Mailman 3 March 2016 - scikit-image

Problem with using sp.ndimage.label to get largest object in a binary image
by Matteo March 8, 2016

March 8, 2016

Hello there I'm putting together some code to grab an image with a map, colorbar, and possibly text and other elements, guess what the largest object in the image is -assuming it is the map - crop the image to the map extent, then reduce the number of colors in the map. My Jupiter notebook is at this location on GitHub: https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.… The issue I have with this code is that: If I run it with the current test image (https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) or even a nimage with map touching the border(https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cma… the code seems to work. However, in the case of an image with larger blocks of text (https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) the output of [9] is an array that is all zeroes, although as far as I know it should not. Can anyone suggest why this is happening? I am sure it is something I am overlooking in my code/understanding of image processing. Thanks Matteo

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Re: failed to build version 0.12
by Emmanuelle Gouillart March 7, 2016

March 7, 2016

Just to be sure: when doing "pip install scikit-image", there's no need for cython to be installed (any version of cython), right? The .c are shipped with the .tar.gz on PyPi, so I guess it should be fine without Cython... Emma On Mon, Mar 07, 2016 at 12:43:04AM -0800, StÃ©fan van der Walt wrote: > Hi Jean-Patrick > On 7 March 2016 at 00:06, Jean-Patrick Pommier > <jeanpatrick.pommier(a)gmail.com> wrote: > > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' > scikit-image now requires a newer version of Cython to build. See: > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > Best regards > StÃ©fan

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failed to build version 0.12
by Jean-Patrick Pommier March 7, 2016

March 7, 2016

Hello, Thank you for this new version of scikit-image. I met the following message when i try to upgrade scikit-image (linux): $ pip install --upgrade scikit-image Collecting scikit-image Using cached scikit-image-0.12.0.tar.gz Complete output from command python setup.py egg_info: Partial import of skimage during the build process. Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 146, in <module> **extra File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 69, in configuration config.add_subpackage('skimage') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 21, in configuration config.add_subpackage('morphology') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/morphology/setup.py", line 19, in configuration cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) File "skimage/_build.py", line 39, in cython if not _changed(pyxfile): File "skimage/_build.py", line 70, in _changed with open(filename, 'rb') as f: IOError: [Errno 2] No such file or directory: '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' I got the same message working with sudo or from a virtual env. Best regards jean-patrick

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Re: failed to build version 0.12
by Himanshu Mishra March 7, 2016

March 7, 2016

> With the next release cycle, I will probably do release candidates > first like all the adults do ;) > > Release candidates, yay ! :) Himanshu Mishra

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Re: failed to build version 0.12
by Jens Nielsen March 7, 2016

March 7, 2016

It does indeed. ✔ ~ pip3 install --upgrade scikit-image Collecting scikit-image Downloading scikit-image-0.12.1.tar.gz (22.5MB) 100% |████████████████████████████████| 22.5MB 75kB/s Requirement already up-to-date: six>=1.7.3 in /usr/local/lib/python3.5/site-packages (from scikit-image) Requirement already up-to-date: networkx>=1.8 in /usr/local/lib/python3.5/site-packages (from scikit-image) Requirement already up-to-date: pillow>=2.1.0 in /usr/local/lib/python3.5/site-packages (from scikit-image) Collecting dask[array]>=0.5.0 (from scikit-image) Requirement already up-to-date: decorator>=3.4.0 in /usr/local/lib/python3.5/site-packages (from networkx>=1.8->scikit-image) Collecting toolz>=0.7.2 (from dask[array]>=0.5.0->scikit-image) Requirement already up-to-date: numpy in /usr/local/lib/python3.5/site-packages (from dask[array]>=0.5.0->scikit-image) Building wheels for collected packages: scikit-image Running setup.py bdist_wheel for scikit-image ... done Stored in directory: /Users/jhn/Library/Caches/pip/wheels/41/88/c2/e86fe4aa654d61f49c7b95776a15f605081851ef3b08c01d2f Successfully built scikit-image Installing collected packages: toolz, dask, scikit-image Found existing installation: scikit-image 0.11.3 Uninstalling scikit-image-0.11.3: Successfully uninstalled scikit-image-0.11.3 Successfully installed dask-0.8.0 scikit-image-0.12.1 toolz-0.7.4 Thanks for the ultra quick turn around Jens On Monday, 7 March 2016 09:47:23 UTC, stefanv wrote: > > On 7 March 2016 at 01:35, Jens Nielsen <jenshn...(a)gmail.com <javascript:>> > wrote: > > The problem is that skimage/morphology/setup.py contains: > > > > cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) > > > > but that file is not in the pypi tar ball. It should presumably try to > > process the template processed file _skeletonize_3d_cy.pyx? > > I've pushed 0.12.1 to pypi to fix the problem; please let me know if > that works for you. > > Thanks > Stéfan >

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Re: failed to build version 0.12
by Jens Nielsen March 7, 2016

