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Commit e4ac0da9 authored by Andrey Filippov's avatar Andrey Filippov
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more on adjustment

parent 2ed1f2f7
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Showing with 461 additions and 59 deletions
src/main/java/Aberration_Calibration.java
View file @ e4ac0da9
......@@ -4388,6 +4388,7 @@ if (MORE_BUTTONS) {
"",//); //String defaultPath); // AtomicInteger stopRequested
this.SYNC_COMMAND.stopRequested);
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
System.out.println("Loaded FocusingField");
if (!FOCUSING_FIELD.configureDataVector("Configure curvature - TODO: fix many settings restored from properties",true,true)) return;
......@@ -4415,6 +4416,7 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
if (!FOCUSING_FIELD.configureDataVector("Re-configure curvature parameters",false,true)) return;
FOCUSING_FIELD.setDataVector(
true, // calibrate mode
......@@ -4454,10 +4456,11 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.LevenbergMarquardt(
null, // measurement
true, // open dialog
false, // filterZ
// false, // filterZ
DEBUG_LEVEL); //boolean openDialog, int debugLevel){
return;
}
......@@ -9719,7 +9722,44 @@ if (MORE_BUTTONS) {
}
if (!allOK) break; // failed
}
if (focusMeasurementParameters.scanTiltReverse) {
if (debugLevel>0) System.out.println("Starting reverse scanning tilt in X direction, number of stops="+ focusMeasurementParameters.scanTiltStepsX+
", step size="+IJ.d2s(scanStepX,0));
for (int numStep=0;numStep<focusMeasurementParameters.scanTiltStepsX;numStep++){
int delta=(int) Math.round(focusMeasurementParameters.scanTiltRangeX*
(1.0*numStep/(focusMeasurementParameters.scanTiltStepsX-1) -0.5));
scanPos[0]=centerMotorPos[0]+delta;
scanPos[1]=centerMotorPos[1]+delta;
scanPos[2]=centerMotorPos[2]-delta;
if (debugLevel>0) System.out.println("Reverse scanning tilt in X direction, step#"+(numStep+1)+" (of "+
focusMeasurementParameters.scanTiltStepsX+") at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
allOK &=moveAndMaybeProbe(
true,
scanPos, // null OK
focusingMotors,
camerasInterface,
lensDistortionParameters,
matchSimulatedPattern, // should not bee null
focusMeasurementParameters,
patternDetectParameters,
distortionParameters,
simulParameters,
colorComponents,
otfFilterParameters,
psfParameters,
threadsMax,
updateStatus,
debugLevel,
loopDebugLevel);
if (this.SYNC_COMMAND.stopRequested.get()>0){
aborted=true;
allOK=false;
System.out.println("Stop requested, command aborted, returning motors to initial position");
break;
}
if (!allOK) break; // failed
}
}
}
if (allOK && (focusMeasurementParameters.scanTiltStepsY >1 )) { // 0 or 1 STOPS - do not scan
double scanStepY=1.0*focusMeasurementParameters.scanTiltRangeY/(focusMeasurementParameters.scanTiltStepsY-1);
......@@ -9759,9 +9799,45 @@ if (MORE_BUTTONS) {
}
if (!allOK) break; // failed
}
if (focusMeasurementParameters.scanTiltReverse) {
if (debugLevel>0) System.out.println("Starting reverse scanning tilt in Y direction, number of stops="+ focusMeasurementParameters.scanTiltStepsY+
", step size="+IJ.d2s(scanStepY,0));
for (int numStep=0;numStep<focusMeasurementParameters.scanTiltStepsY;numStep++){
int delta=(int) Math.round(focusMeasurementParameters.scanTiltRangeY*
(1.0*numStep/(focusMeasurementParameters.scanTiltStepsY-1) -0.5));
scanPos[0]=centerMotorPos[0]+delta;
scanPos[1]=centerMotorPos[1]-delta;
scanPos[2]=centerMotorPos[2]+0;
if (debugLevel>0) System.out.println("Reverse scanning tilt in Y direction, step#"+(numStep+1)+" (of "+
focusMeasurementParameters.scanTiltStepsY+") at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
allOK &=moveAndMaybeProbe(
true,
scanPos, // null OK
focusingMotors,
camerasInterface,
lensDistortionParameters,
matchSimulatedPattern, // should not bee null
focusMeasurementParameters,
patternDetectParameters,
distortionParameters,
simulParameters,
colorComponents,
otfFilterParameters,
psfParameters,
threadsMax,
updateStatus,
debugLevel,
loopDebugLevel);
if (this.SYNC_COMMAND.stopRequested.get()>0){
aborted=true;
allOK=false;
System.out.println("Stop requested, command aborted, returning motors to initial position");
break;
}
if (!allOK) break; // failed
}
}
}
}
if (allOK && focusMeasurementParameters.scanHysteresis && (scanPosLast!=null)){
......
