Mailman 3 March 2015 - scikit-image

Re: Apply segmentation to a large binary image
by Juan Nunez-Iglesias 03 Apr '15

03 Apr '15

Hey Yuta, You'll need to do some stitching out-of-core. That's a really tricky problem and I don't have any ready-made solutions for you. The solution will depend on the nature of your segments. The only thing I would recommend is that you use a format such as HDF5 (you can use the excellent h5py library) that allows random access into the underlying disk data. Other than that, as I said, to my knowledge you'll have to develop your own stitching: segment *overlapping* tiles independently in memory, and when it comes time to write to disk, load the tile and overlapping tiles that have already been segmented, and resolve label mapping then... Generally, think of it this way: tile i has already been segmented and written out. We now want to write out tile j, which overlaps tile i. Labels from tile i that intersect labels from tile j in the overlap region should be matched. labels in tile j that *don't* intersect tile i should be relabelled to ensure they are unique with respect to tile i. Of course this gets a bit more complicated in 2D or 3D... Juan. On Fri, Mar 13, 2015 at 7:20 PM, Yuta Sato <yutaxsato(a)gmail.com> wrote: > Dear SKIMAGE Developers and Users: > I want to use the following algorithm in a large binary image that does not > fit into my PC memory. So, I am thinking to split my large image into tiles > and apply algorithm one by one. However, the original border definition > change when I do it in parts. I need the result as applied in original full > image. How can I do it efficiently? > skimage.segmentation.clear_border(image, buffer_size=0, bgval=0) > Thanks for your ideas. > -- > 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.

3 3

Steerable pyramid
by Dzung Nguyen 31 Mar '15

31 Mar '15

Hi all, I implemented Steerable pyramid (similar to Gabor transform). Would skimage community be interested in this? I am thinking of adding API for image transforms, and have all popular transform out there? (orthogonal, Gabor, steerable etc) https://github.com/andreydung/Steerable-filter

3 4

Re: GSoC: Rewriting scipy.ndimage in Cython
by Jérôme Kieffer 30 Mar '15

30 Mar '15

On Fri, 27 Mar 2015 07:04:10 -0700 Jaime Fernández del Río <jaime.frio(a)gmail.com> wrote: > Similarly, you suggest using Cython's prange to parallelize computations. I > haven't seen OpenMP used anywhere in NumPy or SciPy, and have the feeling > that parallel implementations are left out on purpose. Am I right, or would > parallelizing were possible be OK? OpenMP is tricky under MacOSX: 10.7-10.9 had no support at all (they use clang <3.6). Since 10.10, the support is incomplete, well at least many code I tested fail with OpenMP (they run under linux and windows), I noticed wrong results, not only failure to compile ! Of course on can install gcc or icc, but this is not in Python's philosophy -- Jérôme Kieffer <google(a)terre-adelie.org>

1 0

Lab Color space vs RGB
by Dzung Nguyen 29 Mar '15

29 Mar '15

Is it true that Lab color space is larger than RGB color space? For example, there exists a color in Lab that can't be reproduced in RGB space ( outside of monitor's gamut)? How does the function rgb2lab deal with this case? From the code, I saw that there's always a corresponding mapping one to one between Lab and RGB.

1 1

Re: Water-shedding non-circular particles
by Claiborne Morton 28 Mar '15

28 Mar '15

Hey thanks for all the help, here is the original image. Also I am removing the smallest particles later on in the process using a function that does the removal based on the average size of healthy (highly circular) cells, which is why I had not removed them in the images I have already posted. On Thursday, March 19, 2015 at 6:07:58 PM UTC-4, Claiborne Morton wrote: > > Hey guys, Im still having trouble finding ways to separate touching > particles if the are not both circular. Further when dealing with > elliptical shapes, a single particle tends to incorrectly get cut in half. > Any ideas how I could change parameters in the water-shedding function to > correct for this? Attached are a few problem cases so you can see examples. > > Thanks, > Clay > [image: Inline image 1] > > >

2 1

Re: Website designer volunteer
by Tony Yu 28 Mar '15

28 Mar '15

Hey Stéfan, Do you have some ideas for what improvements you're looking for? -Tony On Wed, Mar 25, 2015 at 9:09 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi folks, > > I know it's a bit of a long shot, but I'd like to find a volunteer to > work on the layout and readability of our website. > > If you know of anyone interested in doing design work the same way we > do software development, please let me know. They will have to be > able to work with our current workflow, so good technical chops are a > must. > > 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. >

1 0

Re: GSoC: Rewriting scipy.ndimage in Cython
by Jaime Fernández del Río 27 Mar '15

