Example 1 with ObjectReferenceWrapper
use of org.vcell.util.ObjectReferenceWrapper in project vcell by virtualcell.
the class RegionImage method calculateRegions.
/**
* Insert the method's description here.
* Creation date: (3/28/2002 10:30:20 AM)
* @param image cbit.image.VCImage
*/
private void calculateRegions(VCImage vcImage) throws cbit.image.ImageException {
long time1 = System.currentTimeMillis();
RegionMask[][] regionMasks = new RegionMask[numZ][];
for (int k = 0; k < vcImage.getNumZ(); k++) {
regionMasks[k] = calculateRegions3D(vcImage.getPixels(), k * numXY, numX, numY);
}
long time2 = System.currentTimeMillis();
// time2 = System.currentTimeMillis();
// RegionMask regionMasksFast[][] = new RegionMask[numZ][];
// for (int k = 0; k < vcImage.getNumZ(); k++){
// regionMasksFast[k] = calculateRegions3Dfaster(vcImage.getPixels(),k*numXY,numX,numY);
// }
// long time3 = System.currentTimeMillis();
// System.out.println("4way recursive took "+((time2-time1)/1000.0)+" s, nonrecursive line took "+((time3-time2)/1000.0)+" s");
//
// consolidate "off-plane contiguous" region indexes
// build a graph of all 2D regions that touch
//
// the final 3D regions are the set of nodes in each of the spanning trees.
//
//
// build graph with 1 node per 2d region
//
Graph connectionGraph = new Graph();
for (int k = 0; k < numZ; k++) {
for (int i = 0; i < regionMasks[k].length; i++) {
Node node = new Node(k + "," + i, new org.vcell.util.ObjectReferenceWrapper(regionMasks[k][i]));
connectionGraph.addNode(node);
}
}
//
// add edges for any slice-slice touching of regions with same pixel value
//
BitSet zeroBitSet = new BitSet();
BitSet intersection = new BitSet(numXY);
for (int k = 0; k < numZ - 1; k++) {
for (int i = 0; i < regionMasks[k].length; i++) {
Node node_i = connectionGraph.getNode(k + "," + i);
for (int j = 0; j < regionMasks[k + 1].length; j++) {
if (regionMasks[k][i].pixelValue == regionMasks[k + 1][j].pixelValue) {
// clear mask
intersection.and(zeroBitSet);
intersection.or(regionMasks[k][i].mask);
intersection.and(regionMasks[k + 1][j].mask);
if (!intersection.equals(zeroBitSet)) {
Node node_j = connectionGraph.getNode((k + 1) + "," + j);
connectionGraph.addEdge(new Edge(node_i, node_j));
}
}
}
}
}
//
// get spanning forest, and for each spanning tree, assign a single regionID to each contained 2d mask
//
Tree[] spanningForest = connectionGraph.getSpanningForest();
regionInfos = new RegionInfo[spanningForest.length];
for (int i = 0; i < spanningForest.length; i++) {
Node[] nodes = spanningForest[i].getNodes();
int pixelValue = -1;
int numPixels = 0;
BitSet fullMask = new BitSet(numXY * numZ);
for (int j = 0; j < nodes.length; j++) {
RegionMask regionMask = (RegionMask) ((ObjectReferenceWrapper) nodes[j].getData()).getObject();
pixelValue = regionMask.pixelValue;
for (int k = 0; k < numXY; k++) {
if (regionMask.mask.get(k)) {
fullMask.set(regionMask.offset + k);
numPixels++;
}
}
}
regionInfos[i] = new RegionInfo(pixelValue, numPixels, i, fullMask);
}
long time3 = System.currentTimeMillis();
System.out.println("4way recursive on slices took " + ((time2 - time1) / 1000.0) + " s, total RegionImage time " + ((time3 - time1) / 1000.0) + " s");
}