Mailman 3 January 2012 - scikit-image

Re: io.plugins freeimage installation issue?
by Christoph Gohlke 26 Jan '12

26 Jan '12

On 1/26/2012 6:10 AM, Sigmund wrote: > First, thank you for your answer! > > Since I'm not in my office today I tried to do the same at my BootCamp > Win 7 64 Partition. Here I encountered a new problem. > If I run the "test_freeimage.py" I get the error that the "OSError: > Could not find libFreeImage in any of the following directories:"(full > error output below). But I'm sure that it is in the right folder and > that "python_freeimage.py" is looking in the right pace. How can that > be? > First idea was that "sys.platform" is returning "win64" instead of > "win32" but it isn't. I also tried changing the case of the > "FreeImage.dll" but didn't help. So as far I could check, everything > is going right, but it is still not taking the FreeImage.dll. > > Running it on the BootCamp machine is not necessary for me but it > might be of interest for you. > > I will get back to the first post tomorrow. > > By the way, it might be better and I think easy to change if the error > "OSError: Could not find libFreeImage in any of the following > directories:" is using the OS specific library name. Thats easier to > understand for people like me that not relay know what they are doing. > > """ > OSError: Could not find libFreeImage in any of the following > directories: 'C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- > win-amd64.egg\skimage\io\_plugins', '/lib', '/usr/lib', '/usr/local/ > lib', '/opt/local/lib', 'C:\Users\Siggi\lib' > """ > > > > Siggi > You are running a 64 bit version of Python. Please verify that the FreeImage.dll is also 64 bit. You may want to try scikits-image-0.4.2.win-amd64-py2.7.exe from <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits-image>, which includes a 64 bit FreeImage.dll. Christoph

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Re: io.plugins freeimage installation issue?
by Zachary Pincus 26 Jan '12

26 Jan '12

> Since I'm not in my office today I tried to do the same at my BootCamp > Win 7 64 Partition. Here I encountered a new problem. > If I run the "test_freeimage.py" I get the error that the "OSError: > Could not find libFreeImage in any of the following directories:"(full > error output below). But I'm sure that it is in the right folder and > that "python_freeimage.py" is looking in the right pace. How can that > be? That is indeed odd. You're certain that FreeImage.dll is in: C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7-win-amd64.egg\skimage\io\_plugins Could you pop up a command window and paste the following in, just to double-check: dir C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7-win-amd64.egg\skimage\io\_plugins > By the way, it might be better and I think easy to change if the error > "OSError: Could not find libFreeImage in any of the following > directories:" is using the OS specific library name. Thats easier to > understand for people like me that not relay know what they are doing. > > """ > OSError: Could not find libFreeImage in any of the following > directories: 'C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- > win-amd64.egg\skimage\io\_plugins', '/lib', '/usr/lib', '/usr/local/ > lib', '/opt/local/lib', 'C:\Users\Siggi\lib' > """ Definitely. All of the FreeImage loading stuff is still far too *NIX specific, in the search paths and also the errors. I'll try to fix that up. Zach

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Re: Need an advice
by David 26 Jan '12

26 Jan '12

On Jan 14, 1:34 am, Stéfan van der Walt <ste...(a)sun.ac.za> wrote: > On Sun, Jan 1, 2012 at 11:02 PM, Nadav Horesh <nadavh.hor...(a)gmail.com> wrote: > > Shouldn't be a way to copy compilation flags from pythonx.x/config/Makefile? > > I think (not sure) that numpy does it. > > I've CCd David Cournapeau on this e-mail; I think he'll be able to > recommend the best route forward > (David, the full message is here:http://groups.google.com/group/scikits-image/browse_thread/thread/a2d... > ). > > One alternative is to simply try the compilation, first with the fast > math flag, then without, and then have a conditional import in the > code that loads whatever survives the compilation process (with > ndimage's convolve as a backup). I would advise against using -ffast-math, which really should be called -funsafe-math. We removed it in scipy some time ago as it had the annoying property of giving completely borked results. David

