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imagej-elphel
Commit 046d8eb3 authored by Andrey Filippov's avatar Andrey Filippov
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working on expansion + bug fixes

parent 89dfef44
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Showing with 1089 additions and 345 deletions
src/main/java/AlignmentCorrection.java
View file @ 046d8eb3
import java.util.ArrayList;
import Jama.Matrix;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
/**
**
** AlignmentCorrection - try to apply minor adjustments to the misaligned camera
......@@ -29,6 +21,13 @@ import ij.WindowManager;
** -----------------------------------------------------------------------------**
**
*/
import java.util.ArrayList;
import Jama.Matrix;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
public class AlignmentCorrection {
static int NUM_SLICES = 10; // disp, strength, dx0, dy0, dx1, dy1, dx2, dy2, dx3, dy3)
......
src/main/java/ExtendSurfaces.java 0 → 100644
View file @ 046d8eb3
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src/main/java/EyesisCorrectionParameters.java
View file @ 046d8eb3
......@@ -2070,6 +2070,9 @@ public class EyesisCorrectionParameters {
public double ex_strength = 0.18; // minimal 4-corr strength to trust tile
public double ex_nstrength = 0.4; // minimal 4-corr strength divided by channel diff for new (border) tiles
public boolean ex_over_bgnd = false; // Allow expansion over previously identified background (infinity)
public double ex_min_over = 1.0; // When expanding over background, disregard lower disparity
public double pt_super_trust = 1.6; // If strength exceeds ex_strength * super_trust, do not apply ex_nstrength and plate_ds
public boolean pt_keep_raw_fg = true; // Do not replace raw tiles by the plates, if raw is closer (like poles)
public double pt_scale_pre = 1.5; // Scale plates strength before comparing to raw strength
......@@ -2417,7 +2420,7 @@ public class EyesisCorrectionParameters {
public boolean tsLoopMulti = true; // Repeat multi-choice assignment while succeeding
public boolean tsReset = false; // Reset tiles to surfaces assignment
public boolean tsShow = false; // Show results of tiles to surfaces assignment
public int tsNumClust = 50; // Number of clusters to keep
public int tsNumClust = 500; // Number of clusters to keep
public int tsConsensMode = 7; // Which assignments to match +1 - combo, +2 grown single, +4 plane seeds
public int tsConsensAgree = 1; // Minimal number of assignments to agree
......@@ -2624,6 +2627,9 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"ex_strength", this.ex_strength +"");
properties.setProperty(prefix+"ex_nstrength", this.ex_nstrength +"");
properties.setProperty(prefix+"ex_over_bgnd", this.ex_over_bgnd+"");
properties.setProperty(prefix+"ex_min_over", this.ex_min_over +"");
properties.setProperty(prefix+"pt_super_trust", this.pt_super_trust +"");
properties.setProperty(prefix+"pt_keep_raw_fg", this.pt_keep_raw_fg+"");
properties.setProperty(prefix+"pt_scale_pre", this.pt_scale_pre +"");
......@@ -3141,6 +3147,9 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"ex_strength")!=null) this.ex_strength=Double.parseDouble(properties.getProperty(prefix+"ex_strength"));
if (properties.getProperty(prefix+"ex_nstrength")!=null) this.ex_nstrength=Double.parseDouble(properties.getProperty(prefix+"ex_nstrength"));
if (properties.getProperty(prefix+"ex_over_bgnd")!=null) this.ex_over_bgnd=Boolean.parseBoolean(properties.getProperty(prefix+"ex_over_bgnd"));
