Mailman 3 July 2015 - scikit-image

Clothes Parsing
by Pelin Gezer 15 Jul '15

15 Jul '15

Hello everyone, Which library do you use for clothes parsing. I found this. <http://vision.is.tohoku.ac.jp/~kyamagu/research/clothing_parsing/>I dont know how I can import in python ? Anyone has experience about that? Thx! Best, Pelin G.

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ANN: "Effective Computation in Physics" Released, 50% Off until Friday July 17th
by Anthony Scopatz 15 Jul '15

15 Jul '15

Hello All! We are ecstatic to announce the release of the first edition of *Effective Computation in Physics - Field Guide to Research with Python* <http://shop.oreilly.com/product/0636920033424.do>, published by O'Reilly Media. *You (or your students and colleagues) can even get a 50% discount if you grab it before July 17th using the code: WKPYDP <http://shop.oreilly.com/product/0636920033424.do?code=WKPYDP>*. This book was heavily inspired by Software Carpentry. Though it draws on many examples from the physical sciences, many of the topics and chapters are broadly applicable to all of scientific computing. We hope that you'll find it useful even if your domain is biological, chemical, or mathematical in nature! For more information, please check out: - The website: http://physics.codes/ - The summary post at Software Carpentry: http://software-carpentry.org/blog/2015/07/effective-physics-book.html - The lightning talk announcement at SciPy 2015: https://youtu.be/yCStple1-28?t=29m20s Don't hesitate to contact us via email at authors(a)physics.codes or on twitter @physics_codes <https://twitter.com/physics_codes> with any questions or concerns that you have. Accompanying Jupyter Notebooks for all of the code in the book can be found on GitHub at https://github.com/physics-codes/examples released under the CC0 license. Please remember to review the book and give feedback online once you have finished reading it. We truly appreciate it, no matter what you say. Sorry if you received this announcement multiple times. We promise this will be the only time we ever send out such an announcement. We couldn't have done it without you! Katy Huff & Anthony Scopatz

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scikit.measure.label
by Shameem A Puthiya Parambath 14 Jul '15

14 Jul '15

Hi, I pass a 3D integer matrix to the label function in scikit.measure My original matrix contains integers in the range {-1..4}. But he output matrix from label function contains label from {1..199}. I am expecting it to be between {-1 .. 4}. Why so ?

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Use my own data in skimage
by Saber Ayoub Chelaghma 07 Jul '15

07 Jul '15

Hi, I successfully run some examples from scikit, like canny or threshold with image provided in the folder data. My questions is : what is the procedure to use my own data and images ? Changing the name of data used is not sufficient, because I think that I have to transform my image into an array. Regards, Saber

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failed to import the optional _tifffile C extension module.\n
by Saber Ayoub Chelaghma 06 Jul '15

06 Jul '15

Hi, I get this error when i try to compile a simple example of scikit. I am using python on Ubuntu : failed to import the optional _tifffile C extension module.\n Regard Saber

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Pattern and object recognition with COSFIRE
by Almar Klein 06 Jul '15

06 Jul '15

Hi all, Just wanted to mention an algorithm which I was very impressed by and which might be an awesome addition to scikit-image. The algorithm is called COSFIRE (Combination of Shifted Filter Responses). I saw a talk by Geore Azzopardi, who presented the use of the algorithm for object and patter recognition. I was very impressed with the quality of segmentation of the shown examples, but also with the wide variety of image data (e.g. retina images, traffic signs, hand-written characters, and more). The filter is inspired by how the brain processes visual information, and according to the author the algorithm is actually quite simple. The algorithm was the topic of his PhD and he's going to continue working on it in his new job. The code (in Matlab) is available, so it might be worth a shot to try and port it to Python. Some links: - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/ - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395 - Paper in MIA: http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-… - Almar

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Re: Enquiring about companies that rely on scikit-image
by Emmanuelle Gouillart 05 Jul '15

05 Jul '15

Hi Kevin, thank you for your question and sorry you didn't get an answer earlier. Most users (and developers) of scikit-image that I know of work in research labs rather than in companies. I also know a few users in national labs (such as synchrotron facilities, for example). I would be very interested in hearing from readers of the mailing-list working outside of academia: are you using scikit-image for your work? If yes, what do you like and do not like about the package, and if not, what keeps you from using scikit-image? A big difference with scikit-learn is that scikit-learn was the first comprehensive and successful Python package for machine learning, whereas other image processing solutions already existed for Python. In particular, openCV is an excellent package for computer vision, with good python bindings and numpy compatibility. In comparison, some of the strengths of scikit-image are its very simple and readable API (functions taking as input numpy arrays and optional parameters as keyword arguments) and its compatibility with 2D and 3D images. The documentation is also getting pretty good, with the example gallery that is a great tool for beginners (and others) to get started. Also, machine learning is a more recent (and more rapidly growing) field than image processing, so that there is more "legacy" in the image processing field. Whereas it was easier for machine learning users to start with new technologies (Python and scikit-learn), a lot of labs have developed image processing tools in C/C++/matlab and are reluctant to switch to a new language. But I'm sure that some companies are using scikit-image for their data processing workflow. It would be very nice to hear from them (shall we tweet about this?), in order to get feedback and maybe to set up a page like the one of scikit-learn. Any other thoughts from the mailing-list? Cheers, Emmanuelle On Sun, Jun 21, 2015 at 07:58:32PM +0100, 'Kevin Keraudren' via scikit-image wrote: > Hi, > I just came back from PyData London, which was a great experience. I thought I > would see a bit more image processing outside of an academic context, but Lyst > is the only one I noticed. > I was surprised by the success of scikit-learn outside of academia [1], and I > was wondering if people on the mailing list were aware of companies that would > similarly rely on scikit-image? > Kind Regards, > Kevin > [1] http://scikit-learn.org/stable/testimonials/testimonials.html

