Mailman 3 December 2011 - scikit-image

Re: Feature requests for 0.5
by Nelle Varoquaux Dec. 6, 2011

Dec. 6, 2011

Hi Stéfan, I have a Harris affine region detector I'd like to integrate, and potentially a panorama stitching example using hogs and harris I'd like to integrate (might be slightly to complicated for the user guide ?). It's work in progress, but I should have time to work on that during the christmas holidays. Cheers, Nelle 2011/12/6 Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi all, > > With 0.4 (and 0.4.1, 0.4.2) out the door, we can start setting > priorities for 0.5. > > Personally, I'd like to see > > - An expansion of the user guide > - Completion of the Debian packaging > - Object convex hulls and > - Graph cut segmentation and/or tri-mapping > > Feel free to weigh in with your own suggestions, then we'll come to an > agreement on the best way forward. > > Regards > Stéfan

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Feature requests for 0.5
by Stéfan van der Walt Dec. 5, 2011

Dec. 5, 2011

Hi all, With 0.4 (and 0.4.1, 0.4.2) out the door, we can start setting priorities for 0.5. Personally, I'd like to see - An expansion of the user guide - Completion of the Debian packaging - Object convex hulls and - Graph cut segmentation and/or tri-mapping Feel free to weigh in with your own suggestions, then we'll come to an agreement on the best way forward. Regards Stéfan

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Re: io plugin issue (8bits 16bits)
by Christoph Gohlke Dec. 5, 2011

Dec. 5, 2011

On 12/5/2011 1:52 PM, StÃ¯Â¿Â½fan van der Walt wrote: > On Mon, Dec 5, 2011 at 1:20 PM, jip<jeanpatrick.pommier(a)gmail.com> wrote: >> I joined an image with that message. > Thanks, JP. This allowed me to narrow down the problem. We currently > do not have logic to support PIL Tiff objects, so they end up embedded > in an object array. > > In the meantime, the matplotlib plugin does work for me: > > import skimage.io as sio > sio.use_plugin('matplotlib') > img = sio.imread('1.tiff') > > Cheers > StÃ¯Â¿Â½fan > Hello, Matplotlib's imread uses PIL and also does not read 16 bit TIFFs correctly. The FreeImage, Qt, and GDAL plugins do. With scikits-image 0.4.2, the following works correctly for me on Windows: import skimage.io skimage.io.use_plugin('freeimage') skimage.io.use_plugin('matplotlib') image = skimage.io.imread('1.tif', plugin='freeimage') skimage.io.imshow(image, cmap='gray') skimage.io.show() skimage.io.use_plugin is somewhat broken (I think). It replaces all previously defined default imread, imwrite, and imshow functions, regardless whether a `kind` argument is provided. For example: skimage.io.use_plugin('freeimage', 'imread') skimage.io.use_plugin('matplotlib', 'imshow') the second call replaces freeimage.imread as the default imread function with matplotlib.imread. Christoph

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Re: io plugin issue (8bits 16bits)
by jip Dec. 5, 2011

Dec. 5, 2011

dear Stéfan, I joined an image with that message. <https://docs.google.com/open?id=0B-YDFMbEy1grYTMzMGRiZDUtNzk2OC00YTAwLTk5NT…> Le lundi 5 décembre 2011 20:08:36 UTC+1, Stefan van der Walt a écrit : > > Hi JP > > Thanks for finding this issue. Would you mind placing a small 12-bit tiff > online somewhere so that I can use it in the test suite? > > It's strange that the matplotlib plugin is not available, since you > mention that you have pylab. Can you import matplotlib without problems? > I can use pylab if the image is loaded with readmagick. I can check skimage.io on an other configuration. Best regards Jean-Patrick > >> >>

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Nowozin
by Andreas Müller Dec. 5, 2011

Dec. 5, 2011

Hi everybody. Sorry I didn't have much time to contribute. Does anyone of you know this library: http://www.nowozin.net/sebastian/tuwo/ It is a C++ computer vision library under MIT license and contains many great features. Maybe it is worth looking into. Cheers, Andy

