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Commit d14a3970 authored by Andrey Filippov's avatar Andrey Filippov
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Implemented simultaneous processing of multiple measurements (averaging, 

thermal scan), fixed adjustment
parent f8e486b9
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Showing with 1724 additions and 504 deletions
src/main/java/Aberration_Calibration.java
View file @ d14a3970
......@@ -784,6 +784,7 @@ if (MORE_BUTTONS) {
addButton("Focus Average",panelFocusing,color_report);
addButton("Power Control",panelFocusing,color_configure);
addButton("Temp. Scan",panelFocusing,color_process);
addButton("Replay Hist",panelFocusing,color_debug);
//
addButton("List History",panelFocusing,color_report);
addButton("Show PSF",panelFocusing,color_report);
......@@ -1006,6 +1007,7 @@ if (MORE_BUTTONS) {
if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
if (label==null) return;
if (FOCUSING_FIELD!=null) FOCUSING_FIELD.setThreads(THREADS_MAX);
/* ======================================================================== */
if (label.equals("Configure Globals")) {
showConfigureGlobalsDialog();
......@@ -2540,6 +2542,7 @@ if (MORE_BUTTONS) {
// reset histories
MOTORS.clearPreFocus();
MOTORS.clearHistory();
POWER_CONTROL.lightsOnWithDelay();
return;
}
/* ======================================================================== */
......@@ -2550,6 +2553,7 @@ if (MORE_BUTTONS) {
CAMERAS.probeCameraState(); // testing detection
CAMERAS.setupCameraAcquisition();
POWER_CONTROL.lightsOnWithDelay();
return;
}
/* ======================================================================== */
......@@ -2557,8 +2561,8 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
CAMERAS.debugLevel=DEBUG_LEVEL;
CAMERAS.setNumberOfThreads(THREADS_MAX);
POWER_CONTROL.lightsOnWithDelay();
CAMERAS.test1(true);
return;
}
/* ======================================================================== */
......@@ -2566,6 +2570,7 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
CAMERAS.debugLevel=DEBUG_LEVEL;
CAMERAS.setNumberOfThreads(THREADS_MAX);
POWER_CONTROL.lightsOnWithDelay();
CAMERAS.test1(false);
return;
}
......@@ -2598,6 +2603,7 @@ if (MORE_BUTTONS) {
}
// acquire camera image here, no lasers.
FOCUS_MEASUREMENT_PARAMETERS.sensorTemperature=CAMERAS.getSensorTemperature(0,FOCUS_MEASUREMENT_PARAMETERS.EEPROM_channel);
POWER_CONTROL.lightsOnWithDelay();
imp_sel= CAMERAS.acquireSingleImage (
false, //boolean useLasers,
UPDATE_STATUS);
......@@ -2625,6 +2631,7 @@ if (MORE_BUTTONS) {
}
DISTORTION_PROCESS_CONFIGURATION.sourceDirectory=src_dir;
CAMERAS.setNumberOfThreads(THREADS_MAX);
POWER_CONTROL.lightsOnWithDelay();
long startTime=System.nanoTime();
CAMERAS.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory,true, UPDATE_STATUS); // true - use lasers
System.out.println("\"Acquire\" command finished in ("+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec");
......@@ -3419,6 +3426,7 @@ if (MORE_BUTTONS) {
}
// acquire camera image here, no lasers.
FOCUS_MEASUREMENT_PARAMETERS.sensorTemperature=CAMERAS.getSensorTemperature(0,FOCUS_MEASUREMENT_PARAMETERS.EEPROM_channel);
POWER_CONTROL.lightsOnWithDelay();
imp_sel= CAMERAS.acquireSingleImage (
false, //boolean useLasers,
UPDATE_STATUS);
......@@ -3533,6 +3541,7 @@ if (MORE_BUTTONS) {
// long startTime=System.nanoTime();
FOCUS_MEASUREMENT_PARAMETERS.sensorTemperature=CAMERAS.getSensorTemperature(0,FOCUS_MEASUREMENT_PARAMETERS.EEPROM_channel);
CAMERAS.debugLevel=DEBUG_LEVEL;
POWER_CONTROL.lightsOnWithDelay();
imp_sel= CAMERAS.acquireSingleImage (
UV_LED_LASERS,
UPDATE_STATUS);
......@@ -3587,6 +3596,7 @@ if (MORE_BUTTONS) {
return;
}
}
POWER_CONTROL.lightsOnWithDelay();
long startTime=System.nanoTime();
FOCUS_MEASUREMENT_PARAMETERS.sensorTemperature=CAMERAS.getSensorTemperature(0,FOCUS_MEASUREMENT_PARAMETERS.EEPROM_channel);
imp_sel= CAMERAS.acquireSingleImage (
......@@ -3874,6 +3884,7 @@ if (MORE_BUTTONS) {
return;
}
}
POWER_CONTROL.lightsOnWithDelay();
if (matchSimulatedPattern==null) {
matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // new instance, all reset
}
......@@ -4145,7 +4156,7 @@ if (MORE_BUTTONS) {
sampleCoord,
this.SYNC_COMMAND.stopRequested);
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.setAdjustMode(false,null);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES, true);
MOTORS.addCurrentHistoryToFocusingField(FOCUSING_FIELD);
System.out.println("Saving measurement history to "+path);
......@@ -4171,10 +4182,12 @@ if (MORE_BUTTONS) {
double rms_pure= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, true);
System.out.println("rms="+rms+", rms_pure="+rms_pure+" - with old parameters may be well off.");
remoteNotifyComplete();
POWER_CONTROL.setPower("light","off");
if (FOCUS_MEASUREMENT_PARAMETERS.scanRunLMA){
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.setAdjustMode(false,null);
boolean OK=FOCUSING_FIELD.LevenbergMarquardt(
null, // measurement
null, //int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
null, // measurements
false, // true, // open dialog
true,// boolean autoSel,
DEBUG_LEVEL); //boolean openDialog, int debugLevel){
......@@ -4601,7 +4614,7 @@ if (MORE_BUTTONS) {
if (!restoreFocusingHistory(false)) return; // try to restore from the saved history file
}
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.setAdjustMode(false,null);
if (!FOCUSING_FIELD.configureDataVector(
false, // boolean silent,
"Re-configure curvature parameters", // String title
......@@ -4662,9 +4675,10 @@ if (MORE_BUTTONS) {
}
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.setAdjustMode(false,null);
boolean OK=FOCUSING_FIELD.LevenbergMarquardt(
null, // measurement
null, // int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
null, // measurements
true, // open dialog
true,// boolean autoSel,
DEBUG_LEVEL); //boolean openDialog, int debugLevel){
......@@ -4871,10 +4885,10 @@ if (MORE_BUTTONS) {
double pX0;
double pY0;
if (FOCUSING_FIELD!=null){
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
sampleCoord=FOCUSING_FIELD.getSampleCoord();
pX0=FOCUSING_FIELD.pX0_distortions;
pY0=FOCUSING_FIELD.pY0_distortions;
} else {
pX0=FOCUS_MEASUREMENT_PARAMETERS.result_PX0;
pY0=FOCUS_MEASUREMENT_PARAMETERS.result_PY0;
......@@ -5240,6 +5254,7 @@ if (MORE_BUTTONS) {
}
double [][][] sampleCoord=null;
if (FOCUSING_FIELD!=null){
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
sampleCoord=FOCUSING_FIELD.getSampleCoord();
FOCUSING_FIELD.testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
} else {
......@@ -5281,18 +5296,56 @@ if (MORE_BUTTONS) {
POWER_CONTROL.showDialog("Configure power control", true);
return;
}
//"Replay Hist"
/* ======================================================================== */
FocusingField ffReplay=null; // will be passed to a next command
if (label.equals("Replay Hist")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) {
String msg="FOCUSING_FIELD is null";
System.out.println("msg");
IJ.showMessage("Error",msg);
return;
}
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
ffReplay=new FocusingField(
false, // true, // boolean smart, // do not open dialog if default matches
FOCUS_MEASUREMENT_PARAMETERS.focusingHistoryFile, // FOCUSING_FIELD_HISTORY_PATH, //"",//); //String defaultPath); // AtomicInteger stopRequested
this.SYNC_COMMAND.stopRequested);
String path=FOCUSING_FIELD.getHistoryPath();
if (path==null) return; // did not load
GenericDialog gd=new GenericDialog("Select Replay mode");
boolean modeTempScan=true;
gd.addCheckbox("Calculate Thermal parameters from the restored history (false - just average)", modeTempScan);
gd.showDialog();
if (gd.wasCanceled()) return;
modeTempScan=gd.getNextBoolean();
label=modeTempScan?"Temp. Scan":"Focus Average";
FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics=true;
// And fall through to the next command
}
// "Restore History"
/* ======================================================================== */
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 replayMode= ffReplay != null;
String [] zTxTyAdjustModeNames={"keep", "common","individual"};
String [] zTxTyNames={"z", "tx","ty"};
// boolean useLMA=true;
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
GenericDialog gd = new GenericDialog("Temperature Scan");
GenericDialog gd = new GenericDialog(modeAverage?"Averaging measurements":"Temperature Scan");
//replayMode
double scanMinutes=modeAverage?2.0:30.0;
if (replayMode){
} else {
if (modeAverage) {
gd.addMessage("This program will repetitively measure focal distance for specified time and average (and record) results.");
} else {
......@@ -5305,10 +5358,9 @@ if (MORE_BUTTONS) {
}
}
gd.addCheckbox("Erase previous measurement history",modeAverage);
gd.addCheckbox("Allow tilt scan when looking for the best fit",!noTiltScan);
// gd.addCheckbox("Allow tilt scan when looking for the best fit",!noTiltScan);
gd.addCheckbox ("Use lens aberration model (if available) for focal distance and tilts", FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics);
// gd.addCheckbox("Use LMA calculations for focus/tilt",useLMA);
double scanMinutes=modeAverage?2.0:30.0;
// gd.addCheckbox("Use LMA calculations for focus/tilt",useLMA);
if (modeAverage) {
gd.addNumericField("Measure for ", scanMinutes , 1,5," minutes");
} else {
......@@ -5317,16 +5369,31 @@ if (MORE_BUTTONS) {
gd.addNumericField("Heater ON time", FOCUS_MEASUREMENT_PARAMETERS.powerControlHeaterOnMinutes, 1,5,"min");
gd.addNumericField("Both heater and fan OFF time", FOCUS_MEASUREMENT_PARAMETERS.powerControlNeitherOnMinutes, 1,5,"min");
gd.addNumericField("Fan ON time", FOCUS_MEASUREMENT_PARAMETERS.powerControlFanOnMinutes, 1,5,"min");
gd.addNumericField("Report focal length at this temperature", FOCUS_MEASUREMENT_PARAMETERS.reportTemperature, 1,5,"C");
}
}
gd.addCheckbox("Allow tilt scan when looking for the best fit",!noTiltScan);
if (FOCUSING_FIELD!=null) {
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
for (int n=0;n<FOCUSING_FIELD.zTxTyAdjustMode.length;n++){
gd.addChoice("Adjust "+zTxTyNames[n]+" mode",zTxTyAdjustModeNames,zTxTyAdjustModeNames[FOCUSING_FIELD.zTxTyAdjustMode[n]]);
}
gd.addChoice("Recalculate tilts during averaging",zTxTyAdjustModeNames,zTxTyAdjustModeNames[FOCUSING_FIELD.recalculateAverageTilts]);
// gd.addCheckbox ("Store new calculated (during averaging) tilts", FOCUSING_FIELD.updateAverageTilts);
}
gd.showDialog();
if (gd.wasCanceled()) return;
if (replayMode){
} else {
if (!modeAverage && gd.getNextBoolean()){ // was only asked in thermal scan mode
UV_LED_LASERS.debugLevel=DEBUG_LEVEL;
UV_LED_LASERS.lasersOff(FOCUS_MEASUREMENT_PARAMETERS);
if (MASTER_DEBUG_LEVEL>0) System.out.println ("Turned laser pointers off to protect from overheating");
}
if (gd.getNextBoolean()) MOTORS.clearHistory();
noTiltScan=!gd.getNextBoolean();
// noTiltScan=!gd.getNextBoolean();
FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics=gd.getNextBoolean();
// Only try to read history if useLMAMetrics is set
if (FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD==null)) {
......@@ -5336,7 +5403,7 @@ if (MORE_BUTTONS) {
}
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
}
boolean useLMA=FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null);
// boolean useLMA=FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null);
if (modeAverage) {
scanMinutes=gd.getNextNumber();
} else {
......@@ -5345,11 +5412,24 @@ if (MORE_BUTTONS) {
FOCUS_MEASUREMENT_PARAMETERS.powerControlHeaterOnMinutes=gd.getNextNumber();
FOCUS_MEASUREMENT_PARAMETERS.powerControlNeitherOnMinutes=gd.getNextNumber();
FOCUS_MEASUREMENT_PARAMETERS.powerControlFanOnMinutes=gd.getNextNumber();
FOCUS_MEASUREMENT_PARAMETERS.reportTemperature=gd.getNextNumber();
scanMinutes=FOCUS_MEASUREMENT_PARAMETERS.powerControlMaximalTemperature+
FOCUS_MEASUREMENT_PARAMETERS.powerControlHeaterOnMinutes+
FOCUS_MEASUREMENT_PARAMETERS.powerControlNeitherOnMinutes+
FOCUS_MEASUREMENT_PARAMETERS.powerControlFanOnMinutes;
}
}
noTiltScan=!gd.getNextBoolean();
if (FOCUSING_FIELD!=null) {
for (int n=0;n<FOCUSING_FIELD.zTxTyAdjustMode.length;n++){
FOCUSING_FIELD.zTxTyAdjustMode[n]=gd.getNextChoiceIndex();
}
FOCUSING_FIELD.recalculateAverageTilts=gd.getNextChoiceIndex();
// FOCUSING_FIELD.updateAverageTilts=gd.getNextBoolean();
}
boolean useLMA=FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null);
long startTime=System.nanoTime();
long endTime=startTime+(long) (6E10*scanMinutes);
if (MASTER_DEBUG_LEVEL>0) System.out.println(" startTime= "+startTime+", endTime="+endTime);
......@@ -5377,7 +5457,9 @@ if (MORE_BUTTONS) {
System.out.println("Optimal Ty="+FOCUSING_FIELD.qualBOptimizationResults[2]);
}
}
if (!replayMode){
long stateEndTime=endTime;
String [] stateNames={"IDLE","HEATING","WAITING","COOLING","FINISHED"};
if (!modeAverage) {
POWER_CONTROL.setPower("fan","off");
POWER_CONTROL.setPower("heater","on");
