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Commit 1a664c2b authored by Andrey Filippov's avatar Andrey Filippov
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removed obsolete data output

parent 82208513
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Showing with 141 additions and 97 deletions
src/main/java/Aberration_Calibration.java
View file @ 1a664c2b
...@@ -829,6 +829,7 @@ if (MORE_BUTTONS) { ...@@ -829,6 +829,7 @@ if (MORE_BUTTONS) {
addButton("Test measurement", panelCurvature,color_debug); addButton("Test measurement", panelCurvature,color_debug);
addButton("Optimize qualB", panelCurvature,color_debug); addButton("Optimize qualB", panelCurvature,color_debug);
addButton("Focus/Tilt LMA", panelCurvature,color_process); addButton("Focus/Tilt LMA", panelCurvature,color_process);
addButton("Post-UV Adjust", panelCurvature,color_process);
add(panelCurvature); add(panelCurvature);
//panelGoniometer //panelGoniometer
...@@ -4372,11 +4373,12 @@ if (MORE_BUTTONS) { ...@@ -4372,11 +4373,12 @@ if (MORE_BUTTONS) {
// int [] mmm= MOTORS.focusingHistory.getPosition(); // int [] mmm= MOTORS.focusingHistory.getPosition();
//System.out.println("@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]); //System.out.println("@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]);
if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distamnce from center PSF MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distamnce from center PSF
FOCUS_MEASUREMENT_PARAMETERS, FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep, MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL); DEBUG_LEVEL);
}
//System.out.println("@@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]); //System.out.println("@@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]);
boolean autoMove= label.equals("Auto Focus/Tilt"); boolean autoMove= label.equals("Auto Focus/Tilt");
boolean fineFocus=label.equals("Fine Focus"); boolean fineFocus=label.equals("Fine Focus");
...@@ -4934,11 +4936,9 @@ if (MORE_BUTTONS) { ...@@ -4934,11 +4936,9 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.testQualB(true); // public double[] testQualB(boolean interactive) FOCUSING_FIELD.testQualB(true); // public double[] testQualB(boolean interactive)
return; return;
} }
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Focus/Tilt LMA")) { if (label.equals("Focus/Tilt LMA") || label.equals("Post-UV Adjust")) {
int adjustMode=label.equals("Focus/Tilt LMA")?0:1;
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) { if (FOCUSING_FIELD==null) {
if (DEBUG_LEVEL>0) System.out.println("FOCUSING_FIELD==null, trying to restore from the previously saved file"); if (DEBUG_LEVEL>0) System.out.println("FOCUSING_FIELD==null, trying to restore from the previously saved file");
...@@ -4959,12 +4959,13 @@ if (MORE_BUTTONS) { ...@@ -4959,12 +4959,13 @@ if (MORE_BUTTONS) {
} }
} }
// Just for old focal distance calculation // Just for old focal distance calculation
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
FOCUS_MEASUREMENT_PARAMETERS, MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
MOTORS.getMicronsPerStep(), //double micronsPerStep, FOCUS_MEASUREMENT_PARAMETERS,
DEBUG_LEVEL); MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
while (adjustFocusTiltLMA()); }
while (adjustFocusTiltLMA(adjustMode));
return; return;
} }
// //
...@@ -5426,11 +5427,12 @@ if (MORE_BUTTONS) { ...@@ -5426,11 +5427,12 @@ if (MORE_BUTTONS) {
FOCUS_MEASUREMENT_PARAMETERS.result_PX0, FOCUS_MEASUREMENT_PARAMETERS.result_PX0,
FOCUS_MEASUREMENT_PARAMETERS.result_PY0); FOCUS_MEASUREMENT_PARAMETERS.result_PY0);
} }
if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS, FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep, MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL); DEBUG_LEVEL);
