multithreaded LMA (41015a35) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+9 −0

Original line number	Original line	Diff line number	Diff line
	@@ -4165,6 +4165,15 @@ if (MORE_BUTTONS) {
	double rms= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, false);		double rms= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, false);
	double rms_pure= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, true);		double rms_pure= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, true);
	System.out.println("rms="+rms+", rms_pure="+rms_pure+" - with old parameters may be well off.");		System.out.println("rms="+rms+", rms_pure="+rms_pure+" - with old parameters may be well off.");
			if (FOCUS_MEASUREMENT_PARAMETERS.scanRunLMA){
			FOCUSING_FIELD.setAdjustMode(false);
			boolean OK=FOCUSING_FIELD.LevenbergMarquardt(
			null, // measurement
			false, // true, // open dialog
			true,// boolean autoSel,
			DEBUG_LEVEL); //boolean openDialog, int debugLevel){
			if (OK) saveCurrentConfig();
			}
	remoteNotifyComplete();		remoteNotifyComplete();
	return;		return;
	}		}

src/main/java/FocusingField.java

+306 −37

Original line number	Original line	Diff line number	Diff line
	@@ -54,6 +54,7 @@ import org.apache.commons.configuration.XMLConfiguration;




	//import Distortions.LMAArrays; // may still reuse?		//import Distortions.LMAArrays; // may still reuse?
	import Jama.LUDecomposition;		import Jama.LUDecomposition;
	import Jama.Matrix;		import Jama.Matrix;
	@@ -236,7 +237,13 @@ public class FocusingField {
	private double firstRMS=-1.0; // RMS before current series of LMA started		private double firstRMS=-1.0; // RMS before current series of LMA started
	private double firstRMSPure=-1.0; // RMS before current series of LMA started		private double firstRMSPure=-1.0; // RMS before current series of LMA started

			public int threadsMax=0; // 0 - old code
			private boolean multiJacobian=true; // to try multithreaded mode


			public void setThreads(int num){
			this.threadsMax=num;
			}
	public void setDefaults(){		public void setDefaults(){
	goodCalibratedSamples=null;		goodCalibratedSamples=null;
	sensorWidth= 2592;		sensorWidth= 2592;
	@@ -1942,9 +1949,187 @@ public double [] createFXandJacobian( double [] vector, boolean createJacobian){
	commitParameterVector(vector);		commitParameterVector(vector);
	return createFXandJacobian(createJacobian);		return createFXandJacobian(createJacobian);
	}		}
			//multiJacobian
			public double [] createFXandJacobian(boolean createJacobian){
			if (multiJacobian && (threadsMax>0)) return createFXandJacobianMulti(createJacobian);
			else return createFXandJacobianSingle(createJacobian);
			}
			public class PartialFXJac{
			public int index; // measurement number
			public double f;
			public double [] jac=null;
			public PartialFXJac (
			int index,
			double f,
			double [] jac){ //, int num){
			this.index=index;
			this.f=f;
			this.jac=jac;
			// if (num>=0) jac=new double [num];
			// else jac=null;
			// jac=null;
			}
			}
			public double [] createFXandJacobianMulti(
			final boolean createJacobian
			){
			long startTime=System.nanoTime();
			int numCorrPar=fieldFitting.getNumberOfCorrParameters();
			boolean [] selChannels=fieldFitting.getSelectedChannels();
			final int [] selChanIndices= new int[selChannels.length];
			selChanIndices[0]=0;
			for (int i=1;i<selChanIndices.length;i++){
			selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
			}
			final int numPars=fieldFitting.getNumberOfParameters(sagittalMaster);
			int numRegPars=fieldFitting.getNumberOfRegularParameters(sagittalMaster);
			final int numSelChn=fieldFitting.getNumberOfChannels();
			final Thread[] threads = newThreadArray(threadsMax);
			final ArrayList<ArrayList<PartialFXJac>> fxList = new ArrayList<ArrayList<PartialFXJac>>();
			for (int ithread = 0; ithread < threads.length; ithread++) {
			fxList.add(new ArrayList<PartialFXJac>());
			}
			// create list of indices of measurements corresponding to new timestamp/sample
			String prevTimeStamp="";
			double prevPx=-1,prevPy=-1;
			final ArrayList<Integer> measIndicesList = new ArrayList<Integer>(dataVector.length/getNumChannels());
			for (int n=0;n<dataVector.length;n++){
			MeasuredSample ms=dataVector[n];
			if (!ms.timestamp.equals(prevTimeStamp) \|\| (ms.px!=prevPx) \|\| (ms.py!=prevPy)){
			measIndicesList.add(new Integer(n));
			}
			}
			// measIndicesList.add(new Integer(dataVector.length));
			final AtomicInteger measIndex = new AtomicInteger(0);
			final AtomicInteger threadIndexAtomic = new AtomicInteger(0);
			// final boolean [] falseFalse={false,false};
			final boolean [] centerSelect=correct_measurement_ST?fieldFitting.getCenterSelect():null; //falseFalse;
			for (int ithread = 0; ithread < threads.length; ithread++) {

