def test_is_attracting_component(self):
assert not nx.is_attracting_component(self.G1)
assert not nx.is_attracting_component(self.G2)
assert not nx.is_attracting_component(self.G3)
g2 = self.G3.subgraph([1, 2])
assert nx.is_attracting_component(g2)
assert not nx.is_attracting_component(self.G4)
def test_is_attracting_component(self):
assert_false(nx.is_attracting_component(self.G1))
assert_false(nx.is_attracting_component(self.G2))
assert_false(nx.is_attracting_component(self.G3))
g2 = self.G3.subgraph([1, 2])
assert_true(nx.is_attracting_component(g2))
assert_false(nx.is_attracting_component(self.G4))
def test_is_attracting_component(self):
assert_false(nx.is_attracting_component(self.G1))
assert_false(nx.is_attracting_component(self.G2))
assert_false(nx.is_attracting_component(self.G3))
g2 = self.G3.subgraph([1, 2])
assert_true(nx.is_attracting_component(g2))
assert_false(nx.is_attracting_component(self.G4))
# clique #list(nx.find_cliques(G)) #list(nx.make_max_clique_graph(G)) #list(nx.make_clique_bipartite(G)) #nx.graph_clique_number(G) #nx.graph_number_of_cliques(G) # components nx.is_strongly_connected(G) nx.number_strongly_connected_components(G) scc = nx.strongly_connected_components(G) nx.strongly_connected_components_recursive(G) nx.condensation(G, scc) # attracting components nx.is_attracting_component(G) nx.number_attracting_components(G) nx.attracting_components(G) # directed acyclic graphs nx.is_directed_acyclic_graph(G) nx.is_aperiodic(G) # distance measure (all for connected graph) nx.center(Gcc) nx.diameter(Gcc) nx.eccentricity(Gcc) nx.periphery(Gcc) nx.radius(Gcc) # flows (seg fault currently)
pos = nx.spring_layout(G, k=0.15, iterations=10)
# pos=nx.graphviz_layout(G)
# pos=layout(G)
G.remove_nodes_from(nx.isolates(G))
print str(" ")
print 'ATTRACTING CONNECTEDNESS OF DIRECTED GRAPHS'
print str(" ")
print str(" ")
print G.name
print str(" ")
print 'Does the graph G consist of a single attracting component?', nx.is_attracting_component(
G)
print 'The number of attracting components of G is:', nx.number_attracting_components(
G)
print str(" ")
print 'List of attracting components:'
print sorted(nx.attracting_components(G), key=len, reverse=True)
print str(" ")
lc = sorted(nx.strongly_connected_components(G), key=len, reverse=True)
print 'List of strongly connected components:'
print lc
print str(" ")
colors_list = ['c', 'b', 'g', 'y', 'k', 'm']
colors_to_select = list(colors_list)
pos=nx.spring_layout(G,k=0.15,iterations=10)
# pos=nx.graphviz_layout(G)
# pos=layout(G)
G.remove_nodes_from(nx.isolates(G))
print str(" ")
print 'ATTRACTING CONNECTEDNESS OF DIRECTED GRAPHS'
print str(" ")
print str(" ")
print G.name
print str(" ")
print 'Does the graph G consist of a single attracting component?', nx.is_attracting_component(G)
print 'The number of attracting components of G is:', nx.number_attracting_components(G)
print str(" ")
print 'List of attracting components:'
print sorted(nx.attracting_components(G), key = len, reverse=True)
print str(" ")
lc=sorted(nx.strongly_connected_components(G), key = len, reverse=True)
print 'List of strongly connected components:'
print lc
print str(" ")
colors_list=['c','b','g','y','k','m']
colors_to_select=list(colors_list)
graphs =sorted(nx.attracting_component_subgraphs(G), key = len, reverse=True)
def output_graphmetrics(pathadd,paths,file_name,data_dir):
'''
output_graphmetrics()
Calculates graph theory metrics from package NetworkX, stores in file and
outputs in .csv file.
'''
# Graph package
#print outputGraphMetrics
#if outputGraphMetrics:
try:
import networkx as nx
except ImportError:
raise ImportError, "NetworkX required."