src/main/java/FocusingField.java
View file @ e4ac0da9
......@@ -80,7 +80,15 @@ public class FocusingField {
int filterInputConcaveMinSeries;
double filterInputConcaveScale;
boolean filterZ; // (adjustment mode)filter samples by Z
double filterByValueScale;
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
double zMin;
double zMax;
double zStep;
double tMin;
double tMax;
double tStep;
double targetRelFocalShift; // target focal shift relative to best composite "sharpness"
// when false - tangential is master
......@@ -216,7 +224,16 @@ public class FocusingField {
filterInputConcaveMinSeries=5;
filterInputConcaveScale=0.9;
filterZ=true; // (adjustment mode)filter samples by Z
filterByValueScale=1.5; // (adjustment mode)filter samples by value - remove higher than scaled best FWHM
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
zMin=-40.0;
zMax= 40.0;
zStep=2.0;
tMin=-15.0;
tMax= 15.0;
tStep=1.0;
targetRelFocalShift=8.0; // target focal shift relative to best composite "sharpness"
// when false - tangential is master
double [] minMeasDflt= {0.5,0.5,0.5,0.5,0.5,0.5}; // pixels
......@@ -325,7 +342,17 @@ public class FocusingField {
properties.setProperty(prefix+"filterInputConcaveMinSeries",filterInputConcaveMinSeries+"");
properties.setProperty(prefix+"filterInputConcaveScale",filterInputConcaveScale+"");
properties.setProperty(prefix+"filterZ",filterZ+"");
properties.setProperty(prefix+"filterByValueScale",filterByValueScale+"");
properties.setProperty(prefix+"minLeftSamples",minLeftSamples+"");
properties.setProperty(prefix+"zMin",zMin+"");
properties.setProperty(prefix+"zMax",zMax+"");
properties.setProperty(prefix+"zStep",zStep+"");
properties.setProperty(prefix+"tMin",tMin+"");
properties.setProperty(prefix+"tMax",tMax+"");
properties.setProperty(prefix+"tStep",tStep+"");
properties.setProperty(prefix+"targetRelFocalShift",targetRelFocalShift+"");
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]+"");
......@@ -415,14 +442,26 @@ public class FocusingField {
filterInputConcaveMinSeries=Integer.parseInt(properties.getProperty(prefix+"filterInputConcaveMinSeries"));
if (properties.getProperty(prefix+"filterInputConcaveScale")!=null)
filterInputConcaveScale=Double.parseDouble(properties.getProperty(prefix+"filterInputConcaveScale"));
if (properties.getProperty(prefix+"filterZ")!=null)
filterZ=Boolean.parseBoolean(properties.getProperty(prefix+"filterZ"));
if (properties.getProperty(prefix+"filterByValueScale")!=null)
filterByValueScale=Double.parseDouble(properties.getProperty(prefix+"filterByValueScale"));
if (properties.getProperty(prefix+"minLeftSamples")!=null)
minLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minLeftSamples"));
if (properties.getProperty(prefix+"zMin")!=null)
zMin=Double.parseDouble(properties.getProperty(prefix+"zMin"));
if (properties.getProperty(prefix+"zMax")!=null)
zMax=Double.parseDouble(properties.getProperty(prefix+"zMax"));
if (properties.getProperty(prefix+"zStep")!=null)
zStep=Double.parseDouble(properties.getProperty(prefix+"zStep"));
if (properties.getProperty(prefix+"tMin")!=null)
tMin=Double.parseDouble(properties.getProperty(prefix+"tMin"));
if (properties.getProperty(prefix+"tMax")!=null)
tMax=Double.parseDouble(properties.getProperty(prefix+"tMax"));
if (properties.getProperty(prefix+"tStep")!=null)
tStep=Double.parseDouble(properties.getProperty(prefix+"tStep"));
if (properties.getProperty(prefix+"targetRelFocalShift")!=null)
targetRelFocalShift=Double.parseDouble(properties.getProperty(prefix+"targetRelFocalShift"));
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)
......@@ -505,6 +544,12 @@ public class FocusingField {
public void setDebugLevel(int debugLevel){
this.debugLevel=debugLevel;
}
public void setAdjustMode(boolean mode){
if ((fieldFitting!=null) && (fieldFitting.mechanicalFocusingModel!=null)) {
fieldFitting.mechanicalFocusingModel.setAdjustMode(mode);
}
}
public class LMAArrays { // reuse from Distortions?
