debugging (47ffc516) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+189 −34

Original line number	Original line	Diff line number	Diff line
	@@ -59,9 +59,11 @@ public class FocusingField {
	public double pY0;		public double pY0;
	public double [][][] sampleCoord;		public double [][][] sampleCoord;
	public ArrayList<FocusingFieldMeasurement> measurements;		public ArrayList<FocusingFieldMeasurement> measurements;
			boolean sagittalMaster=false; // center data is the same, when true sagittal fitting only may change r=0 coefficients,
			// when false - tangential is master
	double [] minMeas= {1.0,1.0,1.0,1.0,1.0,1.0}; // pixels		double [] minMeas= {1.0,1.0,1.0,1.0,1.0,1.0}; // pixels
	double [] maxMeas= {4.5,4.5,4.5,4.5,4.5,4.5}; // pixels		double [] maxMeas= {4.5,4.5,4.5,4.5,4.5,4.5}; // pixels
	double [] thresholdMax= {3.0,3.0,3.0,3.0,3.0,3.0}; // pixels		double [] thresholdMax= {3.0,3.0,3.0,3.0,4.0,3.0}; // pixels
	double [] weightReference=null;		double [] weightReference=null;
	boolean useMinMeas= true;		boolean useMinMeas= true;
	boolean useMaxMeas= true;		boolean useMaxMeas= true;
	@@ -179,6 +181,9 @@ public class FocusingField {
	int [] numCurvPars=tmpFieldFitting.getNumCurvars();		int [] numCurvPars=tmpFieldFitting.getNumCurvars();
	GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));		GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));
	gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");		gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
			gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);


	for (int i=0;i<minMeas.length;i++){		for (int i=0;i<minMeas.length;i++){
	gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");		gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");
	}		}
	@@ -207,6 +212,7 @@ public class FocusingField {
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
			sagittalMaster= gd.getNextBoolean();
	for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();		for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
	useMinMeas= gd.getNextBoolean();		useMinMeas= gd.getNextBoolean();
	for (int i=0;i<maxMeas.length;i++) this.maxMeas[i]= gd.getNextNumber();		for (int i=0;i<maxMeas.length;i++) this.maxMeas[i]= gd.getNextNumber();
	@@ -232,7 +238,7 @@ public class FocusingField {
	}		}
	if (setupMasks) this.fieldFitting.maskSetDialog("Setup parameter masks");		if (setupMasks) this.fieldFitting.maskSetDialog("Setup parameter masks");
	if (setupParameters) this.fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled);		if (setupParameters) this.fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled);
	this.savedVector=this.fieldFitting.createParameterVector();		this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
	// initialVector		// initialVector
	return true;		return true;
	}		}
	@@ -276,7 +282,7 @@ public class FocusingField {

	// for compatibility with Distortions class		// for compatibility with Distortions class
	public double [] createFXandJacobian( double [] vector, boolean createJacobian){		public double [] createFXandJacobian( double [] vector, boolean createJacobian){
	fieldFitting.commitParameterVector(vector);		fieldFitting.commitParameterVector(vector,sagittalMaster);
	return createFXandJacobian(createJacobian);		return createFXandJacobian(createJacobian);
	}		}

