Mailman 3 June 2014 - scikit-image

Re: GSoC project request for comments
by Johannes Schönberger June 12, 2014

June 12, 2014

+1 for optional dependency, but only if optional. My motivation: - possibly better underlying graph library than using our own quick implementation (though, I am not too familiar with networkx) - much faster progress in GSoC project Johannes Schönberger On Jun 11, 2014, at 11:22 AM, Ronnie Ghose <ronnie.ghose(a)gmail.com> wrote: > +1 as an optional module for additional functionality - I'm not a fan of monolithic libraries > > On Jun 11, 2014 11:18 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > Hi all, > > We are trying to make a pretty big decision regarding the API for graph segmentation methods as part of Vighnesh's GSoC project. The main question is whether to implement our own graph class and build on that, or to use networkX. This would add a (potentially optional) dependency to skimage, but would use established classes an APIs. > > Here's where the relevant discussion on the skimage-gsoc mailing list starts: > > https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J > > As such a decision has a major impact on the skimage API going forward, please take some time to respond to this! > > Thanks, > > Juan. > > -- > 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/d/optout. > > -- > 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/d/optout.

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Can a skeleton be defined on a neighbourhood of 8 pixels ?
by Jean-Patrick Pommier June 12, 2014

June 12, 2014

Hi, Is it possible to skeletonize a binary 2D shape such that its skeleton is defined on a neighbourhood of 8 pixels? When skeletonizing with : *morphology.medial_axis()* , I tried two structuring elements (se8 or se4) as mask : se8 = np.array([[True,True,True],[True,True,True],[True,True,True]]) se4 = np.array([[False,True,False],[True,True,True],[False,True,False]]) imK = makeLetterImage('K', 70) skel = *morphology.medial_axis*(imK,mask=se8) Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel) The skeletons returned using se8 or se4 are very similar and look defined on a neighbourhood of 4 pixels (left). To me, this is a problem when trying to label the skeleton edges (right). <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1Pbx…> Jean-Patrick <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1Pbx…>

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Re: GSoC project request for comments
by Ronnie Ghose June 11, 2014

June 11, 2014

+1 as an optional module for additional functionality - I'm not a fan of monolithic libraries On Jun 11, 2014 11:18 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > Hi all, > > We are trying to make a pretty big decision regarding the API for graph > segmentation methods as part of Vighnesh's GSoC project. The main question > is whether to implement our own graph class and build on that, or to use > networkX. This would add a (potentially optional) dependency to skimage, > but would use established classes an APIs. > > Here's where the relevant discussion on the skimage-gsoc mailing list > starts: > > https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J > > As such a decision has a major impact on the skimage API going forward, > please take some time to respond to this! > > Thanks, > > Juan. > > -- > 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/d/optout. >

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GSoC project request for comments
by Juan Nunez-Iglesias June 11, 2014

June 11, 2014

Hi all, We are trying to make a pretty big decision regarding the API for graph segmentation methods as part of Vighnesh's GSoC project. The main question is whether to implement our own graph class and build on that, or to use networkX. This would add a (potentially optional) dependency to skimage, but would use established classes an APIs. Here's where the relevant discussion on the skimage-gsoc mailing list starts: https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J As such a decision has a major impact on the skimage API going forward, please take some time to respond to this! Thanks, Juan.

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ImportError: cannot import name find_contours
by klonuo June 10, 2014

June 10, 2014

I use Python 2.7 64bit on Windows 8, and installed skimage 0.10.0 from Christoph Gohlke packages. In [1]: from skimage.measure import find_contours --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-15313be983b9> in <module>() ----> 1 from skimage.measure import find_contours C:\Python27\lib\site-packages\skimage\measure\__init__.py in <module>() ----> 1 from ._find_contours import find_contours 2 from ._marching_cubes import (marching_cubes, mesh_surface_area, 3 correct_mesh_orientation) 4 from ._regionprops import regionprops, perimeter 5 from ._structural_similarity import structural_similarity ImportError: cannot import name find_contours Any ideas?

