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Commit d3389b58 authored by Andrey Filippov's avatar Andrey Filippov
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More on quaternions - affines

parent 0abd52b8
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Showing with 457 additions and 112 deletions
src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java
View file @ d3389b58
......@@ -177,7 +177,7 @@ public class ComboMatch {
boolean use_saved_collection = true; // false;
boolean save_collection = true;
boolean save_collection = false; // true;
boolean process_correlation = true; // use false to save new version of data
int num_tries_fit = 10;
boolean update_match = true; // use false to save new version of data
......@@ -210,7 +210,7 @@ public class ComboMatch {
pattern_match = false;
}
GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);
GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
// gd.addChoice ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, FILES_LISTS_PATHS[default_list_choice]);
gd.addChoice ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, omtch_img_set);
gd.addCheckbox ("Use saved maps collection ", use_saved_collection, " (if available). If false - use files list.");
......@@ -433,7 +433,7 @@ public class ComboMatch {
};
GenericJTabbedDialog gdo = new GenericJTabbedDialog("Set image pair",1200,900);
GenericJTabbedDialog gdo = new GenericJTabbedDialog("Set image pair",1200,1000);
gdo.addNumericField("Correlation size", corr_size, 0,4,"",
"Correlation size, power of 2");
gdo.addNumericField("Extracted size", extr_size, 0,4,"",
......@@ -858,6 +858,12 @@ public class ComboMatch {
}
if (process_correlation || render_match || pattern_match || test_multi_lma) {
// int [] gpu_pair;
boolean removeTilt = false;
boolean removeRot = false;
boolean removeScale = false;
boolean removeOffset = false;
boolean max_is_scale = false;
if (gpu_spair == null) {
ArrayList<Point> pairs_list = new ArrayList<Point>();
for (OrthoMap map : maps_collection.ortho_maps) {
......@@ -905,7 +911,7 @@ public class ComboMatch {
boolean flt_show_alt = clt_parameters.imp.flt_show_alt; // true;
boolean flt_update_config = false;
String flt_extra_line = "--- select a single image ---";
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,500);
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,600);
gdf.addCheckbox ("Filter pairs", flt_list, "Filter available pairs.");
gdf.addCheckbox ("Keep undefined pairs only", flt_undef_only, "Keep only undefined pairs (affines== null).");
gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap, 3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
......@@ -999,15 +1005,27 @@ public class ComboMatch {
false, // boolean use_tab,
flt_extra_line); // String extra_line)
GenericJTabbedDialog gdc = new GenericJTabbedDialog("Select image pair",1200,100);
GenericJTabbedDialog gdc = new GenericJTabbedDialog("Select image pair",1200,300);
int num_choice_lines = 50;
gdc.addChoice("Image pair:",
choices_all,
choices_all[choices_all.length - 1], // -1],
"Select processed image pair or request a single image selection", num_choice_lines);
gdc.addCheckbox ("Remove tilt", removeTilt, "Remove tilts from the pairwise affine transform.");
gdc.addCheckbox ("Remove Rotation", removeRot, "Remove rotation from the pairwise affine transform.");
gdc.addCheckbox ("Remove Scale", removeScale, "Remove scale from the pairwise affine transform.");
gdc.addCheckbox ("Remove Translation", removeOffset, "Remove translation from the pairwise affine transform.");
gdc.addCheckbox ("Max eigenvalue is scale", max_is_scale, "Maximal eigenvalue is scale (false - minimal is).");
// boolean max_is_scale = false;
gdc.showDialog();
if (gdc.wasCanceled()) return false;
int pair= gdc.getNextChoiceIndex();
removeTilt = gdc.getNextBoolean();
removeRot = gdc.getNextBoolean();
removeScale = gdc.getNextBoolean();
removeOffset = gdc.getNextBoolean();
max_is_scale = gdc.getNextBoolean();
if (pair >= (choices_all.length -1)) {
int default_choice = 0;
int num_scene_lines = 50;
......@@ -1118,7 +1136,36 @@ public class ComboMatch {
} else {
affine1 = pairwiseOrthoMatch.getAffine();
affine1 = pairwiseOrthoMatch.getAffine().clone();
if (debugLevel > -4) {
System.out.println("removeTilt="+ removeTilt);
System.out.println("removeRot="+ removeRot);
System.out.println("removeScale="+ removeScale);
System.out.println("removeOffset="+removeOffset);
System.out.println("max_is_scale="+max_is_scale);
if (removeTilt || removeRot || removeScale || removeOffset) {
SingularValueDecomposition svd_affine_pair = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine1, true); // y_down_ccw); // boolean y_down_ccw)
System.out.println("Full (original) affine transform:");
System.out.println(QuatUtils.affinesToString(affine1, "full_affine"));
