'skimage._shared.geometry' extension > compiling C sources > C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g > -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC > creating build > creating build/temp.linux-x86_64-2.7 > compile options: '-I/usr/lib/python2.7/dist-packages/numpy/core/include > -I/usr/include/python2.7 -c' > x86_64-linux-gnu-gcc: geometry.c > x86_64-linux-gnu-gcc: error: geometry.c: No such file or directory > x86_64-linux-gnu-gcc: fatal error: no input files > compilation terminated. > x86_64-linux-gnu-gcc: error: geometry.c: No such file or directory > x86_64-linux-gnu-gcc: fatal error: no input files > compilation terminated. > error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing > -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC > -I/usr/lib/python2.7/dist-packages/numpy/core/include > -I/usr/include/python2.7 -c geometry.c -o > build/temp.linux-x86_64-2.7/geometry.o" failed with exit status 4 Any idea? Thanks, Jean 2013/10/14 Stéfan van der Walt <stefan(a)sun.ac.za> > On Mon, Oct 14, 2013 at 3:38 PM, Jean K <jean.kossaifi(a)gmail.com> wrote: > >> ipdb> print popenargs > >> (['cython', '-o', > '/homes/jk712/scikit-image/skimage/feature/_template.c', > >> '/homes/jk712/scikit-image/skimage/feature/_template.pyx'],) > > It looks like cython wasn't installed correctly. Could you try the > "cython" command from the terminal? > > Stéfan > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe. > To unsubscribe from this group and all of its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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Build error
by Jean K Oct. 14, 2013

Oct. 14, 2013

Hi all, I'm trying to build scikit-image locally, in my git folder, and to just add it to my PYTHONPATH. I checked that all the requirements were met (confirmed by pip install -r requirements.txt). However, when I do > python setup.py build_ext -i I get an error. I must be missing something but can't really figure out what... This is the output I get: > non-existing path in 'skimage/_shared': 'tests' > non-existing path in 'skimage/_shared': 'geometry.c' > non-existing path in 'skimage/_shared': 'interpolation.c' > non-existing path in 'skimage/_shared': 'transform.c' > non-existing path in 'skimage/draw': '_draw.c' > non-existing path in 'skimage/feature': 'corner_cy.c' > non-existing path in 'skimage/feature': 'censure_cy.c' > non-existing path in 'skimage/feature': '_brief_cy.c' > non-existing path in 'skimage/feature': '_texture.c' > non-existing path in 'skimage/feature': '_template.c' > cython -o /homes/jk712/scikit-image/skimage/filter/_ctmf.c > /homes/jk712/scikit-image/skimage/filter/_ctmf.pyx > Traceback (most recent call last): > File "setup.py", line 146, in <module> > cmdclass={'build_py': build_py}, > File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line > 152, in setup > config = configuration() > File "setup.py", line 48, in configuration > config.add_subpackage('skimage') > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 1003, in add_subpackage > caller_level = 2) > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 972, in get_subpackage > caller_level = caller_level + 1) > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 909, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "skimage/setup.py", line 14, in configuration > config.add_subpackage('filter') > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 1003, in add_subpackage > caller_level = 2) > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 972, in get_subpackage > caller_level = caller_level + 1) > File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", > line 909, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "skimage/filter/setup.py", line 15, in configuration > cython(['_ctmf.pyx'], working_path=base_path) > File "/homes/jk712/scikit-image/skimage/_build.py", line 49, in cython > subprocess.call(['cython', '-o', c_file, pyxfile]) > File "/usr/lib/python2.7/subprocess.py", line 524, in call > return Popen(*popenargs, **kwargs).wait() > File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1308, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory Apparently the problem would be coming from a missing file _template.c > > /usr/lib/python2.7/subprocess.py(524)call() > 523 """ > --> 524 return Popen(*popenargs, **kwargs).wait() > 525 > > ipdb> print popenargs > (['cython', '-o', '/homes/jk712/scikit-image/skimage/feature/_template.c', > '/homes/jk712/scikit-image/skimage/feature/_template.pyx'],) > > ipdb> print kwargs > {} On the other hand, > easy_install --prefix ~/usr scikit-image works. Any idea of what is going on? Thanks, Jean

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Re: CIELUV Transformations
by Isaac Gerg Oct. 11, 2013

Oct. 11, 2013

I am limited on time but am happy to provide code if someone can put it into github for me. On Friday, October 11, 2013 11:08:50 AM UTC-4, Stefan van der Walt wrote: > > Hi Isaac > > On Fri, Oct 11, 2013 at 4:24 PM, Isaac Gerg <isaac...(a)gergltd.com<javascript:>> > wrote: > > Could CIELUV transformation be added? CIELAB was developed for > reflective > > media while CIELUV is for light emitting sources like monitors. Seems > that > > CIELUV would be a more appropriate perceptually uniform colorspace to > > support. > > Would you like to have a go at adding it? It can probably done by > simply adding the weights--we have all the tools in place already. > We'll also help with the pull request, as necessary. > > Regards > Stéfan >