public double [][] jTByJ= null; // jacobian multiplied by Jacobian transposed
public double [] jTByDiff=null; // jacobian multiplied difference vector
......@@ -718,6 +763,11 @@ private boolean [] dataWeightsToBoolean(){
return enable;
}
public int numEnabled(boolean [] en){
int num=0;
if (en!=null) for (boolean e:en) if (e) num++;
return num;
}
private void maskDataWeights(boolean [] enable){
for (int i=0;i<enable.length;i++){
if (!enable[i]) dataWeights[i]=0.0;
......@@ -793,6 +843,33 @@ private boolean [] filterByZRanges (
if (debugLevel>1) System.out.println("filterByZRanges(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
return enable_out;
}
private boolean [] filterByValue (
double scale, // scale to best FWHM - larger are ignored
boolean [] enable_in){
boolean [] enable_out=enable_in.clone();
double [][] fwhm = fieldFitting.getFWHM(
true, // boolean corrected,
true //boolean allChannels
);
int numFiltered=0;
int numLeft=0;
if (scale>0.0) {
for (int index=0;index<dataVector.length;index++) if ((index>=enable_in.length) || enable_in[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
if (dataVector[index].value > scale*fwhm[chn][sample]){
enable_out[index]=false;
numFiltered++;
} else {
numLeft++;
}
}
}
if (debugLevel>0) System.out.println("filterByValue(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
return enable_out;
}
private int getNumEnabledSamples(
boolean [] enable){
int num_en=0;
......@@ -3209,10 +3286,11 @@ public boolean dialogLMAStep(boolean [] state){
public double getAdjustRMS(
FocusingFieldMeasurement measurement,
boolean filterZ,
double filterByValueScale,
double z,
double tx,
double ty){
fieldFitting.selectZTilt();
fieldFitting.selectZTilt(false);
fieldFitting.mechanicalFocusingModel.setZTxTy(z,tx,ty);
double [] sv= fieldFitting.createParameterVector(sagittalMaster);
setDataVector(
......@@ -3228,37 +3306,60 @@ public double getAdjustRMS(
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return Double.NaN;
}
if (filterByValueScale>0.0){
boolean [] en=dataWeightsToBoolean();
en= filterByValue(
filterByValueScale,
en);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return Double.NaN;
}
double [] focusing_fx= createFXandJacobian(sv, false);
double rms_pure= calcErrorDiffY(focusing_fx, true);
// System.out.println("rms_pure="+rms_pure);
return rms_pure;
}
public double findAdjustZ(
public double [] findAdjustZ(
FocusingFieldMeasurement measurement,
boolean filterZ,
double filterByValueScale,
double zMin,
double zMax,
double zStep,
double tx,
double ty){
double tMin,
double tMax,
double tStep){
double zBest=Double.NaN;
double tXBest=Double.NaN;
double tYBest=Double.NaN;
double bestRMS=Double.NaN;
for (double z=zMin;z<=zMax;z+=zStep){
int bestEn=0;
for (double z=zMin;z<=zMax;z+=zStep) for (double tx=tMin;tx<=tMax;tx+=tStep) for (double ty=tMin;ty<=tMax;ty+=tStep){
double rms=getAdjustRMS(
measurement,
filterZ,
filterByValueScale,
z,
tx,
ty);
if (((Double.isNaN(bestRMS) || (bestRMS>=rms)) && !Double.isNaN(rms) && (rms>0.0))){
zBest=z;
tXBest=tx;
tYBest=ty;
bestRMS=rms;
bestEn=numEnabled(dataWeightsToBoolean());
}
if (debugLevel>1) {
int numEn=numEnabled(dataWeightsToBoolean());
System.out.println("findAdjustZ(): z="+z+" tx="+tx+" ty="+ty+" rms="+rms+" used "+numEn+" samples");
}
if (debugLevel>1) System.out.println("findAdjustZ(): z="+z+" rms="+rms);
}
if (debugLevel>0) System.out.println("findAdjustZ()->"+zBest+" (best RMS = "+bestRMS+")");
return zBest;
if (debugLevel>0) System.out.println("findAdjustZ()-> z="+zBest+" tx="+tXBest+" ty="+tYBest+" (best RMS = "+bestRMS+" used "+bestEn+" samples)");
double [] result={zBest,tXBest,tYBest};
return result;
}
......@@ -3266,7 +3367,7 @@ public double findAdjustZ(
public boolean LevenbergMarquardt(
FocusingFieldMeasurement measurement, // null in calibrate mode
boolean openDialog,
boolean filterZ, // for adjust mode
// boolean filterZ, // for adjust mode
int debugLevel){
boolean calibrate=measurement==null;
