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imagej-elphel
Commit 6f8671a4 authored by Andrey Filippov's avatar Andrey Filippov
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parent dbf595ce
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Showing with 134 additions and 9 deletions
src/main/java/FocusingField.java
View file @ 6f8671a4
......@@ -81,7 +81,12 @@ public class FocusingField {
double filterInputConcaveScale;
boolean filterZ; // (adjustment mode)filter samples by Z
double filterByValueScale;
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
int minCenterSamplesBest; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
int minCenterSamplesTotal; // minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
int centerSamples; // number of center samples to consider for minLeftCenterSamples
double maxRMS; // maximal (pure) RMS allowed during adjustment
double zMin;
double zMax;
double zStep;
......@@ -223,16 +228,20 @@ public class FocusingField {
filterInputConcaveRemoveFew=true;
filterInputConcaveMinSeries=5;
filterInputConcaveScale=0.9;
filterZ=true; // (adjustment mode)filter samples by Z
filterZ=true; // (adjustment mode)filter samples by Z
filterByValueScale=1.5; // (adjustment mode)filter samples by value - remove higher than scaled best FWHM
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
minCenterSamplesBest=4; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
minCenterSamplesTotal=0;// minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
centerSamples= 8; // there should remain at least of centerSamples closest to r==0
maxRMS=0.5; // maximal (pure) RMS allowed during adjustment
zMin=-40.0;
zMax= 40.0;
zStep=2.0;
tMin=-15.0;
tMax= 15.0;
tStep=1.0;
tMin=-10.0;
tMax= 10.0;
tStep=2.0;
targetRelFocalShift=8.0; // target focal shift relative to best composite "sharpness"
// when false - tangential is master
......@@ -343,9 +352,12 @@ public class FocusingField {
properties.setProperty(prefix+"filterInputConcaveScale",filterInputConcaveScale+"");
properties.setProperty(prefix+"filterZ",filterZ+"");
properties.setProperty(prefix+"filterByValueScale",filterByValueScale+"");
properties.setProperty(prefix+"minLeftSamples",minLeftSamples+"");
properties.setProperty(prefix+"minCenterSamplesBest",minCenterSamplesBest+"");
properties.setProperty(prefix+"minCenterSamplesTotal",minCenterSamplesTotal+"");
properties.setProperty(prefix+"centerSamples",centerSamples+"");
properties.setProperty(prefix+"maxRMS",maxRMS+"");
properties.setProperty(prefix+"zMin",zMin+"");
properties.setProperty(prefix+"zMax",zMax+"");
properties.setProperty(prefix+"zStep",zStep+"");
......@@ -448,6 +460,14 @@ public class FocusingField {
filterByValueScale=Double.parseDouble(properties.getProperty(prefix+"filterByValueScale"));
if (properties.getProperty(prefix+"minLeftSamples")!=null)
minLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minLeftSamples"));
if (properties.getProperty(prefix+"minCenterSamplesBest")!=null)
minCenterSamplesBest=Integer.parseInt(properties.getProperty(prefix+"minCenterSamplesBest"));
if (properties.getProperty(prefix+"minCenterSamplesTotal")!=null)
minCenterSamplesTotal=Integer.parseInt(properties.getProperty(prefix+"minCenterSamplesTotal"));
if (properties.getProperty(prefix+"centerSamples")!=null)
centerSamples=Integer.parseInt(properties.getProperty(prefix+"centerSamples"));
if (properties.getProperty(prefix+"maxRMS")!=null)
maxRMS=Double.parseDouble(properties.getProperty(prefix+"maxRMS"));
if (properties.getProperty(prefix+"zMin")!=null)
zMin=Double.parseDouble(properties.getProperty(prefix+"zMin"));
if (properties.getProperty(prefix+"zMax")!=null)
......@@ -870,6 +890,50 @@ private boolean [] filterByValue (
return enable_out;
}
public boolean checkEnoughCenter(
boolean [] centerSamples,
boolean [] enable_in,
int minTotalSamples,
int minBestChannelSamples){
int [] numSamples=getNumCenterSamples(
centerSamples,
enable_in);
int total=0;
boolean bestOK=false;
for (int num:numSamples){
total+=num;
if (num>=minBestChannelSamples) bestOK=true;
}
return bestOK && (total>=minTotalSamples);
}
public int [] getNumCenterSamples( // per channel (disabled channels are already removed in enable_in)
boolean [] centerSamples,
boolean [] enable_in){
int [] numSamples=new int [getNumChannels()];
for (int i=0;i<numSamples.length;i++) numSamples[i]=0;
for (int index=0;index<dataVector.length;index++) if ((index>=enable_in.length) || enable_in[index]){
if (centerSamples[dataVector[index].sampleIndex]) numSamples[dataVector[index].channel]++;
}
return numSamples;
}
public boolean [] getCenterSamples(int num){
double [] sampleCorrRadiuses=fieldFitting.getSampleRadiuses();
if (num>sampleCorrRadiuses.length) num = sampleCorrRadiuses.length;