......@@ -5390,7 +5472,6 @@ if (MORE_BUTTONS) {
FOCUS_MEASUREMENT_PARAMETERS.powerControlNeitherOnMinutes+
FOCUS_MEASUREMENT_PARAMETERS.powerControlFanOnMinutes));
}
String [] stateNames={"IDLE","HEATING","WAITING","COOLING","FINISHED"};
while (System.nanoTime()<endTime){
moveAndMaybeProbe(
true, // just move, not probe
......@@ -5420,7 +5501,7 @@ if (MORE_BUTTONS) {
if (FOCUS_MEASUREMENT_PARAMETERS.sensorTemperature>=FOCUS_MEASUREMENT_PARAMETERS.powerControlMaximalTemperature){
POWER_CONTROL.setPower("heater","off");
}
// long secondsLeft=(long) (0.000000001*(endTime-System.nanoTime()));
// long secondsLeft=(long) (0.000000001*(endTime-System.nanoTime()));
long secondsLeft=(long) (0.000000001*(endTime-System.nanoTime()));
if (secondsLeft<0) secondsLeft=0;
long secondsLeftState=(long) (0.000000001*(stateEndTime-System.nanoTime()));
......@@ -5460,11 +5541,21 @@ if (MORE_BUTTONS) {
POWER_CONTROL.setPower("fan","off");
POWER_CONTROL.setPower("heater","off");
}
}
// LMA version
FocusingField ff= null;
double [] ZTM=null;
if (useLMA){
// boolean replayMode= ffReplay != null;
if (replayMode) {
ff=ffReplay;
ff.setDebugLevel(DEBUG_LEVEL);
ff.setAdjustMode(false,null);
if (PROPERTIES!=null) ff.getProperties("FOCUSING_FIELD.", PROPERTIES,true);
runs=ff.measurements.size();
} else {
ff= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
......@@ -5476,42 +5567,29 @@ if (MORE_BUTTONS) {
pY0,
sampleCoord,
this.SYNC_COMMAND.stopRequested);
ff.setDebugLevel(DEBUG_LEVEL);
ff.setAdjustMode(false);
ff.setAdjustMode(false,null);
if (PROPERTIES!=null) ff.getProperties("FOCUSING_FIELD.", PROPERTIES,true);
MOTORS.addCurrentHistoryToFocusingField(
ff,
(runs==0)?0:(MOTORS.historySize()-runs),
MOTORS.historySize()); // all newly acquired
// TODO: Remove after checking average
/*
}
// TODO: Remove after checking average - no, it is needed again as it calculates average through LMA simultaneously
if (modeAverage && (FOCUSING_FIELD!=null)){ // calculate/show average over the last run - only in "average" mode
double [] ZTM=FOCUSING_FIELD.averageZTM(
ZTM= FOCUSING_FIELD.averageZTM( // finds zc, not z0
noTiltScan,
ff, // no tilt scan - faster
true); // noMotors
FOCUSING_FIELD.recalculateAverageTilts); // boolean keepTilt){ // keep existent tilt
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 (absolute - "+IJ.d2s(ZTM[0]+FOCUSING_FIELD.qualBOptimizationResults[0],3)+"um)\n"+
"Relative horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm (absolute - "+IJ.d2s(ZTM[1]+FOCUSING_FIELD.qualBOptimizationResults[1],3)+"um.mm)\n"+
"Relative vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm (absolute - "+IJ.d2s(ZTM[2]+FOCUSING_FIELD.qualBOptimizationResults[2],3)+"um.mm)\n";
if (ZTM.length>3) {
msg+="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) {
if (FOCUS_MEASUREMENT_PARAMETERS.saveResults && !replayMode) {
String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);
File dFile=new File(dir);
if (!dFile.isDirectory() && !dFile.mkdirs()) {
......@@ -5521,7 +5599,6 @@ if (MORE_BUTTONS) {
}
String lensPrefix="";
if (FOCUS_MEASUREMENT_PARAMETERS.includeLensSerial && (FOCUS_MEASUREMENT_PARAMETERS.lensSerial.length()>0)){
// lensPrefix=String.format("LENS%S-",FOCUS_MEASUREMENT_PARAMETERS.lensSerial);
lensPrefix=String.format("LENS%S-S%02d-",FOCUS_MEASUREMENT_PARAMETERS.lensSerial,FOCUS_MEASUREMENT_PARAMETERS.manufacturingState);
}
String path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+
......@@ -5565,14 +5642,18 @@ if (MORE_BUTTONS) {
// Calculate and show average distances and tilts for measured history
if (!modeAverage) {
double [] lastKT;
double [] allKT;
if (!replayMode){
remoteNotifyComplete();
double [] lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
POWER_CONTROL.setPower("light","off");
lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
useLMA,
runs, // number of last samples from history to use, 0 - use all
FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightY
);
double [] allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
useLMA,
0, // number of last samples from history to use, 0 - use all
FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
......@@ -5584,18 +5665,32 @@ if (MORE_BUTTONS) {
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=
"Focal distance temperature expansion is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,2)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,2)+")"+
"Focal distance temperature expansion is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,3)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,3)+")"+
" 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)\n"+
"Focal distance at "+FOCUS_MEASUREMENT_PARAMETERS.reportTemperature+ "C is "+
IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20+
(FOCUS_MEASUREMENT_PARAMETERS.reportTemperature-20)*FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,2)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20+
(FOCUS_MEASUREMENT_PARAMETERS.reportTemperature-20)*FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,2)+")"+
" microns, measured from this run (measured from all the history)";
System.out.println(msg);
IJ.showMessage("Info",msg);
}
}
// Now in LMA mode - recalculate and overwrite
/*
/* */
if (useLMA){
if (replayMode) {
ff=ffReplay;
ff.setDebugLevel(DEBUG_LEVEL);
ff.setAdjustMode(false,null);
if (PROPERTIES!=null) ff.getProperties("FOCUSING_FIELD.", PROPERTIES,true);
runs=ff.measurements.size();
} else {
ff= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
......@@ -5607,50 +5702,94 @@ if (MORE_BUTTONS) {
pY0,
sampleCoord,
this.SYNC_COMMAND.stopRequested);
ff.setDebugLevel(DEBUG_LEVEL);
ff.setAdjustMode(false);
ff.setAdjustMode(false,null);
if (PROPERTIES!=null) ff.getProperties("FOCUSING_FIELD.", PROPERTIES,true);
MOTORS.addCurrentHistoryToFocusingField(ff); // all, not just newly acquired
if (MASTER_DEBUG_LEVEL>0){
System.out.println ("*** Calculating focal distance shift for each of "+MOTORS.historySize()+" recorded measurments ***");
}
boolean noMotors=true;
double [][] allZTM=FOCUSING_FIELD.getAllZTM(
}
// finds zc, not z0
double [][] allZTT=FOCUSING_FIELD.getAllZTT( // z, tx, ty, temperature - may contain null for bad measurements
noTiltScan,
ff, // no tilt scan (supposed to be adjusted
noMotors); // boolean noMotors) // do not calculate correction
ff, // no tilt scan - faster
FOCUSING_FIELD.recalculateAverageTilts); // boolean keepTilt){ // keep existent tilt
lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
allZTM,
allZTT,
runs
);
allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
allZTM,
allZTT,
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)+")"+
}
/* */
}
if (useLMA){
gd=new GenericDialog(modeAverage?"Averaging results":"Thermal scanning results");
String msg="";
if (modeAverage){
if (ZTM!=null) {
msg="Average (through LMA):\n"+
"Relative focal shift "+IJ.d2s(ZTM[0],3)+"um (absolute - "+IJ.d2s(ZTM[0]+FOCUSING_FIELD.qualBOptimizationResults[0],3)+"um)\n"+
"Relative horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm (absolute - "+IJ.d2s(ZTM[1]+FOCUSING_FIELD.qualBOptimizationResults[1],3)+"um.mm)\n"+
"Relative vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm (absolute - "+IJ.d2s(ZTM[2]+FOCUSING_FIELD.qualBOptimizationResults[2],3)+"um.mm)\n";
} else {
msg="Failed to calulate average focus/tilt";
}
}else {
msg=
"Determined by LMA: Focal distance temperature expansion is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,3)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,3)+")"+
" 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)\n"+
"Focal distance at "+FOCUS_MEASUREMENT_PARAMETERS.reportTemperature+ "C is "+
IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20+
(FOCUS_MEASUREMENT_PARAMETERS.reportTemperature-20)*FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,2)+
" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20+
(FOCUS_MEASUREMENT_PARAMETERS.reportTemperature-20)*FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,2)+")"+
" microns, measured from this run (measured from all the history)";
}
System.out.println(msg);
IJ.showMessage("Info",msg);
gd.addMessage(msg);
double [][] zTxTyAbsRel=null;
if (FOCUSING_FIELD.recalculateAverageTilts==1){ // only if recalculated
zTxTyAbsRel=FOCUSING_FIELD.getZ0TxTyAbsRel(); // z - z0, not zc here !
double [][] zcZ0TxTy=FOCUSING_FIELD.getZcZ0TxTy(ff.measurements);
gd.addMessage("----------------------");
msg= "Average relative z0 parameter: "+IJ.d2s(zTxTyAbsRel[1][0],3)+"um (absolute: "+IJ.d2s(zTxTyAbsRel[0][0],3)+"um\n"+
"Average relative tx parameter: "+IJ.d2s(zTxTyAbsRel[1][1],3)+"um/mm (absolute: "+IJ.d2s(zTxTyAbsRel[0][1],3)+"um/mm\n"+
"Average relative ty parameter: "+IJ.d2s(zTxTyAbsRel[1][2],3)+"um/mm (absolute: "+IJ.d2s(zTxTyAbsRel[0][2],3)+"um/mm\n\n";
msg+= "Average zc: "+IJ.d2s(zcZ0TxTy[0][0],3)+"um\n"+
"Average Tilt x: "+IJ.d2s(zcZ0TxTy[0][1],3)+"um/mm\n"+
"Average Tilt y: "+IJ.d2s(zcZ0TxTy[0][2],3)+"um/mm\n";
System.out.println(msg);
gd.addMessage(msg);
gd.addCheckbox("Store calculated tilts, defaultValue",FOCUSING_FIELD.updateAverageTilts);
}
gd.showDialog();
if (!gd.wasCanceled()){
if (FOCUSING_FIELD.recalculateAverageTilts==1){ // only if recalculated
FOCUSING_FIELD.updateAverageTilts=gd.getNextBoolean();
if (FOCUSING_FIELD.updateAverageTilts){
FOCUSING_FIELD.avgTx=zTxTyAbsRel[0][1]; // average absolute tilt X (optionally used when finding Z of the glued SFE)
FOCUSING_FIELD.avgTy=zTxTyAbsRel[0][2]; // average absolute tilt Y (optionally used when finding Z of the glued SFE)
}
}
}
*/
}
saveCurrentConfig();
return;
}
/// "No-move measure"
/* ======================================================================== */
if (label.equals("Configure Goniometer")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
......@@ -5710,12 +5849,14 @@ if (MORE_BUTTONS) {
"Taget angular size vertical: "+IJ.d2s(targetAngleVertical,1)+" degrees\n"
);
GONIOMETER.debugLevel=DEBUG_LEVEL;
POWER_CONTROL.lightsOnWithDelay();
boolean goniometerScanOK=GONIOMETER.scanAndAcquire(
targetAngleHorizontal,
targetAngleVertical,
this.SYNC_COMMAND.stopRequested,
UPDATE_STATUS);
System.out.println ("GONIOMETER.scanAndAcquireI() "+(goniometerScanOK?"finished OK":"failed"));
POWER_CONTROL.setPower("light","off");
return;
}
......@@ -9226,7 +9367,8 @@ if (MORE_BUTTONS) {
if (path==null) return false; // did not load
FOCUS_MEASUREMENT_PARAMETERS.focusingHistoryFile=path;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
FOCUSING_FIELD.setThreads(THREADS_MAX);
FOCUSING_FIELD.setAdjustMode(false, null);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES,true); // keep distortions center from history
System.out.println("Loaded FocusingField from "+path);
if (!FOCUSING_FIELD.configureDataVector(
......@@ -9295,7 +9437,9 @@ if (MORE_BUTTONS) {
//get measurement
FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
// calculate z, tx, ty, m1,m2,m3
int [] adjustModeAllCommon={1,1,1};
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
adjustModeAllCommon, // FOCUSING_FIELD.zTxTyAdjustMode,
false, // allow tilt scan
fFMeasurement,
false, // parallel move
......@@ -9450,7 +9594,9 @@ if (MORE_BUTTONS) {
}
}
if (parallelMove){ // ignore/recalculate newMotors data
int [] adjustZOnly={1,0,0};
zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
adjustZOnly, // adjustAll,
false,// disable tilt scan
fFMeasurement,
true, // recalculate with parallel move only
......@@ -11247,6 +11393,7 @@ if (MORE_BUTTONS) {
"", //String message,
!noHysteresis); //false); //focusMeasurementParameters.compensateHysteresis); //boolean hysteresis)
focusMeasurementParameters.sensorTemperature=camerasInterface.getSensorTemperature(0,focusMeasurementParameters.EEPROM_channel);
POWER_CONTROL.lightsOnWithDelay();
ImagePlus imp= camerasInterface.acquireSingleImage (
false, //boolean useLasers,
updateStatus);
......@@ -11306,13 +11453,17 @@ if (MORE_BUTTONS) {
focusMeasurementParameters.sensorTemperature,
focusingMotors.readElphel10364Motors(), //focusingHistory.getPosition(), //null?
rFullResults[0]); //focusingState.getSamples());
try{
zTxTy=FOCUSING_FIELD.adjustLMA(
FOCUSING_FIELD.zTxTyAdjustMode,
true, // false, // noTiltScan
fFMeasurement,
false, // parallel move
true, // boolean noQualB, // do not re-claculate testQualB
true); // boolean noAdjust); // do not calculate correction
} catch (Exception e){
System.out.println("FOCUSING_FIELD.adjustLMA() failed");
}
if (zTxTy!=null){
metrics[ca][0]=zTxTy[0]; // was far/near
metrics[ca][1]=zTxTy[1];
......@@ -11402,6 +11553,7 @@ if (MORE_BUTTONS) {
focusMeasurementParameters.compensateHysteresis); //boolean hysteresis)
}
focusMeasurementParameters.sensorTemperature=camerasInterface.getSensorTemperature(0,FOCUS_MEASUREMENT_PARAMETERS.EEPROM_channel);
POWER_CONTROL.lightsOnWithDelay();
ImagePlus imp= camerasInterface.acquireSingleImage (
false, //boolean useLasers,
updateStatus);
......