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Re: Release time
by Stéfan van der Walt Oct. 11, 2013

Oct. 11, 2013

On Fri, Oct 11, 2013 at 5:15 PM, Chintak Sheth <chintaksheth(a)gmail.com> wrote: > Can we include exemplar based inpainting? > https://github.com/scikit-image/scikit-image/pull/706 We need more eyes on this--I am not sure whether this is optimized in the right places. Anyone willing to review Chintak's PR? Stéfan

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Re: Release time
by François Boulogne Oct. 11, 2013

Oct. 11, 2013

Hi, I saw this ticket: https://github.com/scikit-image/scikit-image/issues/745 possible issue with numpy 1.8.0. Cheers, -- François Boulogne. http://www.sciunto.org GPG fingerprint: 25F6 C971 4875 A6C1 EDD1 75C8 1AA7 216E 32D5 F22F

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CIELUV Transformations
by Isaac Gerg Oct. 11, 2013

Oct. 11, 2013

Feature request here. Could CIELUV transformation be added? CIELAB was developed for reflective media while CIELUV is for light emitting sources like monitors. Seems that CIELUV would be a more appropriate perceptually uniform colorspace to support. Thanks in advance, Isaac

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Re: umfpack error
by Josh Warner Oct. 6, 2013

Oct. 6, 2013

This would probably involve an API change, but instead of importing umfpack *at all* we could try `import pyamg` first. If pyamg is available, we wouldn't even attempt to import umfpack, instead using `'cg_mg'` instead of `'cg'`. This sidesteps stderr issues. The approach only works because the results are equivalent, differing only in speed/memory. I don't know why we default to the worst brute force option, either. Seems like we could default to `None` and attempt a fallback scheme of pyamg -> umfpack -> brute force in order, with a different warning structure. On Friday, October 4, 2013 8:07:39 AM UTC-5, Juan Nunez-Iglesias wrote: > > Ok so I'm having trouble actually suppressing this thing. The problem is > that to detect whether umfpack is present we try to build the > UmfpackContect() object: > > try: > from scipy.sparse.linalg.dsolve import umfpack > UmfpackContext = umfpack.UmfpackContext()except: > UmfpackContext = None > > > The constructor raises an ImportError, which we duly catch (although that > line should really specify the error type, but whatever). Unfortunately, > the UmfpackContext class has a destructor (__del__) which then tries to > delete some objects that were never created and raises an AttributeError — > which, since we are already in a try: except: clause, gets ignored, hence > the message to stderr. > > Basically this is a bug in scipy I think? > > The standard approach is to temporarily redirect stderr to /dev/null, and > this works interactively: > > In [1]: from scipy.sparse.linalg.dsolve import umfpack > > In [2]: try: > UC = umfpack.UmfpackContext()except ImportError: > print 'hello' > ...: > hello > Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x103938250>> ignored > > In [3]: import sys, os > > In [4]: null = open(os.devnull, 'w') > > In [5]: null.write('hello!') > > In [6]: sys.stdout.write('hello!') > hello! > In [7]: sys.stderr.write('hello') > hello > In [8]: sys.stderr = null > > In [9]: sys.stderr.write('hello') > > In [10]: try: > UC = umfpack.UmfpackContext()except ImportError: > print 'hello' > ....: > hello > > In [11]: sys.stderr = sys.__stderr__ > > In [12]: sys.stderr.write('hello') > hello > > > However, doing this in the code doesn't work, even when I try to flush the > redirected stderr! (I'm not even sure that makes sense!) > > sys.stderr = open(os.devnull, 'w')try: > from scipy.sparse.linalg.dsolve import umfpack > UmfpackContext = umfpack.UmfpackContext()except: > UmfpackContext = Nonefinally: > sys.stderr.flush() > sys.stderr = sys.__stderr__ > > > Thoughts/ideas? > > > > On Fri, Oct 4, 2013 at 10:54 PM, Juan Nunez-Iglesias <jni....(a)gmail.com<javascript:> > > wrote: > >> Thanks! Although in this case I was using pip install *and* it was on an >> EC2 micro instance so I only have 1 CPU. =) >> >> But it is noted and very useful going forward. =) >> >> >> >> On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.g...(a)gmail.com<javascript:> >> > wrote: >> >>> >>> >>> >>> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni....(a)gmail.com<javascript:> >>> > wrote: >>> >>>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Schönberger <js...(a)demuc.de<javascript:> >>>> > wrote: >>>> >>>>> Are you sure you have SWIG installed? >>>>> >>>> >>>> I wasn't and I didn't. =) >>>> >>>> Bloody hell scipy takes a long time to build. =) >>>> >>> >>> $ time python setup.py build_ext -i >>> real 12m6.843s >>> user 6m3.244s >>> sys 0m13.124s >>> >>> $ time ../Bento/bentomaker build -i -j # -j == parallel build (on 4 >>> cores here) >>> real 1m46.466s >>> user 2m54.628s >>> sys 0m10.900s >>> >>> Blame distutils (and start using Bento) :) >>> >>> Ralf >>> >>> >>> >>> >>>> Juan. >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "scikit-image" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to scikit-image...(a)googlegroups.com <javascript:>. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "scikit-image" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to scikit-image...(a)googlegroups.com <javascript:>. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> >