double savedLambda=this.lambda;
......@@ -3285,7 +3386,7 @@ public boolean LevenbergMarquardt(
// }
if (!calibrate) {
this.currentStrategyStep=-1;
fieldFitting.selectZTilt();
fieldFitting.selectZTilt(false);
keepCorrectionParameters=true;
resetCenter=false;
if (!openDialog) stopEachStep=false;
......@@ -3329,6 +3430,17 @@ public boolean LevenbergMarquardt(
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return false;
}
if (filterByValueScale>0.0){
boolean [] en=dataWeightsToBoolean();
en= filterByValue(
filterByValueScale,
en);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return false;
}
fieldFitting.initSampleCorrVector(
flattenSampleCoord(), //double [][] sampleCoordinates,
null); //getSeriesWeights()); //double [][] sampleSeriesWeights);
......@@ -3372,6 +3484,9 @@ public boolean LevenbergMarquardt(
(this.stopEachStep) ||
(this.stopEachSeries && state[1]) ||
(this.stopOnFailure && state[1] && !state[0])){
if (state[1] && !state[0] && !calibrate){
return false;
}
if (debugLevel>0){
if (this.stopRequested.get()>0) System.out.println("User requested stop");
......@@ -3699,23 +3814,27 @@ public boolean LevenbergMarquardt(
public void testMeasurement(){
GenericDialog gd = new GenericDialog("Select measurement");
int nMeas=measurements.size()/2;
double zMin=-40.0;
double zMax= 40.0;
double zStep=2.0;
// double zMin=-40.0;
// double zMax= 40.0;
// double zStep=2.0;
double targetTiltX=0.0; // for testing, normally should be 0 um/mm
double targetTiltY=0.0; // for testing, normally should be 0 um/mm
// fieldFitting.mechanicalFocusingModel.setZTxTy(0.0,0.0,0.0); // to correctly find Z centers,
fieldFitting.mechanicalFocusingModel.setAdjustMode(false); // to correctly find Z centers,
double [] center_z=fieldFitting.getZCenters(false);
double [] centerFWHM={
fieldFitting.getCalcValuesForZ(center_z[0],0.0,null)[1],
fieldFitting.getCalcValuesForZ(center_z[1],0.0,null)[3],
fieldFitting.getCalcValuesForZ(center_z[2],0.0,null)[5]
};
// String path=null;
String title="Test adjustment results";
double [] best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
// double targetRelZShift=8.0; // focus by this closer to lens to compensate for closer tested than used
gd.addMessage("Best composite distance for FWHM^4 "+ IJ.d2s(best_qb_corr[0],3)+" um"+
", FWHM="+IJ.d2s(best_qb_corr[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+" lp/mm");
gd.addMessage("Best center focus for Red (relative to best composite) = "+ IJ.d2s(center_z[0]-best_qb_corr[0],3)+" um"+
......@@ -3725,55 +3844,88 @@ public boolean LevenbergMarquardt(
gd.addMessage("Best center focus for Blue (relative to best composite) = "+ IJ.d2s(center_z[2]-best_qb_corr[0],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[2],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[2],2)+" lp/mm");
gd.addNumericField("Measurement number",nMeas,0,5,"0.."+(measurements.size()-1));
if (fieldFitting.channelSelect==null) fieldFitting.channelSelect=fieldFitting.getDefaultMask();
for (int i=0;i<fieldFitting.channelSelect.length;i++) {
gd.addCheckbox(fieldFitting.getDescription(i), fieldFitting.channelSelect[i]);
}
filterZ=true; // (adjustment mode)filter samples by Z
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
// filterZ=true; // (adjustment mode)filter samples by Z
// minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
gd.addNumericField("Measurement number",nMeas,0,5,"0.."+(measurements.size()-1));
gd.addCheckbox("Filter samples/channels by Z",filterZ);
gd.addNumericField("Filter by value (remove samples above scaled best FWHM for channel/location)",filterByValueScale,2,5,"x");
gd.addNumericField("Minimal required number of channels/samples",minLeftSamples,0,3,"samples");
gd.addNumericField("Z min",zMin,2,5,"um");
gd.addNumericField("Z max",zMax,2,5,"um");
gd.addNumericField("Z step",zStep,2,5,"um");
gd.addNumericField("Tilt min",tMin,2,5,"um/mm");
gd.addNumericField("Tilt max",tMax,2,5,"um/mm");
gd.addNumericField("Tilt step",tStep,2,5,"um/mm");
