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Commit eebf08ba authored by Andrey Filippov's avatar Andrey Filippov
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debugging LMA

parent 1738d70d
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Showing with 229 additions and 52 deletions
src/main/java/FocusingField.java
View file @ eebf08ba
......@@ -65,13 +65,13 @@ public class FocusingField {
// when false - tangential is master
double [] minMeas= {1.0,1.0,1.0,1.0,1.0,1.0}; // pixels
double [] maxMeas= {4.5,4.5,4.5,4.5,4.5,4.5}; // pixels
double [] thresholdMax= {3.0,3.0,3.0,3.0,4.0,3.0}; // pixels
double [] thresholdMax= {2.4,3.0,2.6,3.0,3.1,3.0}; // pixels
double [] weightReference=null;
boolean useMinMeas= true;
boolean useMaxMeas= true;
boolean useThresholdMax=true;
FieldFitting fieldFitting=null;
int weighMode=0; // 0 - same weight, 1 - linear threshold difference, 2 - quadratic thershold difference
int weighMode=2; // 0; // 0 - same weight, 1 - linear threshold difference, 2 - quadratic thershold difference
double weightRadius=2.0; // Gaussian sigma in mm
MeasuredSample [] dataVector;
double [] dataValues;
......@@ -113,9 +113,18 @@ public class FocusingField {
private boolean showAllSamples = true;
private boolean showIgnoredData= false;
private boolean showRad = true;
private boolean [][][][] sampleMask=null;
private boolean [][][][][] sampleMask=null;
private boolean correct_measurement_ST=true;
private boolean updateWeightWhileFitting=false;
public int debugLevel;
public boolean debugDerivatives;
public boolean debugDerivativesFxDxDy=false;
public void setDebugLevel(int debugLevel){
this.debugLevel=debugLevel;
}
public class LMAArrays { // reuse from Distortions?
public double [][] jTByJ= null; // jacobian multiplied by Jacobian transposed
public double [] jTByDiff=null; // jacobian multiplied difference vector
......@@ -218,6 +227,9 @@ public class FocusingField {
gd.addCheckbox("Setup parameter masks?",setupMasks);
gd.addCheckbox("Setup parameter values?",setupParameters);
gd.addCheckbox("Show/modify disabled for auto-adjustment parameters?",showDisabled);
gd.addCheckbox("Debug feature: update measurements and /dxc, /dyc if center is being fitted",correct_measurement_ST);
gd.addCheckbox("Debug feature: update sample weights during fitting",updateWeightWhileFitting);
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
......@@ -238,6 +250,8 @@ public class FocusingField {
setupMasks= gd.getNextBoolean();
setupParameters= gd.getNextBoolean();
showDisabled= gd.getNextBoolean();
correct_measurement_ST= gd.getNextBoolean();
updateWeightWhileFitting= gd.getNextBoolean();
if (forcenew) {
this.fieldFitting= new FieldFitting(
currentPX0,
......@@ -260,6 +274,7 @@ public class FocusingField {
// includes deselected channels
public void setDataVector(MeasuredSample [] vector){ // remove unused channels if any
if (debugLevel>1) System.out.println("+++++ (Re)calculating sample weights +++++");
boolean [] chanSel=fieldFitting.getSelectedChannels();
int numSamples=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) numSamples++;
......@@ -303,10 +318,13 @@ public class FocusingField {
double [] pXY=fieldFitting.getCenterXY();
currentPX0=pXY[0];
currentPY0=pXY[1];
setDataVector(createDataVector(
false, // boolean updateSelection,
pXY[0], //double centerPX,
pXY[1])); //double centerPY
