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imagej-elphel
Commit dfe9ae9d authored by Andrey Filippov's avatar Andrey Filippov
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selecting no-conflict clusters

parent da537ae9
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Showing with 361 additions and 2 deletions
src/main/java/TileSurface.java
View file @ dfe9ae9d
...@@ -2867,6 +2867,357 @@ public class TileSurface { ...@@ -2867,6 +2867,357 @@ public class TileSurface {
sdfa_instance.showArrays(img_clust, imageTilesX, imageTilesY, true, title, titles); sdfa_instance.showArrays(img_clust, imageTilesX, imageTilesY, true, title, titles);
} }
public boolean [][] growClusterOnce( // used from inside threads
final boolean [][] cluster_local_pure,
final int [] window,
final int [] img_indices,
final int [] surf_indices,
final int debugLevel,
final int dbg_X,
final int dbg_Y)
{
int num_tiles = img_indices.length;
int width = window[2];
int height = window[3];
boolean [][] grown_cluster = new boolean [num_tiles][];
for (int neTile = 0; neTile < num_tiles; neTile++){
if (cluster_local_pure[neTile] != null){
grown_cluster[neTile] = cluster_local_pure[neTile].clone();
}
}
int dbg_ntiles1 = 0;
if (debugLevel > 0) {
for (int neTile = 0; neTile < num_tiles; neTile++){
if (grown_cluster[neTile] != null){
for (int nl = 0; nl < grown_cluster[neTile].length; nl++){
if (grown_cluster[neTile][nl]) dbg_ntiles1 ++;
}
}
}
System.out.println("growClusterOnce(): number of tiles = "+dbg_ntiles1);
}
final TileNeibs tnWindow = new TileNeibs(width,height);
for (int neTile0 = 0; neTile0 < num_tiles; neTile0++) if (cluster_local_pure[neTile0] != null){
for (int nl0 = 0; nl0 < cluster_local_pure[neTile0].length; nl0++){
if (cluster_local_pure[neTile0][nl0]){ // source should be single-layer, but ...
int nSurfTile0 = surf_indices[neTile0];
int [] neibs = tileData[nSurfTile0][nl0].getNeighbors();
for (int dir = 0; dir < tnWindow.dirs; dir++) {
int nl1 = neibs[dir];
if (nl1 < 0){
if (debugLevel >-1) {
System.out.println("growClusterOnce(): Expected 8 neighbors for tile nSurfTile0="+
nSurfTile0+" neibs["+dir+"] = "+nl1);
}
} else {
int neTile1 = tnWindow.getNeibIndex(neTile0, dir);
if (neTile1 >= 0) {
if ( ((cluster_local_pure[neTile1] == null) || !cluster_local_pure[neTile1][nl1]) &&
((grown_cluster[neTile1] == null) || !grown_cluster[neTile1][nl1])) {
if (grown_cluster[neTile1] == null) {
int nSurfTile1 = surf_indices[neTile1];
// should never be null as it is connected from nSurfTile0
grown_cluster[neTile1] = new boolean [tileData[nSurfTile1].length];
}
grown_cluster[neTile1][nl1] = true;
}
}
}
}
}
}
}
if (debugLevel > 0) {
int dbg_ntiles2 = 0;
for (int neTile = 0; neTile < num_tiles; neTile++){
if (grown_cluster[neTile] != null){
for (int nl = 0; nl < grown_cluster[neTile].length; nl++){
if (grown_cluster[neTile][nl]) dbg_ntiles2 ++;
}
}
}
System.out.println("growClusterOnce(): new number of tiles = "+dbg_ntiles2+" (was "+dbg_ntiles1+")");
}
return grown_cluster;
}
public int [][] mergeNoConflict(
final int [][] matchedGrown,
final int [][] clusters_grown,
final int [][] clusters_pure,
final int debugLevel,
final int dbg_X,
final int dbg_Y)
{
if (debugLevel >-1){
System.out.println("mergeNoConflict(): groups: "+matchedGrown.length);
}
final int num_grown = matchedGrown.length;
final int [][][] pre_merged_subs = new int [num_grown][][];
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int iGClust = ai.getAndIncrement(); iGClust < num_grown; iGClust = ai.getAndIncrement()) {
int num_subs = matchedGrown[iGClust].length;
if (num_subs < 2){ // nothing to split
pre_merged_subs[iGClust] = new int [num_subs][];
if (num_subs > 0) { // should always be so?
