Mailman 3 May 2012 - scikit-image

Re: Release 0.6
by Tony Yu May 9, 2012

May 9, 2012

On Tue, May 8, 2012 at 3:48 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi everyone, > > It's time for another release of scikits-image! I would very much > appreciate your help in reviewing the following outstanding > pull-requests: > > > - Tony Yu's neat visualization tools, previously packaged as skloupe: > > https://github.com/scikits-image/scikits-image/pull/165 > > - Fast image warping: > > https://github.com/scikits-image/scikits-image/pull/184 > > - RegionProps (still awaiting tests, but review the rest so long) > > https://github.com/scikits-image/scikits-image/pull/183 > > > This release is due in about 10 days. I'm also happy to report that > our Debian package has been submitted for approval; thanks go to > Yaroslav Halchenko! > > Stéfan > I went ahead and merged the fast image-warping PR. I've read through the code a couple of times already, and I think it looks pretty good. (Sorry if anyone else was planning to review it before merging.) -Tony

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Release 0.6
by Stéfan van der Walt May 8, 2012

May 8, 2012

Hi everyone, It's time for another release of scikits-image! I would very much appreciate your help in reviewing the following outstanding pull-requests: - Tony Yu's neat visualization tools, previously packaged as skloupe: https://github.com/scikits-image/scikits-image/pull/165 - Fast image warping: https://github.com/scikits-image/scikits-image/pull/184 - RegionProps (still awaiting tests, but review the rest so long) https://github.com/scikits-image/scikits-image/pull/183 This release is due in about 10 days. I'm also happy to report that our Debian package has been submitted for approval; thanks go to Yaroslav Halchenko! Stéfan

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filter_iter on github
by Nadav Horesh May 8, 2012

May 8, 2012

Just made my first github commit on https://github.com/Nadav-Horesh/filter_iter Nadav

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Re: filter_iter: New version
by Nadav Horesh May 5, 2012

May 5, 2012

Sorry, I had a mix between a working and a nonworking versions. Before I'll commit further changes, I'll take the advice to build a git repo. Thanks, Nadav. 2012/5/2 Tony Yu <tsyu80(a)gmail.com> > > > On Tue, May 1, 2012 at 2:24 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Hi Nadav >> >> On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> >> wrote: >> > I have an unresolved problem (which caused me a delay of ~3 weeks) with >> > applying a cython callback function, which I would like your help: how >> to >> > make demo/example_not_working.py work? >> >> I'd like to help, but unfortunately I can't get demo/example.py to >> work. Did you include all the relevant files in the archive? It >> seems filter_iter.py is missing. I can also help to get this into a >> git repo--feel free to ping me on google talk or via email. >> >> Stéfan >> > > > I got an error when building the main package. For me, commenting the > "package_data" (i.e. the pxd file) fixed the build. For ease of testing, > maybe the demo should be in the parent directory, and there should be a > subdirectory "filter_iter" which contains the filter implementation. That > way you don't have to add "filter_iter" to your path in order to test. > > After all that though, I also get an error with example.py: > > Traceback (most recent call last): > File "example.py", line 18, in <module> > 'rand_select', (3,3)) > File "../../filter_iter/gen_filter.py", line 55, in apply_C_filter > File "_filter_iter.pyx", line 184, in > filter_iter._filter_iter.gen_filter_matrix.filter_with_C_callback_float > (./_filter_iter.c:4819) > TypeError: an integer is required > filter_iter_demo$ > > Changing the call the last argumet to an int gives an "'int' object is > unsubscriptable" TypeError. As Stefan suggests, putting this into a git > repo would be really helpful for testing and review. > > -Tony > >

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Fisheye warping
by Stéfan van der Walt May 3, 2012

May 3, 2012

Hi all, After yesterday's post on warping, another teaser: http://mentat.za.net/refer/lena_warp.png From: def fisheye(xy): center = np.mean(xy, axis=0) c = xy - center r = np.sqrt(np.sum(c**2, axis=1)) theta = np.arctan2(c[:, 1], c[:, 0]) r = 0.87 * np.exp(r**(1/2.5) / 1.75) return np.column_stack(( r * np.cos(theta), r * np.sin(theta) )) + center Stéfan