			threads[ithread] = new Thread() {
			public void run() {
			int threadIndex=threadIndexAtomic.getAndIncrement();
			fxList.get(threadIndex).clear(); // not needed
			double [][] derivs;
			for (int startMeasIndex=measIndex.getAndIncrement(); startMeasIndex<measIndicesList.size();startMeasIndex=measIndex.getAndIncrement()){
			int startMeas=measIndicesList.get(startMeasIndex);
			int endMeas=(startMeasIndex==(measIndicesList.size()-1))?dataVector.length:measIndicesList.get(startMeasIndex+1);
			MeasuredSample ms=dataVector[startMeas];
			derivs=createJacobian?(new double[numSelChn][]):null;
			double [] subData=fieldFitting.getValsDerivatives(
			ms.sampleIndex,
			sagittalMaster,
			ms.motors, // 3 motor coordinates
			ms.px, // pixel x
			ms.py, // pixel y
			derivs);
			for (int n=startMeas;n<endMeas;n++){
			int chn=selChanIndices[ms.channel];
			if (centerSelect!=null){
			int np=0;
			for (int i=0;i<2;i++) if (centerSelect[i]){
			derivs[chn][np++]-=ms.dPxyc[i]; // subtract, as effect is opposite to fX
			}
			}
			PartialFXJac partialFXJac = new PartialFXJac(n,
			subData[chn],
			derivs[chn]);
			fxList.get(threadIndex).add(partialFXJac);
			}

			}

	public double [] createFXandJacobian(boolean createJacobian){		}
			};
			}
			startAndJoin(threads);
			if (debugLevel>1) System.out.println("#1 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),5));
			// Combibe results
			double [] fx=new double[dataVector.length + numCorrPar ];
			if (createJacobian) {
			jacobian=new double [numPars][dataVector.length+numCorrPar];
			for (double [] row : jacobian) Arrays.fill(row, 0.0);
			}

