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imagej-elphel
Commit 08b36456 authored by Andrey Filippov's avatar Andrey Filippov
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modified other distance measurements (like for temperature coefficient) 

to use lens aberration model
parent 77c3afd4
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Showing with 287 additions and 99 deletions
src/main/java/Aberration_Calibration.java
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src/main/java/FocusingField.java
View file @ 08b36456
...@@ -5121,20 +5121,39 @@ public boolean LevenbergMarquardt( ...@@ -5121,20 +5121,39 @@ public boolean LevenbergMarquardt(
public double [][] getAllZTM( public double [][] getAllZTM(
boolean noTiltScan, boolean noTiltScan,
FocusingField ff){ FocusingField ff,
double [][] result =new double[ff.measurements.size()][6]; boolean noMotors){
for (int i=0;i<result.length;i++) result[i]=adjustLMA(noTiltScan,ff.measurements.get(i),false); double [][] result =new double[ff.measurements.size()][];
for (int i=0;i<result.length;i++) result[i]=adjustLMA(
noTiltScan,
ff.measurements.get(i),
false, // boolean parallelMove,
true, // boolean noQualB, // do not re-claculate testQualB
noMotors); // boolean noAdjust) // do not calculate correction
return result; return result;
} }
public double [] averageZTM(// results relative to optimal public double [] averageZTM(// results relative to optimal
boolean noTiltScan, boolean noTiltScan,
FocusingField ff){ FocusingField ff,
double [] result =new double[6]; boolean noMotors){
if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
if (debugLevel>0) {
System.out.println("Optimal absolute Zc="+this.qualBOptimizationResults[0]);
System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]);
System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]);
}
double [] result =new double[noMotors?3:6];
for (int i=0;i<result.length;i++) result[i]=0.0; for (int i=0;i<result.length;i++) result[i]=0.0;
int num=0; int num=0;
for (FocusingFieldMeasurement measurement:ff.measurements){ for (FocusingFieldMeasurement measurement:ff.measurements){
double [] ZTM = adjustLMA(noTiltScan,measurement,false); double [] ZTM = adjustLMA(
noTiltScan,
measurement,
false, // boolean parallelMove,
true, // boolean noQualB, // do not re-claculate testQualB
noMotors); // boolean noAdjust) // do not calculate correction
if (ZTM!=null) { if (ZTM!=null) {
for (int i=0;i<result.length;i++) result[i]+=ZTM[i]; for (int i=0;i<result.length;i++) result[i]+=ZTM[i];
num++; num++;
...@@ -5147,13 +5166,17 @@ public boolean LevenbergMarquardt( ...@@ -5147,13 +5166,17 @@ public boolean LevenbergMarquardt(
public double [] adjustLMA ( // result relative to optimal public double [] adjustLMA ( // result relative to optimal
boolean noTiltScan, boolean noTiltScan,
FocusingFieldMeasurement measurement, FocusingFieldMeasurement measurement,
boolean parallelMove){ boolean parallelMove,
if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode); boolean noQualB, // do not re-claculate testQualB
testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults boolean noAdjust){ // do not calculate correction
if (debugLevel>0) { if (!noQualB) {
System.out.println("Optimal absolute Zc="+this.qualBOptimizationResults[0]); if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]); testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]); if (debugLevel>0) {
System.out.println("Optimal absolute Zc="+this.qualBOptimizationResults[0]);
System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]);
System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]);
}
} }
if (!testMeasurement( if (!testMeasurement(
measurement, measurement,
...@@ -5166,55 +5189,49 @@ public boolean LevenbergMarquardt( ...@@ -5166,55 +5189,49 @@ public boolean LevenbergMarquardt(
if (debugLevel>0) System.out.println("adjustLMA() failed"); if (debugLevel>0) System.out.println("adjustLMA() failed");
return null; return null;
} }
double [] result=new double [6]; double [] result=new double [noAdjust?3:6];
// double [] best_qb_corr= fieldFitting.getBestQualB(
// k_red,
// k_blue,
// true);
double [] zTilts=getCenterZTxTy(measurement); double [] zTilts=getCenterZTxTy(measurement);
result[0]=zTilts[0]-this.qualBOptimizationResults[0]; //best_qb_corr[0]; result[0]=zTilts[0]-this.qualBOptimizationResults[0]; //best_qb_corr[0];
result[1]=zTilts[1]-this.qualBOptimizationResults[1]; result[1]=zTilts[1]-this.qualBOptimizationResults[1];
result[2]=zTilts[2]-this.qualBOptimizationResults[2]; result[2]=zTilts[2]-this.qualBOptimizationResults[2];
double [] zm=null; if (!noAdjust) {
// if (parallelMove){ double [] zm=null;
zm=new double [3]; zm=new double [3];
for (int i=0;i<zm.length;i++) zm[i]=fieldFitting.mechanicalFocusingModel.mToZm(measurement.motors[i], i); for (int i=0;i<zm.length;i++) zm[i]=fieldFitting.mechanicalFocusingModel.mToZm(measurement.motors[i], i);
// } if (this.debugLevel>0){
