Mailman 3 November 2013 - scikit-image

Re: Kakadu JP2000 reader
by Michael Aye Nov. 26, 2013

Nov. 26, 2013

On Friday, November 22, 2013 6:10:52 PM UTC-8, Stefan van der Walt wrote: > > On Sat, Nov 23, 2013 at 4:00 AM, Michael Aye <kmicha...(a)gmail.com<javascript:>> > wrote: > > If this is the driver that is exposed by GDAL, it's far too slow and > crashy > > for HiRISE images. > > These images look like they're about 1GB in size. Do you want to read > the entire image into memory? How large would that NumPy array be? > Are you interested in only loading a specific portion of the image? > > Hi Stéfan, I'm usually not interested in reading the whole image into memory, but would like to successively scan through the image in portions. But even that used to crash with the HiRISE images using open source JP2000 drivers, maybe because they use an exceptional harsh compression algorithm. Do I see it correctly, that the io.imread interface does not yet support partial reading of an image? Michael > Stéfan >

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Re: SLICO
by Michal Romaniuk Nov. 26, 2013

Nov. 26, 2013

Hi Juan, I'll see what I can do about SLICO, although I might need some help with Cython. I also noticed that the scikit-image version doesn't do the seed perturbation step in preprocessing, and doesn't seem to do the connected components step in post-processing. Was there any reason for omitting them? Michal

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Re: What's 'stable' version currently?
by Johannes Schönberger Nov. 26, 2013

Nov. 26, 2013

Stefan, would you merge and push the update to gh-pages? Am 13.11.2013 um 06:52 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > Perfect, thank you. > > On 12 Nov 2013 18:37, "Johannes Schönberger" <jsch(a)demuc.de> wrote: > Sorry, I didn’t see that you were asking for a review, so I just merged. > > See https://github.com/scikit-image/scikit-image-web/pull/14 for a slightly modified layout and automatic release date insertion. > > Am 12.11.2013 um 16:31 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > > > Here's a start--this PR grabs it directly from PyPi: > > > > https://github.com/scikit-image/scikit-image-web/pull/13 > > > > Some spacing issues etc., so some suggestions on how to tweak welcome. > > > > On Tue, Nov 12, 2013 at 4:55 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > >> Easiest way to do that is to just grab it from docversions.js. > >> > >> On 12 Nov 2013 20:20, "Johannes Schönberger" <jsch(a)demuc.de> wrote: > >>> > >>> Yes, but only in the documentation section and not on the home page in the > >>> sidebar on the top left. > >>> > >>> We should change this to automatically update the version number, because > >>> building the docs and uploading it every time is a pain... > >>> > >>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma(a)gmail.com>: > >>> > >>> I thought we had changed the site version string to read "0.9.x"??? > >>> > >>> > >>> On Tue, Nov 12, 2013 at 8:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za> > >>> wrote: > >>>> > >>>> Those are all bug fix releases, but yes: the website needs an update. In > >>>> fact, why don't we have the website builder just query pipy? > >>>> > >>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: > >>>>> > >>>>> I am asking because the website says 0.9.0, but pip just brought me > >>>>> 0.9.3? > >>>>> So either 0.9.3 is stable, and the website needs an update, or pip > >>>>> provides unstable versions, which would not be in line with what is written > >>>>> on skimage's Download page? > >>>>> > >>>>> Cheers, > >>>>> Michael > >>>>> > >>>>> > >>>>> -- > >>>>> 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. > >>>> > >>>> -- > >>>> 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. > >>> > >>> > >>> -- > >>> 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. > >>> > >>> -- > >>> 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. > > > > -- > > 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. > > > > -- > 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. > > -- > 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: Advice on basic operations: zoom, crop and splice
by Adam Hughes Nov. 25, 2013

Nov. 25, 2013

Thanks for all of your help guys. I was unaware of image Inpainting, so thank you Chintak for bringing that fascinating concept to my attention. Josh, thanks for your help. I am capable enough to do such manipulations in numpy and matplotlib; hell,I could even just save a zoomed/crop version of the images of interest. I was certainly interested in doing such manipulations in the notebook. I wouldn't worry about tweaking the viewer, as it would just be easier for me to, as I said, do the manipulations in and save them to separate images. The discussion that followed was quite interesting, and in line with what I expected might be the case. It's really great to see the progress of iPython widgets. I'm fairly competent at traits/chaco, but don't have a javascript background. Stefan, any idea how much javascript competency one might need to begin to approach this effort? On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote: > > Hi everyone, > > I'm used to working with big images of lots of particles. In the > notebook, I'd like to be able to look at a full image, and then at a zoomed > in region of interest. A few basic questions come to mind: > > Is there a zoom/crop function or preffered approach to basic > manipulations of zooming and cropping, or would I have to do this at the > numpy or matplotlib level? I saw that there's a rectangle function that > probably would be useful here. Does anyone have any examples or personal > code built for doing some of these common manipulations? Ideally, I want > to take the fastest approach to: > > 1. Selecting a rectangular region of interest (ROI). > 2. Cropping or zooming in on this region, and storing the ROI as its own > array/image. > 3. If possible, removing the ROI from the original image, and splicing > the original image back together. If this is possible, that would be > amazing. This would allow us to effectively cut out regions of our images > that are obviously contaminates. > > Thanks. > > >

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Re: stupid question: Why is imshow in io module?
by Michael Aye Nov. 25, 2013

