def run_test():
######################################################
#
# Runs a couple sanity checks on the network:
#
# 0 0
# |\ /|
# | 0--0 |
# |/ \|
# 0 0
#
# with the obvious correct grouping followed
# by a slightly non-optimal grouping.
#
# Results should be Q1 ~ .357, Q2 ~ .122
#
######################################################
network = create_test_network()
print "A = ", network
group1 = Grouping.create_from_vector([1, 1, 1, 0, 0, 0], network)
print "S1 = ", group1
group2 = Grouping.create_from_vector([1, 1, 1, 1, 0, 0], network)
print "S2 = ", group2
group3 = Grouping.create_from_vector([1, 1, 0, 1, 0, 0], network)
print "S3 = ", group3
Q1 = group1.get_modularity()
Q2 = group2.get_modularity()
Q3 = group3.get_modularity()
print "Modularities:"
print "Q_1 = ", Q1
print "Q_2 = ", Q2
print "Q_3 = ", Q3
if ((Q1 - 0.357) < 0.001) and ((Q2 - 0.122) < 0.001):
print "Test passed!"
else:
print "*** Test Failed! ***"
return False
print "Trying point patch method..."
pointpatch = PointPatch(3, 0, 1)
Q4 = pointpatch.get_modularity(group1, network)
print "Q_4 = ", Q4
print group1.get_nodes()
print group1.get_groups()
pointpatch.modify(group1)
print group1.get_nodes()
print group1.get_groups()
Q5 = group1.calculate_modularity(network)
print "Q_5 = ", Q5
if Q5 - Q2 < 0.00001:
print "Test passed!"
else:
print "*** Test Failed! ***"
return False
return True
def run_test():
######################################################
#
# Runs a couple sanity checks on the network:
#
# 0 0
# |\ /|
# | 0--0 |
# |/ \|
# 0 0
#
# with the obvious correct grouping followed
# by a slightly non-optimal grouping.
#
# Results should be Q1 ~ .357, Q2 ~ .122
#
######################################################
network = create_test_network()
print "A = ", network
group1 = Grouping.create_from_vector([1, 1, 1, 0, 0, 0], network)
print "S1 = ", group1
group2 = Grouping.create_from_vector([1, 1, 1, 1, 0, 0], network)
print "S2 = ", group2
group3 = Grouping.create_from_vector([1, 1, 0, 1, 0, 0], network)
print "S3 = ", group3
Q1 = group1.get_modularity()
Q2 = group2.get_modularity()
Q3 = group3.get_modularity()
print "Modularities:"
print "Q_1 = ", Q1
print "Q_2 = ", Q2
print "Q_3 = ", Q3
if ((Q1 - .357) < .001) and ((Q2 - .122) < .001):
print "Test passed!"
else:
print "*** Test Failed! ***"
return False
print "Trying point patch method..."
pointpatch = PointPatch(3, 0, 1)
Q4 = pointpatch.get_modularity(group1, network)
print "Q_4 = ", Q4
print group1.get_nodes()
print group1.get_groups()
pointpatch.modify(group1)
print group1.get_nodes()
print group1.get_groups()
Q5 = group1.calculate_modularity(network)
print "Q_5 = ", Q5
if Q5 - Q2 < .00001:
print "Test passed!"
else:
print "*** Test Failed! ***"
return False
return True
def create_graphml_file(self, filename, grouping=None):
"""Creates a graphml file that can be used to generate a visualization
of the network using the optional partition to color the nodes."""
file = open(filename + ".graphml", "w")
if grouping == None:
grouping = Grouping.create_from_vector([0] * self.number_of_nodes)
n = self.number_of_nodes
m = self.number_of_edges
nodes = grouping.get_nodes()
non_empty_groups = grouping.get_non_empty_groups()
c = len(non_empty_groups)
A = self.adjacency_matrix
print n, m, c, len(nodes), len(colors)
# set palettes...
if c <= len(colors):
if c == 1:
palette = ["#FFFFFF"]
else:
palette = graphml_colors
else:
palette = map(lambda x: "gray" + str(x), range(0, 100))