			for (ArrayList<PartialFXJac> partilaList:fxList){
			for (PartialFXJac partialFXJac:partilaList){
			int n=partialFXJac.index;
			fx[n]=partialFXJac.f;
			if (createJacobian){
			for (int i=0;i<numPars;i++){
			jacobian[i][n]=partialFXJac.jac[i];
			}
			}
			}
			}
			if (debugLevel>1) System.out.println("#2 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),5));
			if (createJacobian && (fieldFitting.sampleCorrChnParIndex!=null)) {
			// add mutual dependence of correction parameters. first - values (fx)
			int index=dataVector.length; // add to the end of vector
			int numSamples=getNumSamples();
			for (int chn=0;chn<fieldFitting.sampleCorrChnParIndex.length;chn++) if (fieldFitting.sampleCorrChnParIndex[chn]!=null) {
			for (int np=0;np<fieldFitting.sampleCorrChnParIndex[chn].length;np++){
			int pindex=fieldFitting.sampleCorrChnParIndex[chn][np];
			if (pindex>=0) {
			for (int i=0;i<numSamples;i++){
			double f=0.0;
			for (int j=0;j<numSamples;j++){
			f+=fieldFitting.sampleCorrVector[pindex+j]*fieldFitting.sampleCorrCrossWeights[chn][np][i][j];
			}
			fx[index]=f;
			// f+=fieldFitting.sampleCorrVector[pindex+i]
			if (createJacobian) {
			for (int j=0;j<numSamples;j++){
			jacobian[numRegPars+pindex+j][index]=fieldFitting.sampleCorrCrossWeights[chn][np][i][j];
			}
			}
			index++;
			}
			}
			}
			}
			}
			if (debugLevel>1) System.out.println("#3 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),5));
			if (createJacobian && (debugLevel>1)){
			if (debugPoint>=0) debugJacobianPoint(debugPoint);
			if (debugParameter>=0) debugJacobianParameter(debugParameter);
			}
			if (debugLevel>1) System.out.println("#4 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),5));
			return fx;

			}
			/* Create a Thread[] array as large as the number of processors available.
			* From Stephan Preibisch's Multithreading.java class. See:
			* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
			*/
			private Thread[] newThreadArray(int maxCPUs) {
			int n_cpus = Runtime.getRuntime().availableProcessors();
			if (n_cpus>maxCPUs)n_cpus=maxCPUs;
			return new Thread[n_cpus];
			}
			/* Start all given threads and wait on each of them until all are done.
			* From Stephan Preibisch's Multithreading.java class. See:
			* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
			*/
			private static void startAndJoin(Thread[] threads)
			{
			for (int ithread = 0; ithread < threads.length; ++ithread)
			{
			threads[ithread].setPriority(Thread.NORM_PRIORITY);
			threads[ithread].start();
			}

			try
			{
			for (int ithread = 0; ithread < threads.length; ++ithread)
			threads[ithread].join();
			} catch (InterruptedException ie)
			{
			throw new RuntimeException(ie);
			}
			}

			public double [] createFXandJacobianSingle(boolean createJacobian){
	int numCorrPar=fieldFitting.getNumberOfCorrParameters();		int numCorrPar=fieldFitting.getNumberOfCorrParameters();
	double [] fx=new double[dataVector.length + numCorrPar ];		double [] fx=new double[dataVector.length + numCorrPar ];
	double [][] derivs=null;		double [][] derivs=null;
	@@ -1967,11 +2152,6 @@ public double [] createFXandJacobian(boolean createJacobian){
	double prevPx=-1,prevPy=-1;		double prevPx=-1,prevPy=-1;
	for (int n=0;n<dataVector.length;n++){		for (int n=0;n<dataVector.length;n++){
	MeasuredSample ms=dataVector[n];		MeasuredSample ms=dataVector[n];
	// int saveDebugLevel=debugLevel;
	// if (n==9) {
	// System.out.println("createFXandJacobian(): n="+n);
	// debugLevel=10;
	// }
	if (!ms.timestamp.equals(prevTimeStamp) \|\| (ms.px!=prevPx) \|\| (ms.py!=prevPy)){		if (!ms.timestamp.equals(prevTimeStamp) \|\| (ms.px!=prevPx) \|\| (ms.py!=prevPy)){
	subData=fieldFitting.getValsDerivatives(		subData=fieldFitting.getValsDerivatives(
	ms.sampleIndex,		ms.sampleIndex,
	@@ -1984,7 +2164,6 @@ public double [] createFXandJacobian(boolean createJacobian){
	prevPx=ms.px;		prevPx=ms.px;
	prevPy=ms.py;		prevPy=ms.py;
	}		}
	// debugLevel=saveDebugLevel; // restore debugLevel
	fx[n]=subData[selChanIndices[ms.channel]];		fx[n]=subData[selChanIndices[ms.channel]];
	if (createJacobian) {		if (createJacobian) {
	double [] thisDerivs=derivs[selChanIndices[ms.channel]];		double [] thisDerivs=derivs[selChanIndices[ms.channel]];
	@@ -2011,6 +2190,8 @@ public double [] createFXandJacobian(boolean createJacobian){
	}		}
	}		}
	}		}
			}
			if (createJacobian) {
	// add mutual dependence of correction parameters. first - values (fx)		// add mutual dependence of correction parameters. first - values (fx)
	// System.out.println("Using sampleCorrVector 1");		// System.out.println("Using sampleCorrVector 1");
	int index=dataVector.length; // add to the end of vector		int index=dataVector.length; // add to the end of vector
	@@ -2611,6 +2792,11 @@ d_s2/d_x0= 2delta_xdelta_y^2/r2^2


