Mailman 3 February 2015 - scikit-image

PeerJ Staff Picks 2015
by Stefan van der Walt Feb. 17, 2015

Feb. 17, 2015

Hi everyone Juan just informed me that our scikit-image paper appears on the 2015 PeerJ Staff Picks: https://peerj.com/collections/13-peerjpicks2015/ Congratulations team! Stéfan

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Last blockers for 0.11 release
by Stéfan van der Walt Feb. 17, 2015

Feb. 17, 2015

Hi everyone We're overdue for the 0.11 release, and there are very few issues left to close. I'd appreciate your feedback on this one: https://github.com/scikit-image/scikit-image/pull/1248 (peak detectors) And help in fixing: https://github.com/scikit-image/scikit-image/issues/1048 (doctest failures on Mac OSX) I think this Sunday is a reasonable target for 0.11. Please get any additional documentation updates in before then. Stéfan

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Re: Install difficulties - No module named _hough_transform
by Johannes Schoenberger Feb. 14, 2015

Feb. 14, 2015

Just to make sure: Do you try to import skimage from within the scikit-image source directory? > On Feb 14, 2015, at 12:21 PM, James Jackson <james.a.f.jackson.2(a)googlemail.com> wrote: > > Just tinkering, I wondered if this was related to having multiple versions of Python installed. When auto-config / build scripts are being run I always have a niggling feeling of unease in a multiple-version environment. Looking at the multi-version support in OS X, I came across this nugget to set a global default version to execute: > > sudo defaults write /Library/Preferences/com.apple.versioner.python Version 2.7 > > It looks like the modules are now importing properly. Perhaps worth adding to the install page as a Mac OS X note? > > Yours, > James. > > On Sat, Feb 14, 2015 at 6:17 PM, James Jackson <james.a.f.jackson.2(a)googlemail.com> wrote: > Josh, > > Thanks for the reply - I've just installed cython using the requirements file so should be up-to-date. Looking back at my install log, it seems I've got the latest (0.22). > > Collecting cython>=0.21 (from -r requirements.txt (line 1)) > Downloading Cython-0.22-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7MB) > > Looking in the site-packages directory I do see a _hough_transform library: > > James-Jacksons-MacBook-Air:transform jamesjackson$ pwd > /Library/Python/2.7/site-packages/skimage/transform > James-Jacksons-MacBook-Air:transform jamesjackson$ ll | grep hough > -rwxr-xr-x 1 root wheel 659580 14 Feb 09:41 _hough_transform.so > -rw-r--r-- 1 root wheel 5566 14 Feb 09:41 hough_transform.py > -rw-r--r-- 1 root wheel 5044 14 Feb 09:41 hough_transform.pyc > > So something funny is clearly going on here with it not being picked up... > > Yours, > James. > > On Sat, Feb 14, 2015 at 5:51 PM, Josh Warner <silvertrumpet999(a)gmail.com> wrote: > Hi James, > > These are Cython modules that aren't being found or are not properly compiling. Please let us know what version of Cython you are running. > > Rest assured the modules are there. These are not external dependencies. I suspect an old version of Cython is to blame. > > > Regards, > > > > On Saturday, February 14, 2015 at 7:35:31 AM UTC-7, james.a.f...(a)googlemail.com wrote: > > Hi, > > > > > > I'm trying to install skimage, and having installed the dependencies (from requirements.txt in the source release), and then using pip to install skimage itself, I am having problems importing the transform library: > > > > > > > > Python 2.7.2 (default, Oct 11 2012, 20:14:37) > > [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin > > Type "help", "copyright", "credits" or "license" for more information. > > >>> import skimage.data > > >>> import skimage.transform > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > File "skimage/transform/__init__.py", line 1, in <module> > > from ._hough_transform import (hough_ellipse, hough_line, > > ImportError: No module named _hough_transform > > > > > > This is on Mac OSX 10.8.4 with Python 2.7.2. Is this an external library that needs installing from somewhere else? I have already had to install tifffile separately to get skimage.data working (perhaps should be added to requirements.txt?). I've tried a variety of approaches, but haven't had any success. > > > > > > Any and all advice welcome! > > > > > > Yours, > > James. > > -- > You received this message because you are subscribed to a topic in the Google Groups "scikit-image" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/scikit-image/anOjoI4jW-w/unsubscribe. > To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > > > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout.

