Mailman 3 April 2013 - scikit-image

Re: multi-page TIFF writer
by Juan Nunez-Iglesias 17 Apr '13

17 Apr '13

On Wed, Apr 17, 2013 at 12:32 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Can you give us a gdb traceback perhaps? > Um, I don't really get one, perhaps cos my Python is not configured properly? Here's the gdb output: In [7]: fr.write_multipage(im, 'image.tif') Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x000000000eb74970 0x0000000107ca8786 in FreeImage_AppendPage () (I've trimmed the start because it's littered with tons of "no debug data for file blah" statements.) Here's all I need to reproduce it: import numpy as npfrom skimage.io._plugins import freeimage_plugin as fr im0 = np.zeros((500, 500, 500), uint8) fr.write_multipage(im0, 'im.tif') Example in iPython: ~ $ ipython --pylab Welcome to pylab, a matplotlib-based Python environment [backend: MacOSX]. For more information, type 'help(pylab)'. In [1]: from skimage.io._plugins import freeimage_plugin as fr In [2]: im0 = np.zeros((500, 500, 500), uint8) In [3]: fr.write_multipage(im0, 'im0.tif') Segmentation fault: 11 Let me know if you get the same result...

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Re: Histogram backprojection
by abid rahman 17 Apr '13

17 Apr '13

I am sorry, what does PR means ? Never heard before. On Wed, Apr 17, 2013 at 2:20 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Abid > > On Tue, Apr 16, 2013 at 3:54 PM, abid rahman <abidrahman2(a)gmail.com> > wrote: > > I have sent a pull request for Histogram backprojection ( sorry for > being a > > little late, It is "exam season" for me in this month). Please review the > > request and let me know if any modifications to be done ( as this is my > > first pull request to scikit-image) > > Thanks for the PR! As you'll notice, you've already had feedback from > two of us. We typically use the PR as a place to converse about the > code until it reaches a state where it can be incorporated into the > project. > > Stéfan > > -- > 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/groups/opt_out. > > > -- Abid K. opencvpython.blogspot.com

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Re: Errors while compiling and $make coverage
by Stéfan van der Walt 16 Apr '13

16 Apr '13

Hi Chintak On Apr 16, 2013 10:00 AM, "Chintak Sheth" <chintaksheth(a)gmail.com> wrote: > > I seem to be getting segmentation fault after running : > > $ python setup.py build_ext -i > $ make coverage > nosetests skimage --with-coverage --cover-package=skimage > make: *** [coverage] Segmentation fault: 11 > > Any ideas why this is happening ? With such little information I can't say. Could you send us a gdb traceback? Stéfan

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Histogram backprojection
by abid rahman 16 Apr '13

16 Apr '13

Hi, I would like to add a feature on histogram backprojection as proposed by *Swain & Michael J.* in their paper *"Indexing via color histograms"*.. Earlier, I had written a simple article on that ( it was focussed for OpenCV) in my blog : http://opencvpython.blogspot.in/2013/03/histograms-4-back-projection.html. I can have some simple modification to it to integrate it into scikit-image. So I would like to know the opinion of senior developers on this proposal. Regards Abid K.

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Bug when using float32 arrays and Lab2Rgb
by Isaac Gerg 16 Apr '13

16 Apr '13

I am doing a LAB to RGB conversion. If my LAB matrix is float64, the bounds for the axes must be -100, 100. Upon analysis of the output RGB image, the results look correct. However, if the LAB matrix is float32 the bounds are checked and forced to -1 1 which yields an RGB image that is incorrect. Upon further inspect, the problem looks like it comes from the convert function in dtype.py. image = np.asarray(image) dtypeobj = np.dtype(dtype) dtypeobj_in = image.dtype dtype = dtypeobj.type dtype_in = dtypeobj_in.type if dtype_in == dtype: if force_copy: image = image.copy() return image at the "if dtype_in == dtype:" the types are float32 and float64 causing the if to be skipped. Eventually the code reaches the point: if kind_in == 'f': if np.min(image) < -1.0 or np.max(image) > 1.0: raise ValueError("Images of type float must be between -1 and 1.") if kind == 'f': # floating point -> floating point if itemsize_in > itemsize: prec_loss() return dtype(image) and the bounds are checked, outside of [-1 1] and an error is thrown. Isaac