	public LMAArrays calculateJacobianArrays(double [] fX){		public LMAArrays calculateJacobianArrays(double [] fX){
			if (multiJacobian && (threadsMax>0)) return calculateJacobianArraysMulti(fX);
			else return calculateJacobianArraysSingle(fX);
			}

			public LMAArrays calculateJacobianArraysSingle(double [] fX){
	// calculate JtJ		// calculate JtJ
	double [] diff=calcYminusFx(fX);		double [] diff=calcYminusFx(fX);
	int numPars=this.jacobian.length; // number of parameters to be adjusted		int numPars=this.jacobian.length; // number of parameters to be adjusted
	@@ -2625,7 +2811,6 @@ d_s2/d_x0= 2delta_xdelta_y^2/r2^2
	for (int k=0;k<length;k++) JtByJmod[i][j]+=this.jacobian[i][k]*this.jacobian[j][k];		for (int k=0;k<length;k++) JtByJmod[i][j]+=this.jacobian[i][k]*this.jacobian[j][k];
	}		}
	for (int i=0;i<numPars;i++) { // subtract lambda*diagonal , fill the symmetrical half below the diagonal		for (int i=0;i<numPars;i++) { // subtract lambda*diagonal , fill the symmetrical half below the diagonal
	// JtByJmod[i][i]+=lambda*JtByJmod[i][i]; //Marquardt mod
	for (int j=0;j<i;j++) JtByJmod[i][j]= JtByJmod[j][i]; // it is symmetrical matrix, just copy		for (int j=0;j<i;j++) JtByJmod[i][j]= JtByJmod[j][i]; // it is symmetrical matrix, just copy
	}		}
	for (int i=0;i<numPars;i++) {		for (int i=0;i<numPars;i++) {
	@@ -2642,6 +2827,76 @@ d_s2/d_x0= 2delta_xdelta_y^2/r2^2
	lMAArrays.jTByDiff=JtByDiff;		lMAArrays.jTByDiff=JtByDiff;
	return lMAArrays;		return lMAArrays;
	}		}

			public LMAArrays calculateJacobianArraysMulti(double [] fX){
			// calculate JtJ
			final double [] diff=calcYminusFx(fX);
			final int numPars=this.jacobian.length; // number of parameters to be adjusted
			// int length=diff.length; // should be the same as this.jacobian[0].length
			final double [][] JtByJmod=new double [numPars][numPars]; //Transposed Jacobian multiplied by Jacobian
			final double [] JtByDiff=new double [numPars];

			final double [] fWeights=this.dataWeights;
			// final double [][] fJacobian=this.jacobian;
			final AtomicInteger lineAtomic = new AtomicInteger(0);
			final Thread[] threads = newThreadArray(threadsMax);