boolean [] centerMask=new boolean[sampleCorrRadiuses.length];
for (int i=0;i<centerMask.length;i++) centerMask[i]=false;
for (int pass=0;pass<num;pass++){
double min=0;
int bestIndex=-1;
for (int i=0;i<centerMask.length;i++) if (!centerMask[i] && ((bestIndex<0) || (sampleCorrRadiuses[i] < min))){
bestIndex=i;
min=sampleCorrRadiuses[i];
}
centerMask[bestIndex]=true;
}
return centerMask;
}
private int getNumEnabledSamples(
boolean [] enable){
int num_en=0;
......@@ -3316,6 +3380,27 @@ public double getAdjustRMS(
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return Double.NaN;
}
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
if (!checkEnoughCenter(
centerSampesMask,
en,
minCenterSamplesTotal, //int minTotalSamples,
minCenterSamplesBest )){ //int minBestChannelSamples)){
if (debugLevel>0) {
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
System.out.print("Got:");
for (int n:numSamples) System.out.print(" "+n);
System.out.println();
}
return Double.NaN;
}
}
double [] focusing_fx= createFXandJacobian(sv, false);
double rms_pure= calcErrorDiffY(focusing_fx, true);
// System.out.println("rms_pure="+rms_pure);
......@@ -3441,6 +3526,27 @@ public boolean LevenbergMarquardt(
if (numEn<minLeftSamples) return false;
}
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
if (!checkEnoughCenter(
centerSampesMask,
en,
minCenterSamplesTotal, //int minTotalSamples,
minCenterSamplesBest )){ //int minBestChannelSamples)){
if (debugLevel>0) {
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
System.out.print("Got:");
for (int n:numSamples) System.out.print(" "+n);
System.out.println();
}
return false;
}
}
fieldFitting.initSampleCorrVector(
flattenSampleCoord(), //double [][] sampleCoordinates,
null); //getSeriesWeights()); //double [][] sampleSeriesWeights);
......@@ -3857,6 +3963,11 @@ public boolean LevenbergMarquardt(
gd.addCheckbox("Filter samples/channels by Z",filterZ);
gd.addNumericField("Filter by value (remove samples above scaled best FWHM for channel/location)",filterByValueScale,2,5,"x");
gd.addNumericField("Minimal required number of channels/samples",minLeftSamples,0,3,"samples");
gd.addNumericField("... of them closest to the center, best channel",minCenterSamplesBest,0,3,"samples");
gd.addNumericField("... of them closest to the center, total in all channels",minCenterSamplesTotal,0,3,"samples");
gd.addNumericField("Number of closest samples to consider",centerSamples,0,3,"samples");
gd.addNumericField("Maximal accepted RMS",maxRMS,3,5,"");
gd.addNumericField("Z min",zMin,2,5,"um");
gd.addNumericField("Z max",zMax,2,5,"um");
......@@ -3882,7 +3993,10 @@ public boolean LevenbergMarquardt(
filterZ=gd.getNextBoolean();
filterByValueScale=gd.getNextNumber();
minLeftSamples=(int) gd.getNextNumber();
minCenterSamplesBest=(int) gd.getNextNumber();
minCenterSamplesTotal=(int) gd.getNextNumber();
centerSamples=(int) gd.getNextNumber();
maxRMS=gd.getNextNumber();
zMin= gd.getNextNumber();
zMax= gd.getNextNumber();
zStep=gd.getNextNumber();
......@@ -3905,6 +4019,7 @@ public boolean LevenbergMarquardt(
header+="\t"+fieldFitting.mechanicalFocusingModel.getName(i)+" ("+fieldFitting.mechanicalFocusingModel.getUnits(i)+")";
}
}
header+="\tRMS";
for (int i=0;i<3;i++) header+="\tmz"+i;
for (int i=0;i<3;i++) header+="\tm"+i;
StringBuffer sb = new StringBuffer();
......@@ -3957,6 +4072,7 @@ public boolean LevenbergMarquardt(
sb.append("\t"+IJ.d2s(fieldFitting.mechanicalFocusingModel.paramValues[i],3));
}
}
sb.append("\t"+IJ.d2s(currentRMSPure,3));
if (dmz!=null){
for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
} else {
......@@ -4007,12 +4123,20 @@ public boolean LevenbergMarquardt(
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));
}
if (maxRMS>0.0){
if (currentRMSPure > maxRMS){
if (debugLevel>0) System.out.println("RMS too high, "+IJ.d2s(currentRMSPure,3)+" > "+ IJ.d2s(maxRMS,3));
continue;
}
}
sb.append(nMeas);
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
sb.append("\t"+IJ.d2s(fieldFitting.mechanicalFocusingModel.paramValues[i],3));
}
}
sb.append("\t"+IJ.d2s(currentRMSPure,3));
if (dmz!=null){
for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
} else {
......@@ -4490,7 +4614,8 @@ public boolean LevenbergMarquardt(
int r0Index=2; // index of "r0" parameter (fwhm is twice that)
double [] corrPars=corrected?getCorrPar(channel,sampleIndex):null;
double r=(sampleIndex>=0)?getSampleRadius(sampleIndex):0.0;
double fwhm=2.0 * curvatureModel[channel].getAr( r, corrPars)[r0Index];
// double fwhm=2.0 * curvatureModel[channel].getAr( r, corrPars)[r0Index];
double fwhm=Math.exp(curvatureModel[channel].getAr( r, corrPars)[r0Index]);
return fwhm;
}
......
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