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ImportError when importing skimage subpackages
by Weixun Goh 03 Jul '15

03 Jul '15

I'm running into some issues after upgrading scikit-image, so I tried uninstalling and reinstalling, and it just doesn't seem to work. When I try to import skimage.feature, I run into the following issue: --------------------------------------------------------------------------- > > ImportError Traceback (most recent call > last) > > <ipython-input-3-9ed3c50fda3e> in <module>() > > ----> 1 from skimage import feature > > > /usr/local/lib/python2.7/dist-packages/skimage/feature/__init__.py in > <module>() > > 1 from ._canny import canny > > ----> 2 from ._daisy import daisy > > 3 from ._hog import hog > > 4 from .texture import (greycomatrix, greycoprops, > > 5 local_binary_pattern, > > > /usr/local/lib/python2.7/dist-packages/skimage/feature/_daisy.py in > <module>() > > 2 from scipy import sqrt, pi, arctan2, cos, sin, exp > > 3 from scipy.ndimage import gaussian_filter > > ----> 4 from .. import img_as_float, draw > > 5 from ..color import gray2rgb > > 6 from .._shared.utils import assert_nD > > > /usr/local/lib/python2.7/dist-packages/skimage/draw/__init__.py in > <module>() > > ----> 1 from .draw import circle, ellipse, set_color > > 2 from .draw3d import ellipsoid, ellipsoid_stats > > 3 from ._draw import (line, line_aa, polygon, ellipse_perimeter, > > 4 circle_perimeter, circle_perimeter_aa, > > 5 _bezier_segment, bezier_curve) > > > /usr/local/lib/python2.7/dist-packages/skimage/draw/draw.py in <module>() > > 1 # coding: utf-8 > > 2 import numpy as np > > ----> 3 from ._draw import _coords_inside_image > > 4 > > 5 > > > /scratch/repo/_draw.pyx in init skimage.draw._draw > (skimage/draw/_draw.c:23752)() > > > ImportError: No module named _shared.geometry > Same thing happens with filters and filter --------------------------------------------------------------------------- > ImportError Traceback (most recent call > last) > <ipython-input-9-6bd277fca327> in <module>() > ----> 1 import skimage.filters > /usr/local/lib/python2.7/dist-packages/skimage/filters/__init__.py in > <module>() > 11 from .thresholding import (threshold_adaptive, threshold_otsu, > threshold_yen, > 12 threshold_isodata, threshold_li) > ---> 13 from . import rank > 14 from .rank import median > 15 > ImportError: cannot import name rank Importing skimage.viewer gives me: ImportError: cannot import name _coords_inside_image Those are all that I have tried. skimage.utils works fine. I'm running the numpy and scipy packages provided by Ubuntu, and have tried both installing scikit-image using the pip packages as well as downloading from github then installing pip. Would be great if someone could shed some light on this.

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cannot import name 'generic_cy'
by Saber Ayoub Chelaghma 03 Jul '15

03 Jul '15

Hi, I have a problem when i try to compile a basic example for scikit. I’m using python on Ubuntu : cannot import name 'generic_cy' unfile('/home/stage/Documents/scikit-image/canny_simple.py', wdir='/home/stage/Documents/scikit-image') File "/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 586, in runfile execfile(filename, namespace) File "/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 48, in execfile exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace) File "/home/stage/Documents/scikit-image/canny_simple.py", line 1, in <module> from skimage import data File "/home/stage/Documents/scikit-image/skimage/data/__init__.py", line 13, in <module> from ._binary_blobs import binary_blobs File "/home/stage/Documents/scikit-image/skimage/data/_binary_blobs.py", line 2, in <module> from ..filters import gaussian_filter File "/home/stage/Documents/scikit-image/skimage/filters/__init__.py", line 13, in <module> from . import rank File "/home/stage/Documents/scikit-image/skimage/filters/rank/__init__.py", line 1, in <module> from .generic import (autolevel, bottomhat, equalize, gradient, maximum, mean, File "/home/stage/Documents/scikit-image/skimage/filters/rank/generic.py", line 24, in <module> from . import generic_cy Best regards

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ANN: imageio v1.0
by Almar Klein 03 Jul '15

03 Jul '15

Hi all, I'm pleased to announce version 1.0 of imageio - a library for reading and writing images. This library started as a spin-off of the freeimage plugin in skimage, and is now a fully-fledged library with unit tests and all. Imageio provides an easy interface to read and write a wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy to install. Imageio is plugin-based, making it easy to extend. It could probably use more scientific formats. I welcome anyone who's interested to contribute! install: pip install imageio website: http://imageio.github.io release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html Regards, Almar

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