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imagej-elphel
Commit 67228555 authored by Andrey Filippov's avatar Andrey Filippov
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more tweaking

parent d059a2ac
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Showing with 248 additions and 28 deletions
src/main/java/LinkPlanes.java
View file @ 67228555
......@@ -35,6 +35,7 @@ public class LinkPlanes {
public double plMinStrength; // = 0.1; // Minimal total strength of a plane
public double plMaxEigen; // = 0.05; // Maximal eigenvalue of a plane
public double plEigenFloor; // = 0.01; // Add to eigenvalues of each participating plane and result to validate connections
public double plEigenStick; // = 20.0; // Consider plane to be a "stick" if second eigenvalue is below
public double plWorstWorsening; // = 2.0; // Worst case worsening after merge
public double plWorstWorsening2; // = 5.0; // Worst case worsening for thin planes
......@@ -92,7 +93,8 @@ public class LinkPlanes {
plDispNorm = clt_parameters.plDispNorm;
plMaxEigen = clt_parameters.plMaxEigen;
plEigenFloor = clt_parameters.plEigenFloor; // final double eigenFloor, // Add to eigenvalues of each participating plane and result to validate connections
plEigenFloor = clt_parameters.plEigenFloor;
plEigenStick = clt_parameters.plEigenStick;
plMinStrength = clt_parameters.plMinStrength;
plMaxOverlap = clt_parameters.plMaxOverlap;
......@@ -963,6 +965,9 @@ public class LinkPlanes {
boolean hasConflict(LinkPair lp){
return (src == lp.src) || (dst == lp.dst);
}
public String toString(){
return String.format("%d-(%6.3f)->%d", src,cost,dst);
}
}
for (int ithread = 0; ithread < threads.length; ithread++) {
......@@ -981,16 +986,16 @@ public class LinkPlanes {
if ((nsTile >= 0) && (planes[nsTile] != null)){
int num_dp = planes[nsTile].length;
double [][] inter_costs = new double [num_sp][num_dp];
for (int np0 = 0; np0 < num_sp; np0++) if (planes[np0]!=null){
for (int np = 0; np < num_dp; np++)if (planes[np]!=null){
for (int np0 = 0; np0 < num_sp; np0++) if (planes[nsTile0][np0]!=null){
for (int np = 0; np < num_dp; np++)if (planes[nsTile][np]!=null){
inter_costs[np0][np] = 0.5* (
planes[nsTile0][np0].getLinkCosts(dir, np)+
planes[nsTile][np].getLinkCosts(dir_back, np0));
}
}
HashSet<LinkPair> pairs_set = new HashSet<LinkPair>();
for (int np0 = 0; np0 < num_sp; np0++) if (planes[np0]!=null){
for (int np = 0; np < num_dp; np++)if (planes[np]!=null){
for (int np0 = 0; np0 < num_sp; np0++) if (planes[nsTile0][np0]!=null){
for (int np = 0; np < num_dp; np++)if (planes[nsTile][np]!=null){
if (!Double.isNaN(inter_costs[np0][np]) && (inter_costs[np0][np] <= max_cost)){
pairs_set.add(new LinkPair(np0, np, inter_costs[np0][np]));
}
......@@ -998,7 +1003,7 @@ public class LinkPlanes {
}
HashSet<LinkPair> links_set = new HashSet<LinkPair>();
while (!pairs_set.isEmpty()){
LinkPair link =Collections.max(pairs_set, new Comparator<LinkPair>() {
LinkPair link =Collections.min(pairs_set, new Comparator<LinkPair>() {
@Override
public int compare(LinkPair lhs, LinkPair rhs) { // ascending
return (lhs.cost < rhs.cost) ? -1 : (lhs.cost > rhs.cost ) ? 1 : 0;
......@@ -2324,14 +2329,22 @@ public class LinkPlanes {
ImageDtt.startAndJoin(threads);
return valid_candidates;
}
/**
* Possible problem is that "normalizing" merge quality for low weights is not applicable for "star" plane that include neighhbors
* Switch to a single "cost" function (costSameTileConnectionsAlt())
* @param planes
* @param merge_candidates
* @param valid_candidates
* @param debugLevel
* @param dbg_X
* @param dbg_Y
*/
public void costSameTileConnections(
final boolean ignore_weights,
final double threshold_worst,
final double threshold_world_worst,
final TilePlanes.PlaneData [][] planes,
final int [][][] merge_candidates,
final boolean [][][] valid_candidates, // will be updated
// final boolean merge_low_eigen,
final int debugLevel,
final int dbg_X,
final int dbg_Y)
......@@ -2343,8 +2356,6 @@ public class LinkPlanes {
final int stilesX = (tilesX + superTileSize -1)/superTileSize;
final int stilesY = (tilesY + superTileSize -1)/superTileSize;