	@@ -291,7 +297,7 @@ public class FocusingField {
	for (int i=1;i<selChanIndices.length;i++){		for (int i=1;i<selChanIndices.length;i++){
	selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);		selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
	}		}
	int numPars=fieldFitting.getNumberOfParameters();		int numPars=fieldFitting.getNumberOfParameters(sagittalMaster);
	if (createJacobian) {		if (createJacobian) {
	jacobian=new double [numPars][dataVector.length];		jacobian=new double [numPars][dataVector.length];
	derivs=new double [fieldFitting.getNumberOfChannels()][];		derivs=new double [fieldFitting.getNumberOfChannels()][];
	@@ -302,6 +308,7 @@ public class FocusingField {
	MeasuredSample ms=dataVector[n];		MeasuredSample ms=dataVector[n];
	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(
			sagittalMaster,
	ms.motors, // 3 motor coordinates		ms.motors, // 3 motor coordinates
	ms.px, // pixel x		ms.px, // pixel x
	ms.py, // pixel y		ms.py, // pixel y
	@@ -896,6 +903,7 @@ public class FocusingField {
	for (int i=0;i<sampleCoord.length;i++)		for (int i=0;i<sampleCoord.length;i++)
	for (int j=0;j<sampleCoord[0].length;j++) {		for (int j=0;j<sampleCoord[0].length;j++) {
	double [] subData=fieldFitting.getValsDerivatives(		double [] subData=fieldFitting.getValsDerivatives(
			sagittalMaster, // dependent channel does not have center parameters, but that is only used for derivs.
	ffm.motors, // 3 motor coordinates		ffm.motors, // 3 motor coordinates
	sampleCoord[i][j][0], // pixel x		sampleCoord[i][j][0], // pixel x
	sampleCoord[i][j][1], // pixel y		sampleCoord[i][j][1], // pixel y
	@@ -1049,8 +1057,8 @@ public class FocusingField {
	if (openDialog && !selectLMAParameters()) return false;		if (openDialog && !selectLMAParameters()) return false;
	this.startTime=System.nanoTime();		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
	this.savedVector=this.fieldFitting.createParameterVector();		this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
			this.iterationStepNumber=0;
	this.firstRMS=-1; //undefined		this.firstRMS=-1; //undefined
	// while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series		// while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series
	this.currentVector=null; // invalidate for the new series		this.currentVector=null; // invalidate for the new series
	@@ -1062,7 +1070,7 @@ public class FocusingField {
	String msg="Calculation aborted by user request, restoring saved parameter vector";		String msg="Calculation aborted by user request, restoring saved parameter vector";
	IJ.showMessage(msg);		IJ.showMessage(msg);
	System.out.println(msg);		System.out.println(msg);
	this.fieldFitting.commitParameterVector(this.savedVector);		this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
	return false;		return false;
	}		}

	@@ -1113,13 +1121,13 @@ public class FocusingField {
	// updateCameraParametersFromCalculated(false); // update camera parameters from enabled only images (may overwrite some of the above)		// updateCameraParametersFromCalculated(false); // update camera parameters from enabled only images (may overwrite some of the above)
	}		}
	// if RMS was decreased. this.saveSeries==false after dialogLMAStep(state) only if "cancel" was pressed		// if RMS was decreased. this.saveSeries==false after dialogLMAStep(state) only if "cancel" was pressed
	this.fieldFitting.commitParameterVector(this.savedVector); // either new or original		this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster); // either new or original
	return this.saveSeries; // TODO: Maybe change result?		return this.saveSeries; // TODO: Maybe change result?
	}		}
	//stepLevenbergMarquardtAction();		//stepLevenbergMarquardtAction();
	if (state[1]) {		if (state[1]) {
	if (!state[0]) {		if (!state[0]) {
	this.fieldFitting.commitParameterVector(this.savedVector);		this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
	return false; // sequence failed		return false; // sequence failed
	}		}
	this.savedVector=this.currentVector.clone();		this.savedVector=this.currentVector.clone();
	@@ -1134,11 +1142,12 @@ public class FocusingField {
	// if (wasLastSeries) break;		// if (wasLastSeries) break;
	// } // while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series		// } // while (this.fittingStrategy.isSeriesValid(this.seriesNumber)){ // TODO: Add "stop" tag to series
	if (debugLevel>0) System.out.println("LevenbergMarquardt(): all done"+		if (debugLevel>0) System.out.println("LevenbergMarquardt(): all done"+
			", step="+ this.iterationStepNumber+
	", RMS="+this.currentRMS+		", RMS="+this.currentRMS+
	" ("+this.firstRMS+") "+		" ("+this.firstRMS+") "+
	" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3));		" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3));
	this.savedVector=this.currentVector.clone();		this.savedVector=this.currentVector.clone();
	this.fieldFitting.commitParameterVector(this.savedVector);		this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
	return true; // all series done		return true; // all series done