}
moveAndMaybeProbe( moveAndMaybeProbe(
true, // just move, not probe true, // just move, not probe
null, // no move, just measure null, // no move, just measure
...@@ -5500,10 +5502,12 @@ if (MORE_BUTTONS) { ...@@ -5500,10 +5502,12 @@ if (MORE_BUTTONS) {
String [] zTxTyNames={"z", "tx","ty"}; String [] zTxTyNames={"z", "tx","ty"};
// boolean useLMA=true; // boolean useLMA=true;
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
FOCUS_MEASUREMENT_PARAMETERS, MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
MOTORS.getMicronsPerStep(), //double micronsPerStep, FOCUS_MEASUREMENT_PARAMETERS,
DEBUG_LEVEL); MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
}
GenericDialog gd = new GenericDialog(modeAverage?"Averaging measurements":"Temperature Scan"); GenericDialog gd = new GenericDialog(modeAverage?"Averaging measurements":"Temperature Scan");
//replayMode //replayMode
double scanMinutes=modeAverage?2.0:30.0; double scanMinutes=modeAverage?2.0:30.0;
...@@ -5938,7 +5942,7 @@ if (MORE_BUTTONS) { ...@@ -5938,7 +5942,7 @@ if (MORE_BUTTONS) {
"Average Tilt y: "+IJ.d2s(zcZ0TxTy[0][2],3)+"um/mm\n"; "Average Tilt y: "+IJ.d2s(zcZ0TxTy[0][2],3)+"um/mm\n";
System.out.println(msg); System.out.println(msg);
gd.addMessage(msg); gd.addMessage(msg);
gd.addCheckbox("Store calculated tilts, defaultValue",FOCUSING_FIELD.updateAverageTilts); gd.addCheckbox("Store calculated tilts",FOCUSING_FIELD.updateAverageTilts);
} }
gd.showDialog(); gd.showDialog();
if (!gd.wasCanceled()){ if (!gd.wasCanceled()){
...@@ -9918,7 +9922,11 @@ if (MORE_BUTTONS) { ...@@ -9918,7 +9922,11 @@ if (MORE_BUTTONS) {
} }
public boolean adjustFocusTiltLMA(){ /**
* @param adjustMode - 0 normal, using motors. 1 - post-UV manual adjustment
* @return
*/
public boolean adjustFocusTiltLMA(int adjustMode){
// just for reporting distance old way // just for reporting distance old way
/* /*
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
...@@ -9940,8 +9948,11 @@ if (MORE_BUTTONS) { ...@@ -9940,8 +9948,11 @@ if (MORE_BUTTONS) {
FOCUS_MEASUREMENT_PARAMETERS.result_PX0, FOCUS_MEASUREMENT_PARAMETERS.result_PX0,
FOCUS_MEASUREMENT_PARAMETERS.result_PY0); FOCUS_MEASUREMENT_PARAMETERS.result_PY0);
} }
int [] adjustModeAllCommon={1,1,1};
// save zTxTyAdjustMode used in moveMeasureAndSave, and overwrite it with adjustModeAllCommon (so new tX,tY will be calculated each time)
int [] savedZTxTyAdjustMode=FOCUSING_FIELD.zTxTyAdjustMode.clone();
FOCUSING_FIELD.zTxTyAdjustMode=adjustModeAllCommon.clone();
// No-move measure, add to history // No-move measure, add to history
moveAndMaybeProbe( moveAndMaybeProbe(
true, // just move, not probe true, // just move, not probe
null, // no move, just measure null, // no move, just measure
...@@ -9961,16 +9972,17 @@ if (MORE_BUTTONS) { ...@@ -9961,16 +9972,17 @@ if (MORE_BUTTONS) {
UPDATE_STATUS, UPDATE_STATUS,
MASTER_DEBUG_LEVEL, MASTER_DEBUG_LEVEL,
DISTORTION.loop_debug_level); DISTORTION.loop_debug_level);
// restore configured FOCUSING_FIELD.zTxTyAdjustMode
FOCUSING_FIELD.zTxTyAdjustMode=savedZTxTyAdjustMode.clone();
//get measurement //get measurement
FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD); FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
// calculate z, tx, ty, m1,m2,m3 // calculate z, tx, ty, m1,m2,m3
int [] adjustModeAllCommon={1,1,1};
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA( double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
adjustModeAllCommon, // FOCUSING_FIELD.zTxTyAdjustMode, adjustModeAllCommon, // FOCUSING_FIELD.zTxTyAdjustMode,
false, // allow tilt scan false, // allow tilt scan
fFMeasurement, fFMeasurement,
false, // parallel move false, // parallel move
true, // boolean noQualB, // do not re-claculate testQualB true, // boolean noQualB, // do not re-calculate testQualB