System.out.println("full_affine_svd" + svd_affine_pair.toString(true)); // use_degrees));
}
}
affine1 = SingularValueDecomposition.removeTiltRotScale(
affine1, // double [][] A,
removeTilt, // boolean removeTilt,
removeRot, // boolean removeRot,
removeScale, // boolean removeScale,
removeOffset, // boolean removeOffset)
max_is_scale); //boolean max_is_scale)
if (debugLevel > -4) {
if (removeTilt || removeRot || removeScale || removeOffset) {
SingularValueDecomposition svd_affine_pair = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine1, true); // y_down_ccw); // boolean y_down_ccw)
System.out.println("Final differential affine transform:");
System.out.println(QuatUtils.affinesToString(affine1, "affine1 "));
System.out.println("affine1_svd " + svd_affine_pair.toString(true)); // use_degrees));
}
}
double [][][] affines = {affine0,affine1};
int [] zooms = {initial_zoom, min_zoom_lev, 1000,1000}; // make automatic
// double scale = 2.0; // scale vectors when warping;
......@@ -1239,6 +1286,14 @@ public class ComboMatch {
}
if (render_match) {
String title=String.format("multi_%03d-%03d_%s-%s_zoom%d_%d",gpu_pair[0],gpu_pair[1],gpu_spair[0],gpu_spair[1],min_zoom_lev,zoom_lev);
if (removeTilt || removeRot || removeScale || removeOffset) {
title += "_no-";
if (removeTilt) title += "T";
if (removeRot) title += "R";
if (removeScale) title += "S";
if (removeOffset) title += "O";
if (max_is_scale) title += "X";
}
// Avoid renderMulti() - it duplicates code renderMultiDouble()
int eq_mode = 2; // calculate
ImagePlus imp_img_pair = maps_collection.renderMulti (
......@@ -2077,7 +2132,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
{2139.833, 1474.5},
{ 461.5, 1493.5}}};
boolean set_coords = true; // false;
GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1090,900);
GenericJTabbedDialog gd = new GenericJTabbedDialog("Select processing moder",1090,900);
gd.addStringField ("First image path", image_paths[0], 120, "First image full path");
gd.addStringField ("Second image path", image_paths[1], 120, "Second image full path");
gd.addCheckbox ("Set image markers to following coordinates", set_coords, "Delete markers and set them according to data.");
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java
View file @ d3389b58
......@@ -3732,7 +3732,21 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
final double [] weight,
final int width,
final double [] xy0) {
int debug = -1;
return getPlane(
data, // final double [] data,
mask, // final boolean [] mask,
weight, //final double [] weight,
width, // final int width,
xy0, // final double [] xy0,
null); // String dbg_title)
}
public static double [] getPlane(
final double [] data,
final boolean [] mask,
final double [] weight,
final int width,
final double [] xy0,
String dbg_title) {
final double [][][] mdatai = new double [data.length][][];
AtomicInteger anum_good = new AtomicInteger(0);
final Thread[] threads = ImageDtt.newThreadArray();
......@@ -3770,7 +3784,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
null, // damping, // double [] damping, null OK
-1); // debug level
if (approx2d != null) {
if (debug > 0) {
if (dbg_title != null) {
double [] plane=new double[data.length];
double [] diff=new double[data.length];
double [] dweight = (weight != null) ? weight: new double[data.length];
......@@ -3794,7 +3808,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
width,
data.length/width,
true,
"plane_approximation",
dbg_title,
new String[] {"data","approx","diff","masked","weight","mask"});
}
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMapsCollection.java
View file @ d3389b58
......@@ -5204,7 +5204,7 @@ public class OrthoMapsCollection implements Serializable{
boolean flt_update_config = false;
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);
gdf.addMessage("Filter pairs parameters");
gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap, 3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap, 3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
......@@ -6342,7 +6342,7 @@ public class OrthoMapsCollection implements Serializable{
boolean flt_update_config = false;
boolean select_pairs = false;
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);
gdf.addMessage("Filter pairs parameters");
gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap, 3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap, 3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
......@@ -6581,7 +6581,7 @@ public class OrthoMapsCollection implements Serializable{
boolean flt_update_config = false;
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);
GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);
gdf.addMessage("Filter pairs parameters");
gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap, 3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap, 3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
......