	}		}
	@@ -1495,15 +1504,29 @@ public class FocusingField {
	}		}
	}		}
	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
	parList.add("\t ===== Curvature model parameters for \""+ getDescription(n)+"\"=====\t\t");		parList.add("\t ===== Curvature model parameters for \""+ getDescription(n)+"\"=====\t\t");
			int n1= n ^ 1;
	int index=0;		int index=0;
	for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){		for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
	String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);		String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);
			if ((j==0) && !isMasterDir){ // dependent, copy center coefficients from the master
			if ((curvatureSelect[n1]==null) \|\| curvatureSelect[n1][index] ) {
			parList.add("(master)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
			// debugging
			parList.add("(this)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
			} else if (showDisabled) {
			parList.add("(master_disabled)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
			// debugging
			parList.add("(this_disabled)\t"+name+":\t"+curvatureModel[n1].modelParams[i][j]+"\t");
			}
			} else {
	if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) {		if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) {
	parList.add("\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");		parList.add("\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
	} else if (showDisabled) {		} else if (showDisabled) {
	parList.add("(disabled)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");		parList.add("(disabled)\t"+name+":\t"+curvatureModel[n].modelParams[i][j]+"\t");
	}		}
			}
	index++;		index++;
	}		}
	}		}
	@@ -1523,15 +1546,26 @@ public class FocusingField {
	}		}
	}		}
	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
			int n1= n ^ 1;

	gd.addMessage("===== Curvature model parameters for \""+ getDescription(n)+"\"=====");		gd.addMessage("===== Curvature model parameters for \""+ getDescription(n)+"\"=====");
	int index=0;		int index=0;
	for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){		for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
	String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);		String name=curvatureModel[n].getZDescription(i)+", "+curvatureModel[n].getRadialDecription(j);
			if ((j==0) && !isMasterDir){ // dependent, copy center coefficients from the master
			if ((curvatureSelect[n1]==null) \|\| curvatureSelect[n1][index] ) {
			gd.addNumericField("(copied from master) "+name,curvatureModel[n1].modelParams[i][j],5,8,"");
			} else if (showDisabled) {
			gd.addNumericField("(copied from disabled master) "+name,curvatureModel[n1].modelParams[i][j],5,8,"");
			}
			} else {
	if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) {		if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) {
	gd.addNumericField(name,curvatureModel[n].modelParams[i][j],5,8,"");		gd.addNumericField(name,curvatureModel[n].modelParams[i][j],5,8,"");
	} else if (showDisabled) {		} else if (showDisabled) {
	gd.addNumericField("(disabled) "+name,curvatureModel[n].modelParams[i][j],5,8,"");		gd.addNumericField("(disabled) "+name,curvatureModel[n].modelParams[i][j],5,8,"");
	}		}
			}
	index++;		index++;
	}		}
	}		}
	@@ -1562,15 +1596,16 @@ public class FocusingField {
	/**		/**
	* @return number of selected parameters (including mechanical and each selected - up to 6 - curvature)		* @return number of selected parameters (including mechanical and each selected - up to 6 - curvature)
	*/		*/
	public int getNumberOfParameters(){		public int getNumberOfParameters(boolean sagittalMaster){
	int np=0;		int np=0;
	for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){		for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
	if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) np++;		if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) np++;
	}		}
	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
	int index=0;		int index=0;
	for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){		for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
	if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) np++;		if ((isMasterDir \|\| (j!=0)) && ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] )) np++;
	index++;		index++;
	}		}
	}		}
	@@ -1589,20 +1624,22 @@ public class FocusingField {
	/**		/**
	* @return vector of the current selected parameters values		* @return vector of the current selected parameters values
	*/		*/
	public double [] createParameterVector(){		public double [] createParameterVector(boolean sagittalMaster){
	double [] pars = new double [getNumberOfParameters()];		double [] pars = new double [getNumberOfParameters(sagittalMaster)];
	int np=0;		int np=0;
	for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){		for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
	if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) pars[np++]=mechanicalFocusingModel.paramValues[i];		if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) pars[np++]=mechanicalFocusingModel.paramValues[i];
	}		}
	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
	int index=0;		int index=0;
	for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){		for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
	if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) pars[np++]=curvatureModel[n].modelParams[i][j];		if ((isMasterDir \|\| (j!=0)) && ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] )) {
			pars[np++]=curvatureModel[n].modelParams[i][j];
			}
	index++;		index++;
	}		}
	}		}

