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Commit 0c488df6 authored by Andrey Filippov's avatar Andrey Filippov
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bug fixes

parent 1d7456a6
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Showing with 20 additions and 11 deletions
src/main/java/Aberration_Calibration.java
View file @ 0c488df6
...@@ -5171,9 +5171,9 @@ if (MORE_BUTTONS) { ...@@ -5171,9 +5171,9 @@ if (MORE_BUTTONS) {
if (MASTER_DEBUG_LEVEL>0) { if (MASTER_DEBUG_LEVEL>0) {
String msg="Failed to calulate average focus/tilt"; String msg="Failed to calulate average focus/tilt";
if (ZTM!=null) msg="Average:\n"+ if (ZTM!=null) msg="Average:\n"+
"Relative focal shift "+IJ.d2s(ZTM[0],3)+"um\n"+ "Relative focal shift "+IJ.d2s(ZTM[0],3)+"um (absolute - "+IJ.d2s(ZTM[0]+FOCUSING_FIELD.qualBOptimizationResults[0],3)+"um)\n"+
"Horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm\n"+ "Relative horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm (absolute - "+IJ.d2s(ZTM[1]+FOCUSING_FIELD.qualBOptimizationResults[1],3)+"um.mm)\n"+
"Vertical tilt "+IJ.d2s(ZTM[2],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"+
"Suggested M1 "+IJ.d2s(ZTM[3],0)+"steps\n"+ "Suggested M1 "+IJ.d2s(ZTM[3],0)+"steps\n"+
"Suggested M2 "+IJ.d2s(ZTM[4],0)+"steps\n"+ "Suggested M2 "+IJ.d2s(ZTM[4],0)+"steps\n"+
"Suggested M3 "+IJ.d2s(ZTM[5],0)+"steps"; "Suggested M3 "+IJ.d2s(ZTM[5],0)+"steps";
...@@ -8928,10 +8928,15 @@ if (MORE_BUTTONS) { ...@@ -8928,10 +8928,15 @@ if (MORE_BUTTONS) {
double scaleMovement=1.0; // calculate automatically - reduce when close double scaleMovement=1.0; // calculate automatically - reduce when close
boolean parallelMove=false; boolean parallelMove=false;
if (MASTER_DEBUG_LEVEL>0){ if (MASTER_DEBUG_LEVEL>0){
System.out.println("----- Optimal (for qualB) focus/tilt -----");
System.out.println("Optimal absolute Zc="+FOCUSING_FIELD.qualBOptimizationResults[0]);
System.out.println("Optimal Tx="+FOCUSING_FIELD.qualBOptimizationResults[1]);
System.out.println("Optimal Ty="+FOCUSING_FIELD.qualBOptimizationResults[2]);
System.out.println("----- Focus/tilt measurement results -----"); System.out.println("----- Focus/tilt measurement results -----");
System.out.println("Relative 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("Horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(targetTilts[0],3)+"um/mm)"); System.out.println("Relative to optimal horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(targetTilts[0],3)+"um/mm)");
System.out.println("Vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(targetTilts[1],3)+"um/mm)"); System.out.println("Relative to optimal vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(targetTilts[1],3)+"um/mm)");
for (int i=0;i<newMotors.length;i++){ for (int i=0;i<newMotors.length;i++){
System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")"); System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")");
} }
...@@ -8955,6 +8960,10 @@ if (MORE_BUTTONS) { ...@@ -8955,6 +8960,10 @@ if (MORE_BUTTONS) {
gd.addNumericField("Target horizontal tilt relative to optimal (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")"); gd.addNumericField("Target horizontal tilt relative to optimal (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")");
gd.addNumericField("Target vertical tilt relative to optimal (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")"); gd.addNumericField("Target vertical tilt relative to optimal (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")");
gd.addMessage("Optimal absolute Zc="+FOCUSING_FIELD.qualBOptimizationResults[0]);
gd.addMessage("Optimal Tx="+FOCUSING_FIELD.qualBOptimizationResults[1]);
gd.addMessage("Optimal Ty="+FOCUSING_FIELD.qualBOptimizationResults[2]);
gd.addCheckbox("Optimize focal distance",(FOCUSING_FIELD.qualBOptimizeMode & 1) != 0); gd.addCheckbox("Optimize focal distance",(FOCUSING_FIELD.qualBOptimizeMode & 1) != 0);
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);
......
src/main/java/FocusingField.java
View file @ 0c488df6
...@@ -4790,7 +4790,7 @@ public boolean LevenbergMarquardt( ...@@ -4790,7 +4790,7 @@ public boolean LevenbergMarquardt(
return result; return result;
} }
public double [] averageZTM( public double [] averageZTM(// results relative to optimal
boolean noTiltScan, boolean noTiltScan,
FocusingField ff){ FocusingField ff){
double [] result =new double[6]; double [] result =new double[6];
...@@ -4807,7 +4807,7 @@ public boolean LevenbergMarquardt( ...@@ -4807,7 +4807,7 @@ public boolean LevenbergMarquardt(
for (int i=0;i<result.length;i++) result[i]/=num; for (int i=0;i<result.length;i++) result[i]/=num;
return result; return result;
} }
public double [] adjustLMA ( public double [] adjustLMA ( // result relative to optimal
boolean noTiltScan, boolean noTiltScan,
FocusingFieldMeasurement measurement, FocusingFieldMeasurement measurement,
boolean parallelMove){ boolean parallelMove){
...@@ -4826,9 +4826,9 @@ public boolean LevenbergMarquardt( ...@@ -4826,9 +4826,9 @@ public boolean LevenbergMarquardt(
if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode); if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
if (debugLevel>0) { if (debugLevel>0) {
System.out.println("Target Zc="+this.qualBOptimizationResults[0]); System.out.println("Optimal absolute Zc="+this.qualBOptimizationResults[0]);
System.out.println("Target Tx="+this.qualBOptimizationResults[1]); System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]);
System.out.println("Target Ty="+this.qualBOptimizationResults[2]); System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]);
} }
// double [] best_qb_corr= fieldFitting.getBestQualB( // double [] best_qb_corr= fieldFitting.getBestQualB(
......
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