# get number of nodes nodes = len(g.vs) # get edges in the right format edgelist = np.array( [edge.tuple for edge in g.es], np.int32) print 'igraph baseline' start = time.clock() igLayout = g.layout_fruchterman_reingold() elapsed = time.clock() elapsed = elapsed - start print "Time spent for igraph baseline is: ", elapsed ig.plot(g, "output/plot_baseline_igraph.png", layout=igLayout) print 'float baseline:' start = time.clock() pos = fl.layout_fr(nodes*dimension, edgelist, max_it, temp ) pos = np.reshape(pos, (nodes, dimension)) floatLayout = ig.Layout( tuple(map(tuple, pos )) ) elapsed = time.clock() elapsed = elapsed - start print "Time spent for fastlayout float baseline is: ", elapsed ig.plot(g, "output/plot_baseline_float.png", layout=floatLayout) # NOTE # this one works different as it uses a different layout # for the data, so no reshaping has to be done, but you # have to zip first and second half of the array print 'layout_fr_stride' start = time.clock() pos = fl.layout_fr_stride( nodes*dimension, edgelist, max_it, temp ) float6Layout = ig.Layout( tuple(zip(pos[0:nodes], pos[nodes:2*nodes])) )
_l = len(edges)
#calculate node coords
print "VIZUALISATION TIMER: igraph layouting :",datetime.now()
#read from tmp file
ly_start = datetime.now()
graph = igraph.Graph.Read( tmp_name , directed=directed_graph,format="ncol",weights=False )
#new layouting by rcattano
dimension = 2
max_it = 500
temp = 1
nodes = len(graph.vs)
edges = np.array( [edge.tuple for edge in graph.es], np.int32)
pos = fl.layout_fr(nodes*dimension, edges, max_it, temp )
#get the Layout object here.
#http://igraph.org/python/doc/igraph.layout.Layout-class.html
scl = int( _l/ 100 ) #int( _l * _l / 10 )
if ly_alg == "Fruchterman-Reingold":
ly = igraph.Layout(tuple(zip(pos[0:nodes], pos[nodes:2*nodes])))
scl = scl / 3
elif ly_alg == "LGL":
ly = graph.layout_lgl()
elif ly_alg == "Kamada-Kawai":
ly = graph.layout_kamada_kawai()
scl = scl / 10
elif ly_alg == "Star":
ly = graph.layout_star()
scl = scl * 2
def layout(self, ly_alg = "Fruchterman-Reingold", directed_graph=True):
if ly_alg not in SUPPORTED_LAYOUTS:
return {
"graph_ready": False,
"errors": "Unsuspported layout algorithm"
}
print "VIZUALISATION TIMER: igraph layouting :",datetime.now()
ly_start = datetime.now()
#new layouting by rcattano
dimension = 2
max_it = 500
temp = 1
nodes = len(self.igraph.vs)
edges = np.array( [edge.tuple for edge in self.igraph.es], np.int32)
_l = len(edges)
pos = fl.layout_fr(nodes*dimension, edges, max_it, temp )
#get the Layout object here.
#http://igraph.org/python/doc/igraph.layout.Layout-class.html
scl = int( _l/ 100 ) #int( _l * _l / 10 )
if ly_alg == "Fruchterman-Reingold":
ly = igraph.Layout(tuple(zip(pos[0:nodes], pos[nodes:2*nodes])))
scl = scl / 3
elif ly_alg == "LGL":
ly = self.igraph.layout_lgl()
elif ly_alg == "Kamada-Kawai":
ly = self.igraph.layout_kamada_kawai()
scl = scl / 10
elif ly_alg == "Star":
ly = self.igraph.layout_star()
scl = scl * 2
elif ly_alg == "Random":
ly = self.igraph.layout_random()
scl = scl * 2
else:
#ly = igraph.Layout( tuple(map(tuple, pos )) )
#scl = scl / 3
ly = self.igraph.layout_fruchterman_reingold(dim=2,coolexp =1, area = int( _l * _l / 10 ) )
#ly_alg = "Fruchterman-Reingold"
#OR standard fruchterman reingold
ly_end = datetime.now()
diff = ly_end - ly_start
print "VIZUALISATION TIMER: returning coordinates :",ly_end
print "Layouting took :", diff.seconds, "seconds using", ly_alg
# TODO screws up positioning for graphs with few nodes
#ly.scale( scl * 4)
box = ly.bounding_box()
width = abs(box.left) + abs(box.right)
coords = ly.__dict__['_coords']
#numpy.float64 cannot be jsonified later, so we convert to standard float:
coords = [ [ float( c[0] )* 1 , float( c[1] ) * 1 ] for c in coords ]
#todo we have the node names somewhere already ...