	return pars;		return pars;
	}		}

	@@ -1610,18 +1647,30 @@ public class FocusingField {
	* Apply (modified) parameter values to selected ones		* Apply (modified) parameter values to selected ones
	* @param pars vector corresponding to selected parameters		* @param pars vector corresponding to selected parameters
	*/		*/
	public void commitParameterVector(double [] pars){		public void commitParameterVector(double [] pars, boolean sagittalMaster){
	int np=0;		int np=0;
	for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){		for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
	if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) mechanicalFocusingModel.paramValues[i] = pars[np++];;		if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) mechanicalFocusingModel.paramValues[i] = pars[np++];;
	}		}
	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir=(n%2) == (sagittalMaster?0:1);
	int index=0;		int index=0;
	for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){		for (int i=0;i<curvatureModel[n].modelParams.length;i++) for (int j=0;j<curvatureModel[n].modelParams[0].length;j++){
	if ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] ) curvatureModel[n].modelParams[i][j]=pars[np++];		if ((isMasterDir \|\| (j!=0)) && ((curvatureSelect[n]==null) \|\| curvatureSelect[n][index] )) {
			curvatureModel[n].modelParams[i][j]=pars[np++];
			}
	index++;		index++;
	}		}
	}		}
			// copy center parameters to dependent
			// copy if master is selected, regardless of is dependent selected or not
			for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			boolean isMasterDir = (n%2) == (sagittalMaster?0:1);
			if (isMasterDir){
			curvatureModel[n ^ 1].setCenterVector(curvatureModel[n].getCenterVector());
			}
			}


	}		}
	public double getMotorsZ(		public double getMotorsZ(
	@@ -1653,6 +1702,64 @@ public class FocusingField {
	* @return array of [getNumberOfChannels()] calculated function values		* @return array of [getNumberOfChannels()] calculated function values
	*/		*/
	public double [] getValsDerivatives(		public double [] getValsDerivatives(
			boolean sagittalMaster, // false - tangential master, true - sagittal master (for center coefficients)
			int [] motors, // 3 motor coordinates
			double px, // pixel x
			double py, // pixel y
			double [][] deriv // array of (1..6[][], matching getNumberOfChannels) or null if derivatives are not required
			){
			double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]);
			double [] chnValues=new double [getNumberOfChannels()];
			double mot_z=mechanicalFocusingModel.calc_ZdZ(
			motors,
			px,
			py,
			motorDerivs);
			int nChn=0;
			double [][] deriv_curv = new double [channelSelect.length][];
			for (int c=0;c<channelSelect.length;c++) deriv_curv[c]=null;
			for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
			deriv_curv[c]=(deriv==null)?null:(new double [curvatureModel[c].getSize()]);
			chnValues[nChn++]=curvatureModel[c].getFdF(
			px,
			py,
			mot_z,
			deriv_curv[c]);
			}
			if (deriv!=null){
			nChn=0;
			for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
			boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
			int otherChannel= c ^ 1;
			deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)];
			int np=0;
			// For dependent/master channels no difference for mechanical parameters
			// TOSO: verify they are the same?

