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Commit 47ffc516 authored by Andrey Filippov's avatar Andrey Filippov
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debugging

parent 367449b7
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Showing with 189 additions and 34 deletions
src/main/java/FocusingField.java
View file @ 47ffc516
......@@ -59,9 +59,11 @@ public class FocusingField {
public double pY0;
public double [][][] sampleCoord;
public ArrayList<FocusingFieldMeasurement> measurements;
boolean sagittalMaster=false; // center data is the same, when true sagittal fitting only may change r=0 coefficients,
// 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= {3.0,3.0,3.0,3.0,3.0,3.0}; // pixels
double [] thresholdMax= {3.0,3.0,3.0,3.0,4.0,3.0}; // pixels
double [] weightReference=null;
boolean useMinMeas= true;
boolean useMaxMeas= true;
......@@ -179,6 +181,9 @@ public class FocusingField {
int [] numCurvPars=tmpFieldFitting.getNumCurvars();
GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));
gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
for (int i=0;i<minMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");
}
......@@ -207,6 +212,7 @@ public class FocusingField {
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
sagittalMaster= gd.getNextBoolean();
for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
useMinMeas= gd.getNextBoolean();
for (int i=0;i<maxMeas.length;i++) this.maxMeas[i]= gd.getNextNumber();
......@@ -232,7 +238,7 @@ public class FocusingField {
}
if (setupMasks) this.fieldFitting.maskSetDialog("Setup parameter masks");
if (setupParameters) this.fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled);
this.savedVector=this.fieldFitting.createParameterVector();
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
// initialVector
return true;
}
......@@ -276,7 +282,7 @@ public class FocusingField {
// for compatibility with Distortions class
public double [] createFXandJacobian( double [] vector, boolean createJacobian){
fieldFitting.commitParameterVector(vector);
fieldFitting.commitParameterVector(vector,sagittalMaster);
return createFXandJacobian(createJacobian);
}
......@@ -291,7 +297,7 @@ public class FocusingField {
for (int i=1;i<selChanIndices.length;i++){
selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
}
int numPars=fieldFitting.getNumberOfParameters();
int numPars=fieldFitting.getNumberOfParameters(sagittalMaster);
if (createJacobian) {
jacobian=new double [numPars][dataVector.length];
derivs=new double [fieldFitting.getNumberOfChannels()][];
......@@ -302,6 +308,7 @@ public class FocusingField {
MeasuredSample ms=dataVector[n];
if (!ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){
subData=fieldFitting.getValsDerivatives(
sagittalMaster,
ms.motors, // 3 motor coordinates
ms.px, // pixel x
ms.py, // pixel y
......@@ -896,6 +903,7 @@ public class FocusingField {
for (int i=0;i<sampleCoord.length;i++)
for (int j=0;j<sampleCoord[0].length;j++) {
double [] subData=fieldFitting.getValsDerivatives(
sagittalMaster, // dependent channel does not have center parameters, but that is only used for derivs.
ffm.motors, // 3 motor coordinates
sampleCoord[i][j][0], // pixel x
sampleCoord[i][j][1], // pixel y
......@@ -1049,8 +1057,8 @@ public class FocusingField {
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();
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
this.iterationStepNumber=0;
this.firstRMS=-1; //undefined
// while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series
this.currentVector=null; // invalidate for the new series
......@@ -1062,7 +1070,7 @@ public class FocusingField {
String msg="Calculation aborted by user request, restoring saved parameter vector";
IJ.showMessage(msg);
System.out.println(msg);
this.fieldFitting.commitParameterVector(this.savedVector);
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
return false;
}
......@@ -1113,13 +1121,13 @@ public class FocusingField {
// updateCameraParametersFromCalculated(false); // update camera parameters from enabled only images (may overwrite some of the above)
}
// if RMS was decreased. this.saveSeries==false after dialogLMAStep(state) only if "cancel" was pressed
this.fieldFitting.commitParameterVector(this.savedVector); // either new or original
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster); // either new or original
return this.saveSeries; // TODO: Maybe change result?
