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Commit 87f4c7ce authored by Andrey Filippov's avatar Andrey Filippov
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Debugging derivatives for mechanical variables

parent 1ac965a0
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Showing with 340 additions and 214 deletions
src/main/java/FocusingField.java
View file @ 87f4c7ce
......@@ -27,12 +27,14 @@ import ij.IJ;
import ij.gui.GenericDialog;
import ij.text.TextWindow;
import java.awt.Point;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Properties;
import java.util.concurrent.atomic.AtomicInteger;
......@@ -40,12 +42,6 @@ import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration;
//import Distortions.LMAArrays; // may still reuse?
import Jama.LUDecomposition;
import Jama.Matrix;
......@@ -60,6 +56,7 @@ public class FocusingField {
public double currentPX0;
public double currentPY0;
boolean sagittalMaster=false; // center data is the same, when true sagittal fitting only may change r=0 coefficients,
boolean parallelOnly = true; // only process measurements for parallel moves
// 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
......@@ -78,6 +75,8 @@ public class FocusingField {
private boolean qb_use_corrected=true;
private boolean qb_invert=true;
private boolean z_relative=true; // focal distance relative to center greeen
private boolean rslt_show_z_axial=true;
private boolean rslt_show_z_individual=true;
......@@ -157,12 +156,11 @@ public class FocusingField {
public boolean debugDerivativesFxDxDy=false;
private Properties savedProperties=null; // to-be applied
private String propertiesPrefix=null;
// public double fwhm_to_mtf50=500.0; // put actual number
public double fwhm_to_mtf50=2*Math.log(2.0)/Math.PI*1000; //pi/0.004
public boolean updateStatus=true;
public void setProperties(String prefix,Properties properties){
System.out.println("FocusingField: setProperties()");
if (debugLevel>1) System.out.println("FocusingField: setProperties()");
if (fieldFitting == null) {
System.out.println("fieldFitting is not initioalized, nothing to save");
return;
......@@ -174,6 +172,7 @@ public class FocusingField {
properties.setProperty(prefix+"currentPX0",currentPX0+"");
properties.setProperty(prefix+"currentPY0",currentPY0+"");
properties.setProperty(prefix+"sagittalMaster",sagittalMaster+"");
properties.setProperty(prefix+"parallelOnly",parallelOnly+"");
for (int chn=0; chn<minMeas.length; chn++) properties.setProperty(prefix+"minMeas_"+chn,minMeas[chn]+"");
for (int chn=0; chn<maxMeas.length; chn++) properties.setProperty(prefix+"maxMeas_"+chn,maxMeas[chn]+"");
for (int chn=0; chn<thresholdMax.length; chn++) properties.setProperty(prefix+"thresholdMax_"+chn,thresholdMax[chn]+"");
......@@ -190,6 +189,7 @@ public class FocusingField {
properties.setProperty(prefix+"qb_scan_step",qb_scan_step+"");
properties.setProperty(prefix+"qb_use_corrected",qb_use_corrected+"");
properties.setProperty(prefix+"qb_invert",qb_invert+"");
properties.setProperty(prefix+"z_relative",z_relative+"");
properties.setProperty(prefix+"rslt_show_z_axial",rslt_show_z_axial+"");
properties.setProperty(prefix+"rslt_show_z_individual",rslt_show_z_individual+"");
properties.setProperty(prefix+"rslt_show_f_axial",rslt_show_f_axial+"");
......@@ -204,7 +204,7 @@ public class FocusingField {
public void getProperties(String prefix,Properties properties){
savedProperties=properties;
propertiesPrefix=prefix;
System.out.println("FocusingField: getProperties()");
if (debugLevel>1) System.out.println("FocusingField: getProperties()");
if (fieldFitting == null) {
System.out.println("fieldFitting is not initialized, will apply properties later");
return; //fieldFitting=new FieldFitting();
......@@ -219,7 +219,10 @@ public class FocusingField {
currentPX0=Double.parseDouble(properties.getProperty(prefix+"currentPX0"));
if (properties.getProperty(prefix+"currentPY0")!=null)
currentPY0=Double.parseDouble(properties.getProperty(prefix+"currentPY0"));
if (properties.getProperty(prefix+"sagittalMaster")!=null)
sagittalMaster=Boolean.parseBoolean(properties.getProperty(prefix+"sagittalMaster"));
if (properties.getProperty(prefix+"parallelOnly")!=null)
parallelOnly=Boolean.parseBoolean(properties.getProperty(prefix+"parallelOnly"));
for (int chn=0; chn<minMeas.length; chn++) if (properties.getProperty(prefix+"minMeas_"+chn)!=null)
minMeas[chn]=Double.parseDouble(properties.getProperty(prefix+"minMeas_"+chn));
for (int chn=0; chn<maxMeas.length; chn++) if (properties.getProperty(prefix+"maxMeas_"+chn)!=null)
......@@ -250,6 +253,8 @@ public class FocusingField {
qb_use_corrected=Boolean.parseBoolean(properties.getProperty(prefix+"qb_use_corrected"));
if (properties.getProperty(prefix+"qb_invert")!=null)
qb_invert=Boolean.parseBoolean(properties.getProperty(prefix+"qb_invert"));
if (properties.getProperty(prefix+"z_relative")!=null)
z_relative=Boolean.parseBoolean(properties.getProperty(prefix+"z_relative"));
if (properties.getProperty(prefix+"rslt_show_z_axial")!=null)
rslt_show_z_axial=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_z_axial"));
if (properties.getProperty(prefix+"rslt_show_z_individual")!=null)
......@@ -357,10 +362,12 @@ public boolean configureDataVector(String title, boolean forcenew){
if (tmpFieldFitting==null) tmpFieldFitting= new FieldFitting(); // just to get field description
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("Only use measurements acquired during parallel moves (false - use all)",parallelOnly);
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
for (int i=0;i<minMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");
}
......@@ -392,6 +399,7 @@ public boolean configureDataVector(String title, boolean forcenew){
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
parallelOnly=gd.getNextBoolean();
sagittalMaster= gd.getNextBoolean();
for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
useMinMeas= gd.getNextBoolean();
......@@ -418,7 +426,7 @@ public boolean configureDataVector(String title, boolean forcenew){
numCurvPars[0],
numCurvPars[1]);
if (savedProperties!=null){
System.out.println("configureDataVector(): Applying properties");
if (debugLevel>1) System.out.println("configureDataVector(): Applying properties");
getProperties(propertiesPrefix,savedProperties);
}
}
......@@ -437,17 +445,49 @@ public boolean configureDataVector(String title, boolean forcenew){
}
private int [] getParallelDiff(MeasuredSample [] vector){
HashMap<Point,AtomicInteger> map=new HashMap<Point,AtomicInteger>();
for (MeasuredSample ms:vector) {
Point diff=new Point (ms.motors[1]-ms.motors[0],ms.motors[2]-ms.motors[0]);
if (map.containsKey(diff)) map.get(diff).incrementAndGet();
else map.put(diff, new AtomicInteger(1));
}
Point parallelDiff=new Point(0,0);
int maxRun=0;
for (Point diff:map.keySet()){
if (map.get(diff).get()>maxRun){
maxRun=map.get(diff).get();
parallelDiff=diff;
}
}
if (debugLevel>1) System.out.println("getParallelDiff(): maximal number of parallel measurements is "+
maxRun+", for M2-M1="+parallelDiff.x+", M3-M2="+parallelDiff.y);
int [] result= {parallelDiff.x,parallelDiff.y};
return result;
}
// includes deselected channels
public void setDataVector(MeasuredSample [] vector){ // remove unused channels if any
if (debugLevel>1) System.out.println("+++++ (Re)calculating sample weights +++++");
int [] diffs=null;
if (parallelOnly) diffs=getParallelDiff(vector);
boolean [] chanSel=fieldFitting.getSelectedChannels();
int numSamples=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) numSamples++;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]){
if ((diffs!=null) && (
((vector[i].motors[1]-vector[i].motors[0]) != diffs[0]) ||
((vector[i].motors[2]-vector[i].motors[0]) != diffs[1]))) continue;
numSamples++;
}
dataVector=new MeasuredSample [numSamples];
int n=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) dataVector[n++]=vector[i];
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) {
if ((diffs!=null) && (
((vector[i].motors[1]-vector[i].motors[0]) != diffs[0]) ||
((vector[i].motors[2]-vector[i].motors[0]) != diffs[1]))) continue;
dataVector[n++]=vector[i];
}
int corrLength=fieldFitting.getNumberOfCorrParameters();
dataValues = new double [dataVector.length+corrLength];
dataWeights = new double [dataVector.length+corrLength];
......@@ -811,7 +851,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
// convert to microns from pixels
weightReference[c]*=getPixelUM();
System.out.println("==== weightReference["+c+"]="+weightReference[c]);
if (debugLevel>1) System.out.println("==== weightReference["+c+"]="+weightReference[c]);
}
} else {
thresholdMax=null;
......@@ -994,7 +1034,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
nMeas++;
}
if (debugLevel>3) System.out.println();
if (debugLevel>0) System.out.println("createDataVector -> "+sampleList.size()+" elements");
if (debugLevel>1) System.out.println("createDataVector -> "+sampleList.size()+" elements");
return sampleList.toArray(new MeasuredSample[0]);
}
/**
......@@ -1149,17 +1189,17 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
// if ((this.currentfX==null)|| ((this.jacobian==null) && !this.threadedLMA )) {
if ((this.currentfX==null)|| (this.lMAArrays==null)) {
if (debugLevel>1) {
System.out.println(": initial Jacobian matrix calculation. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length);
}
String msg="initial Jacobian matrix calculation. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
if (debugLevel>1) System.out.println(msg);
if (this.updateStatus) IJ.showStatus(msg);
this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)
this.lMAArrays=calculateJacobianArrays(this.currentfX);
this.currentRMS= calcErrorDiffY(this.currentfX,false);
this.currentRMSPure=calcErrorDiffY(this.currentfX, true);
if (debugLevel>1) {
System.out.println(": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS="+IJ.d2s(this.currentRMSPure,8)+")"+
". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length);
}
msg=": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS"+IJ.d2s(this.currentRMSPure,8)+")"+
". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
if (debugLevel>1) System.out.println(msg);
if (this.updateStatus) IJ.showStatus(msg);
} else {
// continuing, but need to re-build Y vector to match this.currentVector
commitParameterVector(this.currentVector); // may be extra job?
......@@ -1191,6 +1231,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
for (int i=0;i<this.nextVector.length;i++) this.nextVector[i]+=deltas[i];
// another option - do not calculate J now, just fX. and late - calculate both if it was improvement
// save current Jacobian
if (debugLevel>2) {
System.out.println("this.nextVector");
for (int i=0;i<this.nextVector.length;i++){
......@@ -1207,13 +1248,13 @@ this.nextRMS= calcErrorDiffY(this.nextfX,false);
this.nextRMSPure= calcErrorDiffY(this.nextfX,true);
this.lastImprovements[1]=this.lastImprovements[0];
this.lastImprovements[0]=this.currentRMS-this.nextRMS;
if (debugLevel>2) {
System.out.println("stepLMA this.currentRMS="+this.currentRMS+
", this.currentRMSPure="+this.currentRMSPure+
", this.nextRMS="+this.nextRMS+
", this.nextRMSPure="+this.nextRMSPure+
", delta="+(this.currentRMS-this.nextRMS));
}
String msg="currentRMS="+this.currentRMS+
", currentRMSPure="+this.currentRMSPure+
", nextRMS="+this.nextRMS+
", nextRMSPure="+this.nextRMSPure+
", delta="+(this.currentRMS-this.nextRMS);
if (debugLevel>2) System.out.println("stepLMA "+msg);
if (this.updateStatus) IJ.showStatus(msg);
boolean [] status={matrixNonSingular && (this.nextRMS<=this.currentRMS),!matrixNonSingular};
// additional test if "worse" but the difference is too small, it was be caused by computation error, like here:
//stepLevenbergMarquardtAction() step=27, this.currentRMS=0.17068403807026408, this.nextRMS=0.1706840380702647
......@@ -1258,26 +1299,25 @@ this.nextRMSPure= calcErrorDiffY(this.nextfX,true);
}
public void stepLevenbergMarquardtAction(int debugLevel){//
this.iterationStepNumber++;
// apply/revert,modify lambda
if (debugLevel>1) {
System.out.println(
"stepLevenbergMarquardtAction() step="+this.iterationStepNumber+
", this.currentRMS="+this.currentRMS+
", this.currentRMSPure="+this.currentRMSPure+
", this.nextRMS="+this.nextRMS+
", this.nextRMSPure="+this.nextRMSPure+
" lambda="+this.lambda); //+" at "+IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec");
}
if (this.nextRMS<this.currentRMS) { //improved
this.lambda*=this.lambdaStepDown;
this.currentRMS=this.nextRMS;
this.currentfX=this.nextfX;
this.currentVector=this.nextVector;
} else {
this.lambda*=this.lambdaStepUp;
this.lMAArrays=this.savedLMAArrays; // restore Jt*J and Jt*diff
}
this.iterationStepNumber++;
// apply/revert,modify lambda
String msg="currentRMS="+this.currentRMS+
", currentRMSPure="+this.currentRMSPure+
", nextRMS="+this.nextRMS+
", nextRMSPure="+this.nextRMSPure+
", delta="+(this.currentRMS-this.nextRMS)+
", lambda="+this.lambda;
if (debugLevel>1) System.out.println("stepLevenbergMarquardtAction() "+msg);
// if (this.updateStatus) IJ.showStatus(msg);
if (this.nextRMS<this.currentRMS) { //improved
this.lambda*=this.lambdaStepDown;
this.currentRMS=this.nextRMS;
this.currentfX=this.nextfX;
this.currentVector=this.nextVector;
} else {
this.lambda*=this.lambdaStepUp;
this.lMAArrays=this.savedLMAArrays; // restore Jt*J and Jt*diff
}
}
/**
......@@ -1670,6 +1710,8 @@ public void listCombinedResults(){
gd.addCheckbox("Show constant-z sections (axial model)", this.rslt_show_f_axial);
gd.addCheckbox("Show constant-z sections (per-sample adjusted)", this.rslt_show_f_individual);
gd.addCheckbox("Show mtf50 (false - PSF FWHM)", this.rslt_mtf50_mode);
gd.addCheckbox("Show focal distance relative to center green (false - motor absolute)", this.z_relative);
gd.addMessage("Multiple section setup:");
gd.addNumericField("Scan from (relative to green center)", this.rslt_scan_below, 3,7,"um");
gd.addNumericField("Scan to (relative to green center)", this.rslt_scan_above, 3,7,"um");
......@@ -1687,114 +1729,118 @@ public void listCombinedResults(){
this.rslt_show_f_axial= gd.getNextBoolean();
this.rslt_show_f_individual= gd.getNextBoolean();
this.rslt_mtf50_mode= gd.getNextBoolean();
this.rslt_scan_below= gd.getNextNumber();
this.rslt_scan_above= gd.getNextNumber();
this.rslt_scan_step= gd.getNextNumber();
listCombinedResults(
"Field curvature measuremnts results", //String title,
null, //String path,
rslt_show_chn, //boolean [] show_chn,
rslt_show_z_axial, //boolean show_z_axial,
rslt_show_z_individual, //boolean show_z_individual,
rslt_show_f_axial, //boolean show_f_axial,
rslt_show_f_individual, //boolean show_f_individual,
center_z[1]+rslt_scan_below, // double scan_below,
