Mailman 3 April 2013 - scikit-image

Re: Errors while compiling and $make coverage
by Tony Yu 20 Apr '13

20 Apr '13

On Sat, Apr 20, 2013 at 1:49 PM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: <snip> > > Also on another note, is there a function for checking the connectivity of > objects in an image ? How about multiple objects ? > Maybe you're looking for the `label` function? http://scikit-image.org/docs/dev/api/skimage.morphology.html#label

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Fwd: Errors while compiling and $make coverage
by Chintak Sheth 20 Apr '13

20 Apr '13

Alright, I'll come back to this a little later. First, clean the documentation and submit for a PR. Also on another note, is there a function for checking the connectivity of objects in an image ? How about multiple objects ?I'm sure this will be there, but just not sure which function it is. And in case there isn't, is there a better way of finding an initial point in the object that maybe : > #im is a binary image (m, n) = im.shape for i=0:m-1 > for j=0:n-1 > if im(i,j) > # this is my starting point Thanks, Chintak On Sun, Apr 21, 2013 at 12:06 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > On Sat, Apr 20, 2013 at 1:28 PM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: > >> Hi Tony, >> >> On Sat, Apr 20, 2013 at 10:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: >> >>> >>> This is kind of a shot in the dark: Could you try running nosetests in >>> the segmentation subpackage of skimage? >>> >>> >> Strangely so, "nosetests -v" runs in segmentation subpackage. However, it >> gives me a warning : >> >>> warnings.warn('SciPy was built without UMFPACK. Consider rebuilding ' >> >> Does that give any more ideas ? >> > > I was hoping that the umfpack import was broken, but it looks like it's > failing gracefully. > > I don't have any specific ideas. Could you try going into each subpackage > and running nosetests in each? This is a bit brute-force, but there's not a > lot of information to go on right now. > > -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: Errors while compiling and $make coverage
by Tony Yu 20 Apr '13

20 Apr '13

On Sat, Apr 20, 2013 at 1:28 PM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: > Hi Tony, > > On Sat, Apr 20, 2013 at 10:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > >> >> This is kind of a shot in the dark: Could you try running nosetests in >> the segmentation subpackage of skimage? >> >> > Strangely so, "nosetests -v" runs in segmentation subpackage. However, it > gives me a warning : > >> warnings.warn('SciPy was built without UMFPACK. Consider rebuilding ' > > Does that give any more ideas ? > I was hoping that the umfpack import was broken, but it looks like it's failing gracefully. I don't have any specific ideas. Could you try going into each subpackage and running nosetests in each? This is a bit brute-force, but there's not a lot of information to go on right now. -Tony

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Re: Errors while compiling and $make coverage
by Chintak Sheth 20 Apr '13

20 Apr '13

Hi Tony, On Sat, Apr 20, 2013 at 10:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > This is kind of a shot in the dark: Could you try running nosetests in the > segmentation subpackage of skimage? > > Strangely so, "nosetests -v" runs in segmentation subpackage. However, it gives me a warning : > warnings.warn('SciPy was built without UMFPACK. Consider rebuilding ' Does that give any more ideas ? Thanks, Chintak

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Re: scikit-image-example for all basic Morphological techniques
by Chintak Sheth 20 Apr '13

20 Apr '13

Hi Tony, Thanks for the all the suggestions! Working on it. Chintak On Sat, Apr 20, 2013 at 10:45 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Sat, Apr 20, 2013 at 9:43 AM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: > > <snip> > > I have included the documentation provided with functions, a sample code >> which shows how to implement the function (i.e. read the image, create a >> structuring element), show the ouput image vs the input image and some >> comments to give an intuitive feel for the function. >> >> Take a look and tell me if it serves the purpose. I hope this can further >> decrease the "familiarisation" time for skimage :) >> https://github.com/chintak/scikit-image-examples >> > > > Hi Chintak, > > I only took a quick look at the notebook version of this example, but I > think something like this would be useful to a lot of users. Thanks for > posting! > > If you'd be willing to take some time to clean it up and submit it as a PR > to the scikit-image documentation, I think it would be much more accessible > for new users. Here's an example of formatting required for our > documentation (specifically, interleaving code, text, and figures): > > > https://github.com/scikit-image/scikit-image/blob/master/doc/examples/appli… > > and the resulting output > > > http://scikit-image.org/docs/dev/auto_examples/applications/plot_rank_filte… > > The version you have now looks pretty good, but I think it'd be best to > leave off the docstrings for the functions. In their place, you could put > the essential points from the docstring, plus what you have now as comments. > > Also, you can import the phantom image as follows (instead of using your > local directory path): > > > from skimage import data_dir > image = io.imread(data_dir + "/phantom.png", as_grey=True) > > > Same for all the other images that you add to the data directory of > skimage. (I would probably leave off the first text image if you're only > using it for image display.) > > Cheers, > -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: scikit-image-example for all basic Morphological techniques
by Tony Yu 20 Apr '13

