scikit-image March 2013

scikit-image@python.org

16 participants
37 discussions

Announcement: scikits-image 0.8.0
by Johannes Schönberger 05 Mar '13

05 Mar '13

Announcement: scikits-image 0.8.0 ================================= We're happy to announce the 8th version of scikit-image! scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. For more information, examples, and documentation, please visit our website: http://scikit-image.org New Features ------------ - New rank filter package with many new functions and a very fast underlying local histogram algorithm, especially for large structuring elements `skimage.filter.rank.*` - New function for small object removal `skimage.morphology.remove_small_objects` - New circular hough transformation `skimage.transform.hough_circle` - New function to draw circle perimeter `skimage.draw.circle_perimeter` and ellipse perimeter `skimage.draw.ellipse_perimeter` - New dense DAISY feature descriptor `skimage.feature.daisy` - New bilateral filter `skimage.filter.denoise_bilateral` - New faster TV denoising filter based on split-Bregman algorithm `skimage.filter.denoise_tv_bregman` - New linear hough peak detection `skimage.transform.hough_peaks` - New Scharr edge detection `skimage.filter.scharr` - New geometric image scaling as convenience function `skimage.transform.rescale` - New theme for documentation and website - Faster median filter through vectorization `skimage.filter.median_filter` - Grayscale images supported for SLIC segmentation - Unified peak detection with more options `skimage.feature.peak_local_max` - `imread` can read images via URL and knows more formats `skimage.io.imread` Additionally, this release adds lots of bug fixes, new examples, and performance enhancements. Contributors to this release ---------------------------- This release was only possible due to the efforts of many contributors, both new and old. - Adam Ginsburg - Anders Boesen Lindbo Larsen - Andreas Mueller - Christoph Gohlke - Christos Psaltis - Colin Lea - François Boulogne - Jan Margeta - Johannes Schönberger - Josh Warner (Mac) - Juan Nunez-Iglesias - Luis Pedro Coelho - Marianne Corvellec - Matt McCormick - Nicolas Pinto - Olivier Debeir - Paul Ivanov - Sergey Karayev - Stefan van der Walt - Steven Silvester - Thouis (Ray) Jones - Tony S Yu

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Re: Segmenting contours
by zetah 04 Mar '13

04 Mar '13

Sure Stefan, I attached SVG version with a bit of smoothing.

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Re: Segfaults from CTMF
by Tony Yu 01 Mar '13

01 Mar '13

On Fri, Mar 1, 2013 at 9:48 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Thu, Feb 28, 2013 at 8:17 PM, Thouis (Ray) Jones <thouis(a)gmail.com>wrote: > >> I'm on OSX 10.8, python 2.7.3, Cython 0.18. I wonder if it's the >> cython version. Your code works for me. >> >> Do you have a traceback? > > > There's no python traceback, but I've copied the crash report below. The > relevant line in the Cython code is: > > > https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ct… > > > Also, do you know which path it's going down >> (SSE/MMX/Altivec/unaccelerated)? >> >> > > It's crashing on the SSE path. The MMX (and unaccelerated) path works fine. > > Crash report > ~~~~~~~~~ > > Crashed Thread: 0 Dispatch queue: com.apple.main-thread > > Exception Type: EXC_BAD_ACCESS (SIGSEGV) > Exception Codes: EXC_I386_GPFLT > > Thread 0 Crashed:: Dispatch queue: com.apple.main-thread > 0 _ctmf.so 0x058c77ea > __pyx_f_7skimage_6filter_5_ctmf_accumulate + 490 (_ctmf.c:2277) > 1 _ctmf.so 0x058cb4a0 > __pyx_pw_7skimage_6filter_5_ctmf_1median_filter + 8864 (_ctmf.c:3673) > 2 org.python.python 0x000cb2d1 PyEval_EvalFrameEx + 21649 > 3 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042 > 4 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523 > 5 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042 > 6 org.python.python 0x000cd1b7 PyEval_EvalCode + 87 > 7 org.python.python 0x000f1898 PyRun_FileExFlags + 168 > 8 org.python.python 0x000f27c3 PyRun_SimpleFileExFlags + 867 > 9 org.python.python 0x0010ba58 Py_Main + 3560 > 10 org.python.python 0x00001fb6 0x1000 + 4022 > > > >> Ray >> >> >> On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80(a)gmail.com> wrote: >> > I'm getting segfaults when running the median filter due to the >> > SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for >> > testing: >> > >> > >> > from skimage import data >> > from skimage.filter import median_filter >> > >> > median_filter(data.camera()) >> > >> > >> > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel >> Core i7 >> > machine with Cython 0.16, Python 2.7.3. >> > >> > Thanks, >> > -Tony >> >> I forgot to mention in my original email: This is running 32-bit Python. I have a separate machine running 64-bit Python and everything is fine. -T

