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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Re: Segmentation and Granulometry with scikit-image
by Emmanuelle Gouillart 21 Sep '12

21 Sep '12

Hi, the good news is that it is possible to perform the same operations with functions from skimage, plus some functions from scipy.ndimage (not in skimage to avoid code duplication). Below is a correspondence table that you can use for your applications. You can use the online doc to know more about these functions on http://scikits-image.org/docs/dev/api/api.html. You may also want to read the segmentation tutorial on http://scikits-image.org/docs/dev/user_guide/tutorial_segmentation.html Matlab <-> skimage (or scipy.ndimage) imread skimage.io.imread edge skimage.filter.canny strel skimage.morphology.selem imdilate skimage.morphology.dilation imfill ndimage.binary_fill_holes imclearborder skimage.segmentation.clear_border (**) imerode skimage.morphology.erosion bwperim skimage.measure.find_contours or ndimage.morphological_gradient adapthisteq skimage.exposure.equalize imadjust skimage.exposure.rescale_intensity imopen skimage.morphology.opening (**) only in the development version, the code is on https://github.com/scikits-image/scikits-image/blob/master/skimage/segmenta… Hope this is enough to get you started! Cheers, Emmanuelle On Wed, Sep 19, 2012 at 04:01:06AM -0700, ashz wrote: > Hi, > I am very interested in python image analysis and especially in > Scikit-image. > As a newbie would it be possible to get an explanation how to convert the > Matlab codes below to python+scikit-image. > Detecting a Cell Using Image Segmentation: > http://www.mathworks.com/help/images/examples/detecting-a-cell-using-image-… > Granulometry of Snowflakes: > http://www.mathworks.com/products/image/examples.html?file=/products/demos/… > Thanks a lot.

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Re: how to use fast_homography ?
by Stéfan van der Walt 21 Sep '12

21 Sep '12

Hi Nicolas On Wed, Sep 19, 2012 at 4:10 AM, Nicolas Barthe <lordnio101(a)gmail.com> wrote: > I'm trying to use scikits-image to apply an homography to a color image. You should see a factor 2 or so speedup in the latest version of skimage. On my older machine, with the following code, I get roughly 0.3 seconds. Do you require a nearer to real-time response? If you switch of bi-linear interpolation, you can shave off another 25% or so. Regards Stéfan from skimage import transform import numpy as np import datetime image = np.random.random((1280, 720, 3)) (x_scale,y_scale)=(1.05,1.1) (x_skew,y_skew)=(0.31e-3,0) S = np.array([[x_scale, 0, 0], [0, y_scale, 0], [x_skew, y_skew, 1]]) p = transform.ProjectiveTransform(S) t1 = datetime.datetime.now() transform.warp(image, inverse_map=p.inverse) t2 = datetime.datetime.now() print t2 - t1

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Re: how to use fast_homography ?
by Schönberger Johannes 20 Sep '12

20 Sep '12

Hi, what version of skimage do you use? Johannes Schönberger Am 19.09.2012 um 13:10 schrieb Nicolas Barthe <lordnio101(a)gmail.com>: > Hello, > > I'm trying to use scikits-image to apply an homography to a color image. > > Here's my sample script: > > from skimage import data, transform, io > from skimage.util import img_as_float > import numpy, Image > from scipy import ndimage > > img = Image.open("test.jpg") > data = numpy.asarray(img) > > (x_scale,y_scale)=(1.05,1.1) > (x_skew,y_skew)=(0.31e-3,0) > > S = numpy.array([[x_scale, 0, 0], > [0, y_scale, 0], > [x_skew, y_skew, 1]]) > > t1 = datetime.datetime.now() > data = transform.homography(data, S) > img = Image.fromarray(data) > img.show() > > The function transform.homography takes about 0.5 second on my core i7 pc to apply the homography on a 1280x720 color image... Is there a way to improve the performance ? > > I tried to use "fast_homography" instead of "homography" but I got a "ValueError: Buffer has wrong number of dimensions (expected 2, got 3)" error and I couldn't get it work... > > Thanks for your help! > > Nicolas.

