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Commit b2797800 authored by Andrey Filippov's avatar Andrey Filippov
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Will modify squared parameters to exponents to avoid zero crossing when 

fitting
parent 1dbe6bd1
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Showing with 75 additions and 20 deletions
src/main/java/FocusingField.java
View file @ b2797800
......@@ -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)?(-0.5*getPixelMM()*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(kw*r2);
......@@ -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
// 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(dx*dx+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;
}
......
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