false); // boolean noAdjust); // do not calculate correction false); // boolean noAdjust); // do not calculate correction
// show dialog: Apply, re-calculate, exit // show dialog: Apply, re-calculate, exit
int [] currentMotors=fFMeasurement.motors; int [] currentMotors=fFMeasurement.motors;
...@@ -10012,28 +10024,31 @@ if (MORE_BUTTONS) { ...@@ -10012,28 +10024,31 @@ if (MORE_BUTTONS) {
System.out.println("Relative to optimal focal shift "+IJ.d2s(zTxTy[0],3)+" um ("+IJ.d2s(FOCUSING_FIELD.targetRelFocalShift,3)+"um)"); System.out.println("Relative to optimal focal shift "+IJ.d2s(zTxTy[0],3)+" um ("+IJ.d2s(FOCUSING_FIELD.targetRelFocalShift,3)+"um)");
System.out.println("Relative to optimal horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltX,3)+"um/mm)"); System.out.println("Relative to optimal horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltX,3)+"um/mm)");
System.out.println("Relative to optimal vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltY,3)+"um/mm)"); System.out.println("Relative to optimal vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltY,3)+"um/mm)");
for (int i=0;i<newMotors.length;i++){ if (adjustMode==0) {
System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")"); for (int i=0;i<newMotors.length;i++){
} System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")");
if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){ }
double deg=360*Math.abs(manualScrewsCW[i]); if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){
if (manualScrewsCW[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+ double deg=360*Math.abs(manualScrewsCW[i]);
" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)"); if (manualScrewsCW[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+
else System.out.println("Suggested rotation for screw # "+(i+1)+ " "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
}
if (postUVScrews!=null) {
System.out.println("----- Post-UV fixture screw adjustments -----");
for (int i=0;i<postUVScrews.length;i++){
double deg=360*Math.abs(postUVScrews[i]);
if (postUVScrews[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+
" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
else System.out.println("Suggested rotation for screw # "+(i+1)+ else System.out.println("Suggested rotation for screw # "+(i+1)+
" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)"); " "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
}
} else if (adjustMode==1) {
if (postUVScrews!=null) {
System.out.println("----- Post-UV fixture screw adjustments -----");
for (int i=0;i<postUVScrews.length;i++){
double deg=360*Math.abs(postUVScrews[i]);
if (postUVScrews[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+
" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
else System.out.println("Suggested rotation for screw # "+(i+1)+
" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
}
} }
} }
System.out.println("----- end of Focus/tilt measurement results -----"); System.out.println("----- end of Focus/tilt measurement results -----");
if (MASTER_DEBUG_LEVEL>0) System.out.println(FOCUSING_FIELD.showSamples()); if (MASTER_DEBUG_LEVEL>0) System.out.println(FOCUSING_FIELD.showSamples());
} }
GenericDialog gd = new GenericDialog("Adjusting focus/tilt"); GenericDialog gd = new GenericDialog("Adjusting focus/tilt");
...@@ -10053,26 +10068,29 @@ if (MORE_BUTTONS) { ...@@ -10053,26 +10068,29 @@ if (MORE_BUTTONS) {
gd.addCheckbox("Optimize tiltX", (FOCUSING_FIELD.qualBOptimizeMode & 2) != 0); gd.addCheckbox("Optimize tiltX", (FOCUSING_FIELD.qualBOptimizeMode & 2) != 0);
gd.addCheckbox("Optimize tiltY", (FOCUSING_FIELD.qualBOptimizeMode & 4) != 0); gd.addCheckbox("Optimize tiltY", (FOCUSING_FIELD.qualBOptimizeMode & 4) != 0);
if (adjustMode==0) {
gd.addNumericField("Motor 1",newMotors[0],0,5,"steps ("+currentMotors[0]+")"); gd.addNumericField("Motor 1",newMotors[0],0,5,"steps ("+currentMotors[0]+")");
