BUG Fix crash with close_holes

The code did not check correctly for whether the input was 2
dimensional.

ChangeLog

@@ -1,3 +1,6 @@
+Version 1.1.1 2014-07-04 by luispedro
+	* Fix crash in close_holes() with nD images (for n > 2)
+
 Version 1.1.0 2014-02-12 by luispedro
 	* Better error checking
 	* Fix interpolation of integer images using order 1

mahotas/internal.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2011-2012, Luis Pedro Coelho <luis@luispedro.org>
+# Copyright (C) 2011-2014, Luis Pedro Coelho <luis@luispedro.org>
 # vim: set ts=4 sts=4 sw=4 expandtab smartindent:
 #
 # License: MIT (see COPYING file)
@@ -166,3 +166,6 @@ def _check_3(arr, funcname):
     if arr.ndim != 3 or arr.shape[2] != 3:
         raise ValueError('mahotas.%s: this function expects an array of shape (h, w, 3), received an array of shape %s.' % (funcname, arr.shape))
 
+def _check_2(arr, funcname):
+    if arr.ndim != 2:
+        raise ValueError('mahotas.%s: this function can only handle 2D arrays (passed array with shape %s).' % (funcname, arr.shape))

mahotas/morph.py

@@ -6,7 +6,7 @@
 from __future__ import division
 import numpy as np
 
-from .internal import _get_output, _verify_is_integer_type
+from .internal import _get_output, _verify_is_integer_type, _check_2
 from . import _morph
 
 __all__ = [
@@ -273,10 +273,10 @@ def cwatershed(surface, markers, Bc=None, return_lines=False):
     W,WL = cwatershed(surface, markers, Bc=None, return_lines=True)
 
     Seeded watershed in n-dimensions
-    
+
     This function computes the watershed transform on the input surface (which
     may actually be an n-dimensional volume).
-    
+
     This function requires initial seed points. A traditional way of
     initializing watershed is to use regional minima::
 
@@ -477,6 +477,7 @@ def close_holes(ref, Bc=None):
     closed : ndarray
         superset of `ref` (i.e. with closed holes)
     '''
+    _check_2(ref, 'close_holes')
     ref = np.ascontiguousarray(ref, dtype=np.bool_)
     Bc = get_structuring_elem(ref, Bc)
     return _morph.close_holes(ref, Bc)

mahotas/tests/test_morph.py

@@ -1,7 +1,9 @@
+import mahotas as mh
 import numpy as np
 from mahotas.morph import get_structuring_elem, subm, tophat_open, tophat_close
 from nose.tools import raises
 
+
 def test_get_structuring_elem():
     A = np.zeros((10,10), np.bool)
     Bc = np.ones((4,4), dtype=np.bool)
@@ -24,7 +26,7 @@ def bad_dims():
         get_structuring_elem(A, Bc)
 
     bad_dims()
-        
+
 
 def test_open():
     from mahotas.morph import open
@@ -201,7 +203,7 @@ def test_distance_multi():
 
 def test_disk():
     from mahotas.morph import disk
-    D2 = disk(2) 
+    D2 = disk(2)
     assert D2.shape[0] == D2.shape[1]
     assert D2.shape == (5,5)
     assert not D2[0,0]
@@ -226,3 +228,10 @@ def test_negative_dim(dim):
     test_negative_dim(-2)
     test_negative_dim(-1)
     test_negative_dim(0)
+
+
+@raises(ValueError)
+def test_close_holes_3d():
+    'Close holes should raise exception with 3D inputs'
+    f = np.random.rand(100,100,3) > .9
+    mh.close_holes(f)