}
//stepLevenbergMarquardtAction();
if (state[1]) {
if (!state[0]) {
this.fieldFitting.commitParameterVector(this.savedVector);
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
return false; // sequence failed
}
this.savedVector=this.currentVector.clone();
......@@ -1134,11 +1142,12 @@ public class FocusingField {
// if (wasLastSeries) break;
// } // while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series
if (debugLevel>0) System.out.println("LevenbergMarquardt(): all done"+
", step="+ this.iterationStepNumber+
", RMS="+this.currentRMS+
" ("+this.firstRMS+") "+
" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3));
this.savedVector=this.currentVector.clone();
this.fieldFitting.commitParameterVector(this.savedVector);
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
return true; // all series done
}
......@@ -1495,14 +1504,28 @@ public class FocusingField {
}
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
parList.add("\t ===== Curvature model parameters for \""+ getDescription(n)+"\"=====\t\t");
int n1= n ^ 1;
int index=0;
for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) {
parList.add("\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
} else if (showDisabled) {
parList.add("(disabled)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
if ((j==0) && !isMasterDir){ // dependent, copy center coefficients from the master
if ((curvatureSelect[n1]==null) || curvatureSelect[n1][index] ) {
parList.add("(master)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
// debugging
parList.add("(this)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
} else if (showDisabled) {
parList.add("(master_disabled)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
// debugging
parList.add("(this_disabled)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
}
} else {
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) {
parList.add("\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
} else if (showDisabled) {
parList.add("(disabled)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
}
}
index++;
}
......@@ -1523,14 +1546,25 @@ public class FocusingField {
}
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
int n1= n ^ 1;
gd.addMessage("===== Curvature model parameters for \""+ getDescription(n)+"\"=====");
int index=0;
for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) {
gd.addNumericField(name,curvatureModel[n].modelParams[i][j],5,8,"");
} else if (showDisabled) {
gd.addNumericField("(disabled) "+name,curvatureModel[n].modelParams[i][j],5,8,"");
if ((j==0) && !isMasterDir){ // dependent, copy center coefficients from the master
if ((curvatureSelect[n1]==null) || curvatureSelect[n1][index] ) {
gd.addNumericField("(copied from master) "+name,curvatureModel[n1].modelParams[i][j],5,8,"");
} else if (showDisabled) {
gd.addNumericField("(copied from disabled master) "+name,curvatureModel[n1].modelParams[i][j],5,8,"");
}
} else {
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) {
gd.addNumericField(name,curvatureModel[n].modelParams[i][j],5,8,"");
} else if (showDisabled) {
gd.addNumericField("(disabled) "+name,curvatureModel[n].modelParams[i][j],5,8,"");
}
}
index++;
}
......@@ -1562,15 +1596,16 @@ public class FocusingField {
/**
* @return number of selected parameters (including mechanical and each selected - up to 6 - curvature)
*/
public int getNumberOfParameters(){
public int getNumberOfParameters(boolean sagittalMaster){
int np=0;
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) np++;
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
int index=0;
for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) np++;
if ((isMasterDir || (j!=0)) && ((curvatureSelect[n]==null) || curvatureSelect[n][index] )) np++;
index++;
}
}
......@@ -1589,20 +1624,22 @@ public class FocusingField {
/**
* @return vector of the current selected parameters values
*/
public double [] createParameterVector(){
double [] pars = new double [getNumberOfParameters()];
public double [] createParameterVector(boolean sagittalMaster){
double [] pars = new double [getNumberOfParameters(sagittalMaster)];
int np=0;
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) pars[np++]=mechanicalFocusingModel.paramValues[i];
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
int index=0;
for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) pars[np++]=curvatureModel[n].modelParams[i][j];
if ((isMasterDir || (j!=0)) && ((curvatureSelect[n]==null) || curvatureSelect[n][index] )) {
pars[np++]=curvatureModel[n].modelParams[i][j];
}
index++;
}