			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int line=lineAtomic.getAndIncrement(); line<numPars;line=lineAtomic.getAndIncrement()){
			double [] sLine=jacobian[line];
			if (fWeights!=null){
			sLine=jacobian[line].clone();
			for (int i=0;i<sLine.length;i++) sLine[i]*=fWeights[i];
			}
			for (int line2=line;line2<numPars;line2++){
			double d=0;
			for (int i=0;i<sLine.length;i++) if (sLine[i]!=0.0){
			d+=sLine[i]*jacobian[line2][i];
			}
			JtByJmod[line][line2]=d;
			}
			double d=0;
			for (int i=0;i<sLine.length;i++) if (sLine[i]!=0.0){
			d+=sLine[i]*diff[i];
			}
			JtByDiff[line]=d;
			}
			} // public void run() {
			};
			}
			startAndJoin(threads);
			/*
			for (int i=0;i<numPars;i++) for (int j=i;j<numPars;j++){
			JtByJmod[i][j]=0.0;
			if (this.dataWeights!=null)
			for (int k=0;k<length;k++) JtByJmod[i][j]+=this.jacobian[i][k]this.jacobian[j][k]this.dataWeights[k];
			else
			for (int k=0;k<length;k++) JtByJmod[i][j]+=this.jacobian[i][k]*this.jacobian[j][k];
			}
			*/
			for (int i=0;i<numPars;i++) { // subtract lambda*diagonal , fill the symmetrical half below the diagonal
			for (int j=0;j<i;j++) JtByJmod[i][j]= JtByJmod[j][i]; // it is symmetrical matrix, just copy
			}
			/*
			for (int i=0;i<numPars;i++) {
			JtByDiff[i]=0.0;
			if (this.dataWeights!=null)
			for (int k=0;k<length;k++) JtByDiff[i]+=this.jacobian[i][k]diff[k]this.dataWeights[k];
			else
			for (int k=0;k<length;k++) JtByDiff[i]+=this.jacobian[i][k]*diff[k];

			}
			*/
			LMAArrays lMAArrays = new LMAArrays();
			lMAArrays.jTByJ=JtByJmod;
			lMAArrays.jTByDiff=JtByDiff;
			return lMAArrays;
			}



	public double [] solveLMA(		public double [] solveLMA(
	LMAArrays lMAArrays,		LMAArrays lMAArrays,
	double lambda,		double lambda,
	@@ -2763,10 +3018,15 @@ d_s2/d_x0= 2delta_xdelta_y^2/r2^2
	String msg="initial Jacobian matrix calculation. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;		String msg="initial Jacobian matrix calculation. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
	if (debugLevel>1) System.out.println(msg);		if (debugLevel>1) System.out.println(msg);
	if (this.updateStatus) IJ.showStatus(msg);		if (this.updateStatus) IJ.showStatus(msg);
			System.out.println("*** 1 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)		this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)
			System.out.println("*** 2 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.lMAArrays=calculateJacobianArrays(this.currentfX);		this.lMAArrays=calculateJacobianArrays(this.currentfX);
			System.out.println("*** 3 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.currentRMS= calcErrorDiffY(this.currentfX,false);		this.currentRMS= calcErrorDiffY(this.currentfX,false);
			System.out.println("*** 4 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.currentRMSPure=calcErrorDiffY(this.currentfX, true);		this.currentRMSPure=calcErrorDiffY(this.currentfX, true);
			System.out.println("*** 5 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	msg=this.currentStrategyStep+": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS="+IJ.d2s(this.currentRMSPure,8)+")"+		msg=this.currentStrategyStep+": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS="+IJ.d2s(this.currentRMSPure,8)+")"+
	". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;		". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
	if (debugLevel>1) System.out.println(msg);		if (debugLevel>1) System.out.println(msg);
	@@ -2813,10 +3073,16 @@ d_s2/d_x0= 2delta_xdelta_y^2/r2^2
	// this.savedJacobian=this.jacobian;		// this.savedJacobian=this.jacobian;
	this.savedLMAArrays=lMAArrays.clone();		this.savedLMAArrays=lMAArrays.clone();
	this.jacobian=null; // not needed, just to catch bugs		this.jacobian=null; // not needed, just to catch bugs
			if (debugLevel>1) System.out.println("*** 6 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.nextfX=createFXandJacobian(this.nextVector,true);		this.nextfX=createFXandJacobian(this.nextVector,true);
			if (debugLevel>1) System.out.println("*** 7 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.lMAArrays=calculateJacobianArrays(this.nextfX);		this.lMAArrays=calculateJacobianArrays(this.nextfX);
			if (debugLevel>1) System.out.println("*** 8 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.nextRMS= calcErrorDiffY(this.nextfX,false);		this.nextRMS= calcErrorDiffY(this.nextfX,false);
			if (debugLevel>1) System.out.println("*** 9 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));
	this.nextRMSPure= calcErrorDiffY(this.nextfX,true);		this.nextRMSPure= calcErrorDiffY(this.nextfX,true);
			if (debugLevel>1) System.out.println("*** 10 @ "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),5));