if (properties.getProperty(prefix+"ex_min_over")!=null) this.ex_min_over=Double.parseDouble(properties.getProperty(prefix+"ex_min_over"));
if (properties.getProperty(prefix+"pt_super_trust")!=null) this.pt_super_trust=Double.parseDouble(properties.getProperty(prefix+"pt_super_trust"));
if (properties.getProperty(prefix+"pt_keep_raw_fg")!=null) this.pt_keep_raw_fg=Boolean.parseBoolean(properties.getProperty(prefix+"pt_keep_raw_fg"));
if (properties.getProperty(prefix+"pt_scale_pre")!=null) this.pt_scale_pre=Double.parseDouble(properties.getProperty(prefix+"pt_scale_pre"));
......@@ -3680,6 +3689,9 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Minimal 4-corr strength to trust tile", this.ex_strength, 3);
gd.addNumericField("Minimal 4-corr strength divided by channel diff for new (border) tiles", this.ex_nstrength, 3);
gd.addCheckbox ("Allow expansion over previously identified background (infinity)", this.ex_over_bgnd);
gd.addNumericField("When expanding over background, disregard lower disparity ", this.ex_min_over, 3);
gd.addMessage ("********* Plates filetering when building initial z-map *********");
gd.addNumericField("If strength exceeds ex_strength * super_trust, do not apply ex_nstrength and plate_ds", this.pt_super_trust, 3);
gd.addCheckbox ("Do not replace raw tiles by the plates, if raw is closer (like poles)", this.pt_keep_raw_fg);
......@@ -3803,10 +3815,10 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Consider merging initial planes if disparity difference below", this.stSmallDiff, 6);
gd.addNumericField("Consider merging initial planes if jumps between ratio above", this.stHighMix, 6);
gd.addNumericField("Outlayer tiles weaker than this may be replaced from neighbors", this.outlayerStrength, 6);
gd.addNumericField("Replace weak outlayer tiles that do not have neighbors within this disparity difference", this.outlayerDiff, 6);
gd.addNumericField("Replace weak outlayer tiles that have higher disparity than weighted average", this.outlayerDiffPos, 6);
gd.addNumericField("Replace weak outlayer tiles that have lower disparity than weighted average", this.outlayerDiffNeg, 6);
gd.addNumericField("Outlier tiles weaker than this may be replaced from neighbors", this.outlayerStrength, 6);
gd.addNumericField("Replace weak outlier tiles that do not have neighbors within this disparity difference", this.outlayerDiff, 6);
gd.addNumericField("Replace weak outlier tiles that have higher disparity than weighted average", this.outlayerDiffPos, 6);
gd.addNumericField("Replace weak outlier tiles that have lower disparity than weighted average", this.outlayerDiffNeg, 6);
gd.addCheckbox ("Combine with all previous after refine pass", this.combine_refine);
gd.addNumericField("Disregard weaker tiles when combining scans", this.combine_min_strength, 6);
......@@ -4222,6 +4234,9 @@ public class EyesisCorrectionParameters {
this.ex_strength= gd.getNextNumber();
this.ex_nstrength= gd.getNextNumber();
this.ex_over_bgnd= gd.getNextBoolean();
this.ex_min_over= gd.getNextNumber();
this.pt_super_trust= gd.getNextNumber();
this.pt_keep_raw_fg= gd.getNextBoolean();
this.pt_scale_pre= gd.getNextNumber();
......
src/main/java/LinkPlanes.java
View file @ 046d8eb3
......@@ -3879,7 +3879,7 @@ public class LinkPlanes {
weak_pairs, // final boolean [][] weak_fg_pairs,
1.0, // double relax,
plWeakFgRelax, // final double relax_weak_fg,
debugLevel, // final int debugLevel)
1+ debugLevel, // final int debugLevel)
dbg_tileX,
dbg_tileY);
// Calculate costs of merging planes of the same supertile and remove those that are exceed threshold
......