if (debugLevel>1) System.out.println("Updated currentPX0="+currentPX0+", currentPY0="+currentPY0);
if (correct_measurement_ST && updateWeightWhileFitting) {
setDataVector(createDataVector(
false, // boolean updateSelection,
pXY[0], //double centerPX,
pXY[1])); //double centerPY
}
}
}
......@@ -354,7 +372,7 @@ public class FocusingField {
}
//TODO: correct /dpx, /dpy to compensate for measured S,T calcualtion
boolean [] centerSelect=fieldFitting.getCenterSelect();
if (centerSelect[0] || centerSelect[1]){ // do not do that if both X and Y are disabled
if (correct_measurement_ST && (centerSelect[0] || centerSelect[1])){ // do not do that if both X and Y are disabled
int np=0;
for (int i=0;i<2;i++) if (centerSelect[i]){
jacobian[np++][n]-=ms.dPxyc[i]; // subtract, as effect is opposite to fX
......@@ -453,17 +471,20 @@ d_cs/dy0= delta_x*(2*delta_y^2-r2)/r2^2
double [] minMeas, // pixels
double [] maxMeas, // pixels
double [] thresholdMax){ // pixels
debugDerivatives=debugLevel==3;
currentPX0=centerPX;
currentPY0=centerPY;
final int numColors=3;
final int numDirs=2;
if (sampleMask== null) updateSelection=true;
if (updateSelection){
sampleMask= new boolean[sampleCoord.length][sampleCoord[0].length][numColors][numDirs];
for (int i=0;i<sampleMask.length;i++)
for (int j=0;j<sampleMask[i].length;j++)
if (debugLevel>1) System.out.println("createDataVector(true,"+centerPX+","+centerPY+"...)");
sampleMask= new boolean[measurements.size()] [sampleCoord.length][sampleCoord[0].length][numColors][numDirs];
for (int n=0;n<sampleMask.length;n++)
for (int i=0;i<sampleMask[n].length;i++)
for (int j=0;j<sampleMask[n][i].length;j++)
for (int c=0;c<numColors;c++)
for (int d=0;d<numDirs;d++) sampleMask[i][j][c][d]=false;
for (int d=0;d<numDirs;d++) sampleMask[n][i][j][c][d]=false;
}
/*
......@@ -477,13 +498,28 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
2*d_cs/dy0= 2*delta_x*(2*delta_y^2-r2)/r2^2
*/
double [][][] cosSin2Tab=new double[sampleCoord.length][sampleCoord[0].length][3];
double [][][] debugCosSin2Tab_dx=null;
double [][][] debugCosSin2Tab_dy=null;
double debugDelta_x_dx=0,debugDelta_y_dy=0,debugR2_dx=0,debugR2_dy=0;
if (debugDerivatives){
debugCosSin2Tab_dx=new double[sampleCoord.length][sampleCoord[0].length][3];
debugCosSin2Tab_dy=new double[sampleCoord.length][sampleCoord[0].length][3];
}
double [][][] cosSin2Tab_dx0=new double[sampleCoord.length][sampleCoord[0].length][3];
double [][][] cosSin2Tab_dy0=new double[sampleCoord.length][sampleCoord[0].length][3];
for (int i=0;i<sampleMask.length;i++) for (int j=0;j<sampleMask[i].length;j++){
for (int i=0;i<sampleCoord.length;i++) for (int j=0;j<sampleCoord[i].length;j++){
double delta_x=sampleCoord[i][j][0]-currentPX0;
double delta_y=sampleCoord[i][j][1]-currentPY0;
double r2=delta_x*delta_x+delta_y*delta_y;
double r4=r2*r2;
if (debugDerivatives){
debugDelta_x_dx=sampleCoord[i][j][0]-currentPX0-1;
debugDelta_y_dy=sampleCoord[i][j][1]-currentPY0-1;
debugR2_dx=debugDelta_x_dx*debugDelta_x_dx+delta_y*delta_y;
debugR2_dy=delta_x*delta_x+debugDelta_y_dy*debugDelta_y_dy;
}
if (r2>0.0) {
cosSin2Tab[i][j][0]= delta_x*delta_x/r2; // cos^2
cosSin2Tab[i][j][1]= delta_y*delta_y/r2; // sin^2
......@@ -496,6 +532,15 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab_dy0[i][j][0]= 2*delta_y*delta_x*delta_x/r4; // d(cos^2)/d(y0)