final int nStiles = stilesX * stilesY;
final int [][] dirsYX = {{-1, 0},{-1,1},{0,1},{1,1},{1,0},{1,-1},{0,-1},{-1,-1}};
// final boolean [][] merge_pairs = new boolean [nStiles][];
final double [][][][][][] merged_neib_ev = new double [nStiles][][][][][];
final int debug_stile = dbg_Y * stilesX + dbg_X;
final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : st.tileProcessor.threadsMax);
......@@ -2401,8 +2412,153 @@ public class LinkPlanes {
}
}
/// final double threshold_worst,
// final double threshold_world_worst,
if (dl>0){
double [][] costs = new double[2][];
costs[0] = getFitQualities(
planes[nsTile0][np1].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
nsTile0+":"+np1+":"+np2, // String prefix,
0); // int debugLevel)
costs[1] = getFitQualities(
planes[nsTile0][np1].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
nsTile0+":"+np1+":"+np2, // String prefix,
0); // int debugLevel)
System.out.println("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs:");
System.out.print("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs weighted: ");
for (int i = 0; i < costs[0].length;i++) {
System.out.print(costs[0][i]+" ");
}
System.out.println();
System.out.print("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs equalized: ");
for (int i = 0; i < costs[1].length;i++) {
System.out.print(costs[1][i]+" ");
}
System.out.println();
}
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
}
public void costSameTileConnectionsAlt(
final double threshold,
final double threshold_nostar,
final TilePlanes.PlaneData [][] planes,
final int [][][] merge_candidates,
final boolean [][][] valid_candidates, // will be updated
final int debugLevel,
final int dbg_X,
final int dbg_Y)
{
final int tilesX = st.tileProcessor.getTilesX();
final int tilesY = st.tileProcessor.getTilesY();
final int superTileSize = st.tileProcessor.getSuperTileSize();
// final int tileSize = tileProcessor.getTileSize();
final int stilesX = (tilesX + superTileSize -1)/superTileSize;
final int stilesY = (tilesY + superTileSize -1)/superTileSize;
final int nStiles = stilesX * stilesY;
final double [][][][][][] merged_neib_ev = new double [nStiles][][][][][];
final int debug_stile = dbg_Y * stilesX + dbg_X;
final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : st.tileProcessor.threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {
int dl = ((debugLevel > 0) && (nsTile0 == debug_stile)) ? 3: ((debugLevel > 1) ? 2:0);
if (dl > 2){
System.out.println("costSameTileConnectionsAlt(): nsTile="+nsTile0);
}
int n_planes = planes[nsTile0].length;
// overlap_merge_candidates[nsTile] = new boolean [n_planes][n_planes];
merged_neib_ev[nsTile0] = new double [n_planes][n_planes][4][][];
// get original directions
for (int np1 = 0; np1 < planes[nsTile0].length; np1++) if (planes[nsTile0][np1] != null){
for (int np2 = np1 + 1; np2 < planes[nsTile0].length; np2++) if (planes[nsTile0][np2] != null){
if (valid_candidates[nsTile0][np1][np2]) { // only check pair considered valid
String prefix = "costSameTileConnectionsAlt() fit weighted: nsTile0="+nsTile0+" np1="+np1+" np2="+np2;
double [] costs = new double[2];
costs[0] = getLinkCost(
planes[nsTile0][np1].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
prefix, // String prefix,
0); // int debugLevel)
prefix = "costSameTileConnectionsAlt() fit equal weight: nsTile0="+nsTile0+" np1="+np1+" np2="+np2;
costs[1] = getLinkCost(
planes[nsTile0][np1].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
prefix, // String prefix,
0); // int debugLevel)
boolean star1 = (planes[nsTile0][np1].getNonexclusiveStar() != null) && (planes[nsTile0][np2].getNonexclusiveStar() != null);
boolean star2 = (planes[nsTile0][np1].getNonexclusiveStarEq() != null) && (planes[nsTile0][np2].getNonexclusiveStarEq() != null);
boolean fit1 = costs[0] < (star1 ? threshold : threshold_nostar);
boolean fit2 = costs[1] < (star2 ? threshold : threshold_nostar);
if (!fit1 || !fit2){
valid_candidates[nsTile0][np1][np2] = false;
valid_candidates[nsTile0][np2][np1] = false;
if (dl > -1){
System.out.println("costSameTileConnectionsAlt(): nsTile="+nsTile0+":"+np1+":"+np2+
