/*
Copyright 2008-2010 Gephi
Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
Website : http://www.gephi.org
This file is part of Gephi.
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2011 Gephi Consortium. All rights reserved.
The contents of this file are subject to the terms of either the GNU
General Public License Version 3 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with the
License. You can obtain a copy of the License at
http://gephi.org/about/legal/license-notice/
or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
specific language governing permissions and limitations under the
License. When distributing the software, include this License Header
Notice in each file and include the License files at
/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
License Header, with the fields enclosed by brackets [] replaced by
your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
If you wish your version of this file to be governed by only the CDDL
or only the GPL Version 3, indicate your decision by adding
"[Contributor] elects to include this software in this distribution
under the [CDDL or GPL Version 3] license." If you do not indicate a
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your version of this file under either the CDDL, the GPL Version 3 or
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However, if you add GPL Version 3 code and therefore, elected the GPL
Version 3 license, then the option applies only if the new code is
made subject to such option by the copyright holder.
Contributor(s):
Portions Copyrighted 2011 Gephi Consortium.
*/
package org.gephi.layout.plugin.openord;
import gnu.trove.iterator.TIntFloatIterator;
import gnu.trove.map.hash.TIntFloatHashMap;
import gnu.trove.map.hash.TIntIntHashMap;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.concurrent.CyclicBarrier;
import org.gephi.graph.api.Edge;
import org.gephi.graph.api.Graph;
import org.gephi.graph.api.GraphModel;
import org.gephi.graph.api.GraphView;
import org.gephi.graph.api.Interval;
import org.gephi.layout.spi.Layout;
import org.gephi.layout.spi.LayoutBuilder;
import org.gephi.layout.spi.LayoutProperty;
import org.gephi.utils.longtask.spi.LongTask;
import org.gephi.utils.progress.ProgressTicket;
import org.openide.util.Exceptions;
import org.openide.util.NbBundle;
/**
*
* @author Mathieu Bastian
*/
public class OpenOrdLayout implements Layout, LongTask {
//Architecture
private final LayoutBuilder builder;
private GraphModel graphModel;
private boolean running = true;
private ProgressTicket progressTicket;
//Settings
private Params param;
private float edgeCut;
private int numThreads;
private long randSeed;
private int numIterations;
private float realTime;
//Layout
private Worker[] workers;
private Combine combine;
private Control control;
private CyclicBarrier barrier;
private Graph graph;
private boolean firstIteration = true;
public OpenOrdLayout(LayoutBuilder builder) {
this.builder = builder;
}
@Override
public void resetPropertiesValues() {
edgeCut = 0.8f;
numIterations = 750;
numThreads = Math.max(1, Runtime.getRuntime().availableProcessors() - 1);
Random r = new Random();
randSeed = r.nextLong();
running = true;
realTime = 0.2f;
param = Params.DEFAULT;
}
@Override
public void initAlgo() {
//Verify param
if (param.getIterationsSum() != 1f) {
param = Params.DEFAULT;
//throw new RuntimeException("The sum of the time for each stage must be equal to 1");
}
//Get graph
graph = graphModel.getUndirectedGraphVisible();
graph.readLock();
boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
Interval interval = graph.getView().getTimeInterval();
try {
int numNodes = graph.getNodeCount();
//Prepare data structure - nodes and neighbors map
Node[] nodes = new Node[numNodes];
TIntFloatHashMap[] neighbors = new TIntFloatHashMap[numNodes];
//Load nodes and edges
TIntIntHashMap idMap = new TIntIntHashMap(numNodes, 1f);
org.gephi.graph.api.Node[] graphNodes = graph.getNodes().toArray();
for (int i = 0; i < numNodes; i++) {
org.gephi.graph.api.Node n = graphNodes[i];
nodes[i] = new Node(i);
nodes[i].x = n.x();
nodes[i].y = n.y();
nodes[i].fixed = n.isFixed();
OpenOrdLayoutData layoutData = new OpenOrdLayoutData(i);
n.setLayoutData(layoutData);
idMap.put(n.getStoreId(), i);
}
float highestSimilarity = Float.NEGATIVE_INFINITY;
for (Edge e : graph.getEdges()) {
int source = idMap.get(e.getSource().getStoreId());
int target = idMap.get(e.getTarget().getStoreId());
if (source != target) { //No self-loop
float weight = (float) (isDynamicWeight ? e.getWeight(interval) : e.getWeight());
if (neighbors[source] == null) {
neighbors[source] = new TIntFloatHashMap();
}
if (neighbors[target] == null) {
neighbors[target] = new TIntFloatHashMap();
}
neighbors[source].put(target, weight);
neighbors[target].put(source, weight);
highestSimilarity = Math.max(highestSimilarity, weight);
}
}
//Reset position
boolean someFixed = false;
for (Node n : nodes) {
if (!n.fixed) {
n.x = 0;
n.y = 0;
} else {
someFixed = true;
}
}
//Recenter fixed nodes and rescale to fit into grid
if (someFixed) {
float minX = Float.POSITIVE_INFINITY;
float maxX = Float.NEGATIVE_INFINITY;
float minY = Float.POSITIVE_INFINITY;
float maxY = Float.NEGATIVE_INFINITY;
for (Node n : nodes) {
if (n.fixed) {
minX = Math.min(minX, n.x);
maxX = Math.max(maxX, n.x);
minY = Math.min(minY, n.y);
maxY = Math.max(maxY, n.y);
}
}
float shiftX = minX + (maxX - minX) / 2f;
float shiftY = minY + (maxY - minY) / 2f;
float ratio = Math.min(DensityGrid.getViewSize() / (maxX - minX), DensityGrid.getViewSize() / (maxY - minY));
ratio = Math.min(1f, ratio);
for (Node n : nodes) {
if (n.fixed) {
n.x = (float) (n.x - shiftX) * ratio;
n.y = (float) (n.y - shiftY) * ratio;
}
}
}
//Init control and workers
control = new Control();
combine = new Combine(this);
barrier = new CyclicBarrier(numThreads, combine);
control.setEdgeCut(edgeCut);
control.setRealParm(realTime);
control.setProgressTicket(progressTicket);
control.initParams(param, numIterations);
control.setNumNodes(numNodes);
control.setHighestSimilarity(highestSimilarity);
workers = new Worker[numThreads];
for (int i = 0; i < numThreads; ++i) {
workers[i] = new Worker(i, numThreads, barrier);
workers[i].setRandom(new Random(randSeed));
control.initWorker(workers[i]);
}
//Load workers with data
//Deep copy of all nodes positions
//Deep copy of a partition of all neighbors for each workers
for (Worker w : workers) {
Node[] nodesCopy = new Node[nodes.length];
for (int i = 0; i < nodes.length; i++) {
nodesCopy[i] = nodes[i].clone();
}
TIntFloatHashMap[] neighborsCopy = new TIntFloatHashMap[numNodes];
for (int i = 0; i < neighbors.length; i++) {
if (i % numThreads == w.getId() && neighbors[i] != null) {
int neighborsCount = neighbors[i].size();
neighborsCopy[i] = new TIntFloatHashMap(neighborsCount, 1f);
for (TIntFloatIterator itr = neighbors[i].iterator(); itr.hasNext();) {
itr.advance();
float weight = normalizeWeight(itr.value(), highestSimilarity);
neighborsCopy[i].put(itr.key(), weight);
}
}
}
w.setPositions(nodesCopy);
w.setNeighbors(neighborsCopy);
}
//Add real nodes
for (Node n : nodes) {
if (n.fixed) {
for (Worker w : workers) {
w.getDensityGrid().add(n, w.isFineDensity());
}
}
}
running = true;
firstIteration = true;
} finally {
graph.readUnlockAll();
}
}
@Override
public void goAlgo() {
if (firstIteration) {
for (int i = 0; i < numThreads; ++i) {
Thread t = new Thread(workers[i]);
t.setDaemon(true);
t.start();
}
firstIteration = false;
}
combine.waitForIteration();
}
@Override
public void endAlgo() {
running = false;
combine = null;
}
private float normalizeWeight(float weight, float highestSimilarity) {
weight /= highestSimilarity;
weight = weight * Math.abs(weight);
return weight;
}
@Override
public boolean canAlgo() {
return running;
}
@Override
public void setGraphModel(GraphModel graphModel) {
this.graphModel = graphModel;
}
@Override
public LayoutProperty[] getProperties() {
List<LayoutProperty> properties = new ArrayList<>();
final String OPENORD = "OpenOrd";
final String STAGE = "Stages";
try {
properties.add(LayoutProperty.createProperty(
this, Float.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.edgecut.name"),
OPENORD,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.edgecut.description"),
"getEdgeCut", "setEdgeCut"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.numthreads.name"),
OPENORD,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.numthreads.description"),