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io.plugins freeimage installation issue?
by Sigmund 26 Jan '12

26 Jan '12

Hallo! I'm using the freeimage plugin for reading uint8 and float32 Grey- scale TIFF files. The aim is some basic x-ray diffraction image processing. The development is done on MacOSX but some users are Win users. To make it short. The freeimage imread on Windows isn't working. Since it is working on the Mac and I had a hard time getting freeimage installed. I think I might have done something wrong during installation. The readme file from FreeImage didn't help much. So some questions: 1. Do I have to build the freeimage.dll or can I just use the compiled one? (didn't make it to compile) 2. Is just dropping the .dll in the _plugins Folder all I need to do? (thats basically all I did after trying 1. all day) I ended up with having a successful run of the test_freeimage.py and a ValueError for the TIFF files on the Windows machin. Error output: File "00PeakWIN.py", line 32, in <module> img_for_dimentions = array(io.imread(bild, plugin="freeimage" ), dtype=int) File "C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- win32.egg\skimage\io\_io.py", line 72, in imread img = call_plugin('imread', fname, plugin=plugin, **plugin_args) File "C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- win32.egg\skimage\io\_plugins\plugin.py", line 88, in call return func(*args, **kwargs) File "C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- win32.egg\skimage\io\_plugins\freeimage_plugin.py", line 512, in imread img = read(filename) File "C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- win32.egg\skimage\io\_plugins\freeimage_plugin.py", line 282, in read bitmap = _read_bitmap(filename, flags) File "C:\Python27\lib\site-packages\scikits_image-0.4.2-py2.7- win32.egg\skimage\io\_plugins\freeimage_plugin.py", line 326, in _read_bitmap raise ValueError('Cannot determine type of file %s' % filename) ValueError: Cannot determine type of file E Thanks! Siggi

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Re: Need an advice
by Stéfan van der Walt 14 Jan '12

14 Jan '12

On Sun, Jan 1, 2012 at 11:02 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> wrote: > Shouldn't be a way to copy compilation flags from pythonx.x/config/Makefile? > I think (not sure) that numpy does it. I've CCd David Cournapeau on this e-mail; I think he'll be able to recommend the best route forward (David, the full message is here: http://groups.google.com/group/scikits-image/browse_thread/thread/a2d4edb98… ). One alternative is to simply try the compilation, first with the fast math flag, then without, and then have a conditional import in the code that loads whatever survives the compilation process (with ndimage's convolve as a backup). Stéfan

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Re: Harris corner detection (#106)
by Stéfan van der Walt 11 Jan '12

11 Jan '12

On Mon, Jan 9, 2012 at 8:34 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > In any case, I've merged Nelle's corner detection PR, and I've created a new > PR with peak detection factored out. There's a couple open questions, which > I've added as comments on the PR. Thanks for taking care of that, Tony. I'll review the new PRs. Cheers Stéfan

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Re: Adding images to the repository for panorama stitching
by Stéfan van der Walt 10 Jan '12

10 Jan '12

Hi Nelle On Tue, Jan 10, 2012 at 12:36 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > I was working on the panorama stitching example, and adding images to the > repository > (https://github.com/NelleV/scikits.image/commit/50ff69389bc3458eb1cfb263d147…). Out of curiosity, what methods are you implementing? I have some panorama stitching related code that may come in handy. > Talking with Gaël about this, I realized it probably wasn't the best idea to > clutter the repository with images probably no one else will use. > In scikit-learn, data used for examples is downloaded from internet only > when used,, and stored in the user home folder. > > What do you think about implementing this for skimage ? We definitely don't want to clutter the git repo with too much data (we've been very careful in choosing the images in the data and testing modules). If we implement this, we should do it such that packaging systems like Debian can easily modify the data path (e.g., they may want to package python-skimage-data). Do the learn guys already have a caching system in place? Whatever solution we provide, a user should be able to download the files manually as well (otherwise, with Python's poor proxy support, people are going to run into problems). Stéfan