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Re: io plugin issue (8bits 16bits)
by Stéfan van der Walt Dec. 5, 2011

Dec. 5, 2011

Hi JP Thanks for finding this issue. Would you mind placing a small 12-bit tiff online somewhere so that I can use it in the test suite? It's strange that the matplotlib plugin is not available, since you mention that you have pylab. Can you import matplotlib without problems? Regards Stéfan On Dec 5, 2011 5:30 AM, "jip" <jeanpatrick.pommier(a)gmail.com> wrote: > Dear all, > > I meet some problem to open/display 12bits tif (16 bits) gray images. > I can open an image but I fail to display it: > import skimage > path='/media/Elements__/Science/Biologie/QTeloFISH/myoblastes > HPS/JPP55_nFF/16/DAPI' > image='/1.tif' > from skimage import io as io > > print skimage.io.plugin_info('matplotlib') > #skimage.io.use_plugin('matplotlib', 'read') > > #dapi=io.imread(path+image,plugin='matplotlib') > dapi=io.imread(path+image) > > print type(dapi) > print type(dapi) > print 'dapi.dtype',dapi.dtype > > io.imshow(dapi) > #import pylab > #pylab.imshow(dapi) > #pylab.show() > Then I get the following error: > *<type 'numpy.ndarray'> > <type 'numpy.ndarray'> > dapi.dtype object > Traceback (most recent call last): > File "/home/claire/.spyder2/.temp.py", line 28, in <module> > io.imshow(dapi) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", > line 149, in imshow > return call_plugin('imshow', arr, plugin=plugin, **plugin_args) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", > line 88, in call > return func(*args, **kwargs) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", > line 108, in imshow > Image.fromarray(arr).show() > File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in > fromarray > raise TypeError("Cannot handle this data type") > TypeError: Cannot handle this data type > * > The default plugin is PIL.If I try to switch to matplotlib (or freeimage), > the plugin doesn't seem available: > *Traceback (most recent call last): > File "/home/claire/.spyder2/.temp.py", line 16, in <module> > dapi=io.imread(path+image,plugin='matplotlib') > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", > line 72, in imread > img = call_plugin('imread', fname, plugin=plugin, **plugin_args) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", > line 86, in call > (plugin, kind)) > RuntimeError: Could not find the plugin "matplotlib" for imread.* > I can open the same image with plugin='pil' but I fail to display it: > *uint16 > (1024, 1536) > Traceback (most recent call last): > File "/home/claire/.spyder2/.temp.py", line 28, in <module> > io.imshow(dapi0) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", > line 149, in imshow > return call_plugin('imshow', arr, plugin=plugin, **plugin_args) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", > line 88, in call > return func(*args, **kwargs) > File > "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", > line 108, in imshow > Image.fromarray(arr).show() > File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in > fromarray > raise TypeError("Cannot handle this data type") > TypeError: Cannot handle this data type* > > Does io.imshow() support only 8bits image? > > I can open and display the image with readmagick/pylab. > > Best regards > Jean-Patrick > > >

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io plugin issue (8bits 16bits)
by jip Dec. 5, 2011