"getNumThreads", "setNumThreads"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.numiterations.name"),
OPENORD,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.numiterations.description"),
"getNumIterations", "setNumIterations"));
properties.add(LayoutProperty.createProperty(
this, Float.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.realtime.name"),
OPENORD,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.realtime.description"),
"getRealTime", "setRealTime"));
properties.add(LayoutProperty.createProperty(
this, Long.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.seed.name"),
OPENORD,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.seed.description"),
"getRandSeed", "setRandSeed"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.liquid.name"),
STAGE,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.liquid.description"),
"getLiquidStage", "setLiquidStage"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.expansion.name"),
STAGE,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.expansion.description"),
"getExpansionStage", "setExpansionStage"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.cooldown.name"),
STAGE,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.cooldown.description"),
"getCooldownStage", "setCooldownStage"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.crunch.name"),
STAGE,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.crunch.description"),
"getCrunchStage", "setCrunchStage"));
properties.add(LayoutProperty.createProperty(
this, Integer.class,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.simmer.name"),
STAGE,
NbBundle.getMessage(OpenOrdLayout.class, "OpenOrd.properties.stage.simmer.description"),
"getSimmerStage", "setSimmerStage"));
} catch (Exception e) {
Exceptions.printStackTrace(e);
}
return properties.toArray(new LayoutProperty[0]);
}
public Float getEdgeCut() {
return edgeCut;
}
public void setEdgeCut(Float edgeCut) {
edgeCut = Math.min(1f, edgeCut);
edgeCut = Math.max(0, edgeCut);
this.edgeCut = edgeCut;
}
public Integer getNumThreads() {
return numThreads;
}
public void setNumThreads(Integer numThreads) {
numThreads = Math.max(1, numThreads);
this.numThreads = numThreads;
}
public Long getRandSeed() {
return randSeed;
}
public void setRandSeed(Long randSeed) {
this.randSeed = randSeed;
}
public void setRunning(Boolean running) {
this.running = running;
}
public Integer getNumIterations() {
return numIterations;
}
public void setNumIterations(Integer numIterations) {
numIterations = Math.max(100, numIterations);
this.numIterations = numIterations;
}
public Float getRealTime() {
return realTime;
}
public void setRealTime(Float realTime) {
realTime = Math.min(1f, realTime);
realTime = Math.max(0, realTime);
this.realTime = realTime;
}
public Integer getLiquidStage() {
return param.getLiquid().getIterationsPercentage();
}
public Integer getExpansionStage() {
return param.getExpansion().getIterationsPercentage();
}
public Integer getCooldownStage() {
return param.getCooldown().getIterationsPercentage();
}
public Integer getCrunchStage() {
return param.getCrunch().getIterationsPercentage();
}
public Integer getSimmerStage() {
return param.getSimmer().getIterationsPercentage();
}
public void setLiquidStage(Integer value) {
int v = Math.min(100, value);
v = Math.max(0, v);
param.getLiquid().setIterations(v / 100f);
}
public void setExpansionStage(Integer value) {
int v = Math.min(100, value);
v = Math.max(0, v);
param.getExpansion().setIterations(v / 100f);
}
public void setCooldownStage(Integer value) {
int v = Math.min(100, value);
v = Math.max(0, v);
param.getCooldown().setIterations(v / 100f);
}
public void setCrunchStage(Integer value) {
int v = Math.min(100, value);
v = Math.max(0, v);
param.getCrunch().setIterations(v / 100f);
}
public void setSimmerStage(Integer value) {
int v = Math.min(100, value);
v = Math.max(0, v);
param.getSimmer().setIterations(v / 100f);
}
@Override
public LayoutBuilder getBuilder() {
return builder;
}
public Worker[] getWorkers() {
return workers;
}
public Graph getGraph() {
return graph;
}
public Control getControl() {
return control;
}
@Override
public boolean cancel() {
return true;
}
@Override
public void setProgressTicket(ProgressTicket progressTicket) {
this.progressTicket = progressTicket;
}
}