scikit-image October 2011

scikit-image@python.org

12 participants
89 discussions

Re: Bug-fix 0.3.1
by Klonuo Umom 12 Oct '11

12 Oct '11

Thanks for quick fix release. If of any interest here is output of my test: http://pastebin.com/raw.php?i=DJ8JGtGU I have opencv 2.3.1 in /usr/local/lib/ with cv2.so for Python in dist-packages (on Ubuntu) Cheers 2011/10/12 Stéfan van der Walt <stefan(a)sun.ac.za> > Hi everyone, > > Thanks to Christoph Gohlke, the package now runs smoothly on Windows > and Python 3. I've uploaded a 0.3.1 bug-fix release to PyPi. > > There's still one segfault in the OpenCV test suite. If someone files > a bug report against it, I'll try to figure out what is going on, but > that subpackage has already been removed from 0.4dev (it was > deprecated in 0.3). > > Regards > Stéfan >

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Bug-fix 0.3.1
by Stéfan van der Walt 12 Oct '11

12 Oct '11

Hi everyone, Thanks to Christoph Gohlke, the package now runs smoothly on Windows and Python 3. I've uploaded a 0.3.1 bug-fix release to PyPi. There's still one segfault in the OpenCV test suite. If someone files a bug report against it, I'll try to figure out what is going on, but that subpackage has already been removed from 0.4dev (it was deprecated in 0.3). Regards Stéfan

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Re: 'heap_watershed.pxi' not found
by Stéfan van der Walt 12 Oct '11

12 Oct '11

On Wed, Oct 12, 2011 at 11:00 AM, Klonuo Umom <klonuo(a)gmail.com> wrote: > congratulations for your new release :) Thanks! > On Ubuntu I did: `sudo pip install scikits.image` and got this on two > occasions of installing process: > ======================================== > scikits/image/morphology/_watershed.pyx:26:0: 'heap_watershed.pxi' not > found This was missing from our manifest file--it's been fixed in the repo. > ======================================== > Other then that it installed fine and I then tried to run test: `import > scikits.image as si; si.test()` > And got this: > ======================================== > ValueError: Working directory > /usr/local/lib/python2.7/dist-packages/scikits/image/__init__.pyc/.. not > found, or not a directory > ======================================== > Should I worry about it? Aha, you found a bug :) This should now be fixed. Thanks for your feedback! Cheers Stéfan

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Re: Alternative domain
by Emmanuelle Gouillart 12 Oct '11

12 Oct '11

Thanks :-) We owe you a few beers for that! Emmanuelle On Tue, Oct 11, 2011 at 08:52:15AM -0700, StÃ¯Â¿Â½fan van der Walt wrote: > Hi everyone, > A little gift for the 0.3 release :) > http://skimage.org > Regards > StÃ¯Â¿Â½fan

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'heap_watershed.pxi' not found
by Klonuo Umom 12 Oct '11

12 Oct '11

Hi, congratulations for your new release :) On Ubuntu I did: `sudo pip install scikits.image` and got this on two occasions of installing process: ======================================== Error compiling Cython file: ------------------------------------------------------------ ... DTYPE_INT32 = np.int32 ctypedef np.int32_t DTYPE_INT32_t DTYPE_BOOL = np.bool ctypedef np.int8_t DTYPE_BOOL_t include "heap_watershed.pxi" ^ ------------------------------------------------------------ scikits/image/morphology/_watershed.pyx:26:0: 'heap_watershed.pxi' not found ======================================== Other then that it installed fine and I then tried to run test: `import scikits.image as si; si.test()` And got this: ======================================== ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (47, 0)) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (23, 0)) ... <traceback part> ValueError: Working directory /usr/local/lib/python2.7/dist-packages/scikits/image/__init__.pyc/.. not found, or not a directory ======================================== Should I worry about it? Thanks

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Alternative domain
by Stéfan van der Walt 11 Oct '11

11 Oct '11

Hi everyone, A little gift for the 0.3 release :) http://skimage.org Regards Stéfan

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Re: Challenge: Speed up seam carving example
by Stéfan van der Walt 10 Oct '11

10 Oct '11

2011/10/9 Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi all, > > I have placed an example of seam carving here: > > https://github.com/stefanv/scikits.image-1/blob/seam_carving/doc/examples/p… Does anybody have a better (copyright free) test image than the cameraman we can use for this? Something like two trees, or somesuch. If we simply scale the photo down to 256x256, the algorithm is fast enough. Stéfan

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Re: Challenge: Speed up seam carving example
by Emmanuelle Gouillart 10 Oct '11

10 Oct '11

Hi, cool stuff :-). This is not a large improvement, but you can gain a little by removing all pixels of a path at one time, by ravelling the array and using fancy indexing. Something like sx, sy = img.shape inds = np.arange(img.size) removed_inds = p + row_idx * sy img = img.ravel()[np.setdiff1d(inds, removed_inds)] img.shape = sx, sy - 1 Also, is it possible to compute at one time several shortest paths from one side of the array to the other (using MCP), and removing several paths during a single iteration? You might have problems when paths intersect, because then you don't have the same number of pixels to remove for each line, but you might choose a rule for such cases (e.g. removing the pixel on this line that belongs to the next path that would be removed) and maybe it won't be so bad... I don't know, I guess I should have watched the video before giving my advice ;-) Emma On Sun, Oct 09, 2011 at 03:48:20AM -0700, StÃ¯Â¿Â½fan van der Walt wrote: > Hi all, > I have placed an example of seam carving here: > https://github.com/stefanv/scikits.image-1/blob/seam_carving/doc/examples/p… > The idea is super simple, but currently it's too slow. I'm curious to > see if anyone can improve its execution time? > If you haven't seen seam carving before, take a look at the video link > in the docstring. > Regards > StÃ¯Â¿Â½fan

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Re: A big thanks for 0.3!
by Stéfan van der Walt 10 Oct '11

10 Oct '11

Hi Nelle On Mon, Oct 10, 2011 at 11:51 AM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > I can do that, if it can wait until this week-end! I've used grep in the > past for such tasks :) Thanks, that'd be great! Could you also investigate what happens to our pull requests when we change the naming? I have a feeling they may not appreciate it. The scikit-learn guys have both scikits.learn and sklearn subpackages, but we'll stick to one and simply move from scikits.image to skimage for the next release. Other low hanging fruit would be to improve the documentation index: http://scikits-image.org/docs/ (It's currently not themed along with the rest of the website) Then there's also the compatibility table, where I want to list all the functionality we provide: http://scikits-image.org/docs/dev/coverage_table.html At the moment it mainly contains MATLAB features. I think that was a mistake on my part; we should not follow MATLAB, but rather forge our own exciting route ahead (playing catch-up is boring). Lots more to be done, but I'll stop here :) Regards Stéfan

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Re: A big thanks for 0.3!
by Brian Holt 10 Oct '11

10 Oct '11

Congratulations on a successful release! I was just looking through http://scikits-image.org/docs/0.3/contribute.html to find out what else is in the pipeline and it seems like many of the tasks can already be ticked off. What are the next priorities for this project?

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scikit-image October 2011