Author: paperwing
Date: 2012-03-16 11:45:31 -0700 (Fri, 16 Mar 2012)
New Revision: 28563
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/edges/EdgeAnalyser.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
Log:
Modified RenderArcEdgesProcedure to use EdgeAnalyser which recycles analyzed
data, gain in framerate was barely noticeable (remained at 30 for 400 nodes and
1100 edges)
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/edges/EdgeAnalyser.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/edges/EdgeAnalyser.java
2012-03-16 18:25:36 UTC (rev 28562)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/edges/EdgeAnalyser.java
2012-03-16 18:45:31 UTC (rev 28563)
@@ -46,6 +46,8 @@
/** The frame number that the generated edge data is current for */
private Long currentFrame;
+ private Long lastCalculatedTime = 0L;
+
public EdgeAnalyser() {
edgeContainers = new HashMap<View<CyEdge>,
AugmentedEdgeContainer>();
currentFrame = 0L;
@@ -61,9 +63,13 @@
* @return An up-to-date set of analyzed edge data to be used for
rendering.
*/
public Collection<AugmentedEdgeContainer>
getAnalyzedEdges(CyNetworkView networkView, double distanceScale, Long
currentFrame) {
- if (this.currentFrame != currentFrame) {
+
+ if (currentFrame - this.currentFrame > 0) {
calculateEdgeProperties(networkView, distanceScale);
calculateEdgeCoordinates();
+ this.currentFrame = currentFrame;
+ } else {
+ // System.out.println("Reusing edge data");
}
return edgeContainers.values();
@@ -135,14 +141,22 @@
}
}
+ Collection<View<CyEdge>> edgeViews = networkView.getEdgeViews();
+
// Update the value for the total number of edges between this
pair of nodes
for (AugmentedEdgeContainer container :
edgeContainers.values()) {
+
container.setTotalCoincidentEdges(pairCoincidenceCount.get(container.getPairIdentifier()));
// If there was only 1 edge for that pair of nodes,
make it a straight edge
if (container.getTotalCoincidentEdges() == 1 &&
!container.isSelfEdge()) {
container.setStraightEdge(true);
}
+
+ // Check if this edge container holds an edge that is
no longer in the network
+// if (!edgeViews.contains(container.getEdgeView())) {
+// edgeContainers.remove(container.getEdgeView());
+// }
}
}
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
2012-03-16 18:25:36 UTC (rev 28562)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
2012-03-16 18:45:31 UTC (rev 28563)
@@ -2,6 +2,7 @@
import java.awt.Color;
import java.nio.FloatBuffer;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
@@ -14,6 +15,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNode;
+import org.cytoscape.paperwing.internal.cytoscape.edges.AugmentedEdgeContainer;
import org.cytoscape.paperwing.internal.data.GraphicsData;
import org.cytoscape.paperwing.internal.geometric.Vector3;
import org.cytoscape.paperwing.internal.rendering.shapes.EdgeShapeDrawer;
@@ -38,22 +40,13 @@
private static final RenderColor DEFAULT_COLOR =
new RenderColor(0.67, 0.67, 0.67);
- private static final RenderColor DEFAULT_SELECTED_COLOR =
- new RenderColor(0.73, 0.73, 0.6);
- private static final RenderColor DEFAULT_HOVER_COLOR =
- new RenderColor(0.5, 0.5, 0.7);
private static final float DASHED_EDGE_RADIUS = 0.012f;
private static final float DASHED_EDGE_LENGTH = 0.05f;
- private static final float DASHED_EDGE_SPACING = 0.07f;
private static final float DOTTED_EDGE_RADIUS = 0.017f;
- private static final float DOTTED_EDGE_SPACING = 0.057f;
+
- private static final double ARC_SELF_EDGE_MINIMUM_RADIUS = 0.055; //
0.045 default feb 7, 2012
- private static final double ARC_SELF_EDGE_RADIUS_FACTOR = 0.008; //
0.007 default feb 7, 2012
- private static final double ARC_SELF_EDGE_EXPONENTIAL_BASE = 1.25;
-
/**
* The number of straight segments used to approximate a curved edge
*/
@@ -62,111 +55,11 @@
private EdgeShapeDrawer shapeDrawer;
private float edgeRadiusFactor = 1.0f;
-
- // Container for EdgeView objects that also adds information about
whether the
- // edge is part of a series of edges that connect the same pair of nodes
- private class EdgeViewContainer {
- protected View<CyEdge> edgeView;
- // Identifies the pair of nodes that the edge connects
- protected long pairIdentifier;
-
- // The index of this edge compared to all the other edges that
connect the same pair
- // of nodes. If this is the first of 7 edges that connect the
same pair of nodes, its
- // edgeNumber would be set to 1.
- protected int edgeNumber;
-
- // The total number of edges that connect the pair of nodes.
- protected int totalCoincidentEdges;
-
- // Does this edge direct from a node to itself?
- protected boolean selfEdge;
-
- // Should this edge be a straight edge because it is the only
edge between 2 nodes?
- protected boolean straightEdge;
-
- Vector3 start;
- Vector3 end;
- }
-
public RenderArcEdgesProcedure() {
shapeDrawer = new EdgeShapeDrawer();
}
- // Analyze the network to obtain whether each edge is connecting 2
nodes that
- // are already connected by other nodes
- // Maybe add an optimization so we only have to re-analyze the network
each time it changes?
- private Set<EdgeViewContainer> analyzeEdges(CyNetworkView networkView,
double distanceScale) {
-
- // Create the set of containers to be returned
- Set<EdgeViewContainer> edgeViewContainers = new
HashSet<EdgeViewContainer>(
- networkView.getModel().getEdgeCount());
-
- // This map maps each node-pair identifier to the number of
edges between that pair of nodes
- // The identifier is: max(sourceIndex, targetIndex) * nodeCount
+ min(sourceIndex, targetIndex)
- Map<Long, Integer> pairCoincidenceCount = new HashMap<Long,
Integer>(
- networkView.getModel().getNodeCount());
- long identifier;
- int sourceIndex, targetIndex, edgeNumber;
- int nodeCount = networkView.getModel().getNodeCount();
- CyEdge edge;
-
- boolean selfEdge;
-
- for (View<CyEdge> edgeView : networkView.getEdgeViews()) {
- edge = edgeView.getModel();
-
- // Assign an identifier to each pair of nodes
- sourceIndex = edge.getSource().getIndex();
- targetIndex = edge.getTarget().getIndex();
-
- if (sourceIndex >= targetIndex) {
- identifier = (long) nodeCount * sourceIndex +
targetIndex;
- } else {
- identifier = (long) nodeCount * targetIndex +
sourceIndex;
- }
-
- // Assign a value that represents how many edges have
been found between this pair
- if (!pairCoincidenceCount.containsKey(identifier)) {
- edgeNumber = 1;
- } else {
- edgeNumber =
pairCoincidenceCount.get(identifier) + 1;
- }
-
- pairCoincidenceCount.put(identifier, edgeNumber);
-
- // Check if the edge leads from a node to itself
- if (sourceIndex == targetIndex) {
- selfEdge = true;
- } else {
- selfEdge = false;
- }
-
- EdgeViewContainer container = new EdgeViewContainer();
- container.edgeView = edgeView;
- container.pairIdentifier = identifier;
- container.edgeNumber = edgeNumber;
- container.selfEdge = selfEdge;
-
- container.start = obtainCoordinates(edge.getSource(),
networkView, distanceScale);
- container.end = obtainCoordinates(edge.getTarget(),
networkView, distanceScale);
-
- edgeViewContainers.add(container);
- }
-
- // Update the value for the total number of edges between this
pair of nodes
- for (EdgeViewContainer container : edgeViewContainers) {
- container.totalCoincidentEdges =
pairCoincidenceCount.get(container.pairIdentifier);
-
- // If there was only 1 edge for that pair of nodes,
make it a straight edge
- if (container.totalCoincidentEdges == 1 &&
!container.selfEdge) {
- container.straightEdge = true;
- }
- }
-
- return edgeViewContainers;
- }
-
@Override
public void initialize(GraphicsData graphicsData) {
shapeDrawer.initialize(graphicsData.getGlContext());
@@ -184,18 +77,17 @@
double distanceScale = graphicsData.getDistanceScale();
- Set<EdgeViewContainer> edgeViewContainers =
analyzeEdges(networkView, distanceScale);
+ Collection<AugmentedEdgeContainer> edgeContainers =
graphicsData.getEdgeAnalyser().getAnalyzedEdges(networkView, distanceScale,
graphicsData.getFramesElapsed());
View<CyEdge> edgeView;
- Vector3 circleCenter;
+
Number edgeWidth;
- for (EdgeViewContainer container : edgeViewContainers) {
- edgeView = container.edgeView;
+ for (AugmentedEdgeContainer container : edgeContainers) {
+ edgeView = container.getEdgeView();
- if (container.start != null && container.end != null &&
-
(container.end.distance(container.start) >= MIN_LENGTH || container.selfEdge)) {
+ if (container.isSufficientLength()) {
- edgeWidth =
container.edgeView.getVisualProperty(BasicVisualLexicon.EDGE_WIDTH);
+ edgeWidth =
edgeView.getVisualProperty(BasicVisualLexicon.EDGE_WIDTH);
if (edgeWidth != null) {
edgeRadiusFactor =
edgeWidth.floatValue() / 2;
@@ -210,58 +102,25 @@
gl.glLoadName(edgeView.getModel().getIndex());
// General points along the arc
- Vector3[] points;
+ Vector3[] points = container.getCoordinates();
- if (container.straightEdge) {
+
+ // Draw the correct type of edge depending on
the visual property
+ if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
+ ==
LineTypeVisualProperty.EQUAL_DASH) {
+
+ drawDashedArc(gl, points);
+ } else if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
+ == LineTypeVisualProperty.DOT) {
+
+ drawDottedArc(gl, points);
- // Draw the correct type of edge
depending on the visual property
- if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
- ==
LineTypeVisualProperty.EQUAL_DASH) {
- points =
EdgeCoordinateCalculator.generateStraightEdgeSparseCoordinates(
-
container.start, container.end, DASHED_EDGE_SPACING);
-
- drawDashedArc(gl, points);
- } else if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
- ==
LineTypeVisualProperty.DOT) {
- points =
EdgeCoordinateCalculator.generateStraightEdgeSparseCoordinates(
-
container.start, container.end, DOTTED_EDGE_SPACING);
-
- drawDottedArc(gl, points);
-
- // Draw regular edges for the catch-all
case
- } else {
- points =
EdgeCoordinateCalculator.generateStraightEdgeCoordinates(
-
container.start, container.end, 1);
-
- drawRegularArc(gl, points);
- }
-
+ // Draw regular edges for the catch-all case
} else {
- // Find the arc circle's center
- circleCenter =
findCircleCenter(container);
-
- // Draw the correct type of edge
depending on the visual property
- if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
- ==
LineTypeVisualProperty.EQUAL_DASH) {
- points =
EdgeCoordinateCalculator.generateArcEdgeSparseCoordinates(
-
container.start, container.end, circleCenter, DASHED_EDGE_SPACING,
container.selfEdge);
-
- drawDashedArc(gl, points);
- } else if
(edgeView.getVisualProperty(BasicVisualLexicon.EDGE_LINE_TYPE)
- ==
LineTypeVisualProperty.DOT) {
- points =
EdgeCoordinateCalculator.generateArcEdgeSparseCoordinates(
-
container.start, container.end, circleCenter, DOTTED_EDGE_SPACING,
container.selfEdge);
-
- drawDottedArc(gl, points);
-
- // Draw regular edges for the catch-all
case
- } else {
- points =
EdgeCoordinateCalculator.generateArcEdgeCoordinates(
-
container.start, container.end, circleCenter, NUM_SEGMENTS, container.selfEdge);
-
- drawRegularArc(gl, points);
- }
+
+ drawRegularArc(gl, points);
}
+
}
}
}
@@ -296,119 +155,6 @@
RenderColor.setNonAlphaColors(gl, color);
}
- // Obtain the coordinates of a given node, eg. source or target node
- // Returns null if failed to find coordinates
- private Vector3 obtainCoordinates(CyNode node, CyNetworkView
networkView, double distanceScale) {
- Vector3 coordinates = null;
-
- View<CyNode> nodeView = networkView.getNodeView(node);
-
- if (nodeView != null) {
- double x =
nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION) / distanceScale;
- double y =
nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION) / distanceScale;
- double z =
nodeView.getVisualProperty(BasicVisualLexicon.NODE_Z_LOCATION) / distanceScale;
-
- // TODO: Perform a check to ensure none of x, y, z are
null?