gd.addNumericField("Target focus (relative to best composirte)",targetRelFocalShift,2,5,"um");
gd.addNumericField("Target horizontal tilt (normally 0)",targetTiltX,2,5,"um/mm");
gd.addNumericField("Target vertical tilt (normally 0)",targetTiltY,2,5,"um/mm");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return;
nMeas=(int) gd.getNextNumber();
for (int i=0;i<fieldFitting.channelSelect.length;i++) {
fieldFitting.channelSelect[i]=gd.getNextBoolean();
}
filterZ=gd.getNextBoolean();
filterByValueScale=gd.getNextNumber();
minLeftSamples=(int) gd.getNextNumber();
zMin= gd.getNextNumber();
zMax= gd.getNextNumber();
zStep=gd.getNextNumber();
tMin= gd.getNextNumber();
tMax= gd.getNextNumber();
tStep=gd.getNextNumber();
targetRelFocalShift=gd.getNextNumber();
targetTiltX=gd.getNextNumber(); // for testing, normally should be 0 um/mm
targetTiltY=gd.getNextNumber(); // for testing, normally should be 0 um/mm
boolean OK;
/*
double targetRelFocalShift,
double targetTiltX, // for testing, normally should be 0 um/mm
double targetTiltY // for testing, normally should be 0 um/mm
fieldFitting.mechanicalFocusingModel.setAdjustMode(true); // to correctly find Z centers,
fieldFitting.mechanicalSelect=fieldFitting.mechanicalFocusingModel.maskSetZTxTy();
*/
if (nMeas>=0){
String header="# measurement";
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
header+="\t"+fieldFitting.mechanicalFocusingModel.getName(i)+" ("+fieldFitting.mechanicalFocusingModel.getUnits(i)+")";
}
}
for (int i=0;i<3;i++) header+="\tmz"+i;
for (int i=0;i<3;i++) header+="\tm"+i;
StringBuffer sb = new StringBuffer();
boolean single= (nMeas>=0);
if (single){
OK=testMeasurement(
measurements.get(nMeas),
// nMeas,
zMin,
zMax,
zStep
zMin, //+best_qb_corr[0],
zMax, //+best_qb_corr[0],
zStep,
tMin,
tMax,
tStep
);
if (!OK){
if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
} else {
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ========");
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
......@@ -3783,25 +3935,54 @@ public boolean LevenbergMarquardt(
fieldFitting.mechanicalFocusingModel.getUnits(i));
}
}
double [] dmz= getAdjustedMotors(
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
false);
if ((dmz!=null) && (debugLevel>0)){
System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
}
double [] dm= getAdjustedMotors(
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY);
targetTiltY,
true);
if ((dm!=null) && (debugLevel>0)){
System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
}
sb.append(nMeas);
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
sb.append("\t"+IJ.d2s(fieldFitting.mechanicalFocusingModel.paramValues[i],3));
}
}
if (dmz!=null){
for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
} else {
sb.append("\t---\t---\t---");
}
if (dm!=null){
for (int i=0;i<dm.length;i++) sb.append("\t"+IJ.d2s(dm[i],1));
} else {
sb.append("\t---\t---\t---");
}
sb.append("\n");
}
} else {
for (nMeas=0;nMeas<measurements.size();nMeas++){
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
OK=testMeasurement(
measurements.get(nMeas),
// nMeas,
zMin,
zMax,
zStep);
zMin, //+best_qb_corr[0],
zMax, // +best_qb_corr[0],
zStep,
tMin,
tMax,
tStep);
if (!OK){
if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
} else {
// if (debugLevel>0) System.out.println("======== testMeasurement("+nMeas+") ========");
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
System.out.println(
......@@ -3810,19 +3991,59 @@ public boolean LevenbergMarquardt(
fieldFitting.mechanicalFocusingModel.getUnits(i));
}
}
double [] dmz= getAdjustedMotors(
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
false);
if ((dmz!=null) && (debugLevel>0)){
System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
}
double [] dm= getAdjustedMotors(
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY);
targetTiltY,
true);
if ((dm!=null) && (debugLevel>0)){
System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
}
sb.append(nMeas);