cosSin2Tab_dy0[i][j][1]= 2*delta_y*(delta_y*delta_y - r2)/r4; // d(sin^2)/d(y0)
cosSin2Tab_dy0[i][j][2]= 2*delta_x*(2*delta_y*delta_y-r2)/r4; // d(2*cos*sin)/d(y0)
if (debugDerivatives){
debugCosSin2Tab_dx[i][j][0]= debugDelta_x_dx*debugDelta_x_dx/debugR2_dx; // cos^2
debugCosSin2Tab_dx[i][j][1]= delta_y*delta_y/debugR2_dx; // sin^2
debugCosSin2Tab_dx[i][j][2]=2*debugDelta_x_dx*delta_y/debugR2_dx; // 2*cos*sin
debugCosSin2Tab_dy[i][j][0]= delta_x*delta_x/debugR2_dy; // cos^2
debugCosSin2Tab_dy[i][j][1]= debugDelta_y_dy*debugDelta_y_dy/debugR2_dy; // sin^2
debugCosSin2Tab_dy[i][j][2]=2*delta_x*debugDelta_y_dy/debugR2_dy; // 2*cos*sin
}
} else {
cosSin2Tab[i][j][0]=1.0;
......@@ -509,6 +554,15 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab_dy0[i][j][0]=0.0;
cosSin2Tab_dy0[i][j][1]=0.0;
cosSin2Tab_dy0[i][j][2]=0.0;
if (debugDerivatives){
debugCosSin2Tab_dx[i][j][0]= 0.0;
debugCosSin2Tab_dx[i][j][1]= 0.0;
debugCosSin2Tab_dx[i][j][2]= 0.0;
debugCosSin2Tab_dy[i][j][0]= 0.0;
debugCosSin2Tab_dy[i][j][1]= 0.0;
debugCosSin2Tab_dy[i][j][2]= 0.0;
}
}
}
......@@ -543,6 +597,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} else {
thresholdMax=null;
}
int nMeas=0;
for (FocusingFieldMeasurement ffm:measurements){
double [][][][] samples=ffm.samples;
if (samples!=null) for (int i=0;i<sampleCoord.length;i++){
......@@ -550,7 +605,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
if ((j<samples[i].length) && (samples[i][j]!=null)) for (int c=0;c<numColors;c++){
if ((c<samples[i][j].length) && (samples[i][j][c]!=null)){
double sagTan[] = {
double [] sagTan = {
Math.sqrt(
cosSin2Tab[i][j][0]*samples[i][j][c][0]+
cosSin2Tab[i][j][1]*samples[i][j][c][1]+
......@@ -559,8 +614,26 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab[i][j][1]*samples[i][j][c][0]+
cosSin2Tab[i][j][0]*samples[i][j][c][1]-
cosSin2Tab[i][j][2]*samples[i][j][c][2])};
double sagTan_dx0[] = {
double [] debugSagTan_dx={0.0,0.0},debugSagTan_dy={0.0,0.0};
if (debugDerivatives){
debugSagTan_dx[0]= Math.sqrt(
debugCosSin2Tab_dx[i][j][0]*samples[i][j][c][0]+
debugCosSin2Tab_dx[i][j][1]*samples[i][j][c][1]+
debugCosSin2Tab_dx[i][j][2]*samples[i][j][c][2]);
debugSagTan_dx[1]= Math.sqrt(
debugCosSin2Tab_dx[i][j][1]*samples[i][j][c][0]+
debugCosSin2Tab_dx[i][j][0]*samples[i][j][c][1]-
debugCosSin2Tab_dx[i][j][2]*samples[i][j][c][2]);
debugSagTan_dy[0]= Math.sqrt(
debugCosSin2Tab_dy[i][j][0]*samples[i][j][c][0]+
debugCosSin2Tab_dy[i][j][1]*samples[i][j][c][1]+
debugCosSin2Tab_dy[i][j][2]*samples[i][j][c][2]);
debugSagTan_dy[1]= Math.sqrt(
debugCosSin2Tab_dy[i][j][1]*samples[i][j][c][0]+
debugCosSin2Tab_dy[i][j][0]*samples[i][j][c][1]-
debugCosSin2Tab_dy[i][j][2]*samples[i][j][c][2]);
}
double [] sagTan_dx0 = {
(0.5*(
cosSin2Tab_dx0[i][j][0]*samples[i][j][c][0]+
cosSin2Tab_dx0[i][j][1]*samples[i][j][c][1]+
......@@ -571,7 +644,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab_dx0[i][j][2]*samples[i][j][c][2])/sagTan[1])
};
double sagTan_dy0[] = {
double [] sagTan_dy0 = {
(0.5*(
cosSin2Tab_dy0[i][j][0]*samples[i][j][c][0]+
cosSin2Tab_dy0[i][j][1]*samples[i][j][c][1]+
......@@ -582,50 +655,105 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab_dy0[i][j][2]*samples[i][j][c][2])/sagTan[1])
};
System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
if (debugLevel>3) System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
for (int d=0;d<numDirs;d++){
