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	Diff line number	Diff line
		@@ -629,6 +629,21 @@ private void maskDataWeights(boolean [] enable){
		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(
		double sigma,
		@@ -976,13 +991,15 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
		dataValues = new double [dataVector.length+corrLength];
		dataWeights = new double [dataVector.length+corrLength];
		// sumWeights=0.0;
		int mode=weightMode;
		// int mode=weightMode;
		double kw= (weightRadius>0.0)?(-0.5getPixelMM()getPixelMM()/(weightRadius*weightRadius)):0;
		//weightRadius
		if (weightReference==null)mode=0;
		// if (weightReference==null) mode=0;
		for (int i=0;i<dataVector.length;i++){
		MeasuredSample ms=dataVector[i];
		dataValues[i]=ms.value;
		dataWeights[i]=1.0/Math.pow(ms.value,weightMode);
		/*
		double diff=weightReference[ms.channel]-ms.value;
		if (diff<0.0) diff=0;
		switch (mode){
		@@ -991,6 +1008,7 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
		case 2: dataWeights[i]=diff*diff; break;
		default: dataWeights[i]=1.0;
		}
		*/
		if (weightRadius>0.0){
		double r2=(ms.px-currentPX0)(ms.px-currentPX0)+(ms.py-currentPY0)(ms.py-currentPY0);
		dataWeights[i]=Math.exp(kwr2);
		@@ -1028,7 +1046,11 @@ public void setDataVector(MeasuredSample [] vector){ // remove unused channels i
		filterInputConcaveScale,
		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){
		double savedLambda=this.lambda;
		this.debugLevel=debugLevel;
		if (openDialog && !selectLMAParameters()) return false;
		this.startTime=System.nanoTime();
		// 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);
		if (debugDerivativesFxDxDy){
		compareDrDerivatives(this.savedVector);
		@@ -3329,7 +3355,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		if ((curvatureModel[chn]!=null) && (allChannels \|\| channelSelect[chn])){
		result[chn]=new double [numSamples];
		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);
		}

		@@ -3754,7 +3780,10 @@ if ((chn==4) && (sampleIndex==3)){
		* Run in the beginning of fitting series (zeroes the values)
		*/
		// 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;
		this.sampleCoordinates=new double[sampleCoordinates.length][];
		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;
		}
		}
		double normalizedCost=sampleCorrCost[nChn][nPar];
		if (sampleSeriesWeights!=null) normalizedCost*=sampleSeriesWeights[nChn][i];
		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++) {
		if (i!=j){
		sampleCorrCrossWeights[nChn][nPar][i][j]*=sw;
		} 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;
		}
		}
		getCorrVector();

		/*
		sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
		int numPars=0;
		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.
		getCorrVector();
		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;
		/*
		sampleCorrRadius=new double [numberOfLocations];
		//pXY
		for (int i=0;i<numberOfLocations;i++){
		double dx=sampleCoordinates[i][0]-pXY[0];
		double dy=sampleCoordinates[i][1]-pXY[0];
		sampleCorrRadius[i]=getPixelMM()Math.sqrt(dxdx+dy*dy);

		public void initSampleCorrChnParIndex(
		double [][] sampleCoordinates){
		numberOfLocations=sampleCoordinates.length;
		this.sampleCoordinates=new double[sampleCoordinates.length][];
		for (int i=0;i<sampleCoordinates.length;i++) this.sampleCoordinates[i]=sampleCoordinates[i].clone();
		sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
		int numPars=0;
		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(){
		return sampleCoordinates;
		}
		@@ -3994,7 +4049,7 @@ if ((chn==4) && (sampleIndex==3)){
		// initSampleCorr(flattenSampleCoord());
		}
		// 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;
		}