src/main/java/CalibrationHardwareInterface.java
View file @ d14a3970
......@@ -47,6 +47,7 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.Properties;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import javax.xml.parsers.DocumentBuilder;
......@@ -1800,14 +1801,18 @@ public class CalibrationHardwareInterface {
}
public static class PowerControl{
public boolean [] states={false,false,false};
public String [] groups={"heater","fan","light"};
public int debugLevel=1;
private String powerIP="192.168.0.80";
private double lightsDelay=5.0;
private final String urlFormat="http://%s/insteon/index.php?cmd=%s&group=%s";
private final String rootElement="Document";
public boolean powerConrtolEnabled=false;
public void setProperties(String prefix,Properties properties){
properties.setProperty(prefix+"powerIP",this.powerIP+"");
properties.setProperty(prefix+"powerConrtolEnabled",this.powerConrtolEnabled+"");
properties.setProperty(prefix+"lightsDelay",this.lightsDelay+"");
}
//Integer.decode(string)
public void getProperties(String prefix,Properties properties){
......@@ -1815,6 +1820,8 @@ public class CalibrationHardwareInterface {
this.powerIP=properties.getProperty(prefix+"powerIP");
if (properties.getProperty(prefix+"powerConrtolEnabled")!=null)
this.powerConrtolEnabled=Boolean.parseBoolean(properties.getProperty(prefix+"powerConrtolEnabled"));
if (properties.getProperty(prefix+"lightsDelay")!=null)
this.lightsDelay=Double.parseDouble(properties.getProperty(prefix+"lightsDelay"));
}
public boolean setPower (String group, String state){
......@@ -1822,6 +1829,7 @@ public class CalibrationHardwareInterface {
System.out.println("=== Power control is disabled ===");
return false;
}
System.out.println("=== Power control: "+group+":"+state+" ===");
String url=String.format(urlFormat,this.powerIP,state,group);
if (this.debugLevel>2) System.out.println("setPower: "+url);
Document dom=null;
......@@ -1856,16 +1864,22 @@ public class CalibrationHardwareInterface {
se.printStackTrace();
return false;
}
for (int i=0;i<this.groups.length;i++) if (this.groups[i].equals(group)){
this.states[i]=state.equals("on");
}
return true;
}
public boolean showDialog(String title, boolean control) {
GenericDialog gd = new GenericDialog(title);
boolean heaterOn=false, fanOn=false;
gd.addCheckbox("Enable power control (heater, fan) ", this.powerConrtolEnabled);
boolean heaterOn=false, fanOn=false, lightOn=false;
gd.addCheckbox("Enable power control (heater, fan, lights) ", this.powerConrtolEnabled);
gd.addStringField("IP address of the power control",this.powerIP,15);
gd.addNumericField("Delay after lights on", this.lightsDelay, 1,4,"sec");
if (control){
gd.addCheckbox("Heater On", heaterOn);
gd.addCheckbox("Fan On", fanOn);
gd.addCheckbox("Lights On", lightOn);
}
WindowTools.addScrollBars(gd);
if (control) gd.enableYesNoCancel("OK", "Control Power");
......@@ -1873,16 +1887,33 @@ public class CalibrationHardwareInterface {
if (gd.wasCanceled()) return false;
this.powerConrtolEnabled=gd.getNextBoolean();
this.powerIP=gd.getNextString();
this.lightsDelay=gd.getNextNumber();
if (control){
heaterOn=gd.getNextBoolean();
fanOn=gd.getNextBoolean();
lightOn=gd.getNextBoolean();
if (!gd.wasOKed()) {
setPower("heater",heaterOn?"on":"off");
setPower("fan",fanOn?"on":"off");
setPower("light",lightOn?"on":"off");
}
}
return true;
}
public void lightsOnWithDelay(){
if (this.states[2] || !this.powerConrtolEnabled) return; // already on
setPower("light","on");
System.out.print("Sleeping "+this.lightsDelay+" seconds to let lights stibilize on...");
try {
TimeUnit.MILLISECONDS.sleep((long) (1000*this.lightsDelay));
} catch (InterruptedException e) {
System.out.println("Sleep was interrupted");
// TODO Auto-generated catch block
}
System.out.println(" Done");
}
public boolean isPowerControlEnabled(){
return this.powerConrtolEnabled;
}
......@@ -5218,22 +5249,26 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
}
public double [] temperatureLinearApproximation(
double [][] ZTM, // Z, tXx, tY, m1,m2,m3 found with LMA
double [][] ZTT, // Z, tXx, tY, m1,m2,m3 found with LMA - may contain NaN
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;
// if (numSamples<=0) this.history.size();
// if (numSamples>this.history.size()) numSamples=this.history.size();
// int firstSample=this.history.size()-numSamples;
if (numSamples<=0) numSamples=ZTT.length;
if (numSamples>ZTT.length) numSamples=ZTT.length;
int firstSample=ZTT.length-numSamples;
int numGoodSamples=0;
for (int nSample=0;nSample<numSamples;nSample++){
if (ZTM[firstSample+nSample]!=null) numGoodSamples++;
if (ZTT[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
for (int nSample=0;nSample<numSamples;nSample++) if (ZTT[firstSample+nSample]!=null) {
// data[index][0]=this.history.get(firstSample+nSample).getTemperature();
data[index][0]=ZTT[firstSample+nSample][3];
data[index++][1]=ZTT[firstSample+nSample][0]; // Z
}
PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
......
src/main/java/FocusingField.java
View file @ d14a3970
......@@ -93,6 +93,7 @@ public class FocusingField {
double filterSetsByRMS; // remove complete sets (same timestamp) with RMS greater than scaled average
boolean filterSetsByRMSTiltOnly; // only remove non-scan sets
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
int minBestLeftSamples; // minimal number of samples of the best channel/dir for adjustment
int minCenterSamplesBest; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
int minCenterSamplesTotal; // minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
int centerSamples; // number of center samples to consider for minLeftCenterSamples
......@@ -109,6 +110,13 @@ public class FocusingField {
double targetRelTiltX; // target tilt Horizontal
double targetRelTiltY; // target tilt Vertical
public double avgTx; // average absolute tilt X (optionally used when finding Z of the glued SFE)
public double avgTy; // average absolute tilt Y (optionally used when finding Z of the glued SFE)
public int [] zTxTyAdjustMode; //[3] - 0 - keep, 1 adjust common, 2 - adjust individual
public boolean updateAverageTilts; // update avgTx, avgTy after averaging measurements (in "Focus Average" and "Temp. Scan")
public int recalculateAverageTilts; // recalculate tilts during averaging, same values as in zTxTyAdjustMode
// when false - tangential is master
double [] minMeas; // pixels
double [] maxMeas; // pixels
......@@ -223,7 +231,6 @@ public class FocusingField {
double [] currentVector=null;
double [] nextVector=null;
double [] savedVector=null;
boolean [][] goodCalibratedSamples=null;
......@@ -283,6 +290,8 @@ public class FocusingField {
filterSetsByRMSTiltOnly=true; // only remove non-scan sets
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
minBestLeftSamples=5; // minimal number of samples of the best channel/dir for adjustment (FIXME: still may fail if colinear and tilt free)
minCenterSamplesBest=4; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
minCenterSamplesTotal=0;// minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
centerSamples= 8; // there should remain at least of centerSamples closest to r==0
......@@ -298,6 +307,18 @@ public class FocusingField {
targetRelFocalShift=0.0; // target focal shift relative to best composite "sharpness"
targetRelTiltX=0.0; // target tilt Horizontal
targetRelTiltY=0.0; // target tilt Vertical
avgTx=0.0; // average absolute tilt X (optionally used when finding Z of the glued SFE)
avgTy=0.0; // average absolute tilt Y (optionally used when finding Z of the glued SFE)
zTxTyAdjustMode=new int[3]; //[3] - 0 - keep, 1 adjust common, 2 - adjust individual
zTxTyAdjustMode[0]=1;
zTxTyAdjustMode[1]=1;
zTxTyAdjustMode[2]=1;
updateAverageTilts=true;
recalculateAverageTilts=1; // recalculate, common
// when false - tangential is master
double [] minMeasDflt= {0.5,0.5,0.5,0.5,0.5,0.5}; // pixels
minMeas= minMeasDflt; // pixels
......@@ -439,6 +460,8 @@ public class FocusingField {
properties.setProperty(prefix+"filterSetsByRMS",filterSetsByRMS+"");
properties.setProperty(prefix+"filterSetsByRMSTiltOnly",filterSetsByRMSTiltOnly+"");
properties.setProperty(prefix+"minLeftSamples",minLeftSamples+"");
properties.setProperty(prefix+"minBestLeftSamples",minBestLeftSamples+"");
properties.setProperty(prefix+"minCenterSamplesBest",minCenterSamplesBest+"");
properties.setProperty(prefix+"minCenterSamplesTotal",minCenterSamplesTotal+"");
properties.setProperty(prefix+"centerSamples",centerSamples+"");
......@@ -455,6 +478,11 @@ public class FocusingField {
properties.setProperty(prefix+"targetRelTiltX",targetRelTiltX+"");
properties.setProperty(prefix+"targetRelTiltY",targetRelTiltY+"");
properties.setProperty(prefix+"avgTx",avgTx+"");
properties.setProperty(prefix+"avgTy",avgTy+"");
for (int i=0;i<zTxTyAdjustMode.length; i++) properties.setProperty(prefix+"zTxTyAdjustMode_"+i,zTxTyAdjustMode[i]+"");
properties.setProperty(prefix+"updateAverageTilts",updateAverageTilts+"");
properties.setProperty(prefix+"recalculateAverageTilts",recalculateAverageTilts+"");
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]+"");
......@@ -594,6 +622,10 @@ public class FocusingField {
filterSetsByRMSTiltOnly=Boolean.parseBoolean(properties.getProperty(prefix+"filterSetsByRMSTiltOnly"));
if (properties.getProperty(prefix+"minLeftSamples")!=null)
minLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minLeftSamples"));
if (properties.getProperty(prefix+"minBestLeftSamples")!=null)
minBestLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minBestLeftSamples"));
if (properties.getProperty(prefix+"minCenterSamplesBest")!=null)
minCenterSamplesBest=Integer.parseInt(properties.getProperty(prefix+"minCenterSamplesBest"));
if (properties.getProperty(prefix+"minCenterSamplesTotal")!=null)
......@@ -622,6 +654,18 @@ public class FocusingField {
if (properties.getProperty(prefix+"targetRelTiltY")!=null)
targetRelTiltY=Double.parseDouble(properties.getProperty(prefix+"targetRelTiltY"));
if (properties.getProperty(prefix+"avgTx")!=null)
avgTx=Double.parseDouble(properties.getProperty(prefix+"avgTx"));
if (properties.getProperty(prefix+"avgTy")!=null)
avgTy=Double.parseDouble(properties.getProperty(prefix+"avgTy"));
for (int i=0;i<zTxTyAdjustMode.length;i++){
if (properties.getProperty(prefix+"zTxTyAdjustMode_"+i)!=null)
zTxTyAdjustMode[i]=Integer.parseInt(properties.getProperty(prefix+"zTxTyAdjustMode_"+i));
}
if (properties.getProperty(prefix+"updateAverageTilts")!=null)
updateAverageTilts=Boolean.parseBoolean(properties.getProperty(prefix+"updateAverageTilts"));
if (properties.getProperty(prefix+"recalculateAverageTilts")!=null)
recalculateAverageTilts=Integer.parseInt(properties.getProperty(prefix+"recalculateAverageTilts"));
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)
......@@ -735,9 +779,11 @@ public class FocusingField {
public void setDebugLevel(int debugLevel){
this.debugLevel=debugLevel;
}
public void setAdjustMode(boolean mode){
public void setAdjustMode(
boolean mode,
int [] zTxTyMode){ //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
if ((fieldFitting!=null) && (fieldFitting.mechanicalFocusingModel!=null)) {
fieldFitting.mechanicalFocusingModel.setAdjustMode(mode);
fieldFitting.mechanicalFocusingModel.setAdjustMode(mode,zTxTyMode);
}
}
......@@ -796,6 +842,7 @@ public class MeasuredSample{
public double px;
public double py;
public int sampleIndex=0;
public int measurementIndex=-1;
public int channel;
public double value;
public double [] dPxyc=new double[2]; // derivative of the value by optical (aberration) center pixel X,Y
......@@ -809,6 +856,7 @@ public class MeasuredSample{
double px,
double py,
int sampleIndex,
int measurementIndex,
int channel,
double value,
double dPxc,
......@@ -824,6 +872,7 @@ public class MeasuredSample{
this.dPxyc[0]=dPxc;
this.dPxyc[1]=dPyc;
this.sampleIndex=sampleIndex;
this.measurementIndex=measurementIndex;
this.scan=scan;
}
}
......@@ -1210,6 +1259,80 @@ private boolean [] filterByValue (
return enable_out;
}
private boolean [] filterNotEnoughSamples(
boolean [] centerSamples,
boolean [] enable_in,
int minTotalCenterSamples,
int minBestChannelCenterSamples,
int minTotalSamples,
int minBestChannelSamples){
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
boolean [] enable_out=enable_in.clone();
int numFiltered=0;
int lastIndex;
int firstIndex;
int nextIndex=0;
String lastTimestamp="";
while (nextIndex < dataVector.length){
// find first enabled sample
for(firstIndex=nextIndex;(firstIndex<dataVector.length) && ((firstIndex < enable_in.length) && !enable_in[firstIndex]); firstIndex++);
lastTimestamp=dataVector[firstIndex].timestamp;
lastIndex=firstIndex;
for (nextIndex=firstIndex; nextIndex<dataVector.length; nextIndex++) if ((nextIndex >= enable_in.length) || enable_in[nextIndex]){
if (dataVector[nextIndex].timestamp.equals(lastTimestamp)) lastIndex=nextIndex;
else break;
}
int [] numCenterSamples= new int [getNumChannels()];
int [] numSamples= new int [getNumChannels()];
for (int chn=0;chn<getNumChannels();chn++){
numCenterSamples[chn]=0;
numSamples[chn]=0;
}
for (int index=firstIndex;index<=lastIndex;index++) if ((index >= enable_in.length) || enable_in[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
numSamples[chn]++;
if (centerSamples[sample]) numCenterSamples[chn]++;
}
int numTotalCenterSamples=0;
int numBestChannelCenterSamples=0;
int numTotalSamples=0;
int numBestChannelSamples=0;
for (int chn=0;chn<getNumChannels();chn++){
numTotalSamples+= numSamples[chn];
numTotalCenterSamples+=numCenterSamples[chn];
if (numBestChannelSamples<numSamples[chn]) numBestChannelSamples = numSamples[chn];
if (numBestChannelCenterSamples<numCenterSamples[chn]) numBestChannelCenterSamples = numCenterSamples[chn];
}
if (
(numTotalCenterSamples < minTotalCenterSamples) ||
(numBestChannelCenterSamples < minBestChannelCenterSamples) ||
(numTotalSamples < minTotalSamples) ||
(numBestChannelSamples < minBestChannelSamples)){
// Remove all samples in this measurement
for (int index=firstIndex;index<=lastIndex;index++) if ((index >= enable_in.length) || enable_in[index]){
numFiltered++;
enable_out[index]=false;
}
}
}
if (debugLevel > 1) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterNotEnoughSamples("+
minTotalCenterSamples+","+
minBestChannelCenterSamples+","+
minTotalSamples+","+
minBestChannelSamples+"): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
/*
public boolean checkEnoughCenter(
boolean [] centerSamples,
boolean [] enable_in,
......@@ -1236,6 +1359,7 @@ public int [] getNumCenterSamples( // per channel (disabled channels are already
}
return numSamples;
}
*/
public boolean [] getCenterSamples(int num){
double [] sampleCorrRadiuses=fieldFitting.getSampleRadiuses();
......@@ -1515,7 +1639,7 @@ private boolean [] filterTooFar(
double z= fieldFitting.getMotorsZ(
dataVector[index].motors, //int [] motors, // 3 motor coordinates
dataVector[index].px, // double px, // pixel x
dataVector[index].px); // double py)
dataVector[index].py); // double py) / was px!
double w=weightReference[chn]-dataVector[index].value; // maybe use square of w?