System.out.print(" d= "+d+" ");
if (debugLevel>3) System.out.print(" d= "+d+" ");
if (!updateSelection && !sampleMask[i][j][c][d]) continue;
if (!updateSelection && !sampleMask[nMeas][i][j][c][d]) continue;
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=sagTan[d]*2.0;
double value_dx0=sagTan_dx0[d]*2.0;
double value_dy0=sagTan_dy0[d]*2.0;
double debugValue_dx0=0.0,debugValue_dy0=0.0;
if (debugDerivatives){
debugValue_dx0=debugSagTan_dx[d]*2.0;
debugValue_dy0=debugSagTan_dy[d]*2.0;
}
boolean dbg=(debugLevel==3) && (i==1) && (j==3);
double dbg_delta_x=sampleCoord[i][j][0]-currentPX0;
double dbg_delta_y=sampleCoord[i][j][1]-currentPY0;
if (dbg) System.out.print("mot="+ffm.motors[2]+" dx="+dbg_delta_x+" dy="+dbg_delta_y);
if (dbg) System.out.println(" value="+value+" value_dx0="+value_dx0+" value_dy0="+value_dy0);
if (dbg) System.out.println(" value(dx)="+debugValue_dx0+" value(dy)="+debugValue_dy0+
" debugDiff_dx0="+(debugValue_dx0-value)+" debugDiff_dy0="+(debugValue_dy0-value));
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) {
System.out.println("samples["+i+"]["+j+"]["+c+"]["+d+"] = Double.NaN, motors[0]="+ffm.motors[0]);
continue; // bad measurement
if (debugLevel>3) System.out.println("samples["+i+"]["+j+"]["+c+"]["+d+"] = Double.NaN, motors[0]="+ffm.motors[0]);
if (updateSelection) continue; // bad measurement
}
System.out.print(" A "+value);
if (debugLevel>3) System.out.print(" A "+value);
if (thresholdMax != null){
if (value >= thresholdMax[chn]) {
System.out.print(" > "+thresholdMax[chn]);
continue; // bad measurement (above threshold)
if (debugLevel>3) System.out.print(" > "+thresholdMax[chn]);
if (updateSelection) continue; // bad measurement (above threshold)
}
}
System.out.print(" B "+value);
if (debugLevel>3) System.out.print(" B "+value);
// correct for for minimal measurement;
if (minMeas != null){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
if (value<minMeas[chn]) {
if (debugLevel>3) System.out.print(" < "+minMeas[chn]);
if (updateSelection) continue; // bad measurement (smaller than correction)
}
double f=value;
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
value_dx0*=f/value;
value_dy0*=f/value;
if (dbg) {
System.out.println("2. value="+value+" value_dx0="+value_dx0+" value_dy0="+value_dy0);
if (debugDerivatives){
debugValue_dx0=Math.sqrt(debugValue_dx0*debugValue_dx0-minMeas[chn]*minMeas[chn]);
debugValue_dy0=Math.sqrt(debugValue_dy0*debugValue_dy0-minMeas[chn]*minMeas[chn]);
if (dbg) System.out.println("2. value(dx)="+debugValue_dx0+" value(dy)="+debugValue_dy0+
" debugDiff_dx0="+(debugValue_dx0-value)+" debugDiff_dy0="+(debugValue_dy0-value));
}
}
}
System.out.print(" C "+value);
if (debugLevel>3) System.out.print(" C "+value);
// correct for for maximal measurement;
if (maxMeas != null) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
if (value >= maxMeas[chn]){
if (debugLevel>3) System.out.print(" > "+maxMeas[chn]);
if (updateSelection) continue; // bad measurement (larger than correction)
}
double f=value;
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
value_dx0*=1.0/(value*f*f*f);
value_dy0*=1.0/(value*f*f*f);
// value_dx0*=1.0/(value*f*f*f);
// value_dy0*=1.0/(value*f*f*f);
f=value/f;
f*=f*f;
value_dx0*=f;
value_dy0*=f;
if (dbg) {
System.out.println("3. value="+value+" value_dx0="+value_dx0+" value_dy0="+value_dy0);
if (debugDerivatives){
debugValue_dx0 = 1.0/Math.sqrt(1.0/(debugValue_dx0*debugValue_dx0)-1.0/(maxMeas[chn]*maxMeas[chn]));
debugValue_dy0 = 1.0/Math.sqrt(1.0/(debugValue_dy0*debugValue_dy0)-1.0/(maxMeas[chn]*maxMeas[chn]));
if (dbg) System.out.println("3. value(dx)="+debugValue_dx0+" value(dy)="+debugValue_dy0+
" debugDiff_dx0="+(debugValue_dx0-value)+" debugDiff_dy0="+(debugValue_dy0-value));
}
}
}
System.out.print(" D "+value);
if (debugLevel>3) System.out.print(" D "+value);
// convert to microns from pixels
value*=getPixelUM();
value_dx0*=getPixelUM();
value_dy0*=getPixelUM();
if (dbg) {
System.out.println("4. value="+value+" value_dx0="+value_dx0+" value_dy0="+value_dy0);
if (debugDerivatives){
debugValue_dx0*=getPixelUM();
debugValue_dy0*=getPixelUM();
if (dbg) System.out.println("4. value(dx)="+debugValue_dx0+" value(dy)="+debugValue_dy0+
" debugDiff_dx0="+(debugValue_dx0-value)+" debugDiff_dy0="+(debugValue_dy0-value));
}
}
sampleList.add(new MeasuredSample(
ffm.motors,
ffm.timestamp,
......@@ -636,16 +764,17 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X
value_dy0 //double dPyc; // derivative of the value by optical (aberration) center pixel Y
));
System.out.print(" E "+value);
if (updateSelection) sampleMask[i][j][c][d]=true;
if (debugLevel>3) System.out.print(" E "+value);
if (updateSelection) sampleMask[nMeas][i][j][c][d]=true;
}
}
}
}
}
nMeas++;
}
System.out.println();
System.out.println("createDataVector -> "+sampleList.size()+" elements");
if (debugLevel>3) System.out.println();
if (debugLevel>0) System.out.println("createDataVector -> "+sampleList.size()+" elements");
return sampleList.toArray(new MeasuredSample[0]);
}
/**
......@@ -664,7 +793,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
if (this.dataWeights!=null) {
for (int i=0;i<fX.length;i++){
double diff=this.dataValues[i]-fX[i];
result+=diff*diff*this.dataWeights[i]; System.out.println(""+i+"fx="+fX[i]+" data="+this.dataValues[i]+" diff="+diff+" w="+this.dataWeights[i]);
result+=diff*diff*this.dataWeights[i];
if (debugLevel>2) System.out.println(""+i+"fx="+fX[i]+" data="+this.dataValues[i]+" diff="+diff+" w="+this.dataWeights[i]);
sumWeights+=this.dataWeights[i];
}
if (sumWeights>0) result/=sumWeights;
......@@ -715,6 +845,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
LMAArrays lMAArrays,
double lambda,
int debugLevel){
this.debugLevel=debugLevel;
double [][] JtByJmod= lMAArrays.jTByJ.clone();
int numPars=JtByJmod.length;
for (int i=0;i<numPars;i++){
......@@ -750,6 +881,27 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
return Ma.getColumnPackedCopy();
}
public void compareDrDerivatives(double [] vector){
boolean [] centerSelect=fieldFitting.getCenterSelect();
if (!centerSelect[0] || !centerSelect[1]){
System.out.println("compareDrDerivatives(): Both px0 and px1 parameters should be enabled, aborting");
return;
}
double [] vector_dx=vector.clone();
double [] vector_dy=vector.clone();
vector_dx[0]+=1.0;
vector_dy[1]+=1.0;
double [] fx_dx=createFXandJacobian(vector_dx,false);
double [] fx_dy=createFXandJacobian(vector_dy,false);
double [] fx= createFXandJacobian(vector,true);
for (int i=0;i<fx.length;i++){
System.out.println(i+" fx= "+fx[i]+" delta_fx= "+(fx_dx[i]-fx[i])+" delta_fy= "+(fx_dy[i]-fx[i]));
System.out.println(" df/dx= "+jacobian[0][i]+" df/dy= "+jacobian[1][i]);
}
}
/**
