Mailman 3 June 2014 - scikit-image

Re: Example doesn't display in gallery?
by Rishabh Raj 25 Jun '14

25 Jun '14

The ipynb link also seems to be not generated. On Wednesday, June 25, 2014, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > I don't see it either! Yikes, how did that happen? > > -- > 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 <javascript:;>. > For more options, visit https://groups.google.com/d/optout. > -- Best, Rishabh Raj

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Re: Example doesn't display in gallery?
by Stéfan van der Walt 25 Jun '14

25 Jun '14

I don't see it either! Yikes, how did that happen?

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Example doesn't display in gallery?
by Tony Yu 25 Jun '14

25 Jun '14

Is it just me, or is the following example not displaying the gallery? http://scikit-image.org/docs/dev/auto_examples/plot_line_hough_transform.ht… The link works for me, but I can't seem to find it in the gallery. Best, -Tony

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Doctest failures
by Juan Nunez-Iglesias 20 Jun '14

20 Jun '14

Hi all, I'm running this <https://github.com/scikit-image/skimage-tutorials/blob/master/scipy-2014/ch…> on my system (OSX 10.9) and getting some doctest failures, apparently due to precision issues (see below). Can people please run this on theirs and see what happens, and offer ideas re: fixing it? I imagine something like setting the precision of numpy printouts will do, but it would be best if that can be a global setting. In the meantime, I might not run the doctests in this script, so that people don't incorrectly fail their check_env for the SciPy 2014 tutorial... Thoughts? Thanks! Juan. ........................................F.F...................................F./Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py:4: skimage_deprecation: Call to deprecated function ``label``. Use ``skimage.measure.label`` instead. return _label(input, neighbors, background, return_num) ..F....................................................... ====================================================================== FAIL: Doctest: skimage.feature.texture.greycoprops ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 2226, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for skimage.feature.texture.greycoprops File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py", line 125, in greycoprops ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py", line 176, in skimage.feature.texture.greycoprops Failed example: contrast Expected: array([[ 0.58333333, 1. ], [ 1.25 , 2.75 ]]) Got: array([[ 0.5833333333, 1. ], [ 1.25 , 2.75 ]]) ====================================================================== FAIL: Doctest: skimage.filter._gaussian.gaussian_filter ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 2226, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for skimage.filter._gaussian.gaussian_filter File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", line 13, in gaussian_filter ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", line 73, in skimage.filter._gaussian.gaussian_filter Failed example: gaussian_filter(a, sigma=0.4) # mild smoothing Expected: array([[ 0.00163116, 0.03712502, 0.00163116], [ 0.03712502, 0.84496158, 0.03712502], [ 0.00163116, 0.03712502, 0.00163116]]) Got: array([[ 0.0016311596, 0.0371250207, 0.0016311596], [ 0.0371250207, 0.8449615765, 0.0371250207], [ 0.0016311596, 0.0371250207, 0.0016311596]]) ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", line 77, in skimage.filter._gaussian.gaussian_filter Failed example: gaussian_filter(a, sigma=1) # more smooting Expected: array([[ 0.05855018, 0.09653293, 0.05855018], [ 0.09653293, 0.15915589, 0.09653293], [ 0.05855018, 0.09653293, 0.05855018]]) Got: array([[ 0.0585501805, 0.096532928 , 0.0585501805], [ 0.096532928 , 0.1591558917, 0.096532928 ], [ 0.0585501805, 0.096532928 , 0.0585501805]]) ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", line 82, in skimage.filter._gaussian.gaussian_filter Failed example: gaussian_filter(a, sigma=1, mode='reflect') Expected: array([[ 0.08767308, 0.12075024, 0.08767308], [ 0.12075024, 0.16630671, 0.12075024], [ 0.08767308, 0.12075024, 0.08767308]]) Got: array([[ 0.0876730803, 0.1207502431, 0.0876730803], [ 0.1207502431, 0.1663067063, 0.1207502431], [ 0.0876730803, 0.1207502431, 0.0876730803]]) ====================================================================== FAIL: Doctest: skimage.measure._label.label ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 2226, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for skimage.measure._label.label File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line unknown line number, in label ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: x = np.eye(3).astype(int) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[0]>", line 1, in <module> x = np.eye(3).astype(int) NameError: name 'np' is not defined ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: print(x) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[1]>", line 1, in <module> print(x) NameError: name 'x' is not defined ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: print(m.label(x, neighbors=4)) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[2]>", line 1, in <module> print(m.label(x, neighbors=4)) NameError: name 'm' is not defined ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: print(m.label(x, neighbors=8)) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[3]>", line 1, in <module> print(m.label(x, neighbors=8)) NameError: name 'm' is not defined ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: x = np.array([[1, 0, 0], [1, 1, 5], [0, 0, 0]]) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[4]>", line 1, in <module> x = np.array([[1, 0, 0], NameError: name 'np' is not defined ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", line ?, in skimage.measure._label.label Failed example: print(m.label(x, background=0)) Exception raised: Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest skimage.measure._label.label[5]>", line 1, in <module> print(m.label(x, background=0)) NameError: name 'm' is not defined ====================================================================== FAIL: Doctest: skimage.measure.fit.ransac ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 2226, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for skimage.measure.fit.ransac File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py", line 470, in ransac ---------------------------------------------------------------------- File "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py", line 576, in skimage.measure.fit.ransac Failed example: ransac_model.params Expected: array([ 20.12762373, 29.73563063, 4.81499637, 10.4743584 , 0.05217117]) Got: array([ 20.1276237259, 29.7356306313, 4.8149963715, 10.474358404 , 0.0521711691])

