Mailman 3 December 2011 - scikit-image

Re: Feature requests for 0.5
by Anders Klint Dec. 8, 2011

Dec. 8, 2011

Hi, More of a question than a request: Rather long ago I used an image analysis tool called Image Pro which had a rather large set of measurements that could be applied to identified objects. So a possible scenario there could be something like: * Grab image * Segment objects from background * Measure objects * Filter out only objects with a size between 1.5 and 3.3 mm^2 (or relevant pixel measurement) and a roundness (defined in terms of length of object's periphery vs periphery of a circle with same area) over 0.85 * ...and further processing on matching objects Other measurements included for example major and minor axis direction and length, average greyscale value etc etc Could something like this, ie a more comprehensive set of measurements be valuable for skimage users? Regards /Anders On 6 dec 2011, at 01:51, Stéfan van der Walt wrote: > Hi all, > > With 0.4 (and 0.4.1, 0.4.2) out the door, we can start setting > priorities for 0.5. > > Personally, I'd like to see > > - An expansion of the user guide > - Completion of the Debian packaging > - Object convex hulls and > - Graph cut segmentation and/or tri-mapping > > Feel free to weigh in with your own suggestions, then we'll come to an > agreement on the best way forward. > > Regards > Stéfan

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Re: Feature requests for 0.5
by Stéfan van der Walt Dec. 8, 2011

Dec. 8, 2011

Hi Tony On Wed, Dec 7, 2011 at 8:52 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > * A while back, I mentioned the possibility of automatically importing some > submodules (but leaving them in their own namespace). For example, I'd vote > for automatic import of the io module. If we can agree on which submodules > (if any), I could throw together a pull request. This was the original model for NumPy and SciPy, but whenever redesign comes up this is mentioned, and I think those projects would eventually like to step away from it. The important thing to improve may be the root docstring for skimage, so that you can inspect that to know what is available below. > * Automatic threshold algorithms. I started to integrate some code from > CellProfiler, but I got bogged down with some of the details. I can give it > another go, unless someone else wants to do it. We could maybe start with an implementation of Otsu's method, which is really simple: http://en.wikipedia.org/wiki/Otsu's_method Regards Stéfan

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Re: Feature requests for 0.5
by Neil Yager Dec. 7, 2011

Dec. 7, 2011

> * Automatic threshold algorithms. I started to integrate some code from > CellProfiler, but I got bogged down with some of the details. I can give it > another go, unless someone else wants to do it. I agree that thresholding should be a priority, as it is widely used. I also started to look at the CellProfiler. It has a lot of functionality, but even a subset of this would be a good start. Unfortunately I don't think I'll have much time for this in the next few weeks. Another useful method would be histogram equalization. Here's a nice implementation: http://www.janeriksolem.net/2009/06/histogram-equalization-with-python-and.… but we'd have to contact the author about using it. Neil

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Re: Feature requests for 0.5
by Tony Yu Dec. 7, 2011

Dec. 7, 2011

2011/12/6 Stéfan van der Walt <stefan(a)sun.ac.za> > Hi Nelle > > On Mon, Dec 5, 2011 at 10:23 PM, Nelle Varoquaux > <nelle.varoquaux(a)gmail.com> wrote: > > I have a Harris affine region detector I'd like to integrate, and > > Great, that would be a very useful addition! > > > potentially a panorama stitching example using hogs and harris I'd > > like to integrate (might be slightly to complicated for the user guide > > ?). It's work in progress, but I should have time to work on that > > during the christmas holidays. > > We could make this an example chapter in the user guide, since it > would illustrate a number of things. For that, we may want to modify > the auto example generator to allow text snippets to appear between > code. I did quite a bit of work on stitching during my phd, so I'd be > interested to help out with this, if you want. > > Regards > Stéfan > A stitching/image-registration example would be great. Other wish-list items: * A while back, I mentioned the possibility of automatically importing some submodules (but leaving them in their own namespace). For example, I'd vote for automatic import of the io module. If we can agree on which submodules (if any), I could throw together a pull request. * Automatic threshold algorithms. I started to integrate some code from CellProfiler, but I got bogged down with some of the details. I can give it another go, unless someone else wants to do it. Best, -Tony

