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Commit f8cffed4 authored by Andrey Filippov's avatar Andrey Filippov
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Added suggestions for manual screws (handling motors out of range)

parent 3fa095d3
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Showing with 142 additions and 13 deletions
src/main/java/Aberration_Calibration.java
View file @ f8cffed4
......@@ -4544,6 +4544,12 @@ if (MORE_BUTTONS) {
return;
}
}
// Just for old focal distance calculation
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
while (adjustFocusTiltLMA());
return;
}
......@@ -8698,10 +8704,12 @@ if (MORE_BUTTONS) {
/* ===== Other methods ==================================================== */
public boolean adjustFocusTiltLMA(){
// just for reporting distance old way
/*
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
*/
// No-move measure, add to history
moveAndMaybeProbe(
true, // just move, not probe
......@@ -8724,7 +8732,7 @@ if (MORE_BUTTONS) {
//get measurement
FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
// calculate z, tx, ty, m1,m2,m3
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA (fFMeasurement);
double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,false);
// show dialog: Apply, re-calculate, exit
int [] currentMotors=fFMeasurement.motors;
int [] newMotors=currentMotors.clone();
......@@ -8738,15 +8746,47 @@ if (MORE_BUTTONS) {
zTxTy[2]=zTxTyM1M2M3[2];
}
double [] targetTilts={0.0,0.0};
double [] manualScrewsCW=null;
if (zTxTyM1M2M3!=null){
manualScrewsCW=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel. getManualScrews(
zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens
zTxTy[1]-targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens
zTxTy[2]-targetTilts[1]); // double tYErr);
}
double scaleMovement=1.0; // calculate automatically - reduce when close
boolean parallelMove=false;
if (MASTER_DEBUG_LEVEL>0){
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("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)");
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++){
if (manualScrewsCW[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CW)");
else System.out.println("Suggested rotation for screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CCW)");
}
System.out.println("----- end of Focus/tilt measurement results -----");
}
GenericDialog gd = new GenericDialog("Adjusting focus/tilt");
if (zTxTyM1M2M3==null){
gd.addMessage("**** Failed to determine focus/tilt, probably too far out of focus. ****");
gd.addMessage("**** You may cancel the command and try \"Auto pre-focus\" first. ****");
}
gd.addNumericField("Target focus (relative to best composirte)",FOCUSING_FIELD.targetRelFocalShift,2,5,"um ("+IJ.d2s(zTxTy[0],3)+")");
gd.addNumericField("Target horizontal tilt (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")");
gd.addNumericField("Target vertical tilt (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")");
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 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");
if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){
if (manualScrewsCW[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CW)");
else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CCW)");
}
gd.addNumericField("Scale movement",scaleMovement,3,5,"x");
gd.addCheckbox("Recalculate and apply parallel move only",parallelMove); // should be false after manual movement
gd.addCheckbox("Filter samples/channels by Z",FOCUSING_FIELD.filterZ); // should be false after manual movement
gd.addCheckbox("Filter by value (leave lower than maximal fwhm used in focal scan mode)",FOCUSING_FIELD.filterByScanValue);
......@@ -8773,7 +8813,7 @@ if (MORE_BUTTONS) {
newMotors[1]= (int) gd.getNextNumber();
newMotors[2]= (int) gd.getNextNumber();
scaleMovement= gd.getNextNumber();
parallelMove= gd.getNextBoolean();
FOCUSING_FIELD.filterZ= gd.getNextBoolean();
FOCUSING_FIELD.filterByScanValue= gd.getNextBoolean();
FOCUSING_FIELD.filterByValueScale= gd.getNextNumber();
......@@ -8789,6 +8829,18 @@ if (MORE_BUTTONS) {
MASTER_DEBUG_LEVEL=( int) gd.getNextNumber();
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
if (parallelMove){ // ignore/recalculate newMotors data
zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,true); // recalculate with parallel move only
newMotors=currentMotors.clone();
if (zTxTyM1M2M3!=null){
newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);
newMotors[1]=(int) Math.round(zTxTyM1M2M3[4]);
newMotors[2]=(int) Math.round(zTxTyM1M2M3[5]);
}
System.out.println("Parallel move position for motor 1 "+newMotors[0]+" ("+currentMotors[0]+")");
System.out.println("Parallel move position for motor 2 "+newMotors[1]+" ("+currentMotors[1]+")");
System.out.println("Parallel move position for motor 3 "+newMotors[2]+" ("+currentMotors[2]+")");
}
// Scale motor movement
newMotors[0]=currentMotors[0]+((int) Math.round((newMotors[0]-currentMotors[0])*scaleMovement));
......@@ -10042,6 +10094,7 @@ if (MORE_BUTTONS) {
return null;
}
if (allOK) {
if (focusMeasurementParameters.scanMeasureLast) {
allOK &= moveAndMaybeProbe(
true,
centerMotorPos, // null OK
......@@ -10060,6 +10113,16 @@ if (MORE_BUTTONS) {
updateStatus,
debugLevel,
loopDebugLevel);
} else { // just move, no measuring
System.out.println("Returning motors to initial position at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
focusingMotors.moveElphel10364Motors( // return to last direct scan position
true, //boolean wait,
centerMotorPos,
0.0, //double sleep,
true, //boolean showStatus,
"", //String message,
false); //focusMeasurementParameters.compensateHysteresis); //boolean hysteresis)
}
}
if (debugLevel>0) System.out.println("Scanning focus in the center, number of steps="+ focusMeasurementParameters.scanNumber+
......