	this.lastImprovements[1]=this.lastImprovements[0];		this.lastImprovements[1]=this.lastImprovements[0];
	this.lastImprovements[0]=this.currentRMS-this.nextRMS;		this.lastImprovements[0]=this.currentRMS-this.nextRMS;
	String msg="currentRMS="+this.currentRMS+		String msg="currentRMS="+this.currentRMS+
	@@ -2937,6 +3203,8 @@ public boolean selectLMAParameters(boolean autoSel){
	gd.addCheckbox("Show modified parameters", this.showParams);		gd.addCheckbox("Show modified parameters", this.showParams);
	gd.addCheckbox("Show disabled parameters", this.showDisabledParams);		gd.addCheckbox("Show disabled parameters", this.showDisabledParams);
	gd.addCheckbox("Show per-sample correction parameters", this.showCorrectionParams);		gd.addCheckbox("Show per-sample correction parameters", this.showCorrectionParams);
			gd.addNumericField("Maximal number of threads (0 - old code)", this.threadsMax, 0);
			//threadsMax

	// gd.addCheckbox("Reset all per-sample corrections to zero", resetCorrections);		// gd.addCheckbox("Reset all per-sample corrections to zero", resetCorrections);

	@@ -2969,6 +3237,7 @@ public boolean selectLMAParameters(boolean autoSel){
	this.showParams= gd.getNextBoolean();		this.showParams= gd.getNextBoolean();
	this.showDisabledParams= gd.getNextBoolean();		this.showDisabledParams= gd.getNextBoolean();
	this.showCorrectionParams= gd.getNextBoolean();		this.showCorrectionParams= gd.getNextBoolean();
			this.threadsMax= (int) gd.getNextNumber();
	// if (!keepCorrectionParameters) fieldFitting.resetSampleCorr();		// if (!keepCorrectionParameters) fieldFitting.resetSampleCorr();
	return true;		return true;
	}		}
	@@ -6669,7 +6938,7 @@ public boolean LevenbergMarquardt(
	int [] motors, // 3 motor coordinates		int [] motors, // 3 motor coordinates
	double px, // pixel x		double px, // pixel x
	double py, // pixel y		double py, // pixel y
	double [][] deriv // array of (1..6[][], matching getNumberOfChannels) or null if derivatives are not required		double [][] deriv // array of (1..6][], matching getNumberOfChannels) or null if derivatives are not required
	){		){
	// if (sampleIndex==39) {		// if (sampleIndex==39) {
	// System.out.print("?");		// System.out.print("?");