center_z[1]+rslt_scan_above, //double scan_above,
rslt_scan_step, //double scan_step,
rslt_mtf50_mode); //boolean freq_mode)
this.z_relative= gd.getNextBoolean();
this.rslt_scan_below= gd.getNextNumber();
this.rslt_scan_above= gd.getNextNumber();
this.rslt_scan_step= gd.getNextNumber();
listCombinedResults(
"Field curvature measuremnts results", //String title,
null, //String path,
z_relative?center_z[1]:0.0,
rslt_show_chn, //boolean [] show_chn,
rslt_show_z_axial, //boolean show_z_axial,
rslt_show_z_individual, //boolean show_z_individual,
rslt_show_f_axial, //boolean show_f_axial,
rslt_show_f_individual, //boolean show_f_individual,
center_z[1]+rslt_scan_below, // double scan_below,
center_z[1]+rslt_scan_above, //double scan_above,
rslt_scan_step, //double scan_step,
rslt_mtf50_mode); //boolean freq_mode)
}
public void listCombinedResults(
String title,
String path,
boolean [] show_chn,
boolean show_z_axial,
boolean show_z_individual,
boolean show_f_axial,
boolean show_f_individual,
double scan_below,
double scan_above,
double scan_step,
boolean freq_mode){
String [] chnNames={"RS","RT","GS","GT","BS","BT"};
double k=this.fwhm_to_mtf50; //TODO: correct psf fwhm to mtf50 conversion
// double k=2*Math.log(2.0)/Math.PI*1000;
// String header="Z(um)\tComposite\tRed\tGreen\tBlue";
String header="radius(mm)";
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i];
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i]+"*";
}
}
int numSect=0;
if (show_f_axial || show_f_individual) for (double z=scan_below;z<=scan_above;z+=scan_step){
if (show_f_axial) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1);
}
}
if (show_f_individual) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1)+"*";
}
}
numSect++;
}
double [] radiuses=fieldFitting.getSampleRadiuses();
double [][][][] f_values=new double [numSect][2][][];
double [][][] z_values={
(show_z_axial?fieldFitting.getCalcZ(false,true):null),
(show_z_individual?fieldFitting.getCalcZ(true,true):null)};
int sect=0;
for (double z=scan_below;z<=scan_above;z+=scan_step){
f_values[sect][0]=show_f_axial?fieldFitting.getCalcValuesForZ(z, false,true):null;
f_values[sect][1]=show_f_individual?fieldFitting.getCalcValuesForZ(z, true,true):null;
sect++;
}
StringBuffer sb = new StringBuffer();
for (int n=0;n<radiuses.length;n++){
sb.append(IJ.d2s(radiuses[n],3));
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[0][i][n],3));
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[1][i][n],3));
}
}
if (show_f_axial || show_f_individual) for (int s=0;s<numSect;s++){
if (show_f_axial) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][0][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][0][i][n],3));
}
}
if (show_f_individual) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][1][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][1][i][n],3));
}
}
}
sb.append("\n");
}
if (path!=null) {
CalibrationFileManagement.saveStringToFile (
path,
header+"\n"+sb.toString());
} else {
new TextWindow(title, header, sb.toString(), 800,1000);
}
String title,
String path,
double z0, // subtract from z
boolean [] show_chn,
boolean show_z_axial,
boolean show_z_individual,
boolean show_f_axial,
boolean show_f_individual,
double scan_below,
double scan_above,
double scan_step,
boolean freq_mode){
String [] chnNames={"RS","RT","GS","GT","BS","BT"};
double k=this.fwhm_to_mtf50; //TODO: correct psf fwhm to mtf50 conversion
// double k=2*Math.log(2.0)/Math.PI*1000;
// String header="Z(um)\tComposite\tRed\tGreen\tBlue";
String header="radius(mm)";
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i];
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i]+"*";
}
}
int numSect=0;
if (show_f_axial || show_f_individual) for (double z=scan_below;z<=scan_above;z+=scan_step){
if (show_f_axial) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1);
}
}
if (show_f_individual) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1)+"*";
}
}
numSect++;
}
double [] radiuses=fieldFitting.getSampleRadiuses();
double [][][][] f_values=new double [numSect][2][][];
double [][][] z_values={
(show_z_axial?fieldFitting.getCalcZ(false,true):null),
(show_z_individual?fieldFitting.getCalcZ(true,true):null)};
int sect=0;
for (double z=scan_below;z<=scan_above;z+=scan_step){
f_values[sect][0]=show_f_axial?fieldFitting.getCalcValuesForZ(z, false,true):null;