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Detection of digits on a display
by François Boulogne June 9, 2014

June 9, 2014

Hi, I wrote a blog post about the detection of digits on a display. It's written in french (sorry!) there https://blog.sciunto.org/posts/detection_nombres/ but the snippets talk by themself. My point is that it could be a pain to collect data from electronics (no serial port...) and displays are everywhere, camera largely available in labs. Basically, the idea is to use scikit-image and then scikit-learn. Scikit-image to isolate digits and make sub-images with each of them. Scikit-learn to recognize the digits. A training of 3 example per digits gave me a 100% success over 60 images. At the bottom, I show that it is also robust to the superposition of two digits (because of a fluctuation during the snapshot). Best, -- François Boulogne. http://www.sciunto.org GPG fingerprint: 25F6 C971 4875 A6C1 EDD1 75C8 1AA7 216E 32D5 F22F

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Re: Tutorials
by Juan Nunez-Iglesias June 9, 2014

June 9, 2014

Haha I was literally going to do the same tomorrow! Alright, I'll have a look at yours then and start shuffling/adding! Juan. On Sun, Jun 8, 2014 at 3:04 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > Hey Juan, > > Sorry for being so quiet about the SciPy tutorial. I've pushed a template > as well as a skeleton for the tutorial. It's mostly taken from a rough > outline that I wrote up for last year's SciPy. I'm sure it'll get shuffled > around quite a bit, but I thought it'd be nice to start with something. > > Best, > -Tony > > > On Wed, May 21, 2014 at 4:27 AM, Stuart Mumford <stuart(a)mumford.me.uk> > wrote: > >> Hi, >> >> The other thing that the astropy repo does to manage the size of the >> gh-pages branch is make it an orphan branch on every build, so there is no >> history of the built notebooks only the empty ones. >> >> Stuart >> >> >> On 21 May 2014 10:23, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: >> >>> Hi Stuart! >>> >>> This looks like a very good idea on first inspection -- iirc git will not >>> clone/fork a gh-pages branch by default, so having the run notebooks (with >>> a lot of images built-in as Stéfan was concerned about) on that branch >>> should not matter? >>> >>> I'm not sure I have time to get something like this working in time for >>> SciPy... Perhaps I can use my own repo for drafting the tutorial, then move >>> it into the tutorials repo as time allows? >>> >>> >>> On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart(a)mumford.me.uk> >>> wrote: >>> >>>> Hi, >>>> >>>> Astropy have a interesting tutorials repo ( >>>> https://github.com/astropy/astropy-tutorials) we are planning on >>>> implementing something similar using that for SunPy. There was some talk of >>>> building this on a generic framework based on the Astropy repo, though I >>>> don't think this has picked up much momentum. >>>> >>>> If you are interested in something like this as well then we all could >>>> try and work together on a IPython notebook gallery / tutorials framework? >>>> >>>> Stuart >>>> >>>> >>>> On 21 May 2014 08:14, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >>>> >>>>> Hey Juan >>>>> >>>>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias < >>>>> jni.soma(a)gmail.com> wrote: >>>>> > I'd like to have a repo for the tutorial Tony and I are doing at >>>>> SciPy, and >>>>> > all future scikit-image tutorials. I imagine it'll be a mix of >>>>> markdown, >>>>> > Python, and IPython notebooks. Do you think this is a good idea (say >>>>> > github.com/scikit-image/skimage-tutorials), and if so, can you >>>>> create it? >>>>> > I'd suggest all core members should have write access to it. >>>>> >>>>> I think it's a great idea! >>>>> >>>>> https://github.com/scikit-image/skimage-tutorials >>>>> >>>>> With notebooks, I sometimes worry that the repository grows rapidly if >>>>> you don't clear out the images before storing--what do you think is >>>>> the best way to handle that? >>>>> >>>>> I could perhaps add a Travis config that runs all the notebooks (then >>>>> one doesn't need to store the images because you are sure they can be >>>>> generated). Also, another idea is to deploy to readthedocs upon merge. >>>>> >>>>> Thanks! >>>>> 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/d/optout. >>>>> >>>> >>>> -- >>>> 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/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

