saving target tilts (89ea8734) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+30 −15

Original line number	Original line	Diff line number	Diff line
	@@ -106,6 +106,8 @@ public class FocusingField {
	double tStep;		double tStep;

	double targetRelFocalShift; // target focal shift relative to best composite "sharpness"		double targetRelFocalShift; // target focal shift relative to best composite "sharpness"
			double targetRelTiltX; // target tilt Horizontal
			double targetRelTiltY; // target tilt Vertical

	// when false - tangential is master		// when false - tangential is master
	double [] minMeas; // pixels		double [] minMeas; // pixels
	@@ -292,7 +294,9 @@ public class FocusingField {
	tMax= 10.0;		tMax= 10.0;
	tStep=2.0;		tStep=2.0;

	targetRelFocalShift=8.0; // target focal shift relative to best composite "sharpness"		targetRelFocalShift=0.0; // target focal shift relative to best composite "sharpness"
			targetRelTiltX=0.0; // target tilt Horizontal
			targetRelTiltY=0.0; // target tilt Vertical
	// when false - tangential is master		// when false - tangential is master
	double [] minMeasDflt= {0.5,0.5,0.5,0.5,0.5,0.5}; // pixels		double [] minMeasDflt= {0.5,0.5,0.5,0.5,0.5,0.5}; // pixels
	minMeas= minMeasDflt; // pixels		minMeas= minMeasDflt; // pixels
	@@ -446,6 +450,10 @@ public class FocusingField {
	properties.setProperty(prefix+"tStep",tStep+"");		properties.setProperty(prefix+"tStep",tStep+"");

	properties.setProperty(prefix+"targetRelFocalShift",targetRelFocalShift+"");		properties.setProperty(prefix+"targetRelFocalShift",targetRelFocalShift+"");

			properties.setProperty(prefix+"targetRelTiltX",targetRelTiltX+"");
			properties.setProperty(prefix+"targetRelTiltY",targetRelTiltY+"");

	for (int chn=0; chn<minMeas.length; chn++) properties.setProperty(prefix+"minMeas_"+chn,minMeas[chn]+"");		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<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]+"");		for (int chn=0; chn<thresholdMax.length; chn++) properties.setProperty(prefix+"thresholdMax_"+chn,thresholdMax[chn]+"");
	@@ -607,6 +615,12 @@ public class FocusingField {
	tStep=Double.parseDouble(properties.getProperty(prefix+"tStep"));		tStep=Double.parseDouble(properties.getProperty(prefix+"tStep"));
	if (properties.getProperty(prefix+"targetRelFocalShift")!=null)		if (properties.getProperty(prefix+"targetRelFocalShift")!=null)
	targetRelFocalShift=Double.parseDouble(properties.getProperty(prefix+"targetRelFocalShift"));		targetRelFocalShift=Double.parseDouble(properties.getProperty(prefix+"targetRelFocalShift"));

			if (properties.getProperty(prefix+"targetRelTiltX")!=null)
			targetRelTiltX=Double.parseDouble(properties.getProperty(prefix+"targetRelTiltX"));
			if (properties.getProperty(prefix+"targetRelTiltY")!=null)
			targetRelTiltY=Double.parseDouble(properties.getProperty(prefix+"targetRelTiltY"));

	for (int chn=0; chn<minMeas.length; chn++) if (properties.getProperty(prefix+"minMeas_"+chn)!=null)		for (int chn=0; chn<minMeas.length; chn++) if (properties.getProperty(prefix+"minMeas_"+chn)!=null)
	minMeas[chn]=Double.parseDouble(properties.getProperty(prefix+"minMeas_"+chn));		minMeas[chn]=Double.parseDouble(properties.getProperty(prefix+"minMeas_"+chn));
	for (int chn=0; chn<maxMeas.length; chn++) if (properties.getProperty(prefix+"maxMeas_"+chn)!=null)		for (int chn=0; chn<maxMeas.length; chn++) if (properties.getProperty(prefix+"maxMeas_"+chn)!=null)
	@@ -4815,8 +4829,8 @@ public boolean LevenbergMarquardt(
	// double zMin=-40.0;		// double zMin=-40.0;
	// double zMax= 40.0;		// double zMax= 40.0;
	// double zStep=2.0;		// double zStep=2.0;
	double targetTiltX=0.0; // for testing, normally should be 0 um/mm		// double targetTiltX=0.0; // for testing, normally should be 0 um/mm
	double targetTiltY=0.0; // for testing, normally should be 0 um/mm		// 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.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); // to correctly find Z centers,
	@@ -4872,8 +4886,9 @@ public boolean LevenbergMarquardt(
	gd.addNumericField("Tilt step",tStep,2,5,"um/mm");		gd.addNumericField("Tilt step",tStep,2,5,"um/mm");

