def makeGraph(self, img, dia, xScale, yScale):
print 'Building Graph Data Structure'
start = time.time()
G = Graph(directed=False)
vprop = G.new_vertex_property('object')
eprop = G.new_edge_property('object')
epropW = G.new_edge_property("int32_t")
avgScale = (xScale + yScale) / 2
test = np.where(img == True)
ss = np.shape(test)
cccc = 0
percentOld = 0.0
print str(np.round(percentOld, 1)) + '%'
for (i, j) in zip(test[1], test[0]):
cccc += 1
percent = (float(cccc) / float(ss[1])) * 100
if percentOld + 10 < percent:
print str(np.round(percent, 1)) + '%'
percentOld = percent
nodeNumber1 = (float(i) * yScale, float(j) * xScale)
if gu.find_vertex(
G, vprop, {
'imgIdx': (j, i),
'coord': nodeNumber1,
'nrOfPaths': 0,
'diameter': float(dia[j][i]) * avgScale
}):
v1 = gu.find_vertex(
G, vprop, {
'imgIdx': (j, i),
'coord': nodeNumber1,
'nrOfPaths': 0,
'diameter': float(dia[j][i]) * avgScale
})[0]
else:
v1 = G.add_vertex()
vprop[G.vertex(v1)] = {
'imgIdx': (j, i),
'coord': nodeNumber1,
'nrOfPaths': 0,
'diameter': float(dia[j][i]) * avgScale
}
try:
if img[j, i + 1] == True:
nodeNumber2 = (float(i + 1) * yScale, float(j) * xScale)
if gu.find_vertex(
G, vprop, {
'imgIdx': (j, i + 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i + 1]) * avgScale
}):
v2 = gu.find_vertex(
G, vprop, {
'imgIdx': (j, i + 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i + 1]) * avgScale
})[0]
if gu.find_edge(
G, eprop, {
'coord1':
vprop[v2]['coord'],
'coord2':
vprop[v1]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}):
pass
else:
e = G.add_edge(v1, v2)
epropW[e] = (((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2) /
avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}
else:
v2 = G.add_vertex()
vprop[G.vertex(v2)] = {
'imgIdx': (j, i + 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i + 1]) * avgScale
}
e = G.add_edge(v1, v2)
epropW[e] = (
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2) / avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight':
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2)**4,
'RTP':
False
}
except:
pass
try:
if img[j, i - 1] == True:
nodeNumber2 = (float(i - 1) * yScale, float(j) * xScale)
if gu.find_vertex(
G, vprop, {
'imgIdx': (j, i - 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i - 1]) * avgScale
}):
v2 = gu.find_vertex(
G, vprop, {
'imgIdx': (j, i - 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i - 1]) * avgScale
})[0]
if gu.find_edge(
G, eprop, {
'coord1':
vprop[v2]['coord'],
'coord2':
vprop[v1]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}):
pass
else:
e = G.add_edge(v1, v2)
epropW[e] = (((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2) /
avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}
else:
v2 = G.add_vertex()
vprop[G.vertex(v2)] = {
'imgIdx': (j, i - 1),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j][i - 1]) * avgScale
}
e = G.add_edge(v1, v2)
epropW[e] = (
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2) / avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight':
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2)**4,
'RTP':
False
}
except:
pass
try:
if img[j + 1, i] == True:
nodeNumber2 = (float(i) * yScale, float(j + 1) * xScale)
if gu.find_vertex(
G, vprop, {
'imgIdx': (j + 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j + 1][i]) * avgScale
}):
v2 = gu.find_vertex(
G, vprop, {
'imgIdx': (j + 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j + 1][i]) * avgScale
})[0]
if gu.find_edge(
G, eprop, {
'coord1':
vprop[v2]['coord'],
'coord2':
vprop[v1]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}):
pass
else:
e = G.add_edge(v1, v2)
epropW[e] = (((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2) /
avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}
else:
v2 = G.add_vertex()
vprop[G.vertex(v2)] = {
'imgIdx': (j + 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j + 1][i]) * avgScale
}
e = G.add_edge(v1, v2)
epropW[e] = (
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2) / avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight':
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2)**4,
'RTP':
False
}
except:
pass
try:
if img[j - 1, i] == True:
nodeNumber2 = (float(i) * yScale, float(j - 1) * xScale)
if gu.find_vertex(
G, vprop, {
'imgIdx': (j - 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j - 1][i]) * avgScale
}):
v2 = gu.find_vertex(
G, vprop, {
'imgIdx': (j - 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j - 1][i]) * avgScale
})[0]
if gu.find_edge(
G, eprop, {
'coord1':
vprop[v2]['coord'],
'coord2':
vprop[v1]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}):
pass
else:
e = G.add_edge(v1, v2)
epropW[e] = (((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2) /
avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight': ((vprop[v1]['diameter'] +
vprop[v2]['diameter']) / 2)**4,
'RTP':
False
}
else:
v2 = G.add_vertex()
vprop[G.vertex(v2)] = {
'imgIdx': (j - 1, i),
'coord': nodeNumber2,
'nrOfPaths': 0,
'diameter': float(dia[j - 1][i]) * avgScale
}
e = G.add_edge(v1, v2)
epropW[e] = (
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2) / avgScale)**4
eprop[e] = {
'coord1':
vprop[v1]['coord'],
'coord2':
vprop[v2]['coord'],
'weight':
((vprop[v1]['diameter'] + vprop[v2]['diameter']) /
2)**4,
'RTP':
False
}
except:
pass
#
print '100.0%'
print 'selecting largest connected component'
G.edge_properties["ep"] = eprop
G.edge_properties["w"] = epropW
G.vertex_properties["vp"] = vprop
l = gt.label_largest_component(G)
print(l.a)
u = gt.GraphView(G, vfilt=l)
print '# vertices'
print(u.num_vertices())
print(G.num_vertices())
print '# edges'
print(u.num_edges())
print 'building graph finished in: ' + str(time.time() - start) + 's'
return u
def makeGraphFast(self, img, dia, xScale, yScale):
print('Building Graph Data Structure'),
start = time.time()
G = Graph(directed=False)
sumAddVertices = 0
vprop = G.new_vertex_property('object')
eprop = G.new_edge_property('object')
epropW = G.new_edge_property("float")
h, w = np.shape(img)
avgScale = (xScale + yScale) / 2
addedVerticesLine2 = []
vListLine2 = []
percentOld = 0
counter = 0
'''
Sweep over each line in the image except the last line
'''
for idx, i in enumerate(img[:len(img) - 2]):
'''
Get foreground indices in the current line of the image and make vertices
'''
counter += 1
percent = (float(counter) / float(h)) * 100
if percentOld + 10 < percent:
print(str(np.round(percent, 1)) + '% '),
percentOld = percent
line1 = np.where(i == True)
if len(line1[0]) > 0:
line1 = set(line1[0]).difference(set(addedVerticesLine2))
vL = G.add_vertex(len(list(line1)))
if len(line1) > 1:
vList = vListLine2 + list(vL)
else:
vList = vListLine2 + [vL]
line1 = addedVerticesLine2 + list(line1)
for jdx, j in enumerate(line1):
vprop[vList[jdx]] = {
'imgIdx': (j, idx),
'coord': (float(j) * xScale, float(idx) * yScale),
'nrOfPaths': 0,
'diameter': float(dia[idx][j]) * avgScale
}
'''
keep order of the inserted vertices
'''
sumAddVertices += len(line1)
addedVerticesLine2 = []
vListLine2 = []
'''
Connect foreground indices to neighbours in the next line
'''
for v1 in line1:
va = vList[line1.index(v1)]
diagonalLeft = diagonalRight = True
try:
if img[idx][v1 - 1] == True:
diagonalLeft = False