Nov. 25, 2013

On Monday, November 25, 2013 2:29:26 PM UTC-8, Thomas A Caswell wrote: > > I would argue that showing an image is the 'out' part of I/O. > I see your point. It is certainly 'some' kind of output, although I'm used to have the output part more dealing with a file than with a display of it, but YMMV. Never mind, carry on. ;) > > On Mon, Nov 25, 2013 at 4:24 PM, Michael Aye <kmicha...(a)gmail.com<javascript:>> > wrote: > > I just stumbled over the 3 lines of code on scikits' title page: > > > > > > from skimage import data, io, filter > > image = data.coins() # or any NumPy array! > > edges = filter.sobel(image) > > io.imshow(edges) > > > > and wondered: Isn't it a bit funny to require an I/O module to show an > image > > that is already loaded? > > > > My apologies if that has been discussed before. > > > > Michael > > > > -- > > 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. > > > > -- > Thomas A Caswell > PhD Candidate University of Chicago > Nagel and Gardel labs > tcas...(a)uchicago.edu <javascript:> > jfi.uchicago.edu/~tcaswell<http://www.google.com/url?q=http%3A%2F%2Fjfi.uchicago.edu%2F~tcaswell&sa=D&…> > o: 773.702.7204 >

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Kakadu JP2000 reader
by Michael Aye Nov. 25, 2013

Nov. 25, 2013

Hi! I was wondering if it would be possible to implement the Kakadu JP2000 reader into scikit-image? I believe but am not sure that the reader only could be used without licensing fees? At least it's worth investigating because that reader is really the most powerful JP2000 reader out there and the only one that can deal with the large HiRISE images of the MRO spacecraft. Failing the above, a work-around could be to implement or encapsulate system calls to the freely downloadable kdu-expand utilities, converting it to something that is compatible with your current import routines? Best regards, Michael

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Re: Template matching for 3D image
by Kevin Keraudren Nov. 25, 2013

Nov. 25, 2013

I had a look at the SLIC code and I'll try this approach then, replace the 2D code by 3D code and consider 2D images as special cases. Cheers, Kevin Le 25/11/2013 04:02, Juan Nunez-Iglesias a Ã¯Â¿Â½crit : > On Mon, Nov 25, 2013 at 10:41 AM, Johannes SchÃ¯Â¿Â½nberger <jsch(a)demuc.de > <mailto:jsch@demuc.de>> wrote: > > Imo checking for 3D images in the same function is the best option. > > > +1 > > Sorry if I betray my ignorance about template matching, but can the 2D > case not be considered a special case of the 3D with z=1? In other > code (such as SLIC), when we get a 2D image we simply go: > > im = im[np.newaxis, ...] > > and feed that to the 3D code. Can the same be done for template matching? > > Thanks for this, Kevin! > > 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/groups/opt_out.

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Template matching for 3D image
by Kevin Keraudren Nov. 25, 2013

Nov. 25, 2013

Hi, I adapted the 2D code from: https://github.com/scikit-image/scikit-image/blob/master/skimage/feature/te… to 3D: https://github.com/kevin-keraudren/template-matching-3d I use it in my work, I have manual segmentation experts performed on cropped data, and I need the template matching to realign the cropped image with the full image (3D medical images). So thanks a lot for the 2D code! If you think it is of use, I could fork scikit-image and add the 3D version next to the 2D version. I understand there should be as little duplicated code as necessary, but shall I create a function match_template3D or shall match_template check the shape of the input image? Kind regards, Kevin

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SLICO
by Michal Romaniuk Nov. 24, 2013

Nov. 24, 2013

Hi everyone, I'm wondering if anyone is working on implementing SLICO, the more recent version of SLIC which doesn't require the compactness parameter? Michal

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Re: Test coverage
by Michael Aye Nov. 23, 2013

Nov. 23, 2013

I'd like to help here. Can somebody line out briefly how to find/identify uncovered code? Can this website generate a list and paths to the relevant code? Cheers, Michael On Wednesday, November 20, 2013 12:06:55 PM UTC-8, Chintak Sheth wrote: > > Hi Ankit > > Yes, the number of function calls and the lines (?) that have tests for > them. Tests are for ensuring that all the lines of code that is written is > checked against test cases and are correct. > > Chintak > On Nov 21, 2013 1:31 AM, "Ankit Agrawal" <aaaag...(a)gmail.com <javascript:>> > wrote: > >> Hi Stefan, >> >> Can you elaborate briefly what the coverage percentage exactly >> represents? Is it the fraction of API functions that have tests to cover >> their back? Or something else? >> >> Regards, >> Ankit Agrawal, >> Communication and Signal Processing, >> IIT Bombay. >> >> >> On Thu, Nov 21, 2013 at 12:15 AM, Stéfan van der Walt <ste...(a)sun.ac.za<javascript:> >> > wrote: >> >>> Hello, everyone >>> >>> We now have automated test coverage for scikit-image: >>> >>> https://coveralls.io/r/scikit-image/scikit-image<https://www.google.com/url?q=https%3A%2F%2Fcoveralls.io%2Fr%2Fscikit-image%…> >>> >>> Most of the newer modules (those that went through rigorous PR >>> review!) did pretty well, but we are still only at 82%. If ever you >>> find yourself with a bit of spare time on your hands, please hunt down >>> some of these corner cases and write tests for them so that we can >>> start making our way towards 100%. >>> >>> 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. >>> >> >> -- >> 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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