	gd.addNumericField("Target focus (relative to best composirte)",targetRelFocalShift,2,5,"um");		gd.addNumericField("Target focus (relative to best composirte)",targetRelFocalShift,2,5,"um");
	gd.addNumericField("Target horizontal tilt (normally 0)",targetTiltX,2,5,"um/mm");
	gd.addNumericField("Target vertical tilt (normally 0)",targetTiltY,2,5,"um/mm");		gd.addNumericField("Target horizontal tilt (normally 0)",targetRelTiltX,2,5,"um/mm");
			gd.addNumericField("Target vertical tilt (normally 0)",targetRelTiltY,2,5,"um/mm");
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return;		if (gd.wasCanceled()) return;
	@@ -4902,8 +4917,8 @@ public boolean LevenbergMarquardt(
	tStep= gd.getNextNumber();		tStep= gd.getNextNumber();

	targetRelFocalShift= gd.getNextNumber();		targetRelFocalShift= gd.getNextNumber();
	targetTiltX= gd.getNextNumber(); // for testing, normally should be 0 um/mm		targetRelTiltX= gd.getNextNumber(); // for testing, normally should be 0 um/mm
	targetTiltY= gd.getNextNumber(); // for testing, normally should be 0 um/mm		targetRelTiltY= gd.getNextNumber(); // for testing, normally should be 0 um/mm

	boolean OK;		boolean OK;
	fieldFitting.mechanicalFocusingModel.setAdjustMode(true); // to correctly find Z centers,		fieldFitting.mechanicalFocusingModel.setAdjustMode(true); // to correctly find Z centers,
	@@ -4956,8 +4971,8 @@ public boolean LevenbergMarquardt(
	double [] dmz= getAdjustedMotors(		double [] dmz= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	targetTiltX, // for testing, normally should be 0 um/mm		targetRelTiltX, // for testing, normally should be 0 um/mm
	targetTiltY,		targetRelTiltY,
	false);		false);
	if ((dmz!=null) && (debugLevel>0)){		if ((dmz!=null) && (debugLevel>0)){
	System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));		System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
	@@ -4965,8 +4980,8 @@ public boolean LevenbergMarquardt(
	double [] dm= getAdjustedMotors(		double [] dm= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	targetTiltX, // for testing, normally should be 0 um/mm		targetRelTiltX, // for testing, normally should be 0 um/mm
	targetTiltY,		targetRelTiltY,
	true);		true);
	if ((dm!=null) && (debugLevel>0)){		if ((dm!=null) && (debugLevel>0)){
	System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));		System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
	@@ -5028,8 +5043,8 @@ public boolean LevenbergMarquardt(
	double [] dmz= getAdjustedMotors(		double [] dmz= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	targetTiltX, // for testing, normally should be 0 um/mm		targetRelTiltX, // for testing, normally should be 0 um/mm
	targetTiltY,		targetRelTiltY,
	false);		false);
	if ((dmz!=null) && (debugLevel>0)){		if ((dmz!=null) && (debugLevel>0)){
	System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));		System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
	@@ -5037,8 +5052,8 @@ public boolean LevenbergMarquardt(
	double [] dm= getAdjustedMotors(		double [] dm= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	targetTiltX, // for testing, normally should be 0 um/mm		targetRelTiltX, // for testing, normally should be 0 um/mm
	targetTiltY,		targetRelTiltY,
	true);		true);
	if ((dm!=null) && (debugLevel>0)){		if ((dm!=null) && (debugLevel>0)){
	System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));		System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));

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