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
sb.append("\t"+IJ.d2s(fieldFitting.mechanicalFocusingModel.paramValues[i],3));
}
}
if (dmz!=null){
for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
} else {
sb.append("\t---\t---\t---");
}
if (dm!=null){
for (int i=0;i<dm.length;i++) sb.append("\t"+IJ.d2s(dm[i],1));
} else {
sb.append("\t---\t---\t---");
}
sb.append("\n");
}
}
}
if (!single) {
// if (path!=null) {
// CalibrationFileManagement.saveStringToFile (
// path,
// header+"\n"+sb.toString());
// } else {
new TextWindow(title, header, sb.toString(), 800,1000);
// }
}
// fieldFitting.mechanicalFocusingModel.setZTxTy(0.0,0.0,0.0); // restore zeros to correctly find Z centers,
fieldFitting.mechanicalFocusingModel.setAdjustMode(false); // to correctly find Z centers,
}
public double [] getAdjustedMotors(
double targetRelFocalShift,
double targetTiltX, // for testing, normally should be 0 um/mm
double targetTiltY){ // for testing, normally should be 0 um/mm
double targetTiltY,
boolean motorSteps){ // for testing, normally should be 0 um/mm
double [] zM=fieldFitting.mechanicalFocusingModel.getZM(
currentPX0, //fieldFitting.getCenterXY()[0],
currentPY0, //fieldFitting.getCenterXY()[1],
......@@ -3830,7 +4051,8 @@ public boolean LevenbergMarquardt(
targetTiltX,
targetTiltY);
if (zM==null) return null; // not yet used
if (debugLevel>0) System.out.println("Suggested motor linearized positions: "+IJ.d2s(zM[0],2)+":"+IJ.d2s(zM[1],2)+":"+IJ.d2s(zM[2],2));
if (!motorSteps) return zM;
// if (debugLevel>0) System.out.println("Suggested motor linearized positions: "+IJ.d2s(zM[0],2)+":"+IJ.d2s(zM[1],2)+":"+IJ.d2s(zM[2],2));
double [] dm=new double[zM.length];
for (int index=0;index<dm.length;index++){
dm[index]=fieldFitting.mechanicalFocusingModel.zmToM(
......@@ -3845,37 +4067,49 @@ public boolean LevenbergMarquardt(
// int nMeas,
double zMin,
double zMax,
double zStep
double zStep,
double tMin,
double tMax,
double tStep
){
int retryLimit=20;
fieldFitting.mechanicalFocusingModel.setAdjustMode(true);
setDataVector(
false,
createDataVector(measurement)); //measurements.get(nMeas)));
// System.out.println("testMeasurement("+nMeas+")");
double z=findAdjustZ(
// TODO: Adjust by center samples only?
double [] zTxTy=findAdjustZ(
// measurements.get(nMeas),
measurement,
filterZ, //boolean filterZ,
filterByValueScale,
zMin,
zMax,
zStep,
0.0, //double tx,
0.0); // double ty);
fieldFitting.mechanicalFocusingModel.setZTxTy(z,0.0,0.0);// z,tx,ty
tMin,
tMax,
tStep);
if (Double.isNaN(zTxTy[0])) {
if (debugLevel>1) System.out.println("testMeasurement() failed: insufficient data to get z initial estimation");
return false;
}
fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy[0],zTxTy[1],zTxTy[2]); //z,0.0,0.0);// z,tx,ty
boolean [] wasPrevEnable=null;
for (int n=0;n<retryLimit;n++) { // TODO: Watch for the mask remain stable
z=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.z0);
if (debugLevel>0) System.out.println("testMeasurement(), run "+n+" (z="+z+")");
zTxTy[0]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.z0);
zTxTy[1]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.tx);
zTxTy[2]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.ty);
if (debugLevel>0) System.out.println("testMeasurement(), run "+n+" (z="+zTxTy[0]+" tx="+zTxTy[1]+" ty="+zTxTy[2]+")");
boolean [] was2PrevEnable=(wasPrevEnable==null)?null:wasPrevEnable.clone();
wasPrevEnable=(prevEnable==null)?null:prevEnable.clone();
boolean OK=LevenbergMarquardt(
measurement,
false, // true, // open dialog
filterZ, // filterZ
// filterZ, // filterZ
debugLevel);
if (!OK){
// if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
if (debugLevel>1) System.out.println("testMeasurement() failed");
if (debugLevel>1) System.out.println("testMeasurement() failed: LMA failed");
return false;
}
/*
......@@ -4248,6 +4482,18 @@ public boolean LevenbergMarquardt(
return result;
}
public double getChannelBestFWHM(
int channel,
int sampleIndex, // -1 for center
boolean corrected //
