move unpack_unique_verts to Cython for speed

skimage/measure/_marching_cubes.py

@@ -116,46 +116,7 @@ def marching_cubes(volume, level, sampling=(1., 1., 1.)):
 
     # Find and collect unique vertices, storing triangle verts as indices.
     # Removes much redundancy and eliminates degenerate "triangles".
-    vert_list, tri_list = _unpack_unique_verts(raw_tris)
-
-    return vert_list, tri_list
-
-
-def _unpack_unique_verts(trilist):
-    """
-    Converts a list of lists of tuples corresponding to triangle vertices into
-    a unique vertex list, and a list of triangle faces w/indices corresponding
-    to entries of the vertex list.
-
-    """
-    idx = 0
-    vert_index = {}
-    vert_list = []
-    tri_list = []
-
-    # Iterate over triangles
-    for i in range(len(trilist)):
-        templist = []
-
-        # Only parse vertices from non-degenerate triangles
-        if not ((trilist[i][0] == trilist[i][1]) or
-                (trilist[i][0] == trilist[i][2]) or
-                (trilist[i][1] == trilist[i][2])):
-
-            # Iterate over vertices within each triangle
-            for j in range(3):
-                vert = trilist[i][j]
-
-                # Check if a new unique vertex found
-                if vert not in vert_index:
-                    vert_index[vert] = idx
-                    templist.append(idx)
-                    vert_list.append(vert)
-                    idx += 1
-                else:
-                    templist.append(vert_index[vert])
-
-            tri_list.append(templist)
+    vert_list, tri_list = _marching_cubes_cy.unpack_unique_verts(raw_tris)
 
     return vert_list, tri_list
 

skimage/measure/_marching_cubes_cy.pyx

@@ -13,6 +13,48 @@ cdef inline double _get_fraction(double from_value, double to_value,
     return ((level - from_value) / (to_value - from_value))
 
 
+def unpack_unique_verts(list trilist):
+    """
+    Converts a list of lists of tuples corresponding to triangle vertices into
+    a unique vertex list, and a list of triangle faces w/indices corresponding
+    to entries of the vertex list.
+
+    """
+    cdef Py_ssize_t idx = 0
+    cdef Py_ssize_t n_tris = len(trilist)
+    cdef Py_ssize_t i, j
+    cdef dict vert_index = {}
+    cdef list vert_list = []
+    cdef list tri_list = []
+    cdef list templist
+
+    # Iterate over triangles
+    for i in range(n_tris):
+        templist = []
+
+        # Only parse vertices from non-degenerate triangles
+        if not ((trilist[i][0] == trilist[i][1]) or
+                (trilist[i][0] == trilist[i][2]) or
+                (trilist[i][1] == trilist[i][2])):
+
+            # Iterate over vertices within each triangle
+            for j in range(3):
+                vert = trilist[i][j]
+
+                # Check if a new unique vertex found
+                if vert not in vert_index:
+                    vert_index[vert] = idx
+                    templist.append(idx)
+                    vert_list.append(vert)
+                    idx += 1
+                else:
+                    templist.append(vert_index[vert])
+
+            tri_list.append(templist)
+
+    return vert_list, tri_list
+
+
 def iterate_and_store_3d(cnp.ndarray[double, ndim=3] arr,
                          double level, tuple sampling=(1., 1., 1.)):
     """Iterate across the given array in a marching-cubes fashion,