Mailman 3 May 2012 - scikit-image

io.imsave() problems with passing arguments to plugin "freeimage"
by Sigmund 12 Jul '12

12 Jul '12

Hallo! To read uncompressed TIFF files I use the freeimage plugin. The reading works great but since last week I need to save a summed Image. I used the io.imsave() with the freeimage plugin but by default it writs a compressed TIFF file. The freeimage documentation provides Flags to use for different compressions or for a non compressed type (TIFF_NONE). Can someone tell me how to pass theses Flags to the plugin? I saw that Christophs 'tifffile' plugin does the job but still I would like to know how to use the freeimage plug-n for it. Thanks! Siggi

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Re: Test error with tifffile plugin
by Tony Yu 31 May '12

31 May '12

On Wed, May 30, 2012 at 1:25 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Tue, May 29, 2012 at 8:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call` > looks > > in `skimage.io.plugin_store`. But `plugin_store` is populated by the > first > > installed plugin in a list of preferred plugins. Whatever matches, takes > > over all io operations (more or less). If that plugin doesn't provide > > `imread_collection`, then that entry in `plugin_store` remains empty. (In > > other words, after accepting a plugin, there's no additional check > > afterwards to fill in the functions not provided by that plugin.) > > That's not the way it should behave; we should fix it to transparently > fall back to whatever is available. > I've addressed this specific issue in PR 196<https://github.com/scikits-image/scikits-image/pull/196>. Note: It still doesn't fix the original test error (but if the tifffile plugin gained an `imread_collection` function, then that would fix it). > > > Is there any reason why there's no default `imread_collection` which just > > passes arguments to `ImageCollection`? > > No, that would probably make sense. And I think ImageCollection uses > the plugin version of imread. > Yup: any plugin that provides `imread` should be able to provide an `imread_collection`. I can take care of this at a later date. (It'd be great if someone beat me to it, though ;) -Tony

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Re: Valgrind please?
by Stéfan van der Walt 30 May '12

30 May '12

On Tue, May 29, 2012 at 6:04 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > I ran all of the scikits-image examples through valgrind (following > instructions from the scikits-learn website) and didn't see any leaks. Not > all Cython functions are tested in the examples, though (for example > functions in morphology and io) so this isn't a thorough test. Thanks a lot, Tony--that's very helpful. Stéfan

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Re: Test error with tifffile plugin
by Stéfan van der Walt 30 May '12

30 May '12

On Tue, May 29, 2012 at 8:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call` looks > in `skimage.io.plugin_store`. But `plugin_store` is populated by the first > installed plugin in a list of preferred plugins. Whatever matches, takes > over all io operations (more or less). If that plugin doesn't provide > `imread_collection`, then that entry in `plugin_store` remains empty. (In > other words, after accepting a plugin, there's no additional check > afterwards to fill in the functions not provided by that plugin.) That's not the way it should behave; we should fix it to transparently fall back to whatever is available. > Is there any reason why there's no default `imread_collection` which just > passes arguments to `ImageCollection`? No, that would probably make sense. And I think ImageCollection uses the plugin version of imread. Stéfan

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Re: Test error with tifffile plugin
by Tony Yu 29 May '12

29 May '12

On Tue, May 29, 2012 at 9:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Tue, May 29, 2012 at 5:51 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > Are there any other plugins that should explicitly state that they > provide > > 'imread_collection'? I can run `skimage.io.ImageCollection` but not > > `skimage.io.imread_collection` so presumably some other plugin(s) can > read > > image collections. > > Would it help to modify the test plugin to handle image collections? > I'm not sure if that is loaded by default in the test suite. The idea > was to eventually have the tiff loader handle multiple layers as an > ImageCollection as well (and the video loading routines, too). > > Stéfan Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call` looks in `skimage.io.plugin_store`. But `plugin_store` is populated by the first installed plugin in a list of preferred plugins<https://github.com/scikits-image/scikits-image/blob/master/skimage/io/__ini…>. Whatever matches, takes over all io operations (more or less). If that plugin doesn't provide `imread_collection`, then that entry in `plugin_store` remains empty. (In other words, after accepting a plugin, there's no additional check afterwards to fill in the functions not provided by that plugin.) Is there any reason why there's no default `imread_collection` which just passes arguments to `ImageCollection`? -Tony

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Re: Test error with tifffile plugin
by Stéfan van der Walt 29 May '12

29 May '12

On Tue, May 29, 2012 at 5:51 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > Are there any other plugins that should explicitly state that they provide > 'imread_collection'? I can run `skimage.io.ImageCollection` but not > `skimage.io.imread_collection` so presumably some other plugin(s) can read > image collections. Would it help to modify the test plugin to handle image collections? I'm not sure if that is loaded by default in the test suite. The idea was to eventually have the tiff loader handle multiple layers as an ImageCollection as well (and the video loading routines, too). Stéfan

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Re: Valgrind please?
by James Turner 29 May '12

29 May '12

> Does anyone have time to run the current version of scikits-image > through Valgrind? We're getting a segfault on the SPARC platform (via > the Debian builders), and I wanted to make sure there are no strange > allocations going on that we're missing. > > Thanks > StÃ¯Â¿Â½fan > > > I ran all of the scikits-image examples through valgrind (following instructions > from the scikits-learn website > <http://scikit-learn.org/dev/developers/debugging.html>) and didn't see any > leaks. Not all Cython functions are tested in the examples, though (for example > functions in morphology and io) so this isn't a thorough test. > > -Tony Isn't a segfault likely to be in SciPy (especially if it's calling something like ATLAS)? That's where I've seen most problems in the past, though I'm not really familiar with the extensions in scikits.image itself. Just an idea. Cheers, James.

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Re: Valgrind please?
by Tony Yu 29 May '12

29 May '12

On Tue, May 29, 2012 at 12:03 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi, > > Does anyone have time to run the current version of scikits-image > through Valgrind? We're getting a segfault on the SPARC platform (via > the Debian builders), and I wanted to make sure there are no strange > allocations going on that we're missing. > > Thanks > Stéfan > I ran all of the scikits-image examples through valgrind (following instructions from the scikits-learn website<http://scikit-learn.org/dev/developers/debugging.html>) and didn't see any leaks. Not all Cython functions are tested in the examples, though (for example functions in morphology and io) so this isn't a thorough test. -Tony

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Test error with tifffile plugin
by Tony Yu 29 May '12

29 May '12

I'm getting an error for one of the tifffile plugin tests. Basically, the teardown function<https://github.com/scikits-image/scikits-image/blob/master/skimage/io/tests…>of the test is trying to reset all the io functions to their defaults. But, it turns out that the default for 'imread_collection' is empty on my system. I'm not sure if 'imread_collection' should be empty (the fits plugin seems to be the only one that explicitly states that it reads collections and I don't have pyfits installed), but the teardown function should be able to handle that case. I've fixed the test error in PR 195<https://github.com/scikits-image/scikits-image/pull/195> . Are there any other plugins that should explicitly state that they provide 'imread_collection'? I can run `skimage.io.ImageCollection` but not `skimage.io.imread_collection` so presumably some other plugin(s) can read image collections. -Tony

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Valgrind please?
by Stéfan van der Walt 29 May '12

29 May '12

Hi, Does anyone have time to run the current version of scikits-image through Valgrind? We're getting a segfault on the SPARC platform (via the Debian builders), and I wanted to make sure there are no strange allocations going on that we're missing. Thanks Stéfan

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scikit-image May 2012