pre_merged_subs[iGClust][0] = matchedGrown[iGClust].clone();
}
} else { //>= 2 clusters
int nGClust = iGClust + 1;
int dl = ((debugLevel > -1) && (num_subs > 3)) ? 3: 0;
if (dl > 0){
System.out.println("mergeNoConflict(): nGClust: "+nGClust+" num_subs= "+num_subs);
}
// create window for the grown cluster, it will include all subs
int [] window = getClusterBBox(
nGClust, // 1-based
0, // border,
clusters_grown);
int [][] tile_indices = getClusterBBoxIndices(
window, // final int [] window,
0); // border); // final int border) // maybe 0, actual value just saves time
int [] img_tile_indices = tile_indices[0];
int [] surf_tile_indices = tile_indices[1];
int num_tiles = img_tile_indices.length;
int [] clust_sizes = new int [num_subs];
boolean [][][] subs_pure = new boolean [num_subs][][];
boolean [][][] subs_grown = new boolean [num_subs][][];
for (int nSub = 0; nSub < num_subs; nSub++){
subs_pure[nSub] = extractCluster(
matchedGrown[iGClust][nSub], // final int numToSplit, // 1-based
0, // border, // final int border,
clusters_pure, // final int [][] clusters,
window, // final int [] window,
img_tile_indices, // final int [] bbox_indices,
debugLevel, // final int debugLevel,
dbg_X, // final int dbg_X,
dbg_Y); // final int dbg_Y)
subs_grown[nSub] = growClusterOnce( // used from inside threads
subs_pure[nSub], // final boolean [][] cluster_local_pure,
window, // final int [] window,
img_tile_indices, // final int [] bbox_indices,
surf_tile_indices, // final int [] surf_indices,
0, // dl, // debugLevel, // final int debugLevel,
dbg_X, // final int dbg_X,
dbg_Y); // final int dbg_Y)
}
// now build sets of clusters
// a) connected to current (and having higher number)
// b) conflicting with current (and having higher number)
ArrayList<HashSet<Integer>> touching_list = new ArrayList<HashSet<Integer>>();
ArrayList<HashSet<Integer>> conflict_list = new ArrayList<HashSet<Integer>>();
for (int nSub = 0; nSub < num_subs; nSub++){
touching_list.add(new HashSet<Integer>());
conflict_list.add(new HashSet<Integer>());
}
for (int neTile = 0; neTile < num_tiles; neTile++){
for (int nSub = 0; nSub < num_subs; nSub++){
if (subs_grown[nSub][neTile] != null){
for (int nl1 = 0; nl1 < subs_grown[nSub][neTile].length; nl1++){
if (subs_grown[nSub][neTile][nl1]){
clust_sizes[nSub] ++;
for (int nSub2 = nSub+1; nSub2 < num_subs; nSub2++) if (subs_grown[nSub2][neTile] != null){
for (int nl2 = 0; nl2 < subs_grown[nSub2][neTile].length; nl2++){ //*
if (subs_grown[nSub2][neTile][nl2]){
if (nl1 == nl2) {
touching_list.get(nSub).add(new Integer(nSub2));
touching_list.get(nSub2).add(new Integer(nSub)); // both ways
} else {
conflict_list.get(nSub).add(new Integer(nSub2));
conflict_list.get(nSub2).add(new Integer(nSub)); // both ways
}
}
}
}
}
}
}
}
}
ArrayList<HashSet<Integer>> groups_list = new ArrayList<HashSet<Integer>>();
HashSet<Integer> clusters_left = new HashSet<Integer>();
for (int nSub = 0; nSub < num_subs; nSub++){
clusters_left.add(new Integer(nSub));
}
while (!clusters_left.isEmpty()){
HashSet<Integer> new_group = new HashSet<Integer>();
HashSet<Integer> candidates = new HashSet<Integer>();
HashSet<Integer> conflicts = new HashSet<Integer>();
// HashSet<Integer> touching = new HashSet<Integer>();
// start with the largest of the remaining clusters
Integer best_sub = -1;
for (Integer sc:clusters_left){
if ((best_sub < 0) || (clust_sizes[best_sub] < clust_sizes[sc])){
best_sub = sc;
}
}
if ( !clusters_left.remove(best_sub)) {
System.out.println("mergeNoConflict() bug: can not remove"+best_sub);
}
new_group.add(best_sub);
conflicts.addAll(conflict_list.get(best_sub)); // keep track of all accumulated conflicts
candidates.addAll(touching_list.get(best_sub)); // add all clusters that are touching the current selection
candidates.removeAll(conflicts); // remove all conflicts
while (!candidates.isEmpty()) { // add more clusters if possible
// Find the largest one
best_sub = -1;
for (Integer sc:candidates){
if ((best_sub < 0) || (clust_sizes[best_sub] < clust_sizes[sc])){
best_sub = sc;
}
}
// add that new cluster
clusters_left.remove(best_sub);
new_group.add(best_sub);
conflicts.addAll(conflict_list.get(best_sub)); // keep track of all accumulated conflicts
candidates.addAll(touching_list.get(best_sub)); // add all clusters that are touching the current selection
candidates.removeAll(conflicts); // remove all conflicts
candidates.removeAll(new_group); // remove all what is already included
}
groups_list.add(new_group);