}
return pars;
}
......@@ -1610,18 +1647,30 @@ public class FocusingField {
* Apply (modified) parameter values to selected ones
* @param pars vector corresponding to selected parameters
*/
public void commitParameterVector(double [] pars){
public void commitParameterVector(double [] pars, boolean sagittalMaster){
int np=0;
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) mechanicalFocusingModel.paramValues[i] = pars[np++];;
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
int index=0;
for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
if ((curvatureSelect[n]==null) || curvatureSelect[n][index] ) curvatureModel[n].modelParams[i][j]=pars[np++];
if ((isMasterDir || (j!=0)) && ((curvatureSelect[n]==null) || curvatureSelect[n][index] )) {
curvatureModel[n].modelParams[i][j]=pars[np++];
}
index++;
}
}
// copy center parameters to dependent
// copy if master is selected, regardless of is dependent selected or not
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
boolean isMasterDir = (n%2) == (sagittalMaster?0:1);
if (isMasterDir){
curvatureModel[n ^ 1].setCenterVector(curvatureModel[n].getCenterVector());
}
}
}
public double getMotorsZ(
......@@ -1653,6 +1702,64 @@ public class FocusingField {
* @return array of [getNumberOfChannels()] calculated function values
*/
public double [] getValsDerivatives(
boolean sagittalMaster, // false - tangential master, true - sagittal master (for center coefficients)
int [] motors, // 3 motor coordinates
double px, // pixel x
double py, // pixel y
double [][] deriv // array of (1..6[][], matching getNumberOfChannels) or null if derivatives are not required
){
double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]);
double [] chnValues=new double [getNumberOfChannels()];
double mot_z=mechanicalFocusingModel.calc_ZdZ(
motors,
px,
py,
motorDerivs);
int nChn=0;
double [][] deriv_curv = new double [channelSelect.length][];
for (int c=0;c<channelSelect.length;c++) deriv_curv[c]=null;
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
deriv_curv[c]=(deriv==null)?null:(new double [curvatureModel[c].getSize()]);
chnValues[nChn++]=curvatureModel[c].getFdF(
px,
py,
mot_z,
deriv_curv[c]);
}
if (deriv!=null){
nChn=0;
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
int otherChannel= c ^ 1;
deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)];
int np=0;
// For dependent/master channels no difference for mechanical parameters
// TOSO: verify they are the same?
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) {
deriv[nChn][np++]=-motorDerivs[i]*deriv_curv[c][0]; // minus d/dz0 const part
}
}
// other parameters - for dependent - skip center (j==0), for master add dependent
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
int [] ncp=curvatureModel[n].getNumPars(); // {(z),(r)}
boolean isDependMasterDir=(n%2) == (sagittalMaster?0:1);
for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){
if (((i%ncp[1])!=0) || isDependMasterDir) {
int dependOnChannel=(((i%ncp[1])==0) && !isMasterDir)?otherChannel:c;
deriv[nChn][np++]=(n==dependOnChannel)?(deriv_curv[n][i]):0.0;
}
}
}
nChn++;
}
}
return chnValues;
}
public double [] getValsDerivativesOld(
boolean sagittalMaster,
int [] motors, // 3 motor coordinates
double px, // pixel x
double py, // pixel y
......@@ -1674,12 +1781,13 @@ public class FocusingField {
mot_z,
deriv_curv);
if (deriv!=null){
deriv[nChn]=new double [getNumberOfParameters()];
deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)];
int np=0;
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) deriv[nChn][np++]=-motorDerivs[i]*deriv_curv[0]; // minus d/dz0 const part
}
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){
deriv[nChn][np++]=(n==c)?(deriv_curv[i]):0.0;
......@@ -1690,7 +1798,9 @@ public class FocusingField {
}
return chnValues;
}
}
public class MechanicalFocusingModel{
......@@ -1990,6 +2100,19 @@ public class FocusingField {
this.modelParams[1][0]=dflt_na;
this.modelParams[2][0]=dflt_r0;
}
public double [] getCenterVector(){
double [] vector=new double [this.modelParams.length];
for (int i=0;i<this.modelParams.length;i++){
vector[i]=this.modelParams[i][0];
}
return vector;
}
public void setCenterVector(double [] vector){
for (int i=0;i<this.modelParams.length;i++){
this.modelParams[i][0]=vector[i];
}
}
public double [] getVector(){
double [] vector=new double [this.modelParams.length*this.modelParams[0].length];
int index=0;
......@@ -2036,6 +2159,11 @@ modified parameters, r0 - PSF FWHM at z=0, k (instead of a0), so that old r0 now
r0*exp(-k), old a0= r0*(1-exp(-k)).
f=sqrt((a*(zin-z0))^2 + (r0*(exp(-k))^2)+r0*(1-exp(-k))+ a1*(zin-z0)+...aN*(zin-z0)^N
z0 - ar[0]
a - ar[1]
r0 - ar[2]
k - ar[3]
ar1 - ar[4]
*/
double r=Math.sqrt((pX-pX0)*(pX-pX0)+(pY-pY0)*(pY-pY0))*PIXEL_SIZE; // in mm
......@@ -2050,13 +2178,24 @@ f=sqrt((a*(zin-z0))^2 + (r0*(exp(-k))^2)+r0*(1-exp(-k))+ a1*(zin-z0)+...aN*(zin-
}
}
double z=z_in-ar[0];
double sqrt=Math.sqrt((ar[1]*z)*(ar[1]*z) + ar[2]*ar[2]);
double f=sqrt;
double exp=Math.exp(-ar[3]);
double reff=ar[2]*exp;
// double sqrt=Math.sqrt((ar[1]*z)*(ar[1]*z) + ar[2]*ar[2]);
double sqrt=Math.sqrt((ar[1]*z)*(ar[1]*z) + reff*reff);
double f=sqrt+ar[2]*(1-exp);
double zp=1.0;
/*
for (int i=3;i<ar.length;i++){
f+=ar[i]*zp;
zp*=z;
}
*/
for (int i=4;i<ar.length;i++){
zp*=z;
f+=ar[i]*zp;
}
if (deriv==null) return f; // only value, no derivatives
double [] df_da=new double[this.modelParams.length]; // last element - derivative for dz
// derivative for z0 (shift) - ar[0]
......@@ -2069,13 +2208,24 @@ f=sqrt((a*(zin-z0))^2 + (r0*(exp(-k))^2)+r0*(1-exp(-k))+ a1*(zin-z0)+...aN*(zin-
// derivative for a (related to numeric aperture) - ar[1]
df_da[1]=1.0/sqrt*ar[1]*z*z;
// derivative for a (related to lowest PSF radius) - ar[2]
df_da[2]=1.0/sqrt*ar[2];
// df_da[2]=1.0/sqrt*ar[2];
df_da[2]=1.0/sqrt*reff*exp + (1-exp); // * exp(-k)
// derivative for k (ar[3]
df_da[3]=1.0/sqrt*reff*ar[2]*exp*(-1) + ar[2]*exp;
// derivatives for rest (polynomial) coefficients
zp=1.0;
/*
for (int i=3;i<this.modelParams.length;i++){
df_da[i]=zp;
zp*=z;
}
*/
for (int i=4;i<this.modelParams.length;i++){
zp*=z;
df_da[i]=zp;
}
// derivative for z (to be combined with mechanical is just negative of derivative for z0, no need to calcualate separately
// calculate even powers of radius
double [] dar= new double [this.modelParams[0].length];
......@@ -2178,15 +2328,20 @@ f=sqrt((a*(zin-z0))^2 + (r0*(exp(-k))^2)+r0*(1-exp(-k))+ a1*(zin-z0)+...aN*(zin-
return mask;
}
public boolean showModifyParameterValues(String title, boolean showDisabled, boolean [] mask){
public boolean showModifyParameterValues(String title, boolean showDisabled, boolean [] mask, boolean isMaster){
GenericDialog gd = new GenericDialog(title);
int index=0;
for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){
String name=getZDescription(i)+", "+getRadialDecription(j);
if ((mask==null) || mask[index] ) {
boolean dependent=!isMaster && (j==0);
if (((mask==null) || mask[index] ) && !dependent) {
gd.addNumericField(name,this.modelParams[i][j],5,8,"");
} else if (showDisabled) {
gd.addNumericField("(disabled) "+name,this.modelParams[i][j],5,8,"");
if (dependent) {
gd.addNumericField("(from master) "+name,this.modelParams[i][j],5,8,"");
} else {
gd.addNumericField("(disabled) "+name,this.modelParams[i][j],5,8,"");
}
// gd.addMessage(name +": "+this.modelParams[i][j]);
}
index++;
......
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