* Calculates next parameters vector, holds some arrays
* @param numSeries
......@@ -766,6 +918,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
lastImprovements[0]=-1.0;
lastImprovements[1]=-1.0;
}
this.debugLevel=debugLevel;
// calculate this.currentfX, this.jacobian if needed
if (debugLevel>2) {
System.out.println("this.currentVector");
......@@ -786,7 +939,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length);
}
} else {
this.currentRMS= calcErrorDiffY(this.currentfX);
// continuing, but need to re-build Y vector to match this.currentVector
commitParameterVector(this.currentVector); // may be extra job?
this.currentRMS= calcErrorDiffY(this.currentfX); // Verify - currentfX is correct, but Y vector is modified! Yes, it is so
}
if (this.firstRMS<0) {
this.firstRMS=this.currentRMS;
......@@ -801,7 +956,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
for (int i=0;i<deltas.length;i++) deltas[i]=0.0;
matrixNonSingular=false;
}
if (debugLevel>2) {
if (debugLevel>1) {
System.out.println("deltas");
for (int i=0;i<deltas.length;i++){
System.out.println(i+": "+ deltas[i]);
......@@ -901,6 +1056,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
public boolean selectLMAParameters(){
// int numSeries=fittingStrategy.getNumSeries();
GenericDialog gd = new GenericDialog("Levenberg-Marquardt algorithm parameters for cameras distortions/locations");
gd.addCheckbox("Debug df/dX0, df/dY0", false);
// gd.addNumericField("Iteration number to start (0.."+(numSeries-1)+")", this.seriesNumber, 0);
gd.addNumericField("Initial LMA Lambda ", this.lambda, 5);
gd.addNumericField("Multiply lambda on success", this.lambdaStepDown, 5);
......@@ -923,6 +1079,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
// gd.addCheckbox("Use memory-saving/multithreaded version", this.threadedLMA);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.debugDerivativesFxDxDy=gd.getNextBoolean();
// this.seriesNumber= (int) gd.getNextNumber();
this.lambda= gd.getNextNumber();
this.lambdaStepDown= gd.getNextNumber();
......@@ -1039,7 +1196,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
}
double [][][] cosSin2Tab=new double[sampleCoord.length][sampleCoord[0].length][3];
for (int i=0;i<sampleMask.length;i++) for (int j=0;j<sampleMask[i].length;j++){
for (int i=0;i<sampleCoord.length;i++) for (int j=0;j<sampleCoord[i].length;j++){
double delta_x=sampleCoord[i][j][0]-currentPX0;
double delta_y=sampleCoord[i][j][1]-currentPY0;
double r2=delta_x*delta_x+delta_y*delta_y;
......@@ -1102,39 +1259,45 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
cosSin2Tab[i][j][1]*samples[i][j][c][0]+
cosSin2Tab[i][j][0]*samples[i][j][c][1]-
cosSin2Tab[i][j][2]*samples[i][j][c][2])};
System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
if (debugLevel>3) System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
for (int d=0;d<numDirs;d++){
System.out.print(" d= "+d+" ");
if (debugLevel>3) System.out.print(" d= "+d+" ");
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=sagTan[d]*2.0;
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) continue; // bad measurement
System.out.print(" A "+value);
if (debugLevel>3) System.out.print(" A "+value);
if (!showIgnoredData && (thresholdMax != null)){
if (value >= thresholdMax[chn]){
System.out.print(" > "+thresholdMax[chn]);
if (debugLevel>3) System.out.print(" > "+thresholdMax[chn]);