20 Apr '13

On Sat, Apr 20, 2013 at 9:43 AM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: <snip> I have included the documentation provided with functions, a sample code > which shows how to implement the function (i.e. read the image, create a > structuring element), show the ouput image vs the input image and some > comments to give an intuitive feel for the function. > > Take a look and tell me if it serves the purpose. I hope this can further > decrease the "familiarisation" time for skimage :) > https://github.com/chintak/scikit-image-examples > Hi Chintak, I only took a quick look at the notebook version of this example, but I think something like this would be useful to a lot of users. Thanks for posting! If you'd be willing to take some time to clean it up and submit it as a PR to the scikit-image documentation, I think it would be much more accessible for new users. Here's an example of formatting required for our documentation (specifically, interleaving code, text, and figures): https://github.com/scikit-image/scikit-image/blob/master/doc/examples/appli… and the resulting output http://scikit-image.org/docs/dev/auto_examples/applications/plot_rank_filte… The version you have now looks pretty good, but I think it'd be best to leave off the docstrings for the functions. In their place, you could put the essential points from the docstring, plus what you have now as comments. Also, you can import the phantom image as follows (instead of using your local directory path): from skimage import data_dir image = io.imread(data_dir + "/phantom.png", as_grey=True) Same for all the other images that you add to the data directory of skimage. (I would probably leave off the first text image if you're only using it for image display.) Cheers, -Tony

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Re: Errors while compiling and $make coverage
by Tony Yu 20 Apr '13

20 Apr '13

Hi Chintak, This is kind of a shot in the dark: Could you try running nosetests in the segmentation subpackage of skimage? -Tony On Sat, Apr 20, 2013 at 11:40 AM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: > > > > On Thu, Apr 18, 2013 at 6:25 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: >> >> 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. > > > Even "nosetests -v" seems to give a segmentation fault. I've posted the > output after running "python setup.py build_ext -i" here. > http://pastebin.com/s1y9RESz > > Chintak > > -- > 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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GSoC 2013
by Ankit Agrawal 20 Apr '13

20 Apr '13

Hi everyone, I apologize for introducing myself a bit late on this list. I am Ankit Agrawal(ankit-maverick <https://github.com/ankit-maverick> on github), a third year student enrolled in Dual Degree program(B.Tech + Masters) in Electrical Engineering at IIT Bombay, with Masters specialization in Communication and Signal Processing. I would like to participate with scikit-image in GSoC this year and currently, I am thinking on building the proposal along the idea of Implementing Feature Detection algorithms or Video Manipulation Framework. I would be discussing about these ideas in more detail in the coming days. The relevant courses that I have taken in the past are Linear Algebra, Image Processing, Computer Vision and Digital Signal Processing. I have end-term exams going on currently, and hence I maybe be a little slower in responding to posts or pushing commits. Thank you. Regards, Ankit Agrawal, Communication and Signal Processing, IIT Bombay.

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Re: Errors while compiling and $make coverage
by Chintak Sheth 20 Apr '13

20 Apr '13

On Thu, Apr 18, 2013 at 6:25 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > > 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. Even "nosetests -v" seems to give a segmentation fault. I've posted the output after running "python setup.py build_ext -i" here. http://pastebin.com/s1y9RESz Chintak

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scikit-image-example for all basic Morphological techniques
by Chintak Sheth 20 Apr '13

20 Apr '13

Hi, Since this is my first exposure with open source development, while getting familiar with scikit-image morphological processing functions, I thought why not create an example (tutorial) that could walk you through all the functions and provide you with some intuitive feel about what is happening physically rather than mathematically. Although the documentation is sufficient and has an example included. This example is with a binary array. So I created some examples using images and really showing the whole procedure. So a beginner can straight away start coding with just this one document. I have included the documentation provided with functions, a sample code which shows how to implement the function (i.e. read the image, create a structuring element), show the ouput image vs the input image and some comments to give an intuitive feel for the function. Take a look and tell me if it serves the purpose. I hope this can further decrease the "familiarisation" time for skimage :) https://github.com/chintak/scikit-image-examples Thanks, Chintak

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