Mailman 3 September 2012 - scikit-image

A word of thanks to our 0.7 release manager
by Stéfan van der Walt 30 Sep '12

30 Sep '12

Hi everyone, I just wanted to give a big shout-out to Tony, who handled the v0.7.0 release. Thanks for all your effort, Tony--this version's a big one! Thanks also to everyone else who contributed so enthusiastically over the past few months, as well as our sprinters at the USA and Europe SciPy conferences. Stéfan

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ANN: scikits-image 0.7.0 release
by Tony Yu 30 Sep '12

30 Sep '12

Announcement: scikits-image 0.7.0 ================================= We're happy to announce the 7th version of scikits-image! Scikits-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. For more information, examples, and documentation, please visit our website http://skimage.org New Features ------------ It's been only 3 months since scikits-image 0.6 was released, but in that short time, we've managed to add plenty of new features and enhancements, including - Geometric image transforms - 3 new image segmentation routines (Felsenzwalb, Quickshift, SLIC) - Local binary patterns for texture characterization - Morphological reconstruction - Polygon approximation - CIE Lab color space conversion - Image pyramids - Multispectral support in random walker segmentation - Slicing, concatenation, and natural sorting of image collections - Perimeter and coordinates measurements in regionprops - An extensible image viewer based on Qt and Matplotlib, with plugins for edge detection, line-profiling, and viewing image collections Plus, this release adds a number of bug fixes, new examples, and performance enhancements. Contributors to this release ---------------------------- This release was only possible due to the efforts of many contributors, both new and old. - Andreas Mueller - Andreas Wuerl - Andy Wilson - Brian Holt - Christoph Gohlke - Dharhas Pothina - Emmanuelle Gouillart - Guillaume Gay - Josh Warner - James Bergstra - Johannes Schonberger - Jonathan J. Helmus - Juan Nunez-Iglesias - Leon Tietz - Marianne Corvellec - Matt McCormick - Neil Yager - Nicolas Pinto - Nicolas Poilvert - Pavel Campr - Petter Strandmark - Stefan van der Walt - Tim Sheerman-Chase - Tomas Kazmar - Tony S Yu - Wei Li

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Re: Preparing for scikits-image release 0.7
by Andreas Mueller 28 Sep '12

28 Sep '12

Hi StÃ¯Â¿Â½fan. >> Any reviews urgently needed? > I think we're done with most of those. Good to hear :) > We do have a bug report by a > certain A. Mueller from about a year ago that you could work on :) > > https://github.com/scikits-image/scikits-image/issues/32 Will have a look! Cheers and keep up the good work. Andy

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Re: Preparing for scikits-image release 0.7
by Andreas Mueller 28 Sep '12

28 Sep '12

Hey Team scikits-image! Is there a plan for the release? Any reviews urgently needed? I could also give the sphinx a look and the pep8. As always to busy to have helped much :-/ Cheers, Andy

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Re: Segmentation and Granulometry with scikit-image
by Tony Yu 24 Sep '12