}
pre_merged_subs[iGClust] = new int [groups_list.size()][];
for (int ng = 0; ng < groups_list.size(); ng++) {
pre_merged_subs[iGClust][ng] = new int [groups_list.get(ng).size()];
int nc = 0;
for (Integer cl: groups_list.get(ng)){
pre_merged_subs[iGClust][ng][nc++] = cl;
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
// "flatten" pre_merged_subs
int num_new_groups = 0;
for (int ng = 0; ng < pre_merged_subs.length; ng ++) {
num_new_groups += pre_merged_subs[ng].length;
}
if (debugLevel >-1){
System.out.println("mergeNoConflict(): groups: " + num_new_groups + " (was : "+matchedGrown.length+")");
}
final int [][] merged_subs = new int [num_new_groups][];
int indx = 0;
for (int ng = 0; ng < pre_merged_subs.length; ng ++) {
for (int nc = 0; nc < pre_merged_subs[ng].length; nc ++){
merged_subs[indx++] = pre_merged_subs[ng][nc];
}
}
if (debugLevel > -1) {
for (int i = 0; i < num_new_groups; i++){
System.out.print("mergeNoConflict(): "+ (i+1)+" [");
for (int j = 0; j < merged_subs[i].length; j++) {
if (j > 0) System.out.print(", ");
System.out.print(merged_subs[i][j]);
}
System.out.println(" ]");
}
}
return merged_subs;
}
/**
* Grow each of the clusters (encoded as positive cluster numbers per tile per layer) by 1 in each
* of 8 directions. As they now may overlap they are encoded in boolean array [cluster][tile][layer]
* @param clusters_pure cluster numbers (>0) for each tile, each layer
* @param debugLevel
* @param dbg_X
* @param dbg_Y
* @return boolean array [cluster-1][tile][layer]
*/
public boolean [][][] growEachCluster (
final int [][] clusters_pure,
final int debugLevel,
final int dbg_X,
final int dbg_Y)
{
final int num_clusters = getNumClusters(clusters_pure);
final boolean [][][] clusters = new boolean [num_clusters][clusters_pure.length][];
final TileNeibs tnImage = new TileNeibs(imageTilesX, imageTilesY);
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int iClust = ai.getAndIncrement(); iClust < num_clusters; iClust = ai.getAndIncrement()) {
int nClust = iClust + 1; // 1-based
for (int nTile0 = 0; nTile0 < clusters_pure.length; nTile0++) if (clusters_pure[nTile0] != null){
for (int nl0 = 0; nl0 < clusters_pure[nTile0].length; nl0++){
if (clusters_pure[nTile0][nl0] == nClust){ // source should be single-layer, but ...
if (clusters[iClust][nTile0]==null) {
clusters[iClust][nTile0] = new boolean [clusters_pure[nTile0].length];
}
clusters[iClust][nTile0][nl0] = true;
int nSurfTile0 = getSurfaceTileIndex(nTile0);
int [] neibs = tileData[nSurfTile0][nl0].getNeighbors();
for (int dir = 0; dir < tnImage.dirs; dir++) {
int nl1 = neibs[dir];
if (nl1 < 0){
if (debugLevel >-1) {
System.out.println("growEachCluster(): Expected 8 neighbors for tile nSurfTile0="+
nSurfTile0+" neibs["+dir+"] = "+nl1);
}
int nTile1 = tnImage.getNeibIndex(nTile0, dir);
if (nTile1 >= 0) {
if ( ((clusters_pure[nTile1] == null) || (clusters_pure[nTile1][nl1] != nClust)) &&
((clusters[iClust][nTile1] == null) || !clusters[iClust][nTile1][nl1])) {
if (clusters[iClust][nTile1] == null) {
int nSurfTile1 = getSurfaceTileIndex(nTile1);
clusters[iClust][nTile1] = new boolean [tileData[nSurfTile1].length];
}
clusters[iClust][nTile1][nl1] = true;
}
}
}
}
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return clusters;
}
/**
* Match grown/merged clusters to the ones they were made of
* @param clusters_grown per-tile, per layer array of positive merged cluster numbers (0 - empty)
* @param clusters_pure per-tile, per layer array of positive pure cluster numbers (0 - empty)
* @param debugLevel
* @param dbg_X
* @param dbg_Y
* @return array for each of the merged clusters array of pure cluster numbers it is made of
*/
public int [][] matchPureGrown ( public int [][] matchPureGrown (
final int [][] clusters_grown, final int [][] clusters_grown,
final int [][] clusters_pure, final int [][] clusters_pure,
...@@ -2915,7 +3266,7 @@ public class TileSurface { ...@@ -2915,7 +3266,7 @@ public class TileSurface {
System.out.println(" ]"); System.out.println(" ]");
} }
} }
return null; return grown_subs;
} }
...@@ -3413,7 +3764,15 @@ public class TileSurface { ...@@ -3413,7 +3764,15 @@ public class TileSurface {
debugLevel, debugLevel,
dbg_X, dbg_X,
dbg_Y); dbg_Y);
int [][] merged_no_conflict = mergeNoConflict(
grown_sub_clusters,
clusters_grown,
clusters_pure,
debugLevel,
dbg_X,
dbg_Y);
System.out.println("mergeAndGrow() done"); System.out.println("mergeAndGrow() done");
......
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