Dec. 5, 2011

Dear all, I meet some problem to open/display 12bits tif (16 bits) gray images. I can open an image but I fail to display it: import skimage path='/media/Elements__/Science/Biologie/QTeloFISH/myoblastes HPS/JPP55_nFF/16/DAPI' image='/1.tif' from skimage import io as io print skimage.io.plugin_info('matplotlib') #skimage.io.use_plugin('matplotlib', 'read') #dapi=io.imread(path+image,plugin='matplotlib') dapi=io.imread(path+image) print type(dapi) print type(dapi) print 'dapi.dtype',dapi.dtype io.imshow(dapi) #import pylab #pylab.imshow(dapi) #pylab.show() Then I get the following error: *<type 'numpy.ndarray'> <type 'numpy.ndarray'> dapi.dtype object Traceback (most recent call last): File "/home/claire/.spyder2/.temp.py", line 28, in <module> io.imshow(dapi) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", line 149, in imshow return call_plugin('imshow', arr, plugin=plugin, **plugin_args) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 88, in call return func(*args, **kwargs) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", line 108, in imshow Image.fromarray(arr).show() File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in fromarray raise TypeError("Cannot handle this data type") TypeError: Cannot handle this data type * The default plugin is PIL.If I try to switch to matplotlib (or freeimage), the plugin doesn't seem available: *Traceback (most recent call last): File "/home/claire/.spyder2/.temp.py", line 16, in <module> dapi=io.imread(path+image,plugin='matplotlib') File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", line 72, in imread img = call_plugin('imread', fname, plugin=plugin, **plugin_args) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 86, in call (plugin, kind)) RuntimeError: Could not find the plugin "matplotlib" for imread.* I can open the same image with plugin='pil' but I fail to display it: *uint16 (1024, 1536) Traceback (most recent call last): File "/home/claire/.spyder2/.temp.py", line 28, in <module> io.imshow(dapi0) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", line 149, in imshow return call_plugin('imshow', arr, plugin=plugin, **plugin_args) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", line 88, in call return func(*args, **kwargs) File "/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", line 108, in imshow Image.fromarray(arr).show() File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in fromarray raise TypeError("Cannot handle this data type") TypeError: Cannot handle this data type* Does io.imshow() support only 8bits image? I can open and display the image with readmagick/pylab. Best regards Jean-Patrick

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Re: scikits-image 0.4 release
by Emmanuelle Gouillart Dec. 5, 2011

Dec. 5, 2011

Very cool :-). I was very excited to talk about the new release during my talk at Scipy India (a few hours ago), thanks for the opportunity to advertise the release! During questions, I was asked if during the sprint, it would be possible to contribute to the Debian/Ubuntu packaging. I don't know the status of the packaging, and if something could be done to help with the packaging. What should I answer to the person who asked about packaging? Cheers, Emmanuelle On Sat, Dec 03, 2011 at 02:42:41PM -0800, StÃ¯Â¿Â½fan van der Walt wrote: > Announcement: scikits-image 0.4 > =============================== > We're happy to announce the 0.4 release of scikits-image, an image processing > toolbox for SciPy. > Please visit our examples gallery to see what we've been up to: > http://scikits-image.org/docs/0.3/auto_examples/ > Note that, in this release, we renamed the module from ``scikits.image`` to > ``skimage``, to work around name space conflicts with other scikits (similarly, > the machine learning scikit is now imported as ``sklearn``). > A big shout-out also to everyone currently at SciPy India; have fun, and > remember to join the scikits-image sprint! > This release runs under all major operating systems where Python (>=2.6 or > 3.x), NumPy and SciPy can be installed. > For more information, visit our website > http://scikits-image.org > New Features > ------------ > - Module rename from ``scikits.image`` to ``skimage`` > - Contour finding > - Grey-level co-occurrence matrices > - Skeletonization and medial axis transform > - Convex hull images > - New test data sets > - GDAL I/O plugin > ... as well as some bug fixes. > Contributors to this release > ---------------------------- > * Andreas Mueller > * Christopher Gohlke > * Emmanuelle Gouillart > * Neil Yager > * Nelle Varoquaux > * Riaan van den Dool > * Stefan van der Walt > * Thouis (Ray) Jones > * Tony S Yu > * Zachary Pincus

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Re: scikits-image 0.4 release
by jip Dec. 4, 2011

Dec. 4, 2011

Thank you, I just upgrade Jean-Patrick Pommier

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sprint @Scipy India on Thursday 8th
by Emmanuelle Gouillart Dec. 3, 2011

Dec. 3, 2011

Hi all, the day for sprints at Scipy India is next Thursday (Dec 8th). How about having a skimage sprint during this day? Tomorrow is the first day of the conference, I'll try to see if some attendees could be interested. If some people here use image processing for their work, I'll try to make them write examples about their usecases. I'm only catching up after two weeks of travelling in India, but I'll try to make more precise suggestions for the sprint in the next few days. Anyone interested in joining in? Cheers, Emmanuelle

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