def ChangeEdgeWeights(self):
if self.G == None:
return
n = self.edgeWeightVar.get()
k = self.G.edgeWeights.keys()
if self.G.edgeWeights[0].QInteger():
initialWeight = 0
else:
initialWeight = 0.0
if n == 1 or n == 2:
if 2 in k:
del (self.G.edgeWeights[2])
else:
if 2 not in k:
self.G.edgeWeights[2] = EdgeWeight(self.G, initialWeight)
if self.G.edgeWeights[0].QInteger():
self.G.edgeWeights[2].Integerize()
if n == 1:
if 1 in k:
del (self.G.edgeWeights[1])
else:
if 1 not in k:
self.G.edgeWeights[1] = EdgeWeight(self.G, initialWeight)
if self.G.edgeWeights[0].QInteger():
self.G.edgeWeights[1].Integerize()
def Clear(self):
""" Delete all vertices and edges from the subgraph. """
self.vertices = []
self.adjLists = {}
self.invAdjLists = {} # Inverse Adjazenzlisten
self.size = 0
self.totalWeight = 0
self.edgeWeights = {} # Dictionary of edge labellings
self.edgeWeights[0] = EdgeWeight(self)
self.vertexWeights.clear() # None by default
self.highVertexID = 0 # INTERNAL
def OpenDotGraph(fileName):
""" Reads in a graph from file fileName. File-format is supposed
to be dot (*.dot) used in """
G = Graph.Graph()
G.directed = 1
E = VertexLabeling()
W = EdgeWeight(G)
L = VertexLabeling()
VLabel = VertexLabeling()
ELabel = EdgeLabeling()
import re
file = open(fileName, 'r')
lines = file.readlines()
file.close()
dot2graph = {}
for l in lines[3:]:
items = string.split(l)
if len(items) < 2:
break
if items[1] != '->':
v = G.AddVertex()
dot_v = int(items[0])
L[v] = "%d" % dot_v
dot2graph[dot_v] = v
m = re.search('label=("[^"]+")', l)
VLabel[v] = m.group(1)[1:-1]
m = re.search('pos="(\d+),(\d+)"', l)
x = int(m.group(1))
y = int(m.group(2))
E[v] = Point2D(x,y)
else:
m = re.search('(\d+) -> (\d+)', l)
v = dot2graph[int(m.group(1))]
w = dot2graph[int(m.group(2))]
m = re.search('label=("[^"]+")', l)
#print l
#print v,w,m.group(1)
G.AddEdge(v,w)
weight = float(m.group(1)[1:-1])
W[(v,w)] = weight
ELabel[(v,w)] = "%0.2f" % weight
G.embedding = E
G.labeling = L
G.nrEdgeWeights = 1
G.edgeWeights[0] = W
G.vertexAnnotation = VLabel
G.edgeAnnotation = ELabel
return G
def __init__(self, vertexClass, edgeClass):
self.vertexClass = vertexClass
self.edgeClass = edgeClass
self.vertices = {}
self.edges = {}
self.highVertexID = 0 # INTERNAL
self.simple = 1
self.euclidian = 1
self.directed = 0
self.edgeWeights = {} # Dictionary of edge labellings
self.edgeWeights[0] = EdgeWeight(self)
self.vertexWeights = {} # None by default
self.size = 0
self.edgeWidth = None
self.vertexAnnotation = None
self.edgeAnnotation = None
self.properties = {}
def __init__(self):
self.simple = 1
self.euclidian = 1
self.directed = 0
self.vertices = []
self.adjLists = {}
self.invAdjLists = {} # Inverse Adjazenzlisten
self.highVertexID = 0 # INTERNAL
self.embedding = VertexLabeling() # 2D-Positions
self.labeling = VertexLabeling() # Names of vertices
self.edgeWeights = {} # Dictionary of edge labellings
self.edgeWeights[0] = EdgeWeight(self)
self.vertexWeights = {} # None by default
self.size = 0
self.edgeWidth = None
