Mailman 3 December 2011 - scikit-image

Re: Need an advice
by Stéfan van der Walt Dec. 23, 2011

Dec. 23, 2011

On Thu, Dec 22, 2011 at 10:44 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> wrote: > The application is not too sophisticated, and I do use numpy, scipy and > skimage for all I need. The only problem is speed, I need the processing to > be at l5-10 time faster. Convolutions take most of the processing time. I > prefer a flexible solution that would speed up also common nonlinear filters > (i.e. a median filter). We have a PR in the pipeline for doing really, really fast convolutions... but it needs a bit of work. Would you like to have a look at it? Stéfan

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PKG: Cant seem to build scikits debian package from source
by harish badrinath Dec. 23, 2011

Dec. 23, 2011

Hello, I cant seem to build scikits-image from source using debuild. Here are the steps i followed: a)I checkout master and debian branches in seprate directories. b) export master branch as a tar ball c) run dh_make (a debian specific packaging helper script) d) copy the contents of the debian directory to the directory in which i ran dh_make e) run debbuild The log of the build is <snip> dh clean --buildsystem python_distutils dh_testdir -O--buildsystem=python_distutils dh_auto_clean -O--buildsystem=python_distutils Traceback (most recent call last): File "setup.py", line 101, in <module> cmdclass={'build_py': build_py}, File "/usr/lib/pymodules/python2.5/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 42, in configuration config.add_subpackage('skimage') File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 957, in add_subpackage caller_level = 2) File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 926, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 863, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 8, in configuration config.add_subpackage('graph') File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 957, in add_subpackage caller_level = 2) File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 926, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/pymodules/python2.5/numpy/distutils/misc_util.py", line 848, in _get_configuration_from_setup_py ('.py', 'U', 1)) File "skimage/graph/setup.py", line 3, in <module> from skimage._build import cython File "/home/code/projs/scikits-image-master/scikits-image-0.4/skimage/__init__.py", line 64 from .util.dtype import * SyntaxError: 'import *' not allowed with 'from .' dh_auto_clean: python2.5 setup.py clean -a returned exit code 1 make: *** [clean] Error 1 dpkg-buildpackage: error: fakeroot debian/rules clean gave error exit status 2 debuild: fatal error at line 1325: dpkg-buildpackage -rfakeroot -D -us -uc failed </snip> Since i have very little experience with python, its build system, etc any help would be appreciated. Regards, Harish

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Re: Need an advice
by Nadav Horesh Dec. 23, 2011

Dec. 23, 2011

The application is not too sophisticated, and I do use numpy, scipy and skimage for all I need. The only problem is speed, I need the processing to be at l5-10 time faster. Convolutions take most of the processing time. I prefer a flexible solution that would speed up also common nonlinear filters (i.e. a median filter). Nadav, 2011/12/22 Jaidev Deshpande <deshpande.jaidev(a)gmail.com> > On Fri, Dec 23, 2011 at 1:42 AM, Nadav Horesh <nadavh.horesh(a)gmail.com> > wrote: > > > >Currently in use are filters and array processing from numpy, > scipy.signal, scipy.ndimage and numexpr. I am looking for faster tools that > cold be used without any extensive learning period. > > Are filters all you're looking for? If yes, and if your application > isn't too sophisticated, you can simply use NumPy arrays as filters. > Or else try scikits-image. > > What kind of filtering is it, and what's the application? > > Best, > Jaidev >

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Re: Need an advice
by Emmanuelle Gouillart Dec. 22, 2011

Dec. 22, 2011

Hi Nadav, would you need everything to be faster, or do you have some identified bottlenecks that take most of the computing time? In the latter case, you may want to keep using the most standard tools for most image processing steps, and pick a specialized and fast module for the most critical steps, like OpenCV. Also, the algorithms in scikits-image shouldn't do too bad in terms of executing speed, since they rely either on numpy arrays or on Cython code: what speed factor would you expect to gain with another library such as OpenCV? As for alternative librairies, ITK is very powerful and fast and has Python bindings. The learning curve looks a bit steep, though. Cheers, Emmanuelle On Thu, Dec 22, 2011 at 10:12:59PM +0200, Nadav Horesh wrote: > I have several scripts dealing with image procession of digital cameras > raw data. Currently in use are filters and array processing from numpy, > scipy.signal, scipy.ndimage and numexpr. I am looking for faster tools > that cold be used without any extensive learning period. I came up of the > following options: > 1, Theano: Can be very fast, but missing some important features� like a > median filter > 2. OpenCV: Fast and features rich, but the interface is not easy to learn. > Any recommendation for alternative libraries or easy interfaces to opencv? > (I looked at pyopencv, but the project doen't seems to be alive these > days) > �� Nadav

