Mailman 3 September 2012 - scikit-image

Re: Segmentation and Granulometry with scikit-image
by Emmanuelle Gouillart Sept. 21, 2012

Sept. 21, 2012

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 Sept. 21, 2012

Sept. 21, 2012

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 Sept. 20, 2012

Sept. 20, 2012

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 Sept. 18, 2012

Sept. 18, 2012

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 Sept. 17, 2012

Sept. 17, 2012

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 Sept. 14, 2012

Sept. 14, 2012

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 Sept. 8, 2012

Sept. 8, 2012

> - 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 Sept. 8, 2012

Sept. 8, 2012

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 Sept. 6, 2012

Sept. 6, 2012

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 Sept. 3, 2012

Sept. 3, 2012

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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