gd.addNumericField("Motor 2",newMotors[1],0,5,"steps ("+currentMotors[1]+")"); gd.addNumericField("Motor 2",newMotors[1],0,5,"steps ("+currentMotors[1]+")");
gd.addNumericField("Motor 3",newMotors[2],0,5,"steps ("+currentMotors[2]+")"); gd.addNumericField("Motor 3",newMotors[2],0,5,"steps ("+currentMotors[2]+")");
gd.addMessage("Suggested rotation of the top screws, use if motor positions are out of limits - outside of +/-25,000"); gd.addMessage("Suggested rotation of the top screws, use if motor positions are out of limits - outside of +/-25,000");
if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){ if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){
double deg=360*Math.abs(manualScrewsCW[i]); double deg=360*Math.abs(manualScrewsCW[i]);
if (manualScrewsCW[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)"); if (manualScrewsCW[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)"); else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
} }
if (postUVScrews!=null) { } else if (adjustMode==1) {
gd.addMessage("Suggested rotation of the post-UV fixture screws (far left, near left, right) ---");
for (int i=0;i<postUVScrews.length;i++){ if (postUVScrews!=null) {
double deg=360*Math.abs(postUVScrews[i]); gd.addMessage("Suggested rotation of the post-UV fixture screws (far left, near left, right) ---");
if (postUVScrews[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)"); for (int i=0;i<postUVScrews.length;i++){
else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)"); double deg=360*Math.abs(postUVScrews[i]);
} if (postUVScrews[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
gd.addMessage("--- Post-UV fixture screws sensitivity ---"); else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){ }
gd.addNumericField("Screw "+i+" sensitivity", FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i], 4,6,"um/turn CW"); gd.addMessage("--- Post-UV fixture screws sensitivity ---");
for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){
gd.addNumericField("Screw "+i+" sensitivity", FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i], 4,6,"um/turn CW");
}
} }
} }
gd.addNumericField("Scale movement",scaleMovement,3,5,"x"); gd.addNumericField("Scale movement",scaleMovement,3,5,"x");
...@@ -10089,11 +10107,13 @@ if (MORE_BUTTONS) { ...@@ -10089,11 +10107,13 @@ if (MORE_BUTTONS) {
gd.addNumericField("Tilt min",FOCUSING_FIELD.tMin,2,5,"um/mm"); gd.addNumericField("Tilt min",FOCUSING_FIELD.tMin,2,5,"um/mm");
gd.addNumericField("Tilt max",FOCUSING_FIELD.tMax,2,5,"um/mm"); gd.addNumericField("Tilt max",FOCUSING_FIELD.tMax,2,5,"um/mm");
gd.addNumericField("Tilt step",FOCUSING_FIELD.tStep,2,5,"um/mm"); gd.addNumericField("Tilt step",FOCUSING_FIELD.tStep,2,5,"um/mm");
gd.addCheckbox("Store calculated tilts",FOCUSING_FIELD.updateAverageTilts);
gd.addCheckbox("Show current PSF",showPSF); gd.addCheckbox("Show current PSF",showPSF);
if (adjustMode==0) {
gd.addNumericField("Motor anti-hysteresis travel (last measured was "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.measuredHysteresis,0)+")", FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis, 0,7,"motors steps"); gd.addNumericField("Motor anti-hysteresis travel (last measured was "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.measuredHysteresis,0)+")", FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis, 0,7,"motors steps");
}
gd.addNumericField("Debug Level:", MASTER_DEBUG_LEVEL, 0); gd.addNumericField("Debug Level:", MASTER_DEBUG_LEVEL, 0);
gd.enableYesNoCancel("Apply movement","Re-measure"); // default OK (on enter) - "Apply" if (adjustMode==0) gd.enableYesNoCancel("Apply movement","Re-measure"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
