debugging (d82b993c) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+37 −7

Original line number	Original line	Diff line number	Diff line
	@@ -4390,8 +4390,8 @@ public boolean LevenbergMarquardt(
	// if ((comment.length()>10) && comment.substring(0,9).equals("<![CDATA[")) comment=comment.substring(9,comment.length()-3);		// if ((comment.length()>10) && comment.substring(0,9).equals("<![CDATA[")) comment=comment.substring(9,comment.length()-3);

	PIXEL_SIZE=Double.parseDouble(hConfig.getString("PIXEL_SIZE",PIXEL_SIZE+""));		PIXEL_SIZE=Double.parseDouble(hConfig.getString("PIXEL_SIZE",PIXEL_SIZE+""));
	sensorWidth=Integer.parseInt(hConfig.getString("sensorWidth","0"));		sensorWidth=Integer.parseInt(hConfig.getString("sensorWidth",sensorWidth+""));
	sensorHeight=Integer.parseInt(hConfig.getString("sensorHeight","0"));		sensorHeight=Integer.parseInt(hConfig.getString("sensorHeight",sensorHeight+""));

	serialNumber= hConfig.getString("serialNumber","???");		serialNumber= hConfig.getString("serialNumber","???");
	lensSerial= hConfig.getString("lensSerial","???");		lensSerial= hConfig.getString("lensSerial","???");
	@@ -8473,6 +8473,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]

