Author: pwang
Date: 2010-09-24 16:54:32 -0700 (Fri, 24 Sep 2010)
New Revision: 22058
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayoutTask.java
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
Log:
Refactored
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-09-24 23:28:44 UTC (rev 22057)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-09-24 23:54:32 UTC (rev 22058)
@@ -5,39 +5,26 @@
package csplugins.layout.algorithms.graphPartition;
import java.util.Iterator;
-import java.util.List;
+//import java.util.List;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
+import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
-import cern.colt.list.IntArrayList;
-import cern.colt.map.OpenIntIntHashMap;
-import cern.colt.map.OpenIntObjectHashMap;
-import cern.colt.map.PrimeFinder;
-import cern.colt.matrix.DoubleMatrix1D;
-import cern.colt.matrix.impl.DenseDoubleMatrix1D;
-
-
/**
*
*/
-public class ISOMLayout extends AbstractGraphPartition {
+public class ISOMLayout extends AbstractLayout implements TunableValidator {
@Tunable(description="Number of iterations")
public int maxEpoch = 5000;
- private int epoch;
@Tunable(description="Radius constant")
public int radiusConstantTime = 100;
@Tunable(description="Radius")
public int radius = 20;
@Tunable(description="Minimum radius")
public int minRadius = 1;
- private double adaption;
@Tunable(description="Initial adaptation")
public double initialAdaptation = 90.0D / 100.0D;
@Tunable(description="Minimum adaptation value")
@@ -46,25 +33,26 @@
public double sizeFactor = 100;
@Tunable(description="Cooling factor")
public double coolingFactor = 2;
- private LayoutPartition partition;
- //Queue, First In First Out, use add() and get(0)/remove(0)
- private IntArrayList q;
- OpenIntObjectHashMap nodeIndexToDataMap;
- OpenIntIntHashMap nodeIndexToLayoutIndex;
- double globalX;
- double globalY;
- double squared_size;
/**
* Creates a new ISOMLayout object.
*/
public ISOMLayout(UndoSupport undoSupport) {
super(undoSupport);
-
- q = new IntArrayList();
}
+ // TODO
+ public boolean tunablesAreValid(final Appendable errMsg) {
+ return true;
+ }
+
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new ISOMLayoutTask(networkView,
getName(), selectedOnly, staticNodes,
+
maxEpoch,radiusConstantTime,radius,minRadius,initialAdaptation,
+ minAdaptation,sizeFactor,coolingFactor));
+ }
+
/**
* DOCUMENT ME!
*
@@ -82,234 +70,13 @@
public String getName() {
return "isom";
}
-
+
/**
- * DOCUMENT ME!
+ * We do support selected only
*
- * @param partition DOCUMENT ME!
+ * @return true
*/
- public void layoutPartion(LayoutPartition partition) {
- this.partition = partition;
-
- int nodeCount = partition.nodeCount();
- nodeIndexToDataMap = new
OpenIntObjectHashMap(PrimeFinder.nextPrime(nodeCount));
- nodeIndexToLayoutIndex = new
OpenIntIntHashMap(PrimeFinder.nextPrime(nodeCount));
- squared_size = network.getNodeCount() * sizeFactor;
-
- epoch = 1;
-
- adaption = initialAdaptation;
-
- System.out.println("Epoch: " + epoch + " maxEpoch: " +
maxEpoch);
-
- while (epoch < maxEpoch) {
- partition.resetNodes();
- adjust();
- updateParameters();
-
- if (canceled)
- break;
- }
+ public boolean supportsSelectedOnly() {
+ return true;
}
-
- /**
- * @return the index of the closest NodeView to these coords.
- */
- public int getClosestPosition(double x, double y) {
- double minDistance = Double.MAX_VALUE;
- int closest = 0;
- Iterator nodeIter = partition.nodeIterator();
-
- while (nodeIter.hasNext()) {
- LayoutNode node = (LayoutNode) nodeIter.next();
- int rootGraphIndex = node.getNode().getIndex();
-
- nodeIndexToLayoutIndex.put(rootGraphIndex,
node.getIndex());
-
- double dx = node.getX();
- double dy = node.getY();
- double dist = (dx * dx) + (dy * dy);
-
- if (dist < minDistance) {
- minDistance = dist;
- closest = rootGraphIndex;
- }
- }
-
- return closest;
- }
-
- /**
- * DOCUMENT ME!
- */
- public void adjust() {
- //Generate random position in graph space
- ISOMVertexData tempISOM = new ISOMVertexData();
-
- // creates a new XY data location
- globalX = 10 + (Math.random() * squared_size);
- globalY = 10 + (Math.random() * squared_size);
-
- //Get closest vertex to random position
- int winner = getClosestPosition(globalX, globalY);
-
- Iterator nodeIter = partition.nodeIterator();
-
- while (nodeIter.hasNext()) {
- int nodeIndex = ((LayoutNode)
nodeIter.next()).getNode().getIndex();
- ISOMVertexData ivd = getISOMVertexData(nodeIndex);
- ivd.distance = 0;
- ivd.visited = false;
- }
-
- adjustVertex(winner);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateParameters() {
- epoch++;
-
- double factor = Math.exp(-1 * coolingFactor * ((1.0 * epoch) /
maxEpoch));
- adaption = Math.max(minAdaptation, factor * initialAdaptation);
-
- if ((radius > minRadius) && ((epoch % radiusConstantTime) ==
0)) {
- radius--;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void adjustVertex(int v) {
- q.clear();
-
- ISOMVertexData ivd = getISOMVertexData(v);
- ivd.distance = 0;
- ivd.visited = true;
- q.add(v);
-
- int current;
- List<LayoutNode> nodeList = partition.getNodeList();
-
- while (!q.isEmpty()) {
- current = q.get(0);
- q.remove(0);
-
- int layoutIndex = nodeIndexToLayoutIndex.get(current);
- LayoutNode currentNode = (LayoutNode)
nodeList.get(layoutIndex);
-
- ISOMVertexData currData = getISOMVertexData(current);
-
- double current_x = currentNode.getX();
- double current_y = currentNode.getY();
-
- double dx = globalX - current_x;
- double dy = globalY - current_y;
-
- // possible mod
- double factor = adaption / Math.pow(2,
currData.distance);
-
- currentNode.setX(current_x + (factor * dx));
- currentNode.setY(current_y + (factor * dy));
- partition.moveNodeToLocation(currentNode);
-
- if (currData.distance < radius) {
- int[] neighbors = neighborsArray(network,
currentNode.getNode());
-
- for (int neighbor_index = 0; neighbor_index <
neighbors.length; ++neighbor_index) {
- ISOMVertexData childData =
getISOMVertexData(neighbors[neighbor_index]);
-
- if (!childData.visited) {
- childData.visited = true;
- childData.distance =
currData.distance + 1;
-
q.add(neighbors[neighbor_index]);
- }
- }
- }
- }
-
- // Add check to make sure we don't put nodes on top of each
other
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ISOMVertexData getISOMVertexData(int v) {
- ISOMVertexData vd = (ISOMVertexData) nodeIndexToDataMap.get(v);
-
- if (vd == null) {
- vd = new ISOMVertexData();
- nodeIndexToDataMap.put(v, vd);
- }
-
- return vd;
- }
-
- public static class ISOMVertexData {
- public DoubleMatrix1D disp;
- int distance;
- boolean visited;
-
- public ISOMVertexData() {
- initialize();
- }
-
- public void initialize() {
- disp = new DenseDoubleMatrix1D(2);
-
- distance = 0;
- visited = false;
- }
-
- public double getXDisp() {
- return disp.get(0);
- }
-
- public double getYDisp() {
- return disp.get(1);
- }
-
- public void setDisp(double x, double y) {
- disp.set(0, x);
- disp.set(1, y);
- }
-
- public void incrementDisp(double x, double y) {
- disp.set(0, disp.get(0) + x);
- disp.set(1, disp.get(1) + y);
- }
-
- public void decrementDisp(double x, double y) {
- disp.set(0, disp.get(0) - x);
- disp.set(1, disp.get(1) - y);
- }
- }
-
- // This is here to replace the deprecated neighborsArray function
- /**
- * DOCUMENT ME!
- *
- * @param network DOCUMENT ME!