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The asymmetry of licensing
by Stéfan van der Walt Dec. 6, 2011

Dec. 6, 2011

Hi all, Here's a link to a (potentially controversial) post I made on Google Plus: https://plus.google.com/104831275312843762750/posts/fcdAoLarutu Basically, it briefly touches on why we are using BSD and not GPL. Your comments are welcome. Regards Stéfan

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Re: io plugin issue (8bits 16bits)
by Neil Yager Dec. 6, 2011

Dec. 6, 2011

> I'll commit that as soon as it has been reviewed by at least one other person. I just pulled 88, 90 and 91, and everything works for me. Neli

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Re: installation -- error on the download webpage
by Emmanuelle Gouillart Dec. 6, 2011

Dec. 6, 2011

> For future reference: > To start, clone git@github.com:scikits-image/scikits-image-web.git > 1. Make the changes necessary. > 2. "make html" and check that the build/html output looks ok. > 3. "make gh-pages" > 4. If all looks ok, "cd gh-pages ; git commit" Thanks, this will be useful! Emmanuelle

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installation -- error on the download webpage
by Emmanuelle Gouillart Dec. 6, 2011

Dec. 6, 2011

Hi all, in the download webpage http://scikits-image.org/download.html, the PyPi link points to http://pypi.python.org/pypi/scikits.image (this produces an error), whereas it should be http://pypi.python.org/pypi/scikits-image I'll try to correct this but I first have to understand how this webpage is generated, so if anybody is quicker than me, it'd be good to correct this ASAP. Emmanuelle

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Re: io plugin issue (8bits 16bits)
by Neil Yager Dec. 6, 2011

Dec. 6, 2011

Coincidentally, I also noticed the 16-bit tiff issue the other day, and started working on a fix. I was using an approach based on this: http://stackoverflow.com/questions/7684695/numpy-array-of-an-i16-image-file Changing the last line of imread in pil_plugin to: return np.array(im.getdata()).reshape(im.size[::-1]) fixes that specific problems, but causes others (e.g. can't load colour images). At that point I got side-tracked by something else, so I'm not sure if it's a good fix. Neil On Dec 6, 12:32 am, Stéfan van der Walt <ste...(a)sun.ac.za> wrote: > On Mon, Dec 5, 2011 at 2:40 PM, Christoph Gohlke <cjgoh...(a)gmail.com> wrote: > > skimage.io.use_plugin is somewhat broken (I think). It replaces all > > previously defined default imread, imwrite, and imshow functions, regardless > > whether a `kind` argument is provided. For example: > > Between Chris and myself, we should have this fixed tonight. Follow along here: > > https://github.com/scikits-image/scikits-image/pull/88https://github.com/sc… > > PR90 provides a new function called "plugin_order", which allows the > user to see under the hood which function skimage will try to use. > > Cheers > Stéfan

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Re: Feature requests for 0.5
by Stéfan van der Walt Dec. 5, 2011

Dec. 5, 2011

Hi Nelle On Mon, Dec 5, 2011 at 10:23 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > I have a Harris affine region detector I'd like to integrate, and Great, that would be a very useful addition! > potentially a panorama stitching example using hogs and harris I'd > like to integrate (might be slightly to complicated for the user guide > ?). It's work in progress, but I should have time to work on that > during the christmas holidays. We could make this an example chapter in the user guide, since it would illustrate a number of things. For that, we may want to modify the auto example generator to allow text snippets to appear between code. I did quite a bit of work on stitching during my phd, so I'd be interested to help out with this, if you want. Regards Stéfan

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