def testWriteToFile3(self):
"""
We will test out writing out some random graphs to Pajek
"""
numVertices = 20
numFeatures = 0
vList = VertexList(numVertices, numFeatures)
graph = SparseGraph(vList)
p = 0.1
generator = ErdosRenyiGenerator(p)
graph = generator.generate(graph)
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
pw.writeToFile(directory + "erdosRenyi20", graph)
#Now write a small world graph
p = 0.2
k = 3
graph.removeAllEdges()
generator = SmallWorldGenerator(p, k)
graph = generator.generate(graph)
pw.writeToFile(directory + "smallWorld20", graph)
def testWriteToFile3(self):
"""
We will test out writing out some random graphs to Pajek
"""
numVertices = 20
numFeatures = 0
vList = VertexList(numVertices, numFeatures)
graph = SparseGraph(vList)
p = 0.1
generator = ErdosRenyiGenerator(p)
graph = generator.generate(graph)
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
pw.writeToFile(directory + "erdosRenyi20", graph)
#Now write a small world graph
p = 0.2
k = 3
graph.removeAllEdges()
generator = SmallWorldGenerator(p, k)
graph = generator.generate(graph)
pw.writeToFile(directory + "smallWorld20", graph)
def testWriteToFile(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
#Have to check the files
fileName1 = directory + "denseTestUndirected"
pw.writeToFile(fileName1, self.dGraph1)
fileName2 = directory + "denseTestDirected"
pw.writeToFile(fileName2, self.dGraph2)
fileName3 = directory + "sparseTestUndirected"
pw.writeToFile(fileName3, self.sGraph1)
fileName4 = directory + "sparseTestDirected"
pw.writeToFile(fileName4, self.sGraph2)
fileName5 = directory + "dictTestUndirected"
pw.writeToFile(fileName5, self.dctGraph1)
fileName6 = directory + "dictTestDirected"
pw.writeToFile(fileName6, self.dctGraph2)
def testWriteToFile2(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
def setVertexColour(vertexIndex, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex]
def setVertexSize(vertexIndex, graph):
return vertexIndex
def setEdgeColour(vertexIndex1, vertexIndex2, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex1]
def setEdgeSize(vertexIndex1, vertexIndex2, graph):
return vertexIndex1 + vertexIndex2
pw.setVertexColourFunction(setVertexColour)
fileName1 = directory + "vertexColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexColourFunction(None)
pw.setVertexSizeFunction(setVertexSize)
fileName1 = directory + "vertexSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexSizeFunction(None)
pw.setEdgeColourFunction(setEdgeColour)
fileName1 = directory + "edgeColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
pw.setEdgeSizeFunction(setEdgeSize)
fileName1 = directory + "edgeSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
def testWriteToFile(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
#Have to check the files
fileName1 = directory + "denseTestUndirected"
pw.writeToFile(fileName1, self.dGraph1)
fileName2 = directory + "denseTestDirected"
pw.writeToFile(fileName2, self.dGraph2)
fileName3 = directory + "sparseTestUndirected"
pw.writeToFile(fileName3, self.sGraph1)
fileName4 = directory + "sparseTestDirected"
pw.writeToFile(fileName4, self.sGraph2)
fileName5 = directory + "dictTestUndirected"
pw.writeToFile(fileName5, self.dctGraph1)
fileName6 = directory + "dictTestDirected"
pw.writeToFile(fileName6, self.dctGraph2)
def testWriteToFile2(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
def setVertexColour(vertexIndex, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex]
def setVertexSize(vertexIndex, graph):
return vertexIndex
def setEdgeColour(vertexIndex1, vertexIndex2, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex1]
def setEdgeSize(vertexIndex1, vertexIndex2, graph):
return vertexIndex1+vertexIndex2
pw.setVertexColourFunction(setVertexColour)
fileName1 = directory + "vertexColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexColourFunction(None)
pw.setVertexSizeFunction(setVertexSize)
fileName1 = directory + "vertexSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexSizeFunction(None)
pw.setEdgeColourFunction(setEdgeColour)
fileName1 = directory + "edgeColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
pw.setEdgeSizeFunction(setEdgeSize)
fileName1 = directory + "edgeSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
from apgl.viroscopy.HIVGraphReader import HIVGraphReader
from apgl.io.PajekWriter import PajekWriter
from apgl.util import *
import logging
import sys
import math
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
"""
A script to load up the HIV data in its entirity.
"""
hivReader = HIVGraphReader()
graph = hivReader.readHIVGraph()
def getVertexSize(vertexIndex, graph):
return math.sqrt(len(graph.neighbours(vertexIndex)))
def getEdgeWeight(vertexIndex1, vertexIndex2, graph):
return graph.getEdge(vertexIndex1, vertexIndex2, 0)
outputDirectory = PathDefaults.getOutputDir()
fileName = outputDirectory + "hivGraph"
pajekWriter = PajekWriter()
pajekWriter.setVertexSizeFunction(getVertexSize)
pajekWriter.setEdgeWeightFunction(getEdgeWeight)
pajekWriter.writeToFile(fileName, graph)