src/main/java/FocusingField.java
View file @ f8cffed4
......@@ -4255,6 +4255,7 @@ public boolean LevenbergMarquardt(
}
}
double [] dmz= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
......@@ -4263,6 +4264,7 @@ public boolean LevenbergMarquardt(
System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
}
double [] dm= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
......@@ -4312,6 +4314,7 @@ public boolean LevenbergMarquardt(
}
}
double [] dmz= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
......@@ -4320,6 +4323,7 @@ public boolean LevenbergMarquardt(
System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
}
double [] dm= getAdjustedMotors(
null, // double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift+best_qb_corr[0],
targetTiltX, // for testing, normally should be 0 um/mm
targetTiltY,
......@@ -4369,7 +4373,9 @@ public boolean LevenbergMarquardt(
}
//,
public double [] adjustLMA (FocusingFieldMeasurement measurement){
public double [] adjustLMA (
FocusingFieldMeasurement measurement,
boolean parallelMove){
if (!testMeasurement(
measurement,
zMin, //+best_qb_corr[0],
......@@ -4390,7 +4396,13 @@ public boolean LevenbergMarquardt(
result[0]=zTilts[0]-best_qb_corr[0];
result[1]=zTilts[1];
result[2]=zTilts[2];
double [] zm=null;
if (parallelMove){
zm=new double [3];
for (int i=0;i<zm.length;i++) zm[i]=fieldFitting.mechanicalFocusingModel.mToZm(measurement.motors[i], i);
}
double [] dm= getAdjustedMotors(
zm,
targetRelFocalShift+best_qb_corr[0],
0.0, // targetTiltX, // for testing, normally should be 0 um/mm
0.0, // targetTiltY,
......@@ -4426,11 +4438,13 @@ public boolean LevenbergMarquardt(
}
public double [] getAdjustedMotors(
double [] zM0, // current linearized motors (or null for full adjustment)
double targetRelFocalShift,
double targetTiltX, // for testing, normally should be 0 um/mm
double targetTiltY, // for testing, normally should be 0 um/mm
boolean motorSteps){
double [] zM=fieldFitting.mechanicalFocusingModel.getZM(
zM0,
currentPX0, //fieldFitting.getCenterXY()[0],
currentPY0, //fieldFitting.getCenterXY()[1],
targetRelFocalShift,
......@@ -4516,7 +4530,7 @@ public boolean LevenbergMarquardt(
break;
}
if (!changedEnable) {
if (debugLevel>0) System.out.println("No filter chnage, finished in "+(n+1)+" steps");
if (debugLevel>0) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
return true;
} else {
if ((was2PrevEnable!=null) && (prevEnable!=null) && (was2PrevEnable.length==prevEnable.length)){
......@@ -4541,7 +4555,7 @@ public boolean LevenbergMarquardt(
private double [] pXY=null;
private boolean [] centerSelect=null;
private boolean [] centerSelectDefault={true,true};
private MechanicalFocusingModel mechanicalFocusingModel;
public MechanicalFocusingModel mechanicalFocusingModel;
private CurvatureModel [] curvatureModel=new CurvatureModel[6]; // 3 colors, sagittal+tangential each
private boolean [] channelSelect=null;
private boolean [] mechanicalSelect=null;
......@@ -6609,9 +6623,44 @@ public boolean LevenbergMarquardt(
}
return m;
}
/**
* Calculate manual screw adjustments for focus/tilt to reduce amount of motor travel (when it is out of limits)
* @param zErr current focal distance error in microns, positive - away from lens
* @param tXErr current horizontal tilt in microns/mm , positive - 1,2 away from lens, 3 - to the lens
* @param tYErr current vertical tilt in microns/mm , positive - 2 away from lens, 1 - to the lens
* @return array of optimal CW rotations of each screw (1.0 == 360 deg)
* Screw locations:
* 5 2
* 3 +
* 4 1
* + - center
* 1,2 M2x0.4 set screws (push)
* 3 - M2x0.4 socket screw (push)
* 4 - M2x0.4 socket screw (pull)
* 5 - M2.5x0.45 screw (pull)
*/
public double [] getManualScrews(
double zErr, // positive - away from lens
double tXErr,// positive - 1,2 away from lens, 3 - to the lens
double tYErr){// positive - 2 away from lens
double [][] screws={ // right, down, thread pitch (pull)
{ 20.5 ,17.5, -0.4},
{ 20.5,-17.5, -0.4},
{-20.5, 0.0, -0.4},
{ 0.0, 17.5, 0.4},
{ 0.0,-17.5, 0.45}};
double [] moveDownUm=new double [screws.length];
double [] turnCW=new double [screws.length];
for (int i=0;i<screws.length;i++){
moveDownUm[i]=zErr + screws[i][0]*tXErr+screws[i][1]*tYErr;
turnCW[i]=0.001*moveDownUm[i]/screws[i][2];
}
return turnCW;
}
/**
* Calculate three linearized values of motor positions for current parameters, target center focal shift and tilt
* @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
......@@ -6620,6 +6669,7 @@ public boolean LevenbergMarquardt(
* @return array of 3 linearized motor positions (microns)
*/
public double [] getZM(
double [] zMCurrent, // current linearized motors (or null for full adjustment)
double px,
double py,
double targetZ,
......@@ -6627,6 +6677,16 @@ public boolean LevenbergMarquardt(
double targetTy){
double dx=PIXEL_SIZE*(px-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
if (zMCurrent!=null){
// 0.25* zM1+ 0.25* zM2+ 0.5 * zM3 = targetZ-getValue(MECH_PAR.z0);
// 0.25* (zM1+dzM)+ 0.25* (zM2+dzM)+ 0.5 * (zM3+dzM) = targetZ-getValue(MECH_PAR.z0);
// 0.25* (dzM+ 0.25* dzM+ 0.5 * dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
// dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
double dZM=targetZ-getValue(MECH_PAR.z0)-(0.25* zMCurrent[0]+ 0.25* zMCurrent[1]+ 0.5 * zMCurrent[2]);
double [] zM=zMCurrent.clone();
for (int i=0;i<zM.length;i++) zM[i]+=dZM;
return zM;
}
// double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
// 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)));//!
......