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Re: Preparing for scikits-image release 0.7
by Tony Yu 18 Sep '12

18 Sep '12

On Mon, Sep 10, 2012 at 2:15 AM, KuantKid <kuantkid(a)gmail.com> wrote: > Issue 263: Fixed in pull request #307<https://github.com/scikits-image/scikits-image/pull/307> > > > On Saturday, September 8, 2012 11:37:33 PM UTC+8, Tony S Yu wrote: >> >> There have been a ton of new features added to scikits-image since >> version 0.6 was released at the end of June. So, now is a good time to >> prepare for a 0.7 release. >> >> To that end, it would be great to have fixes for a couple of pending >> issues. My list would include: >> >> - Issue 217 <https://github.com/scikits-image/scikits-image/issues/217>: >> Add check for dependency versions. >> - Issue 232 <https://github.com/scikits-image/scikits-image/issues/232>: >> measure.find_contours fails if ndarray is not C-contiguous >> - Issue 263 <https://github.com/scikits-image/scikits-image/issues/263>: >> IPython inline display does not work for binary images >> - Issue 271 <https://github.com/scikits-image/scikits-image/issues/271>: >> Test failure with nose 1.1.2 >> >> Are there any other fixes (or *small* enhancements) that people are >> itching to get into 0.7? >> >> Let's aim to get fixes in by next weekend (Sept 16th) and release the >> following weekend (Sept 23rd). >> >> Cheers! >> -Tony >> > Great! It looks like all these issues are fixed. (Thanks to Johannes and KuantKid!) Johannes is already hard at work adding PRs for new features (PR 321<https://github.com/scikits-image/scikits-image/pull/321>, PR 319 <https://github.com/scikits-image/scikits-image/pull/319>) and there are a couple of lingering PRs that deserve some attention after the the release (PR 293 <https://github.com/scikits-image/scikits-image/pull/293>, PR 242 <https://github.com/scikits-image/scikits-image/pull/242>, PR 235<https://github.com/scikits-image/scikits-image/pull/235>). So, it's probably best to push this release out the door soon. Unfortunately, I'll be traveling for the next week, but I don't know release procedure anyway, so that may not matter. Stefan: do you have time to cut a release? Actually, while we're on the topic, I don't really understand the requirements for Debian packaging: Why is there a separate debian branch? Couldn't the debian directory simply be put on master? I imagine there's a good reason, I just couldn't find it after a quick search. Best, -Tony

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Re: Multispectral random walker segmentation
by Emmanuelle Gouillart 17 Sep '12

17 Sep '12

Hi Josh, extending the random walker algorithm to multichannel images sounds like a very nice idea, and I'm sure that it would be useful for other people (including myself!). In fact, I had started working on some improvements of the random walker code but didn't go as far as proposing the pull request. I have a branch for that on https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, maybe you can include these changes when you contribute your changes? Cheers, Emmanuelle On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote: > I have modified the existing random walker algorithm into a fully > backwards-compatible version which allows inclusion of multispectral data, > e.g. RGBA channels or different (registered) image modalities. Ã¯Â¿Â½I really > liked the existing algorithm, so I just extended it rather than write one > from scratch for my own purposes. Ã¯Â¿Â½The overhead is minimal; multispectral > processing is triggered if data is passed as an iterable of arrays rather > than just an array. Ã¯Â¿Â½ > This amounts to combining image gradients as sqrt(sum-of-squares) and > dividing by sqrt(#channels). Ã¯Â¿Â½For obvious reasons, the several channels > must be pre-processed to have data on similar ranges by whitening or a > similar method. Ã¯Â¿Â½Not usually a problem for RGB, but in medical imaging > this rears its head. > Would this be of interest to the community? Ã¯Â¿Â½I'd be happy to contribute > the changes if there is interest.

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Re: Error building docs
by Tony Yu 14 Sep '12