f_values[sect][1]=show_f_individual?fieldFitting.getCalcValuesForZ(z, true,true):null;
sect++;
}
StringBuffer sb = new StringBuffer();
for (int n=0;n<radiuses.length;n++){
sb.append(IJ.d2s(radiuses[n],3));
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[0][i][n]-z0,3));
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[1][i][n]-z0,3));
}
}
if (show_f_axial || show_f_individual) for (int s=0;s<numSect;s++){
if (show_f_axial) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][0][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][0][i][n],3));
}
}
if (show_f_individual) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][1][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][1][i][n],3));
}
}
}
sb.append("\n");
}
if (path!=null) {
CalibrationFileManagement.saveStringToFile (
path,
header+"\n"+sb.toString());
} else {
new TextWindow(title, header, sb.toString(), 800,1000);
}
}
......@@ -1821,7 +1867,9 @@ public void listScanQB(){
gd.addNumericField("Relative (to green) weight of red channel",100* this.k_red, 3,7,"%");
gd.addNumericField("Relative (to green) weight of blue channel",100* this.k_blue, 3,7,"%");
gd.addCheckbox("Use per-sample location corrected data", this.qb_use_corrected);
gd.addCheckbox("Use per-sample location corrected data", this.qb_invert);
gd.addCheckbox("Show mtf50 (false - PSF FWHM)", this.qb_invert);
gd.addCheckbox("Show focal distance relative to center green (false - motor absolute)", this.z_relative);
gd.showDialog();
if (gd.wasCanceled()) {
return;
......@@ -1833,10 +1881,13 @@ public void listScanQB(){
this.k_blue= 0.01*gd.getNextNumber();
this.qb_use_corrected= gd.getNextBoolean();
this.qb_invert= gd.getNextBoolean();
this.z_relative= gd.getNextBoolean();
listScanQB(
"Focus quality vs. distance", // String title,
null, //String path,
z_relative?center_z[1]:0.0,
center_z[1]+this.qb_scan_below, //double min_z, // absolute
center_z[1]+this.qb_scan_above, //double max_z,
this.qb_scan_step , //double step_z,
......@@ -1849,6 +1900,7 @@ public void listScanQB(){
public void listScanQB(
String title,
String path,
double z0,
double min_z, // absolute
double max_z,
double step_z,
......@@ -1869,9 +1921,9 @@ public void listScanQB(
z,
corrected);
if (freq_mode){
sb.append(z+"\t"+IJ.d2s(k/qb_w,3)+"\t"+IJ.d2s(k/qb_rgb[0],3)+"\t"+IJ.d2s(k/qb_rgb[1],3)+"\t"+IJ.d2s(k/qb_rgb[2],3) +"\n");
sb.append(IJ.d2s(z-z0,3)+"\t"+IJ.d2s(k/qb_w,3)+"\t"+IJ.d2s(k/qb_rgb[0],3)+"\t"+IJ.d2s(k/qb_rgb[1],3)+"\t"+IJ.d2s(k/qb_rgb[2],3) +"\n");
} else {
sb.append(z+"\t"+IJ.d2s(qb_w,3)+"\t"+IJ.d2s(qb_rgb[0],3)+"\t"+IJ.d2s(qb_rgb[1],3)+"\t"+IJ.d2s(qb_rgb[2],3) +"\n");
sb.append(IJ.d2s(z-z0,3)+"\t"+IJ.d2s(qb_w,3)+"\t"+IJ.d2s(qb_rgb[0],3)+"\t"+IJ.d2s(qb_rgb[1],3)+"\t"+IJ.d2s(qb_rgb[2],3) +"\n");
}
}
......@@ -2015,17 +2067,14 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
// if (this.showNextImages) showDiff (this.nextfX, "fit-"+(this.iterationStepNumber+1));
}
stepLevenbergMarquardtAction(debugLevel); // apply step - in any case?
/*
if (this.updateStatus){
IJ.showStatus(this.seriesNumber+": "+"Step #"+this.iterationStepNumber+
IJ.showStatus("Step #"+this.iterationStepNumber+
" RMS="+IJ.d2s(this.currentRMS,8)+
" ("+IJ.d2s(this.firstRMS,8)+")"+
" RMSPure="+IJ.d2s(this.currentRMSPure,8)+
" ("+IJ.d2s(this.firstRMSPure,8)+")"+
" ");
// showStatus(this.seriesNumber+": "+"Step #"+this.iterationStepNumber+" RMS="+IJ.d2s(this.currentRMS,8)+ " ("+IJ.d2s(this.firstRMS,8)+")",0);
}
*/
if (!cont){
if (this.saveSeries) {
savedLambda=this.lambda;
......@@ -2058,23 +2107,23 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
// 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();
commitParameterVector(this.savedVector);
return true; // all series done
}
String msg="RMS="+this.currentRMS+" ("+this.firstRMS+") "+
", pure RMS="+this.currentRMSPure+" ("+this.firstRMSPure+") "+
" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3);
if (debugLevel>0) System.out.println("stepLevenbergMarquardtAction() "+msg);
// if (this.updateStatus) IJ.showStatus(msg);
if (this.updateStatus){
IJ.showStatus("Done: Step #"+this.iterationStepNumber+
" RMS="+IJ.d2s(this.currentRMS,8)+
" ("+IJ.d2s(this.firstRMS,8)+")"+
" RMSPure="+IJ.d2s(this.currentRMSPure,8)+
" ("+IJ.d2s(this.firstRMSPure,8)+")"+
" ");
}
this.savedVector=this.currentVector.clone();
commitParameterVector(this.savedVector);
