Mailman 3 Doctest failures - scikit-image

20 Jun 2014

      Hi all,

I'm running this
<https://github.com/scikit-image/skimage-tutorials/blob/master/scipy-2014/che...>
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])

Doctest failures

Juan Nunez-Iglesias

tags

participants (1)