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Commit b75d6c0f authored by Andrey Filippov's avatar Andrey Filippov
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Adding LMA version to averaging/temperature scan commands

parent 0a57888e
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Showing with 163 additions and 11 deletions
src/main/java/Aberration_Calibration.java
View file @ b75d6c0f
......@@ -50,6 +50,7 @@ import java.util.regex.Pattern;
//import FocusingField.FocusingFieldMeasurement;
//import FocusingField.MeasuredSample;
import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
......@@ -5018,6 +5019,8 @@ if (MORE_BUTTONS) {
if (label.equals("Temp. Scan") || label.equals("Focus Average")) {
checkSerialAndRestore(); // returns true if did not change or was restored
boolean modeAverage=label.equals("Focus Average");
boolean noTiltScan=true;
boolean useLMA=true;
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS,
......@@ -5033,6 +5036,8 @@ if (MORE_BUTTONS) {
gd.addCheckbox("Turn lasers off to protect from overheating",true);
}
gd.addCheckbox("Erase previous measurement history",modeAverage);
gd.addCheckbox("Allow tilt scan when looking for the best fit",!noTiltScan);
gd.addCheckbox("Use LMA calculations for focus/tilt",useLMA);
double scanMinutes=modeAverage?1.0:30.0;
gd.addNumericField("Measure for ", scanMinutes , 1,5," minutes");
gd.showDialog();
......@@ -5043,6 +5048,9 @@ if (MORE_BUTTONS) {
if (MASTER_DEBUG_LEVEL>0) System.out.println ("Turned laser pointers off to protect from overheating");
}
if (gd.getNextBoolean()) MOTORS.clearHistory();
noTiltScan=!gd.getNextBoolean();
useLMA=gd.getNextBoolean();
// int startHistPos=MOTORS.historySize();
scanMinutes=gd.getNextNumber();
long startTime=System.nanoTime();
long endTime=startTime+(long) (6E10*scanMinutes);
......@@ -5079,7 +5087,45 @@ if (MORE_BUTTONS) {
}
}
// LMA version
double pX0=FOCUS_MEASUREMENT_PARAMETERS.result_PX0;
double pY0=FOCUS_MEASUREMENT_PARAMETERS.result_PY0;
double [][][] sampleCoord=FOCUS_MEASUREMENT_PARAMETERS.sampleCoordinates( //{x,y,r}
pX0, // lens center on the sensor
pY0);
if (useLMA){
FOCUSING_FIELD= new FocusingField(
FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
pX0,
pY0,
sampleCoord,
this.SYNC_COMMAND.stopRequested);
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
MOTORS.addCurrentHistoryToFocusingField(
FOCUSING_FIELD,
(runs==0)?0:(MOTORS.historySize()-runs),
MOTORS.historySize()); // all newly acquired
if (modeAverage){ // calculate/show average over the last run - only in "average" mode
double [] ZTM=FOCUSING_FIELD.averageZTM(noTiltScan); // no tilt scan - faster
if (MASTER_DEBUG_LEVEL>0) {
String msg="Failed to calulate average focus/tilt";
if (ZTM!=null) msg="Average:\n"+
"Relative focal shift "+IJ.d2s(ZTM[0],3)+"um\n"+
"Horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm\n"+
"Vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm\n"+
"Suggested M1 "+IJ.d2s(ZTM[3],0)+"steps\n"+
"Suggested M2 "+IJ.d2s(ZTM[4],0)+"steps\n"+
"Suggested M3 "+IJ.d2s(ZTM[5],0)+"steps";
System.out.println(msg);
IJ.showMessage(msg);
}
}
}
if (FOCUS_MEASUREMENT_PARAMETERS.saveResults) {
String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);
File dFile=new File(dir);
......@@ -5113,8 +5159,16 @@ if (MORE_BUTTONS) {
FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,
FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT
);
if (useLMA){
String focusingPath=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml";
System.out.println("Saving measurement history to "+focusingPath);
FOCUSING_FIELD.saveXML(focusingPath);
}
}
// Calculate and showaverage distances and tilts for measured history
if (!modeAverage) {
double [] lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
runs, // number of last samples from history to use, 0 - use all
FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
......@@ -5140,6 +5194,48 @@ if (MORE_BUTTONS) {
System.out.println(msg);
IJ.showMessage("Info",msg);
}
// Now in LMA mode - recalculate and overwrite
if (useLMA){
FOCUSING_FIELD= new FocusingField(
FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
pX0,
pY0,
sampleCoord,
this.SYNC_COMMAND.stopRequested);
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
MOTORS.addCurrentHistoryToFocusingField(FOCUSING_FIELD); // all, not just newly acquired
if (MASTER_DEBUG_LEVEL>0){
System.out.println ("*** Calculating focal distance shift for each of "+MOTORS.historySize()+" recorded measurments ***");
}
double [][] allZTM=FOCUSING_FIELD.getAllZTM(noTiltScan); // no tilt scan (supposed to be adjusted
lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
allZTM,
runs
);
allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
allZTM,
0
);
FOCUS_MEASUREMENT_PARAMETERS.result_lastKT=lastKT[1]; // focal distance temperature coefficient (um/C), measured from last run
FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20=lastKT[0]+20*lastKT[1]; // focal distance for 20C, measured from last run
FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT=allKT[1]; // focal distance temperature coefficient (um/C), measured from all the measurement histgory
FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20=allKT[0]+20*allKT[1]; // focal distance for 20C, measured from all the measurement histgory
if (MASTER_DEBUG_LEVEL>0){
String msg=
"Determined by LMA: Focal distance temperature expansion is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,2)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,2)+")"+
" microns per C, measured from this run (measured from all the history)\n"+
"Focal distance at 20C is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20,2)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20,2)+")"+
" microns, measured from this run (measured from all the history)";
System.out.println(msg);
IJ.showMessage("Info",msg);
}
}
}
saveCurrentConfig();
return;
......@@ -8738,7 +8834,7 @@ if (MORE_BUTTONS) {
//get measurement
FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
// calculate z, tx, ty, m1,m2,m3
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,false);
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,false); // allow tilt scan
// show dialog: Apply, re-calculate, exit
int [] currentMotors=fFMeasurement.motors;
int [] newMotors=currentMotors.clone();
......@@ -8836,7 +8932,7 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
if (parallelMove){ // ignore/recalculate newMotors data
zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,true); // recalculate with parallel move only
zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,true); // recalculate with parallel move only, allow tilt scan
newMotors=currentMotors.clone();
if (zTxTyM1M2M3!=null){
newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);
......
src/main/java/CalibrationHardwareInterface.java
View file @ b75d6c0f
......@@ -3100,15 +3100,22 @@ public class CalibrationHardwareInterface {
return null;
}
// public void addCurrentHistoryToFocusingField(FocusingField focusingField){
// this.focusingHistory.addCurrentHistory(focusingField);
// }
public void addCurrentHistoryToFocusingField(FocusingField focusingField){
for (int i=0;i<historySize();i++){
public void addCurrentHistoryToFocusingField(
FocusingField focusingField,
int start,
int end){
for (int i=start;i<end;i++){
addCurrentHistoryToFocusingField(focusingField,i);
}
// this.focusingHistory.addCurrentHistory(focusingField);
}
}
public void addCurrentHistoryToFocusingField(FocusingField focusingField){
addCurrentHistoryToFocusingField(
focusingField,
0,
historySize()
);
}
public void addCurrentHistoryToFocusingField(
FocusingField focusingField,
......@@ -5086,6 +5093,31 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
return polyCoeff;
}
public double [] temperatureLinearApproximation(
double [][] ZTM, // Z, tXx, tY, m1,m2,m3 found with LMA
int numSamples // number of last samples from history to use, 0 - use all
){
if (numSamples<=0) numSamples=this.history.size();
if (numSamples>this.history.size()) numSamples=this.history.size();
int firstSample=this.history.size()-numSamples;
int numGoodSamples=0;
for (int nSample=0;nSample<numSamples;nSample++){
if (ZTM[firstSample+nSample]!=null) numGoodSamples++;
}
double [][] data =new double [numGoodSamples][2]; // no weights
int index=0;
for (int nSample=0;nSample<numSamples;nSample++) if (ZTM[firstSample+nSample]!=null) {
data[index][0]=this.history.get(firstSample+nSample).getTemperature();
data[index++][1]=ZTM[firstSample+nSample][0]; // Z
}
PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
return polyCoeff;
}
/**
* will return same coordinates if tolerances are met
* @param useTheBest
......
src/main/java/FocusingField.java
View file @ b75d6c0f
......@@ -4373,7 +4373,31 @@ public boolean LevenbergMarquardt(
}
//,
public double [][] getAllZTM(
boolean noTiltScan){
double [][] result =new double[measurements.size()][6];
for (int i=0;i<result.length;i++) result[i]=adjustLMA(noTiltScan,measurements.get(i),false);
return result;
}
public double [] averageZTM(
boolean noTiltScan){
double [] result =new double[6];
for (int i=0;i<result.length;i++) result[i]=0.0;
int num=0;
for (FocusingFieldMeasurement measurement:measurements){
double [] ZTM = adjustLMA(noTiltScan,measurement,false);
if (ZTM!=null) {
for (int i=0;i<result.length;i++) result[i]+=ZTM[i];
num++;
}
}
if (num==0) return null;
for (int i=0;i<result.length;i++) result[i]/=num;
return result;
}
public double [] adjustLMA (
boolean noTiltScan,
FocusingFieldMeasurement measurement,
boolean parallelMove){
if (!testMeasurement(
......@@ -4381,8 +4405,8 @@ public boolean LevenbergMarquardt(
zMin, //+best_qb_corr[0],
zMax, //+best_qb_corr[0],
zStep,
tMin,
tMax,
(noTiltScan?0.0:tMin),
(noTiltScan?0.0:tMax),
tStep)) {
if (debugLevel>0) System.out.println("adjustLMA() failed");
return null;
......
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