System.out.println("Current linearized motor positions, center="+(0.25*zm[0]+0.25*zm[1]+0.5*zm[2]));
if (this.debugLevel>0){ for (int i=0;i<zm.length;i++) {
System.out.println("Current linearized motor positions, center="+(0.25*zm[0]+0.25*zm[1]+0.5*zm[2])); System.out.println(i+": "+zm[i]+" um");
for (int i=0;i<zm.length;i++) { }
System.out.println(i+": "+zm[i]+" um"); double [] rzm=new double [3];
for (int i=0;i<zm.length;i++) rzm[i]=fieldFitting.mechanicalFocusingModel.zmToM(zm[i], i);
System.out.println("Checking back to motor positions, center="+(0.25*rzm[0]+0.25*rzm[1]+0.5*rzm[2])+
"steps (current="+(0.25*measurement.motors[0]+0.25*measurement.motors[1]+0.5*measurement.motors[2])+" steps)");
for (int i=0;i<zm.length;i++) {
System.out.println(i+": "+rzm[i]+" steps (was "+measurement.motors[i]+" steps)");
}
}
double [] dm= getAdjustedMotors(
parallelMove?zm:null,
targetRelFocalShift+this.qualBOptimizationResults[0] , //targetRelFocalShift+best_qb_corr[0],
this.qualBOptimizationResults[1], //0.0, // targetTiltX, // for testing, normally should be 0 um/mm
this.qualBOptimizationResults[2], //0.0, // targetTiltY,
true); // motor steps
if ((dm!=null) && (debugLevel>1)){
System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
} }
double [] rzm=new double [3]; if (dm!=null) {
for (int i=0;i<zm.length;i++) rzm[i]=fieldFitting.mechanicalFocusingModel.zmToM(zm[i], i); result[3]=dm[0];
System.out.println("Checking back to motor positions, center="+(0.25*rzm[0]+0.25*rzm[1]+0.5*rzm[2])+ result[4]=dm[1];
"steps (current="+(0.25*measurement.motors[0]+0.25*measurement.motors[1]+0.5*measurement.motors[2])+" steps)"); result[5]=dm[2];
for (int i=0;i<zm.length;i++) { } else {
System.out.println(i+": "+rzm[i]+" steps (was "+measurement.motors[i]+" steps)"); result[3]=Double.NaN;
result[4]=Double.NaN;
result[5]=Double.NaN;
} }
} }
double [] dm= getAdjustedMotors( return result;
parallelMove?zm:null,
targetRelFocalShift+this.qualBOptimizationResults[0] , //targetRelFocalShift+best_qb_corr[0],
this.qualBOptimizationResults[1], //0.0, // targetTiltX, // for testing, normally should be 0 um/mm
this.qualBOptimizationResults[2], //0.0, // targetTiltY,
true); // motor steps
if ((dm!=null) && (debugLevel>1)){
System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
}
if (dm!=null) {
result[3]=dm[0];
result[4]=dm[1];
result[5]=dm[2];
} else {
result[3]=Double.NaN;
result[4]=Double.NaN;
result[5]=Double.NaN;
}
return result;
} }
// add tx, ty? // add tx, ty?
...@@ -5310,7 +5327,7 @@ public boolean LevenbergMarquardt( ...@@ -5310,7 +5327,7 @@ public boolean LevenbergMarquardt(
zTxTy[0]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.z0); zTxTy[0]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.z0);
zTxTy[1]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.tx); zTxTy[1]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.tx);
zTxTy[2]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.ty); 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]+")"); if (debugLevel>1) System.out.println("testMeasurement(), run "+n+" (z="+zTxTy[0]+" tx="+zTxTy[1]+" ty="+zTxTy[2]+")");
boolean [] was2PrevEnable=(wasPrevEnable==null)?null:wasPrevEnable.clone(); boolean [] was2PrevEnable=(wasPrevEnable==null)?null:wasPrevEnable.clone();
wasPrevEnable=(prevEnable==null)?null:prevEnable.clone(); wasPrevEnable=(prevEnable==null)?null:prevEnable.clone();
this.lambda=this.adjustmentInitialLambda; this.lambda=this.adjustmentInitialLambda;
...@@ -5340,8 +5357,8 @@ public boolean LevenbergMarquardt( ...@@ -5340,8 +5357,8 @@ public boolean LevenbergMarquardt(
break; break;
} }
if (!changedEnable) { if (!changedEnable) {
if (debugLevel>0) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s")); if (debugLevel>1) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
if (debugLevel>0) { if (debugLevel>1) {
System.out.println("=== Absolute shift/tilt from the measuremet ==="); System.out.println("=== Absolute shift/tilt from the measuremet ===");
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){ for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) { if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
...@@ -9609,7 +9626,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -9609,7 +9626,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
String msg="QualB="+this.currentQualB+" ("+this.firstQualB+") "+ String msg="QualB="+this.currentQualB+" ("+this.firstQualB+") "+
" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.qStartTime),3); " at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.qStartTime),3);
if (debugLevel>0) System.out.println("qStepLevenbergMarquardtAction() "+msg); if (debugLevel>1) System.out.println("qStepLevenbergMarquardtAction() "+msg);
// if (this.updateStatus) IJ.showStatus(msg); // if (this.updateStatus) IJ.showStatus(msg);
if (updateStatus){ if (updateStatus){
IJ.showStatus("Done: Step #"+this.iterationStepNumber+ IJ.showStatus("Done: Step #"+this.iterationStepNumber+
......
