Doctest failures

Josh Warner silvertrumpet999 at gmail.com
Fri Jun 20 19:27:52 EDT 2014


Several of these might be solved by globally forcing the expected 
numpy.set_printoptions 
<http://docs.scipy.org/doc/numpy/reference/generated/numpy.set_printoptions.html> 
prior to running the doctests. I'm not sure why this would differ in 
certain platforms, but for whatever reason it looks like on OSX 10.9 you're 
reliably printing an additional two digits.

The second to last error, in skimage.measure._label.label, looks like a 
real error / malformed example to me.

Josh


On Friday, June 20, 2014 9:18:34 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Hi all,
>
> I'm running this 
> <https://github.com/scikit-image/skimage-tutorials/blob/master/scipy-2014/check_env.py> 
> 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])
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20140620/14305e5c/attachment.html>


More information about the scikit-image mailing list