return true; // all series done
}
public class FocusingFieldMeasurement{
public String timestamp;
......@@ -2348,7 +2397,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
public void setProperties(String prefix,Properties properties){
if (mechanicalFocusingModel==null){
System.out.println ("Mechanical properties not yet initialized, will save properties later");
if (debugLevel>1) System.out.println ("Mechanical properties not yet initialized, will save properties later");
return;
}
properties.setProperty(prefix+"numberOfLocations",numberOfLocations+"");
......@@ -2400,7 +2449,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
if (properties.getProperty(prefix+"centerSelect_Y")!=null)
centerSelect[1]=Boolean.parseBoolean(properties.getProperty(prefix+"centerSelect_Y"));
if (mechanicalFocusingModel==null){
System.out.println ("Mechanical properties not yet initialized, will apply properties later");
if (debugLevel>1) System.out.println ("Mechanical properties not yet initialized, will apply properties later");
return;
}
mechanicalFocusingModel.getProperties(prefix+"mechanicalFocusingModel.",properties);
......@@ -2500,13 +2549,19 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
for (int np=0;np<numPars;np++) for (int i=0;i<numberOfLocations;i++)
correctionParameters[chn][np][i]=0.0;
}
for (int np=0;np<numPars;np++) for (int i=0;i<numberOfLocations;i++)
if (properties.getProperty(prefix+"correctionParameters_"+chn+"_"+np+"_"+i)!=null) {
correctionParameters[chn][np][i]=Double.parseDouble(properties.getProperty(prefix+"correctionParameters_"+chn+"_"+np+"_"+i));
for (int np=0;np<numPars;np++) {
if ((correctionParameters[chn][np]==null) || (correctionParameters[chn][np].length!=numberOfLocations)){
correctionParameters[chn][np]=new double [numberOfLocations];
for (int i=0;i<numberOfLocations;i++) correctionParameters[chn][np][i]=0.0;
}
for (int i=0;i<numberOfLocations;i++)
if (properties.getProperty(prefix+"correctionParameters_"+chn+"_"+np+"_"+i)!=null) {
correctionParameters[chn][np][i]=Double.parseDouble(properties.getProperty(prefix+"correctionParameters_"+chn+"_"+np+"_"+i));
}
}
}
} else {
System.out.println("numberOfLocations==0, can not restore");
if (debugLevel>1) System.out.println("numberOfLocations==0, can not restore");
}
......@@ -2533,7 +2588,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
if (numCorrPar==0){
String msg="No correction parameters are enabled";
IJ.showMessage(msg);
System.out.println(msg);
if (debugLevel>1) System.out.println(msg);
return;
}
double [][] pixels=new double [numCorrPar][numSamples];
......@@ -2861,7 +2916,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
}
}
System.out.println("getCorrVector 1");
if (debugLevel>1) System.out.println("getCorrVector 1");
sampleCorrVector=new double [numPars];
for (int nChn=0; nChn< sampleCorrChnParIndex.length;nChn++) {
if (sampleCorrChnParIndex[nChn]!=null){
......@@ -2873,7 +2928,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
else {
sampleCorrVector[sampleCorrChnParIndex[nChn][nPar]+i]=0.0;
if ((correctionParameters[nChn]!=null) && (correctionParameters[nChn][nPar]!=null) && (correctionParameters[nChn][nPar].length<i)){
System.out.println("correctionParameters["+nChn+"]["+nPar+"].length < "+i);
if (debugLevel>1) System.out.println("correctionParameters["+nChn+"]["+nPar+"].length < "+i);
}
}
}
......@@ -2885,7 +2940,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
public void commitCorrVector(){
System.out.println("commitCorrVector()");
if (debugLevel>1) System.out.println("commitCorrVector()");
commitCorrVector(sampleCorrVector);
}
......@@ -2897,7 +2952,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
if(correctionParameters[nChn]==null)
correctionParameters[nChn]=new double [sampleCorrChnParIndex[nChn].length][];
if ((correctionParameters[nChn][nPar]==null) || (correctionParameters[nChn][nPar].length!=numberOfLocations)){
System.out.println("commitCorrVector(): correctionParameters["+nChn+"]["+nPar+"].length < "+numberOfLocations);
if (debugLevel>1) System.out.println("commitCorrVector(): correctionParameters["+nChn+"]["+nPar+"].length < "+numberOfLocations);
correctionParameters[nChn][nPar]=new double [numberOfLocations];
}
......@@ -2975,7 +3030,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
// currently all correction parameters are initialized as zeros.