data[chn][sample][0]+=w;
data[chn][sample][1]+=w*z;
......@@ -1636,10 +1760,11 @@ private boolean [] filterSets(
double scaleRMS,
boolean [] scanMask // if not null, will not touch samples where true
){
double [] sv=fieldFitting.createParameterVector(sagittalMaster);
double [] sv=fieldFitting.createParameterVector(sagittalMaster); // FIXME:
double [] fX= createFXandJacobian(sv, false);
double maxRMS= scaleRMS*calcErrorDiffY(fX, true);
int [] indices=getSetIndices();
// int [] indices=getSetIndices();
Integer [] indices=getSetIndices().toArray(new Integer[0]); // uses dataVector; - new measurements
double [] setRMA=calcErrorsPerSet(fX);
if (enable_in==null) {
......@@ -1697,9 +1822,6 @@ private boolean [] filterLowNeighbors(
while (nextIndex < dataVector.length){
// find first enabled sample
for(firstIndex=nextIndex;(firstIndex<dataVector.length) && ((firstIndex < enable_in.length) && !enable_in[firstIndex]); firstIndex++);
// if (firstIndex>=dataVector.length){
// break;
// }
lastTimestamp=dataVector[firstIndex].timestamp;
lastIndex=firstIndex;
for (nextIndex=firstIndex; nextIndex<dataVector.length; nextIndex++) if ((nextIndex >= enable_in.length) || enable_in[nextIndex]){
......@@ -1717,9 +1839,6 @@ private boolean [] filterLowNeighbors(
boolean [] left=usedSamples[chn].clone();
for (int y=0;y<height;y++) for (int x=0;x<width;x++) if (usedSamples[chn][y*width+x]){
int n=0;
// if ((chn==2) && (y==4) && (x==0)){ // debugging
// n=0;
// }
for (int d=0;d<dirs.length;d++){
int [] dXY=dirs[d].clone();
if (((x==0) && (dXY[0]<0)) || ((x==(width-1)) && (dXY[0]>0))) dXY[0]=-dXY[0];
......@@ -1939,7 +2058,14 @@ public void setDataVector(
// for compatibility with Distortions class\
public void commitParameterVector(double [] vector){
public void commitParameterVector(
double [] vector){
int [] zTxTyMode=fieldFitting.mechanicalFocusingModel.getZTxTyMode();
// fieldFitting.setCurrentVectorLength(vector.length);
if (zTxTyMode!=null) {
fieldFitting.commitParameterVectorZTxTy(vector);
return;
}
fieldFitting.commitParameterVector(vector,sagittalMaster);
// recalculate measured S,T (depend on center) if center is among fitted parameters
boolean [] centerSelect=fieldFitting.getCenterSelect();
......@@ -1960,7 +2086,9 @@ public void commitParameterVector(double [] vector){
}
}
public double [] createFXandJacobian( double [] vector, boolean createJacobian){
public double [] createFXandJacobian(
double [] vector,
boolean createJacobian){
commitParameterVector(vector);
return createFXandJacobian(createJacobian);
}
......@@ -1989,6 +2117,8 @@ public double [] createFXandJacobianMulti(
final boolean createJacobian
){
long startTime=System.nanoTime();
// final int [] zTxTyMode=fieldFitting.mechanicalFocusingModel.getZTxTyMode();
final boolean useZTxTy=fieldFitting.mechanicalFocusingModel.getZTxTyMode() != null;
int numCorrPar=fieldFitting.getNumberOfCorrParameters();
boolean [] selChannels=fieldFitting.getSelectedChannels();
final int [] selChanIndices= new int[selChannels.length];
......@@ -1996,17 +2126,25 @@ public double [] createFXandJacobianMulti(
for (int i=1;i<selChanIndices.length;i++){
selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
}
// if (zTxTyMode!=null) {
// fieldFitting.commitParameterVectorZTxTy(vector);
// return;
// }
final int numPars=fieldFitting.getNumberOfParameters(sagittalMaster);
int numRegPars=fieldFitting.getNumberOfRegularParameters(sagittalMaster);
final int numSelChn=fieldFitting.getNumberOfChannels();
final Thread[] threads = newThreadArray(threadsMax);
final ArrayList<ArrayList<PartialFXJac>> fxList = new ArrayList<ArrayList<PartialFXJac>>();
for (int ithread = 0; ithread < threads.length; ithread++) {
fxList.add(new ArrayList<PartialFXJac>());
}
// create list of indices of measurements corresponding to new timestamp/sample
String prevTimeStamp="";
// create list of indices of measurements corresponding to new timestamp/sample (up to 6 increment)
final ArrayList<Integer> measIndicesList=getSetSampleIndices(); // uses dataVector;
/* String prevTimeStamp="";
double prevPx=-1,prevPy=-1;
final ArrayList<Integer> measIndicesList = new ArrayList<Integer>(dataVector.length/getNumChannels());
for (int n=0;n<dataVector.length;n++){
MeasuredSample ms=dataVector[n];
......@@ -2014,10 +2152,9 @@ public double [] createFXandJacobianMulti(
measIndicesList.add(new Integer(n));
}
}
// measIndicesList.add(new Integer(dataVector.length));
*/
final AtomicInteger measIndex = new AtomicInteger(0);
final AtomicInteger threadIndexAtomic = new AtomicInteger(0);
// final boolean [] falseFalse={false,false};
final boolean [] centerSelect=correct_measurement_ST?fieldFitting.getCenterSelect():null; //falseFalse;
for (int ithread = 0; ithread < threads.length; ithread++) {
......@@ -2026,12 +2163,46 @@ public double [] createFXandJacobianMulti(
int threadIndex=threadIndexAtomic.getAndIncrement();
fxList.get(threadIndex).clear(); // not needed
double [][] derivs;
double [] blankPars=null;
if (useZTxTy){
if (createJacobian){
blankPars=new double[numPars];
for (int i=0;i<numPars;i++) blankPars[i]=0.0;
}
}
for (int startMeasIndex=measIndex.getAndIncrement(); startMeasIndex<measIndicesList.size();startMeasIndex=measIndex.getAndIncrement()){
int startMeas=measIndicesList.get(startMeasIndex);
int endMeas=(startMeasIndex==(measIndicesList.size()-1))?dataVector.length:measIndicesList.get(startMeasIndex+1);
MeasuredSample ms=dataVector[startMeas];
derivs=createJacobian?(new double[numSelChn][]):null;
double [] subData=fieldFitting.getValsDerivatives(
double [] subData;
if (useZTxTy){
subData=fieldFitting.getValsDerivativesZTxTy(
ms.measurementIndex, //-1, // <0 - use mechanicalFocusingModel z, tx, ty
ms.sampleIndex,
ms.motors, // 3 motor coordinates
ms.px, // pixel x
ms.py, // pixel y
derivs);
for (int n=startMeas;n<endMeas;n++){
ms=dataVector[n];
int chn=selChanIndices[ms.channel];
double [] zTxTyDerivs=null;
if (createJacobian && (derivs[chn]!=null)){
zTxTyDerivs=blankPars.clone();
for (int i=0;i<derivs[chn].length;i++){
int parIndex=fieldFitting.getZTMap(ms.measurementIndex, i); //n);
if (parIndex>=0) zTxTyDerivs[parIndex] = derivs[chn][i];
}
}
PartialFXJac partialFXJac = new PartialFXJac(n,
subData[chn],
zTxTyDerivs); // createJacobian?derivs[chn]:null);
fxList.get(threadIndex).add(partialFXJac);
}
} else {
subData=fieldFitting.getValsDerivatives(
// ms.measurementIndex, //-1, // <0 - use mechanicalFocusingModel z, tx, ty
ms.sampleIndex,
sagittalMaster,
ms.motors, // 3 motor coordinates
......@@ -2039,6 +2210,7 @@ public double [] createFXandJacobianMulti(
ms.py, // pixel y
derivs);
for (int n=startMeas;n<endMeas;n++){
ms=dataVector[n];
int chn=selChanIndices[ms.channel];
if (createJacobian && (centerSelect!=null)){
int np=0;
......@@ -2051,6 +2223,7 @@ public double [] createFXandJacobianMulti(
createJacobian?derivs[chn]:null);
fxList.get(threadIndex).add(partialFXJac);
}
}
}
......@@ -2078,7 +2251,7 @@ public double [] createFXandJacobianMulti(
}
}
if (debugLevel>1) System.out.println("#2 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),5));
if (createJacobian && (fieldFitting.sampleCorrChnParIndex!=null)) {
if (createJacobian && !useZTxTy && (fieldFitting.sampleCorrChnParIndex!=null)) {
// add mutual dependence of correction parameters. first - values (fx)
int index=dataVector.length; // add to the end of vector
int numSamples=getNumSamples();
......@@ -2145,6 +2318,8 @@ public double [] createFXandJacobianMulti(
}
public double [] createFXandJacobianSingle(boolean createJacobian){
final boolean useZTxTy=fieldFitting.mechanicalFocusingModel.getZTxTyMode() != null;
int numCorrPar=fieldFitting.getNumberOfCorrParameters();
double [] fx=new double[dataVector.length + numCorrPar ];
double [][] derivs=null;
......@@ -2168,7 +2343,19 @@ public double [] createFXandJacobianMulti(
for (int n=0;n<dataVector.length;n++){
MeasuredSample ms=dataVector[n];
if (!ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){
if (useZTxTy){
subData=fieldFitting.getValsDerivativesZTxTy( // fixed length derivative- 3 elements
ms.measurementIndex, //-1, // <0 - use mechanicalFocusingModel z, tx, ty
ms.sampleIndex,
ms.motors, // 3 motor coordinates
ms.px, // pixel x
ms.py, // pixel y
derivs);
} else {
subData=fieldFitting.getValsDerivatives(
// null, // double [] zTxTy, // null - use mechanicalFocusingModel data
//FIXME: - ***************** here needs actual index **************************
// ms.measurementIndex, //-1, // <0 - use mechanicalFocusingModel z, tx, ty
ms.sampleIndex,
sagittalMaster,
ms.motors, // 3 motor coordinates
......@@ -2179,16 +2366,24 @@ public double [] createFXandJacobianMulti(
prevPx=ms.px;
prevPy=ms.py;
}
}
fx[n]=subData[selChanIndices[ms.channel]];
if (createJacobian) {
double [] thisDerivs=derivs[selChanIndices[ms.channel]];
if (useZTxTy){
for (int i=0;i<numPars;i++) jacobian[i][n]=0.0;
for (int i=0;i<thisDerivs.length;i++){
int parIndex=fieldFitting.getZTMap(ms.measurementIndex, i); //n);
if (parIndex>=0) jacobian[parIndex][n] = thisDerivs[i];
}
} else {
// for (int i=0;i<numRegPars;i++){
if ((debugLevel>1) && (debugParameter>=0)){
if ((debugParameter<thisDerivs.length) && (thisDerivs[debugParameter]!=0.0)){
System.out.println("createFXandJacobian(): n="+n+" channel="+ms.channel+" chn. index="+selChanIndices[ms.channel]+
", sample="+ms.sampleIndex+" timestamp="+ms.timestamp+" derivative="+thisDerivs[debugParameter]);
}
}
// contains derivatives for normal and correction parameters
......@@ -2206,9 +2401,10 @@ public double [] createFXandJacobianMulti(
}
}
}
if (createJacobian) {
}
if (createJacobian && !useZTxTy) {
// add mutual dependence of correction parameters. first - values (fx)
// System.out.println("Using sampleCorrVector 1");
// System.out.println("Using sampleCorrVector 1");
int index=dataVector.length; // add to the end of vector
if (fieldFitting.sampleCorrChnParIndex!=null){
int numSamples=getNumSamples();
......@@ -2240,7 +2436,7 @@ public double [] createFXandJacobianMulti(
if (debugParameter>=0) debugJacobianParameter(debugParameter);
}
return fx;
}
}
public void debugJacobianPoint(int nPoint){
System.out.println("==== Non-zero parameters on which point #"+nPoint+" depends:");
......@@ -2305,11 +2501,21 @@ public double getRMS(double [] fx, boolean pure){
return Math.sqrt(sum);
}
public ArrayList<FocusingFieldMeasurement> singleMeasurement(FocusingFieldMeasurement measurement){
ArrayList<FocusingFieldMeasurement> sm=new ArrayList<FocusingFieldMeasurement>();
sm.add(measurement);
return sm;
}
public MeasuredSample [] createDataVector(FocusingFieldMeasurement measurement){
ArrayList<FocusingFieldMeasurement> singleMeasurement=new ArrayList<FocusingFieldMeasurement>();
singleMeasurement.add(measurement);
return createDataVector(singleMeasurement(measurement));
}
public MeasuredSample [] createDataVector(ArrayList<FocusingFieldMeasurement> measurements){
return createDataVector(
singleMeasurement,
measurements,
false, // calibrate
true, // update selection
currentPX0, // ignored
......@@ -2320,7 +2526,6 @@ public MeasuredSample [] createDataVector(FocusingFieldMeasurement measurement){
}
public MeasuredSample [] createDataVector(){
return createDataVector(
true, // boolean updateSelection,
......@@ -2691,6 +2896,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
sampleCoord[i][j][0], // px,
sampleCoord[i][j][1], // py,
flattenIndex(i,j),
nMeas,
chn,
value,
value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X
......@@ -2722,6 +2928,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
public double calcErrorDiffY(double [] fX, boolean pure){
int len=pure?dataVector.length:fX.length;
// if (debugLevel>0) System.out.println("debug calcErrorDiffY(): fX.length="+fX.length+", dataVector.length="+dataVector.length);
double result=0;
double sumWeights=0;
if (this.dataWeights!=null) {
......@@ -2752,7 +2959,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
public void printSetRMS(double [] fX){
int [] indices=getSetIndices();
// int [] indices=getSetIndices();
Integer [] indices=getSetIndices().toArray(new Integer[0]); // uses dataVector;
double [] setRMA=calcErrorsPerSet(fX);
for (int numSet=0;numSet<indices.length;numSet++){
System.out.println(numSet+" "+IJ.d2s(setRMA[numSet],3)+" "+
......@@ -2762,8 +2970,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
public double [] calcErrorsPerSet(double [] fX){
int [] indices=getSetIndices();
double [] setRMA=new double[indices.length];
// int [] indices=getSetIndices();
Integer [] indices=getSetIndices().toArray(new Integer[0]); // uses dataVector;
double [] setRMS=new double[indices.length];
double [] weights=this.dataWeights;
if (weights==null){
weights=new double [fX.length];
......@@ -2779,13 +2988,13 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
sumWeights+=weights[i];
}
if (sumWeights>0) result/=sumWeights;
setRMA[numSet]=Math.sqrt(result);
setRMS[numSet]=Math.sqrt(result);
}
return setRMA;
return setRMS;
}
public int [] getSetIndices(){
public int [] getSetIndices_old(){
String lastTimestamp="";
int numMeas=0;
for (int i=0;i<dataVector.length;i++){
......@@ -2805,6 +3014,56 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
return indices;
}
public ArrayList<Integer> getSetSampleIndices(){ // indices of data with anything new but channel (maximum - 6 increment)
String prevTimeStamp="";
int prevMeasurementIndex=-1;
double prevPx=-1,prevPy=-1;
final ArrayList<Integer> measIndicesList = new ArrayList<Integer>(dataVector.length/getNumChannels());
for (int n=0;n<dataVector.length;n++){
MeasuredSample ms=dataVector[n];
if ((ms.measurementIndex!=prevMeasurementIndex) || !ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){
measIndicesList.add(new Integer(n));
prevMeasurementIndex=ms.measurementIndex;
prevTimeStamp=ms.timestamp;
prevPx=ms.px;
prevPy=ms.py;
}
}
return measIndicesList;
}
public ArrayList<Integer> getSetIndices(){
String prevTimeStamp="";
int prevMeasurementIndex=-1;
// double prevPx=-1,prevPy=-1;
final ArrayList<Integer> measIndicesList = new ArrayList<Integer>(dataVector.length/getNumChannels());
for (int n=0;n<dataVector.length;n++){
MeasuredSample ms=dataVector[n];
// if (!ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){
if ((ms.measurementIndex!=prevMeasurementIndex) || !ms.timestamp.equals(prevTimeStamp)){
measIndicesList.add(new Integer(n));
prevMeasurementIndex=ms.measurementIndex;
prevTimeStamp=ms.timestamp;
// prevPx=ms.px;
// prevPy=ms.py;
}
}
return measIndicesList;
}
public boolean [] getMeasurementsMask(){
ArrayList<Integer> indices=getSetIndices(); // uses dataVector;
boolean [] en=dataWeightsToBoolean();
boolean [] measMask=new boolean[indices.size()];
for (int i=0;i<measMask.length;i++) {
int startIndex=indices.get(i);
int endIndex=(i<(measMask.length-1))?indices.get(i+1):en.length;
measMask[i]=false;
for (int index=startIndex;index<endIndex;index++) measMask[i] |= en[index];
}
return measMask;
}
public LMAArrays calculateJacobianArrays(double [] fX){
if (multiJacobian && (threadsMax>0)) return calculateJacobianArraysMulti(fX);
......@@ -3031,7 +3290,7 @@ 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)) {
String msg="initial Jacobian matrix calculation. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
if (debugLevel>1) System.out.println(msg);
if (debugLevel>0) System.out.println(msg);
if (this.updateStatus) IJ.showStatus(msg);
if (debugLevel>1) System.out.println("*** 1 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)
......@@ -3482,10 +3741,8 @@ public void listData(String title,
if ((i==0) && (j==3) && (ffm.motors[0]==2209)){
System.out.println("listData(), i="+i+", j="+j);
}
// if ((i==4) && (j==7)) {
// System.out.print("-");
// }
double [] subData=fieldFitting.getValsDerivatives(
// -1, // <0 - use mechanicalFocusingModel z, tx, ty
flattenIndex(i,j),
sagittalMaster, // dependent channel does not have center parameters, but that is only used for derivs.
