Will modify squared parameters to exponents to avoid zero crossing when (b2797800) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+75 −20

Original line number	Original line	Diff line number	Diff line
	@@ -629,6 +629,21 @@ private void maskDataWeights(boolean [] enable){
	if (!enable[i]) dataWeights[i]=0.0;		if (!enable[i]) dataWeights[i]=0.0;
	}		}
	}		}
			public double [][] getSeriesWeights(){
			double [][] seriesWeights=new double [getNumChannels()][getNumSamples()];
			for (int chn=0;chn<seriesWeights.length;chn++) for (int sample=0;sample<seriesWeights[chn].length;sample++) seriesWeights[chn][sample]=0.0;
			for (int index=0;index<dataVector.length;index++) if (dataWeights[index]>0.0){
			seriesWeights[dataVector[index].channel][dataVector[index].sampleIndex]+=dataWeights[index];
			}
			if (debugLevel>1){
			System.out.println("==== getSeriesWeights():");
			for (int chn=0;chn<seriesWeights.length;chn++) for (int sample=0;sample<seriesWeights[chn].length;sample++){
			System.out.println("chn="+chn+" sample="+sample+" weight="+IJ.d2s(seriesWeights[chn][sample],3));
			}
			}
			return seriesWeights;
			}


	private boolean [] filterConcave(		private boolean [] filterConcave(
	double sigma,		double sigma,
	@@ -976,13 +991,15 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
	dataValues = new double [dataVector.length+corrLength];		dataValues = new double [dataVector.length+corrLength];
	dataWeights = new double [dataVector.length+corrLength];		dataWeights = new double [dataVector.length+corrLength];
	// sumWeights=0.0;		// sumWeights=0.0;
	int mode=weightMode;		// int mode=weightMode;
	double kw= (weightRadius>0.0)?(-0.5getPixelMM()getPixelMM()/(weightRadius*weightRadius)):0;		double kw= (weightRadius>0.0)?(-0.5getPixelMM()getPixelMM()/(weightRadius*weightRadius)):0;
	//weightRadius		//weightRadius
	if (weightReference==null)mode=0;		// if (weightReference==null) mode=0;
	for (int i=0;i<dataVector.length;i++){		for (int i=0;i<dataVector.length;i++){
	MeasuredSample ms=dataVector[i];		MeasuredSample ms=dataVector[i];
	dataValues[i]=ms.value;		dataValues[i]=ms.value;
			dataWeights[i]=1.0/Math.pow(ms.value,weightMode);
			/*
	double diff=weightReference[ms.channel]-ms.value;		double diff=weightReference[ms.channel]-ms.value;
	if (diff<0.0) diff=0;		if (diff<0.0) diff=0;
	switch (mode){		switch (mode){
	@@ -991,6 +1008,7 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
	case 2: dataWeights[i]=diff*diff; break;		case 2: dataWeights[i]=diff*diff; break;
	default: dataWeights[i]=1.0;		default: dataWeights[i]=1.0;
	}		}
			*/
	if (weightRadius>0.0){		if (weightRadius>0.0){
	double r2=(ms.px-currentPX0)(ms.px-currentPX0)+(ms.py-currentPY0)(ms.py-currentPY0);		double r2=(ms.px-currentPX0)(ms.px-currentPX0)+(ms.py-currentPY0)(ms.py-currentPY0);
	dataWeights[i]=Math.exp(kwr2);		dataWeights[i]=Math.exp(kwr2);
	@@ -1028,7 +1046,11 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
	filterInputConcaveScale,		filterInputConcaveScale,
	en);		en);
	maskDataWeights(en);		maskDataWeights(en);

	}		}
			fieldFitting.initSampleCorrVector(
			flattenSampleCoord(), //double [][] sampleCoordinates,
			getSeriesWeights()); //double [][] sampleSeriesWeights);


	}		}
	@@ -2676,13 +2698,17 @@ public boolean dialogLMAStep(boolean [] state){
	}		}



	public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){		public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
	double savedLambda=this.lambda;		double savedLambda=this.lambda;
	this.debugLevel=debugLevel;		this.debugLevel=debugLevel;
	if (openDialog && !selectLMAParameters()) return false;		if (openDialog && !selectLMAParameters()) return false;
	this.startTime=System.nanoTime();		this.startTime=System.nanoTime();
	// create savedVector (it depends on parameter masks), restore from it if aborted		// create savedVector (it depends on parameter masks), restore from it if aborted
			fieldFitting.initSampleCorrVector(
			flattenSampleCoord(), //double [][] sampleCoordinates,
			getSeriesWeights()); //double [][] sampleSeriesWeights);


	this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);		this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
	if (debugDerivativesFxDxDy){		if (debugDerivativesFxDxDy){
	compareDrDerivatives(this.savedVector);		compareDrDerivatives(this.savedVector);
	@@ -3329,7 +3355,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
	if ((curvatureModel[chn]!=null) && (allChannels \|\| channelSelect[chn])){		if ((curvatureModel[chn]!=null) && (allChannels \|\| channelSelect[chn])){
	result[chn]=new double [numSamples];		result[chn]=new double [numSamples];
	for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {		for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
	if ((chn==4) && (sampleIndex==3)){		if ((chn==3) && (sampleIndex==23)){
	System.out.println("getCalcValuesForZ(), chn="+chn+", sampleIndex="+sampleIndex);		System.out.println("getCalcValuesForZ(), chn="+chn+", sampleIndex="+sampleIndex);
	}		}