- * @param nodeIndex DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int[] neighborsArray(CyNetwork network, CyNode node) {
- // Get a list of edges
- List<CyNode> neighborList = network.getNeighborList(node,
CyEdge.Type.ANY);
- int [] neighbors = new int[neighborList.size()];
- int offset = 0;
- for (CyNode n: neighborList){
- neighbors[offset++]=n.getIndex();
- }
- return neighbors;
- }
}
Added:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayoutTask.java
(rev 0)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayoutTask.java
2010-09-24 23:54:32 UTC (rev 22058)
@@ -0,0 +1,301 @@
+package csplugins.layout.algorithms.graphPartition;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.work.Tunable;
+
+import cern.colt.list.IntArrayList;
+import cern.colt.map.OpenIntIntHashMap;
+import cern.colt.map.OpenIntObjectHashMap;
+import cern.colt.map.PrimeFinder;
+import cern.colt.matrix.DoubleMatrix1D;
+import cern.colt.matrix.impl.DenseDoubleMatrix1D;
+
+public class ISOMLayoutTask extends AbstractGraphPartition {
+
+ public int maxEpoch;
+ private int epoch;
+ public int radiusConstantTime;
+ public int radius;
+ public int minRadius;
+ private double adaption;
+ public double initialAdaptation;
+ public double minAdaptation;
+ public double sizeFactor;
+ public double coolingFactor;
+ private LayoutPartition partition;
+
+ //Queue, First In First Out, use add() and get(0)/remove(0)
+ private IntArrayList q;
+ OpenIntObjectHashMap nodeIndexToDataMap;
+ OpenIntIntHashMap nodeIndexToLayoutIndex;
+ double globalX;
+ double globalY;
+ double squared_size;
+
+ CyNetwork network;
+
+ public ISOMLayoutTask(final CyNetworkView networkView, final String
name,
+ final boolean selectedOnly, final Set<View<CyNode>>
staticNodes,
+ final int maxEpoch,final int radiusConstantTime,final
int radius,final int minRadius,
+ final double initialAdaptation,final double
minAdaptation,final double sizeFactor,final double coolingFactor)
+ {
+
+ super(networkView, name, selectedOnly, staticNodes);
+
+
+ this.maxEpoch = maxEpoch;
+ this.radiusConstantTime = radiusConstantTime;
+ this.radius = radius;
+ this.minRadius = minRadius;
+ this.initialAdaptation = initialAdaptation;
+ this.minAdaptation = minAdaptation;
+ this.sizeFactor = sizeFactor;
+ this.coolingFactor = coolingFactor;
+
+ network = networkView.getModel();
+ q = new IntArrayList();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartion(LayoutPartition partition) {
+ this.partition = partition;
+
+ int nodeCount = partition.nodeCount();
+ nodeIndexToDataMap = new
OpenIntObjectHashMap(PrimeFinder.nextPrime(nodeCount));
+ nodeIndexToLayoutIndex = new
OpenIntIntHashMap(PrimeFinder.nextPrime(nodeCount));
+ squared_size = network.getNodeCount() * sizeFactor;
+
+ epoch = 1;
+
+ adaption = initialAdaptation;
+
+ System.out.println("Epoch: " + epoch + " maxEpoch: " +
maxEpoch);
+
+ while (epoch < maxEpoch) {
+ partition.resetNodes();
+ adjust();
+ updateParameters();
+
+ if (cancelled)
+ break;
+ }
+ }
+
+ /**
+ * @return the index of the closest NodeView to these coords.