ffm.motors, // 3 motor coordinates
......@@ -4144,7 +4401,9 @@ public boolean dialogLMAStep(boolean [] state){
return gd.wasOKed();
}
public double getAdjustRMS(
FocusingFieldMeasurement measurement,
// FocusingFieldMeasurement measurement,
int [] zTxTyAdjustMode, //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
ArrayList<FocusingFieldMeasurement> measurements,
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
......@@ -4152,12 +4411,12 @@ public double getAdjustRMS(
double z,
double tx,
double ty){
fieldFitting.selectZTilt(false);
fieldFitting.selectZTilt(false,zTxTyAdjustMode);
fieldFitting.mechanicalFocusingModel.setZTxTy(z,tx,ty);
double [] sv= fieldFitting.createParameterVector(sagittalMaster);
// double [] sv= fieldFitting.createParameterVector(sagittalMaster);
setDataVector(
false, // calibrate mode
createDataVector(measurement));
createDataVector(measurements));
if (filterZ) {
boolean [] en=dataWeightsToBoolean();
en= filterByZRanges(
......@@ -4199,7 +4458,7 @@ public double getAdjustRMS(
false); // calib mode for debug print
maskDataWeights(en);
}
/*
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
......@@ -4212,23 +4471,40 @@ public double getAdjustRMS(
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
// System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
System.out.print("Got:");
for (int n:numSamples) System.out.print(" "+n);
System.out.println(" - not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
// System.out.println();
}
return Double.NaN;
}
}
*/
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0) || (minLeftSamples>0) || (minBestLeftSamples>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
en=filterNotEnoughSamples(
centerSampesMask,
en,
minCenterSamplesTotal, // int minTotalCenterSamples,
minCenterSamplesBest, //int minBestChannelCenterSamples,
minLeftSamples, //int minTotalSamples,
minBestLeftSamples); //int minBestChannelSamples);
maskDataWeights(en);
}
int numEn=getNumEnabledSamples(dataWeightsToBoolean());
if ((numEn<minLeftSamples) || (numEn<1)) return Double.NaN;
// double [] sv= fieldFitting.createParameterVector(sagittalMaster);
double [] sv= fieldFitting.createParameterVectorZTxTy(zTxTyAdjustMode); //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
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(
FocusingFieldMeasurement measurement,
public double [] findAdjustZ( // Mode should already be set to adjustment!
// int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
// FocusingFieldMeasurement measurement,
ArrayList<FocusingFieldMeasurement> measurements,
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
......@@ -4239,14 +4515,31 @@ public double [] findAdjustZ(
double tMin,
double tMax,
double tStep){
int [] zTxTyAdjustMode=fieldFitting.mechanicalFocusingModel.getZTxTyMode();
double zBest=Double.NaN;
double tXBest=Double.NaN;
double tYBest=Double.NaN;
double bestRMS=Double.NaN;
double tMinX=tMin,tMinY=tMin,tMaxX=tMax,tMaxY=tMax, tStepX=tStep,tStepY=tStep;
// Disable scanning tilts according to zTxTyAdjustMode (null - old way)
if (zTxTyAdjustMode!=null){
double [] zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy(); // current values
if (zTxTyAdjustMode[1]==0){
tMinX=zTxTy[1];
tMaxX=zTxTy[1];
}
if (zTxTyAdjustMode[2]==0){
tMinY=zTxTy[2];
tMaxY=zTxTy[2];
}
}
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){
for (double z=zMin;z<=zMax;z+=zStep) for (double tx=tMinX;tx<=tMaxX;tx+=tStepX) for (double ty=tMinY;ty<=tMaxY;ty+=tStepY){
double rms=getAdjustRMS(
measurement,
zTxTyAdjustMode,
// measurement,
measurements,
filterZ,
filterByScanValue,
filterByValueScale,
......@@ -4289,12 +4582,14 @@ public void calculateGoodSamples(){
public boolean LevenbergMarquardt(
FocusingFieldMeasurement measurement, // null in calibrate mode
// FocusingFieldMeasurement measurement, // null in calibrate mode
int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
ArrayList<FocusingFieldMeasurement> measurements,
boolean openDialog,
boolean autoSel,
// boolean filterZ, // for adjust mode
int debugLevel){
boolean calibrate=measurement==null;
boolean calibrate=measurements==null;
// FocusingFieldMeasurement measurement=measurements.get(0); // FIXME: - process all measurements
double savedLambda=this.lambda;
this.debugLevel=debugLevel;
if (openDialog && !selectLMAParameters(autoSel)) return false;
......@@ -4317,7 +4612,8 @@ public boolean LevenbergMarquardt(
// }
if (!calibrate) {
this.currentStrategyStep=-1;
fieldFitting.selectZTilt(false);
// int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
fieldFitting.selectZTilt(false,zTxTyAdjustMode); // still need to create a parameter vector
keepCorrectionParameters=true;
resetVariableParameters=false;
resetCenter=false;
......@@ -4353,10 +4649,12 @@ public boolean LevenbergMarquardt(
flattenSampleCoord(), //double [][] sampleCoordinates,
getSeriesWeights()); //double [][] sampleSeriesWeights);
fieldFitting.setEstimatedZ0( z0_estimates, false); // boolean force)
} else {
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
} else { // adjustment mode
setDataVector(
false, // calibrate mode
createDataVector(measurement)); // Make it different for adjustment mode
// createDataVector(measurement)); // Make it different for adjustment mode
createDataVector(measurements)); // Make it different for adjustment mode
if (filterZ) {
boolean [] en=dataWeightsToBoolean();
en= filterByZRanges(
......@@ -4398,7 +4696,21 @@ public boolean LevenbergMarquardt(
false); // calibrate mode - for debug print
maskDataWeights(en);
}
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0) || (minLeftSamples>0) || (minBestLeftSamples>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
en=filterNotEnoughSamples(
centerSampesMask,
en,
minCenterSamplesTotal, // int minTotalCenterSamples,
minCenterSamplesBest, //int minBestChannelCenterSamples,
minLeftSamples, //int minTotalSamples,
minBestLeftSamples); //int minBestChannelSamples);
maskDataWeights(en);
}
int numEn=getNumEnabledSamples(dataWeightsToBoolean());
if ((numEn<minLeftSamples) || (numEn<1)) return false;
/*
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
......@@ -4418,15 +4730,16 @@ public boolean LevenbergMarquardt(
return false;
}
}
*/
fieldFitting.initSampleCorrVector(
flattenSampleCoord(), //double [][] sampleCoordinates,
null); //getSeriesWeights()); //double [][] sampleSeriesWeights);
// fieldFitting.setEstimatedZ0( z0_estimates, false); // boolean force)
// this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
this.savedVector=this.fieldFitting.createParameterVectorZTxTy(zTxTyAdjustMode); //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
this.fieldFitting.commitParameterVectorZTxTy( // to populate fieldFitting.mechanicalFocusingModel.replaceParameters array
this.savedVector);
}
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
// this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
if (debugDerivativesFxDxDy){
compareDrDerivatives(this.savedVector);
}
......@@ -4841,6 +5154,8 @@ public boolean LevenbergMarquardt(
return this.historyPath;
}
public void testMeasurement(){
String [] zTxTyAdjustModeNames={"keep", "common","individual"};
String [] zTxTyNames={"z", "tx","ty"};
GenericDialog gd = new GenericDialog("Select measurement");
int nMeas=measurements.size()/2;
// double zMin=-40.0;
......@@ -4850,7 +5165,9 @@ public boolean LevenbergMarquardt(
// 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,
fieldFitting.mechanicalFocusingModel.setAdjustMode(false,null); // to correctly find Z centers,
double [] center_z=fieldFitting.getZCenters(false);
double [] centerFWHM={
......@@ -4888,6 +5205,7 @@ public boolean LevenbergMarquardt(
gd.addNumericField("Filter by value (remove samples above scaled best FWHM for channel/location)",filterByValueScale,2,5,"x");
gd.addNumericField("Remove samples having less neighbors (same channel) that this during ",filterByNeib,0,1,"");
gd.addNumericField("Minimal required number of channels/samples",minLeftSamples,0,3,"samples");
gd.addNumericField("Minimal required number of samples in the best channel",minBestLeftSamples,0,3,"samples");
gd.addNumericField("... of them closest to the center, best channel",minCenterSamplesBest,0,3,"samples");
gd.addNumericField("... of them closest to the center, total in all channels",minCenterSamplesTotal,0,3,"samples");
gd.addNumericField("Number of closest samples to consider",centerSamples,0,3,"samples");
......@@ -4906,6 +5224,11 @@ public boolean LevenbergMarquardt(
gd.addNumericField("Target horizontal tilt (normally 0)",targetRelTiltX,2,5,"um/mm");
gd.addNumericField("Target vertical tilt (normally 0)",targetRelTiltY,2,5,"um/mm");
for (int n=0;n<this.zTxTyAdjustMode.length;n++){
gd.addChoice("Adjust "+zTxTyNames[n]+" mode",zTxTyAdjustModeNames,zTxTyAdjustModeNames[this.zTxTyAdjustMode[n]]);
}
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return;
......@@ -4921,6 +5244,7 @@ public boolean LevenbergMarquardt(
filterByNeib= (int) gd.getNextNumber();
minLeftSamples= (int) gd.getNextNumber();
minBestLeftSamples= (int) gd.getNextNumber();
minCenterSamplesBest= (int) gd.getNextNumber();
minCenterSamplesTotal= (int) gd.getNextNumber();
centerSamples= (int) gd.getNextNumber();
......@@ -4936,10 +5260,13 @@ public boolean LevenbergMarquardt(
targetRelFocalShift= gd.getNextNumber();
targetRelTiltX= gd.getNextNumber(); // for testing, normally should be 0 um/mm
targetRelTiltY= gd.getNextNumber(); // for testing, normally should be 0 um/mm
for (int n=0;n<this.zTxTyAdjustMode.length;n++){
this.zTxTyAdjustMode[n]=gd.getNextChoiceIndex();
}
boolean OK;
fieldFitting.mechanicalFocusingModel.setAdjustMode(true); // to correctly find Z centers,
fieldFitting.mechanicalSelect=fieldFitting.mechanicalFocusingModel.maskSetZTxTy();
fieldFitting.mechanicalFocusingModel.setAdjustMode(true,this.zTxTyAdjustMode); // to correctly find Z centers,
fieldFitting.mechanicalSelect=fieldFitting.mechanicalFocusingModel.maskSetZTxTy(null); // all: z, tx, ty
String header="# measurement";
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
......@@ -4959,7 +5286,8 @@ public boolean LevenbergMarquardt(
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
OK=testMeasurement(
measurements.get(nMeas),
null, // FIXME: zTxTyAdjustMode
singleMeasurement(measurements.get(nMeas)),
// nMeas,
zMin, //+best_qb_corr[0],
zMax, //+best_qb_corr[0],
......@@ -4983,7 +5311,7 @@ public boolean LevenbergMarquardt(
fieldFitting.mechanicalFocusingModel.getUnits(i));
}
}
double [] zTilts=getCenterZTxTy(measurements.get(nMeas));
double [] zTilts=getCenterZTxTy(measurements.get(nMeas),-1); // common parameters
double [] dmz= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
......@@ -5034,7 +5362,8 @@ public boolean LevenbergMarquardt(
for (nMeas=0;nMeas<measurements.size();nMeas++){
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
OK=testMeasurement(
measurements.get(nMeas),
null, // FIXME: zTxTyAdjustMode
singleMeasurement(measurements.get(nMeas)),
zMin, //+best_qb_corr[0],
zMax, // +best_qb_corr[0],
zStep,
......@@ -5056,7 +5385,7 @@ public boolean LevenbergMarquardt(
fieldFitting.mechanicalFocusingModel.getUnits(i));
}
}
double [] zTilts=getCenterZTxTy(measurements.get(nMeas));
double [] zTilts=getCenterZTxTy(measurements.get(nMeas),-1); // <0 - common parameters
double [] dmz= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift+best_qb_corr[0],
......@@ -5121,7 +5450,7 @@ public boolean LevenbergMarquardt(
// }
}
// 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,
fieldFitting.mechanicalFocusingModel.setAdjustMode(false,null); // to correctly find Z centers,
}
//,
......@@ -5151,24 +5480,43 @@ public boolean LevenbergMarquardt(
return s;
}
public double [][] getAllZTM(
public double [][] getAllZTT( // z, tx, ty, temperature - skips bad measurements - no, some may be null; have NaN
boolean noTiltScan,
FocusingField ff,
boolean noMotors){
int tiltAdjustMode){
if (debugLevel>0) System.out.println("getAllZTM(): 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]);
}
// int [] zTxTyMode={1,tiltAdjustMode,tiltAdjustMode}; // all common parameters
int [] zTxTyMode={2,tiltAdjustMode,tiltAdjustMode}; // z - individual, tilt - as specified
double [][] results=matchSeriesAbsoluteLMA ( // result absolute (not relative to optimal)
zTxTyMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
true, //boolean noTiltScan,
ff.measurements);
if (results==null) {
System.out.println("getAllZTM() FAILED");
return null;
}
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;
for (int i=0;i<result.length;i++) {
result[i]=new double [results.length+1];
for (int j=0;j<results.length;j++){
result[i][j]=results[j][(i>=results[j].length)?0:i]-this.qualBOptimizationResults[j];
}
result[i][results.length]=ff.measurements.get(i).temperature;
if ((result[i]!=null) && Double.isNaN(result[i][0])) result[i]=null;
}
return result; // may contain bad measurements (NaN for Z)
}
public double [] averageZTM(// results relative to optimal
boolean noTiltScan,
FocusingField ff,
boolean noMotors){
int tiltAdjustMode){ // keep existent tilt
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) {
......@@ -5176,31 +5524,100 @@ public boolean LevenbergMarquardt(
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, // 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++;
}
}
if (num==0) return null;
for (int i=0;i<result.length;i++) result[i]/=num;
int [] zTxTyMode={1,tiltAdjustMode,tiltAdjustMode}; // all common parameters
double [][] results=matchSeriesAbsoluteLMA ( // result absolute (not relative to optimal)
zTxTyMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
true, //boolean noTiltScan,
ff.measurements);
// here results should not contain null - at least for z
if (results==null) {
System.out.println("averageZTM() FAILED");
return null;
}
double [] result =new double[results.length];
for (int n=0;n<result.length;n++){
result[n]=results[n][0]-this.qualBOptimizationResults[n];
}
return result;
}
public double [][] getZ0TxTyAbsRel(){ // z0, not zc!??
double [][]zTxTyAbsRel = new double[2][];
zTxTyAbsRel[0]=fieldFitting.mechanicalFocusingModel.getZTxTy();
zTxTyAbsRel[1]=zTxTyAbsRel[0].clone();
for (int i=0;i<this.qualBOptimizationResults.length;i++) zTxTyAbsRel[1][i]-=this.qualBOptimizationResults[i];
return zTxTyAbsRel;
}
public double [][] getZcZ0TxTy( // 0, zc, 1 - z0 abs, 2 - z0-rel
ArrayList<FocusingFieldMeasurement> measurements){
double [][]zcZ0TxTy = new double[2][];
zcZ0TxTy[0]=getCenterZTxTy(measurements.get(0),-1);
zcZ0TxTy[1]=fieldFitting.mechanicalFocusingModel.getZTxTy();
// zTxTyAbsRel[1]=zTxTyAbsRel[0].clone();
// for (int i=0;i<this.qualBOptimizationResults.length;i++) zTxTyAbsRel[1][i]-=this.qualBOptimizationResults[i];
return zcZ0TxTy;
}
public double [][] matchSeriesAbsoluteLMA ( // result absolute (not relative to optimal)
int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
boolean noTiltScan,
ArrayList<FocusingFieldMeasurement> measurements){
if (measurements.size()<1) return null;
if (!testMeasurement(
zTxTyAdjustMode,
measurements,
zMin, //+best_qb_corr[0],
zMax, //+best_qb_corr[0],
zStep,
(noTiltScan?0.0:tMin),
(noTiltScan?0.0:tMax),
tStep)) {
if (debugLevel>0) System.out.println("adjustLMA() failed");
return null;
}
double [] zTilts=getCenterZTxTy(measurements.get(0),-1); // common values
double [][] zTiltsIndiv=null;
boolean indiv=false;
if (measurements.size()>1){
for (int n=0;n<zTilts.length;n++) if (zTxTyAdjustMode[n]>1) indiv=true;
}
if (indiv){
zTiltsIndiv=new double [measurements.size()][];
for (int i=0;i<zTiltsIndiv.length;i++){
zTiltsIndiv[i]=getCenterZTxTy(measurements.get(0),i); // individual values // may be null
}
}
// May contain NaN !!
