Mailman 3 February 2012 - scikit-image

Re: random walker segmentation / blob detection
by Stéfan van der Walt 10 Feb '12

10 Feb '12

On Thu, Feb 9, 2012 at 12:26 AM, Thouis Jones <thouis.jones(a)curie.fr> wrote: > Or take a look at ilastik (ilastik.org). We've been using this in a What a neat project! I've added a link to our front page. Stéfan

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Re: 0.5 release soon?
by Stéfan van der Walt 10 Feb '12

10 Feb '12

On Thu, Feb 9, 2012 at 9:07 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > There has been a surprising amount of new features, fixes, and doc > improvements since 0.4, so I'm wondering if it's time for a new release. You're right, it's about time! > Are there any major todos before that? - Finish the Debian packaging. Really, this is so close, we should just do it: 1. Edit the skivi.1 man-page template (anyone with Troff skills here?) 2. Update the copyright file. 3. Ping Yaroslav to check and upload. If possible, we should get permission from everyone with per-file copyright messages and move their names to the CONTRIBUTORS.txt file, so that we have a single license covering all our code. > * Maybe doc additions if they're close. I've got some unpushed user guide changes that I'll be done with soon. > * Of the current pull requests, only SSIM and template-matching are close, > but I don't think I'll have much time to sort out the issues with > template-matching for awhile. For now, I'm pretty much done with SSIM, so if you think it looks OK please merge. > * I was really excited about the image stitching example using HoGs, > suggested by Nelle. If it's not close, though, no pressure. Since Nelle's indicated that she's very busy at the moment, we can push that back to 0.6 (and yes, it would make a great feature!). The end of February gets crazy for me time-wise, so shall we aim for the 19th of February? That gives us two more weekends. Stéfan

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Error when building from git
by Guillaume 10 Feb '12

10 Feb '12

Hey list, First thanks for the great work. I am planning to use skimage for some fluorescence microscopy analysis. Today I installed from the git repository and an error occurred when compiling: File "/home/guillaume/Python/lib/scikits-image/skimage/util/ dtype.py", line 20, in <module> in <module> np.float16, np.float32, np.float64) AttributeError: 'module' object has no attribute 'float16' taking out 'float16' in the _supported_types tuple solves the issue (at least it compiles), but I don't know whether it could have consequences later on. _supported_types = (np.uint8, np.uint16, np.uint32, np.int8, np.int16, np.int32, #np.float16, ### Commented this out... np.float32, np.float64) I am running Python 2.7.2+ with numpy 1.5.1 (that is what you get with apt-get install python-numpy) Thanks...

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Re: 0.5 release soon?
by Nelle Varoquaux 10 Feb '12

10 Feb '12

On 10 February 2012 06:07, Tony Yu <tsyu80(a)gmail.com> wrote: > There has been a surprising amount of new features, fixes, and doc > improvements since 0.4, so I'm wondering if it's time for a new release. > Are there any major todos before that? > > * Maybe doc additions if they're close. > > * Of the current pull requests, only SSIM and template-matching are close, > but I don't think I'll have much time to sort out the issues with > template-matching for awhile. > > * I was really excited about the image stitching example using HoGs, > suggested by Nelle. If it's not close, though, no pressure. > I'm a bit swamped with work right now, so I'll think we'll have to delay that if you want to do a release before end of February Cheers, Nelle > > Anything else? > > Cheers! > -Tony >

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0.5 release soon?
by Tony Yu 09 Feb '12

09 Feb '12

There has been a surprising amount of new features, fixes, and doc improvements since 0.4, so I'm wondering if it's time for a new release. Are there any major todos before that? * Maybe doc additions if they're close. * Of the current pull requests, only SSIM and template-matching are close, but I don't think I'll have much time to sort out the issues with template-matching for awhile. * I was really excited about the image stitching example using HoGs, suggested by Nelle. If it's not close, though, no pressure. Anything else? Cheers! -Tony

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image conversions
by Michael Aye 09 Feb '12

09 Feb '12

I am working through the docs of skimage and tried out the image conversions. The docs say that these functions *properly rescale* the values, but I'm not sure what is meant with *properly? * *IF *rescaling is meant to exploit the defined range between 0 and 1 for floats, that does not seem to happen: In [13]: data=np.uint(data) In [14]: data.max() Out[14]: 27 In [15]: data.min() Out[15]: 17 In [16]: fimg = skimage.img_as skimage.img_as_float skimage.img_as_int skimage.img_as_ubyte skimage.img_as_uint In [16]: fimg = skimage.img_as_float(data) In [17]: fimg.max() Out[17]: 6.2864273801181529e-09 In [18]: fimg.min() Out[18]: 3.9581209430373555e-09 In [19]: imshow(fimg) Out[19]: <matplotlib.image.AxesImage at 0xe38b1f0> In [20]: data.dtype Out[20]: dtype('uint32') Or do I misunderstand something? Best regards, Michael

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Re: Fixing image loading in Python: imread
by Luis Pedro Coelho 09 Feb '12

09 Feb '12

I had a look at matplotlib. It is very similar to what I did (I mean, it's just a call to libpng, there is just a few variations on the same theme), but not as flexible as they are not using anything but libpng. Luis

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Re: random walker segmentation / blob detection
by Michael Aye 09 Feb '12

09 Feb '12

Hi Thouis, ilastik does not seem to have a programmatic interface, is that right? I can't do it via GUI's, my end goal is to find features programmatically in possibly thousands of images...

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Understanding HoG output
by bricklemacho 09 Feb '12

09 Feb '12

Hi, new to group, new to image processing starting to explore HoG. Looking for a python implementation and discovered skimage.feature.hog(). My plan to run skimage.features.hog over some positive/negative images and use this to train a svm classifier from scikits-learn. I am trying to understand the output hog before I proceed further. When I run skimag.feature.hog() it over a region of interest it appears to returns an array. How do I interpret this array? Is there a way to reshape the array to see what it was like before it was flattened or that doesn't make any sense? Can I plot the descriptor returned in any meaningful way? Also when I choose to visualise the HoG often where I expected to see vertical line dominate, say on the edge of builds, the line drawn often appears to be more dominant at the 45 deg. Is this expected as the line drawn is really just the sum of all surrounding orientations for the "cell"? Thanks in advance, Michael. --

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Re: Documentation sprint over the weekend
by Ralf Gommers 09 Feb '12

09 Feb '12

On Thu, Feb 9, 2012 at 4:56 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > 2012/2/8 Stéfan van der Walt <stefan(a)sun.ac.za> > >> On Wed, Feb 8, 2012 at 12:12 PM, Ralf Gommers >> <ralf.gommers(a)googlemail.com> wrote: >> > On http://scikits-image.org/docs/dev/ it points to >> > http://scikits-image.org/docs/dev/. >> > On http://scikits-image.org/ it points to http://scikits-image.org/. >> > On http://scikits-image.org/docs/ it points to >> > http://scikits-image.org/docs/. >> > On http://scikits-image.org/docs/0.3/ it points to >> > http://scikits-image.org/docs/0.3/. >> >> I rebuilt the docs. The logo now links to the webpage, and there is >> an additional navigation item in the sidebar to take you to the >> documentation root. >> >> Regards >> Stéfan >> > > Nice! Not only did you add the navigation link, but the sidebar looks much > cleaner now, also. > > Indeed, looks great. Ralf

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