Qhull error

[Juan Nunez-Iglesias]

Hi all. I'm getting the below error when computing regionprops(...,
['Solidity']). Does anyone know what's going on? At first I thought maybe
it was passing a singleton array or something, but this array looks like a
reasonable thing to compute a convex hull on, no?

If I'm not being totally stupid (which is a big if), perhaps we should add
a try/except around the convex hull calculation and return a non-value,
e.g. -1, when the calculation fails?

 In [49]: test_im = array([[ 0.,  0.,  0.,  0.,  1.,  0.,  0.],
       [ 0.,  0.,  1.,  1.,  1.,  1.,  1.],
       [ 1.,  1.,  1.,  0.,  0.,  0.,  0.]], np.int)

In [50]: test_im
Out[50]:
array([[0, 0, 0, 0, 1, 0, 0],
       [0, 0, 1, 1, 1, 1, 1],
       [1, 1, 1, 0, 0, 0, 0]])

In [51]: measure.regionprops(test_im.astype(int), ['Solidity'])
QH6228
Qhull internal error (qh_findbestlower): all neighbors of facet 8 are
flipped or upper Delaunay.
Please report this error to qhull_bug at qhull.org with the input and all
of the output.
ERRONEOUS FACET:
- f8
    - flags: bottom simplicial upperDelaunay
    - normal:   -0.8366  -0.5167    0.182
    - offset:   1.254902
    - center: 0.7380952380952381 2.30952380952381 3.054054054054054
    - vertices: p30(v6) p56(v3) p28(v0)
    - neighboring facets: f3 f23 f22

While executing:  | qhull d Qz Qbb Qt
Options selected for Qhull 2010.1 2010/01/14:
  run-id 1680623163  delaunay  Qz-infinity-point  Qbbound-last  Qtriangulate
  _pre-merge  _zero-centrum  Pgood  _max-width  7  Error-roundoff 9.7e-15
  _one-merge 6.8e-14  _near-inside 3.4e-13  Visible-distance 1.9e-14
  U-coplanar-distance 1.9e-14  Width-outside 3.9e-14  _wide-facet 1.2e-13
Last point added to hull was p33.  Last merge was #1.

At error exit:

Delaunay triangulation by the convex hull of 57 points in 3-d:

  Number of input sites and at-infinity: 10
  Number of nearly incident points: 10
  Number of Delaunay regions: 0
  Number of non-simplicial Delaunay regions: 1

Statistics for:  | qhull d Qz Qbb Qt

  Number of points processed: 10
  Number of hyperplanes created: 27
  Number of facets in hull: 15
  Number of distance tests for qhull: 512
  Number of distance tests for merging: 127
  Number of distance tests for checking: 0
  Number of merged facets: 1

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-51-efe47406d455> in <module>()
----> 1 measure.regionprops(test_im.astype(int), ['Solidity'])

/Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/scikit_image-0.9dev-py2.7-macosx-10.5-x86_64.egg/skimage/measure/_regionprops.pyc
in regionprops(label_image, properties, intensity_image)
    363         if 'Solidity' in properties:
    364             if _convex_image is None:
--> 365                 _convex_image = convex_hull_image(array)
    366             obj_props['Solidity'] = m[0, 0] / np.sum(_convex_image)
    367

/Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/scikit_image-0.9dev-py2.7-macosx-10.5-x86_64.egg/skimage/morphology/convex_hull.pyc
in convex_hull_image(image)
     52
     53     # Find the convex hull
---> 54     chull = Delaunay(coords).convex_hull
     55     v = coords[np.unique(chull)]
     56

/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/scipy/spatial/qhull.so
in scipy.spatial.qhull.Delaunay.__init__
(scipy/spatial/qhull.c:4109)()

/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/scipy/spatial/qhull.so
in scipy.spatial.qhull._construct_delaunay
(scipy/spatial/qhull.c:1314)()

RuntimeError: Qhull error
> /Users/nuneziglesiasj/Data/images-work/qhull.pyx(172)scipy.spatial.qhull._construct_delaunay (scipy/spatial/qhull.c:1314)()
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