// TODO: change order to skip nulls (bad measurements), and also - invert indices?
double [][] result=new double [3][];
for (int n=0;n<result.length;n++){
if (zTxTyAdjustMode[n]<=1){
result[n]=new double[1];
result[n][0]=zTilts[n];
} else {
result[n]=new double[zTiltsIndiv.length];
for (int i=0;i<zTiltsIndiv.length;i++){
if (zTiltsIndiv[i]!=null) result[n][i]=zTiltsIndiv[i][n];
else result[n][i]=Double.NaN;
}
}
}
return result;
}
public double [] adjustLMA ( // result relative to optimal
int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
boolean noTiltScan,
FocusingFieldMeasurement measurement,
boolean parallelMove,
boolean noQualB, // do not re-claculate testQualB
boolean noAdjust){ // do not calculate correction
System.out.println("adjustLMA(): mode="+zTxTyAdjustMode[0]+"/"+zTxTyAdjustMode[1]+"/"+zTxTyAdjustMode[2]+
", noTiltScan="+noTiltScan+", parallelMove="+parallelMove+", noQualB="+noQualB+", noAdjust="+noAdjust);
if (!noQualB) {
if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
......@@ -5211,7 +5628,8 @@ public boolean LevenbergMarquardt(
}
}
if (!testMeasurement(
measurement,
zTxTyAdjustMode,
singleMeasurement(measurement),
zMin, //+best_qb_corr[0],
zMax, //+best_qb_corr[0],
zStep,
......@@ -5223,10 +5641,21 @@ public boolean LevenbergMarquardt(
}
double [] result=new double [noAdjust?3:6];
double [] zTilts=getCenterZTxTy(measurement);
double [] zTilts=getCenterZTxTy(measurement,-1);
if (zTilts==null){
System.out.println("Failed to get getCenterZTxTy()");
return null;
}
if (this.qualBOptimizationResults==null){
System.out.println("this.qualBOptimizationResults is null (yet), absolute focal distance is wrong ");
result[0]=zTilts[0]; // not calibrated
result[1]=zTilts[1];
result[2]=zTilts[2];
} else {
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];
}
if (!noAdjust) {
double [] zm=null;
zm=new double [3];
......@@ -5267,10 +5696,14 @@ public boolean LevenbergMarquardt(
}
// add tx, ty?
public double[] getCenterZTxTy(FocusingFieldMeasurement measurement){
double [] tilts= fieldFitting.mechanicalFocusingModel.getTilts(measurement.motors);
public double[] getCenterZTxTy(
FocusingFieldMeasurement measurement,
int index){ // <0 - use mechanicalFocusingModel z, tx, ty, >=0 - use individual if available
double [] tilts= fieldFitting.mechanicalFocusingModel.getTilts(measurement.motors, index);
if (tilts==null) return null;// bad measurement
double [] result = {
fieldFitting.mechanicalFocusingModel.calc_ZdZ(
index, // <0 - use mechanicalFocusingModel z, tx, ty
measurement.motors,
currentPX0, //fieldFitting.getCenterXY()[0],
currentPY0, //fieldFitting.getCenterXY()[1],
......@@ -5278,10 +5711,11 @@ public boolean LevenbergMarquardt(
tilts[0],
tilts[1]
};
return result;
// if (Double.isNaN(result[0])) return null;
return result; // may contain Double.NaN - no, all null
}
public double [] getAdjustedMotors(
public double [] getAdjustedMotors( // Target - absolute Zc, axial tilts
double [] zM0, // current linearized motors (or null for full adjustment)
double targetRelFocalShift,
double targetTiltX, // for testing, normally should be 0 um/mm
......@@ -5320,8 +5754,9 @@ public boolean LevenbergMarquardt(
}
public boolean testMeasurement(
FocusingFieldMeasurement measurement, // null in calibrate mode
// int nMeas,
int [] zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
// FocusingFieldMeasurement measurement, // null in calibrate mode
ArrayList<FocusingFieldMeasurement> measurements,
double zMin,
double zMax,
double zStep,
......@@ -5331,14 +5766,23 @@ public boolean LevenbergMarquardt(
){
debugDerivativesFxDxDy=false;
int retryLimit=20;
fieldFitting.mechanicalFocusingModel.setAdjustMode(true);
fieldFitting.mechanicalFocusingModel.setAdjustMode(true,zTxTyAdjustMode);
double [] zTxTy;
if (zTxTyAdjustMode!=null) {
zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy(); // current values - will be ignored and overwritten
// if (zTxTyAdjustMode[1]==0)
zTxTy[1]=avgTx;
zTxTy[2]=avgTy;
fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy); // may be used in findAdjustZ()
}
setDataVector(
false,
createDataVector(measurement)); //measurements.get(nMeas)));
createDataVector(measurements)); //measurements.get(nMeas)));
// TODO: Adjust by center samples only?
double [] zTxTy=findAdjustZ(
// measurements.get(nMeas),
measurement,
zTxTy=findAdjustZ(
// zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual (will ignore tilt Min/Max and use current if not adjusted)
// measurement,
measurements,
filterZ, //boolean filterZ,
filterByScanValue,
filterByValueScale,
......@@ -5364,7 +5808,9 @@ public boolean LevenbergMarquardt(
wasPrevEnable=(prevEnable==null)?null:prevEnable.clone();
this.lambda=this.adjustmentInitialLambda;
boolean OK=LevenbergMarquardt(
measurement,
// measurement,
zTxTyAdjustMode, // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
measurements,
false, // true, // open dialog
true,// boolean autoSel,
debugLevel);
......@@ -5422,6 +5868,7 @@ public boolean LevenbergMarquardt(
}
public class FieldFitting{
// private Properties savedProperties=null;
private int currentVectorLength=0;
private double [] pXY=null;
private boolean [] centerSelect=null;
private boolean [] centerSelectDefault={true,true};
......@@ -5461,10 +5908,34 @@ public boolean LevenbergMarquardt(
private double [] dflt_sampleCorrCost= {0.01,1.0,1.0,1.0,1.0};
private double dflt_sampleCorrSigma= 2.0; // mm
private double dflt_sampleCorrPullZero= 0.75; // fraction
// outer index - parameter [0..2], inner - number of measurement
// element may be null if this parameter is not used or [num] - common parameter
private int [][] zTMap=null;
public final String [] channelDescriptions={
"Red, sagittal","Red, tangential",
"Green, sagittal","Green, tangential",
"Blue, sagittal","Blue, tangential"};
public int getCurrentVectorLength(){
return this.currentVectorLength;
}
public void setCurrentVectorLength(int vectorlength){
this.currentVectorLength=vectorlength;
}
public void setZTMap(int [][] map){
this.zTMap=map;
}
public int getZTMap(int meas, int parIndex){
try {
if (meas>=this.zTMap[parIndex].length) meas=0; // common parameter, use spec ified for measurement 0
} catch (Exception e){
}
try {
return this.zTMap[parIndex][meas];
} catch (Exception e){
return -1;
}
}
public void setProperties(String prefix,Properties properties){
if (mechanicalFocusingModel==null){
......@@ -6665,8 +7136,11 @@ public boolean LevenbergMarquardt(
return true;
}
public void selectZTilt(boolean allChannels){
mechanicalSelect=mechanicalFocusingModel.maskSetZTxTy(); // enable z0, tx, ty
public void selectZTilt(
boolean allChannels,
int [] zTxTyAdjustMode){ // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
mechanicalSelect=mechanicalFocusingModel.maskSetZTxTy(zTxTyAdjustMode); // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
mechanicalFocusingModel.setAdjustMode(true,zTxTyAdjustMode);
// enable all color/dir channels (add separate selection dialog?)
for (int i=0;i<channelSelect.length;i++) {
if (allChannels) channelSelect[i]=true;
......@@ -6826,16 +7300,19 @@ public boolean LevenbergMarquardt(
}
public int getNumberOfCorrParameters(){ // selected for fitting
return (sampleCorrVector!=null)?sampleCorrVector.length:0;
if (mechanicalFocusingModel.getZTxTyMode()!=null) return 0;
return ((sampleCorrVector!=null) && (mechanicalFocusingModel.getZTxTyMode()==null))?sampleCorrVector.length:0;
}
public int getNumberOfParameters(boolean sagittalMaster){
if (mechanicalFocusingModel.getZTxTyMode()!=null) return currentVectorLength;
return getNumberOfRegularParameters(sagittalMaster)+getNumberOfCorrParameters();
}
/**
* @return number of selected parameters (including center, mechanical and each selected - up to 6 - curvature)
*/
public int getNumberOfRegularParameters(boolean sagittalMaster){
if (mechanicalFocusingModel.getZTxTyMode()!=null) return currentVectorLength;
int np=0;
for (int i=0;i<2;i++){
if ( centerSelect[i]) np++;
......@@ -6868,6 +7345,11 @@ public boolean LevenbergMarquardt(
*/
public double [] createParameterVector(boolean sagittalMaster){
int debugThreshold=0;
int [] zTxTyMode=mechanicalFocusingModel.getZTxTyMode();
if (zTxTyMode!=null) return createParameterVectorZTxTy(zTxTyMode);
double [] pars = new double [getNumberOfParameters(sagittalMaster)];
int np=0;
if (debugLevel>debugThreshold) debugParameterNames=new String [pars.length];
......@@ -6908,14 +7390,155 @@ public boolean LevenbergMarquardt(
System.out.println(i+" "+debugParameterNames[i]+" = "+pars[i]);
}
}
fieldFitting.setCurrentVectorLength(pars.length); // maybe not needed
return pars;
}
/**
* Apply (modified) parameter values to selected ones
private int [] getNumSubPars(int [] zTxTyMode, int numMeas){
// Integer [] indices=getSetIndices().toArray(new Integer[0]); // uses dataVector;
int [] numSubPars=new int[zTxTyMode.length];
for (int n=0;n<zTxTyMode.length;n++) {
if (zTxTyMode[n]==2) numSubPars[n]=numMeas; // indices.length;
else if (zTxTyMode[n]==1) numSubPars[n]=1;
else numSubPars[n]=0;
}
return numSubPars;
}
//TODO: create mask for measurements
public double [] createParameterVectorZTxTy(
// double [] zTxTy,
int [] zTxTyMode){ //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
// int numMeas=0;
boolean needMask=false; // shortcut if there are no individual parameters at all
boolean [] measMask=null;
for (int m:zTxTyMode) if (m>1) {
needMask=true;
break;
}
if (needMask) {
measMask=getMeasurementsMask();
// for (boolean b:measMask) if (b) numMeas++;
}
int [][] map=new int [zTxTyMode.length][];
for (int n=0;n<map.length;n++){
if (zTxTyMode[n]<1){
map[n]=null;
} else {
map[n]=new int [(zTxTyMode[n]>1)?measMask.length:1];
for (int i=0;i<map[n].length;i++) map[n][i]=-1;
}
}
int debugThreshold=0;
String [] dbgParNames={"Z","tX","tY"};
// int [] numSubPars=getNumSubPars(zTxTyMode, numMeas);
int numPars=0;
for (int n=0;n<zTxTyMode.length;n++) {
// numPars+=numSubPars[n];
switch(zTxTyMode[n]){
case 1:
numPars++;
break;
case 2:
for (int i=0;i<measMask.length;i++){
if (measMask[i]) numPars++;
}
}
}
double [] pars=new double[numPars];
if (debugLevel>debugThreshold) debugParameterNames=new String [pars.length];
double [] zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();
int index=0;
for (int n=0;n<zTxTyMode.length;n++) {
switch(zTxTyMode[n]){
case 1:
if (debugLevel>debugThreshold){
debugParameterNames[index]=dbgParNames[n];
}
map[n][0]=index;
pars[index++]=zTxTy[n];
break;
case 2:
for (int i=0;i<measMask.length;i++){
if (measMask[i]){
if (debugLevel>debugThreshold){
debugParameterNames[index]=dbgParNames[n]+"-"+i;
}
map[n][i]=index;
pars[index++]=zTxTy[n];
} else {
map[n][i]=-1;
}
}
}
// for (int i=0;i<numSubPars[n];i++){
// if (debugLevel>debugThreshold){
// debugParameterNames[index]=dbgParNames[n]+((numSubPars[n]>1)?("-"+i):"");
// }
// pars[index++]=zTxTy[n];
// }
}
fieldFitting.setCurrentVectorLength(pars.length);
fieldFitting.setZTMap(map);
// create parameter map here
return pars;
}
public void commitParameterVectorZTxTy(
double [] vector){ //
// int [] zTxTyMode){ //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
// fieldFitting.commitParameterVector(vector, sagittalMaster); // Hereit does not matter ???
int [] zTxTyMode=mechanicalFocusingModel.getZTxTyMode(); // Probably is not needed - already set
int numMeas=0;
int [] numSubParsAll=null;
boolean [] measMask=null;
if (mechanicalFocusingModel.isNeededMask()){
measMask=getMeasurementsMask();
for (boolean b:measMask) if (b) numMeas++;
numSubParsAll=getNumSubPars(zTxTyMode,measMask.length);
}
int [] numSubPars=getNumSubPars(zTxTyMode,numMeas);
if (numSubParsAll==null) numSubParsAll=numSubPars;
double [] zTxTy=mechanicalFocusingModel.getZTxTy();
int parIndex=0;
for (int n=0;n<zTxTyMode.length;n++) {
// if (numSubPars[n]>1){
if (zTxTyMode[n]>1){
double v=0; // not used?
double [] pars=new double [numSubParsAll[n]];
for (int i=0;i<pars.length;i++){
if (measMask[i]) {
v+=vector[parIndex]; // not used?
pars[i]=vector[parIndex++];
} else {
pars[i]=Double.NaN;
}
}
zTxTy[n]=v/numSubPars[n]; // not used?
