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Fix - add try/finally logic to wrap graph reentrant locks for layouts #1487

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Fix - add try/finally logic to wrap graph reentrant locks for layouts #1487

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142 changes: 83 additions & 59 deletions modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/force/yifanHu/YifanHuLayout.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,6 @@ Development and Distribution License("CDDL") (collectively, the
*/
package org.gephi.layout.plugin.force.yifanHu;

import java.util.ArrayList;
import java.util.List;
import org.gephi.graph.api.Edge;
import org.gephi.graph.api.Graph;
import org.gephi.graph.api.Node;
Expand All @@ -58,6 +56,9 @@ Development and Distribution License("CDDL") (collectively, the
import org.gephi.layout.spi.LayoutProperty;
import org.openide.util.NbBundle;

import java.util.ArrayList;
import java.util.List;

/**
* Hu's basic algorithm
*
Expand Down Expand Up @@ -229,88 +230,111 @@ public void initAlgo() {
return;
}
graph = graphModel.getGraphVisible();
energy = Float.POSITIVE_INFINITY;
for (Node n : graph.getNodes()) {
n.setLayoutData(new ForceVector());
graph.readLock();
try
{
energy = Float.POSITIVE_INFINITY;
for (Node n : graph.getNodes())
{
n.setLayoutData(new ForceVector());
}
progress = 0;
setConverged(false);
setStep(initialStep);
} finally {
graph.readUnlock();
}
progress = 0;
setConverged(false);
setStep(initialStep);
}

@Override
public void endAlgo() {
for (Node n : graph.getNodes()) {
n.setLayoutData(null);
graph.readLock();
try
{
for (Node n : graph.getNodes())
{
n.setLayoutData(null);
}
} finally {
graph.readUnlock();
}
}

@Override
public void goAlgo() {
graph = graphModel.getGraphVisible();
graph.readLock();
Node[] nodes = graph.getNodes().toArray();
for (Node n : nodes) {
if (n.getLayoutData() == null || !(n.getLayoutData() instanceof ForceVector)) {
n.setLayoutData(new ForceVector());
try
{
Node[] nodes = graph.getNodes().toArray();
for (Node n : nodes)
{
if (n.getLayoutData() == null || !(n.getLayoutData() instanceof ForceVector))
{
n.setLayoutData(new ForceVector());
}
}
}

// Evaluates n^2 inter node forces using BarnesHut.
QuadTree tree = QuadTree.buildTree(graph, getQuadTreeMaxLevel());
// Evaluates n^2 inter node forces using BarnesHut.
QuadTree tree = QuadTree.buildTree(graph, getQuadTreeMaxLevel());

// double electricEnergy = 0; ///////////////////////
// double springEnergy = 0; ///////////////////////
BarnesHut barnes = new BarnesHut(getNodeForce());
barnes.setTheta(getBarnesHutTheta());
for (Node node : nodes) {
ForceVector layoutData = node.getLayoutData();
// double electricEnergy = 0; ///////////////////////
// double springEnergy = 0; ///////////////////////
BarnesHut barnes = new BarnesHut(getNodeForce());
barnes.setTheta(getBarnesHutTheta());
for (Node node : nodes)
{
ForceVector layoutData = node.getLayoutData();

ForceVector f = barnes.calculateForce(node, tree);
layoutData.add(f);
// electricEnergy += f.getEnergy();
}
ForceVector f = barnes.calculateForce(node, tree);
layoutData.add(f);
// electricEnergy += f.getEnergy();
}

// Apply edge forces.
// Apply edge forces.

for (Edge e : graph.getEdges()) {
if (!e.getSource().equals(e.getTarget())) {
Node n1 = e.getSource();
Node n2 = e.getTarget();
ForceVector f1 = n1.getLayoutData();
ForceVector f2 = n2.getLayoutData();

ForceVector f = getEdgeForce().calculateForce(n1, n2);
f1.add(f);
f2.subtract(f);
for (Edge e : graph.getEdges())
{
if (!e.getSource().equals(e.getTarget()))
{
Node n1 = e.getSource();
Node n2 = e.getTarget();
ForceVector f1 = n1.getLayoutData();
ForceVector f2 = n2.getLayoutData();

ForceVector f = getEdgeForce().calculateForce(n1, n2);
f1.add(f);
f2.subtract(f);
}
}
}

// Calculate energy and max force.
energy0 = energy;
energy = 0;
double maxForce = 1;
for (Node n : nodes) {
ForceVector force = n.getLayoutData();
// Calculate energy and max force.
energy0 = energy;
energy = 0;
double maxForce = 1;
for (Node n : nodes)
{
ForceVector force = n.getLayoutData();

energy += force.getNorm();
maxForce = Math.max(maxForce, force.getNorm());
}
energy += force.getNorm();
maxForce = Math.max(maxForce, force.getNorm());
}

// Apply displacements on nodes.
for (Node n : nodes) {
if (!n.isFixed()) {
ForceVector force = n.getLayoutData();
// Apply displacements on nodes.
for (Node n : nodes)
{
if (!n.isFixed())
{
ForceVector force = n.getLayoutData();

force.multiply((float) (1.0 / maxForce));
getDisplacement().moveNode(n, force);
force.multiply((float) (1.0 / maxForce));
getDisplacement().moveNode(n, force);
}
}
postAlgo();
} finally {
graph.readUnlock();
}
postAlgo();
// springEnergy = energy - electricEnergy;
// System.out.println("electric: " + electricEnergy + " spring: " + springEnergy);
// System.out.println("energy0 = " + energy0 + " energy = " + energy);
graph.readUnlock();
}


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