self.vertexAnnotation = None
self.edgeAnnotation = None
self.properties = {}
def OpenGMLGraph(fileName):
""" Reads in a graph from file fileName. File-format is supposed
to be GML (*.gml) """
G = Graph.Graph()
G.directed = 0
E = VertexLabeling()
W = EdgeWeight(G)
L = VertexLabeling()
VLabel = VertexLabeling()
ELabel = EdgeLabeling()
file = open(fileName, 'r')
g = ParseGML(file)
file.close()
if g[0][0] != 'graph':
log.error("Serious format error in %s. first key is not graph" % fileName)
return
else:
l = g[0][1]
for i in xrange(len(l)):
key = l[i][0]
value = l[i][1]
if key == 'node':
d = PairListToDictionary(value)
v = G.AddVertex()
try:
VLabel[v] = eval(d['label'])
P = PairListToDictionary(d['graphics'])
E[v] = Point2D(eval(P['x']), eval(P['y']))
except:
d = None
P = None
elif key == 'edge':
d = PairListToDictionary(value)
try:
s = eval(d['source'])
t = eval(d['target'])
G.AddEdge(s,t)
ELabel[(s,t)] = eval(d['label'])
W[(s,t)] = 0
except:
d = None
elif key == 'directed':
G.directed = 1
for v in G.vertices:
L[v] = v
G.embedding = E
G.labeling = L
G.nrEdgeWeights = 1
G.edgeWeights[0] = W
G.vertexAnnotation = VLabel
G.edgeAnnotation = ELabel
return G
def OpenCATBoxGraph(_file):
""" Reads in a graph from file fileName. File-format is supposed
to be from old CATBOX++ (*.cat) """
G = Graph.Graph()
E = VertexLabeling()
W = EdgeWeight(G)
L = VertexLabeling()
# get file from name or file object
graphFile=None
if type(_file) in types.StringTypes:
graphFile = open(_file, 'r')
elif type(_file)==types.FileType or issubclass(_file.__class__,StringIO.StringIO):
graphFile=_file
else:
raise Exception("got wrong argument")
lineNr = 1
firstVertexLineNr = -1
lastVertexLineNr = -1
firstEdgeLineNr = -1
lastEdgeLineNr = -1
intWeights = 0
while 1:
line = graphFile.readline()
if not line:
break
if lineNr == 2: # Read directed and euclidian
splitLine = split(line[:-1],';')
G.directed = eval(split(splitLine[0],':')[1])
G.simple = eval(split(splitLine[1],':')[1])
G.euclidian = eval(split(splitLine[2],':')[1])
intWeights = eval(split(splitLine[3],':')[1])
nrOfEdgeWeights = eval(split(splitLine[4],':')[1])
nrOfVertexWeights = eval(split(splitLine[5],':')[1])
for i in xrange(nrOfEdgeWeights):
G.edgeWeights[i] = EdgeWeight(G)
for i in xrange(nrOfVertexWeights):
G.vertexWeights[i] = VertexWeight(G)
if lineNr == 5: # Read nr of vertices
nrOfVertices = eval(split(line[:-2],':')[1]) # Strip of "\n" and ;
firstVertexLineNr = lineNr + 1
lastVertexLineNr = lineNr + nrOfVertices
if firstVertexLineNr <= lineNr and lineNr <= lastVertexLineNr:
splitLine = split(line[:-1],';')
v = G.AddVertex()
x = eval(split(splitLine[1],':')[1])
y = eval(split(splitLine[2],':')[1])
for i in xrange(nrOfVertexWeights):
w = eval(split(splitLine[3+i],':')[1])
G.vertexWeights[i][v] = w
E[v] = Point2D(x,y)
if lineNr == lastVertexLineNr + 1: # Read Nr of edges
nrOfEdges = eval(split(line[:-2],':')[1]) # Strip of "\n" and ;
firstEdgeLineNr = lineNr + 1
lastEdgeLineNr = lineNr + nrOfEdges
if firstEdgeLineNr <= lineNr and lineNr <= lastEdgeLineNr:
splitLine = split(line[:-1],';')
h = eval(split(splitLine[0],':')[1])
t = eval(split(splitLine[1],':')[1])
G.AddEdge(t,h,False)
for i in xrange(nrOfEdgeWeights):
G.edgeWeights[i][(t,h)] = eval(split(splitLine[3+i],':')[1])
lineNr = lineNr + 1
graphFile.close()
for v in G.vertices:
L[v] = v
G.embedding = E
G.labeling = L
if intWeights:
G.Integerize('all')
for i in xrange(nrOfVertexWeights):
G.vertexWeights[i].Integerize()
return G
def fromDOM(self, XMLNode):
# self.hmmClass.fromDOM(XMLNode.getElementsByTagName("hmm:class")[0])
for tag in XMLNode.getElementsByTagName("hmm:class"):
self.hmmClass.fromDOM(tag)
nameNodes = XMLNode.getElementsByTagName("hmm:name")
if (len(nameNodes) > 0):
self.modelType = nameNodes[0].firstChild.nodeValue
# model type node
modelTypeNodes = XMLNode.getElementsByTagName("hmm:modeltype")
if (len(modelTypeNodes) > 0):
self.modelType = modelTypeNodes[0].firstChild.nodeValue
if (self.modelType == "pairHMM"):
alphabetNodes = XMLNode.getElementsByTagName("hmm:alphabet")
for alphabetNode in alphabetNodes:
alphabet = DiscreteHMMAlphabet()
alphabet.fromDOM(alphabetNode)
self.hmmAlphabets[alphabet.id] = alphabet
transitionFunctionNodes = XMLNode.getElementsByTagName(
"hmm:transitionfunction")
for transitionFunctionNode in transitionFunctionNodes:
transitionFunction = TransitionFunction()
transitionFunction.fromDom(transitionFunctionNode)
self.transitionFunctions[
transitionFunction.id] = transitionFunction
else:
# If it is no pair hmm One "hmm:alphabet" XML element
self.hmmAlphabets[0] = DiscreteHMMAlphabet()
self.hmmAlphabets[0].fromDOM(
XMLNode.getElementsByTagName("hmm:alphabet")[0])
self.backgroundDistributions.fromDOM(XMLNode)
nodes = XMLNode.getElementsByTagName("node")
for n in nodes:
state = HMMState(-1, self)
state.fromDOM(n)
self.state[state.index] = state # key must be string
self.id2index[state.id] = state.index
self.G.embedding[state.index] = state.pos
self.G.labeling[state.index] = "%s\n%s" % (state.id, state.label
) # XXX Hack Aaaargh!
edges = XMLNode.getElementsByTagName("edge")
# nr_classes = int(self.hmmClass.high()-self.hmmClass.low())+1
nr_classes = 1
# search in all states for the maximal kclasses
for s in self.state.values():
if (s.kclasses > nr_classes):
nr_classes = s.kclasses
for i in range(nr_classes):
self.G.edgeWeights[i] = EdgeWeight(self.G)
for edge in edges:
i = self.id2index[int(edge.attributes['source'].nodeValue)]
j = self.id2index[int(edge.attributes['target'].nodeValue)]
source = self.state[i]
datas = edge.getElementsByTagName("data")
for data in datas:
dataKey = data.attributes['key'].nodeValue
# dataValue = data.firstChild.nodeValue
if dataKey == 'prob':
#p = float(dataValue)
# collect all strings from childnodes
dataValue = ""
for child in data.childNodes:
dataValue += child.nodeValue
p = listFromCSV(dataValue, types.FloatType)
self.G.AddEdge(i, j)
if len(p) == 1: # only one class
for cl in range(source.kclasses - 1):
p.append(0.0)
for cl in range(source.kclasses):
self.G.edgeWeights[cl][(i, j)] = p[cl]