mechanicalFocusingModel.setReplaceParam(pars,n);
} else {
if (numSubPars[n]==1){
zTxTy[n]=vector[parIndex++];
}
mechanicalFocusingModel.setReplaceParam(null,n); // use common parameter (z0,tx,ty) from mechanicalFocusingModel
}
}
mechanicalFocusingModel.setZTxTy(zTxTy);
}
/**
* Apply (modified) parameter values to selected ones
* @param pars vector corresponding to selected parameters
*/
public void commitParameterVector(double [] pars, boolean sagittalMaster){
if (mechanicalFocusingModel.getZTxTyMode()!=null) {
commitParameterVectorZTxTy(pars);
return;
}
int np=0;
for (int i=0;i<2;i++){
if ( centerSelect[i]) pXY[i]=pars[np++];
......@@ -6957,6 +7580,7 @@ public boolean LevenbergMarquardt(
double px, // pixel x
double py) {// pixel y
return mechanicalFocusingModel.calc_ZdZ(
-1, // <0 - use mechanicalFocusingModel z, tx, ty
motors,
px,
py,
......@@ -6980,6 +7604,8 @@ public boolean LevenbergMarquardt(
/**
* Generate vector of function values (up to 6 - 1 per selected channel), corresponding to motor positions and pixel
* coordinates, optionally generate partial derivatives for each channel and parameter
* //@param zTxTy - optional z0, tx, ty instead of mechanical model parameters (used when null)
* @param measurementIndex - <0 -use mechanical model regular parameters, >=0 - overwrite with per-measurement parameters
* @param motors array of 3 motors positions
* @param px pixel X-coordinate of the sample center
* @param py pixel Y-coordinate of the sample center
......@@ -6988,6 +7614,7 @@ public boolean LevenbergMarquardt(
* @return array of [getNumberOfChannels()] calculated function values
*/
public double [] getValsDerivatives(
// int measurementIndex, // <0 - use mechanicalFocusingModel z, tx, ty
int sampleIndex, // double [][] corrPars, // [6][nParZ]
boolean sagittalMaster, // false - tangential master, true - sagittal master (for center coefficients)
int [] motors, // 3 motor coordinates
......@@ -6995,15 +7622,12 @@ public boolean LevenbergMarquardt(
double py, // pixel y
double [][] deriv // array of (1..6][], matching getNumberOfChannels) or null if derivatives are not required
){
// if (sampleIndex==39) {
// System.out.print("?");
// }
double [][] corrPars=getCorrPar(sampleIndex);
double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]);
double [] chnValues=new double [getNumberOfChannels()];
double mot_z=mechanicalFocusingModel.calc_ZdZ(
-1, // measurementIndex,
motors,
px,
py,
......@@ -7089,6 +7713,62 @@ public boolean LevenbergMarquardt(
}
return chnValues;
}
public double [] getValsDerivativesZTxTy( // Version for adjustment mode - returns fixed width (3)
int measurementIndex, // <0 - use mechanicalFocusingModel z, tx, ty
int sampleIndex, // double [][] corrPars, // [6][nParZ]
int [] motors, // 3 motor coordinates
double px, // pixel x
double py, // pixel y
double [][] deriv // array of (1..6][], matching getNumberOfChannels) or null if derivatives are not required
){
double [][] corrPars=getCorrPar(sampleIndex);
double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]);
double [] chnValues=new double [getNumberOfChannels()];
double mot_z=mechanicalFocusingModel.calc_ZdZ(
measurementIndex,
motors,
px,
py,
motorDerivs);
int nChn=0;
double [][] deriv_curv = new double [channelSelect.length][];
for (int c=0;c<channelSelect.length;c++) deriv_curv[c]=null;
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
deriv_curv[c]=(deriv==null)?null:(new double [curvatureModel[c].getSize()]); // nr*nz+1
chnValues[nChn++]=curvatureModel[c].getFdF(
(corrPars==null)?null:corrPars[c], // param_corr
px,
py,
mot_z,
deriv_curv[c]);
}
if (deriv!=null){
double dX=px-pXY[0];
double dY=py-pXY[1];
double r=Math.sqrt(dX*dX+dY*dY);
double [] dr_dxy={1.0,1.0};
if (r>0.0){
dr_dxy[0]=-dX/r;
dr_dxy[1]=-dY/r;
}
nChn=0;
for (int i=0;i<2;i++){
dr_dxy[i]*=getPixelMM(); // radius in mm, dx, dy - in pixels
}
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){ // c -full, nChn - disabled skipped - dependent COMPONET
deriv[nChn]=new double [3];
deriv[nChn][0]=-motorDerivs[mechanicalFocusingModel.getIndex(MECH_PAR.z0)]*deriv_curv[c][0]; // minus d/dz0 const part
deriv[nChn][1]=-motorDerivs[mechanicalFocusingModel.getIndex(MECH_PAR.tx)]*deriv_curv[c][0]; // minus d/dz0 const part
deriv[nChn][2]=-motorDerivs[mechanicalFocusingModel.getIndex(MECH_PAR.ty)]*deriv_curv[c][0]; // minus d/dz0 const part
nChn++;
}
}
return chnValues;
}
}
public class MechanicalFocusingModel{
......@@ -7115,11 +7795,41 @@ public boolean LevenbergMarquardt(
public double [] paramValues=new double [descriptions.length];
public double [] paramValuesCalibrate=null; // save calibration mode parameters while adjusting
public boolean adjustMode=false;
private int [] zTxTyMode=null;
public double [][] replaceZTxTy={null,null,null};
private boolean needMask=false;
public void setReplaceParam(double [] pars, int index){
replaceZTxTy[index]=pars;
}
public double [] getReplaceParam(int index){
return replaceZTxTy[index];
}
public double [][] getReplaceParam(){
return replaceZTxTy;
}
public void setZTxTyMode(int [] zTxTyMode){
if (zTxTyMode==null) this.zTxTyMode=null;
else this.zTxTyMode=zTxTyMode.clone(); // clone() needed?
needMask=false; // shortcut if there are no individual parameters at all
for (int m:zTxTyMode) if (m>1) {
needMask=true;
break;
}
}
public boolean isNeededMask(){
return needMask;
}
public int [] getZTxTyMode(){
return adjustMode?this.zTxTyMode:null;
}
public MechanicalFocusingModel(){ // add arguments?
initDefaults();
}
public void setAdjustMode(boolean mode){
public void setAdjustMode(
boolean mode,
int [] zTxTyMode){ //0 - do not adjust, 1 - commonn adjust, 2 - individual adjust
if (mode && (zTxTyMode!=null)) setZTxTyMode(zTxTyMode);
if (mode==adjustMode) return;
if (adjustMode) restoreCalibration();
else saveCalibration();
......@@ -7141,7 +7851,7 @@ public boolean LevenbergMarquardt(
}
public void setProperties(String prefix,Properties properties){
setAdjustMode(false); // restore if needed
setAdjustMode(false,null); // restore if needed
if (paramValues!=null) {
for (int i=0;i<paramValues.length;i++){
properties.setProperty(prefix+descriptions[i][0],paramValues[i]+"");
......@@ -7265,9 +7975,15 @@ public boolean LevenbergMarquardt(
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);
double zm=calc_ZdZ(
// null, //double [] zTxTy, // null - old way
-1, // <0 - use mechanicalFocusingModel z, tx, ty
motors,px,py,null);
paramValues[i]=initialVector[i]+scale*derivSteps[i];
double zp=calc_ZdZ(motors,px,py,null);
double zp=calc_ZdZ(
// null, //double [] zTxTy, // null - old way
-1, // <0 - use mechanicalFocusingModel z, tx, ty
motors,px,py,null);
paramValues[i]=initialVector[i];
derivs[i]=(zp-zm)/(2.0*scale*derivSteps[i]);
}
......@@ -7288,9 +8004,11 @@ public boolean LevenbergMarquardt(
boolean calDerivs){
double [] result= new double [calDerivs?4:1];
double [] derivs=(calDerivs)? (new double [getNumPars()]):null;
int [] zeroMot={0,0,0};
// int [] zeroMot={0,0,0};
result[0]=calc_ZdZ(
zeroMot,
// null, //double [] zTxTy, // null - old way
-1, // <0 - use mechanicalFocusingModel z, tx, ty
null, //zeroMot,
px,
py,
derivs);
......@@ -7312,7 +8030,7 @@ public boolean LevenbergMarquardt(
* @param deriv returns partial derivatives if array is provided. If null - does not calculate derivatives
* @return array of partial derivatives
*/
public double calc_ZdZ(
public double calc_ZdZ_old(
int [] motors,
double px,
double py,
......@@ -7470,7 +8188,196 @@ public boolean LevenbergMarquardt(
}
return z;
}
public double [] getTilts(int [] motors){
/**
* Calculate focal shift of the specified pixel location and optionally derivatives by parameters
* @param measIndex measurement index to replace z0,tx,ty with individual values, or -1 to use model parameters
* @param motors 3 motor steps
* @param px absolute position of the pixel, X
* @param py absolute position of the pixel, Y
* @param deriv null or the proper length array to accommodate derivatives calculated here
* @return focal shift of the specified pixel
*/
public double calc_ZdZ(
int measIndex, // only used in adjustment mode
int [] motors,
double px,
double py,
double[] deriv){
int [] zeroMot={0,0,0};
if (motors==null) motors=zeroMot.clone();
double [] zTxTy=getZTxTy();
if (adjustMode && (measIndex>=0)){
for (int n=0;n<zTxTy.length;n++) if (replaceZTxTy[n]!=null) {
if (measIndex<replaceZTxTy[n].length) zTxTy[n]=replaceZTxTy[n][measIndex];
else zTxTy[n]=replaceZTxTy[n][0]; // maybe not needed - common parameter
if (Double.isNaN(zTxTy[n])) {
zTxTy[n]=getZTxTy()[0]; // use common parameter?
// return Double.NaN;// bad measurement, no derivatives calculated
}
}
}
double debugMot=6545;
int debugThreshold=2;
boolean dbg = (debugLevel>debugThreshold);
/*
kM3=K0+KD3
kM1=K0+KD1-KD3
kM2=K0-KD1-KD3
K0 may be fixed (overall scale), kM1, kM2 - variable
dZc(m1)= 0.25* kM1 * (m1 + sM1*P/(2*pi)*sin(2pi*m1/P) + cM1*P/(2*pi)*cos(2pi*m1/P))
dZc(m2)= 0.25* kM2 * (m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P))
dZc(m3)= 0.5 * kM3 *( m3 + sM3*P/(2*pi)*sin(2pi*m3/P) + cM3*P/(2*pi)*cos(2pi*m3/P))
Assuming X - towards M3, Y - towards M1
d2Z/dX/dm1=-ps/(4*Lx)* kM1 * (m1 + sM1*P/(2*pi)*sin(2pi*m1/P) + cM1*P/(2*pi)*cos(2pi*m1/P))
d2Z/dX/dm2=-ps/(4*Lx)* kM2 *( m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P))
d2Z/dX/dm3= ps/(2*Lx)* kM3 * (m3 + sM3*P/(2*pi)*sin(2pi*m3/P) + cM3*P/(2*pi)*cos(2pi*m3/P))
d2Z/dY/dm1= -ps/(2*Ly)* kM1 * (m1 + sM1*P/(2*pi)*sin(2pi*m1/P) + cM1*P/(2*pi)*cos(2pi*m1/P)) //!
d2Z/dY/dm2= +ps/(2*Ly)* kM2 * (m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P)) //!
d2Z/dY/dm3= 0
*/
// double [] deriv=new double [paramValues.length];
double kM1= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM2= getValue(MECH_PAR.K0)-getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM3= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD3);
double p2pi= PERIOD/2/Math.PI;
double m1=motors[0],m2=motors[1],m3=motors[2];
double aM1=(m1 + getValue(MECH_PAR.sM1)*p2pi*Math.sin(m1/p2pi) + getValue(MECH_PAR.cM1)*p2pi*Math.cos(m1/p2pi));
double aM2=(m2 + getValue(MECH_PAR.sM2)*p2pi*Math.sin(m2/p2pi) + getValue(MECH_PAR.cM2)*p2pi*Math.cos(m2/p2pi));
double aM3=(m3 + getValue(MECH_PAR.sM3)*p2pi*Math.sin(m3/p2pi) + getValue(MECH_PAR.cM3)*p2pi*Math.cos(m3/p2pi));
double zM1=kM1 * aM1;
double zM2=kM2 * aM2;
double zM3=kM3 * aM3;
double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+zTxTy[0]; // getValue(MECH_PAR.z0);
double dx=PIXEL_SIZE*(px-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
//zTxTy
// double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
// double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))); //!
double zx=dx*(zTxTy[1]+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
double zy=dy*(zTxTy[2]-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))); //!
double z=zc+zx+zy;
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*zTxTy[1],3)+":"+IJ.d2s(dy*zTxTy[2],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;
double dy_mpY0=-PIXEL_SIZE;
double zM1_K0= aM1;
double zM1_KD1= aM1;
double zM1_KD3=-aM1;
double zM2_K0= aM2;
double zM2_KD1=-aM2;
double zM2_KD3=-aM2;
double zM3_K0= aM3;
// 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);
double zM2_cM2= kM2*p2pi*Math.cos(m2/p2pi);
double zM3_sM3= kM3*p2pi*Math.sin(m3/p2pi);
double zM3_cM3= kM3*p2pi*Math.cos(m3/p2pi);
double zc_K0= 0.25* zM1_K0+ 0.25* zM2_K0+ 0.5 * zM3_K0;
double zc_KD1= 0.25* zM1_KD1+ 0.25* zM2_KD1+ 0.5 * zM3_KD1;
double zc_KD3= 0.25* zM1_KD3+ 0.25* zM2_KD3+ 0.5 * zM3_KD3;
double zc_sM1= 0.25* zM1_sM1;
double zc_cM1= 0.25* zM1_cM1;
double zc_sM2= 0.25* zM2_sM2;
double zc_cM2= 0.25* zM2_cM2;
double zc_sM3= 0.5* zM3_sM3;
double zc_cM3= 0.5* zM3_cM3;
// double zx_K0=(2*zM3-zM1-zM2)* dx/(4*getValue(MECH_PAR.Lx));
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_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;
double zx_cM2= (-zM2_cM2)*zx_a;
double zx_sM3= (2*zM3_sM3)*zx_a;
double zx_cM3= (2*zM3_cM3)*zx_a;
// double zx_mpX0=dx_mpX0*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))); // double zx_mpX0=dx_mpX0/(4*getValue(MECH_PAR.Lx));
double zx_mpX0=dx_mpX0*(zTxTy[1]+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))); // 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= -dy/(2*getValue(MECH_PAR.Ly)); //!
double zy_K0= (zM2_K0- zM1_K0) *zy_a;
double zy_KD1= (zM2_KD1-zM1_KD1)*zy_a;
double zy_KD3= (zM2_KD3-zM1_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_sM3= 0.0;
double zy_cM3= 0.0;
// double zy_mpY0=dy_mpY0*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//! // double zy_mpY0=-dy_mpY0/(2*getValue(MECH_PAR.Ly));//!
double zy_mpY0=dy_mpY0*(zTxTy[2]-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//! // double zy_mpY0=-dy_mpY0/(2*getValue(MECH_PAR.Ly));//!
