Mailman 3 April 2013 - scikit-image

Re: Edge detectors in filter package
by Johannes Schönberger 21 Apr '13

21 Apr '13

Basically, "filter" is a very universal term that may be used for lots of image processing related tasks… On the one hand, edge operators probably fit well into the feature package, on the other hand Tony just used the very common term > edge filters So, I am +-0 on this… Johannes Schönberger Am 21.04.2013 um 17:56 schrieb Tony Yu <tsyu80(a)gmail.com>: > > On Sun, Apr 21, 2013 at 8:15 AM, Ankit Agrawal <aaaagrawal(a)gmail.com> wrote: > Hi everyone, > > I would like to know the motivation behind keeping edges.py(edge detectors) in filters package. Based on the Image Processing terminology , I think features package is a more appropriate place for it. Thank you. > > > I've always thought that edge filters belonged in the features package, too. There's always the question of whether deprecating the current behavior is worth the trouble. I'm +1, despite the pain of deprecation. > > 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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Edge detectors in filter package
by Ankit Agrawal 21 Apr '13

21 Apr '13

Hi everyone, I would like to know the motivation behind keeping edges.py(edge detectors) in filters package. Based on the Image Processing terminology , I think features package is a more appropriate place for it. Thank you. Regards, Ankit Agrawal, Communication and Signal Processing, IIT Bombay.

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Re: imageio progress
by Juan Nunez-Iglesias 21 Apr '13

21 Apr '13

I wrote a lot of image io stuff for my own projects before I became aware of skimage. I spent some time thinking about how people could add and maintain their own modules, and came up with the following: io/ __init__.py tiff.py read() write() png.py read() write() etc. This isn't coded, it was just on my todo. Adding new formats is then a matter of dumping in a file containing read() and write() functions, and importing that in the __init__.py file. This results in very clean syntax: io.png.read() There could also be io.read() and io.write() defined in __init__ or some generic name, e.g. io.auto.read(), that would call the right format based on filename. Thoughts? On Fri, Apr 19, 2013 at 10:47 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Almar > > On Wed, Mar 27, 2013 at 4:33 PM, Almar Klein <almar.klein(a)gmail.com> > wrote: > > The project is called imageio and it is now a plugin-based library with a > > relatively small core. The freeimage plugin that started it all currently > > provides most file formats. Its now at a stage where I think the core is > > pretty much finished, and focus can shift towards different plugins for > > various scientific formats. But I am not going to do that alone :) > > Is there a way to add plugins by simply "dumping" plugin files into > place? This was part of the thinking when we designed the skimage.io > plugin infrastructure (so it would be easy for, e.g., Debian to add > new formats by simply unpacking into the right location). > > I am not entirely happy with the complexity of the io module in > skimage, and would love to hear ideas about how it can be simplified, > perhaps integrating with imageio. > > 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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Test failures in graph subpackage
by Tony Yu 20 Apr '13

20 Apr '13

Can anyone reproduce the test failures that the Travis buildbot is raising on master: https://travis-ci.org/scikit-image/scikit-image/jobs/6472929#L2274 The tests pass on my setup, so I can't really figure out what's wrong. Thanks, -Tony

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Re: multi-page TIFF writer
by Tony Yu 20 Apr '13

20 Apr '13

On Thu, Apr 18, 2013 at 10:47 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Thu, Apr 18, 2013 at 5:12 PM, Zachary Pincus <zachary.pincus(a)yale.edu> > wrote: > > Also, BTW, I get the below test failure when I have matplotlib but no > PIL installed. I think test_imread_url or the test right before it must be > making some incorrect assumptions. (If I re-run the tests after this > failure, then also all of the tifffile tests fail, so it seems that some > test isn't doing proper teardown of the image loading plugins?) > > Ah, I see what's happening. This one might be a job for @tonysyu -- > Tony, this looks weird because matplotlib is supposed to be able to > handle pngs (and you are reading in a png in that test). So perhaps a > bug in matplotlib when providing a "file-like object"? > > Fixed in PR 515: https://github.com/scikit-image/scikit-image/pull/515 Unfortunately, I can't reproduce Zach's issue with the test failure leaking into into the tifffile tests. Best, -Tony

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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 1:49 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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Re: Google Summer of Code 2013
by Umesh Sharma 20 Apr '13

20 Apr '13

Hi All, I implemented Robert's Edge Detection algorithm ( http://homepages.inf.ed.ac.uk/rbf/HIPR2/roberts.htm). I have made an issue on GitHub( https://github.com/scikit-image/scikit-image/issues/513) and I have the implementation with me. I also created a new topic for this in this group. Should I submit a pull request on GitHub? Regards, Umesh

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_mask_filter_result function
by Umesh Sharma 20 Apr '13

20 Apr '13

hello, can anyone tell me what "_mask_filter_result" function is doing in edges.py (skimage/filer/edges.py), i am getting error when i am calling sobel edge detector in latest version of scikit-image . and why we are using it , i mean in sobel edge detection after applying the convolution , can't we directly return that new matrix. Thanks Umesh Kumar Sharma 4th year UG student CSE IIT kharagpur