src/main/java/MeasuredLayers.java
View file @ 046d8eb3
......@@ -337,7 +337,7 @@ public class MeasuredLayers {
* @return [smplSide * smplSide]array of weights, 1.0 in the center
*/
public double [] getSampleWindow(int smplSide, boolean all1){
static double [] getSampleWindow(int smplSide, boolean all1){
double [] weights = new double [smplSide * smplSide];
for (int sy = 0; sy < smplSide; sy++){
for (int sx = 0; sx < smplSide; sx++){
......@@ -898,6 +898,9 @@ public class MeasuredLayers {
boolean null_if_none,
int debugLevel)
{
boolean use_new = true; // false;
if (use_new) {
return getDisparityStrength (
num_layer, // int num_layer,
stX, // int stX,
......@@ -914,6 +917,25 @@ public class MeasuredLayers {
0.2, // double max_rel_tilt, // = 0.2; // (pix / disparity) per tile
null_if_none, // boolean null_if_none,
debugLevel); // int debugLevel)
} else {
return getDisparityStrength_old (
num_layer, // int num_layer,
stX, // int stX,
stY, // int stY,
sel_in, // boolean [] sel_in,
// null, // double [] tiltXY, // null - free with limit on both absolute (2.0?) and relative (0.2) values
strength_floor, // double strength_floor,
strength_pow, // double strength_pow,
smplSide, // int smplSide, // = 2; // Sample size (side of a square)
smplNum, // int smplNum, // = 3; // Number after removing worst (should be >1)
smplRms, // double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
smplWnd, // boolean smplWnd, //
// 2.0, // double max_abs_tilt, // = 2.0; // pix per tile
// 0.2, // double max_rel_tilt, // = 0.2; // (pix / disparity) per tile
null_if_none, // boolean null_if_none,
debugLevel); // int debugLevel)
}
}
public double[][] getDisparityStrength (
......@@ -921,7 +943,9 @@ public class MeasuredLayers {
int stX,
int stY,
boolean [] sel_in,
double [] tiltXY, // null - free with limit on both absolute (2.0?) and relative (0.2) values
double [][] atiltXY, // null - free with limit on both absolute (2.0?) and relative (0.2) values
// if it has just one element - apply to all tiles, otherwise it is supposed
// to be per-tile of a supertile array
double strength_floor,
double strength_pow,
int smplSide, // = 2; // Sample size (side of a square)
......@@ -1018,7 +1042,7 @@ public class MeasuredLayers {
if (num_in_sample >= smplNum){ // try, remove worst
sample_loop:
{
boolean en_tilt = (tiltXY == null);
boolean en_tilt = (atiltXY == null);
if (en_tilt) { // make sure there are enough samples and not all of them are on the same line
if (!notColinear(smpl_sel,smplSide)){
en_tilt = false;
......@@ -1128,7 +1152,10 @@ public class MeasuredLayers {
}
}
if (iworst < 0){
System.out.println("**** this is a BUG in getDisparityStrength() can not find the worst sample ****");
if (debugLevel > 0) {
System.out.println("**** this may be BUG in getDisparityStrength() can not find the worst sample - all tiles fit perfectly ****");
}
// this can happen if some samples are the same and all the pixels fit exactly - use all of them
break;
}
// remove worst sample
......@@ -1158,6 +1185,15 @@ public class MeasuredLayers {
} else { // fixed tilt
// tilt around center
double [] tiltXY= {0.0,0.0};
if (atiltXY != null){ // if null ( free but failed co-linear test - keep both tilts == 0.0
if (atiltXY.length == 1){
tiltXY = atiltXY[0]; // common for all tiles (such as constant disparity)
} else if (atiltXY[indx] != null){
tiltXY = atiltXY[indx];
}
}
if ((tiltXY != null) && (tiltXY[0] != 0.0) && (tiltXY[1] != 0.0)){
for (int sy = 0; sy < smplSide; sy++){
for (int sx = 0; sx < smplSide; sx++){
......
src/main/java/PolynomialApproximation.java
View file @ 046d8eb3
This diff is collapsed.
src/main/java/QuadCLT.java
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This diff is collapsed.
src/main/java/SuperTiles.java
View file @ 046d8eb3
......@@ -1436,13 +1436,17 @@ public class SuperTiles{
// TODO: Remove when promoting PlaneData
final TilePlanes tpl = new TilePlanes(tileSize,superTileSize, geometryCorrection);
final double [][][][] plane_disp_strength = new double [nStiles][][][];
// DEBUG feature:
final double [][] zero_tilts = {{0.0,0.0}}; // set to null for float
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
double [][][] plane_tilts = null; // used only forworld_plane_norm != null
// to get tile disparities needed to calculate tilts