vertices = []
for i in self.igraph.vs:
vertices.append( i['name'] )
all_coords = dict( zip( vertices, coords ) )
#add coords to each layer and get the nodes in each layer intersect with the nodes in the next layer
layer_neighborhoods = []
for i,_l in enumerate(self.layer_names):
_layer_data = self.data[_l]
_layer_data['name'] = _l
try:
_layer_data_next = data[ self.layer_names[i+1] ]
except:
#last layer
_layer_data_next = self.data[ self.layer_names[i-1] ]
#possible with namedtuples
#nodes1 = _layer_data.nodes
#nodes2 = _layer_data_next.nodes
#indegs = _layer_data.in_degrees
max_in_deg = 0
max_out_deg = 0
max_total_deg = 0
nodes1 = _layer_data['nodes']
nodes2 = _layer_data_next['nodes']
indegs = _layer_data['in_degrees']
outdegs = _layer_data['out_degrees']
coords = {}
common_nodes = list( set( nodes1 ).intersection( set( nodes2 ) ) )
for node_id in nodes1:
_common = 1 if node_id in common_nodes else 0
try:
indeg = indegs[ node_id ]
outdeg = outdegs[ node_id ]
except Exception,e:
indeg = 0
outdeg = 0
coords[node_id] = [ all_coords[ node_id ], _common, indeg, outdeg, indeg + outdeg, self.custom_scale.get(node_id, 1)]
max_out_deg = max(max_out_deg, outdeg)
max_in_deg = max(max_in_deg, indeg)
max_total_deg = max(max_total_deg, outdeg + indeg)
#possible with namedtuples
#_layer_data.coords = coords
_layer_data['coords'] = coords
# add dummy 0 values, so max_in_degree and max_out_degree have to
# same offset as the node's degrees
_layer_data['maxDeg'] = [0, 0, max_in_deg, max_out_deg, max_total_deg, 1.0]
if directed_graph:
get_key = lambda v1, v2: ''.join([v1, v2])
else:
get_key = lambda v1, v2: ''.join(sorted([v1, v2]))
edge_dict = { get_key(x[0], x[1]): x[2] for x in _layer_data['edges']}
neighborhood = {}
for i, nb in enumerate(self.igraph.neighborhood()):
l = []
neighborhood[vertices[i]] = neighborhood.get(vertices[i], l) + [[vertices[j], edge_dict[get_key(vertices[i], vertices[j])]] for j in nb if get_key(vertices[i], vertices[j]) in edge_dict]
_layer_data['neighborhood'] = neighborhood
float5Pos = np.copy( pos.astype(np.float32) ) float6Pos = np.copy( pos.astype(np.float32) ) #print np.array_str( floatPos ) #print np.array_str( float2Pos ) print 'igraph' start = time.clock() igLayout = g.layout_fruchterman_reingold() elapsed = time.clock() elapsed = elapsed - start print "Time spent in (function name) is: ", elapsed ig.plot(g, "output/plot_igraph.png", layout=igLayout) print 'float baseline:' fl.layout_fr( edges, floatPos, max_it, temp ) floatLayout = ig.Layout( tuple(map(tuple, floatPos )) ) ig.plot(g, "output/plot_float_baseline.png", layout=floatLayout) #print 'layout_fr_omp' #fl.layout_fr_omp( edges, float2Pos, max_it, temp ) #float2Layout = ig.Layout( tuple(map(tuple, float2Pos)) ) #ig.plot(g, "output/plot_fr_omp.png", layout=float2Layout) #print 'layout_fr_simd' #fl.layout_fr_simd( edges, float3Pos, max_it, temp ) #float3Layout = ig.Layout( tuple(map(tuple, float3Pos)) ) #ig.plot(g, "output/plot_fr_simd.png", layout=float3Layout) #print 'layout_fr_simd_1x4' #fl.layout_fr_simd_1x4( edges, float4Pos, max_it, temp )