src/main/java/LensAdjustment.java
View file @ 08b36456
...@@ -195,6 +195,7 @@ public class LensAdjustment { ...@@ -195,6 +195,7 @@ public class LensAdjustment {
public String gridGeometryFile=""; public String gridGeometryFile="";
public String initialCalibrationFile=""; public String initialCalibrationFile="";
public String focusingHistoryFile=""; public String focusingHistoryFile="";
public boolean useLMAMetrics=true; // measure/report focal distance and tilts using lens model/LMA (when available)
public String strategyFile=""; public String strategyFile="";
public String resultsSuperDirectory=""; // directory with subdirectories named as serial numbers to stro results public String resultsSuperDirectory=""; // directory with subdirectories named as serial numbers to stro results
public int EEPROM_channel=1; // EEPROM channel to read serial number from public int EEPROM_channel=1; // EEPROM channel to read serial number from
...@@ -430,6 +431,7 @@ public class LensAdjustment { ...@@ -430,6 +431,7 @@ public class LensAdjustment {
String strategyFile, String strategyFile,
String resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results String resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
String focusingHistoryFile, String focusingHistoryFile,
boolean useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
int EEPROM_channel, // EEPROM channel to read serial number from int EEPROM_channel, // EEPROM channel to read serial number from
boolean saveResults, // save focusing results boolean saveResults, // save focusing results
boolean showResults, // show focusing (includingh intermediate) results boolean showResults, // show focusing (includingh intermediate) results
...@@ -577,6 +579,7 @@ public class LensAdjustment { ...@@ -577,6 +579,7 @@ public class LensAdjustment {
this.strategyFile=strategyFile; this.strategyFile=strategyFile;
this.resultsSuperDirectory=resultsSuperDirectory; // directory with subdirectories named as serial numbers to stro results this.resultsSuperDirectory=resultsSuperDirectory; // directory with subdirectories named as serial numbers to stro results
this.focusingHistoryFile=focusingHistoryFile; this.focusingHistoryFile=focusingHistoryFile;
this.useLMAMetrics=useLMAMetrics; // measure/report focal distance and tilts using lens model/LMA (when available)
this.EEPROM_channel=EEPROM_channel; // EEPROM channel to read serial number from this.EEPROM_channel=EEPROM_channel; // EEPROM channel to read serial number from
this.saveResults=saveResults; // save focusing results this.saveResults=saveResults; // save focusing results
this.showResults=showResults; // show focusing (includingh intermediate) results this.showResults=showResults; // show focusing (includingh intermediate) results
...@@ -725,6 +728,7 @@ public class LensAdjustment { ...@@ -725,6 +728,7 @@ public class LensAdjustment {
this.strategyFile, this.strategyFile,
this.resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results this.resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
this.focusingHistoryFile, this.focusingHistoryFile,
this.useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
this.EEPROM_channel,// EEPROM channel to read serial number from this.EEPROM_channel,// EEPROM channel to read serial number from
this.saveResults, // save focusing results this.saveResults, // save focusing results
this.showResults, // show focusing (includingh intermediate) results this.showResults, // show focusing (includingh intermediate) results
...@@ -871,6 +875,7 @@ public class LensAdjustment { ...@@ -871,6 +875,7 @@ public class LensAdjustment {
properties.setProperty(prefix+"strategyFile",this.strategyFile+""); properties.setProperty(prefix+"strategyFile",this.strategyFile+"");
properties.setProperty(prefix+"resultsSuperDirectory",this.resultsSuperDirectory+""); properties.setProperty(prefix+"resultsSuperDirectory",this.resultsSuperDirectory+"");
properties.setProperty(prefix+"focusingHistoryFile",this.focusingHistoryFile+""); properties.setProperty(prefix+"focusingHistoryFile",this.focusingHistoryFile+"");