vb = vList[line1.index(v1 - 1)]
e = G.add_edge(va, vb)
eprop[e] = {
'coord1':
vprop[va]['coord'],
'coord2':
vprop[vb]['coord'],
'weight': ((vprop[va]['diameter'] +
vprop[vb]['diameter']) / 2),
'RTP':
False
}
epropW[e] = 2. / (eprop[e]['weight']**2)
except:
print 'Boundary vertex at: ' + str(
[v1, idx - 1]) + ' image size: ' + str([w, h])
pass
try:
if img[idx][v1 + 1] == True:
diagonalRight = False
vb = vList[line1.index(v1 + 1)]
e = G.add_edge(va, vb)
eprop[e] = {
'coord1':
vprop[va]['coord'],
'coord2':
vprop[vb]['coord'],
'weight': ((vprop[va]['diameter'] +
vprop[vb]['diameter']) / 2),
'RTP':
False
}
epropW[e] = 2. / (eprop[e]['weight']**2)
except:
print 'Boundary vertex at: ' + str(
[v1 + 1, idx]) + ' image size: ' + str([w, h])
pass # just if we are out of bounds
try:
if img[idx + 1][v1] == True:
diagonalRight = False
diagonalLeft = False
vNew = G.add_vertex()
vprop[vNew] = {
'imgIdx': (v1, idx + 1),
'coord':
(float(v1) * xScale, float(idx + 1) * yScale),
'nrOfPaths':
0,
'diameter':
float(dia[idx + 1][v1]) * avgScale
}
vListLine2.append(vNew)
e = G.add_edge(vList[line1.index(v1)], vNew)
eprop[e] = {
'coord1':
vprop[va]['coord'],
'coord2':
vprop[vNew]['coord'],
'weight': ((vprop[va]['diameter'] +
vprop[vNew]['diameter']) / 2),
'RTP':
False
}
epropW[e] = 1. / (eprop[e]['weight']**2)
if v1 not in addedVerticesLine2:
addedVerticesLine2.append(v1)
except:
print 'Boundary vertex at: ' + str(
[v1, idx + 1]) + ' image size: ' + str([w, h])
pass
try:
if diagonalRight == True and img[idx + 1][v1 +
1] == True:
vNew = G.add_vertex()
vprop[vNew] = {
'imgIdx': (v1 + 1, idx + 1),
'coord': (float(v1 + 1) * xScale,
float(idx + 1) * yScale),
'nrOfPaths':
0,
'diameter':
float(dia[idx + 1][v1 + 1]) * avgScale
}
vListLine2.append(vNew)
e = G.add_edge(vList[line1.index(v1)], vNew)
eprop[e] = {
'coord1':
vprop[va]['coord'],
'coord2':
vprop[vNew]['coord'],
'weight': ((vprop[va]['diameter'] +
vprop[vNew]['diameter']) / 2),
'RTP':
False
}
epropW[e] = 1.41 / (eprop[e]['weight']**2)
if v1 + 1 not in addedVerticesLine2:
addedVerticesLine2.append(v1 + 1)
except:
print 'Boundary vertex at: ' + str(
[v1 + 1, idx + 1]) + ' image size: ' + str([w, h])
pass
try:
if diagonalLeft == True and img[idx + 1][v1 -
1] == True:
vNew = G.add_vertex()
vprop[vNew] = {
'imgIdx': (v1 - 1, idx + 1),
'coord': (float(v1 - 1) * xScale,
float(idx + 1) * yScale),
'nrOfPaths':
0,
'diameter':
float(dia[idx + 1][v1 - 1]) * avgScale
}
vListLine2.append(vNew)
e = G.add_edge(vList[line1.index(v1)], vNew)
eprop[e] = {
'coord1':
vprop[va]['coord'],
'coord2':
vprop[vNew]['coord'],
'weight': ((vprop[va]['diameter'] +
vprop[vNew]['diameter']) / 2),
'RTP':
False
}
epropW[e] = 1.41 / (eprop[e]['weight']**2)
if v1 - 1 not in addedVerticesLine2:
addedVerticesLine2.append(v1 - 1)
except:
print 'Boundary vertex at: ' + str(
[v1 - 1, idx + 1]) + ' image size: ' + str([w, h])
pass
try:
if img[idx][v1 + 1] == False and img[idx][
v1 - 1] == False and img[idx + 1][
v1] == False and diagonalLeft == False and diagonalRight == False:
print 'tip detected'
if img[idx - 1][v1 - 1] == False and img[idx - 1][
v1 + 1] == False and img[idx -
1][v1] == False:
print 'floating pixel'
except:
pass
print 'done!'
G.edge_properties["ep"] = eprop
G.edge_properties["w"] = epropW
G.vertex_properties["vp"] = vprop
print 'graph build in ' + str(time.time() - start)
l = gt.label_largest_component(G)
u = gt.GraphView(G, vfilt=l)
print '# vertices'
print(u.num_vertices())
print(G.num_vertices())
if u.num_vertices() != G.num_vertices():
self.__fail = float((G.num_vertices() - u.num_vertices())) / float(
G.num_vertices())
return u, u.num_vertices()