Mailman 3 May 2011 - scikit-image

FreeImage_GetPitch not found (on Win7 x64)
by Dan Farmer 31 May '11

31 May '11

I see there has been some recent activity on Windows issues in the last few days, but I didn't see anything exactly related to this issue, so I opened ticket: https://github.com/stefanv/scikits.image/issues/22 (I only mention this because I don't know if anyone besides Stefan gets notified when an issue is created). The traceback and other details are in the issue on github. I tried manually loading FreeImage.dll using ctypes in an ipython session and had the same issue, checking FreeImage's header file shows that the function should be there though. Anyone have any ideas on what else I can try? Thanks, Dan

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total variation denoising
by Emmanuelle Gouillart 31 May '11

31 May '11

Dear all, I finally found some time to do some polishing on the TV denoising code that MaÃ¯Â¿Â½l had written a while ago. I added a new module to my branch https://github.com/emmanuelle/scikits.image/tree/tv_denoise (https://github.com/emmanuelle/scikits.image/blob/tv_denoise/scikits/image/f…). I'd like to have your opinion on how the code could be improved before a pull request. Cheers, Emmanuelle

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Re: Re : Re: Re : Re: multispectral imaging: rgb image
by Stéfan van der Walt 24 May '11

24 May '11

Hi Jean-Patrick 2011/5/23 jip <jeanpatrick.pommier(a)gmail.com>: > Hi > I have written a simpler script without linear algebra. In the attached version I tried to clean up the script to avoid code repetition. Regards Stéfan

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Re : Re: Re : Re: multispectral imaging: rgb image
by jip 23 May '11

23 May '11

Hi I have written a simpler script without linear algebra<http://dip4fish.blogspot.com/2011/05/making-mfish-image.html> . Jean-Patrick

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Re: Re : Re: multispectral imaging: rgb image
by Zachary Pincus 22 May '11

22 May '11

> red=c3_r.reshape(c3,shape) > TypeError: only length-1 arrays can be converted to Python scalars I assume you want red = c3_r.reshape(c3.shape) ? The method signature for the reshape method of numpy.ndarray is: ndarray.reshape(shape, order='C')

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multispectral imaging: rgb image
by jip 20 May '11

20 May '11

Dear all, Is there something available in scikits-image to produce a rgb image from a 4 or more channels multispectral<http://dip4fish.blogspot.com/2011/05/mfish-image-to-rgb-with-image5d.html>image? Thanks Jean-Patrick

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PyOpenCL computing backend
by Stéfan van der Walt 18 May '11

18 May '11

Hi all, As you may know, we now have a GSoC student working on a new backend engine for scikits.image: http://pythonimaging.blogspot.com/2011/04/gsoc2011.html One of these will be a PyOpenCL-backend, which I hope will be able to leverage this PyOpenCL-subproject: https://github.com/inducer/compyte Cheers Stéfan

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Scikits.image convore forum
by Chris Colbert 17 May '11

17 May '11

I've created a Convore forum for scikits.image https://convore.com/scikitsimage/ Just request membership and I'll approve you.

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Re: Cython on windows (again?)
by Dan Farmer 16 May '11

16 May '11

So I was able to resolve this. In EPD the cython.py file is located in site-packages, but cython.exe evidently expects it to be in Scripts. So I moved cython.py to c:\Python27\Scripts and it worked (incidentally, I compared this to python x,y and it defaults to putting cython.py in Scripts, so scikits.image builds out of the box with python x,y on windows). I don't know distutils well enough to say if something should change on the scikits.image side or if Enthought just needs to tweak their setup. Unfortunately that's not the end of the issues, but I'll send a separate email for future Google searchers. Thanks, Dan On Thu, May 12, 2011 at 8:53 AM, Dan Farmer <dfarmernv(a)gmail.com> wrote: > Hi Guys, > So the semester is over and I'm starting to gear back up (sorry for dropping > off the map for bit :( ). Since my last work on the project I got a new > computer so I'm now working in Windows using EPD 7. I checked everything out > last night and updated, but when I tried to build in place I get the > traceback below. EPD 7 does come with cython 0.14.1 > Any ideas to help me get up and running again? > Thanks, > Dan > cython -o C:\source\scikits.image\scikits\image\opencv\opencv_backend.c.new > C:\source\scikits.image\scikits\image\opencv\opencv_backend.pyx > Cython compilation of opencv_backend.pyx failed. Falling back on > pre-generated file. > python.exe : C:\Python27\python.exe: can't open file > 'C:\Python27\Scripts\cython.py': [Errno 2] No such file or directory > > Traceback (most recent call last): > File "setup.py", line 97, in <module> > cmdclass={'build_py': build_py}, > File "C:\Python27\lib\site-packages\numpy\distutils\core.py", line 152, in > setup > config = configuration() > File "setup.py", line 44, in configuration > config.add_subpackage(DISTNAME) > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 972, in add_subpackage > caller_level = 2) > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 941, in get_subpackage > caller_level = caller_level + 1) > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 878, in _get_configuration_from_s > etup_py > config = setup_module.configuration(*args) > File "scikits\image\setup.py", line 8, in configuration > config.add_subpackage('opencv') > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 972, in add_subpackage > caller_level = 2) > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 941, in get_subpackage > caller_level = caller_level + 1) > File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line > 878, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "scikits\image\opencv\setup.py", line 20, in configuration > cython(cython_files, working_path=base_path) > File "C:\source\scikits.image\scikits\image\_build.py", line 51, in cython > os.remove(c_file_new) > WindowsError: [Error 2] The system cannot find the file specified: > 'C:\\source\\scikits.image\\scikits\\ima > ge\\opencv\\opencv_backend.c.new'

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Cython on windows (again?)
by Dan Farmer 12 May '11

12 May '11

Hi Guys, So the semester is over and I'm starting to gear back up (sorry for dropping off the map for bit :( ). Since my last work on the project I got a new computer so I'm now working in Windows using EPD 7. I checked everything out last night and updated, but when I tried to build in place I get the traceback below. EPD 7 does come with cython 0.14.1 Any ideas to help me get up and running again? Thanks, Dan cython -o C:\source\scikits.image\scikits\image\opencv\opencv_backend.c.new C:\source\scikits.image\scikits\image\opencv\opencv_backend.pyx Cython compilation of opencv_backend.pyx failed. Falling back on pre-generated file. python.exe : C:\Python27\python.exe: can't open file 'C:\Python27\Scripts\cython.py': [Errno 2] No such file or directory Traceback (most recent call last): File "setup.py", line 97, in <module> cmdclass={'build_py': build_py}, File "C:\Python27\lib\site-packages\numpy\distutils\core.py", line 152, in setup config = configuration() File "setup.py", line 44, in configuration config.add_subpackage(DISTNAME) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 972, in add_subpackage caller_level = 2) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 878, in _get_configuration_from_s etup_py config = setup_module.configuration(*args) File "scikits\image\setup.py", line 8, in configuration config.add_subpackage('opencv') File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 972, in add_subpackage caller_level = 2) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scikits\image\opencv\setup.py", line 20, in configuration cython(cython_files, working_path=base_path) File "C:\source\scikits.image\scikits\image\_build.py", line 51, in cython os.remove(c_file_new) WindowsError: [Error 2] The system cannot find the file specified: 'C:\\source\\scikits.image\\scikits\\ima ge\\opencv\\opencv_backend.c.new'

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