March 7, 2016

Sorry but I am also seeing this happening with Cython 0.23.4 so I doubt that the Cython version is the problem. (test) ✔ ~ pip list cycler (0.10.0) Cython (0.23.4) dask (0.8.0) decorator (4.0.9) matplotlib (1.5.1) networkx (1.11) numpy (1.10.4) Pillow (3.1.1) pip (8.1.0) pyparsing (2.1.0) python-dateutil (2.5.0) pytz (2015.7) scipy (0.17.0) setuptools (20.2.2) six (1.10.0) toolz (0.7.4) wheel (0.29.0) (test) ✔ ~ pip install scikit-image Collecting scikit-image Using cached scikit-image-0.12.0.tar.gz Complete output from command python setup.py egg_info: Partial import of skimage during the build process. Traceback (most recent call last): File "<string>", line 1, in <module> File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 146, in <module> **extra File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 69, in configuration config.add_subpackage('skimage') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 21, in configuration config.add_subpackage('morphology') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/morphology/setup.py", line 19, in configuration cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 39, in cython if not _changed(pyxfile): File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 70, in _changed with open(filename, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/ The problem is that skimage/morphology/setup.py contains: cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) but that file is not in the pypi tar ball. It should presumably try to process the template processed file _skeletonize_3d_cy.pyx? Best Jens On Monday, 7 March 2016 08:43:25 UTC, stefanv wrote: > > Hi Jean-Patrick > > On 7 March 2016 at 00:06, Jean-Patrick Pommier > <jeanpatri...(a)gmail.com <javascript:>> wrote: > > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_ > skeletonize_3d_cy.pyx.in' > > scikit-image now requires a newer version of Cython to build. See: > > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > > Best regards > Stéfan >

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Re: failed to build version 0.12
by Johannes Schönberger March 7, 2016

March 7, 2016

For the 0.12.1 release, maybe we can fail more in a more informative error message in this case? Maybe I am wrong, but I think someone else had the same problem very recently? > On Mar 7, 2016, at 9:43 AM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > > Hi Jean-Patrick > > On 7 March 2016 at 00:06, Jean-Patrick Pommier > <jeanpatrick.pommier(a)gmail.com> wrote: >> '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' > > scikit-image now requires a newer version of Cython to build. See: > > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > > Best regards > 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. > To post to this group, send an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnVf5_J0nEL2P-Q7%3Doar…. > For more options, visit https://groups.google.com/d/optout.

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Re: 0.12 release
by Emmanuelle Gouillart March 6, 2016

March 6, 2016

Awesome!! I'm tagging right now, so please don't merge any PRs!!! On Fri, Mar 04, 2016 at 11:40:18AM -0800, StÃ©fan van der Walt wrote: > Who wants to merge the last outstanding PR for 0.12! > https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+mile… > On 2 March 2016 at 18:50, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > > Aren't these pre-existing bugs? At any rate, as you say, might be a moot > > point, finally. =) > > On Thu, Mar 3, 2016 at 1:29 PM, StÃ©fan van der Walt <stefanv(a)berkeley.edu> > > wrote: > >> On 2 March 2016 at 16:00, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > >> > Bug fixes seem precisely inessential to get done ahead of release? > >> > Anything > >> > that doesn't break the API can be added in 0.12.1? > >> You can't really release a package with a broken test suite. So you > >> have the option to temporarily disable the tests, but shipping with a > >> known bug feels kind of weird? > >> Either way, I think I've zapped most of the outstanding ones. Waiting > >> for Travis. > >> StÃ©fan > >> -- > >> 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. > >> To post to this group, send an email to scikit-image(a)googlegroups.com. > >> To view this discussion on the web, visit > >> https://groups.google.com/d/msgid/scikit-image/CABDkGQnz%2BdW7-oC2CpcEpxRYj…. > >> For more options, visit https://groups.google.com/d/optout. > > -- > > 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. > > To post to this group, send email to scikit-image(a)googlegroups.com. > > To view this discussion on the web, visit > > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKRUYPFNz7n3OARY1rhpZ…. > > For more options, visit https://groups.google.com/d/optout.

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Re: jpeg image being read differently skimage.io.imread
by François Boulogne March 5, 2016

March 5, 2016

> Can you please try > > skimage.io.imread(image_name, plugin='matplotlib') ? > I think Vimal said that it works with matplotlib, or misunderstood. To get PIL's version, you can try python -c 'import PIL; print(PIL.VERSION)' Best, -- François Boulogne. http://www.sciunto.org GPG: 32D5F22F

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jpeg image being read differently skimage.io.imread
by Vimal Thilak March 4, 2016

March 4, 2016

Hi, I have two servers on which I have installed skimage. When I do an skimage.io.imread on these two machines with the same image file, I noticed a difference in the shape of the returned image array: Machine 1: image_name = /path/to/JPEG img = skimage.io.imread(image_name) >>> img.shape (3000, 4000, 3) Machine 2: img = skimage.io.imread(image_name) >>> img.shape (2, ) Both machines have skimage version '0.11.3'. I believe that both systems have Pillow installed. I do not know the version of Pillow. I did change the plug-in to matplotlib on Machine 2 and saw that the image was being read correctly. However, I'm curious to know the reason for this difference and what I can do to fix my machine #2 Furthermore, how do I find the version of Pillow installed on my system? A google search didn't come up with anything that was helpful (i.e, copy-pastable solution) :) Thanks, -Vimal

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