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Test Failure
by abid rahman 19 Apr '13

19 Apr '13

Hi, 1 - I had send a PR on histogram backprojection. at that time travis build was successful. Then i made some modifications for PEP8, but travis build shows errors which i don't understand. https://travis-ci.org/scikit-image/scikit-image/jobs/6472929. But i haven't changed any functionality of code and it works fine in my system as good as old. 2 - Also, I didn't get the concept of writing of tests for my code. What actually the tests do and how should I write a good test code? Regards Abid K

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Re: Feature detection
by Harsh Bhatia 19 Apr '13

19 Apr '13

thank u very much for attending and replying ... i will search about more binary features and list them which can be useful by numpy/cython array. i m looking at the bug fixing area n trying to contribute asap. thanks

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Re: Feature detection
by Stéfan van der Walt 19 Apr '13

19 Apr '13

Hi Harsh On Fri, Apr 19, 2013 at 3:08 PM, Harsh Bhatia <horrorbyharsh(a)gmail.com> wrote: > My proposal for this year's GSoC is to implement Feature detection (STAR, > Speeded Up Robust Feature) as given in the project ideas list. The STAR code is in OpenCV, so this would be modifying that code for using the numpy / cython array structures. Also, to give the project sufficient scope, we'd need to implement some other features as well, e.g. binary features. Please note that it is important to have contributed some code changes to scikit-image in order to be considered for the GSoC, so please have a go at fixing some bugs or implementing a new feature as soon as possible. Thanks Stéfan

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Re: imageio progress
by Stéfan van der Walt 19 Apr '13

19 Apr '13

Hi Almar On Wed, Mar 27, 2013 at 4:33 PM, Almar Klein <almar.klein(a)gmail.com> wrote: > The project is called imageio and it is now a plugin-based library with a > relatively small core. The freeimage plugin that started it all currently > provides most file formats. Its now at a stage where I think the core is > pretty much finished, and focus can shift towards different plugins for > various scientific formats. But I am not going to do that alone :) Is there a way to add plugins by simply "dumping" plugin files into place? This was part of the thinking when we designed the skimage.io plugin infrastructure (so it would be easy for, e.g., Debian to add new formats by simply unpacking into the right location). I am not entirely happy with the complexity of the io module in skimage, and would love to hear ideas about how it can be simplified, perhaps integrating with imageio. Stéfan

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Re: Mentor for GSoC
by abid rahman 19 Apr '13

19 Apr '13

Thank you for the answer , although I have already found who might be the mentors from the discussion on github. :) Regards, Abid K. opencvpython.blogspot.com On Fri, Apr 19, 2013 at 4:03 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Mon, Apr 8, 2013 at 9:31 PM, abid rahman <abidrahman2(a)gmail.com> wrote: > > Can I know who is the mentor for scikit-image GSoC projects? Can I get > > mentor's mail id, IRC nickname etc, please? > > I'm sorry, for some reason these messages slipped by my radar > completely unnoticed. We've been communicating in the mean time, but > here's your answer: > > GSoC project leaders: > > Emmanuelle Guillart > Stéfan van der Walt > Tony Yu > > and Aron Ahmadia for projects relating to a proper backend / > dispatching system with integration of numba and opencl backends. I'm > sure the other members of the team will also help out--these are just > the people who signed up. > > 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: Cython memoryviews
by Juan Nunez-Iglesias 19 Apr '13

19 Apr '13

On Fri, Apr 19, 2013 at 12:32 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > The example I gave does take an array of any dimension? > Haha yes of course, I forgot that you Cython could just be Python where you don't need to optimise it. =)

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Re: Mentor for GSoC
by Stéfan van der Walt 19 Apr '13

19 Apr '13

On Mon, Apr 8, 2013 at 9:31 PM, abid rahman <abidrahman2(a)gmail.com> wrote: > Can I know who is the mentor for scikit-image GSoC projects? Can I get > mentor's mail id, IRC nickname etc, please? I'm sorry, for some reason these messages slipped by my radar completely unnoticed. We've been communicating in the mean time, but here's your answer: GSoC project leaders: Emmanuelle Guillart Stéfan van der Walt Tony Yu and Aron Ahmadia for projects relating to a proper backend / dispatching system with integration of numba and opencl backends. I'm sure the other members of the team will also help out--these are just the people who signed up. Stéfan

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Re: multi-page TIFF writer
by Zachary Pincus 19 Apr '13

19 Apr '13

>>> Nope! Not your fault. In these situations, doing another push or >>> close/open or rebase will all re-trigger the tests. >> >> Oh great, thanks. Is there a clean / recommended way to do a nop push / close/open / rebase? My git is limited... sorry for the trouble here! > > I think just clicking the "Close" and then "Re-open" buttons will do the trick. Ah, at the risk of sounding even more like an idiot... on what page are the close/reopen buttons? I can't find ones on the GH pull-request page, or on the Travis-ci build. Sorry! Haven't interacted with the codebase since travis was added and clearly I've no idea what I'm doing. Definitely won't merge my own PRs anymore. Hahaha. Zach

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