24 Sep '12

On Fri, Sep 21, 2012 at 8:46 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz10001(a)gmail.com> wrote: > > > Granulometry of Snowflakes: > > > http://www.mathworks.com/products/image/examples.html?file=/products/demos/… > > Tony, do you think the morphological reconstruction would work for > this? Yes and no. Morphological reconstruction (specifically, h-dome, a.k.a. h-maxima or regional max) tries to enhance features (maxima) based on the local region. So the h-dome of a dim snowflake and bright snowflake will look similar if they have a similar peakiness. In the original example, dim peaks are still much dimmer than the bright peaks, even after the adaptive histogram equalization. Also, the h-dome of an image will tend to remove the corona-like blurring around the larger snowflakes since the middle is so much brighter than the surrounding region. I've attached an image of the results, along with the code to generate it (although you can't run it without the snowflakes image, which I probably shouldn't email). You'll notice that dim peaks are much brighter than in the example, and the large snowflakes are smaller (because of suppression of the corona region). These differences alter the intensity curve quite a bit (I'm not sure what the "right" output is, though). > Otherwise perhaps one of the segmentation algorithms. > Translating the example line-by-line is pretty easy, except that we do > not have adaptive histogram equalization implemented yet. > BTW, there's a pending PR to add adaptive histogram equalization<https://github.com/scikits-image/scikits-image/pull/242>. (Although, I'm not sure how I feel about the large header file required for that PR.) As for the original post about these Matlab examples: Thanks for bringing this up, ashz! These are exactly the type of examples I'd like to see in the user guide: Something that takes the user all the way from image loading to data extraction. We'd probably want to write our own instead of simply translating the Matlab examples. It'd be great if people on this list could provide examples from their own research. Best, -Tony [image: Inline image 1] # Code to generate image above # Note: this won't run without image from Matlab install: # toolbox/images/imdemos/snowflakes.png from skimage import io from skimage import img_as_float import skimage.morphology as morph from skimage import exposure from scipy import ndimage # snowflake image from a Matlab install img = io.imread('snowflakes.png') # convert from uint8 to float since we'll be subtracting (prevent underflow) orig = img_as_float(img) img = exposure.equalize(img) img = ndimage.gaussian_filter(img, 1) # look for regional maxima greater than surrounding regions by h h = 0.2 img_background = morph.reconstruction(img-h, img) img_hdome = img - img_background img = exposure.rescale_intensity(img_hdome) io.imshow(img) # io.imsave('snowflakes_enhanced.png', img) io.show()

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Re: Error importing package. Skimage, Scipy or Macports error?
by bricklemacho 24 Sep '12

24 Sep '12

Yes I get the same error. I look at rebuilding scipy. On Tuesday, 25 September 2012 02:51:05 UTC+8, Tony S Yu wrote: > > > > On Sun, Sep 23, 2012 at 8:07 AM, Brian Holt <bdh...(a)gmail.com<javascript:> > > wrote: > >> My first guess would the the PYTHONPATH... Could you have a look to see >> if adding scikits-image root directory makes any difference? >> >> Brian >> On Sep 23, 2012 8:48 AM, "bricklemacho" <brickl...(a)gmail.com<javascript:>> >> wrote: >> >>> >>> I am trying to run the plot_hog.py demo an I get the error below. If >>> I copy skimage/feature/hog.py and import form the current working directory >>> the plot_hog.py runs. >>> >>> The error seems to be something to do with importing match_template. >>> Not sure where to start , all packages were installed via macports. Is >>> this a scikits-image, scipy or a macports issue? >>> >>> Any help appreciated, error message below. >>> >>> Brickle. >>> >>> ------------- >>> $ python plot_hog.py >>> Traceback (most recent call last): >>> File "scikitsHoG.py", line 1, in <module> >>> from skimage.feature import hog >>> File >>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", >>> line 5, in <module> >>> from .template import match_template >>> File >>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", >>> line 4, in <module> >>> from . import _template >>> File "_template.pyx", line 36, in init skimage.feature._template >>> (skimage/feature/_template.c:3980) >>> File >>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", >>> line 198, in <module> >>> from spline import * >>> ImportError: >>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, >>> 2): Symbol not found: ___ieee_divdc3 >>> Referenced from: >>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >>> Expected in: flat namespace >>> in >>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >>> >> > > Hey Brickle, > > Do you get the same error if you just call: > > from scipy import signal > > If so, you may need to rebuild scipy. > > Best, > -Tony >

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Re: Error importing package. Skimage, Scipy or Macports error?
by bricklemacho 24 Sep '12