getCorrVector();
System.out.println("was resetting sampleCorrVector here");
if (debugLevel>1) System.out.println("was resetting sampleCorrVector here");
// sampleCorrVector=new double [numPars];
// for (int i=0;i<numPars;i++)sampleCorrVector[i]=0.0;
......@@ -3002,7 +3057,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double [] corr =new double [correctionParameters[chn].length];
for (int i=0;i<corr.length;i++){
if ((correctionParameters[chn][i] !=null) && (correctionParameters[chn][i].length<=i)){
System.out.println("getCorrPar(): correctionParameters["+chn+"]["+i+"].length="+correctionParameters[chn][i].length);
if (debugLevel>1) System.out.println("getCorrPar(): correctionParameters["+chn+"]["+i+"].length="+correctionParameters[chn][i].length);
}
if ((correctionParameters[chn][i] !=null) && (correctionParameters[chn][i].length>i)) corr[i]=correctionParameters[chn][i][sampleIndex];
else corr[i]=0.0;
......@@ -3213,7 +3268,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
} else {
if ((correctionParameters[n][np]!=null) && (correctionParameters[n][np].length!=numberOfLocations)){
System.out.println("getParameterValueStrings(): correctionParameters["+n+"]["+np+"].length="+correctionParameters[n][np].length);
if (debugLevel>1) System.out.println("getParameterValueStrings(): correctionParameters["+n+"]["+np+"].length="+correctionParameters[n][np].length);
}
}
}
......@@ -3357,7 +3412,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
index++;
}
}
System.out.println("createParameterVector(): using sampleCorrVector - do we need to create it first?");
if (debugLevel>1) System.out.println("createParameterVector(): using sampleCorrVector - do we need to create it first?");
getCorrVector(); // do we need that?
int nCorrPars=getNumberOfCorrParameters();
for (int i=0;i<nCorrPars;i++) pars[np++]=sampleCorrVector[i];
......@@ -3387,7 +3442,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
}
}
// copy correction parameters
System.out.println("commitParameterVector(): Creating and committing sampleCorrVector");
if (debugLevel>1) System.out.println("commitParameterVector(): Creating and committing sampleCorrVector");
int nCorrPars=getNumberOfCorrParameters();
for (int i=0;i<nCorrPars;i++) sampleCorrVector[i]=pars[np++];
commitCorrVector();
......@@ -3663,7 +3718,44 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
public Double getValue(MECH_PAR mech_par){
return paramValues[mech_par.ordinal()];
}
public double [] debugDeriv_ZdZ(
double scale,
int [] motors,
double px,
double py){
double [] derivSteps ={
0.001, // [0] K0 843.6001052876973
0.001, // [1] KD1 1600.0723700390713
0.001, // [2] KD3 -2428.8998947123027
0.1, // [3] sM1 -1.1720600074585734
0.1, // [4] cM1 0.6081060292866338
0.1, // [5] sM2 -2.3717384278673035
0.1, // [6] cM2 1.2305414643438266
0.1, // [7] sM3 2.7345656468251707
0.1, // [8] cM3 1.4187890097199358
1.0, // [9] Lx -0.535718420298317
1.0, // [10] Ly 0.0
10.0, // [11] mpX0 -2.816702366108815E-5
10.0, // [12] mpY0 -8.351458550253758E-5
1.0, // [13] z0 1.0
0.1, // [14] tx -2.5168000000000004
0.1 // [15] ty -1.76
};
double [] initialVector=paramValues.clone();
double [] derivs=new double [paramValues.length];
for (int i=0;i<derivs.length;i++){
paramValues[i]=initialVector[i]-scale*derivSteps[i];
double zm=calc_ZdZ(motors,px,py,null);
paramValues[i]=initialVector[i]+scale*derivSteps[i];
double zp=calc_ZdZ(motors,px,py,null);
paramValues[i]=initialVector[i];
derivs[i]=(zp-zm)/(2.0*scale*derivSteps[i]);
}
return derivs;
}
/**
* Calculate distance from the selected sensor pixel to the common "focal" plane
......@@ -3679,6 +3771,9 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double px,
double py,
double[] deriv){
double debugMot=6545;
int debugThreshold=1;
boolean dbg = (debugLevel>debugThreshold);
/*
kM3=K0+KD3
kM1=K0+KD1-KD3
......@@ -3713,13 +3808,24 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double zM2=kM2 * aM2;
double zM3=kM3 * aM3;
double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3;
double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
double dx=PIXEL_SIZE*(px-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
