Harden the trace boundary code

A one pixel object could get stuck in an infinite loop in the moore
boundary call.

histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx

@@ -26,8 +26,8 @@ def _trace_object_boundaries_cython(long[:, :] im_label not None, long connectiv
         # find starting x and y points if not defined
         if (x_start == -1) & (y_start == -1):
 
-          for i in range(nrows):
-            for j in range(ncols):
+          for i in range(1, nrows - 1):
+            for j in range(1, ncols - 1):
 
               if (im_label[i, j] > 0) & (flag == 0):
                 # check if the number of points is one
@@ -41,16 +41,17 @@ def _trace_object_boundaries_cython(long[:, :] im_label not None, long connectiv
 
     bx = []
     by = []
+    if x_start >= 0 and y_start >= 0:
 
-    if connectivity == 4:
-        bx, by = _isbf(
-            im_label, im_label_90, im_label_180, im_label_270,
-            x_start, y_start, max_length);
+        if connectivity == 4:
+            bx, by = _isbf(
+                im_label, im_label_90, im_label_180, im_label_270,
+                x_start, y_start, max_length);
 
-    else:
-        bx, by = _moore(
-            im_label, im_label_90, im_label_180, im_label_270,
-            x_start, y_start, max_length);
+        else:
+            bx, by = _moore(
+                im_label, im_label_90, im_label_180, im_label_270,
+                x_start, y_start, max_length);
 
     return np.asarray(bx), np.asarray(by)
 
@@ -126,11 +127,25 @@ def _moore(long[:, :] mask, long[:, :] mask_90, long[:, :] mask_180, long[:, :]
 
     cdef long i, j
 
+    cdef long itercount = 0
+    cdef long last_len = 0
+
     if sum > 1:
 
       # loop until true
       while(True):
 
+        if len(list_bx) > last_len:
+            last_len = len(list_bx)
+            # itercount = 0
+            itercount += 1
+        else:
+            itercount += 1
+        if itercount > 10:
+            list_bx.clear()
+            list_by.clear()
+            break
+
         h = np.zeros((row_isbf, col_isbf), dtype=int)
 
         with nogil:
@@ -277,6 +292,8 @@ def _isbf(long[:, :] mask, long[:, :] mask_90, long[:, :] mask_180, long[:, :] m
 
     # check degenerate case where mask contains 1 pixel
     cdef long sum = np.sum(mask)
+    cdef long itercount = 0
+    cdef long last_len = 0
 
     if sum > 1:
         with nogil:
@@ -286,6 +303,15 @@ def _isbf(long[:, :] mask, long[:, :] mask_90, long[:, :] mask_180, long[:, :] m
 
         while(True):
 
+            if len(list_bx) > last_len:
+                last_len = len(list_bx)
+                itercount = 0
+            else:
+                itercount += 1
+            if itercount > 10:
+                list_bx.clear()
+                list_by.clear()
+                break
             h = np.zeros((row_isbf, col_isbf), dtype=int)
 
             with nogil:

tests/test_segmentation_label.py

@@ -22,7 +22,7 @@ def test_trace_boundary(self):
                                [0, 0, 0, 0, 0, 0, 0, 1, 1, 0],
                                [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=bool)
 
-        # refenece neighbors for isbf
+        # reference neighbors for isbf
         rx_isbf = [1, 1, 2, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 8, 7, 7, 7,
                    7, 6, 6, 5, 5, 5, 4, 4, 3, 3, 3, 3, 2, 1]
         ry_isbf = [7, 8, 8, 7, 6, 6, 6, 6, 6, 7, 8, 8, 7, 7, 6, 5, 4,
@@ -46,6 +46,16 @@ def test_trace_boundary(self):
         np.testing.assert_allclose(rx_moore, x_moore[0])
         np.testing.assert_allclose(ry_moore, y_moore[0])
 
+    def test_trace_boundary_bad(self):
+        # Make sure the algorithms terminate work in a degenerate case
+        m_neighbor = np.array([[0, 0, 0, 0, 0],
+                               [0, 1, 0, 1, 0],
+                               [0, 0, 0, 0, 0]], dtype=bool)
+        x, y = trace_object_boundaries(m_neighbor, simplify_colinear_spurs=False)
+        assert not len(x)
+        x, y = trace_object_boundaries(m_neighbor, 8, simplify_colinear_spurs=False)
+        assert not len(x)
+
 
 class TestDeleteBorderLabel: