def setPercentil(self):
self.spinLowerThreshold = self.histogram.minValue
net = orngNetwork.Network(self.matrix.dim, 0)
lower, upper = net.getDistanceMatrixThreshold(self.matrix,
self.percentil / 100)
self.spinUpperThreshold = upper
self.generateGraph()
import orngNetwork
from pylab import *
# create graph object of type GraphAsList
net = orngNetwork.Network(5, 0)
# set edges
for i in range(4):
for j in range(i + 1, 5):
net[i, j] = 1
# vertices are placed randomly in NetworkOptimization constructor
networkOptimization = orngNetwork.NetworkOptimization(net)
# optimize verices layout with one of included algorithms
networkOptimization.fruchtermanReingold(100, 1000)
# read all edges and plot a line
for u, v in net.getEdges():
x1, y1 = net.coors[0][u], net.coors[1][u]
x2, y2 = net.coors[0][v], net.coors[1][v]
plot([x1, x2], [y1, y2], 'b-')
# read x and y coordinates to Python list
x = net.coors[0]
y = net.coors[1]
# plot vertices
plot(x, y, 'ro')
show()
def generateGraph(self, N_changed = False):
self.searchStringTimer.stop()
self.attributeCombo.box.setEnabled(False)
self.error()
matrix = None
self.warning('')
if N_changed:
self.netOption = 1
if self.matrix == None:
self.infoa.setText("No data loaded.")
self.infob.setText("")
return
#print len(self.histogram.yData), len(self.histogram.xData)
nEdgesEstimate = 2 * sum([self.histogram.yData[i] for i,e in enumerate(self.histogram.xData) if self.spinLowerThreshold <= e <= self.spinUpperThreshold])
if nEdgesEstimate > 200000:
self.graph = None
nedges = 0
n = 0
self.error('Estimated number of edges is too high (%d).' % nEdgesEstimate)
else:
graph = orngNetwork.Network(self.matrix.dim, 0)
matrix = self.matrix
if hasattr(self.matrix, "items"):
if type(self.matrix.items) == type(orange.ExampleTable(orange.Domain(orange.StringVariable('tmp')))):
#graph.setattr("items", self.data.items)
graph.items = self.matrix.items
else:
data = [[str(x)] for x in self.matrix.items]
items = orange.ExampleTable(orange.Domain(orange.StringVariable('label'), 0), data)
#graph.setattr("items", list(items))
graph.items = list(items)
# set the threshold
# set edges where distance is lower than threshold
self.warning(0)
if self.kNN >= self.matrix.dim:
self.warning(0, "kNN larger then supplied distance matrix dimension. Using k = %i" % (self.matrix.dim - 1))
nedges = graph.fromDistanceMatrix(self.matrix, self.spinLowerThreshold, self.spinUpperThreshold, min(self.kNN, self.matrix.dim - 1), self.andor)
edges = graph.getEdges()
#print graph.nVertices, self.matrix.dim
if self.dstWeight == 1:
if graph.directed:
for u,v in edges:
foo = 1
if str(graph[u,v]) != "0":
foo = 1.0 - float(graph[u,v])
graph[u,v] = foo
else:
for u,v in edges:
if u <= v:
foo = 1
if str(graph[u,v]) != "0":
foo = 1.0 - float(graph[u,v])
graph[u,v] = foo
n = len(edges)
#print 'self.netOption',self.netOption
# exclude unconnected
if str(self.netOption) == '1':
components = [x for x in graph.getConnectedComponents() if len(x) > self.excludeLimit]
if len(components) > 0:
include = reduce(lambda x,y: x+y, components)
if len(include) > 1:
self.graph = orngNetwork.Network(graph.getSubGraph(include))
matrix = self.matrix.getitems(include)
else:
self.graph = None
matrix = None
else:
self.graph = None
matrix = None
# largest connected component only
elif str(self.netOption) == '2':
component = graph.getConnectedComponents()[0]
if len(component) > 1:
self.graph = orngNetwork.Network(graph.getSubGraph(component))
matrix = self.matrix.getitems(component)
else:
self.graph = None
matrix = None
# connected component with vertex by label
elif str(self.netOption) == '3':
self.attributeCombo.box.setEnabled(True)
self.graph = None
matrix = None
#print self.attributeCombo.currentText()
if self.attributeCombo.currentText() != '' and self.label != '':
components = graph.getConnectedComponents()
txt = self.label.lower()
#print 'txt:',txt
nodes = [i for i, values in enumerate(self.matrix.items) if txt in str(values[str(self.attributeCombo.currentText())]).lower()]
#print "nodes:",nodes
if len(nodes) > 0:
vertices = []
for component in components:
for node in nodes:
if node in component:
if len(component) > 0:
vertices.extend(component)
if len(vertices) > 0:
#print "n vertices:", len(vertices), "n set vertices:", len(set(vertices))
vertices = list(set(vertices))
self.graph = orngNetwork.Network(graph.getSubGraph(vertices))
matrix = self.matrix.getitems(vertices)
else:
self.graph = graph
if matrix != None:
self.matrix = matrix
self.pconnected = nedges
self.nedges = n
if hasattr(self, "infoa"):
self.infoa.setText("%d vertices" % self.matrix.dim)
if hasattr(self, "infob"):
self.infob.setText("%d connected (%3.1f%%)" % (nedges, nedges / float(self.matrix.dim) * 100))
if hasattr(self, "infoc"):
self.infoc.setText("%d edges (%d average)" % (n, n / float(self.matrix.dim)))
#print 'self.graph:',self.graph+
if hasattr(self, "sendSignals"):
self.sendSignals()
self.histogram.setBoundary(self.spinLowerThreshold, self.spinUpperThreshold)
def exportNetwork(self,
absolute_int=10,
positive_int=0,
negative_int=0,
best_attributes=0,
significant_digits=2,
pretty_names=1,
widget_coloring=1,
pcutoff=1):
NA = len(self.names)
### SELECTION OF INTERACTIONS AND ATTRIBUTES ###
# prevent crashes
best_attributes = min(best_attributes, len(self.attlist))
positive_int = min(positive_int, len(self.list))
absolute_int = min(absolute_int, len(self.list))
negative_int = min(negative_int, len(self.list))
# select the top interactions
ins = []
if positive_int > 0:
ins += self.list[-positive_int:]
ins += self.list[:negative_int]
if absolute_int > 0:
ins += self.abslist[-absolute_int:]
# pick best few attributes
atts = []
if best_attributes > 0:
atts += [i for (x, i) in self.attlist[-best_attributes:]]
# disregard the insignificant attributes, interactions
if len(self.plist) > 0 and pcutoff < 1:
# attributes
oats = atts
atts = []
for i in oats:
if self.plut[(i, -1)] < pcutoff:
atts.append(i)
# interactions
oins = ins
ins = []
for y in oins:
(ig, i, j) = y[1]
if self.plut[(i, j, -1)] < pcutoff:
ins.append(y)
ints = []
max_igain = -1e6
min_gain = 1e6 # lowest information gain of involved attributes
# remove duplicates and sorting keys
for (x, v) in ins:
if v not in ints:
ints.append(v)
# add to attribute list
(ig, i, j) = v
max_igain = max(abs(ig), max_igain)
for x in [i, j]:
if x not in atts:
atts.append(x)
min_gain = min(min_gain, self.gains[x])
# fill-in the attribute list with all possibly more important attributes
## todo
### NODE DRAWING ###
map = {}
graph = orngNetwork.Network(len(atts), 0)
table = []
for i in range(len(atts)):
map[atts[i]] = i
ndx = atts[i]
t = '%s' % self.names[ndx]
if pretty_names:
t = string.replace(t, "ED_", "")
t = string.replace(t, "D_", "")
t = string.replace(t, "M_", "")
t = string.replace(t, " ", "\\n")
t = string.replace(t, "-", "\\n")
t = string.replace(t, "_", "\\n")
r = self.gains[ndx] * 100.0 / self.entropy
table.append([i + 1, t, r])
d = orange.Domain([
orange.FloatVariable('index'),
orange.StringVariable('label'),
orange.FloatVariable('norm. gain')
])
data = orange.ExampleTable(d, table)
graph.items = data
table = []
for (ig, i, j) in ints:
j = map[j]
i = map[i]
perc = int(
abs(ig) * 100.0 / max(max_igain, self.attlist[-1][0]) + 0.5)
graph[i, j] = perc / 30 + 1
if self.entropy > 1e-6:
mc = _nicefloat(100.0 * ig / self.entropy,
significant_digits) + "%"
else:
mc = _nicefloat(0.0, significant_digits)
if len(self.plist) > 0 and pcutoff < 1:
mc += "\\nP\<%.3f" % self.plut[(i, j, -1)]
if ig > 0:
if widget_coloring:
color = "green"
else:
color = '"0.0 %f 0.9"' % (0.3 + 0.7 * perc / 100.0
) # adjust saturation
dir = "both"
else:
if widget_coloring:
color = "red"
else:
color = '"0.5 %f 0.9"' % (0.3 + 0.7 * perc / 100.0
) # adjust saturation
dir = 'none'
table.append([i, j, mc, dir, color])
d = orange.Domain([
orange.FloatVariable('u'),
orange.FloatVariable('v'),
orange.StringVariable('label'),
orange.EnumVariable('dir', values=["both", "none"]),
orange.EnumVariable('color', values=["green", "red"])
])
data = orange.ExampleTable(d, table)
graph.links = data
return graph