continue; // bad measurement (above threshold)
}
}
System.out.print(" B "+value);
if (debugLevel>3) System.out.print(" B "+value);
// correct for for minimal measurement;
if (useMinMeas && (minMeas != null)){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
if (value<minMeas[chn]) {
if (debugLevel>3) System.out.print(" < "+minMeas[chn]);
continue; // bad measurement (smaller than correction)
}
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
}
System.out.print(" C "+value);
if (debugLevel>3) System.out.print(" C "+value);
// correct for for maximal measurement;
if (useMaxMeas && (maxMeas != null)) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
if (value >= maxMeas[chn]) {
if (debugLevel>3) System.out.print(" > "+maxMeas[chn]);
continue; // bad measurement (larger than correction)
}
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
}
System.out.print(" D "+value);
if (debugLevel>3) System.out.print(" D "+value);
// convert to microns from pixels
value*=getPixelUM();
samplesFull[i][j][c][d]=value;
System.out.print(" E "+value);
if (debugLevel>3) System.out.print(" E "+value);
}
}
}
......@@ -1192,7 +1355,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
sb.append("\n");
}
System.out.println();
if (debugLevel>3) System.out.println();
if (showRad){
sb.append(header+"\n");
......@@ -1299,10 +1462,15 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double savedLambda=this.lambda;
this.debugLevel=debugLevel;
if (openDialog && !selectLMAParameters()) return false;
this.startTime=System.nanoTime();
// create savedVector (it depends on parameter masks), restore from it if aborted
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
if (debugDerivativesFxDxDy){
compareDrDerivatives(this.savedVector);
}
this.iterationStepNumber=0;
this.firstRMS=-1; //undefined
// while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series
......@@ -1316,6 +1484,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
IJ.showMessage(msg);
System.out.println(msg);
commitParameterVector(this.savedVector);
this.lambda=savedLambda;
return false;
}
......@@ -1360,6 +1529,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
*/
if (!cont){
if (this.saveSeries) {
savedLambda=this.lambda;
this.savedVector=this.currentVector.clone();
// saveFittingSeries(); // will save series even if it ended in failure, vector will be only updated
// updateCameraParametersFromCalculated(true); // update camera parameters from all (even disabled) images
......@@ -1367,12 +1538,14 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
// if RMS was decreased. this.saveSeries==false after dialogLMAStep(state) only if "cancel" was pressed
commitParameterVector(this.savedVector); // either new or original
this.lambda=savedLambda;
return this.saveSeries; // TODO: Maybe change result?
}
//stepLevenbergMarquardtAction();
if (state[1]) {
if (!state[0]) {
commitParameterVector(this.savedVector);
this.lambda=savedLambda;
return false; // sequence failed
}
this.savedVector=this.currentVector.clone();
......@@ -2060,6 +2233,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
dr_dxy[1]=-dY/r;
}
nChn=0;
for (int i=0;i<2;i++){
dr_dxy[i]*=getPixelMM(); // radius in mm, dx, dy - in pixels
// dr_dxy[i]*=2; //?????
}
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
int otherChannel= c ^ 1;
......
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