double zy=dy*(getValue(MECH_PAR.ty)+(zM1-zM2)/(2*getValue(MECH_PAR.Ly)));
// double zy=dy*(getValue(MECH_PAR.ty)+(zM1-zM2)/(2*getValue(MECH_PAR.Ly)));
double zy=dy*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));
double z=zc+zx+zy;
if (deriv==null) return z;
if (dbg) if ((Math.abs(m1)==debugMot)&& (Math.abs(m2)==debugMot)){
System.out.print ("M: "+((int)m1)+":"+((int)m2)+":"+((int)m3)+
" dxy="+IJ.d2s(dx,3)+":"+IJ.d2s(dy,3)+" zcxy="+IJ.d2s(zc,3)+":"+IJ.d2s(zx,3)+":"+IJ.d2s(zy,3)+
" zxy(t)="+IJ.d2s(dx*getValue(MECH_PAR.tx),3)+":"+IJ.d2s(dy*getValue(MECH_PAR.ty),3));
}
if (deriv==null) {
if (dbg) if ((Math.abs(m1)==debugMot)&& (Math.abs(m2)==debugMot)){
System.out.println();
}
return z;
}
for (int i=0;i<deriv.length;i++) deriv[i]=0.0;
// Above same as calc_Z
double dx_mpX0=-PIXEL_SIZE;
......@@ -3731,8 +3837,10 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double zM2_KD1=-aM2;
double zM2_KD3=-aM2;
double zM3_K0= aM3;
double zM3_KD1=-aM3;
double zM3_KD3= 0.0;
// double zM3_KD1=-aM3;
// double zM3_KD3= 0.0;
double zM3_KD1= 0.0;
double zM3_KD3= aM3;
double zM1_sM1= kM1*p2pi*Math.sin(m1/p2pi);
double zM1_cM1= kM1*p2pi*Math.cos(m1/p2pi);
double zM2_sM2= kM2*p2pi*Math.sin(m2/p2pi);
......@@ -3754,7 +3862,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double zx_a=dx/(4*getValue(MECH_PAR.Lx));
double zx_K0= (2*zM3_K0-zM1_K0-zM2_K0)*zx_a;
double zx_KD1=(2*zM3_KD1-zM1_KD1-zM2_KD1)*zx_a;
double zx_KD3=(2*zM3_K0-zM1_K0-zM2_K0)*zx_a;
double zx_KD3=(2*zM3_KD3-zM1_KD3-zM2_KD3)*zx_a;
double zx_sM1= (-zM1_sM1)*zx_a;
double zx_cM1= (-zM1_cM1)*zx_a;
double zx_sM2= (-zM2_sM2)*zx_a;
......@@ -3764,20 +3872,21 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
double zx_mpX0=dx_mpX0/(4*getValue(MECH_PAR.Lx));
double zx_tx= dx;
double zx_Lx= -dx*(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)*getValue(MECH_PAR.Lx));
double zy_a=dx/(2*getValue(MECH_PAR.Ly));
double zy_K0= (zM1_K0- zM2_K0) *zy_a;
double zy_KD1= (zM1_KD1-zM2_KD1)*zy_a;
double zy_KD3= (zM1_KD3-zM2_KD3)*zy_a;
double zy_sM1= (zM1_sM1)*zy_a;
double zy_cM1= (zM1_cM1)*zy_a;
double zy_sM2= (-zM2_sM2)*zy_a;
double zy_cM2= (-zM2_cM2)*zy_a;
// double zy=dy*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));
double zy_a=dy/(2*getValue(MECH_PAR.Ly));
double zy_K0= (zM2_K0- zM1_K0) *zy_a; // double zy_K0= (zM1_K0- zM2_K0) *zy_a;
double zy_KD1= (zM2_KD1-zM1_KD1)*zy_a; // double zy_KD1= (zM2_KD1-zM1_KD1)*zy_a;
double zy_KD3= (zM2_KD3-zM1_KD3)*zy_a; // double zy_KD3= (zM1_KD3-zM2_KD3)*zy_a;
double zy_sM1= (-zM1_sM1)*zy_a; // double zy_sM1= (zM1_sM1)*zy_a;
double zy_cM1= (-zM1_cM1)*zy_a; // double zy_cM1= (zM1_cM1)*zy_a;
double zy_sM2= (zM2_sM2)*zy_a; // double zy_sM2= (-zM2_sM2)*zy_a;
double zy_cM2= (zM2_cM2)*zy_a; // double zy_cM2= (-zM2_cM2)*zy_a;
double zy_sM3= 0.0;
double zy_cM3= 0.0;
double zy_mpY0=dy_mpY0/(2*getValue(MECH_PAR.Ly));
double zy_ty= dy;
double zy_Ly= -dy*(zM1-zM2)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly));
// double zy_Ly= -dy*(zM1-zM2)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly));
double zy_Ly= -dy*(zM2-zM1)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly));
deriv[getIndex(MECH_PAR.K0)]= zc_K0+zx_K0+zy_K0;
deriv[getIndex(MECH_PAR.KD1)]=zc_KD1+zx_KD1+zy_KD1;
......@@ -3792,8 +3901,25 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
deriv[getIndex(MECH_PAR.Ly)] = zy_Ly;
deriv[getIndex(MECH_PAR.mpX0)] = zx_mpX0;
deriv[getIndex(MECH_PAR.mpY0)] = zy_mpY0;
deriv[getIndex(MECH_PAR.z0)] = 1.0;
deriv[getIndex(MECH_PAR.tx)] = zx_tx;
deriv[getIndex(MECH_PAR.ty)] = zy_ty;
if (dbg) if ((Math.abs(m1)==debugMot)&& (Math.abs(m2)==debugMot)){
if (m1*m2>0){
System.out.println("same sign");
} else {
System.out.println("opposite sign");
}
System.out.println (" zxy_txy="+IJ.d2s(zx_tx,3)+":"+IJ.d2s(zy_ty,3)+" zxy_Lxy="+IJ.d2s(zx_Lx,5)+":"+IJ.d2s(zy_Ly,5));
double [] dbg_derivs= debugDeriv_ZdZ(
0.1, //scale,
motors,
px,
py);
for (int i=0;i<deriv.length;i++){
System.out.println(i+": "+descriptions[i][0]+" deriv="+deriv[i]+", dbg_derivs="+dbg_derivs[i]);
}
}
return z;
}
public boolean[] getDefaultMask(){
......
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