src/main/java/com/elphel/imagej/orthomosaic/QuatUtils.java
View file @ d3389b58
......@@ -45,7 +45,8 @@ public final class QuatUtils { // static class
String fmt_deg = "[%12.9f, %12.9f,%12.9f, %12.9f], tilt=%12.7f\u00B0, dir=%12.7f\u00B0, scale=%12.10f";
double s = degrees ? (180/Math.PI):1;
String fmt=degrees ? fmt_deg : fmt_rad;
return String.format(fmt, quat[0], quat[1],quat[2],quat[3], s*2*Math.acos(quat[0]), s*Math.atan2(quat[2],quat[1]), scale);
String rslt=String.format(fmt, quat[0], quat[1],quat[2],quat[3], s*2*Math.acos(quat[0]), s*Math.atan2(quat[2],quat[1]), scale);
return rslt;
}
/**
......@@ -300,7 +301,10 @@ public final class QuatUtils { // static class
if (t == 0) {
return UNIT_QUAT;
}
double [] axis = {ty/t,-tx/t,0}; // pi/2 CW
tx/=t;
ty/=t;
double [] axis = {ty,-tx,0}; // pi/2 CW
/* sin (A/2) = +-sqrt((1 - cos(A))/2)
* cos (A/2) = +-sqrt((1 + cos(A))/2)
......@@ -313,6 +317,64 @@ public final class QuatUtils { // static class
return quat;
}
public static String tiltToString (
double [] txy,
boolean y_down_ccw,
boolean degrees) {
String fmt_rad = " tilt= %10.7f, dir=%10.7f";
String fmt_deg = " tilt= %10.5f\u00B0, dir=%10.5f\u00B0";
double k = degrees ? (180/Math.PI):1;
String fmt=degrees ? fmt_deg : fmt_rad;
String s = String.format(" = [%12.9f, %12.9f, %15.9f]", txy[0], txy[1], txy[2]);
double tx = txy[0], ty = y_down_ccw?-txy[1]:txy[1]; // invert y
double t2 = tx*tx + ty*ty;
double t = Math.sqrt(t2);
if (t == 0) {
return s;
}
tx/=t;
ty/=t;
double [] axis = {ty,-tx,0}; // pi/2 CW
double dir = Math.atan2(axis[1],axis[0]);
double tilt = Math.atan(t);
s+= String.format(fmt, k*tilt, k*dir);
return s;
}
public static double [] sceneRelLocalGround(
double [] txy,
double [][] affine, // used for rot and scale Now can be null
boolean y_down_ccw) { // boolean y_down_ccw) for tilts and affine
double [] qtilts = tiltToQuaternion(txy,y_down_ccw);
boolean inv_aff = true; // invert affine
double scale = 1.0;
double rot = 0;
if (affine != null) {
if (inv_aff) {
affine = matInverse2x2(affine);
}
SingularValueDecomposition svd= SingularValueDecomposition.singularValueDecomposeScaleTiltBeta(
affine,
y_down_ccw);
scale = svd.getMaxScale();
rot = svd.getRotAngle(); // TODO: check sign !
}
// Now beta,rot correspond to Y - up
double chalfrot = Math.cos(rot/2);
double shalfrot = Math.sin(rot/2);
double [] qrot = {chalfrot,0,0,shalfrot}; // rotation around vertical axis
double [] qinv_tilts = invert(qtilts); //scene to ground
double [] qrt= multiply(qrot,qinv_tilts);
// double [] quat= scale(multiply(qrot,qinv_tilts),scale);
double [] quat= scale(multiply(qinv_tilts,qrot),scale);
return quat;
}
/**
* Remove rotation around Z-axis, keep only tilt around axis in XY plane
* @param quat_in input rotation that may include rotation around Z (vertical) axis
......@@ -563,7 +625,7 @@ q11 - q22 = c3
*/
public static double [][] affineToQuatScaled (
double [][] affine,
boolean stretch,
boolean stretch,// false
boolean y_down_ccw) {
affine = matInverse2x2(affine);
......
src/main/java/com/elphel/imagej/orthomosaic/SingularValueDecomposition.java
View file @ d3389b58
......@@ -29,10 +29,16 @@ public class SingularValueDecomposition {
}
// A = getR1() * getW() getR2() = getR1() * getW() * getIR1() * getRot()
public static double [][] getUnity(){
return new double [][] {{1,0},{0,1}};
}
public double [][] getR1(){ return rotMatrix(beta);}
public double [][] getR2(){ return rotMatrix(gamma);}
public double [][] getIR1(){return rotMatrix(-beta);}
public double [][] getIR1(){return rotMatrix(-beta);} // never used
public double [][] getRot(){return rotMatrix(rot);}
public double [][] getW(){
return new double [][] {{w1,0},{0,w1}};
}
public double getTiltAngle() {
if (ratio <= 1.0) return Math.acos(ratio);
else return Math.acos(1/ratio);
......@@ -46,19 +52,16 @@ public class SingularValueDecomposition {
public String toString(boolean degrees) {
//System.out.println("svd_affine_pair= ["+svd_affine_pair.scale+ ","+svd_affine_pair.getTiltAngle()+ ","+svd_affine_pair.gamma+ ","+svd_affine_pair.rot+
// "] tilt="+(svd_affine_pair.getTiltAngle()*180/Math.PI)+ "\u00B0, dir="+(svd_affine_pair.gamma*180/Math.PI)+"\u00B0");
String fmt_rad = "scale=%10.8f,tilt= %10.7f, gamma=%10.7f, beta=%10.7f, rot=%10.7f, w1=%10.8f, w2=%10.8f, ratio=%10.8f";
String fmt_deg = "scale=%10.8f,tilt= %10.5f\u00B0, gamma=%10.5f\u00B0, beta=%10.5f\u00B0, rot=%10.5f\u00B0, w1=%10.8f, w2=%10.8f, ratio=%10.8f";
String fmt_rad = " scale=%10.8f,tilt= %10.7f, gamma=%10.7f, beta=%10.7f, rot=%10.7f, w1=%10.8f, w2=%10.8f, ratio=%10.8f";
String fmt_deg = " scale=%10.8f,tilt= %10.5f\u00B0, gamma=%10.5f\u00B0, beta=%10.5f\u00B0, rot=%10.5f\u00B0, w1=%10.8f, w2=%10.8f, ratio=%10.8f";
double s = degrees ? (180/Math.PI):1;
String fmt=degrees ? fmt_deg : fmt_rad;
return String.format(fmt, scale, s*getTiltAngle(), s*gamma, s*beta, s*rot, w1, w2, ratio);
}
public double [][] getW(){
return new double [][] {{w1,0},{0,w1}};
}
/**
* Decomposing linear transform into rotation
* Decomposing linear transform into rotations and scales. OK to use full 2x3 affine
* R1={{cos(beta),sin(beta)},{-sin(beta), cos(beta)}} ,
* non-uniform scale transform W={{w1,0}{0,w2}}, and rotation
* R2={{cos(gamma),sin(gamma)},{-sin(gamma), cos(gamma)}}
......@@ -91,6 +94,64 @@ public class SingularValueDecomposition {
return svd;
}
public static double [][] removeTiltRotScale(
double [][] A,
boolean removeTilt,
boolean removeRot,
boolean removeScale,
boolean removeOffset,
boolean max_is_scale) {
SingularValueDecomposition svd = singularValueDecompose(A);
double [][] AR = removeTiltRotScale(
svd, // SingularValueDecomposition svd,
removeTilt, // boolean removeTilt,
removeRot, // boolean removeRot,
removeScale, // boolean removeScale)
max_is_scale); // boolean max_is_scale)
if (A[0].length < 3) {
return AR;
}
A=A.clone();
if (removeOffset) {
for (int i = 0; i < 2; i++) {
A[i][2] = 0;
}
}
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
A[i][j] = AR[i][j];
}
}
return A;
}
public static double [][] removeTiltRotScale(
SingularValueDecomposition svd,
boolean removeTilt,
boolean removeRot,
boolean removeScale,
boolean max_is_scale) {
double [][] R1 = svd.getR1();
double [][] IR1 = svd.getIR1();
// double [][] W = svd.getW();
double scale = max_is_scale?Math.max(svd.w1,svd.w2):Math.min(svd.w1,svd.w2);
double w1 =svd.w1, w2 = svd.w2;
if (removeScale) {
w1 /= scale;
w2 /= scale;
scale = 1.0;
}
if (removeTilt) {
w1 = scale;
w2 = scale;
}
double [][]W = {{w1,0},{0, w2}};
double [][] R = removeRot? getUnity() : svd.getRot();
double [][] A = QuatUtils.matMult2x2(QuatUtils.matMult2x2(QuatUtils.matMult2x2(R1, W), IR1), R);
return A;
}
public static double [] getMinMaxEigenValues(double [][] A) {
double a00=A[0][0],a01=A[0][1],a10=A[1][0],a11=A[1][1];
double b00=(a00+a11)/2; // , b11 = b00;
......
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