	@@ -3754,7 +3780,10 @@ if ((chn==4) && (sampleIndex==3)){
	* Run in the beginning of fitting series (zeroes the values)		* Run in the beginning of fitting series (zeroes the values)
	*/		*/
	// once per fitting series (or parameter change		// once per fitting series (or parameter change
	public void initSampleCorrVector(double [][] sampleCoordinates){		public void initSampleCorrVector(
			double [][] sampleCoordinates,
			double [][] sampleSeriesWeights){
			System.out.println("initSampleCorrVector()");
	numberOfLocations=sampleCoordinates.length;		numberOfLocations=sampleCoordinates.length;
	this.sampleCoordinates=new double[sampleCoordinates.length][];		this.sampleCoordinates=new double[sampleCoordinates.length][];
	for (int i=0;i<sampleCoordinates.length;i++) this.sampleCoordinates[i]=sampleCoordinates[i].clone();		for (int i=0;i<sampleCoordinates.length;i++) this.sampleCoordinates[i]=sampleCoordinates[i].clone();
	@@ -3778,13 +3807,15 @@ if ((chn==4) && (sampleIndex==3)){
	sw+=a;		sw+=a;
	}		}
	}		}
			double normalizedCost=sampleCorrCost[nChn][nPar];
			if (sampleSeriesWeights!=null) normalizedCost*=sampleSeriesWeights[nChn][i];
	if ((sampleCorrPullZero[nChn][nPar]==0) \|\|(sampleCorrCost[nChn][nPar]==0)) sw=0.0;		if ((sampleCorrPullZero[nChn][nPar]==0) \|\|(sampleCorrCost[nChn][nPar]==0)) sw=0.0;
	else if (sw!=0.0) sw=-sampleCorrCost[nChn][nPar]*sampleCorrPullZero[nChn][nPar]/sw;		else if (sw!=0.0) sw=-normalizedCost*sampleCorrPullZero[nChn][nPar]/sw;
	for (int j=0;j<numberOfLocations;j++) {		for (int j=0;j<numberOfLocations;j++) {
	if (i!=j){		if (i!=j){
	sampleCorrCrossWeights[nChn][nPar][i][j]*=sw;		sampleCorrCrossWeights[nChn][nPar][i][j]*=sw;
	} else {		} else {
	sampleCorrCrossWeights[nChn][nPar][i][j]=sampleCorrCost[nChn][nPar];		sampleCorrCrossWeights[nChn][nPar][i][j]=normalizedCost;
	}		}
	}		}
	}		}
	@@ -3796,6 +3827,9 @@ if ((chn==4) && (sampleIndex==3)){
	sampleCorrCrossWeights[nChn]=null;		sampleCorrCrossWeights[nChn]=null;
	}		}
	}		}
			getCorrVector();

			/*
	sampleCorrChnParIndex=new int [sampleCorrSelect.length][];		sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
	int numPars=0;		int numPars=0;
	for (int nChn=0; nChn< sampleCorrCrossWeights.length;nChn++) {		for (int nChn=0; nChn< sampleCorrCrossWeights.length;nChn++) {
	@@ -3816,19 +3850,40 @@ if ((chn==4) && (sampleIndex==3)){
	// currently all correction parameters are initialized as zeros.		// currently all correction parameters are initialized as zeros.
	getCorrVector();		getCorrVector();
	if (debugLevel>1) System.out.println("was resetting sampleCorrVector here");		if (debugLevel>1) System.out.println("was resetting sampleCorrVector here");
			*/
			}

	// sampleCorrVector=new double [numPars];
	// for (int i=0;i<numPars;i++)sampleCorrVector[i]=0.0;		public void initSampleCorrChnParIndex(
	/*		double [][] sampleCoordinates){
	sampleCorrRadius=new double [numberOfLocations];		numberOfLocations=sampleCoordinates.length;
	//pXY		this.sampleCoordinates=new double[sampleCoordinates.length][];
	for (int i=0;i<numberOfLocations;i++){		for (int i=0;i<sampleCoordinates.length;i++) this.sampleCoordinates[i]=sampleCoordinates[i].clone();
	double dx=sampleCoordinates[i][0]-pXY[0];		sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
	double dy=sampleCoordinates[i][1]-pXY[0];		int numPars=0;
	sampleCorrRadius[i]=getPixelMM()Math.sqrt(dxdx+dy*dy);		for (int nChn=0; nChn< sampleCorrSelect.length;nChn++) {
			if (channelSelect[nChn]) {
			sampleCorrChnParIndex[nChn]=new int [sampleCorrSelect[nChn].length];
			for (int nPar=0;nPar< sampleCorrChnParIndex[nChn].length;nPar++) {
			if (sampleCorrSelect[nChn][nPar]) {
			sampleCorrChnParIndex[nChn][nPar]=numPars; // pointer to the first sample
			numPars+=numberOfLocations;
			} else {
			sampleCorrChnParIndex[nChn][nPar]=-1;
	}		}
	*/
	}		}
			} else {
			sampleCorrChnParIndex[nChn]=null;
			}
			}
			System.out.println("initSampleCorrChnParIndex()");
			// currently all correction parameters are initialized as zeros.
			getCorrVector();
			}




	public double [][] getSampleCoordinates(){		public double [][] getSampleCoordinates(){
	return sampleCoordinates;		return sampleCoordinates;
	}		}
	@@ -3994,7 +4049,7 @@ if ((chn==4) && (sampleIndex==3)){
	// initSampleCorr(flattenSampleCoord());		// initSampleCorr(flattenSampleCoord());
	}		}
	// will modify		// will modify
	initSampleCorrVector(flattenSampleCoord()); // run always regardless of configured or not (to create zero-length array of corr)		initSampleCorrChnParIndex(flattenSampleCoord()); // run always regardless of configured or not (to create zero-length array of corr)
	return true;		return true;
	}		}

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