# Preamble stuff...
file.write(
'<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n<graphml xmlns="http://graphml.graphdrawing.org/xmlns/graphml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:y="http://www.yworks.com/xml/graphml" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns/graphml http://www.yworks.com/xml/schema/graphml/1.0/ygraphml.xsd">\n<key for="node" id="d0" yfiles.type="nodegraphics"/>\n<key attr.name="description" attr.type="string" for="node" id="d1"/>\n<key for="edge" id="d2" yfiles.type="edgegraphics"/>\n<key attr.name="description" attr.type="string" for="edge" id="d3"/>\n<key for="graphml" id="d4" yfiles.type="resources"/>\n'
)
# Graph header
file.write(
"""<graph edgedefault="directed" id="G" parse.edges="%d" parse.nodes="%d" parse.order="free">\n""" % (m, n)
)
# Now we write the nodes...
for i in xrange(0, n):
file.write(
"""<node id="n%d">
<data key="d0">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="80.56138057743618" y="0.0"/>
<y:Fill color="%s" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="18.701171875" modelName="internal" modelPosition="c" textColor="#000000" visible="true" width="33.0" x="-1.5" y="5.6494140625">%d</y:NodeLabel>
<y:Shape type="ellipse"/>
</y:ShapeNode>
</data>
<data key="d1"/>
</node>\n"""
% (i, palette[non_empty_groups.index(nodes[i])], i)
)
current_edge = 0
# Now we do the edges...
for i in range(0, n):
for j in range(0, i + 1):
if A[i, j] == 1:
file.write(
"""<edge id="e%d" source="n%d" target="n%d">
<data key="d2">
<y:PolyLineEdge>
<y:Path sx="0.0" sy="0.0" tx="0.0" ty="0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="none"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
<data key="d3"/>
</edge>\n"""
% (current_edge, i, j)
)
current_edge += 1
# close off tags...
file.write(
""" </graph>
<data key="d4">
<y:Resources/>
</data>
</graphml>"""
)
file.close()
def create_graphml_file(self, filename, grouping=None):
"""Creates a graphml file that can be used to generate a visualization
of the network using the optional partition to color the nodes."""
file = open(filename + ".graphml", "w")
if grouping == None:
grouping = Grouping.create_from_vector([0] * self.number_of_nodes)
n = self.number_of_nodes
m = self.number_of_edges
nodes = grouping.get_nodes()
non_empty_groups = grouping.get_non_empty_groups()
c = len(non_empty_groups)
A = self.adjacency_matrix
print n, m, c, len(nodes), len(colors)
# set palettes...
if c <= len(colors):
if c == 1:
palette = ["#FFFFFF"]
else:
palette = graphml_colors
else:
palette = map(lambda x: "gray" + str(x), range(0, 100))
# Preamble stuff...
file.write(
'<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n<graphml xmlns="http://graphml.graphdrawing.org/xmlns/graphml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:y="http://www.yworks.com/xml/graphml" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns/graphml http://www.yworks.com/xml/schema/graphml/1.0/ygraphml.xsd">\n<key for="node" id="d0" yfiles.type="nodegraphics"/>\n<key attr.name="description" attr.type="string" for="node" id="d1"/>\n<key for="edge" id="d2" yfiles.type="edgegraphics"/>\n<key attr.name="description" attr.type="string" for="edge" id="d3"/>\n<key for="graphml" id="d4" yfiles.type="resources"/>\n'
)
# Graph header
file.write(
"""<graph edgedefault="directed" id="G" parse.edges="%d" parse.nodes="%d" parse.order="free">\n"""
% (m, n))
# Now we write the nodes...
for i in xrange(0, n):
file.write("""<node id="n%d">
<data key="d0">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="80.56138057743618" y="0.0"/>
<y:Fill color="%s" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="18.701171875" modelName="internal" modelPosition="c" textColor="#000000" visible="true" width="33.0" x="-1.5" y="5.6494140625">%d</y:NodeLabel>
<y:Shape type="ellipse"/>
</y:ShapeNode>
</data>
<data key="d1"/>
</node>\n""" % (i, palette[non_empty_groups.index(nodes[i])], i))
current_edge = 0
# Now we do the edges...
for i in range(0, n):
for j in range(0, i + 1):
if A[i, j] == 1:
file.write("""<edge id="e%d" source="n%d" target="n%d">
<data key="d2">
<y:PolyLineEdge>
<y:Path sx="0.0" sy="0.0" tx="0.0" ty="0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="none"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
<data key="d3"/>
</edge>\n""" % (current_edge, i, j))
current_edge += 1
# close off tags...
file.write(""" </graph>
<data key="d4">
<y:Resources/>
</data>
</graphml>""")
file.close()