...@@ -10105,14 +10125,15 @@ if (MORE_BUTTONS) { ...@@ -10105,14 +10125,15 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?1:0; FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?1:0;
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?2:0; FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?2:0;
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?4:0; FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?4:0;
if (adjustMode==0) {
newMotors[0]= (int) gd.getNextNumber(); newMotors[0]= (int) gd.getNextNumber();
newMotors[1]= (int) gd.getNextNumber(); newMotors[1]= (int) gd.getNextNumber();
newMotors[2]= (int) gd.getNextNumber(); newMotors[2]= (int) gd.getNextNumber();
} else if (adjustMode==1) {
if (postUVScrews!=null) { if (postUVScrews!=null) {
for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){ for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){
FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i]=gd.getNextNumber(); FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i]=gd.getNextNumber();
}
} }
} }
scaleMovement= gd.getNextNumber(); scaleMovement= gd.getNextNumber();
...@@ -10128,11 +10149,27 @@ if (MORE_BUTTONS) { ...@@ -10128,11 +10149,27 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.tMin= gd.getNextNumber(); FOCUSING_FIELD.tMin= gd.getNextNumber();
FOCUSING_FIELD.tMax= gd.getNextNumber(); FOCUSING_FIELD.tMax= gd.getNextNumber();
FOCUSING_FIELD.tStep= gd.getNextNumber(); FOCUSING_FIELD.tStep= gd.getNextNumber();
FOCUSING_FIELD.updateAverageTilts= gd.getNextBoolean();
showPSF= gd.getNextBoolean(); showPSF= gd.getNextBoolean();
FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis= (int) gd.getNextNumber(); if (adjustMode==0) {
FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis= (int) gd.getNextNumber();
}
MASTER_DEBUG_LEVEL=( int) gd.getNextNumber(); MASTER_DEBUG_LEVEL=( int) gd.getNextNumber();
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL); FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
if (FOCUSING_FIELD.updateAverageTilts){
double[][]zTxTyAbsRel=FOCUSING_FIELD.getZ0TxTyAbsRel(); // z - z0, not zc here !
if (zTxTyAbsRel!=null){
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)
FOCUS_MEASUREMENT_PARAMETERS.result_fDistance=zTxTy[0];
FOCUS_MEASUREMENT_PARAMETERS.result_tiltX= zTxTy[1];
FOCUS_MEASUREMENT_PARAMETERS.result_tiltY= zTxTy[2];
}
}
if (showPSF){ if (showPSF){
if (PSF_KERNEL_MAP==null){ if (PSF_KERNEL_MAP==null){
IJ.showMessage("Warning","PSF_KERNEL_MAP is null, nothing to show" ); IJ.showMessage("Warning","PSF_KERNEL_MAP is null, nothing to show" );
...@@ -10156,6 +10193,7 @@ if (MORE_BUTTONS) { ...@@ -10156,6 +10193,7 @@ if (MORE_BUTTONS) {
} }
} }
} }
if (parallelMove){ // ignore/recalculate newMotors data if (parallelMove){ // ignore/recalculate newMotors data
int [] adjustZOnly={1,0,0}; int [] adjustZOnly={1,0,0};
zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA( zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
...@@ -10182,7 +10220,7 @@ if (MORE_BUTTONS) { ...@@ -10182,7 +10220,7 @@ if (MORE_BUTTONS) {
newMotors[1]=currentMotors[1]+((int) Math.round((newMotors[1]-currentMotors[1])*scaleMovement)); newMotors[1]=currentMotors[1]+((int) Math.round((newMotors[1]-currentMotors[1])*scaleMovement));
newMotors[2]=currentMotors[2]+((int) Math.round((newMotors[2]-currentMotors[2])*scaleMovement)); newMotors[2]=currentMotors[2]+((int) Math.round((newMotors[2]-currentMotors[2])*scaleMovement));
if (gd.wasOKed()){ if ((adjustMode==0) && gd.wasOKed()){
// Move, no measure // Move, no measure
MOTORS.moveElphel10364Motors( MOTORS.moveElphel10364Motors(
true, //boolean wait, true, //boolean wait,
...@@ -12046,14 +12084,16 @@ if (MORE_BUTTONS) { ...@@ -12046,14 +12084,16 @@ if (MORE_BUTTONS) {
if ((debugLevel>0) && (metrics!=null)){ if ((debugLevel>0) && (metrics!=null)){
