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add parallel graphviz processing #12
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@xchrdw
xchrdw committed Mar 3, 2015
1 parent 43f24e6 commit 9b7c1d5
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Showing 3 changed files with 91 additions and 90 deletions.
5 changes: 1 addition & 4 deletions src/graphlod/GraphFeatures.java
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Original file line number Diff line number Diff line change
Expand Up @@ -146,10 +146,7 @@ public boolean containsCycles() {
}

public boolean isBipartite() {
if (GraphTests.isBipartite(this.undirectedG)) {
return true;
}
return false;
return GraphTests.isBipartite(this.undirectedG);
}

public boolean isPathGraph() {
Expand Down
112 changes: 46 additions & 66 deletions src/graphlod/GraphLOD.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,14 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Set;

import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.BasicConfigurator;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.jgrapht.alg.StrongConnectivityInspector;

import com.google.common.base.Charsets;
import com.google.common.base.Preconditions;
Expand All @@ -37,12 +36,12 @@
public class GraphLOD {
private static final Logger logger = Logger.getLogger(GraphLOD.class);
public static final int MAX_SIZE_FOR_DIAMETER = 500;

private final GraphCsvOutput graphCsvOutput;
private final VertexCsvOutput vertexCsvOutput;
private final GraphRenderer graphRenderer;
private String name;

List<GraphFeatures> connectedGraphs = new ArrayList<>();
List<GraphFeatures> stronglyConnectedGraphs = new ArrayList<>();
List<GraphFeatures> pathGraphs = new ArrayList<>();
Expand All @@ -55,11 +54,13 @@ public class GraphLOD {
List<GraphFeatures> completeGraphs = new ArrayList<>();
List<GraphFeatures> bipartiteGraphs = new ArrayList<>();
List<GraphFeatures> unrecognizedStructure = new ArrayList<>();

List<String> htmlFiles = new ArrayList<>();
private String output;

public GraphLOD(String name, Collection<String> datasetFiles, boolean skipChromaticNumber, boolean skipGraphviz, String namespace, Collection<String> excludedNamespaces, int minImportantSubgraphSize, int importantDegreeCount, String output, boolean debugMode) {

public GraphLOD(String name, Collection<String> datasetFiles, boolean skipChromaticNumber, boolean skipGraphviz,
String namespace, Collection<String> excludedNamespaces, int minImportantSubgraphSize,
int importantDegreeCount, String output, boolean debugMode, int threadcount) {
if (debugMode) {
logger.setLevel(Level.DEBUG);
} else {
Expand All @@ -79,7 +80,7 @@ public GraphLOD(String name, Collection<String> datasetFiles, boolean skipChroma
graphCsvOutput = new GraphCsvOutput(name, MAX_SIZE_FOR_DIAMETER);
vertexCsvOutput = new VertexCsvOutput(name);
if (!skipGraphviz) {
graphRenderer = new GraphRenderer(name, debugMode, this.output);
graphRenderer = new GraphRenderer(name, debugMode, this.output, threadcount);
} else {
graphRenderer = null;
}
Expand All @@ -93,8 +94,8 @@ public GraphLOD(String name, Collection<String> datasetFiles, boolean skipChroma

if (graphRenderer != null) {
Stopwatch sw = Stopwatch.createStarted();
graphRenderer.render(this);
logger.debug("visualization took " + sw);
htmlFiles = graphRenderer.render();
logger.debug("visualization took " + sw);
}
createHtmlStructures();
createHtmlConnectedSets();
Expand Down Expand Up @@ -129,19 +130,19 @@ private void analyze(GraphFeatures graphFeatures, int minImportantSubgraphSize,
List<Set<String>> sci_sets = graphFeatures.getStronglyConnectedSets();
System.out.println("Strongly connected components: " + formatInt(sci_sets.size()));
printComponentSizeAndCount(sci_sets);
stronglyConnectedGraphs = graphFeatures.createSubGraphFeatures(sci_sets);
stronglyConnectedGraphs = graphFeatures.createSubGraphFeatures(sci_sets);
logger.debug("Getting the connectivity took " + sw + " to execute.");