for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
// int dl = (nsTile == debug_stile) ? 3 : 0;
int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
if (dl > 1){
if (dl > 2){
System.out.println("getPlaneDispStrengths(): nsTile="+nsTile);
}
int stileY = nsTile / stilesX;
......@@ -1457,7 +1461,48 @@ public class SuperTiles{
measuredLayers, // MeasuredLayers measuredLayers,
plPreferDisparity); // boolean preferDisparity)
if (smplMode && (world_plane_norm != null)) {
plane_tilts = new double [measuredLayers.getNumLayers()][][];
for (int ml = 0; ml < plane_tilts.length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){
double [][] tile_disp_strengths = measuredLayers.getDisparityStrength(
ml, // int num_layer,
stileX, // int stX,
stileY, // int stY,
null, // boolean [] sel_in,
strength_floor, // double strength_floor,
strength_pow, // double strength_pow,
true); // boolean null_if_none);
if (tile_disp_strengths == null){
plane_tilts[ml] = zero_tilts;
} else {
plane_tilts[ml] = pd0.getDisparityTilts(
world_plane_norm, // double [] world_normal_xyz,
tile_disp_strengths, // double [][] tile_disp_strengths,
debugLevel); // int debugLevel);
if(dl > 2){
if (plane_tilts[ml] != null){
for (int k = 0; k < 2; k++) {
System.out.println((k > 0) ? "tilt Y, pix/tile" : "tilt X, pix/tile");
for (int i = 0; i < 2 * superTileSize; i++){
System.out.print(i+",");
for (int j = 0; j < 2 * superTileSize; j++){
int it = j + 2 * superTileSize * i;
if (plane_tilts[ml][it] !=null){
System.out.print(String.format("%f7.4", plane_tilts[ml][it][k]));
}
if (j < (2 * superTileSize - 1)){
System.out.print(", ");
}
}
System.out.println();
}
System.out.println();
}
}
}
}
}
}
plane_disp_strength[nsTile] = new double[measuredLayers.getNumLayers()][][];
......@@ -1469,13 +1514,18 @@ public class SuperTiles{
stileX, // int stX,
stileY, // int stY,
null, // boolean [] sel_in,
// ((world_plane_norm == null)? zero_tilts: null), // double [] tiltXY, // null - free with limit on both absolute (2.0?) and relative (0.2) values
((world_plane_norm == null)? zero_tilts: plane_tilts[ml]), // double [] tiltXY, // null - free with limit on both absolute (2.0?) and relative (0.2) values
strength_floor, // double strength_floor,
strength_pow, // double strength_pow,
smplSide, // int smplSide, // = 2; // Sample size (side of a square)
smplNum, //int smplNum, // = 3; // Number after removing worst (should be >1)
smplRms, //double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
true, // boolean null_if_none);
// true, // boolean null_if_none);
smplWnd, // boolean smplWnd, //
2.0, // double max_abs_tilt, // = 2.0; // pix per tile
0.2, // double max_rel_tilt, // = 0.2; // (pix / disparity) per tile
true, // boolean null_if_none);
dl);
} else {
plane_disp_strength[nsTile][ml] = measuredLayers.getDisparityStrength(
......@@ -1505,7 +1555,7 @@ public class SuperTiles{
if (dl > 0) {
System.out.println("Plane tilted disparity for stileX = "+stileX+" stileY="+stileY+", average disparity "+(sd/sw));
}
if (dl>1) {
if (dl>2) {
String [] dbg_titles = showSupertileSeparationTitles( plane_disp_strength[nsTile], null);
double [][] dbg_img = showSupertileSeparation(false, plane_disp_strength[nsTile], null); // plane_sels);
showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays();
......@@ -1519,7 +1569,7 @@ public class SuperTiles{
null, // boolean [][] tile_sel, // null - do not use, {} use all (will be modified)
plane_disp_strength[nsTile], // double [][][] disp_str, // calculate just once if null
dl); // 1); // int debugLevel);
if (dl>1) {
if (dl>2) {
String [] dbg_titles = showSupertileSeparationTitles( plane_disp_strength[nsTile], null);
double [][] dbg_img = showSupertileSeparation(false, plane_disp_strength[nsTile], null); // plane_sels);
showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays();
......@@ -2623,7 +2673,7 @@ public class SuperTiles{
highMix, //final double highMix, // stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above
world_hor, // final double [] world_hor, // horizontal plane normal (default [0.0, 1.0, 0.0])
show_histograms, // final boolean show_histograms,
debugLevel+0, // final int debugLevel,
debugLevel+1, // final int debugLevel,
dbg_X, // final int dbg_X,
dbg_Y); // final int dbg_Y)
......
src/main/java/TilePlanes.java
View file @ 046d8eb3
......@@ -972,6 +972,82 @@ public class TilePlanes {
return true;
}
/**
* This method is used to filter sample plates by averaging subset of the square
* sample and removing outliers. Currently only constant disparity and horizontal
* surfaces are used, this method is used for horizontal ones to find tilts
* d_disp/d_tx, d_disp/d_ty measured in pixels per tile
* @param world_normal_xyz world space normal vector, currently only "up" - (0,1,0) is used
* @param tile_disp_strengths [0] - unfiltered disparities for the supertile,
* [1] - unfiltered correlation strengths for the
* supertile (just 0/non-0)
* @param debugLevel
* @return per tile arrays of either nulls or tilt-x, tilt-y pairs
*/
public double [][] getDisparityTilts(
double [] world_normal_xyz,
double [][] tile_disp_strengths,
int debugLevel)
{
final int stSize2 = 2* stSize;
final int stCenter = (stSize2 + 1) * superTileSize / 2;
final double [][] tile_tilts = new double [stSize2*stSize2][];
final double [] apy_vector = {0.0, 0.0, 1.0};
final Matrix py_vector = new Matrix(apy_vector,3);
invalidateCalculated();
double [] px_py = getCenterPxPy();
Matrix normal_row = new Matrix(world_normal_xyz,1); // 1x3
Matrix normal_col = new Matrix(world_normal_xyz,3); // 3x1
// find world coordinates of the center of tile intersection with the plane
for (int lTile = 0; lTile < tile_disp_strengths[1].length; lTile++) if (tile_disp_strengths[1][lTile] > 0.0){
int tY = lTile / stSize2;
int tX = lTile % stSize2;
double px = px_py[0] + tX - stCenter;
double py = px_py[1] + tY - stCenter;
double disp = tile_disp_strengths[0][lTile];
// get world coordinates for each tile as determined individually
Matrix t_xyz = new Matrix(geometryCorrection.getWorldCoordinates(
px,
px,
disp,
this.correctDistortions),3);
// double n_by_w = normal_row.times(t_xyz).get(0, 0);
// take pixel vector parallel to py and convert it to the world space
Matrix jacobian = new Matrix(geometryCorrection.getWorldJacobian(
px,
py,
disp,
this.correctDistortions,
(debugLevel > 2)
));
Matrix inv_jacobian = jacobian.inverse();
Matrix wpy_vector = jacobian.times(py_vector); // 3 rows, 1 column py vector in the real world
// get 2 in-plane vectors in the real world
Matrix wv1 = cross3d(normal_col, wpy_vector);
Matrix wv2 = cross3d(normal_col, wv1);
// convert then to pixel space
Matrix pv1 = inv_jacobian.times(wv1);
Matrix pv2 = inv_jacobian.times(wv2);
// Get plane normal in the pixel space
Matrix pn = cross3d(pv1, pv2);
// convert to the two tilts (d/dpx, d/dpy). We will need in pix/tile, not pix/pix
double [] txty = {
-pn.get(1, 0)/pn.get(0, 0)*stSize,
-pn.get(2, 0)/pn.get(0, 0)*stSize};
tile_tilts[lTile] = txty;
}
// if (debugLevel > 1) {
// System.out.println("st_xyz = {"+st_xyz.get(0, 0)+","+st_xyz.get(1, 0)+","+st_xyz.get(2, 0)+"}"+" ="+n_by_w);
// }
return tile_tilts;
}
/**
* Tilt disparity values around the supertile center (this.zxy) so constant disparity in the output
* corresponds to the real world plane parallel to the provided one. Used to discriminate tiles by
......@@ -995,7 +1071,7 @@ public class TilePlanes {
{
final int stSize2 = 2* stSize;
invalidateCalculated();
double [] px_py = getCenterPxPy();
double [] px_py = getCenterPxPy(); // tile center
// find world coordinates of the center of tile intersection with the plane
Matrix st_xyz = new Matrix(geometryCorrection.getWorldCoordinates(
px_py[0],
......@@ -2251,7 +2327,8 @@ public class TilePlanes {
double val = values[0];
if ((dispNorm > 0.0) && (zxy[0] > dispNorm)){
double k = dispNorm / zxy[0];
val *= k*k;
// val *= k*k;
val *= k ; // reducing correction for the large disparities (making it sqrt() )
}
return val;
}
......@@ -3671,6 +3748,13 @@ public class TilePlanes {
int debugLevel){
return getWorldXYZ(this.correctDistortions, debugLevel);
}
/**
* Get vector from the camera perpendicular to the plane converted to the real world
* @param correct_distortions
* @param debugLevel
* @return
*/
public double [] getWorldXYZ(
boolean correct_distortions,
int debugLevel)
......
src/main/java/TileProcessor.java
View file @ 046d8eb3
This diff is collapsed.
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