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Re: multi-page TIFF writer
by Stéfan van der Walt 16 Apr '13

16 Apr '13

On Tue, Apr 16, 2013 at 6:58 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Thanks all. tifffile.py solved my problem. Stefan, the FreeImage plugin > segfaulted when I fed it my data... =\ Can you give us a gdb traceback perhaps? Stéfan

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Re: multi-page TIFF writer
by Jerome Kieffer 16 Apr '13

16 Apr '13

On Fri, 12 Apr 2013 17:16:46 +0530 Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Hi everyone, > > Do any of you know about *writing* a numpy array to a multi-page TIFF file > in Python? Last time I checked, you could only read those with PIL, not > write. A quick Googling led me to > Tiffany<https://bitbucket.org/pydica/tiffany>, > but it doesn't seem to be particularly numpy-friendly... Have a look at TiffIO from PyMca (or FabIO which are the same) which has this capabilities. Cheers, -- Jerome Kieffer <google(a)terre-adelie.org>

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Re: Morphological techniques
by Ankit Agrawal 16 Apr '13

16 Apr '13

Hi Stefan, Can you please elaborate in brief what is expected from convex_hull_objects functions as compared to the existing convex_hull_image<http://scikit-image.org/docs/dev/auto_examples/plot_convex_hull.html#exampl…>function? Thank you. Regards, Ankit Agrawal, Communication and Signal Processing, IIT Bombay.

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Re: Morphological techniques
by Johannes Schönberger 16 Apr '13

16 Apr '13

Hi Chintak, I am not working on this yet, but I recommend to directly ask for it in the issue thread. Maybe some of the other involved people are already working on it. Johannes Schönberger Am 15.04.2013 um 20:38 schrieb Chintak Sheth <chintaksheth(a)gmail.com>: > Hi Stefan, > > Thanks for the prompt reply. I'll try working on the convex_hull_objects function to start with. And go through IEEE Transactions on IP. > > Actually, I did go through the bugs and in particular was looking at 'Add function to resample arrays by a given factor?' (https://github.com/scikit-image/scikit-image/issues/492), in case no one is working on it already. > > Chintak > > -- > 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/groups/opt_out. > >

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Re: Errors while compiling and $make coverage
by Chintak Sheth 16 Apr '13

16 Apr '13

Hi, I seem to be getting segmentation fault after running : $ python setup.py build_ext -i $ make coverage nosetests skimage --with-coverage --cover-package=skimage make: *** [coverage] Segmentation fault: 11 Any ideas why this is happening ? On Tue, Apr 16, 2013 at 4:19 AM, Ankit Agrawal <aaaagrawal(a)gmail.com> wrote: > Hi Stefan, > > Thanks again, that worked. > > Regards, > Ankit Agrawal > > > On Tue, Apr 16, 2013 at 3:58 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> On Tue, Apr 16, 2013 at 12:27 AM, Ankit Agrawal <aaaagrawal(a)gmail.com> >> wrote: >> > I get these test errors. If I want to test the code before issuing a PR, >> > this will be a problem. Any way to sort it out? Thank you again. >> >> It's because that version is trying to run the tests in-place. To fix >> it, you can also build the modules in-place: >> >> python setup.py build_ext -i >> >> Stéfan >> >> -- >> 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/groups/opt_out. >> >> >> > > > -- > Regards, > Ankit Agrawal, > Senior Undergraduate in Electrical Engineering. > IIT Bombay. > +91 9833427046 > > -- > 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/groups/opt_out. > > >

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