int i = 0;

sw = Stopwatch.createStarted();

if (graphFeatures.isConnected()) {
connectedGraphs.add(graphFeatures);
} else {
connectedGraphs = graphFeatures.createSubGraphFeatures(graphFeatures.getConnectedSets());
}
}

for (GraphFeatures subGraph : connectedGraphs) {
if (subGraph.getVertexCount() < minImportantSubgraphSize) {
continue;
Expand All @@ -158,7 +159,7 @@ private void analyze(GraphFeatures graphFeatures, int minImportantSubgraphSize,

boolean cycles = subGraph.containsCycles();
System.out.printf("\tContains cycles: %s\n", cycles);

boolean isTree = false;
boolean isCaterpillar = false;
if (!cycles) {
Expand All @@ -173,13 +174,13 @@ private void analyze(GraphFeatures graphFeatures, int minImportantSubgraphSize,
}
}
}

boolean isCompleteGraph = subGraph.isCompleteGraph();
if (isCompleteGraph) {
System.out.printf("\tComplete graph: %s\n", isCompleteGraph);
completeGraphs.add(subGraph);
}

boolean isBipartiteGraph = false;
/* TODO Takes too long for some graphs and results in OutOfMemoryError. Deal with that first.
boolean isBipartiteGraph = subGraph.isBipartite();
Expand All @@ -188,13 +189,13 @@ private void analyze(GraphFeatures graphFeatures, int minImportantSubgraphSize,
bipartiteGraphs.add(subGraph);
}
*/

boolean isPathGraph = false;
boolean isDirectedPathGraph = false;
boolean isMixedDirectedStarGraph = false;
boolean isOutboundStarGraph = false;
boolean isInboundStarGraph = false;

if (subGraph.getVertexCount() < MAX_SIZE_FOR_DIAMETER) {
isPathGraph = subGraph.isPathGraph();
System.out.printf("\tPath graph: %s\n", isPathGraph);
Expand Down Expand Up @@ -227,52 +228,32 @@ private void analyze(GraphFeatures graphFeatures, int minImportantSubgraphSize,
inboundStarGraphs.add(subGraph);
}
}

}
}
}

if (!isTree && !isBipartiteGraph && !isCaterpillar && !isCompleteGraph && !isPathGraph && !isMixedDirectedStarGraph && !isOutboundStarGraph && !isInboundStarGraph) {
unrecognizedStructure.add(subGraph);
}

}

if (graphRenderer != null) {
graphRenderer.writeDotFiles( "connected", connectedGraphs);
graphRenderer.writeDotFiles( "strongly-connected", graphFeatures.createSubGraphFeatures(sci_sets));
if (!pathGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "pathgraphs", pathGraphs);
}
if (!directedPathGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "directedpathgraphs", directedPathGraphs);
}
if (!outboundStarGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "outboundstargraphs", outboundStarGraphs);
}
if (!inboundStarGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "inboundstargraphs", inboundStarGraphs);
}
if (!mixedDirectedStarGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "stargraphs", mixedDirectedStarGraphs);
}
if (!treeGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "trees", treeGraphs);
}
if (!caterpillarGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "caterpillargraphs", caterpillarGraphs);
}
if (!completeGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "completegraphs", completeGraphs);
}
if (!bipartiteGraphs.isEmpty()) {
graphRenderer.writeDotFiles( "bipartitegraphs", completeGraphs);
}
if (!unrecognizedStructure.isEmpty()) {
graphRenderer.writeDotFiles( "unrecognized", unrecognizedStructure);
}
graphRenderer.writeDotFiles("connected", connectedGraphs);
graphRenderer.writeDotFiles("strongly-connected", graphFeatures.createSubGraphFeatures(sci_sets));
graphRenderer.writeDotFiles("pathgraphs", pathGraphs);
graphRenderer.writeDotFiles("directedpathgraphs", directedPathGraphs);
graphRenderer.writeDotFiles("outboundstargraphs", outboundStarGraphs);
graphRenderer.writeDotFiles("inboundstargraphs", inboundStarGraphs);
graphRenderer.writeDotFiles("stargraphs", mixedDirectedStarGraphs);
graphRenderer.writeDotFiles("trees", treeGraphs);
graphRenderer.writeDotFiles("caterpillargraphs", caterpillarGraphs);
graphRenderer.writeDotFiles("completegraphs", completeGraphs);
graphRenderer.writeDotFiles("bipartitegraphs", completeGraphs);
graphRenderer.writeDotFiles("unrecognized", unrecognizedStructure);
}

