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Variable edge buf size. int64 coordinates. #22

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Variable edge buf size. int64 coordinates. #22

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86f818b
Variable edge buf size. int64 coordinates.
ausrasul Mar 22, 2022
9b1dc50
Change pixel type int16 to int64
ausrasul Mar 23, 2022
6bef547
Return exception if
ausrasul Mar 23, 2022
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33 changes: 22 additions & 11 deletions sknw/sknw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ def mark(img, nbs): # mark the array use (0, 1, 2)

@jit(nopython=True) # trans index to r, c...
def idx2rc(idx, acc):
rst = np.zeros((len(idx), len(acc)), dtype=np.int16)
rst = np.zeros((len(idx), len(acc)), dtype=np.int64)
for i in range(len(idx)):
for j in range(len(acc)):
rst[i,j] = idx[i]//acc[j]
Expand Down Expand Up @@ -57,6 +57,8 @@ def trace(img, p, nbs, acc, buf):
c1 = 0; c2 = 0;
newp = 0
cur = 1
buf_len = len(buf)
buf_overflow = False
while True:
buf[cur] = p
img[p] = 0
Expand All @@ -74,12 +76,15 @@ def trace(img, p, nbs, acc, buf):
newp = cp
p = newp
if c2!=0:break
return (c1-10, c2-10, idx2rc(buf[:cur+1], acc))
if cur >= buf_len:
buf_overflow = True
break
return (c1-10, c2-10, idx2rc(buf[:cur+1], acc)), buf_overflow

@jit(nopython=True) # parse the image then get the nodes and edges
def parse_struc(img, nbs, acc, iso, ring):
def parse_struc(img, nbs, acc, iso, ring, buf_size):
img = img.ravel()
buf = np.zeros(131072, dtype=np.int64)
buf = np.zeros(buf_size, dtype=np.int64)
num = 10
nodes = []
for p in range(len(img)):
Expand All @@ -93,18 +98,22 @@ def parse_struc(img, nbs, acc, iso, ring):
if img[p] <10: continue
for dp in nbs:
if img[p+dp]==1:
edge = trace(img, p+dp, nbs, acc, buf)
edge, buf_overflow = trace(img, p+dp, nbs, acc, buf)
if buf_overflow:
return nodes, edges, buf_overflow
edges.append(edge)
if not ring: return nodes, edges
if not ring: return nodes, edges, False
for p in range(len(img)):
if img[p]!=1: continue
img[p] = num; num += 1
nodes.append(idx2rc([p], acc))
for dp in nbs:
if img[p+dp]==1:
edge = trace(img, p+dp, nbs, acc, buf)
edge, buf_overflow = trace(img, p+dp, nbs, acc, buf)
if buf_overflow:
return nodes, edges, buf_overflow
edges.append(edge)
return nodes, edges
return nodes, edges, False

# use nodes and edges build a networkx graph
def build_graph(nodes, edges, multi=False, full=True):
Expand All @@ -126,12 +135,14 @@ def mark_node(ske):
mark(buf, nbs)
return buf

def build_sknw(ske, multi=False, iso=True, ring=True, full=True):
buf = np.pad(ske, (1,1), mode='constant').astype(np.uint16)
def build_sknw(ske, buf_size=131072, multi=False, iso=True, ring=True, full=True):
buf = np.pad(ske, (1,1), mode='constant').astype(np.int64)
nbs = neighbors(buf.shape)
acc = np.cumprod((1,)+buf.shape[::-1][:-1])[::-1]
mark(buf, nbs)
nodes, edges = parse_struc(buf, nbs, acc, iso, ring)
nodes, edges, buf_overflow = parse_struc(buf, nbs, acc, iso, ring, buf_size)
if buf_overflow:
raise Exception('Buffer overflow')
return build_graph(nodes, edges, multi, full)

# draw the graph
Expand Down