){
int r0Index=2; // index of "r0" parameter
double [] corrPars=corrected?getCorrPar(channel,sampleIndex):null;
double r=(sampleIndex>=0)?getSampleRadius(sampleIndex):0.0;
double fwhm=curvatureModel[channel].getAr( r, corrPars)[r0Index];
return fwhm;
}
public double [] getCalcZ(double r,
boolean solve // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
){
......@@ -4383,6 +4629,44 @@ public boolean LevenbergMarquardt(
return result;
}
/**
* calculate FWHM of the "best focus" for each channel (color and S/T) for each sample
* @param corrected when false - provide averaged (axial model) for radius, if true - with individual correction applied
* @param allChannels calculate for all (even disabled) channels, false - only for currently selected
* @return outer dimension - number of channel, inner - number of sample (use getSampleRadiuses for radius of each)
*/
public double [][] getFWHM(
boolean corrected,
boolean allChannels
){
double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length;
boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()];
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
double [][] result=new double [6][];
for (int chn=0;chn<result.length;chn++) {
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
if (goodSamples[chn][sampleIndex]) {
result[chn][sampleIndex]=getChannelBestFWHM(
chn, // int channel,
sampleIndex, // int sampleIndex,
corrected); //boolean corrected,
} else {
result[chn][sampleIndex]=Double.NaN;
}
}
} else {
result[chn]=null;
}
}
return result;
}
public double getGreenZCenter(){
int chn=3; // Green, Tangential
return curvatureModel[chn].getCenterVector()[0];
......@@ -5031,11 +5315,11 @@ public boolean LevenbergMarquardt(
return true;
}
public void selectZTilt(){
public void selectZTilt(boolean allChannels){
mechanicalSelect=mechanicalFocusingModel.maskSetZTxTy(); // enable z0, tx, ty
// enable all color/dir channels (add separate selection dialog?)
for (int i=0;i<channelSelect.length;i++) {
channelSelect[i]=true;
if (allChannels) channelSelect[i]=true;
curvatureSelect[i]=curvatureModel[0].maskAllDisabled();
}
if (sampleCorrSelect!=null){
......@@ -5481,12 +5765,35 @@ public boolean LevenbergMarquardt(
public double PERIOD=3584.0; // steps/revolution
// public double PIXEL_SIZE=0.0022; // mm
public double [] paramValues=new double [descriptions.length];
public double [] paramValuesCalibrate=null; // save calibration mode parameters while adjusting
public boolean adjustMode=false;
public MechanicalFocusingModel(){ // add arguments?
initDefaults();
}
public void setAdjustMode(boolean mode){
if (mode==adjustMode) return;
if (adjustMode) restoreCalibration();
else saveCalibration();
adjustMode=mode;
}
private void saveCalibration(boolean force){ // do not save if in adjust mode
if (force) adjustMode=false;
saveCalibration();
}
private void saveCalibration(){ // do not save if in adjust mode
if (paramValues!=null){
if (!adjustMode) paramValuesCalibrate=paramValues.clone();
else System.out.println("Possible BUG - tried to save mechanical parameters while in adjust mode");
}
}
private void restoreCalibration(){
if (paramValuesCalibrate!=null) paramValues=paramValuesCalibrate.clone();
adjustMode=false;
}
public void setProperties(String prefix,Properties properties){
setAdjustMode(false); // restore if needed
if (paramValues!=null) {
for (int i=0;i<paramValues.length;i++){
properties.setProperty(prefix+descriptions[i][0],paramValues[i]+"");
......@@ -5500,10 +5807,12 @@ public boolean LevenbergMarquardt(
if (properties.getProperty(prefix+descriptions[i][0])!=null)
paramValues[i]=Double.parseDouble(properties.getProperty(prefix+descriptions[i][0]));
}
saveCalibration(true);
}
public void initDefaults(){
paramValues=new double [descriptions.length];
for (int i=0;i<descriptions.length;i++) paramValues[i]=Double.parseDouble(descriptions[i][3]);
saveCalibration(true);
}
public void setVector(double[] vector){
paramValues=new double [descriptions.length];
......