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Re: plugin freeimage vs gdal on 0.5dev
by jip Dec. 22, 2011

Dec. 22, 2011

thanks, JP On 22 déc, 20:18, Nelle Varoquaux <nelle.varoqu...(a)gmail.com> wrote: > Hi JP, > > You need to upgrade numpy to at least 1.4 > > Thanks, > N > > On 22 December 2011 20:10, jip <jeanpatrick.pomm...(a)gmail.com> wrote: > > > > > > > > > Hi Stéfan, > > my numpy install seems to be broken: > > > In [1]: import numpy as np > > > In [2]: print np.__version__ > > 1.3.0 > > > In [3]: import numpy.compat > > --------------------------------------------------------------------------- > > ImportError Traceback (most recent call > > last) > > /home/claire/Applications/ProjetPython/<ipython-input-3-2f9167a96fc7> > > in <module>() > > ----> 1 import numpy.compat > > > ImportError: No module named compat > > > Thanks > > JP > > > On 22 déc, 18:33, Stéfan van der Walt <ste...(a)sun.ac.za> wrote: > > > Hi JP > > > > It seems like there is something wrong with your numpy. Could you > > > please execute the following: > > > > import numpy as np > > > print np.__version__ > > > print np > > > > import numpy.compat > > > print numpy.compat > > > > Thanks > > > Stéfan > > > > On Thu, Dec 22, 2011 at 5:51 AM, jip <jeanpatrick.pomm...(a)gmail.com> > > wrote: > > > > Dear all, > > > > If I try to load a 12bits TIF image: > > > > sk.io.use_plugin('freeimage', 'imread') > > > > sk.io.use_plugin('matplotlib', 'imshow') > > > > dapi=io.imread(path+CC+im) > > > > > I have the following message: > > > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > > > Traceback (most recent call last): > > > > File "/home/claire/Applications/ProjetPython/projet particule et > > > > objet/Nuclei/QuantSpots-skimage.py", line 49, in <module> > > > > sk.io.use_plugin('freeimage', 'imread') > > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 128, in use > > > > _load(name) > > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 190, in > > > > _load > > > > fromlist=[modname]) > > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > > py2.6-linux-i686.egg/skimage/io/_plugins/freeimage_plugin.py", line 6, > > > > in <module> > > > > from numpy.compat import asbytes > > > > ImportError: No module named compat > > > > > What is that compat module? I have numpy 1.30 installed. > > > > > Anyway,I can load the image with gdal (sk.io.use_plugin('gdal', > > > > 'imread') with some warnings: > > > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > > > encountered > > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > > > encountered > > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > > > encountered > > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > > > encountered > > > > > best regards > > > > Jean-Patrick

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Re: Need an advice
by Jaidev Deshpande Dec. 22, 2011

Dec. 22, 2011

On Fri, Dec 23, 2011 at 1:42 AM, Nadav Horesh <nadavh.horesh(a)gmail.com> wrote: > >Currently in use are filters and array processing from numpy, scipy.signal, scipy.ndimage and numexpr. I am looking for faster tools that cold be used without any extensive learning period. Are filters all you're looking for? If yes, and if your application isn't too sophisticated, you can simply use NumPy arrays as filters. Or else try scikits-image. What kind of filtering is it, and what's the application? Best, Jaidev

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Need an advice
by Nadav Horesh Dec. 22, 2011

Dec. 22, 2011

I have several scripts dealing with image procession of digital cameras raw data. Currently in use are filters and array processing from numpy, scipy.signal, scipy.ndimage and numexpr. I am looking for faster tools that cold be used without any extensive learning period. I came up of the following options: 1, Theano: Can be very fast, but missing some important features like a median filter 2. OpenCV: Fast and features rich, but the interface is not easy to learn. Any recommendation for alternative libraries or easy interfaces to opencv? (I looked at pyopencv, but the project doen't seems to be alive these days) Nadav

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Re: plugin freeimage vs gdal on 0.5dev
by Nelle Varoquaux Dec. 22, 2011