pathG = nx.Graph()
# Get nrows and columns
nrows = len(pathadd)
ncols = len(pathadd[0])
# Now loop through pathadd rows
for irow in xrange(nrows):
# Begin loop through pathadd columns
for icol in xrange(ncols):
# Skip -9999. values
if pathadd[irow][icol] != -9999.0:
# Get spot node number
nodenumber = ncols*irow+icol
# Add node to pathG
pathG.add_node(nodenumber)
# Check neighbors for edges all 8 conditions
# Count 0,1,2,3,4,5,6,7 in counter-clockwise
# around center cell starting 0 in lower
# left corner
# Left top corner:
if irow == 0 and icol == 0:
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 2
if pathadd[irow+1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Right top corner
elif irow == 0 and icol == ncols-1:
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 0
if pathadd[irow+1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Left bottom corner
elif irow == nrows-1 and icol == 0:
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 4
if pathadd[irow-1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Right bottom corner
elif irow == nrows-1 and icol == ncols-1:
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 6
if pathadd[irow-1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Top side
elif irow == 0 and icol != 0 and icol != ncols-1:
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 0
if pathadd[irow+1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 2
if pathadd[irow+1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Left side
elif icol == 0 and irow != 0 and irow != nrows-1:
# Get neighbors -spots 1,2,3,4,5
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 2
if pathadd[irow+1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 4
if pathadd[irow-1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Right side
elif icol == ncols-1 and irow != 0 and irow != nrows-1:
# Get neighbors - spots 0,1,5,6,7
# Get neighbors: spot 0
if pathadd[irow+1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 6
if pathadd[irow-1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Bottom side:
elif irow == nrows-1 and icol != 0 and icol != ncols-1:
# Get neighbors - spots 3,4,5,6,7
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 4
if pathadd[irow-1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 6
if pathadd[irow-1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Everything else:
else:
# Get neighbors: spot 0
if pathadd[irow+1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 1
if pathadd[irow+1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 2
if pathadd[irow+1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow+1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 3
if pathadd[irow][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 4
if pathadd[irow-1][icol+1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol+1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 5
if pathadd[irow-1][icol] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+icol
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 6
if pathadd[irow-1][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow-1)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Get neighbors: spot 7
if pathadd[irow][icol-1] != -9999.:
# Then get egde number
edgenumber = ncols*(irow)+(icol-1)
# Then add edge to pathG
pathG.add_edge(nodenumber,edgenumber)
# Calculate properties from path lengths: min, max, average
pathlen = []
for i in xrange(len(paths)):
pathlen.append(paths[i][2])
# Create file to write info to
try:
fout = open(data_dir+file_name, 'w')
except(IOerror,OSerror) as e:
print("UNICOROutputs %s, error%s"(filename,e))
sys.exit(-1)
# Write header information
fout.write('Minimum Path Length,')
fout.write(str(min(pathlen))+'\n')
fout.write('Maximum Path Length,')
fout.write(str(max(pathlen))+'\n')
fout.write('Average Path Length,')
fout.write(str(sum(pathlen)/len(paths))+'\n')
fout.write('Density of Graph,')
fout.write(str(nx.density(pathG))+'\n')
fout.write('Number of nodes,')
fout.write(str(nx.number_of_nodes(pathG))+'\n')
fout.write('Number of edges,')
fout.write(str(nx.number_of_edges(pathG))+'\n')
fout.write('Is the graph a bipartite,')
fout.write(str(nx.is_bipartite(pathG))+'\n')
fout.write('Size of the largest clique,')
fout.write(str(nx.graph_clique_number(pathG))+'\n')
fout.write('Number of maximal cliques,')
fout.write(str(nx.graph_number_of_cliques(pathG))+'\n')
fout.write('Transitivity,')
fout.write(str(nx.transitivity(pathG))+'\n')
fout.write('Average clustering coefficient,')
fout.write(str(nx.average_clustering(pathG))+'\n')
fout.write('Test graph connectivity,')
fout.write(str(nx.is_connected(pathG))+'\n')
fout.write('Number of connected components,')
fout.write(str(nx.number_connected_components(pathG))+'\n')
fout.write('Consists of a single attracting component,')
fout.write(str(nx.is_attracting_component(pathG))+'\n')
if nx.is_attracting_component(pathG) == True:
fout.write('Number of attracting components,')
fout.write(str(nx.number_attracting_components(pathG))+'\n')
if nx.is_connected(pathG):
fout.write('Center,')
fout.write(str(nx.center(pathG))+'\n')
fout.write('Diameter,')
fout.write(str(nx.diameter(pathG))+'\n')
#fout.write('Eccentricity,')
#fout.write(str(nx.eccentricity(pathG))+'\n')
fout.write('Periphery,')
fout.write(str(nx.periphery(pathG))+'\n')
fout.write('Radius,')
fout.write(str(nx.radius(pathG))+'\n')
fout.write('Degree assortativity,')
fout.write(str(nx.degree_assortativity(pathG))+'\n')
fout.write('Degree assortativity Pearsons r,')
fout.write(str(nx.degree_pearsonr(pathG))+'\n')
# Close file
fout.close
del(pathG)
# End::output_graphmetrics()
# clique #list(nx.find_cliques(G)) #list(nx.make_max_clique_graph(G)) #list(nx.make_clique_bipartite(G)) #nx.graph_clique_number(G) #nx.graph_number_of_cliques(G) # components nx.is_strongly_connected(G) nx.number_strongly_connected_components(G) scc = nx.strongly_connected_components(G) nx.strongly_connected_components_recursive(G) nx.condensation(G, scc) # attracting components nx.is_attracting_component(G) nx.number_attracting_components(G) nx.attracting_components(G) # directed acyclic graphs nx.is_directed_acyclic_graph(G) nx.is_aperiodic(G) # distance measure (all for connected graph) nx.center(Gcc) nx.diameter(Gcc) nx.eccentricity(Gcc) nx.periphery(Gcc) nx.radius(Gcc) # flows (seg fault currently)