+ */
+ public int getClosestPosition(double x, double y) {
+ double minDistance = Double.MAX_VALUE;
+ int closest = 0;
+ Iterator nodeIter = partition.nodeIterator();
+
+ while (nodeIter.hasNext()) {
+ LayoutNode node = (LayoutNode) nodeIter.next();
+ int rootGraphIndex = node.getNode().getIndex();
+
+ nodeIndexToLayoutIndex.put(rootGraphIndex,
node.getIndex());
+
+ double dx = node.getX();
+ double dy = node.getY();
+ double dist = (dx * dx) + (dy * dy);
+
+ if (dist < minDistance) {
+ minDistance = dist;
+ closest = rootGraphIndex;
+ }
+ }
+
+ return closest;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void adjust() {
+ //Generate random position in graph space
+ ISOMVertexData tempISOM = new ISOMVertexData();
+
+ // creates a new XY data location
+ globalX = 10 + (Math.random() * squared_size);
+ globalY = 10 + (Math.random() * squared_size);
+
+ //Get closest vertex to random position
+ int winner = getClosestPosition(globalX, globalY);
+
+ Iterator nodeIter = partition.nodeIterator();
+
+ while (nodeIter.hasNext()) {
+ int nodeIndex = ((LayoutNode)
nodeIter.next()).getNode().getIndex();
+ ISOMVertexData ivd = getISOMVertexData(nodeIndex);
+ ivd.distance = 0;
+ ivd.visited = false;
+ }
+
+ adjustVertex(winner);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateParameters() {
+ epoch++;
+
+ double factor = Math.exp(-1 * coolingFactor * ((1.0 * epoch) /
maxEpoch));
+ adaption = Math.max(minAdaptation, factor * initialAdaptation);
+
+ if ((radius > minRadius) && ((epoch % radiusConstantTime) ==
0)) {
+ radius--;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void adjustVertex(int v) {
+ q.clear();
+
+ ISOMVertexData ivd = getISOMVertexData(v);
+ ivd.distance = 0;
+ ivd.visited = true;
+ q.add(v);
+
+ int current;
+ List<LayoutNode> nodeList = partition.getNodeList();
+
+ while (!q.isEmpty()) {
+ current = q.get(0);
+ q.remove(0);
+
+ int layoutIndex = nodeIndexToLayoutIndex.get(current);
+ LayoutNode currentNode = (LayoutNode)
nodeList.get(layoutIndex);
+
+ ISOMVertexData currData = getISOMVertexData(current);
+
+ double current_x = currentNode.getX();
+ double current_y = currentNode.getY();
+
+ double dx = globalX - current_x;
+ double dy = globalY - current_y;
+
+ // possible mod
+ double factor = adaption / Math.pow(2,
currData.distance);
+
+ currentNode.setX(current_x + (factor * dx));
+ currentNode.setY(current_y + (factor * dy));
+ partition.moveNodeToLocation(currentNode);
+
+ if (currData.distance < radius) {
+ int[] neighbors = neighborsArray(network,
currentNode.getNode());
+
+ for (int neighbor_index = 0; neighbor_index <
neighbors.length; ++neighbor_index) {
+ ISOMVertexData childData =
getISOMVertexData(neighbors[neighbor_index]);
+
+ if (!childData.visited) {
+ childData.visited = true;
+ childData.distance =
currData.distance + 1;
+
q.add(neighbors[neighbor_index]);
+ }
+ }
+ }
+ }
+
+ // Add check to make sure we don't put nodes on top of each
other
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ISOMVertexData getISOMVertexData(int v) {
+ ISOMVertexData vd = (ISOMVertexData) nodeIndexToDataMap.get(v);
+
+ if (vd == null) {
+ vd = new ISOMVertexData();
+ nodeIndexToDataMap.put(v, vd);
+ }
+
+ return vd;
+ }
+
+ public static class ISOMVertexData {
+ public DoubleMatrix1D disp;
+ int distance;
+ boolean visited;
+
+ public ISOMVertexData() {
+ initialize();
+ }
+
+ public void initialize() {
+ disp = new DenseDoubleMatrix1D(2);
+
+ distance = 0;
+ visited = false;
+ }
+
+ public double getXDisp() {
+ return disp.get(0);
+ }
+
+ public double getYDisp() {
+ return disp.get(1);
+ }
+
+ public void setDisp(double x, double y) {
+ disp.set(0, x);
+ disp.set(1, y);
+ }
+
+ public void incrementDisp(double x, double y) {
+ disp.set(0, disp.get(0) + x);
+ disp.set(1, disp.get(1) + y);
+ }
+
+ public void decrementDisp(double x, double y) {
+ disp.set(0, disp.get(0) - x);
+ disp.set(1, disp.get(1) - y);
+ }
+ }
+
+ // This is here to replace the deprecated neighborsArray function
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ * @param nodeIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] neighborsArray(CyNetwork network, CyNode node) {
+ // Get a list of edges
+ List<CyNode> neighborList = network.getNeighborList(node,
CyEdge.Type.ANY);
+ int [] neighbors = new int[neighborList.size()];
+ int offset = 0;
+ for (CyNode n: neighborList){
+ neighbors[offset++]=n.getIndex();
+ }
+ return neighbors;
+ }
+
+}
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