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Adding images to the repository for panorama stitching
by Nelle Varoquaux 10 Jan '12

10 Jan '12

Hi everyone, I was working on the panorama stitching example, and adding images to the repository ( https://github.com/NelleV/scikits.image/commit/50ff69389bc3458eb1cfb263d147… ). Talking with Gaël about this, I realized it probably wasn't the best idea to clutter the repository with images probably no one else will use. In scikit-learn, data used for examples is downloaded from internet only when used,, and stored in the user home folder. What do you think about implementing this for skimage ? Thanks, N

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Re: Harris corner detection (#106)
by Tony Yu 10 Jan '12

10 Jan '12

On Mon, Jan 9, 2012 at 1:55 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com>wrote: > > 2012/1/9 Stéfan van der Walt <stefan(a)sun.ac.za> > >> On Mon, Jan 9, 2012 at 8:05 AM, Tony Yu <tsyu80(a)gmail.com> wrote: >> > You know what: I think I'm just going to merge your Harris detection >> pull >> > request as it is now, and then I'll start a new pull request with the >> peak >> > detection part factored out. >> >> I think that's the way to go. Peak detection would be very useful--it >> crops up all over the place. >> > > I indeed thing peak detection would be very useful. I've used it recently > to do segmentation, on handwriting dataset, and face detection, with > probability score associated to a point. > > >> >> I was trying to recall who recently shared a review of peak detection >> algorithms with me, and I think it might have been you :) > > Actually, if you're referring to the review paper [1] I mentioned in my PR for a grayscale reconstruction function, I'm inclined to say that that paper was on spot detection, as opposed to peak detection. I'm not sure if this is an accepted classification, but in my mind: peaks are *pixels* of high intensity, while spots are *regions* of high intensity. The spot detection algorithms described in [1] find regions of high intensity and then look for the centroids of those regions. This distinction between "spot" and "peak" may be artificial---I'm sort of making it up as I go along :) In any case, I've merged Nelle's corner detection PR, and I've created a new PR with peak detection factored out<https://github.com/scikits-image/scikits-image/pull/110>. There's a couple open questions, which I've added as comments on the PR. -Tony [1] Smal, et al., "Quantitative comparison of spot detection methods in fluorescence microscopy", IEEE Trans Med Imaging. (2010) > There are >> so many out there, almost all heuristics. Typically, there are two >> varieties: those that simply consider the input data (e.g., dividing >> the image into windows and choosing the maximum value in each), and >> those that in addition consider other peaks found (e.g., to avoid >> identifying very closely spaced peaks). The problem takes on an >> interesting twist when working with noisy data, where many points seem >> like peaks but aren't. Here, multi-level decompositions such as the >> Gaussian scale space or wavelets are often employed. >> >> Regards >> Stéfan >> >

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Re: Harris corner detection (#106)
by Nelle Varoquaux 09 Jan '12

09 Jan '12

2012/1/9 Stéfan van der Walt <stefan(a)sun.ac.za> > On Mon, Jan 9, 2012 at 8:05 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > You know what: I think I'm just going to merge your Harris detection pull > > request as it is now, and then I'll start a new pull request with the > peak > > detection part factored out. > > I think that's the way to go. Peak detection would be very useful--it > crops up all over the place. > I indeed thing peak detection would be very useful. I've used it recently to do segmentation, on handwriting dataset, and face detection, with probability score associated to a point. > > I was trying to recall who recently shared a review of peak detection > algorithms with me, and I think it might have been you :) There are > so many out there, almost all heuristics. Typically, there are two > varieties: those that simply consider the input data (e.g., dividing > the image into windows and choosing the maximum value in each), and > those that in addition consider other peaks found (e.g., to avoid > identifying very closely spaced peaks). The problem takes on an > interesting twist when working with noisy data, where many points seem > like peaks but aren't. Here, multi-level decompositions such as the > Gaussian scale space or wavelets are often employed. > > Regards > Stéfan >

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