			for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
			if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) {
			deriv[nChn][np++]=-motorDerivs[i]*deriv_curv[c][0]; // minus d/dz0 const part
			}
			}
			// other parameters - for dependent - skip center (j==0), for master add dependent
			for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
			int [] ncp=curvatureModel[n].getNumPars(); // {(z),(r)}
			boolean isDependMasterDir=(n%2) == (sagittalMaster?0:1);
			for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){
			if (((i%ncp[1])!=0) \|\| isDependMasterDir) {
			int dependOnChannel=(((i%ncp[1])==0) && !isMasterDir)?otherChannel:c;
			deriv[nChn][np++]=(n==dependOnChannel)?(deriv_curv[n][i]):0.0;
			}
			}
			}
			nChn++;
			}
			}
			return chnValues;
			}

			public double [] getValsDerivativesOld(
			boolean sagittalMaster,
	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
	@@ -1674,12 +1781,13 @@ public class FocusingField {
	mot_z,		mot_z,
	deriv_curv);		deriv_curv);
	if (deriv!=null){		if (deriv!=null){
	deriv[nChn]=new double [getNumberOfParameters()];		deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)];
	int np=0;		int np=0;

	for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){		for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
	if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) deriv[nChn][np++]=-motorDerivs[i]*deriv_curv[0]; // minus d/dz0 const part		if ((mechanicalSelect==null) \|\| mechanicalSelect[i] ) deriv[nChn][np++]=-motorDerivs[i]*deriv_curv[0]; // minus d/dz0 const part
	}		}

	for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){		for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
	for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){		for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){
	deriv[nChn][np++]=(n==c)?(deriv_curv[i]):0.0;		deriv[nChn][np++]=(n==c)?(deriv_curv[i]):0.0;
	@@ -1691,6 +1799,8 @@ public class FocusingField {
	return chnValues;		return chnValues;
	}		}



	}		}

	public class MechanicalFocusingModel{		public class MechanicalFocusingModel{
	@@ -1990,6 +2100,19 @@ public class FocusingField {
	this.modelParams[1][0]=dflt_na;		this.modelParams[1][0]=dflt_na;
	this.modelParams[2][0]=dflt_r0;		this.modelParams[2][0]=dflt_r0;
	}		}
			public double [] getCenterVector(){
			double [] vector=new double [this.modelParams.length];
			for (int i=0;i<this.modelParams.length;i++){
			vector[i]=this.modelParams[i][0];
			}
			return vector;
			}
			public void setCenterVector(double [] vector){
			for (int i=0;i<this.modelParams.length;i++){
			this.modelParams[i][0]=vector[i];
			}
			}

	public double [] getVector(){		public double [] getVector(){
	double [] vector=new double [this.modelParams.length*this.modelParams[0].length];		double [] vector=new double [this.modelParams.length*this.modelParams[0].length];
	int index=0;		int index=0;
	@@ -2036,6 +2159,11 @@ modified parameters, r0 - PSF FWHM at z=0, k (instead of a0), so that old r0 now
	r0exp(-k), old a0= r0(1-exp(-k)).		r0exp(-k), old a0= r0(1-exp(-k)).

	f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-z0)^N		f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-z0)^N
			z0 - ar[0]
			a - ar[1]
			r0 - ar[2]
			k - ar[3]
			ar1 - ar[4]

	*/		*/
	double r=Math.sqrt((pX-pX0)(pX-pX0)+(pY-pY0)(pY-pY0))*PIXEL_SIZE; // in mm		double r=Math.sqrt((pX-pX0)(pX-pX0)+(pY-pY0)(pY-pY0))*PIXEL_SIZE; // in mm
	@@ -2050,13 +2178,24 @@ f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-
	}		}
	}		}
	double z=z_in-ar[0];		double z=z_in-ar[0];
	double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + ar[2]ar[2]);		double exp=Math.exp(-ar[3]);
	double f=sqrt;		double reff=ar[2]*exp;
			// double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + ar[2]ar[2]);
			double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + reffreff);