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Fast coordinate transformations
by Stéfan van der Walt May 3, 2012

May 3, 2012

Hi all, I just added a PR which provides a "warp" function, with signature `warp(image, transformation_function, ...)` where the function would be, e.g.: def transformation_function(xy): xy[:, 0] *= 2 return xy This is very similar to ndimage.geometric_transform, except that it is blazingly fast because it is built on top of the much faster ndimage.map_coordinates. With this change it becomes trivial to implement transformations such as swirl (the included example), ripple, the log-polar transform, etc. by writing the appropriate transformation_functions. I'd appreciate a review: https://github.com/scikits-image/scikits-image/pull/184 Thanks! Stéfan

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Re: filter_iter: New version
by Tony Yu May 2, 2012

May 2, 2012

On Tue, May 1, 2012 at 2:24 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Nadav > > On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> > wrote: > > I have an unresolved problem (which caused me a delay of ~3 weeks) with > > applying a cython callback function, which I would like your help: how to > > make demo/example_not_working.py work? > > I'd like to help, but unfortunately I can't get demo/example.py to > work. Did you include all the relevant files in the archive? It > seems filter_iter.py is missing. I can also help to get this into a > git repo--feel free to ping me on google talk or via email. > > Stéfan > I got an error when building the main package. For me, commenting the "package_data" (i.e. the pxd file) fixed the build. For ease of testing, maybe the demo should be in the parent directory, and there should be a subdirectory "filter_iter" which contains the filter implementation. That way you don't have to add "filter_iter" to your path in order to test. After all that though, I also get an error with example.py: Traceback (most recent call last): File "example.py", line 18, in <module> 'rand_select', (3,3)) File "../../filter_iter/gen_filter.py", line 55, in apply_C_filter File "_filter_iter.pyx", line 184, in filter_iter._filter_iter.gen_filter_matrix.filter_with_C_callback_float (./_filter_iter.c:4819) TypeError: an integer is required filter_iter_demo$ Changing the call the last argumet to an int gives an "'int' object is unsubscriptable" TypeError. As Stefan suggests, putting this into a git repo would be really helpful for testing and review. -Tony

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Re: filter_iter: New version
by Stéfan van der Walt May 1, 2012

May 1, 2012

Hi Nadav On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> wrote: > I have an unresolved problem (which caused me a delay of ~3 weeks) with > applying a cython callback function, which I would like your help: how to > make demo/example_not_working.py work? I'd like to help, but unfortunately I can't get demo/example.py to work. Did you include all the relevant files in the archive? It seems filter_iter.py is missing. I can also help to get this into a git repo--feel free to ping me on google talk or via email. Stéfan

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Re: Bizarre error
by Tony Yu May 1, 2012

May 1, 2012

On Tue, May 1, 2012 at 1:04 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Mon, Apr 30, 2012 at 8:51 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > Actually I'm not too surprised that you can't reproduce this since you > never > > got a failure with the SSIM tests. But, yes, this is very strange. > > Good point :) Do you have any more information on your system? > Linux, 64-bit? Standard processor? NumPy compiled from source? > > Stéfan > Well, I guess if I'm suggesting this issue is system dependent, I should actually describe my system ;) OS X 10.6.8, 64-bit Intel Core 2 Duo Python 2.6.1 Numpy from github (an older master that was at least 3 months old and also with the current master) -Tony

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filter_iter: New version
by Nadav Horesh May 1, 2012

May 1, 2012

Hi all, Attached here the 2nd version of filter_iter which compiled with the help of Tony Yu, Stefan van der Walt, Travis Oliphant and Mark Florisson. My plan for the next version is to make the package useful rather than a proof of concept (probably making an advantage of cython 0.16 fused types). I have an unresolved problem (which caused me a delay of ~3 weeks) with applying a cython callback function, which I would like your help: how to make demo/example_not_working.py work? Nadav,

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