scikit-image October 2013

scikit-image@python.org

27 participants
74 discussions

Re: umfpack error
by Josh Warner 04 Oct '13

04 Oct '13

Final note - umfpack enables mode='cg' in random_walker, which is better than brute force but not the fastest or most efficient mode. The multi-grid preconditioned conjugate gradient method is: mode='cg_mg'. This is enabled by pyamg, which is independent of umfpack and is considerably easier to install and use than the method I just described. Come to think of it, we probably should suppress that warning if import pyamg works. It incorrectly implies the user doesn't have the fastest mode available. On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote: Hi guys, > > How do I build scipy with umfpack to silence this error: > > Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored > > and speed up random_walker? I've just been doing a pip install scipy till > now. > > Juan. >

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Re: umfpack error
by Josh Warner 04 Oct '13

04 Oct '13

SciPy has a number of optional dependencies, which `pip` doesn't attempt to install. Largely because several of them are not directly Python based, and `pip` isn't a true package manager. Without them SciPy builds and runs, but certain pieces either run slower (in this case, parts of `scipy.sparse`) or don't exist at all. Near the top of the very lengthy build and compile log for SciPy there is a brief report on which optional dependencies are present at time of build. Presumably you don't have umfpack. It's also possible you do, but lack the development headers - but for the purposes of this argument, let's assume you don't. 1. The first step is to get umfpack. Doing this varies across platforms, but if you're on linux check repos first. If not, look online for the best method; I've always gotten it this way. 2. Next step is to get the development headers for umfpack. Usually in Linux package managers (yum, apt, etc.) these have the same name with `'-dev'` appended. They're what SciPy needs to find and use umfpack. 3. Finally, you'll need to remove and rebuild SciPy with `$ pip uninstall scipy` followed by `$pip install scipy`. The new build should auto-detect umfpack and build appropriately. Hopefully that helps. God help you if you're on Windows; I sure can't. Josh On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote: > > Hi guys, > > How do I build scipy with umfpack to silence this error: > > Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored > > and speed up random_walker? I've just been doing a pip install scipy till > now. > > Juan. >

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Re: Screenshots for PyCon
by Payal Gupta 03 Oct '13

03 Oct '13

hey juan, i am using threshold_otsu for thresholding but i am not getting appropriate result. And how to use threshold_adapt? i want to convert gray image to binary image. how can i do? anybody help in this problem. thanks On Thursday, October 3, 2013 7:28:44 AM UTC+5:30, Juan Nunez-Iglesias wrote: > > Hi Stefan, > > I hope this isn't too late. I recently had to segment out the chromosomes > in this picture: > > [image: Inline image 1] > > You can see the illumination is really uneven, so `threshold_otsu` does > really poorly. `threshold_adapt` works as advertised but you get some > artifacts: > > [image: Inline image 2] > > The key to getting around this was seeing the "grain" in the outside > regions compared to the chromosomes themselves. So after a `binary_opening` > with the right parameters (don't have them off the top of my head), > followed by a `remove_small_objects`: > > [image: Inline image 3] > > Hope that helps! > > Juan. > > PS: I also made this notebook<http://nbviewer.ipython.org/urls/github.com/jni/notebooks/raw/master/pothol…>to help Mehmet Kunt, a civil engineering professor Emmanuelle and I met at > EuroSciPy, measure potholes in images. > > > > On Thu, Oct 3, 2013 at 2:21 AM, Stéfan van der Walt <ste...(a)sun.ac.za<javascript:> > > wrote: > >> Hi folks, >> >> I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for >> a few screenshots or for one demo. If anyone has a particularly nice >> example, please send it my way. >> >> 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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >

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Re: Screenshots for PyCon
by Payal Gupta 03 Oct '13

03 Oct '13

On Wednesday, October 2, 2013 9:51:21 PM UTC+5:30, Stefan van der Walt wrote: > > Hi folks, > > I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a > few screenshots or for one demo. If anyone has a particularly nice example, > please send it my way. > > Thanks! > Stéfan >

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umfpack error
by Juan Nunez-Iglesias 03 Oct '13

03 Oct '13

Hi guys, How do I build scipy with umfpack to silence this error: Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored and speed up random_walker? I've just been doing a pip install scipy till now. Juan.

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Re: Screenshots for PyCon
by Stéfan van der Walt 03 Oct '13

03 Oct '13

On Thu, Oct 3, 2013 at 3:58 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > I hope this isn't too late. I recently had to segment out the chromosomes in this picture: Very nicely done, thank you! Stéfan

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Re: Screenshots for PyCon
by Juan Nunez-Iglesias 03 Oct '13

03 Oct '13

Hi Stefan, I hope this isn't too late. I recently had to segment out the chromosomes in this picture: [image: Inline image 1] You can see the illumination is really uneven, so `threshold_otsu` does really poorly. `threshold_adapt` works as advertised but you get some artifacts: [image: Inline image 2] The key to getting around this was seeing the "grain" in the outside regions compared to the chromosomes themselves. So after a `binary_opening` with the right parameters (don't have them off the top of my head), followed by a `remove_small_objects`: [image: Inline image 3] Hope that helps! Juan. PS: I also made this notebook<http://nbviewer.ipython.org/urls/github.com/jni/notebooks/raw/master/pothol…>to help Mehmet Kunt, a civil engineering professor Emmanuelle and I met at EuroSciPy, measure potholes in images. On Thu, Oct 3, 2013 at 2:21 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi folks, > > I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a > few screenshots or for one demo. If anyone has a particularly nice example, > please send it my way. > > 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/groups/opt_out. >

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Screenshots for PyCon
by Stéfan van der Walt 02 Oct '13

02 Oct '13

Hi folks, I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a few screenshots or for one demo. If anyone has a particularly nice example, please send it my way. Thanks! Stéfan

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Re: Release time
by Stéfan van der Walt 02 Oct '13

02 Oct '13

On Wed, Oct 2, 2013 at 5:35 PM, Jostein Bø Fløystad <jostein.floystad(a)gmail.com> wrote: > The changes suggested here would require raising deprecation warnings in > 0.9: > > https://github.com/scikit-image/scikit-image/issues/744 > > It would be nice to discuss these before the new release. Good, let's get these discussions started, then we can tag in about a week from now. Stéfan

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Re: Release time
by Johannes Schönberger 02 Oct '13

02 Oct '13

I'll do that tonight. Is there as special syntax for marking a function as "experimental"? Am 02.10.2013 um 14:55 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > On Wed, Oct 2, 2013 at 2:48 PM, Johannes Schönberger <jsch(a)demuc.de> wrote: >> Couldn't we just simply remove those functions from __all__ in the feature/__init__.py in the mean time? > > Good suggestion--can you update the docstrings to label them as experimental? > > 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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scikit-image October 2013