logger.debug("Analysing the components took " + sw + " to execute.");

logger.info("Vertex Degrees:");
Expand Down Expand Up @@ -362,7 +343,7 @@ private void printStats(BufferedWriter out, List<GraphFeatures> graphs, String s
stringNormalized = "strongly-connected";
}
exportEntities(graphs, stringNormalized);

out.write("<td>\n");
for (String file : htmlFiles) {
String htmlFile = new File(file).getName();
Expand All @@ -374,7 +355,7 @@ private void printStats(BufferedWriter out, List<GraphFeatures> graphs, String s

out.write("</tr>\n");
}

private void createHtmlConnectedSets() {
try {
File file = new File(this.output + this.name + "_cs_statistics.html");
Expand All @@ -393,7 +374,7 @@ private void createHtmlConnectedSets() {

private void createHtmlStructures() {
logger.info("\nStructure Statistics");

try {
File file = new File(this.output + this.name + "_statistics.html");
Files.createParentDirs(file);
Expand Down Expand Up @@ -432,7 +413,7 @@ private void printTableHeader(BufferedWriter out) throws IOException {
out.write("</tr>\n");
}


private double calculateAverage(List<Integer> sizes) {
Integer sum = 0;
if (!sizes.isEmpty()) {
Expand All @@ -443,7 +424,7 @@ private double calculateAverage(List<Integer> sizes) {
}
return sum;
}

private double round(double value, int places) {
if (places < 0) throw new IllegalArgumentException();
BigDecimal bd = new BigDecimal(value);
Expand Down Expand Up @@ -499,6 +480,7 @@ public static void main(final String[] args) {
parser.addArgument("--skipGraphviz").action(Arguments.storeTrue());
parser.addArgument("--minImportantSubgraphSize").type(Integer.class).action(Arguments.store()).setDefault(1);
parser.addArgument("--importantDegreeCount").type(Integer.class).action(Arguments.store()).setDefault(5);
parser.addArgument("--threadcount").type(Integer.class).action(Arguments.store()).setDefault(4);
parser.addArgument("--debug").action(Arguments.storeTrue());
parser.addArgument("--output").type(String.class).setDefault("");
Namespace result = null;
Expand All @@ -520,9 +502,11 @@ public static void main(final String[] args) {
boolean skipGraphviz = result.getBoolean("skipGraphviz");
int minImportantSubgraphSize = result.getInt("minImportantSubgraphSize");
int importantDegreeCount = result.getInt("importantDegreeCount");
int threadcount = result.getInt("threadcount");
boolean debugMode = result.getBoolean("debug");
String output = result.getString("output");

BasicConfigurator.configure();
logger.info("reading: " + dataset);
logger.info("name: " + name);
logger.info("namespace: " + namespace);
Expand All @@ -531,16 +515,12 @@ public static void main(final String[] args) {
logger.info("excluded namespaces: " + excludedNamespaces);
logger.info("min important subgraph size: " + minImportantSubgraphSize);
logger.info("number of important degrees: " + importantDegreeCount);
logger.info("threadcount: " + threadcount);
logger.info("output: " + output);

Locale.setDefault(Locale.US);

new GraphLOD(name, dataset, skipChromatic, skipGraphviz, namespace, excludedNamespaces, minImportantSubgraphSize, importantDegreeCount, output, debugMode);
new GraphLOD(name, dataset, skipChromatic, skipGraphviz, namespace, excludedNamespaces, minImportantSubgraphSize, importantDegreeCount, output, debugMode, threadcount);
}

public void addHtmlFile(String file) {
//logger.debug("Added "+ file);
htmlFiles.add(file);
}

}
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