14 Sep '12

On Thu, Sep 13, 2012 at 8:01 PM, Melissa Cline <melissa.s.cline(a)gmail.com>wrote: > > Did you ever get this problem figured out? I'm having exactly the same > problem... > Hi Melissa, This was fixed back in May: https://github.com/scikits-image/scikits-image/commit/01d86e3317e63d9428616… Which version of scikits-image are you using? The latest release (0.6, released in June) shouldn't have this issue. Best, -Tony > > On Tuesday, May 8, 2012 8:06:56 PM UTC-7, Tony S Yu wrote: >> >> I'm getting an IOError when rebuilding the docs and I can't figure out >> the cause. The error is raised during the build of the api docs and appears >> to be in `source/api/skimage.filter.**lpi_filter.txt`: >> >> writing output... [ 22%] api/skimage.filter.lpi_filter >> >> Exception occurred: >> File "/Library/Python/2.6/site-**packages/sphinx/ext/graphviz.**py", >> line 219, in render_dot_html >> mapfile = open(outfn + '.map', 'rb') >> IOError: [Errno 2] No such file or directory: '/Users/Tony/python/devel/* >> *skimage/doc/build/html/_**images/inheritance-** >> f7d294ea888e27c920fbf193effa64**2a3152b1be.png.map' >> >> The full sphinx traceback is at the end of this email. NOTE: this error >> only occurs when *RE*building. Running `make clean` and then `make html` in >> the doc directory works fine, but re-running `make html` will raise this >> error. >> >> Any ideas what's going on here? >> >> -Tony >> >> >> # Sphinx version: 1.1.3 >> # Python version: 2.6.1 >> # Docutils version: 0.9 release >> # Jinja2 version: 2.6 >> Traceback (most recent call last): >> File "/Library/Python/2.6/site-**packages/sphinx/cmdline.py", line >> 189, in main >> app.build(force_all, filenames) >> File "/Library/Python/2.6/site-**packages/sphinx/application.**py", >> line 204, in build >> self.builder.build_update() >> File "/Library/Python/2.6/site-**packages/sphinx/builders/__**init__.py", >> line 196, in build_update >> 'out of date' % len(to_build)) >> File "/Library/Python/2.6/site-**packages/sphinx/builders/__**init__.py", >> line 252, in build >> self.write(docnames, list(updated_docnames), method) >> File "/Library/Python/2.6/site-**packages/sphinx/builders/__**init__.py", >> line 292, in write >> self.write_doc(docname, doctree) >> File "/Library/Python/2.6/site-**packages/sphinx/builders/html.**py", >> line 419, in write_doc >> self.docwriter.write(doctree, destination) >> File "/Library/Python/2.6/site-**packages/docutils/writers/__**init__.py", >> line 77, in write >> self.translate() >> File "/Library/Python/2.6/site-**packages/sphinx/writers/html.**py", >> line 38, in translate >> self.document.walkabout(**visitor) >> File "/Library/Python/2.6/site-**packages/docutils/nodes.py", line >> 173, in walkabout >> if child.walkabout(visitor): >> File "/Library/Python/2.6/site-**packages/docutils/nodes.py", line >> 173, in walkabout >> if child.walkabout(visitor): >> File "/Library/Python/2.6/site-**packages/docutils/nodes.py", line >> 165, in walkabout >> visitor.dispatch_visit(self) >> File "/Library/Python/2.6/site-**packages/docutils/nodes.py", line >> 1611, in dispatch_visit >> return method(node) >> File "/Library/Python/2.6/site-**packages/sphinx/ext/**inheritance_diagram.py", >> line 340, in html_visit_inheritance_diagram >> alt='Inheritance diagram of ' + node['content']) >> File "/Library/Python/2.6/site-**packages/sphinx/ext/graphviz.**py", >> line 219, in render_dot_html >> mapfile = open(outfn + '.map', 'rb') >> IOError: [Errno 2] No such file or directory: '/Users/Tony/python/devel/* >> *skimage/doc/build/html/_**images/inheritance-** >> f7d294ea888e27c920fbf193effa64**2a3152b1be.png.map' >> >

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Re: Preparing for scikits-image release 0.7
by Johannes Schönberger 08 Sep '12

08 Sep '12

> - Issue 217: Add check for dependency versions. Fixed. > - Issue 232: measure.find_contours fails if ndarray is not C-contiguous Fixed.

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Preparing for scikits-image release 0.7
by Tony Yu 08 Sep '12

08 Sep '12

There have been a ton of new features added to scikits-image since version 0.6 was released at the end of June. So, now is a good time to prepare for a 0.7 release. To that end, it would be great to have fixes for a couple of pending issues. My list would include: - Issue 217 <https://github.com/scikits-image/scikits-image/issues/217>: Add check for dependency versions. - Issue 232 <https://github.com/scikits-image/scikits-image/issues/232>: measure.find_contours fails if ndarray is not C-contiguous - Issue 263 <https://github.com/scikits-image/scikits-image/issues/263>: IPython inline display does not work for binary images - Issue 271 <https://github.com/scikits-image/scikits-image/issues/271>: Test failure with nose 1.1.2 Are there any other fixes (or *small* enhancements) that people are itching to get into 0.7? Let's aim to get fixes in by next weekend (Sept 16th) and release the following weekend (Sept 23rd). Cheers! -Tony

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Timing comparisons between mahotas & scikits-image
by Luis Pedro Coelho 06 Sep '12

06 Sep '12

Hello, In the context of my previous email to pythonvision https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion I made a timing comparison between mahotas & scikits-image. operation | mahotas | pymorph | skimage ------------+----------+----------+--------- erode | 10.80 | 14.33 | 80.17 dilate | 11.44 | 8.93 | 41.59 open | 22.45 | 23.20 | 80.18 center mass | 7.05 | NA | NA sobel | 75.03 | NA | 105.72 cwatershed | 201.03 | 56586.50 | 290.41 daubechies | 19.05 | NA | NA haralick | 306.48 | NA | 7391.37 (Best viewed with fixed-width fonts) The unit of measurement is the time it takes to run ``numpy.max(image)`` Mahotas is always faster than skimage (although pymorph is better for certain morphological basic operations). I used GCLM in skimage to stand for Haralick, which is a rough approximation. I attach the script that generates these (against github skimage). If you think that I have used skimage incorrectly, please let me know. Best, -- Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