24 Sep '12

Thanks for the suggestion. Adding to the PYTHONPATH didn't change anything. On Sunday, 23 September 2012 16:07:47 UTC+8, Brian Holt wrote: > > My first guess would the the PYTHONPATH... Could you have a look to see if > adding scikits-image root directory makes any difference? > > Brian > On Sep 23, 2012 8:48 AM, "bricklemacho" <brickl...(a)gmail.com <javascript:>> > wrote: > >> >> I am trying to run the plot_hog.py demo an I get the error below. If I >> copy skimage/feature/hog.py and import form the current working directory >> the plot_hog.py runs. >> >> The error seems to be something to do with importing match_template. >> Not sure where to start , all packages were installed via macports. Is >> this a scikits-image, scipy or a macports issue? >> >> Any help appreciated, error message below. >> >> Brickle. >> >> ------------- >> $ python plot_hog.py >> Traceback (most recent call last): >> File "scikitsHoG.py", line 1, in <module> >> from skimage.feature import hog >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", >> line 5, in <module> >> from .template import match_template >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", >> line 4, in <module> >> from . import _template >> File "_template.pyx", line 36, in init skimage.feature._template >> (skimage/feature/_template.c:3980) >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", >> line 198, in <module> >> from spline import * >> ImportError: >> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, >> 2): Symbol not found: ___ieee_divdc3 >> Referenced from: >> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >> Expected in: flat namespace >> in >> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >> >

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Re: Error importing package. Skimage, Scipy or Macports error?
by Tony Yu 24 Sep '12

24 Sep '12

On Sun, Sep 23, 2012 at 8:07 AM, Brian Holt <bdholt1(a)gmail.com> wrote: > My first guess would the the PYTHONPATH... Could you have a look to see if > adding scikits-image root directory makes any difference? > > Brian > On Sep 23, 2012 8:48 AM, "bricklemacho" <bricklemacho(a)gmail.com> wrote: > >> >> I am trying to run the plot_hog.py demo an I get the error below. If I >> copy skimage/feature/hog.py and import form the current working directory >> the plot_hog.py runs. >> >> The error seems to be something to do with importing match_template. >> Not sure where to start , all packages were installed via macports. Is >> this a scikits-image, scipy or a macports issue? >> >> Any help appreciated, error message below. >> >> Brickle. >> >> ------------- >> $ python plot_hog.py >> Traceback (most recent call last): >> File "scikitsHoG.py", line 1, in <module> >> from skimage.feature import hog >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", >> line 5, in <module> >> from .template import match_template >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", >> line 4, in <module> >> from . import _template >> File "_template.pyx", line 36, in init skimage.feature._template >> (skimage/feature/_template.c:3980) >> File >> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", >> line 198, in <module> >> from spline import * >> ImportError: >> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, >> 2): Symbol not found: ___ieee_divdc3 >> Referenced from: >> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >> Expected in: flat namespace >> in >> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so >> > Hey Brickle, Do you get the same error if you just call: from scipy import signal If so, you may need to rebuild scipy. Best, -Tony

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Error importing package. Skimage, Scipy or Macports error?
by bricklemacho 23 Sep '12

23 Sep '12

I am trying to run the plot_hog.py demo an I get the error below. If I copy skimage/feature/hog.py and import form the current working directory the plot_hog.py runs. The error seems to be something to do with importing match_template. Not sure where to start , all packages were installed via macports. Is this a scikits-image, scipy or a macports issue? Any help appreciated, error message below. Brickle. ------------- $ python plot_hog.py Traceback (most recent call last): File "scikitsHoG.py", line 1, in <module> from skimage.feature import hog File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", line 5, in <module> from .template import match_template File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", line 4, in <module> from . import _template File "_template.pyx", line 36, in init skimage.feature._template (skimage/feature/_template.c:3980) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", line 198, in <module> from spline import * ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, 2): Symbol not found: ___ieee_divdc3 Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so Expected in: flat namespace in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so

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Re: Segmentation and Granulometry with scikit-image
by Stéfan van der Walt 21 Sep '12

21 Sep '12

On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz10001(a)gmail.com> wrote: > Granulometry of Snowflakes: > http://www.mathworks.com/products/image/examples.html?file=/products/demos/… Tony, do you think the morphological reconstruction would work for this? Otherwise perhaps one of the segmentation algorithms. Translating the example line-by-line is pretty easy, except that we do not have adaptive histogram equalization implemented yet. > Detecting a Cell Using Image Segmentation: > http://www.mathworks.com/help/images/examples/detecting-a-cell-using-image-… This one is straightforward, except that convex_hull_objects would have made it simpler. We should also spruce up skimage.segmentation.visualize_boundaries, which could have been of use here. https://gist.github.com/3763784 Regards Stéfan

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