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Re: The scikit-image paper is here!
by Juan Nunez-Iglesias 20 Jun '14

20 Jun '14

On Fri, Jun 20, 2014 at 3:29 AM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > import this > print("".join([this.d.get(c, c) for c in this.s]).split("\n")[-6]) > > :) > I did not know of this black magic and I wish I still didn't! =P

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Re: The scikit-image paper is here!
by Nelle Varoquaux 19 Jun '14

19 Jun '14

Congrats ! On 19 June 2014 14:49, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi Ankit > > On Thu, Jun 19, 2014 at 11:10 PM, Ankit Agrawal <aaaagrawal(a)gmail.com> > wrote: > > Congratulations to everyone!! I am humbled to have worked with such > > committed and talented group of people. > > As you may have noticed, your and Johannes's work features fairly > prominently in the paper--thanks for that contribution! > > 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/d/optout. >

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Re: The scikit-image paper is here!
by Ankit Agrawal 19 Jun '14

19 Jun '14

Congratulations to everyone!! I am humbled to have worked with such committed and talented group of people. On Thursday, June 19, 2014 7:30:53 PM UTC+2, Stefan van der Walt wrote: > > On Thu, Jun 19, 2014 at 1:44 PM, Johannes Sch önberger <js...(a)demuc.de > <javascript:>> wrote: > > Let us update the website... @Stefan: are you still working on something > or is it safe to make commits? > > I've got it open, so let me update it quickly. > > Stéfan >

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Re: The scikit-image paper is here!
by Johannes Schönberger 19 Jun '14

19 Jun '14

> This is a significant milestone for the project. Thank you to everyone on the paper and all others who have contributed to the project. I feel extremely lucky to be a part of it. +1, It was a pleasure to work with you on this. Let us update the website… @Stefan: are you still working on something or is it safe to make commits? Johannes Schönberger On Jun 19, 2014, at 7:30 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Hi everyone! > > I was going to let Stéfan announce this, but he's taking way too long. =P The scikit-image paper is here! > > https://peerj.com/articles/453/ > > This is a significant milestone for the project. Thank you to everyone on the paper and all others who have contributed to the project. I feel extremely lucky to be a part of it. (I still remember Stéfan inviting me to the sprint in SciPy 2012, when it all started for me!) > > Stéfan, it looks like they still got your last name wrong in "how to cite"! (van der Walt instead of Van der Walt!) Hopefully that can be fixed by them without too much trouble...! > > Juan. > > -- > 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/d/optout.

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Re: The scikit-image paper is here!
by Stéfan van der Walt 19 Jun '14

19 Jun '14

On Thu, Jun 19, 2014 at 1:30 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > The scikit-image paper is here! > > https://peerj.com/articles/453/ This is super exciting! Thanks so much to the whole team for their hard work--it's been a lot of fun. A special word of thanks to Juan for handling most of the communications with PeerJ. > Stéfan, it looks like they still got your last name wrong in "how to cite"! > (van der Walt instead of Van der Walt!) Hopefully that can be fixed by them > without too much trouble...! There are many lessons in the Zen of Python! import this print("".join([this.d.get(c, c) for c in this.s]).split("\n")[-6]) :) Stéfan

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The scikit-image paper is here!
by Juan Nunez-Iglesias 19 Jun '14

19 Jun '14

Hi everyone! I was going to let Stéfan announce this, but he's taking way too long. =P The scikit-image paper is here! https://peerj.com/articles/453/ This is a significant milestone for the project. Thank you to everyone on the paper and all others who have contributed to the project. I feel extremely lucky to be a part of it. (I still remember Stéfan inviting me to the sprint in SciPy 2012, when it all started for me!) Stéfan, it looks like they still got your last name wrong in "how to cite"! (van der Walt instead of Van der Walt!) Hopefully that can be fixed by them without too much trouble...! Juan.

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