Merge pull request #270 from tonysyu/cython-0.15-compat

BUG: Make reconstruction compatible with Cython 0.15.

DEPENDS.txt

@@ -2,7 +2,7 @@ Build Requirements
 ------------------
 * `Python >= 2.5 <http://python.org>`__
 * `Numpy >= 1.6 <http://numpy.scipy.org/>`__
-* `Cython >= 0.16 <http://www.cython.org/>`__
+* `Cython >= 0.15 <http://www.cython.org/>`__
 
 `Matplotlib >= 1.0 <http://matplotlib.sf.net>`__ is needed to generate the
 examples in the documentation.

skimage/morphology/_greyreconstruct.pyx

@@ -8,12 +8,21 @@ All rights reserved.
 Original author: Lee Kamentsky
 
 """
+cimport numpy as cnp
 cimport cython
 
 
 @cython.boundscheck(False)
-def reconstruction_loop(unsigned int[:] ranks, int[:] prev, int[:] next,
-                        int[:] strides, int current_idx, int image_stride):
+def reconstruction_loop(cnp.ndarray[dtype=cnp.uint32_t, ndim=1,
+                                    negative_indices=False, mode='c'] aranks,
+                        cnp.ndarray[dtype=cnp.int32_t, ndim=1,
+                                    negative_indices=False, mode='c'] aprev,
+                        cnp.ndarray[dtype=cnp.int32_t, ndim=1,
+                                    negative_indices=False, mode='c'] anext,
+                        cnp.ndarray[dtype=cnp.int32_t, ndim=1,
+                                    negative_indices=False, mode='c'] astrides,
+                        int current_idx,
+                        int image_stride):
     """The inner loop for reconstruction.
 
     This algorithm uses the rank-order of pixels. If low intensity pixels have
@@ -28,20 +37,24 @@ def reconstruction_loop(unsigned int[:] ranks, int[:] prev, int[:] next,
 
     Parameters
     ----------
-    ranks : array
+    aranks : array
         The rank order of the flattened seed and mask images.
-    prev, next: arrays
+    aprev, anext: arrays
         Indices of previous and next pixels in rank sorted order.
-    strides : array
+    astrides : array
         Strides to neighbors of the current pixel.
     current_idx : int
         Index of highest-ranked pixel used as starting point in loop.
     image_stride : int
-        Stride between seed image and mask image in `ranks`.
+        Stride between seed image and mask image in `aranks`.
     """
     cdef unsigned int neighbor_rank, current_rank, mask_rank
-    cdef int i, current_link, neighbor_idx, nprev, nnext
-    cdef int nstrides = strides.shape[0]
+    cdef int i, neighbor_idx, current_link, nprev, nnext
+    cdef int nstrides = astrides.shape[0]
+    cdef cnp.uint32_t *ranks = <cnp.uint32_t *>(aranks.data)
+    cdef cnp.int32_t *prev = <cnp.int32_t *>(aprev.data)
+    cdef cnp.int32_t *next = <cnp.int32_t *>(anext.data)
+    cdef cnp.int32_t *strides = <cnp.int32_t *>(astrides.data)
 
     while current_idx != -1:
         if current_idx < image_stride:

skimage/morphology/greyreconstruct.py

@@ -11,7 +11,7 @@ Original author: Lee Kamentsky
 """
 import numpy as np
 
-from skimage.filter.rank_order import rank_order
+from skimage.filter._rank_order import rank_order
 
 
 def reconstruction(seed, mask, method='dilation', selem=None, offset=None):