src/main/java/LensAdjustment.java
View file @ e4ac0da9
......@@ -304,6 +304,7 @@ public class LensAdjustment {
public int scanHysteresisNumber=5; // number of test points for the Hysteresis measurement
public boolean scanTiltEnable=true; // enable scanning tilt
public boolean scanTiltReverse=false; // enable scanning tilt in both directions
public int scanTiltRangeX=14336; // 4 periods
public int scanTiltRangeY=14336; // 4 periods
public int scanTiltStepsX=24;
......@@ -518,6 +519,7 @@ public class LensAdjustment {
int scanHysteresisNumber, // number of test points for the Hysteresis measurement
boolean scanTiltEnable, //=true; // enable scanning tilt
boolean scanTiltReverse,
int scanTiltRangeX, //=14336; // 4 periods
int scanTiltRangeY, //=14336; // 4 periods
int scanTiltStepsX, //=24;
......@@ -660,6 +662,7 @@ public class LensAdjustment {
this.scanHysteresisNumber=scanHysteresisNumber; // number of test points for the Hysteresis measurement
this.scanTiltEnable=scanTiltEnable; //=true; // enable scanning tilt
this.scanTiltReverse=scanTiltReverse;
this.scanTiltRangeX=scanTiltRangeX; //, //=14336; // 4 periods
this.scanTiltRangeY=scanTiltRangeY; //, //=14336; // 4 periods
this.scanTiltStepsX=scanTiltStepsX; //=24;
......@@ -803,6 +806,7 @@ public class LensAdjustment {
this.scanHysteresisNumber, // number of test points for the Hysteresis measurement
this.scanTiltEnable, // enable scanning tilt
this.scanTiltReverse,
this.scanTiltRangeX, // 4 periods
this.scanTiltRangeY, // 4 periods
this.scanTiltStepsX,
......@@ -953,6 +957,8 @@ public class LensAdjustment {
properties.setProperty(prefix+"scanHysteresisNumber",this.scanHysteresisNumber+"");
properties.setProperty(prefix+"scanTiltEnable",this.scanTiltEnable+""); // enable scanning tilt
properties.setProperty(prefix+"scanTiltReverse",this.scanTiltReverse+"");
properties.setProperty(prefix+"scanTiltRangeX",this.scanTiltRangeX+""); // 4 periods
properties.setProperty(prefix+"scanTiltRangeY",this.scanTiltRangeY+""); // 4 periods
properties.setProperty(prefix+"scanTiltStepsX",this.scanTiltStepsX+"");
......@@ -1207,6 +1213,10 @@ public class LensAdjustment {
if (properties.getProperty(prefix+"scanTiltEnable")!=null)
this.scanTiltEnable=Boolean.parseBoolean(properties.getProperty(prefix+"scanTiltEnable"));
if (properties.getProperty(prefix+"scanTiltReverse")!=null)
this.scanTiltReverse=Boolean.parseBoolean(properties.getProperty(prefix+"scanTiltReverse"));
if (properties.getProperty(prefix+"scanTiltRangeX")!=null)
this.scanTiltRangeX=Integer.parseInt(properties.getProperty(prefix+"scanTiltRangeX"));
if (properties.getProperty(prefix+"scanTiltRangeY")!=null)
......@@ -1353,6 +1363,9 @@ public class LensAdjustment {
gd.addNumericField("Number of scan steps during hysteresis (play) measurement", this.scanHysteresisNumber, 0);
gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);
gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
gd.addNumericField("Number of stops measurements when tilting in X-deirection", this.scanTiltStepsX, 0);
......@@ -1372,6 +1385,7 @@ public class LensAdjustment {
this.scanHysteresisNumber= (int) gd.getNextNumber();
this.scanTiltEnable= gd.getNextBoolean();
this.scanTiltReverse= gd.getNextBoolean();
this.scanTiltRangeX= (int) gd.getNextNumber();
this.scanTiltRangeY= (int) gd.getNextNumber();
this.scanTiltStepsX= (int) gd.getNextNumber();
......@@ -1503,6 +1517,8 @@ public class LensAdjustment {
gd.addNumericField("Number of scan steps during hysteresis (play) measurement", this.scanHysteresisNumber, 0);
gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);
gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
gd.addNumericField("Number of stops measurements when tilting in X-deirection", this.scanTiltStepsX, 0);
......@@ -1667,6 +1683,7 @@ public class LensAdjustment {
this.scanHysteresisNumber= (int) gd.getNextNumber();
this.scanTiltEnable= gd.getNextBoolean();
this.scanTiltReverse= gd.getNextBoolean();
this.scanTiltRangeX= (int) gd.getNextNumber();
this.scanTiltRangeY= (int) gd.getNextNumber();
this.scanTiltStepsX= (int) gd.getNextNumber();
......
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