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GSoC update on graph structures
by Stéfan van der Walt June 8, 2014

June 8, 2014

Hi everyone As part of this year's GSoC, Vighnesh is working on a graph region representation. He made several test implementations so far, outlined here: http://vcansimplify.wordpress.com/2014/06/04/gsoc-graph-data-structures-com… If you are interested in following along, please join us on the skimage-gsoc group [0]. Stéfan [0] https://groups.google.com/group/skimage-gsoc

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Re: Tutorials
by Tony Yu June 8, 2014

June 8, 2014

Hey Juan, Sorry for being so quiet about the SciPy tutorial. I've pushed a template as well as a skeleton for the tutorial. It's mostly taken from a rough outline that I wrote up for last year's SciPy. I'm sure it'll get shuffled around quite a bit, but I thought it'd be nice to start with something. Best, -Tony On Wed, May 21, 2014 at 4:27 AM, Stuart Mumford <stuart(a)mumford.me.uk> wrote: > Hi, > > The other thing that the astropy repo does to manage the size of the > gh-pages branch is make it an orphan branch on every build, so there is no > history of the built notebooks only the empty ones. > > Stuart > > > On 21 May 2014 10:23, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > >> Hi Stuart! >> >> This looks like a very good idea on first inspection — iirc git will not >> clone/fork a gh-pages branch by default, so having the run notebooks (with >> a lot of images built-in as Stéfan was concerned about) on that branch >> should not matter? >> >> I'm not sure I have time to get something like this working in time for >> SciPy... Perhaps I can use my own repo for drafting the tutorial, then move >> it into the tutorials repo as time allows? >> >> >> On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart(a)mumford.me.uk> >> wrote: >> >>> Hi, >>> >>> Astropy have a interesting tutorials repo ( >>> https://github.com/astropy/astropy-tutorials) we are planning on >>> implementing something similar using that for SunPy. There was some talk of >>> building this on a generic framework based on the Astropy repo, though I >>> don't think this has picked up much momentum. >>> >>> If you are interested in something like this as well then we all could >>> try and work together on a IPython notebook gallery / tutorials framework? >>> >>> Stuart >>> >>> >>> On 21 May 2014 08:14, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >>> >>>> Hey Juan >>>> >>>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias < >>>> jni.soma(a)gmail.com> wrote: >>>> > I'd like to have a repo for the tutorial Tony and I are doing at >>>> SciPy, and >>>> > all future scikit-image tutorials. I imagine it'll be a mix of >>>> markdown, >>>> > Python, and IPython notebooks. Do you think this is a good idea (say >>>> > github.com/scikit-image/skimage-tutorials), and if so, can you >>>> create it? >>>> > I'd suggest all core members should have write access to it. >>>> >>>> I think it's a great idea! >>>> >>>> https://github.com/scikit-image/skimage-tutorials >>>> >>>> With notebooks, I sometimes worry that the repository grows rapidly if >>>> you don't clear out the images before storing--what do you think is >>>> the best way to handle that? >>>> >>>> I could perhaps add a Travis config that runs all the notebooks (then >>>> one doesn't need to store the images because you are sure they can be >>>> generated). Also, another idea is to deploy to readthedocs upon merge. >>>> >>>> Thanks! >>>> 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/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

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Re: "Cythonize" not working on OSX?
by Stéfan van der Walt June 6, 2014

June 6, 2014

On Mon, 03 Feb 2014 16:44:07 +1100, Juan Nunez-Iglesias wrote: > I didn't know this was a possible course of action! =) I have no idea how > many people are affected, or how quick a fix can be... Is it worth > exploring a bit more before reversing it? I actually have very little idea > about the entire build process so I can't offer much insight here... It broke the build on my system too (perhaps it does not check correctly for old versions), so my preference is to revert and have another look at it. StÃ©fan

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