Dec. 22, 2011

Hi JP, You need to upgrade numpy to at least 1.4 Thanks, N On 22 December 2011 20:10, jip <jeanpatrick.pommier(a)gmail.com> wrote: > Hi Stéfan, > my numpy install seems to be broken: > > In [1]: import numpy as np > > In [2]: print np.__version__ > 1.3.0 > > In [3]: import numpy.compat > --------------------------------------------------------------------------- > ImportError Traceback (most recent call > last) > /home/claire/Applications/ProjetPython/<ipython-input-3-2f9167a96fc7> > in <module>() > ----> 1 import numpy.compat > > ImportError: No module named compat > > Thanks > JP > > On 22 déc, 18:33, Stéfan van der Walt <ste...(a)sun.ac.za> wrote: > > Hi JP > > > > It seems like there is something wrong with your numpy. Could you > > please execute the following: > > > > import numpy as np > > print np.__version__ > > print np > > > > import numpy.compat > > print numpy.compat > > > > Thanks > > Stéfan > > > > > > > > > > > > > > > > On Thu, Dec 22, 2011 at 5:51 AM, jip <jeanpatrick.pomm...(a)gmail.com> > wrote: > > > Dear all, > > > If I try to load a 12bits TIF image: > > > sk.io.use_plugin('freeimage', 'imread') > > > sk.io.use_plugin('matplotlib', 'imshow') > > > dapi=io.imread(path+CC+im) > > > > > I have the following message: > > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > > Traceback (most recent call last): > > > File "/home/claire/Applications/ProjetPython/projet particule et > > > objet/Nuclei/QuantSpots-skimage.py", line 49, in <module> > > > sk.io.use_plugin('freeimage', 'imread') > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 128, in use > > > _load(name) > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 190, in > > > _load > > > fromlist=[modname]) > > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > > py2.6-linux-i686.egg/skimage/io/_plugins/freeimage_plugin.py", line 6, > > > in <module> > > > from numpy.compat import asbytes > > > ImportError: No module named compat > > > > > What is that compat module? I have numpy 1.30 installed. > > > > > Anyway,I can load the image with gdal (sk.io.use_plugin('gdal', > > > 'imread') with some warnings: > > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > > encountered > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > > encountered > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > > encountered > > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > > encountered > > > > > best regards > > > Jean-Patrick >

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Re: plugin freeimage vs gdal on 0.5dev
by jip Dec. 22, 2011

Dec. 22, 2011

Hi Stéfan, my numpy install seems to be broken: In [1]: import numpy as np In [2]: print np.__version__ 1.3.0 In [3]: import numpy.compat --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /home/claire/Applications/ProjetPython/<ipython-input-3-2f9167a96fc7> in <module>() ----> 1 import numpy.compat ImportError: No module named compat Thanks JP On 22 déc, 18:33, Stéfan van der Walt <ste...(a)sun.ac.za> wrote: > Hi JP > > It seems like there is something wrong with your numpy. Could you > please execute the following: > > import numpy as np > print np.__version__ > print np > > import numpy.compat > print numpy.compat > > Thanks > Stéfan > > > > > > > > On Thu, Dec 22, 2011 at 5:51 AM, jip <jeanpatrick.pomm...(a)gmail.com> wrote: > > Dear all, > > If I try to load a 12bits TIF image: > > sk.io.use_plugin('freeimage', 'imread') > > sk.io.use_plugin('matplotlib', 'imshow') > > dapi=io.imread(path+CC+im) > > > I have the following message: > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > Traceback (most recent call last): > > File "/home/claire/Applications/ProjetPython/projet particule et > > objet/Nuclei/QuantSpots-skimage.py", line 49, in <module> > > sk.io.use_plugin('freeimage', 'imread') > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 128, in use > > _load(name) > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 190, in > > _load > > fromlist=[modname]) > > File "/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev- > > py2.6-linux-i686.egg/skimage/io/_plugins/freeimage_plugin.py", line 6, > > in <module> > > from numpy.compat import asbytes > > ImportError: No module named compat > > > What is that compat module? I have numpy 1.30 installed. > > > Anyway,I can load the image with gdal (sk.io.use_plugin('gdal', > > 'imread') with some warnings: > > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > encountered > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > encountered > > Warning 1: TIFFReadDirectory:Unknown field with tag 34959 (0x888f) > > encountered > > Warning 1: TIFFReadDirectory:Unknown field with tag 34960 (0x8890) > > encountered > > > best regards > > Jean-Patrick

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How to update skimage 0.5dev
by jip Dec. 22, 2011

Dec. 22, 2011

Dear all, I'd like to update skimage 0.5dev. I read somewhere that I need not to download the whole archive from github and rebuild from scratch for every update. sudo easy_install -U skimage fails I there a command to do the work? Thank you. Jean-Patrick Pommier

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