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Re: umfpack error
by Juan Nunez-Iglesias Oct. 4, 2013

Oct. 4, 2013

Ok so I'm having trouble actually suppressing this thing. The problem is that to detect whether umfpack is present we try to build the UmfpackContect() object: try: from scipy.sparse.linalg.dsolve import umfpack UmfpackContext = umfpack.UmfpackContext()except: UmfpackContext = None The constructor raises an ImportError, which we duly catch (although that line should really specify the error type, but whatever). Unfortunately, the UmfpackContext class has a destructor (__del__) which then tries to delete some objects that were never created and raises an AttributeError — which, since we are already in a try: except: clause, gets ignored, hence the message to stderr. Basically this is a bug in scipy I think? The standard approach is to temporarily redirect stderr to /dev/null, and this works interactively: In [1]: from scipy.sparse.linalg.dsolve import umfpack In [2]: try: UC = umfpack.UmfpackContext()except ImportError: print 'hello' ...: hello Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x103938250>> ignored In [3]: import sys, os In [4]: null = open(os.devnull, 'w') In [5]: null.write('hello!') In [6]: sys.stdout.write('hello!') hello! In [7]: sys.stderr.write('hello') hello In [8]: sys.stderr = null In [9]: sys.stderr.write('hello') In [10]: try: UC = umfpack.UmfpackContext()except ImportError: print 'hello' ....: hello In [11]: sys.stderr = sys.__stderr__ In [12]: sys.stderr.write('hello') hello However, doing this in the code doesn't work, even when I try to flush the redirected stderr! (I'm not even sure that makes sense!) sys.stderr = open(os.devnull, 'w')try: from scipy.sparse.linalg.dsolve import umfpack UmfpackContext = umfpack.UmfpackContext()except: UmfpackContext = Nonefinally: sys.stderr.flush() sys.stderr = sys.__stderr__ Thoughts/ideas? On Fri, Oct 4, 2013 at 10:54 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Thanks! Although in this case I was using pip install *and* it was on an > EC2 micro instance so I only have 1 CPU. =) > > But it is noted and very useful going forward. =) > > > > On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: > >> >> >> >> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: >> >>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Schönberger <jsch(a)demuc.de>wrote: >>> >>>> Are you sure you have SWIG installed? >>>> >>> >>> I wasn't and I didn't. =) >>> >>> Bloody hell scipy takes a long time to build. =) >>> >> >> $ time python setup.py build_ext -i >> real 12m6.843s >> user 6m3.244s >> sys 0m13.124s >> >> $ time ../Bento/bentomaker build -i -j # -j == parallel build (on 4 >> cores here) >> real 1m46.466s >> user 2m54.628s >> sys 0m10.900s >> >> Blame distutils (and start using Bento) :) >> >> Ralf >> >> >> >> >>> Juan. >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "scikit-image" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to scikit-image+unsubscribe(a)googlegroups.com. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >

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Re: umfpack error
by Juan Nunez-Iglesias Oct. 4, 2013

Oct. 4, 2013

Thanks! Although in this case I was using pip install *and* it was on an EC2 micro instance so I only have 1 CPU. =) But it is noted and very useful going forward. =) On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: > > > > On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Schönberger <jsch(a)demuc.de>wrote: >> >>> Are you sure you have SWIG installed? >>> >> >> I wasn't and I didn't. =) >> >> Bloody hell scipy takes a long time to build. =) >> > > $ time python setup.py build_ext -i > real 12m6.843s > user 6m3.244s > sys 0m13.124s > > $ time ../Bento/bentomaker build -i -j # -j == parallel build (on 4 > cores here) > real 1m46.466s > user 2m54.628s > sys 0m10.900s > > Blame distutils (and start using Bento) :) > > Ralf > > > > >> Juan. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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