// see if lens is calibrated // see if lens is calibrated
double [] resolutions={1.0/metrics[1][6],1.0/metrics[5][6],1.0/metrics[2][6]}; // R,G,B double [] resolutions={1.0/metrics[1][6],1.0/metrics[5][6],1.0/metrics[2][6]}; // R,G,B
double fDistanceOld=focusingMotors.focusingHistory.getLensDistance( double fDistanceOld=Double.NaN;
resolutions, // {R-sharpness,G-sharpness,B-sharpness} if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy) {
true, // boolean absolute, // return absolutely calibrated data fDistanceOld=focusingMotors.focusingHistory.getLensDistance(
focusMeasurementParameters.lensDistanceWeightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives resolutions, // {R-sharpness,G-sharpness,B-sharpness}
focusMeasurementParameters.lensDistanceWeightY, // R-frac, B-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution true, // boolean absolute, // return absolutely calibrated data
debugLevel focusMeasurementParameters.lensDistanceWeightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives
); focusMeasurementParameters.lensDistanceWeightY, // R-frac, B-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
debugLevel
);
}
// int ca=6; // int ca=6;
String sZTxTy=""; String sZTxTy="";
if (zTxTy!=null){ if (zTxTy!=null){
...@@ -12063,8 +12103,7 @@ if (MORE_BUTTONS) { ...@@ -12063,8 +12103,7 @@ if (MORE_BUTTONS) {
System.out.println("##"+focusingMotors.historySize()+": "+actualPosition[0]+", "+actualPosition[1]+", "+actualPosition[2]+ System.out.println("##"+focusingMotors.historySize()+": "+actualPosition[0]+", "+actualPosition[1]+", "+actualPosition[2]+
": "+ ": "+
sZTxTy+ sZTxTy+
" fDistanceOld="+IJ.d2s(fDistanceOld,3)+"um"+ (FOCUS_MEASUREMENT_PARAMETERS.showLegacy?(" fDistanceOld="+IJ.d2s(fDistanceOld,3)+"um"+" Far/Near="+IJ.d2s(oldFarNear,3)):"")+
" Far/Near="+IJ.d2s(oldFarNear,3)+
" Tilt X="+IJ.d2s(oldTx,3)+ " Tilt X="+IJ.d2s(oldTx,3)+
" Tilt Y="+IJ.d2s(oldTy,3)+ " Tilt Y="+IJ.d2s(oldTy,3)+
" R50% average="+IJ.d2s(metrics[ca][3],3)+" sensor pixels,"+ " R50% average="+IJ.d2s(metrics[ca][3],3)+" sensor pixels,"+
...@@ -12096,8 +12135,6 @@ if (MORE_BUTTONS) { ...@@ -12096,8 +12135,6 @@ if (MORE_BUTTONS) {
} }
} }
public boolean moveAndMeasureSharpness( public boolean moveAndMeasureSharpness(
int [] newMotorPos, // null OK int [] newMotorPos, // null OK
CalibrationHardwareInterface.FocusingMotors focusingMotors, CalibrationHardwareInterface.FocusingMotors focusingMotors,
src/main/java/LensAdjustment.java
View file @ 1a664c2b
...@@ -231,9 +231,9 @@ public class LensAdjustment { ...@@ -231,9 +231,9 @@ public class LensAdjustment {
public String comment="no comments"; // Comment to add to the results public String comment="no comments"; // Comment to add to the results
public int lensSerialLength=4; public int lensSerialLength=4;
public String lensSerial=""; // Lens serial number public String lensSerial=""; // Lens serial number
public boolean askLensSerial=true; // Ask lens serial on camera power cycle public boolean askLensSerial=true; // Ask lens serial on camera power cycle
public double reportTemperature=50; // temperature to report focal length public double reportTemperature=50; // temperature to report focal length
public boolean showLegacy=false; // Show old focusing parameters (most are not supported anyway)
public boolean includeLensSerial=true; // add lens serial to config filename 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 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 public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center
...@@ -606,7 +606,8 @@ public class LensAdjustment { ...@@ -606,7 +606,8 @@ public class LensAdjustment {
boolean cameraIsConfigured, boolean cameraIsConfigured,
int [] motorPos, 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 double reportTemperature, // temperature to report focal length