" REMOVING PAIR, fit1="+fit1+" fit2="+fit2+ " (star1="+star1+", star2="+star2+")");
}
} else {
if (dl > -1){
System.out.println("costSameTileConnectionsAlt(): nsTile="+nsTile0+":"+np1+":"+np2+
" KEEPING PAIR, fit1="+fit1+" fit2="+fit2+ " (star1="+star1+", star2="+star2+")");
}
}
if (dl>0){
double [][] costs0 = new double[2][];
costs0[0] = getFitQualities(
planes[nsTile0][np1].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
nsTile0+":"+np1+":"+np2, // String prefix,
0); // int debugLevel)
costs0[1] = getFitQualities(
planes[nsTile0][np1].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane1, // should belong to the same supertile (or be converted for one)
planes[nsTile0][np2].getNonexclusiveStarEqFb(), // TilePlanes.PlaneData plane2,
Double.NaN, // double merged_ev, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_ev_eq, // if NaN will calculate assuming the same supertile
Double.NaN, // double merged_wev, // if NaN will calculate assuming the same supertile - for world
Double.NaN, // double merged_wev_eq, // if NaN will calculate assuming the same supertile - for world
nsTile0+":"+np1+":"+np2, // String prefix,
0); // int debugLevel)
System.out.println("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs:");
System.out.print("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs weighted: ");
for (int i = 0; i < costs0[0].length;i++) {
System.out.print(costs0[0][i]+" ");
}
System.out.println();
System.out.print("costSameTileConnections(): nsTile="+nsTile0+":"+np1+":"+np2+" costs equalized: ");
for (int i = 0; i < costs0[1].length;i++) {
System.out.print(costs0[1][i]+" ");
}
System.out.println();
}
}
}
}
......@@ -2411,7 +2567,6 @@ public class LinkPlanes {
};
}
ImageDtt.startAndJoin(threads);
// return merged_neib_ev;
}
public double [][][][][][] costSameTileConnectionsOld(
......
src/main/java/TilePlanes.java
View file @ 67228555
......@@ -237,7 +237,7 @@ public class TilePlanes {
double [] px_py = getCenterPxPy();
if (zxy != null) s += String.format("\nzxy = [%8.3f, %8.3f, %8.3f] (pix)",zxy[0],zxy[1]+px_py[0],zxy[2]+px_py[1]);
else s += "\nzxy = null";
if (values != null) s += String.format(", values = [%8.3f, %8.3f, %8.3f] pix^2",values[0],values[1],values[2]);
if (values != null) s += String.format(", values = [%8.5f, %8.4f, %8.3f] pix^2",values[0],values[1],values[2]);
else s += " values = null";
if (vectors != null) s += String.format("\nvectors = [%8.5f, %8.5f, %8.5f], [%8.5f, %8.5f, %8.5f], [%8.5f, %8.5f, %8.5f]",
vectors[0][0],vectors[0][1],vectors[0][2], vectors[1][0],vectors[1][1],vectors[1][2], vectors[2][0],vectors[2][1],vectors[2][2]);
......@@ -247,7 +247,7 @@ public class TilePlanes {
else s += " normal = null";
if (wxyz != null) s += String.format("\nwxyz = [%8.2f, %8.2f, %8.2f] (m)",wxyz[0],wxyz[1],wxyz[2]);
else s += "\nwxyz = null";
if (wvalues != null) s += String.format(" wvals = [%8.2f, %8.2f, %8.2f] (m^2)",wvalues[0],wvalues[1],wvalues[2]);
if (wvalues != null) s += String.format(" wvals = [%8.4f, %8.3f, %8.2f] (m^2)",wvalues[0],wvalues[1],wvalues[2]);
else s += " wvals = null";
if (wvectors != null) s += String.format("\nwvect = [%8.5f, %8.5f, %8.5f], [%8.5f, %8.5f, %8.5f], [%8.5f, %8.5f, %8.5f]",
wvectors[0][0],wvectors[0][1],wvectors[0][2], wvectors[1][0],wvectors[1][1],wvectors[1][2], wvectors[2][0],wvectors[2][1],wvectors[2][2]);
......@@ -287,7 +287,30 @@ public class TilePlanes {
nonexclusiveStarEq.world_xyz[0],nonexclusiveStarEq.world_xyz[1],nonexclusiveStarEq.world_xyz[2]);
else s += " normal = null";
}
s+="\n\n";
s+="\n";
if (link_costs != null){
for (int dir = 0; dir < link_costs.length; dir++){
s+=String.format("dir=%d: ", dir);
if (link_costs[dir] != null) {
int best_np = -1;
for (int np = 0; np < link_costs[dir].length; np++){
if (!Double.isNaN(link_costs[dir][np]) && ((best_np < 0) || (link_costs[dir][np] < link_costs[dir][best_np]))){
best_np = np;
}
}
for (int np = 0; np < link_costs[dir].length; np++){
if (np == best_np){
s+=String.format("%7.3f[%d] ", link_costs[dir][np],np);
} else {
s+=String.format("%7.3f ", link_costs[dir][np]);
}
}
}
s+="\n";
}
}
s+="\n";
return s;
}
......