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Re: Numpydoc question
by Stéfan van der Walt 03 Sep '12

03 Sep '12

On Sep 3, 2012 2:32 AM, "Tony Yu" <tsyu80(a)gmail.com> wrote: > > I did manage to fix a number of Sphinx warnings. See PR 295. Thanks very much! Merged. Stéfan

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Re: Numpydoc question
by Tony Yu 02 Sep '12

02 Sep '12

On Sun, Sep 2, 2012 at 5:05 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Sep 2, 2012 7:15 PM, "Tony Yu" <tsyu80(a)gmail.com> wrote: > > > > While looking through the sphinx config file, I noticed that we have > config settings for the `plot_directive` extension and also include the > sphinx extension in `doc/ext/`. A quick grep of the doc directory suggests > that we don't actually use the plot directive anywhere. Is it worth keeping > for future use or should I remove that as part of this doc clean up? > > There's probably some legacy cruft left over--few people ever read that > file, so feel free to clean it up. > > Is the plot directive non needed to build figures for the user guide? > > Thanks! > Stéfan > > > > -Tony > It's not needed for the user guide, but I later noticed that it's used in a couple of the docstrings (e.g. API docs of hough transform). I'll just leave the plot directive as is, since it is actually being used. I did manage to fix a number of Sphinx warnings. See PR 295<https://github.com/scikits-image/scikits-image/pull/295/files> . -Tony

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Re: Numpydoc question
by Stéfan van der Walt 02 Sep '12

02 Sep '12

On Sep 2, 2012 7:15 PM, "Tony Yu" <tsyu80(a)gmail.com> wrote: > > While looking through the sphinx config file, I noticed that we have config settings for the `plot_directive` extension and also include the sphinx extension in `doc/ext/`. A quick grep of the doc directory suggests that we don't actually use the plot directive anywhere. Is it worth keeping for future use or should I remove that as part of this doc clean up? There's probably some legacy cruft left over--few people ever read that file, so feel free to clean it up. Is the plot directive non needed to build figures for the user guide? Thanks! Stéfan > > -Tony

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Re: Timing comparisons between mahotas & scikits-image
by Luis Pedro Coelho 02 Sep '12

02 Sep '12

Great! I will redo the timings in the next round of manuscript corrections (I already submitted last weeks results yesterday) for the mahotas paper. I might try to speed up things on mahotas' side too :) A little friendly competition always gets users better software. Best, Luis On 09/02/2012 03:41 PM, Stéfan van der Walt wrote: > On Thu, Aug 30, 2012 at 9:46 AM, Luis Pedro Coelho <luis(a)luispedro.org > <mailto:luis@luispedro.org>> wrote: > > I made a timing comparison between mahotas & scikits-image. > > > > operation | mahotas | pymorph | skimage > > ------------+----------+----------+--------- > > dilate | 11.44 | 8.93 | 41.59 > > With the latest versions of skimage and mahotas, I have: > > | mahotas | skimage > ----------+------------+-------- > erode | 9.60 | 16.18 > dilate | 11.69 | 8.01 > open | 20.53 | 16.16 > > Thanks to Johannes Schönberger for the speed-ups. > > Stéfan >

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Re: Numpydoc question
by Tony Yu 02 Sep '12

02 Sep '12

On Sun, Sep 2, 2012 at 12:12 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Sun, Sep 2, 2012 at 8:11 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > I'm inclined to just add `numpydoc_show_class_members = False` to > > `doc/source/conf.py` to reduce the noise during the build. Objections? > > Go ahead--for now, having a clean doc build is more important, until > someone can investigate the issue in more depth. > > Stéfan > While looking through the sphinx config file, I noticed that we have config settings for the `plot_directive` extension and also include the sphinx extension in `doc/ext/`. A quick grep of the doc directory suggests that we don't actually use the plot directive anywhere. Is it worth keeping for future use or should I remove that as part of this doc clean up? -Tony

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Re: Numpydoc question
by Stéfan van der Walt 02 Sep '12

02 Sep '12

On Sun, Sep 2, 2012 at 8:11 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > I'm inclined to just add `numpydoc_show_class_members = False` to > `doc/source/conf.py` to reduce the noise during the build. Objections? Go ahead--for now, having a clean doc build is more important, until someone can investigate the issue in more depth. Stéfan

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scikit-image September 2012