double zy_ty= dy;
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;
deriv[getIndex(MECH_PAR.KD3)]=zc_KD3+zx_KD3+zy_KD3;
deriv[getIndex(MECH_PAR.sM1)]=zc_sM1+zx_sM1+zy_sM1;
deriv[getIndex(MECH_PAR.cM1)]=zc_cM1+zx_cM1+zy_cM1;
deriv[getIndex(MECH_PAR.sM2)]=zc_sM2+zx_sM2+zy_sM2;
deriv[getIndex(MECH_PAR.cM2)]=zc_cM2+zx_cM2+zy_cM2;
deriv[getIndex(MECH_PAR.sM3)]=zc_sM3+zx_sM3+zy_sM3;
deriv[getIndex(MECH_PAR.cM3)]=zc_cM3+zx_cM3+zy_cM3;
deriv[getIndex(MECH_PAR.Lx)] = zx_Lx;
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 double [] getTilts(int [] motors, int measIndex){
double [] zTxTy=getZTxTy();
if (adjustMode && (measIndex>=0)){
for (int n=0;n<zTxTy.length;n++) if (replaceZTxTy[n]!=null) {
if (measIndex<replaceZTxTy[n].length) zTxTy[n]=replaceZTxTy[n][measIndex];
else zTxTy[n]=replaceZTxTy[n][0]; // maybe not needed - common parameter
if (Double.isNaN(zTxTy[n])) return null;// bad measurement
}
}
double kM1= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM2= getValue(MECH_PAR.K0)-getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM3= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD3);
......@@ -7483,11 +8390,99 @@ public boolean LevenbergMarquardt(
double zM2=kM2 * aM2;
double zM3=kM3 * aM3;
double [] result ={
getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)),
getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))};
// getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)),
// getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))};
zTxTy[1]+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)),
zTxTy[2]-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))};
return result;
}
/**
* Correction for z0,tx,ty to zc, tilt X (axial), tilt Y (axial) for the specified pixel (optical center)
* and current parameters (including z0,tx,ty), motors are assumed all 0
* @param centerPx optical center X (mechanical parameters are referenced to mechanical only)
* @param centerPy optical center Y
* @return 3-element array to add to z0,tx,ty to get zc, tx axial, ty axial
*/
public double [] getZTxTyCorr(
double centerPx, // optical center X
double centerPy){
double kM1= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM2= getValue(MECH_PAR.K0)-getValue(MECH_PAR.KD1)-getValue(MECH_PAR.KD3);
double kM3= getValue(MECH_PAR.K0)+getValue(MECH_PAR.KD3);
double p2pi= PERIOD/2/Math.PI;
double m1=0.0,m2=0.0,m3=0.0;
double aM1=(m1 + getValue(MECH_PAR.sM1)*p2pi*Math.sin(m1/p2pi) + getValue(MECH_PAR.cM1)*p2pi*Math.cos(m1/p2pi));
double aM2=(m2 + getValue(MECH_PAR.sM2)*p2pi*Math.sin(m2/p2pi) + getValue(MECH_PAR.cM2)*p2pi*Math.cos(m2/p2pi));
double aM3=(m3 + getValue(MECH_PAR.sM3)*p2pi*Math.sin(m3/p2pi) + getValue(MECH_PAR.cM3)*p2pi*Math.cos(m3/p2pi));
double zM1=kM1 * aM1;
double zM2=kM2 * aM2;
double zM3=kM3 * aM3;
double diff_zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3;
double dx=PIXEL_SIZE*(centerPx-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(centerPy-getValue(MECH_PAR.mpY0));
double diff_tx=(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)) ;
double diff_ty=-(zM2-zM1)/(2*getValue(MECH_PAR.Ly));
double zx=dx*(getValue(MECH_PAR.tx)+diff_tx);
double zy=dy*(getValue(MECH_PAR.ty)+diff_ty);
double diff_z=diff_zc+zx+zy;
double [] result ={
diff_z,
diff_tx,
diff_ty
};
return result;
}
/**
* Correction for z0,tx,ty to zc, tilt X (axial), tilt Y (axial) for the specified pixel (optical center)
* and current parameters (including z0,tx,ty), motors are assumed all 0
* @param zM - 3 linearized (in linear um, thread waves removed) motor positions
* @param centerPx optical center X (mechanical parameters are referenced to mechanical only)
* @param centerPy optical center Y
* @return 3-element array to add to z0,tx,ty to get zc, tx axial, ty axial
*/
public double [] getZTxTyCorr(
double [] zM, // linearized motor coordinates
double centerPx, // optical center X
double centerPy){
double zM1=zM[0];
double zM2=zM[1];
double zM3=zM[2];
double diff_zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3;
double dx=PIXEL_SIZE*(centerPx-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(centerPy-getValue(MECH_PAR.mpY0));
double diff_tx=(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)) ;
double diff_ty=-(zM2-zM1)/(2*getValue(MECH_PAR.Ly));
double zx=dx*(getValue(MECH_PAR.tx)+diff_tx);
double zy=dy*(getValue(MECH_PAR.ty)+diff_ty);
double diff_z=diff_zc+zx+zy;
double [] result ={
diff_z,
diff_tx,
diff_ty
};
return result;
}
/**
* Correction for z0 to zc for the specified pixel (optical center)
* and current parameters (including z0,tx,ty), for all linearized
* (in linear um, thread waves removed) mounts positions set to 0.
* No correction for tilts is needed, only for z.
* @param centerPx optical center X (mechanical parameters are referenced to mechanical only)
* @param centerPy optical center Y
* @return 3-element array to add to z0,tx,ty to get zc, tx axial, ty axial
*/
public double getZCorr(
double centerPx, // optical center X
double centerPy){
double dx=PIXEL_SIZE*(centerPx-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(centerPy-getValue(MECH_PAR.mpY0));
double zx=dx*getValue(MECH_PAR.tx);
double zy=dy*getValue(MECH_PAR.ty);
return zx+zy;
}
/**
......@@ -7637,13 +8632,15 @@ public boolean LevenbergMarquardt(
}
/**
* Calculate three linearized values of motor positions for current parameters, target center focal shift and tilt
* Calculate three linearized values of motor positions for current parameters, target center focal
* shift and tilt (from the optic axis)
* Use current values of MECH_PAR.z0, MECH_PAR.tx,MECH_PAR.ty
* @param zM0 current linearized position (for parallel adjustment) or null for full adjustment
* @param px lens center X (pixels)
* @param py lens center Y (pixels)
* @param targetZ target focal shift uin the center, microns, positive - away
* @param targetTx target horizontal tilt (normally 0)
* @param targetTy target vertical tilt (normallty 0)
* @param targetZ target focal shift in the center, microns, positive - away
* @param targetTx target horizontal tilt from the optical axis
* @param targetTy target vertical tilt from the optical axis
* @return array of 3 linearized motor positions (microns)
*/
public double [] getZM(
......@@ -7686,8 +8683,10 @@ public boolean LevenbergMarquardt(
0.0
}
};
double zCenterCorr=getZCorr(px,py);// optical center X
System.out.println("Correcting Z_center by "+zCenterCorr+" um (caused by Tx, Ty and difference between mechanical and optical centers");
double [][] B={
{targetZ-getValue(MECH_PAR.z0)}, // calc_ZdZ()?
{targetZ-getValue(MECH_PAR.z0)-zCenterCorr}, // calc_ZdZ()?
{targetTx-getValue(MECH_PAR.tx)},
{targetTy-getValue(MECH_PAR.ty)}
};
......@@ -7736,12 +8735,18 @@ public boolean LevenbergMarquardt(
}
return mask;
}
public boolean [] maskSetZTxTy(){
public boolean [] maskSetZTxTy(
int [] zTxTyAdjustMode){ // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
boolean [] mask = new boolean[this.paramValues.length];
for (int i=0;i<mask.length;i++) mask[i]=false;
mask[getIndex(MECH_PAR.z0)]=true;
mask[getIndex(MECH_PAR.tx)]=true;
mask[getIndex(MECH_PAR.ty)]=true;
if (zTxTyAdjustMode!=null) { // z, tx, ty - 0 - fixed, 1 - common, 2 - individual
if (zTxTyAdjustMode[0]<=0) mask[getIndex(MECH_PAR.z0)]=false;
if (zTxTyAdjustMode[1]<=0) mask[getIndex(MECH_PAR.tx)]=false;
if (zTxTyAdjustMode[2]<=0) mask[getIndex(MECH_PAR.ty)]=false;
}
return mask;
}
public boolean showModifyParameterValues(String title, boolean showDisabled, boolean [] mask){
......@@ -8977,7 +9982,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
return zTxTy; // no LMA, return zc for optimal qualB, zero tilts
}
fieldFitting.mechanicalFocusingModel.setAdjustMode(true);
fieldFitting.mechanicalFocusingModel.setAdjustMode(true,null);
qualBOptimize.initCorrPars();
double [][] sampleCoord=flattenSampleCoord();
......@@ -9035,9 +10040,20 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
if (OK){
zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();
System.out.println("qualBOptimize returned:\n"+
"zc="+IJ.d2s((zTxTy[0]),3)+"um ("+IJ.d2s((zTxTy[0]-best_qb_corr[0]),3)+"um from best_qb_corr)\n"+
"z0="+IJ.d2s((zTxTy[0]),3)+"um ("+IJ.d2s((zTxTy[0]-best_qb_corr[0]),3)+"um from best_qb_corr)\n"+
"tX="+IJ.d2s(zTxTy[1],3)+"um/mm\n"+
"tY="+IJ.d2s(zTxTy[2],3)+"um/mm");
double [] zTxTyCorr=fieldFitting.mechanicalFocusingModel.getZTxTyCorr(
currentPX0, // optical center X
currentPY0); // optical center Y
for (int i=0;i<zTxTyCorr.length;i++){
zTxTy[i]+=zTxTyCorr[i];
}
System.out.println("qualBOptimize corrected to Zc, tx axial, ty axial:\n"+
"zc="+IJ.d2s((zTxTy[0]),3)+"um ("+IJ.d2s((zTxTy[0]-best_qb_corr[0]),3)+"um from best_qb_corr)\n"+
"tX axial="+IJ.d2s(zTxTy[1],3)+"um/mm\n"+
"tY axial="+IJ.d2s(zTxTy[2],3)+"um/mm");
} else {
System.out.println("qualBOptimize LMA failed");
}
......
src/main/java/LensAdjustment.java
View file @ d14a3970
......@@ -226,13 +226,14 @@ public class LensAdjustment {
public int lensSerialLength=4;
public String lensSerial=""; // Lens serial number
public boolean askLensSerial=true; // Ask lens serial on camera power cycle
public double reportTemperature=50; // temperature to report focal length
public boolean includeLensSerial=true; // add lens serial to config filename
public double centerDeltaX=0.0; // required X-difference between lens center and sensor center
public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center
// with the seam in the middle - make even # of samples horizontally
public Rectangle margins=new Rectangle (100,100,2392,1736) ; // maximal height 1816 (1936-120)
public int [] numSamples={4,3}; // number of samples in x and y directions
public int [] numSamples={8,5}; // number of samples in x and y directions
public int sampleSize=256;// 512; // size of square (2^n), in sensor pixels (twice FFT size)
public int numInCenter=(numSamples[0]-2)*(numSamples[1]-2);// 2 - number of "center" samples
public boolean centerSamples=true; // Select samples in the WOI symmetrical around the lens center
......@@ -583,7 +584,8 @@ public class LensAdjustment {
int numIterations, // maximal number of iterations
boolean cameraIsConfigured,
int [] motorPos,
double [] ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored)
double [] ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
double reportTemperature // temperature to report focal length
){
this.gridGeometryFile=gridGeometryFile;
this.initialCalibrationFile=initialCalibrationFile;
......@@ -734,7 +736,7 @@ public class LensAdjustment {
this.cameraIsConfigured=cameraIsConfigured;
this.motorPos=motorPos;
this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored)
this.reportTemperature=reportTemperature;
}
public FocusMeasurementParameters clone(){
......@@ -887,7 +889,8 @@ public class LensAdjustment {
this.numIterations,
this.cameraIsConfigured,
this.motorPos,
this.ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored)
this.ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
this.reportTemperature
);
}
public void setProperties(String prefix,Properties properties){
......@@ -1049,6 +1052,7 @@ public class LensAdjustment {
properties.setProperty(prefix+"numIterations",this.numIterations+"");
for (int i=0;i<this.ampsSeconds.length;i++)
properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+"");
properties.setProperty(prefix+"reportTemperature",this.reportTemperature+"");
}
public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"gridGeometryFile")!=null)
......@@ -1368,9 +1372,10 @@ public class LensAdjustment {
this.thresholdFinish=Double.parseDouble(properties.getProperty(prefix+"thresholdFinish"));
if (properties.getProperty(prefix+"numIterations")!=null)
this.numIterations=Integer.parseInt(properties.getProperty(prefix+"numIterations"));
for (int i=0;i<this.ampsSeconds.length;i++) if (properties.getProperty(prefix+"ampsSeconds_"+i)!=null)
this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i));
if (properties.getProperty(prefix+"reportTemperature")!=null)
this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature"));
}
public boolean getLensSerial(){
while (true) { // loop until OK-ed
......@@ -1628,13 +1633,23 @@ public class LensAdjustment {
gd.addNumericField("Expand during extrapolation (relative to the average grid period)", this.flatFieldExpand, 3);
gd.addNumericField("Threshold RMS to exit LMA", this.thresholdFinish, 7,9,"pix");
gd.addNumericField("Maximal number of LMA iterations per series",this.numIterations, 0);
gd.addMessage("-----");
gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");
if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C");
if (!Double.isNaN(this.result_lastKT)) gd.addMessage("Temperature focal distance coefficient measured in last run is "+this.result_lastKT+"microns/C");
if (!Double.isNaN(this.result_lastFD20)) gd.addMessage("Focal distance @20C measured at last run is "+this.result_lastFD20+" microns");
if (!Double.isNaN(this.result_lastKT) && !Double.isNaN(this.result_lastFD20)){
gd.addMessage("Focal distance @"+this.reportTemperature+"C measured at last run is "+
(this.result_lastFD20+(this.reportTemperature-20.0)*this.result_lastKT)+" microns");
}
if (!Double.isNaN(this.result_allHistoryKT)) gd.addMessage("Temperature focal distance coefficient calculated from all measurements is "+this.result_allHistoryKT+" microns");
if (!Double.isNaN(this.result_allHistoryFD20)) gd.addMessage("Focal distance @20C calculated from all measurements is "+this.result_allHistoryFD20+" microns");
if (!Double.isNaN(this.result_allHistoryKT) && !Double.isNaN(this.result_allHistoryFD20)){
gd.addMessage("Focal distance @"+this.reportTemperature+"C calculated from all measurements is "+
(this.result_allHistoryFD20+(this.reportTemperature-20.0)*this.result_allHistoryKT)+" microns");
}
if (!Double.isNaN(this.result_fDistance)) gd.addMessage("Focal distance is "+this.result_fDistance+" microns");
if (!Double.isNaN(this.result_tiltX)) gd.addMessage("Horizontal angular/tangential asymmetry "+this.result_tiltX);
if (!Double.isNaN(this.result_tiltY)) gd.addMessage("Vertical angular/tangential asymmetry "+this.result_tiltY);
......@@ -1650,6 +1665,7 @@ public class LensAdjustment {
if (!Double.isNaN(this.result_FocalLength)) gd.addMessage("Lens focal length "+this.result_FocalLength+" mm");
gd.addMessage("Cumulative currents that ran through UV LEDs:");
for (int i=0;i<this.ampsSeconds.length;i++) gd.addMessage("UV LED "+(i+1)+":"+IJ.d2s(this.ampsSeconds[i],3)+" coulombs (amp-seconds)");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
......@@ -1803,6 +1819,7 @@ public class LensAdjustment {
this.flatFieldExpand= gd.getNextNumber();
this.thresholdFinish= gd.getNextNumber();
this.numIterations= (int) gd.getNextNumber();
this.reportTemperature= gd.getNextNumber();
return true;
}
/* ======================================================================== */
......
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