src/main/java/LensAdjustment.java
View file @ f8cffed4
......@@ -305,6 +305,7 @@ public class LensAdjustment {
public boolean scanTiltEnable=true; // enable scanning tilt
public boolean scanTiltReverse=false; // enable scanning tilt in both directions
public boolean scanMeasureLast=false; // Calculate PSF after last move (to original position)
public int scanTiltRangeX=14336; // 4 periods
public int scanTiltRangeY=14336; // 4 periods
public int scanTiltStepsX=24;
......@@ -520,6 +521,7 @@ public class LensAdjustment {
boolean scanTiltEnable, //=true; // enable scanning tilt
boolean scanTiltReverse,
boolean scanMeasureLast,
int scanTiltRangeX, //=14336; // 4 periods
int scanTiltRangeY, //=14336; // 4 periods
int scanTiltStepsX, //=24;
......@@ -663,6 +665,7 @@ public class LensAdjustment {
this.scanTiltEnable=scanTiltEnable; //=true; // enable scanning tilt
this.scanTiltReverse=scanTiltReverse;
this.scanMeasureLast=scanMeasureLast;
this.scanTiltRangeX=scanTiltRangeX; //, //=14336; // 4 periods
this.scanTiltRangeY=scanTiltRangeY; //, //=14336; // 4 periods
this.scanTiltStepsX=scanTiltStepsX; //=24;
......@@ -807,6 +810,7 @@ public class LensAdjustment {
this.scanTiltEnable, // enable scanning tilt
this.scanTiltReverse,
this.scanMeasureLast,
this.scanTiltRangeX, // 4 periods
this.scanTiltRangeY, // 4 periods
this.scanTiltStepsX,
......@@ -952,24 +956,18 @@ public class LensAdjustment {
properties.setProperty(prefix+"scanStep",this.scanStep+"");
properties.setProperty(prefix+"scanNumber",this.scanNumber+"");
properties.setProperty(prefix+"scanNumberNegative",this.scanNumberNegative+"");
properties.setProperty(prefix+"scanHysteresis",this.scanHysteresis+"");
properties.setProperty(prefix+"scanHysteresisNumber",this.scanHysteresisNumber+"");
properties.setProperty(prefix+"scanTiltEnable",this.scanTiltEnable+""); // enable scanning tilt
properties.setProperty(prefix+"scanTiltReverse",this.scanTiltReverse+"");
properties.setProperty(prefix+"scanMeasureLast",this.scanMeasureLast+"");
properties.setProperty(prefix+"scanTiltRangeX",this.scanTiltRangeX+""); // 4 periods
properties.setProperty(prefix+"scanTiltRangeY",this.scanTiltRangeY+""); // 4 periods
properties.setProperty(prefix+"scanTiltStepsX",this.scanTiltStepsX+"");
properties.setProperty(prefix+"scanTiltStepsY",this.scanTiltStepsY+"");
properties.setProperty(prefix+"motorHysteresis",this.motorHysteresis+"");
properties.setProperty(prefix+"measuredHysteresis",this.measuredHysteresis+"");
properties.setProperty(prefix+"motorCalm",this.motorCalm+"");
properties.setProperty(prefix+"linearReductionRatio",this.linearReductionRatio+"");
properties.setProperty(prefix+"motorDebug",this.motorDebug+"");
properties.setProperty(prefix+"lensDistanceNumPoints",this.lensDistanceNumPoints+"");
......@@ -1217,6 +1215,9 @@ public class LensAdjustment {
this.scanTiltReverse=Boolean.parseBoolean(properties.getProperty(prefix+"scanTiltReverse"));
if (properties.getProperty(prefix+"scanMeasureLast")!=null)
this.scanMeasureLast=Boolean.parseBoolean(properties.getProperty(prefix+"scanMeasureLast"));
if (properties.getProperty(prefix+"scanTiltRangeX")!=null)
this.scanTiltRangeX=Integer.parseInt(properties.getProperty(prefix+"scanTiltRangeX"));
if (properties.getProperty(prefix+"scanTiltRangeY")!=null)
......@@ -1364,7 +1365,7 @@ public class LensAdjustment {
gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);
gd.addCheckbox ("Calculate PSF after returning to the initial position", this.scanMeasureLast);
gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
......@@ -1386,6 +1387,8 @@ public class LensAdjustment {
this.scanTiltEnable= gd.getNextBoolean();
this.scanTiltReverse= gd.getNextBoolean();
this.scanMeasureLast= gd.getNextBoolean();
this.scanTiltRangeX= (int) gd.getNextNumber();
this.scanTiltRangeY= (int) gd.getNextNumber();
this.scanTiltStepsX= (int) gd.getNextNumber();
......@@ -1518,6 +1521,8 @@ public class LensAdjustment {
gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);
gd.addCheckbox ("Calculate PSF after returning to the initial position", this.scanMeasureLast);
gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
......@@ -1684,6 +1689,7 @@ public class LensAdjustment {
this.scanTiltEnable= gd.getNextBoolean();
this.scanTiltReverse= gd.getNextBoolean();
this.scanMeasureLast= gd.getNextBoolean();
this.scanTiltRangeX= (int) gd.getNextNumber();
this.scanTiltRangeY= (int) gd.getNextNumber();
this.scanTiltStepsX= (int) gd.getNextNumber();
......
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