- coordinates = new Vector3(x, y, z);
- }
-
- return coordinates;
- }
-
-
- /**
- * Finds the center of a circle passing through 2 points, rotated about
the displacement axis
- * by a certain angle.
- *
- * @param container The EdgeViewContainer object holding additional
information about the
- * edge, including its index amongst the other edges that connect the
same pair of nodes
- * @return A position vector representing the center of the circle
- */
- private Vector3 findCircleCenter(EdgeViewContainer container) {
-
- double[] edgeMetrics = findArcEdgeMetrics(container);
-
- double radius = edgeMetrics[0];
- double angle = edgeMetrics[1];
-
- if (container.selfEdge) {
- Vector3 offset = (new Vector3(1, 0,
0)).multiply(radius).rotate(
- (new Vector3(0, 1, 0)), angle);
-
- return container.start.plus(offset);
- } else {
-
- Vector3 displacement =
container.end.subtract(container.start);
-
- double displacementLength = displacement.magnitude();
-
- // Radius adjustment (can't draw an arc from start to
end if the radius of the arc is less than half that
- // distance)
- // radius = Math.max(displacementLength * 2, radius);
-
- // Use cosine law
- double arcAngle;
- arcAngle = GeometryToolkit.saferArcCos(
- (2 * radius * radius -
displacementLength * displacementLength)
- / (2 * radius * radius));
-
- double nearCornerAngle = Math.PI / 2 - (arcAngle / 2);
-
- // Set the angle of rotation along the node-to-node
displacement axis
- Vector3 targetDirection = new Vector3(0, 1, 0);
- targetDirection = targetDirection.rotate(displacement,
angle);
-
- // Offset vector that points from first node to the
circle's center
- Vector3 circleCenterOffset =
displacement.rotate(targetDirection.cross(displacement), nearCornerAngle);
- circleCenterOffset.normalizeLocal();
- circleCenterOffset.multiplyLocal(radius);
-
- return container.start.plus(circleCenterOffset);
- }
- }
-
- /**
- * Return a 2-tuple containing the appropriate radius for the circular
edge arc, as well
- * as how much it should be rotated in the node-to-node displacement
axis.
- *
- * @param container The EdgeViewContainer object holding additional
information about the
- * edge, including its index amongst the other edges that connect the
same pair of nodes
- * @param selfEdge Whether or not the edge leads from a node to itself
- */
- private double[] findArcEdgeMetrics(EdgeViewContainer container) {
-
- // Level 1 has 2^2 - 1^1 = 3 edges, level 2 has 3^3 - 2^2 = 5,
level 3 has 7
- int edgeLevel = (int) (Math.sqrt((double)
container.edgeNumber));
- int maxLevel = (int) (Math.sqrt((double)
container.totalCoincidentEdges));
-
- int edgesInLevel = edgeLevel * 2 + 1;
-
- double curvedEdgeRadius;
-
- if (container.selfEdge) {
- // For self-edges, want greater edge level -> greater
radius
- curvedEdgeRadius = ARC_SELF_EDGE_MINIMUM_RADIUS
- + ARC_SELF_EDGE_RADIUS_FACTOR *
Math.pow(edgeLevel, ARC_SELF_EDGE_EXPONENTIAL_BASE);
- } else {
- // For regular edges, want greater edge level ->
smaller radius (more curvature)
- curvedEdgeRadius =
container.start.distance(container.end) * (0.5 + (double) 3.5 /
Math.pow(edgeLevel, 2));
- }
-
- // The outmost level is usually not completed
- if (edgeLevel == maxLevel) {
- edgesInLevel = (int) (container.totalCoincidentEdges -
Math.pow(maxLevel, 2) + 1);
- }
-
- double edgeRadialAngle = (double) (container.edgeNumber -
Math.pow(edgeLevel, 2)) / edgesInLevel * Math.PI * 2;
-
- // Flip the angle by 180 degrees for every other edge level for
aesthetic effect
- if (edgeLevel % 2 == 0) {
- edgeRadialAngle = Math.PI - edgeRadialAngle;
- }
-
- return new double[]{curvedEdgeRadius, edgeRadialAngle};
- }
-
private void drawRegularArc(GL2 gl, Vector3[] points) {
Vector3 displacement;
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