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Re: Install difficulties - No module named _hough_transform
by James Jackson Feb. 14, 2015

Feb. 14, 2015

Just tinkering, I wondered if this was related to having multiple versions of Python installed. When auto-config / build scripts are being run I always have a niggling feeling of unease in a multiple-version environment. Looking at the multi-version support in OS X, I came across this nugget to set a global default version to execute: sudo defaults write /Library/Preferences/com.apple.versioner.python Version 2.7 It looks like the modules are now importing properly. Perhaps worth adding to the install page as a Mac OS X note? Yours, James. On Sat, Feb 14, 2015 at 6:17 PM, James Jackson < james.a.f.jackson.2(a)googlemail.com> wrote: > Josh, > > Thanks for the reply - I've just installed cython using the requirements > file so should be up-to-date. Looking back at my install log, it seems > I've got the latest (0.22). > > Collecting cython>=0.21 (from -r requirements.txt (line 1)) > Downloading > Cython-0.22-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl > (3.7MB) > > Looking in the site-packages directory I do see a _hough_transform library: > > James-Jacksons-MacBook-Air:transform jamesjackson$ pwd > /Library/Python/2.7/site-packages/skimage/transform > James-Jacksons-MacBook-Air:transform jamesjackson$ ll | grep hough > -rwxr-xr-x 1 root wheel 659580 14 Feb 09:41 _hough_transform.so > -rw-r--r-- 1 root wheel 5566 14 Feb 09:41 hough_transform.py > -rw-r--r-- 1 root wheel 5044 14 Feb 09:41 hough_transform.pyc > > So something funny is clearly going on here with it not being picked up... > > Yours, > James. > > On Sat, Feb 14, 2015 at 5:51 PM, Josh Warner <silvertrumpet999(a)gmail.com> > wrote: > >> Hi James, >> >> These are Cython modules that aren't being found or are not properly >> compiling. Please let us know what version of Cython you are running. >> >> Rest assured the modules are there. These are not external dependencies. >> I suspect an old version of Cython is to blame. >> >> >> Regards, >> >> >> >> On Saturday, February 14, 2015 at 7:35:31 AM UTC-7, >> james.a.f...(a)googlemail.com wrote: >> > Hi, >> > >> > >> > I'm trying to install skimage, and having installed the dependencies >> (from requirements.txt in the source release), and then using pip to >> install skimage itself, I am having problems importing the transform >> library: >> > >> > >> > >> > Python 2.7.2 (default, Oct 11 2012, 20:14:37) >> > [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on >> darwin >> > Type "help", "copyright", "credits" or "license" for more information. >> > >>> import skimage.data >> > >>> import skimage.transform >> > Traceback (most recent call last): >> > File "<stdin>", line 1, in <module> >> > File "skimage/transform/__init__.py", line 1, in <module> >> > from ._hough_transform import (hough_ellipse, hough_line, >> > ImportError: No module named _hough_transform >> > >> > >> > This is on Mac OSX 10.8.4 with Python 2.7.2. Is this an external >> library that needs installing from somewhere else? I have already had to >> install tifffile separately to get skimage.data working (perhaps should be >> added to requirements.txt?). I've tried a variety of approaches, but >> haven't had any success. >> > >> > >> > Any and all advice welcome! >> > >> > >> > Yours, >> > James. >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/anOjoI4jW-w/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > >

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Install difficulties - No module named _hough_transform
by james.a.f.jackson.2＠googlemail.com Feb. 14, 2015