src/main/java/LensAdjustment.java

+12 −1

Original line number	Original line	Diff line number	Diff line
	@@ -307,6 +307,7 @@ public class LensAdjustment {
	public boolean scanTiltEnable=false; //true; // enable scanning tilt		public boolean scanTiltEnable=false; //true; // enable scanning tilt
	public boolean scanTiltReverse=false; // enable scanning tilt in both directions		public boolean scanTiltReverse=false; // enable scanning tilt in both directions
	public boolean scanMeasureLast=false; // Calculate PSF after last move (to original position)		public boolean scanMeasureLast=false; // Calculate PSF after last move (to original position)
			public boolean scanRunLMA=true; // Calculate PSF after last move (to original position)
	public int scanTiltRangeX=14336; // 4 periods		public int scanTiltRangeX=14336; // 4 periods
	public int scanTiltRangeY=14336; // 4 periods		public int scanTiltRangeY=14336; // 4 periods
	public int scanTiltStepsX=24;		public int scanTiltStepsX=24;
	@@ -524,6 +525,7 @@ public class LensAdjustment {
	boolean scanTiltEnable, //=true; // enable scanning tilt		boolean scanTiltEnable, //=true; // enable scanning tilt
	boolean scanTiltReverse,		boolean scanTiltReverse,
	boolean scanMeasureLast,		boolean scanMeasureLast,
			boolean scanRunLMA,
	int scanTiltRangeX, //=14336; // 4 periods		int scanTiltRangeX, //=14336; // 4 periods
	int scanTiltRangeY, //=14336; // 4 periods		int scanTiltRangeY, //=14336; // 4 periods
	int scanTiltStepsX, //=24;		int scanTiltStepsX, //=24;
	@@ -669,6 +671,7 @@ public class LensAdjustment {
	this.scanTiltEnable=scanTiltEnable; //=true; // enable scanning tilt		this.scanTiltEnable=scanTiltEnable; //=true; // enable scanning tilt
	this.scanTiltReverse=scanTiltReverse;		this.scanTiltReverse=scanTiltReverse;
	this.scanMeasureLast=scanMeasureLast;		this.scanMeasureLast=scanMeasureLast;
			this.scanRunLMA=scanRunLMA;
	this.scanTiltRangeX=scanTiltRangeX; //, //=14336; // 4 periods		this.scanTiltRangeX=scanTiltRangeX; //, //=14336; // 4 periods
	this.scanTiltRangeY=scanTiltRangeY; //, //=14336; // 4 periods		this.scanTiltRangeY=scanTiltRangeY; //, //=14336; // 4 periods
	this.scanTiltStepsX=scanTiltStepsX; //=24;		this.scanTiltStepsX=scanTiltStepsX; //=24;
	@@ -815,6 +818,7 @@ public class LensAdjustment {
	this.scanTiltEnable, // enable scanning tilt		this.scanTiltEnable, // enable scanning tilt
	this.scanTiltReverse,		this.scanTiltReverse,
	this.scanMeasureLast,		this.scanMeasureLast,
			this.scanRunLMA,
	this.scanTiltRangeX, // 4 periods		this.scanTiltRangeX, // 4 periods
	this.scanTiltRangeY, // 4 periods		this.scanTiltRangeY, // 4 periods
	this.scanTiltStepsX,		this.scanTiltStepsX,
	@@ -966,6 +970,7 @@ public class LensAdjustment {
	properties.setProperty(prefix+"scanTiltEnable",this.scanTiltEnable+""); // enable scanning tilt		properties.setProperty(prefix+"scanTiltEnable",this.scanTiltEnable+""); // enable scanning tilt
	properties.setProperty(prefix+"scanTiltReverse",this.scanTiltReverse+"");		properties.setProperty(prefix+"scanTiltReverse",this.scanTiltReverse+"");
	properties.setProperty(prefix+"scanMeasureLast",this.scanMeasureLast+"");		properties.setProperty(prefix+"scanMeasureLast",this.scanMeasureLast+"");
			properties.setProperty(prefix+"scanRunLMA",this.scanRunLMA+"");
	properties.setProperty(prefix+"scanTiltRangeX",this.scanTiltRangeX+""); // 4 periods		properties.setProperty(prefix+"scanTiltRangeX",this.scanTiltRangeX+""); // 4 periods
	properties.setProperty(prefix+"scanTiltRangeY",this.scanTiltRangeY+""); // 4 periods		properties.setProperty(prefix+"scanTiltRangeY",this.scanTiltRangeY+""); // 4 periods
	properties.setProperty(prefix+"scanTiltStepsX",this.scanTiltStepsX+"");		properties.setProperty(prefix+"scanTiltStepsX",this.scanTiltStepsX+"");

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