src/main/java/TileProcessor.java
View file @ 67228555
......@@ -3317,19 +3317,33 @@ public class TileProcessor {
clt_parameters.tileX,
clt_parameters.tileY);
// * Possible problem is that "normalizing" merge quality for low weights is not applicable for "star" plane that include neighhbors
// * Switch to a single "cost" function (costSameTileConnectionsAlt())
// Still - how to merge stray tiles that do not have neighbors/star? Still merge them "old way" (costSameTileConnections()) if at least 1 does not
// have a "star"
// double [][][][][][] merge_cost_data =
lp.costSameTileConnections(
false, // final boolean ignore_weights,
1000.0, // final double threshold_worst,
1000.0, //final double threshold_world_worst,
st.planes, // ffinal TilePlanes.PlaneData [][] planes,
st.planes, // final TilePlanes.PlaneData [][] planes,
merge_candidates, // final int [][][] merge_candidates,
plane_nooverlaps, // final boolean [][][] valid_candidates, // will be updated
2, // -1, // debugLevel, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.tileY);
// System.out.println("merge_cost_data.length = " + merge_cost_data.length);
lp.costSameTileConnectionsAlt(
5.0, // final double threshold,
10.0, // final double threshold_nostar,
st.planes, // final TilePlanes.PlaneData [][] planes,
merge_candidates, // final int [][][] merge_candidates,
plane_nooverlaps, // final boolean [][][] valid_candidates, // will be updated
2, // -1, // debugLevel, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.tileY);
int [][][] merge_groups = lp.extractMergeSameTileGroups(
st.planes, // final TilePlanes.PlaneData [][] planes,
merge_candidates, // final int [][][] merge_candidates,
......@@ -3805,6 +3819,12 @@ public class TileProcessor {
0, // 1,// 0, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.tileY);
lp.interPlaneCosts(
st.planes_mod, // final TilePlanes.PlaneData [][] planes,
2, // -1, // debugLevel, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.tileY);
// recalculate links? more smooth?
} else {
st.planes_mod = st.planes; // just use the measured ones
......@@ -3824,6 +3844,22 @@ public class TileProcessor {
clt_parameters.tileY);
int [] wh = st.getShowPlanesWidthHeight();
double [][] plane_data_nonan_meas = st.getShowPlanes(
st.getPlanes(),
clt_parameters.plMinStrength, // minWeight,
clt_parameters.plMaxEigen, // maxEigen,
clt_parameters.plDispNorm,
false, //boolean use_NaN)
0.0,
10.0);
double [][] plane_data_nan_meas = st.getShowPlanes(
st.getPlanes(),
clt_parameters.plMinStrength, // minWeight,
clt_parameters.plMaxEigen, // maxEigen,
clt_parameters.plDispNorm,
true, //boolean use_NaN)
0.0,
10.0);
double [][] plane_data_nonan = st.getShowPlanes(
(planes_mod != null) ? st.getPlanesMod():st.getPlanes(),
clt_parameters.plMinStrength, // minWeight,
......@@ -3840,8 +3876,14 @@ public class TileProcessor {
true, //boolean use_NaN)
0.0,
10.0);
double [][] plane_data = new double [plane_data_nonan.length + plane_data_nan.length + 3][];
double [][] plane_data = new double [plane_data_nonan_meas.length + plane_data_nan_meas.length+ plane_data_nonan.length + plane_data_nan.length + 3][];
int indx = 0;
for (int i = 0; i < plane_data_nonan_meas.length; i++){
plane_data[indx++] = plane_data_nonan_meas[i];
}
for (int i = 0; i < plane_data_nan_meas.length; i++){
plane_data[indx++] = plane_data_nan_meas[i];
}
for (int i = 0; i < plane_data_nonan.length; i++){
plane_data[indx++] = plane_data_nonan[i];
}
......
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