			double f=sqrt+ar[2]*(1-exp);
	double zp=1.0;		double zp=1.0;
			/*
	for (int i=3;i<ar.length;i++){		for (int i=3;i<ar.length;i++){
	f+=ar[i]*zp;		f+=ar[i]*zp;
	zp*=z;		zp*=z;
	}		}
			*/
			for (int i=4;i<ar.length;i++){
			zp*=z;
			f+=ar[i]*zp;
			}

	if (deriv==null) return f; // only value, no derivatives		if (deriv==null) return f; // only value, no derivatives
	double [] df_da=new double[this.modelParams.length]; // last element - derivative for dz		double [] df_da=new double[this.modelParams.length]; // last element - derivative for dz
	// derivative for z0 (shift) - ar[0]		// derivative for z0 (shift) - ar[0]
	@@ -2069,13 +2208,24 @@ f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-
	// derivative for a (related to numeric aperture) - ar[1]		// derivative for a (related to numeric aperture) - ar[1]
	df_da[1]=1.0/sqrtar[1]z*z;		df_da[1]=1.0/sqrtar[1]z*z;
	// derivative for a (related to lowest PSF radius) - ar[2]		// derivative for a (related to lowest PSF radius) - ar[2]
	df_da[2]=1.0/sqrt*ar[2];		// df_da[2]=1.0/sqrt*ar[2];
			df_da[2]=1.0/sqrtreffexp + (1-exp); // * exp(-k)
			// derivative for k (ar[3]

			df_da[3]=1.0/sqrtreffar[2]exp(-1) + ar[2]*exp;

	// derivatives for rest (polynomial) coefficients		// derivatives for rest (polynomial) coefficients
	zp=1.0;		zp=1.0;
			/*
	for (int i=3;i<this.modelParams.length;i++){		for (int i=3;i<this.modelParams.length;i++){
	df_da[i]=zp;		df_da[i]=zp;
	zp*=z;		zp*=z;
	}		}
			*/
			for (int i=4;i<this.modelParams.length;i++){
			zp*=z;
			df_da[i]=zp;
			}
	// derivative for z (to be combined with mechanical is just negative of derivative for z0, no need to calcualate separately		// derivative for z (to be combined with mechanical is just negative of derivative for z0, no need to calcualate separately
	// calculate even powers of radius		// calculate even powers of radius
	double [] dar= new double [this.modelParams[0].length];		double [] dar= new double [this.modelParams[0].length];
	@@ -2178,15 +2328,20 @@ f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-
	return mask;		return mask;
	}		}

	public boolean showModifyParameterValues(String title, boolean showDisabled, boolean [] mask){		public boolean showModifyParameterValues(String title, boolean showDisabled, boolean [] mask, boolean isMaster){
	GenericDialog gd = new GenericDialog(title);		GenericDialog gd = new GenericDialog(title);
	int index=0;		int index=0;
	for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){		for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){
	String name=getZDescription(i)+", "+getRadialDecription(j);		String name=getZDescription(i)+", "+getRadialDecription(j);
	if ((mask==null) \|\| mask[index] ) {		boolean dependent=!isMaster && (j==0);
			if (((mask==null) \|\| mask[index] ) && !dependent) {
	gd.addNumericField(name,this.modelParams[i][j],5,8,"");		gd.addNumericField(name,this.modelParams[i][j],5,8,"");
	} else if (showDisabled) {		} else if (showDisabled) {
			if (dependent) {
			gd.addNumericField("(from master) "+name,this.modelParams[i][j],5,8,"");
			} else {
	gd.addNumericField("(disabled) "+name,this.modelParams[i][j],5,8,"");		gd.addNumericField("(disabled) "+name,this.modelParams[i][j],5,8,"");
			}
	// gd.addMessage(name +": "+this.modelParams[i][j]);		// gd.addMessage(name +": "+this.modelParams[i][j]);
	}		}
	index++;		index++;

Admin message