Skip to content

I
imagej-elphel
Commit 08b36456 authored by Andrey Filippov's avatar Andrey Filippov
Browse files
Options

modified other distance measurements (like for temperature coefficient) 

to use lens aberration model
parent 77c3afd4
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 287 additions and 99 deletions
src/main/java/Aberration_Calibration.java
View file @ 08b36456
This diff is collapsed.
src/main/java/FocusingField.java
View file @ 08b36456
......@@ -5121,20 +5121,39 @@ public boolean LevenbergMarquardt(
public double [][] getAllZTM(
boolean noTiltScan,
FocusingField ff){
double [][] result =new double[ff.measurements.size()][6];
for (int i=0;i<result.length;i++) result[i]=adjustLMA(noTiltScan,ff.measurements.get(i),false);
FocusingField ff,
boolean noMotors){
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;
}
public double [] averageZTM(// results relative to optimal
boolean noTiltScan,
FocusingField ff){
double [] result =new double[6];
FocusingField ff,
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;
int num=0;
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) {
for (int i=0;i<result.length;i++) result[i]+=ZTM[i];
num++;
......@@ -5147,13 +5166,17 @@ public boolean LevenbergMarquardt(
public double [] adjustLMA ( // result relative to optimal
boolean noTiltScan,
FocusingFieldMeasurement measurement,
boolean parallelMove){
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]);
boolean parallelMove,
boolean noQualB, // do not re-claculate testQualB
boolean noAdjust){ // do not calculate correction
if (!noQualB) {
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]);
}
}
if (!testMeasurement(
measurement,
......@@ -5166,55 +5189,49 @@ public boolean LevenbergMarquardt(
if (debugLevel>0) System.out.println("adjustLMA() failed");
return null;
}
double [] result=new double [6];
// double [] best_qb_corr= fieldFitting.getBestQualB(
// k_red,
// k_blue,
// true);
double [] result=new double [noAdjust?3:6];
double [] zTilts=getCenterZTxTy(measurement);
result[0]=zTilts[0]-this.qualBOptimizationResults[0]; //best_qb_corr[0];
result[1]=zTilts[1]-this.qualBOptimizationResults[1];
result[2]=zTilts[2]-this.qualBOptimizationResults[2];
double [] zm=null;
// if (parallelMove){
if (!noAdjust) {
double [] zm=null;
zm=new double [3];
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]));
for (int i=0;i<zm.length;i++) {
System.out.println(i+": "+zm[i]+" um");
if (this.debugLevel>0){
System.out.println("Current linearized motor positions, center="+(0.25*zm[0]+0.25*zm[1]+0.5*zm[2]));
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];
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)");
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;
}
}
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));
}
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;
return result;
}
// add tx, ty?
......@@ -5310,7 +5327,7 @@ public boolean LevenbergMarquardt(
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]+")");
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();
wasPrevEnable=(prevEnable==null)?null:prevEnable.clone();
this.lambda=this.adjustmentInitialLambda;
......@@ -5340,8 +5357,8 @@ public boolean LevenbergMarquardt(
break;
}
if (!changedEnable) {
if (debugLevel>0) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
if (debugLevel>0) {
if (debugLevel>1) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
if (debugLevel>1) {
System.out.println("=== Absolute shift/tilt from the measuremet ===");
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;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]
String msg="QualB="+this.currentQualB+" ("+this.firstQualB+") "+
" 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 (updateStatus){
IJ.showStatus("Done: Step #"+this.iterationStepNumber+
......
src/main/java/LensAdjustment.java
View file @ 08b36456
......@@ -195,6 +195,7 @@ public class LensAdjustment {
public String gridGeometryFile="";
public String initialCalibrationFile="";
public String focusingHistoryFile="";
public boolean useLMAMetrics=true; // measure/report focal distance and tilts using lens model/LMA (when available)
public String strategyFile="";
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
......@@ -430,6 +431,7 @@ public class LensAdjustment {
String strategyFile,
String resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
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
boolean saveResults, // save focusing results
boolean showResults, // show focusing (includingh intermediate) results
......@@ -577,6 +579,7 @@ public class LensAdjustment {
this.strategyFile=strategyFile;
this.resultsSuperDirectory=resultsSuperDirectory; // directory with subdirectories named as serial numbers to stro results
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.saveResults=saveResults; // save focusing results
this.showResults=showResults; // show focusing (includingh intermediate) results
......@@ -725,6 +728,7 @@ public class LensAdjustment {
this.strategyFile,
this.resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
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.saveResults, // save focusing results
this.showResults, // show focusing (includingh intermediate) results
......@@ -871,6 +875,7 @@ public class LensAdjustment {
properties.setProperty(prefix+"strategyFile",this.strategyFile+"");
properties.setProperty(prefix+"resultsSuperDirectory",this.resultsSuperDirectory+"");
properties.setProperty(prefix+"focusingHistoryFile",this.focusingHistoryFile+"");
properties.setProperty(prefix+"useLMAMetrics",this.useLMAMetrics+"");
properties.setProperty(prefix+"serialNumber",this.serialNumber+"");
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+"");
......@@ -1029,6 +1034,9 @@ public class LensAdjustment {
this.resultsSuperDirectory=properties.getProperty(prefix+"resultsSuperDirectory");
if (properties.getProperty(prefix+"focusingHistoryFile")!=null)
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)
this.serialNumber=properties.getProperty(prefix+"serialNumber");
......@@ -1441,7 +1449,8 @@ public class LensAdjustment {
gd.addStringField ("Initial camera intrinsic/extrinsic parametres file", this.initialCalibrationFile,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 ("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.addCheckbox ("Save SFE focusing results (including intermediate) ", this.saveResults);
gd.addCheckbox ("Show SFE focusing results (including intermediate) ", this.showResults);
......@@ -1618,6 +1627,8 @@ public class LensAdjustment {
this.strategyFile= gd.getNextString();
this.resultsSuperDirectory= gd.getNextString();
this.focusingHistoryFile= gd.getNextString();
this.useLMAMetrics = gd.getNextBoolean();
this.EEPROM_channel= (int) gd.getNextNumber();
this.saveResults= gd.getNextBoolean();
this.showResults= gd.getNextBoolean();
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment