Mailman 3 April 2013 - scikit-image

Re: multi-page TIFF writer
by Zachary Pincus 18 Apr '13

18 Apr '13

> I think Zach knows better than I what the source of the error was, so he should probably handle it. ;) Yes, that's more than fair! I keep forgetting to put in unit tests with my bug fixes, because I am a bad person... :) So the gentle reminders are helpful. Stéfan, I'll try to get something in shortly. Zach > On Thu, Apr 18, 2013 at 12:52 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi Juan > > > On Apr 18, 2013 2:35 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > > Yep, I've confirmed that your PR solved the problem for me! So I'll spare you that backtrace, Stefan. ;) > > Great! Now, for some extra brownie points and our eternal gratitude: a unit test? > > Stéfan > > -- > 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: Cython memoryviews
by Stéfan van der Walt 18 Apr '13

18 Apr '13

On Tue, Apr 16, 2013 at 5:45 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: >> cnp.ndarray[dtype=float, ndim=2] -> double[:, ::1] > > Can you explain this syntax to me? I'd understand double[:, :], but not sure > I get double[:, ::1]. Are you indicating that the array should be > interpreted in C order? Would double[::1, :] indicate a Fortran-order array? > And is double[:, ::1, :] invalid? Finally, can you take any array as input > and reinterpret as a one-dimensional array? Yes, the ::1 indicates the contiguous dimension, and can only be used in the first and last places. I'm not sure I understand your last question correctly, but you can do: def foo(x): cdef double[:] y = x.ravel() return y[0] Stéfan

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Re: Errors while compiling and $make coverage
by Stéfan van der Walt 18 Apr '13

18 Apr '13

On Wed, Apr 17, 2013 at 7:30 PM, Chintak Sheth <chintaksheth(a)gmail.com> wrote: > After getting the segmentation error it just says "Python quit > unexpectedly". Can we get any information from Seg fault "11". Any idea what > the error code represents ? Does your build segfault? That's odd. Try building first, and if that works run "nosetests -v" to see which test breaks. Then start "gdb python" and then provide the given test file, e.g. Stéfan

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Re: multi-page TIFF writer
by Juan Nunez-Iglesias 18 Apr '13

18 Apr '13

I think Zach knows better than I what the source of the error was, so he should probably handle it. ;) On Thu, Apr 18, 2013 at 12:52 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Juan > > On Apr 18, 2013 2:35 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > > Yep, I've confirmed that your PR solved the problem for me! So I'll > spare you that backtrace, Stefan. ;) > > Great! Now, for some extra brownie points and our eternal gratitude: a > unit test? > > Stéfan > > -- > 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: Image Feature Suggestion
by Zachary Pincus 18 Apr '13

18 Apr '13

Hi Ronnie, Identifying features to track between frames is a pretty classic task in computer vision. Things that come to mind would include the simple Harris corner detector (in skimage), or more recent things like SIFT features and its variants like SURF etc. (DAISY is in skimage) might be of use. All of these tools should be in OpenCV too, IIRC. (Time to spend a while on wikipedia reading about these things and related, if it's all totally unfamiliar.) Alternately, you could try optical flow based techniques to densely track local pixel patches between frames. In either case, the first thing to do would be to get a robust estimate of the global camera translation and subtract out that shake (very common operation these days... I think this is all packaged up in openCV). Then you could do the optical flow / feature tracking specifically on your spinning thing. One basic flow might be: (1) subtract out global camera shake (2) find feature points to track (e.g. good Harris corners) that are not static from frame to frame (e.g. by using background estimation and subtraction) (3) optimize an estimate of the center-of-rotaion and angle-of-rotation parameters, based on how well the feature points match between frames after applying the estimated rotation parameters. If you provide a few sample frames, folks might be able to offer better suggestions. Over all, I think most of the tools you need for this sort of thing are in OpenCV... Zach On Apr 16, 2013, at 12:04 AM, Ronnie Ghose wrote: > Hey guys, > > I was wondering if you could suggest feature extraction methods to try on an image. So I was wondering given for example a gif of a wheel spinning or (something easier I should think because it has discrete branches spinning) a carousel spinning how could you identify the branches in each frame and tell the approximate radian shift, and then also do that given a slight translation in the picture - ex. a shaky video camera? > > Thanks, > Ronnie > > -- > 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: multi-page TIFF writer
by Stéfan van der Walt 18 Apr '13

18 Apr '13

Hi Juan On Apr 18, 2013 2:35 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > Yep, I've confirmed that your PR solved the problem for me! So I'll spare you that backtrace, Stefan. ;) Great! Now, for some extra brownie points and our eternal gratitude: a unit test? Stéfan

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Re: multi-page TIFF writer
by Zachary Pincus 17 Apr '13

17 Apr '13

This is a lurking 64-bit bug that I failed to squash the last time. Problem solved: https://github.com/scikit-image/scikit-image/pull/507 Thanks, Juan, for identifying this problem! It should be fixed in the github version of skimage. Zach On Apr 17, 2013, at 12:49 PM, Stéfan van der Walt wrote: > On Wed, Apr 17, 2013 at 6:02 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: >> In [3]: fr.write_multipage(im0, 'im0.tif') >> Segmentation fault: 11 >> >> Let me know if you get the same result... > > Works perfectly here. Could you run it through gdb? > > gdb python > > then > > run myscript.py > > and after it fails type "bt" for backtrace. > > Stéfan > > -- > 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: Errors while compiling and $make coverage
by Chintak Sheth 17 Apr '13

17 Apr '13

Sorry for the delay, exams going on. So i ran it with "gdb python" but still nothing : Working directory /Users/chintak/Repositories/scikit-image. > (gdb) run setup.py build_ext -i > The program being debugged has been started already. > Start it from the beginning? (y or n) y > Starting program: /usr/local/bin/python setup.py build_ext -i > Program received signal SIGTRAP, Trace/breakpoint trap. > 0x00007fff5fc01028 in __dyld__dyld_start () > (gdb) bt > #0 0x00007fff5fc01028 in __dyld__dyld_start () > #1 0x0000000100000000 in ?? () > (gdb) make coverage > nosetests skimage --with-coverage --cover-package=skimage > make: *** [coverage] Segmentation fault: 11 > (gdb) bt > #0 0x00007fff5fc01028 in __dyld__dyld_start () > #1 0x0000000100000000 in ?? () > (gdb) After getting the segmentation error it just says "Python quit unexpectedly". Can we get any information from Seg fault "11". Any idea what the error code represents ? Chintak

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Re: multi-page TIFF writer
by Stéfan van der Walt 17 Apr '13

17 Apr '13

On Wed, Apr 17, 2013 at 6:02 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > In [3]: fr.write_multipage(im0, 'im0.tif') > Segmentation fault: 11 > > Let me know if you get the same result... Works perfectly here. Could you run it through gdb? gdb python then run myscript.py and after it fails type "bt" for backtrace. Stéfan

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Re: Histogram backprojection
by Stéfan van der Walt 16 Apr '13

16 Apr '13

On Apr 17, 2013 5:53 AM, "abid rahman" <abidrahman2(a)gmail.com> wrote: > > I am sorry, what does PR means ? Never heard before. It stands for "pull request". Stéfan

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