properties.setProperty(prefix+"useLMAMetrics",this.useLMAMetrics+"");
properties.setProperty(prefix+"serialNumber",this.serialNumber+""); properties.setProperty(prefix+"serialNumber",this.serialNumber+"");
if (!Double.isNaN(this.sensorTemperature))properties.setProperty(prefix+"sensorTemperature",this.sensorTemperature+""); if (!Double.isNaN(this.sensorTemperature))properties.setProperty(prefix+"sensorTemperature",this.sensorTemperature+"");
if (!Double.isNaN(this.result_lastKT))properties.setProperty(prefix+"result_lastKT",this.result_lastKT+""); if (!Double.isNaN(this.result_lastKT))properties.setProperty(prefix+"result_lastKT",this.result_lastKT+"");
...@@ -1029,6 +1034,9 @@ public class LensAdjustment { ...@@ -1029,6 +1034,9 @@ public class LensAdjustment {
this.resultsSuperDirectory=properties.getProperty(prefix+"resultsSuperDirectory"); this.resultsSuperDirectory=properties.getProperty(prefix+"resultsSuperDirectory");
if (properties.getProperty(prefix+"focusingHistoryFile")!=null) if (properties.getProperty(prefix+"focusingHistoryFile")!=null)
this.focusingHistoryFile=properties.getProperty(prefix+"focusingHistoryFile"); this.focusingHistoryFile=properties.getProperty(prefix+"focusingHistoryFile");
if (properties.getProperty(prefix+"useLMAMetrics")!=null)
this.useLMAMetrics=Boolean.parseBoolean(properties.getProperty(prefix+"useLMAMetrics"));
if (properties.getProperty(prefix+"serialNumber")!=null) if (properties.getProperty(prefix+"serialNumber")!=null)
this.serialNumber=properties.getProperty(prefix+"serialNumber"); this.serialNumber=properties.getProperty(prefix+"serialNumber");
...@@ -1441,7 +1449,8 @@ public class LensAdjustment { ...@@ -1441,7 +1449,8 @@ public class LensAdjustment {
gd.addStringField ("Initial camera intrinsic/extrinsic parametres file", this.initialCalibrationFile,40); gd.addStringField ("Initial camera intrinsic/extrinsic parametres file", this.initialCalibrationFile,40);
gd.addStringField ("Levenberg-Marquardt algorithm strategy file", this.strategyFile,40); gd.addStringField ("Levenberg-Marquardt algorithm strategy file", this.strategyFile,40);
gd.addStringField ("Focusing results superdirectory (individual will be named by serial numbers)", this.resultsSuperDirectory,40); gd.addStringField ("Focusing results superdirectory (individual will be named by serial numbers)", this.resultsSuperDirectory,40);
gd.addStringField ("Measurement history (acquired during \"Scan Calib LMA\" file", this.focusingHistoryFile,80); gd.addStringField ("Measurement history (acquired during \"Scan Calib LMA\") file", this.focusingHistoryFile,80);
gd.addCheckbox ("Use lens aberration model (if available) for focal distance and tilts", this.useLMAMetrics);
gd.addNumericField("EEPROM channel to read sensor serial number from", this.EEPROM_channel, 0,4,""); gd.addNumericField("EEPROM channel to read sensor serial number from", this.EEPROM_channel, 0,4,"");
gd.addCheckbox ("Save SFE focusing results (including intermediate) ", this.saveResults); gd.addCheckbox ("Save SFE focusing results (including intermediate) ", this.saveResults);
gd.addCheckbox ("Show SFE focusing results (including intermediate) ", this.showResults); gd.addCheckbox ("Show SFE focusing results (including intermediate) ", this.showResults);
...@@ -1618,6 +1627,8 @@ public class LensAdjustment { ...@@ -1618,6 +1627,8 @@ public class LensAdjustment {
this.strategyFile= gd.getNextString(); this.strategyFile= gd.getNextString();
this.resultsSuperDirectory= gd.getNextString(); this.resultsSuperDirectory= gd.getNextString();
this.focusingHistoryFile= gd.getNextString(); this.focusingHistoryFile= gd.getNextString();
this.useLMAMetrics = gd.getNextBoolean();
this.EEPROM_channel= (int) gd.getNextNumber(); this.EEPROM_channel= (int) gd.getNextNumber();
this.saveResults= gd.getNextBoolean(); this.saveResults= gd.getNextBoolean();
this.showResults= gd.getNextBoolean(); this.showResults= gd.getNextBoolean();
......
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