Doctest failures
Juan Nunez-Iglesias
jni.soma at gmail.com
Fri Jun 20 10:18:13 EDT 2014
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])
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