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Fix buf bounds checking in trace and fill #2

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Fix buf bounds checking in trace and fill #2

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f2c02ec
Fix buf bounds checking in trace and fill
Alex-Richman Apr 27, 2019
fa12729
Add additional bounds check to fill() inner loop
Alex-Richman Apr 28, 2019
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24 changes: 12 additions & 12 deletions sknw/sknw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,14 @@ def idx2rc(idx, acc):
idx[i] -= rst[i,j]*acc[j]
rst -= 1
return rst

@jit # fill a node (may be two or more points)
def fill(img, p, num, nbs, acc, buf):
back = img[p]
img[p] = num
buf[0] = p
cur = 0; s = 1;

while True:
p = buf[cur]
for dp in nbs:
Expand All @@ -50,8 +50,9 @@ def fill(img, p, num, nbs, acc, buf):
img[cp] = num
buf[s] = cp
s+=1
if s >= len(buf):break
cur += 1
if cur==s:break
if cur==s or s >= len(buf):break
return idx2rc(buf[:s], acc)

@jit # trace the edge and use a buffer, then buf.copy, if use [] numba not works
Expand All @@ -72,16 +73,16 @@ def trace(img, p, nbs, acc, buf):
if img[cp] == 1:
newp = cp
p = newp
if c2!=0:break
if c2!=0 or cur >= len(buf):break
return (c1-10, c2-10, idx2rc(buf[:cur], acc))

@jit # parse the image then get the nodes and edges
def parse_struc(img):
def parse_struc(img, buf_size):
nbs = neighbors(img.shape)
acc = np.cumprod((1,)+img.shape[::-1][:-1])[::-1]
img = img.ravel()
pts = np.array(np.where(img==2))[0]
buf = np.zeros(131072, dtype=np.int64)
buf = np.zeros(buf_size, dtype=np.int64)
num = 10
nodes = []
for p in pts:
Expand All @@ -97,7 +98,7 @@ def parse_struc(img):
edge = trace(img, p+dp, nbs, acc, buf)
edges.append(edge)
return nodes, edges

# use nodes and edges build a networkx graph
def build_graph(nodes, edges, multi=False):
graph = nx.MultiGraph() if multi else nx.Graph()
Expand All @@ -113,12 +114,12 @@ def buffer(ske):
buf[tuple([slice(1,-1)]*buf.ndim)] = ske
return buf

def build_sknw(ske, multi=False):
def build_sknw(ske, buf_size=131072, multi=False):
buf = buffer(ske)
mark(buf)
nodes, edges = parse_struc(buf)
nodes, edges = parse_struc(buf, buf_size)
return build_graph(nodes, edges, multi)

# draw the graph
def draw_graph(img, graph, cn=255, ce=128):
acc = np.cumprod((1,)+img.shape[::-1][:-1])[::-1]
Expand All @@ -142,4 +143,3 @@ def draw_graph(img, graph, cn=255, ce=128):
print('d')
print(a)
print('d')