Feb. 14, 2015

Hi, I'm trying to install skimage, and having installed the dependencies (from requirements.txt in the source release), and then using pip to install skimage itself, I am having problems importing the transform library: Python 2.7.2 (default, Oct 11 2012, 20:14:37) [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import skimage.data >>> import skimage.transform Traceback (most recent call last): File "<stdin>", line 1, in <module> File "skimage/transform/__init__.py", line 1, in <module> from ._hough_transform import (hough_ellipse, hough_line, ImportError: No module named _hough_transform This is on Mac OSX 10.8.4 with Python 2.7.2. Is this an external library that needs installing from somewhere else? I have already had to install tifffile separately to get skimage.data working (perhaps should be added to requirements.txt?). I've tried a variety of approaches, but haven't had any success. Any and all advice welcome! Yours, James.

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Google Summer of Code 2015
by Stefan van der Walt Feb. 8, 2015

Feb. 8, 2015

Hi everyone It's almost time to submit project outlines for Google Summer of Code projects, so please make suggestions here or update the wiki at https://github.com/scikit-image/scikit-image/wiki/GSoC-2015 Thanks! Stéfan

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Transparent output
by Marcel Gutsche Feb. 6, 2015

Feb. 6, 2015

Hi all, I'm not sure if it is a bug, or whether I've just overlooked something obvious, but the internet did not offer much regarding this issue. I try to get slices from an image cube which consists of several images s = 1,...,n with the same dimensions. My new slice should have the width of the original images and the height of the number of images. Here is the code to do this: from skimage.io import ImageCollection, imsave from os.path import join import numpy as np def main(dir): ic = ImageCollection( join(dir, '*.png' ) ) row = 0 img = np.empty((len(ic), ic[0].shape[1], ic[0].shape[2] ) ) for s in range(len(ic)): img[s,...] = ic[s][row,...] # fname = 'new_{0:03d}.jpg'.format(v) # -> wrong colors fname = 'new_{0:03d}.png'.format(v) # -> output image is transparent imsave(fname, img) The problem is that the output images are all transparent. My input files are .png images with an alpha channel. I have also checked the values of the alpha channel of the output which are all set to 255, which, at least to my knowledge, should set the opacity to 100%. Regards, Marcel

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Interactive Mona Lisa Demo
by Adam Hughes Feb. 5, 2015

Feb. 5, 2015

Hey everyone, I made an interactive demo for a class I'm TAing where the user loads an image (default is mona lisa prado) and they can dynamically change HSV or RGB values with sliders, and the altered image is updated in realtime. The point of this excercise is to try to mimic the fading of the mona lisa prado colors into the tinged yellow version of the original Mona Lisa on display today. This program uses TraitsUI and Chaco for its interactivity, so probably isn't of direct use for the image viewer; however, in the spirit of interactive examples, I thought it would be cool to share. It was much easier to get Chaco and play nicely with image data than I thought it would be. /home/glue/Desktop/monolisa.tar.gz *Note: this will be very slow if you use the high-res version of the mona lisa prado, so please start by trying the lowres files*. Requirements: scikit-image numpy chaco traits traitsui enable

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Labels on GitHub issues
by Stefan van der Walt Feb. 5, 2015

Feb. 5, 2015

Hi all Our current set of GitHub labels are not utilized, probably because they don't make much sense i.t.o. our workflow. If you've seen any good usage patterns for labels out there, i.e. ways we can use them to improve our development process, please let me know. Thanks Stéfan

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Image viewer plugin, refreshing low and high values of the slider widget
by Marcel Gutsche Feb. 4, 2015

Feb. 4, 2015

Hi folks, another image viewer plugin related question. Is it possible to update the low and high values of the slider widget based on the return values of plugin function? E.g something like this? custom_plugin = Plugin(image_filter = calc_and_show) custom_plugin += Slider('parameter1', low = calc_and_show.lower_bound(), high = calc_and_show.upper_bound() ) Thanks for the great support so far! Marcel

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