	public double[] testQualB(boolean interactive){		public double[] testQualB(boolean interactive){
	double [] targetZTxTy={0.0,0.0,0.0};		double [] targetZTxTy={0.0,0.0,0.0};
			boolean debugScan=false;
	if (interactive){		if (interactive){
	GenericDialog gd = new GenericDialog("Calculate optimal focus/tilt");		GenericDialog gd = new GenericDialog("Calculate optimal focus/tilt");
	gd.addNumericField("Initial focus (relative to best composirte)",targetZTxTy[0],2,5,"um");		gd.addNumericField("Initial focus (relative to best composirte)",targetZTxTy[0],2,5,"um");
	@@ -8493,6 +8494,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	gd.addNumericField("Relative weight of peripheral areas",100*this.k_qualBFractionPeripheral, 1,7,"%");		gd.addNumericField("Relative weight of peripheral areas",100*this.k_qualBFractionPeripheral, 1,7,"%");
	gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, large sensor dimension",100*this.k_qualBFractionHor, 1,5,"%");		gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, large sensor dimension",100*this.k_qualBFractionHor, 1,5,"%");
	gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, small sensor dimension",100*this.k_qualBFractionVert, 1,5,"%");		gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, small sensor dimension",100*this.k_qualBFractionVert, 1,5,"%");
			gd.addCheckbox("Debug scan", debugScan);
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return null;		if (gd.wasCanceled()) return null;
	@@ -8515,6 +8517,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	this.k_qualBFractionPeripheral= 0.01*gd.getNextNumber();		this.k_qualBFractionPeripheral= 0.01*gd.getNextNumber();
	this.k_qualBFractionHor= 0.01*gd.getNextNumber();		this.k_qualBFractionHor= 0.01*gd.getNextNumber();
	this.k_qualBFractionVert= 0.01*gd.getNextNumber();		this.k_qualBFractionVert= 0.01*gd.getNextNumber();
			debugScan=gd.getNextBoolean();
	}		}
	boolean [] selectQualBPars={		boolean [] selectQualBPars={
	((this.qualBOptimizeMode & 1) != 0),		((this.qualBOptimizeMode & 1) != 0),
	@@ -8581,13 +8584,16 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	selectQualBPars);		selectQualBPars);
	// Set all 3 parameter values, even if some are not selected		// Set all 3 parameter values, even if some are not selected
	fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy);		fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy);
			if (debugScan){
			qualBOptimize.runDebugScan(-20.0,20.0,1.0);
			}
	boolean OK= qualBOptimize.qLevenbergMarquardt(		boolean OK= qualBOptimize.qLevenbergMarquardt(
	interactive, // boolean openDialog,		interactive, // boolean openDialog,
	debugLevel+1);		debugLevel+1);
	if (OK){		if (OK){
	zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();		zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();
	System.out.println("qualBOptimize returned:\n"+		System.out.println("qualBOptimize returned:\n"+
	"zc="+IJ.d2s((zTxTy[0]-best_qb_corr[0]),3)+"um\n"+		"zc="+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"+		"tX="+IJ.d2s(zTxTy[1],3)+"um/mm\n"+
	"tY="+IJ.d2s(zTxTy[2],3)+"um/mm");		"tY="+IJ.d2s(zTxTy[2],3)+"um/mm");
	} else {		} else {
	@@ -8670,8 +8676,8 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	double sumWeights=0.0;		double sumWeights=0.0;
	for (int c=0;c<colorWeights.length;c++) for (int d=0;d<dirWeights.length;d++){		for (int c=0;c<colorWeights.length;c++) for (int d=0;d<dirWeights.length;d++){
	int chn=c*dirWeights.length+d;		int chn=c*dirWeights.length+d;
	double w=0.0;
	for (int sample=0;sample<numSamples;sample++){		for (int sample=0;sample<numSamples;sample++){
			double w=0.0;
	if ((goodSamples==null) \|\| goodSamples[chn][sample]) {		if ((goodSamples==null) \|\| goodSamples[chn][sample]) {
	w=colorWeights[c]*dirWeights[d];		w=colorWeights[c]*dirWeights[d];
	}		}
	@@ -9026,10 +9032,10 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	gd.addMessage("Lambda="+this.qLambda);		gd.addMessage("Lambda="+this.qLambda);
	}		}
	gd.addNumericField("Lambda ", this.qLambda, 5);		gd.addNumericField("Lambda ", this.qLambda, 5);
	gd.addNumericField("Multiply lambda on success", this.qLambdaStepDown, 5);		gd.addNumericField("Multiply lambda on success", this.qLambdaStepDown, 10);
	gd.addNumericField("Threshold RMS to exit LMA", this.qThresholdFinish, 7,9,"pix");		gd.addNumericField("Threshold RMS to exit LMA", this.qThresholdFinish, 7,9,"pix");
	gd.addNumericField("Multiply lambda on failure", this.qLambdaStepUp, 5);		gd.addNumericField("Multiply lambda on failure", this.qLambdaStepUp, 10);
	gd.addNumericField("Threshold lambda to fail", this.qMaxLambda, 5);		gd.addNumericField("Threshold lambda to fail", this.qMaxLambda, 10);
	gd.addNumericField("Maximal number of iterations", this.qNumIterations, 0);		gd.addNumericField("Maximal number of iterations", this.qNumIterations, 0);
	gd.addCheckbox("Dialog after each iteration step", this.qStopEachStep);		gd.addCheckbox("Dialog after each iteration step", this.qStopEachStep);
	gd.addCheckbox("Dialog after each failure", this.qStopOnFailure);		gd.addCheckbox("Dialog after each failure", this.qStopOnFailure);
	@@ -9090,6 +9096,30 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
	this.showDisabledQParams= gd.getNextBoolean();		this.showDisabledQParams= gd.getNextBoolean();
	return true;		return true;
	}		}
			public void runDebugScan(
			double low,
			double high,
			double step){
			double [] best_qb_corr= fieldFitting.getBestQualB(
			k_red,
			k_blue,
			true);

			double [] saveZTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();
			double [] zTxTy=saveZTxTy.clone();
			String header="Z absolute\tZ relative\tqualB";
			StringBuffer sb = new StringBuffer();

			for (double dz=low;dz<=high;dz+=step){
			zTxTy[0]=best_qb_corr[0]+dz;
			fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy);
			double qualB=getQualB();
			sb.append(IJ.d2s(zTxTy[0],3)+"\t"+IJ.d2s(dz,3)+"\t"+IJ.d2s(qualB,5)+"\n");
			}

			fieldFitting.mechanicalFocusingModel.setZTxTy(saveZTxTy);
			new TextWindow("qualB scan, Tx="+IJ.d2s(zTxTy[1],3)+" Ty="+IJ.d2s(zTxTy[1],3), header, sb.toString(), 800,1000);
			}

	public boolean qLevenbergMarquardt(		public boolean qLevenbergMarquardt(
	boolean openDialog,		boolean openDialog,

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