Commit 6f8671a4 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

next snapshot

parent dbf595ce

src/main/java/FocusingField.java

+134 −9
Original line number Diff line number Diff line
@@ -82,6 +82,11 @@ public class FocusingField { 
	boolean    filterZ;    // (adjustment mode)filter samples by Z

	double  filterByValueScale;

	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;
@@ -226,13 +231,17 @@ public class FocusingField { 
    	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

    	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;

        }