27 Mar '15

On Fri, Mar 27, 2015 at 2:27 AM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > On Thu, Mar 26, 2015 at 8:40 PM, AMAN singh <ug201310004(a)iitj.ac.in> > wrote: > >> Thank you everyone for your insightful comments. >> I have tried to incorporate your suggestion in the proposal. Kindly have >> a look at the new proposal here >> <https://docs.google.com/document/d/11RTVaDQDu38mrEv3WPdguxprJ-ha5kGnx2LhpEU…> >> and suggest the improvements. >> > > Hi Aman, this looks quite good to me. For the timeline I think it will > take longer to get the iterators right and shorter to port the last > functions at the end - once you get the hang of it you'll be able to do the > last ones quickly I expect. > That sounds about right. I think that breaking down the schedule to what function will be ported what week is little more than wishful thinking, and that keeping things at the file level would make more sense. But I think you are getting your proposal there. One idea that just crossed my mind: checking your implementation of the iterators and other stuff in support.c for correctness and performance is going to be an important part of the project. Perhaps it is a good idea to identify, either now or very early on the project, a few current ndimage top level functions that use each of those objects, if possible without interaction with the others, and build a sequence that could look something like (I am making this up in a hurry, so don't take the actual function names proposed too seriously, although they may actually make sense): Port NI_PointIterator -> Port NI_CenterOfMass, benchmark and test Port NI_LineBuffer -> Port NI_UniformFilter1D, benchmark and test ... This would very likely extend the time you will need to implement all the items in support.c. But by the time you were finished with that we would both have high confidence that things were going well, plus a "Rosetta Stone" that should make it a breeze to finish the job, both for you and anyone else. We would also have an intermediate milestone (everything in support ported plus a working example of each being used, with correctness and performance verified), that would be a worthy deliverable on its own: if we are terribly miscalculating task duration, and everything slips and is delayed, getting there could still be considered a success, since it would make finishing the job for others much, much simpler. One little concern of mine, and the questions don't really go to Aman, but to the scipy devs: the Cython docs on fused types have a big fat warning at the top on support still being experimental. Also, this is going to bump the version requirements for Cython to a very recent one. Are we OK with this? Similarly, you suggest using Cython's prange to parallelize computations. I haven't seen OpenMP used anywhere in NumPy or SciPy, and have the feeling that parallel implementations are left out on purpose. Am I right, or would parallelizing were possible be OK? Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes de dominación mundial.

1 0

GSoC: Rewriting scipy.ndimage in Cython
by AMAN singh 27 Mar '15

27 Mar '15

Hi developers My name is Aman Singh and I am currently a second year undergraduate student of Computer Science department at Indian Institute of Technology, Jodhpur. I want to participate in GSoC'15 and the project I am aiming for is *porting scipy.ndimage to cython*. I have been following scipy for the last few months and have also made some contributions. I came across this project on their GSoC'15 ideas' page and found it interesting. I have done some research in the last week on my part. I am going through Cython documentation, scipy lecture on github and Richard's work of GSoC' 14 in which he ported cluster package to cython. While going through the module scipy.ndimage I also found that Thouis Jones had already ported a function ndimage.label() to cython. I can use that as a reference for the rest of the project. Please tell me whether I am on right track or not. If you can suggest me some resources which will be helpful to me in understanding the project, I would be highly obliged. Also, I would like to know that how much part of ndimage is to be ported under this project since it is a big module. Kindly provide me some suggestions and guide me through this. Regards, Aman Singh

4 6

Re: Water-shedding non-circular particles
by Claiborne Morton 27 Mar '15

27 Mar '15

Also Juan, When you say, "There have been some recent developments on that function," are you referring to the peak_local_max() function? On Thursday, March 19, 2015 at 6:07:58 PM UTC-4, Claiborne Morton wrote: > > Hey guys, Im still having trouble finding ways to separate touching > particles if the are not both circular. Further when dealing with > elliptical shapes, a single particle tends to incorrectly get cut in half. > Any ideas how I could change parameters in the water-shedding function to > correct for this? Attached are a few problem cases so you can see examples. > > Thanks, > Clay > [image: Inline image 1] > > >

2 1

Re: The right way to access red channel in Lena
by Adam Hughes 27 Mar '15

27 Mar '15

Thanks! On Thu, Mar 26, 2015 at 8:38 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi Adam > > On Thu, Mar 26, 2015 at 4:31 PM, Adam Hughes <hughesadam87(a)gmail.com> > wrote: > >> ax1.imshow(lena*(1,0,0)) >> ax2.imshow(lena*(255,0,0)) >> > > The multiplication turns your image's dtype into uint64, which causes the > scaling problems. > > I prefer with float images, always ensuring that they are in [0, 1] and > then specifying vmin=0 and vmax=1 to matplotlib. > > Regards > Stéfan > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/JzmfEbBJKYU/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

1 0