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Re: Segfaults from CTMF
by Tony Yu 01 Mar '13

01 Mar '13

On Thu, Feb 28, 2013 at 8:17 PM, Thouis (Ray) Jones <thouis(a)gmail.com>wrote: > I'm on OSX 10.8, python 2.7.3, Cython 0.18. I wonder if it's the > cython version. Your code works for me. > > Do you have a traceback? There's no python traceback, but I've copied the crash report below. The relevant line in the Cython code is: https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ct… Also, do you know which path it's going down > (SSE/MMX/Altivec/unaccelerated)? > > It's crashing on the SSE path. The MMX (and unaccelerated) path works fine. Crash report ~~~~~~~~~ Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 _ctmf.so 0x058c77ea __pyx_f_7skimage_6filter_5_ctmf_accumulate + 490 (_ctmf.c:2277) 1 _ctmf.so 0x058cb4a0 __pyx_pw_7skimage_6filter_5_ctmf_1median_filter + 8864 (_ctmf.c:3673) 2 org.python.python 0x000cb2d1 PyEval_EvalFrameEx + 21649 3 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042 4 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523 5 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042 6 org.python.python 0x000cd1b7 PyEval_EvalCode + 87 7 org.python.python 0x000f1898 PyRun_FileExFlags + 168 8 org.python.python 0x000f27c3 PyRun_SimpleFileExFlags + 867 9 org.python.python 0x0010ba58 Py_Main + 3560 10 org.python.python 0x00001fb6 0x1000 + 4022 > Ray > > > On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > I'm getting segfaults when running the median filter due to the > > SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for > > testing: > > > > > > from skimage import data > > from skimage.filter import median_filter > > > > median_filter(data.camera()) > > > > > > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core > i7 > > machine with Cython 0.16, Python 2.7.3. > > > > Thanks, > > -Tony > > > > -- > > 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: Segfaults from CTMF
by Johannes Schönberger 01 Mar '13

01 Mar '13

Works for me on OSX 10.8, Python 2.7.3, Cython 0.18 and Cython 0.16 (Intel Core i7). Johannes Schönberger Am 01.03.2013 um 01:35 schrieb Tony Yu <tsyu80(a)gmail.com>: > I'm getting segfaults when running the median filter due to the SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for testing: > > from skimage import data > from skimage.filter import median_filter > > median_filter(data.camera()) > > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7 machine with Cython 0.16, Python 2.7.3. > > Thanks, > -Tony > > -- > 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: Segfaults from CTMF
by Thouis (Ray) Jones 28 Feb '13

28 Feb '13

I'm on OSX 10.8, python 2.7.3, Cython 0.18. I wonder if it's the cython version. Your code works for me. Do you have a traceback? Also, do you know which path it's going down (SSE/MMX/Altivec/unaccelerated)? Ray On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > I'm getting segfaults when running the median filter due to the > SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for > testing: > > > from skimage import data > from skimage.filter import median_filter > > median_filter(data.camera()) > > > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7 > machine with Cython 0.16, Python 2.7.3. > > Thanks, > -Tony > > -- > 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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Segfaults from CTMF
by Tony Yu 28 Feb '13

28 Feb '13

I'm getting segfaults when running the median filter due to the SSE/MMX/Altivec speed ups for ctmf (PR #432<https://github.com/scikit-image/scikit-image/pull/432>). Here's a short snippet for testing: from skimage import data from skimage.filter import median_filter median_filter(data.camera()) Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7 machine with Cython 0.16, Python 2.7.3. Thanks, -Tony

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scikit-image March 2013