예제 #1
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    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)
예제 #2
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    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)
예제 #3
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    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)
예제 #4
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    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)
예제 #5
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    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)
예제 #6
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    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)
예제 #7
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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)