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Change GraphModificationFunctions to only save edges if graph data is cached

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efischer
2022-02-24 15:32:27 -06:00
parent dd64ac2731
commit 3d9890e16a
2 changed files with 61 additions and 38 deletions
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82
src/main/java/GraphModificationFunctions.java
View File

@@ -9,56 +9,71 @@ import java.util.Set;
public interface GraphModificationFunctions {
//remove over- and under-weight edges
public static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
int low, int high) {
static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
int low, int high, boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
for(DefaultWeightedEdge e: graph.edgeSet()){
if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)){
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
for (DefaultWeightedEdge e : graph.edgeSet()) {
if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
if(saveEdges) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
}
else {
graph.setEdgeWeight(e, 0.0);
}
}
}
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
if(saveEdges) {
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
}
}
return removedEdges;
}
//Remove edges for pairs with large occupancy discrepancy
public static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
Integer maxOccupancyDifference) {
Integer maxOccupancyDifference, boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
if (saveEdges) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
}
else {
graph.setEdgeWeight(e, 0.0);
}
}
}
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
if(saveEdges) {
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
}
}
return removedEdges;
}
//Remove edges for pairs where overlap size is significantly lower than the well occupancy
public static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
Integer minOverlapPercent) {
Integer minOverlapPercent,
boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
@@ -66,20 +81,27 @@ public interface GraphModificationFunctions {
double weight = graph.getEdgeWeight(e);
double min = minOverlapPercent / 100.0;
if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer intWeight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, intWeight};
removedEdges.add(edge);
if(saveEdges) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer intWeight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, intWeight};
removedEdges.add(edge);
}
else {
graph.setEdgeWeight(e, 0.0);
}
}
}
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
if(saveEdges) {
for (Integer[] edge : removedEdges) {
graph.removeEdge(edge[0], edge[1]);
}
}
return removedEdges;
}
public static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
List<Integer[]> removedEdges) {
for (Integer[] edge : removedEdges) {
DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);

17
src/main/java/Simulator.java
View File

@@ -147,8 +147,8 @@ public class Simulator implements GraphModificationFunctions {
Integer highThreshold, Integer maxOccupancyDifference,
Integer minOverlapPercent, boolean verbose) {
Instant start = Instant.now();
//Integer arrays will contain TO VERTEX, FROM VERTEX, and WEIGHT (which I'll need to cast to double)
List<Integer[]> removedEdges = new ArrayList<>();
boolean saveEdges = BiGpairSEQ.cacheGraph();
int numWells = data.getNumWells();
Integer alphaCount = data.getAlphaCount();
Integer betaCount = data.getBetaCount();
@@ -161,21 +161,21 @@ public class Simulator implements GraphModificationFunctions {
//remove edges with weights outside given overlap thresholds, add those to removed edge list
if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold));
removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold, saveEdges));
if(verbose){System.out.println("Over- and under-weight edges removed");}
//remove edges between vertices with too small an overlap size, add those to removed edge list
if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
" percent of vertex occupancy value.");}
removedEdges.addAll(GraphModificationFunctions.filterByOverlapPercent(graph, alphaWellCounts, betaWellCounts,
plateVtoAMap, plateVtoBMap, minOverlapPercent));
plateVtoAMap, plateVtoBMap, minOverlapPercent, saveEdges));
if(verbose){System.out.println("Edges with weights too far below a vertex occupancy value removed");}
//Filter by relative occupancy
if(verbose){System.out.println("Eliminating edges between vertices with occupancy difference > "
+ maxOccupancyDifference);}
removedEdges.addAll(GraphModificationFunctions.filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts,
plateVtoAMap, plateVtoBMap, maxOccupancyDifference));
plateVtoAMap, plateVtoBMap, maxOccupancyDifference, saveEdges));
if(verbose){System.out.println("Edges between vertices of with excessively different occupancy values " +
"removed");}
@@ -310,10 +310,11 @@ public class Simulator implements GraphModificationFunctions {
}
}
//put the removed edges back on the graph
System.out.println("Restoring removed edges to graph.");
GraphModificationFunctions.addRemovedEdges(graph, removedEdges);
if(saveEdges) {
//put the removed edges back on the graph
System.out.println("Restoring removed edges to graph.");
GraphModificationFunctions.addRemovedEdges(graph, removedEdges);
}
//return MatchingResult object
return output;
}