boolean showLegacy
){ ){
this.gridGeometryFile=gridGeometryFile; this.gridGeometryFile=gridGeometryFile;
this.initialCalibrationFile=initialCalibrationFile; this.initialCalibrationFile=initialCalibrationFile;
...@@ -763,7 +764,7 @@ public class LensAdjustment { ...@@ -763,7 +764,7 @@ public class LensAdjustment {
this.motorPos=motorPos; this.motorPos=motorPos;
this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored) this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored)
this.reportTemperature=reportTemperature; this.reportTemperature=reportTemperature;
this.showLegacy=showLegacy;
} }
public FocusMeasurementParameters clone(){ public FocusMeasurementParameters clone(){
return new FocusMeasurementParameters( return new FocusMeasurementParameters(
...@@ -921,7 +922,8 @@ public class LensAdjustment { ...@@ -921,7 +922,8 @@ public class LensAdjustment {
this.cameraIsConfigured, this.cameraIsConfigured,
this.motorPos, 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 this.reportTemperature,
this.showLegacy
); );
} }
public void setProperties(String prefix,Properties properties){ public void setProperties(String prefix,Properties properties){
...@@ -1092,6 +1094,7 @@ public class LensAdjustment { ...@@ -1092,6 +1094,7 @@ public class LensAdjustment {
for (int i=0;i<this.ampsSeconds.length;i++) for (int i=0;i<this.ampsSeconds.length;i++)
properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+""); properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+"");
properties.setProperty(prefix+"reportTemperature",this.reportTemperature+""); properties.setProperty(prefix+"reportTemperature",this.reportTemperature+"");
properties.setProperty(prefix+"showLegacy",this.showLegacy+"");
} }
public void getProperties(String prefix,Properties properties){ public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"gridGeometryFile")!=null) if (properties.getProperty(prefix+"gridGeometryFile")!=null)
...@@ -1427,6 +1430,8 @@ public class LensAdjustment { ...@@ -1427,6 +1430,8 @@ public class LensAdjustment {
this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i)); this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i));
if (properties.getProperty(prefix+"reportTemperature")!=null) if (properties.getProperty(prefix+"reportTemperature")!=null)
this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature")); this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature"));
if (properties.getProperty(prefix+"showLegacy")!=null)
this.showLegacy=Boolean.parseBoolean(properties.getProperty(prefix+"showLegacy"));
} }
public boolean getLensSerial(){ public boolean getLensSerial(){
while (true) { // loop until OK-ed while (true) { // loop until OK-ed
...@@ -1696,6 +1701,7 @@ public class LensAdjustment { ...@@ -1696,6 +1701,7 @@ public class LensAdjustment {
gd.addMessage("-----"); gd.addMessage("-----");
gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C"); gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");
gd.addCheckbox ("Show legacy focusing parameters (most are already not supported anyway)", this.showLegacy);
if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C"); if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C");
...@@ -1888,6 +1894,7 @@ public class LensAdjustment { ...@@ -1888,6 +1894,7 @@ public class LensAdjustment {
this.postUVscrewSensitivity[i]= gd.getNextNumber(); this.postUVscrewSensitivity[i]= gd.getNextNumber();
} }
this.reportTemperature= gd.getNextNumber(); this.reportTemperature= gd.getNextNumber();
this.showLegacy= gd.getNextBoolean();
return true; return true;
} }
/* ======================================================================== */ /* ======================================================================== */
......
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