Working on the model of the PSF dependence on the distance, height, (367449b7) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+110 −19

Original line number	Original line	Diff line number	Diff line
	@@ -34,26 +34,18 @@ import ij.text.TextWindow;

	import java.awt.*;		import java.awt.*;
	import java.awt.event.*;		import java.awt.event.*;

	import java.io.*; // FIle		import java.io.*; // FIle

	import java.io.File;
	import java.io.FileInputStream;
	import java.io.FileNotFoundException;
	import java.io.FileOutputStream;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStream;
	import java.util.Properties;		import java.util.Properties;


	import javax.swing.*; // TODO: modify methods that depend on it, use class CalibrationFileManagement		import javax.swing.*; // TODO: modify methods that depend on it, use class CalibrationFileManagement

	import java.util.*;		import java.util.*;
	import java.util.List;		import java.util.List;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;
	import java.util.regex.Matcher;		import java.util.regex.Matcher;
	import java.util.regex.Pattern;		import java.util.regex.Pattern;

			//import FocusingField.MeasuredSample;
	import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/		import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/

	public class Aberration_Calibration extends PlugInFrame implements ActionListener {		public class Aberration_Calibration extends PlugInFrame implements ActionListener {
	@@ -530,7 +522,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi

	public static LensAdjustment.FocusMeasurementParameters FOCUS_MEASUREMENT_PARAMETERS= new LensAdjustment.FocusMeasurementParameters(MOTORS.curpos);		public static LensAdjustment.FocusMeasurementParameters FOCUS_MEASUREMENT_PARAMETERS= new LensAdjustment.FocusMeasurementParameters(MOTORS.curpos);
	public static CalibrationHardwareInterface.GoniometerMotors GONIOMETER_MOTORS= new CalibrationHardwareInterface.GoniometerMotors();		public static CalibrationHardwareInterface.GoniometerMotors GONIOMETER_MOTORS= new CalibrationHardwareInterface.GoniometerMotors();
			public static FocusingField FOCUSING_FIELD=null;
	//GoniometerParameters		//GoniometerParameters
	public static Goniometer.GoniometerParameters GONIOMETER_PARAMETERS= new Goniometer.GoniometerParameters(GONIOMETER_MOTORS);		public static Goniometer.GoniometerParameters GONIOMETER_PARAMETERS= new Goniometer.GoniometerParameters(GONIOMETER_MOTORS);

	@@ -767,9 +759,13 @@ if (MORE_BUTTONS) {
	panelFocusing = new Panel();		panelFocusing = new Panel();
	panelFocusing.setLayout(new GridLayout(1, 0, 5, 5));		panelFocusing.setLayout(new GridLayout(1, 0, 5, 5));
	addButton("Configure Focusing",panelFocusing,color_configure);		addButton("Configure Focusing",panelFocusing,color_configure);
			if (MORE_BUTTONS) {
	addButton("Head Orientation",panelFocusing);		addButton("Head Orientation",panelFocusing);
			}
	addButton("Lens Center",panelFocusing,color_process);		addButton("Lens Center",panelFocusing,color_process);
			if (MORE_BUTTONS) {
	addButton("Find Grid",panelFocusing,color_lenses);		addButton("Find Grid",panelFocusing,color_lenses);
			}
	addButton("Select WOI",panelFocusing,color_lenses);		addButton("Select WOI",panelFocusing,color_lenses);
	addButton("Reset Histories",panelFocusing,color_lenses);		addButton("Reset Histories",panelFocusing,color_lenses);
	addButton("Motors Home",panelFocusing,color_lenses);		addButton("Motors Home",panelFocusing,color_lenses);
	@@ -781,6 +777,12 @@ if (MORE_BUTTONS) {
	addButton("Temp. Scan",panelFocusing,color_process);		addButton("Temp. Scan",panelFocusing,color_process);
	//		//
	addButton("List History",panelFocusing,color_report);		addButton("List History",panelFocusing,color_report);
			addButton("Save History",panelFocusing,color_debug);
			addButton("Restore History",panelFocusing,color_debug);
			addButton("Modify LMA",panelFocusing,color_debug);
			addButton("LMA History",panelFocusing,color_debug);
			addButton("List curv pars",panelFocusing,color_debug);
			addButton("List curv data",panelFocusing,color_debug);
	addButton("Show PSF",panelFocusing,color_report);		addButton("Show PSF",panelFocusing,color_report);
	add(panelFocusing);		add(panelFocusing);
	//panelGoniometer		//panelGoniometer
	@@ -2643,7 +2645,7 @@ if (MORE_BUTTONS) {
	// /getPointersXY(ImagePlus imp, int numPointers){ if		// /getPointersXY(ImagePlus imp, int numPointers){ if
	// calculate distortion grid for it		// calculate distortion grid for it

	matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Filed calibration - different image.		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
	matchSimulatedPattern.invalidateFocusMask();		matchSimulatedPattern.invalidateFocusMask();
	int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
	DISTORTION, //		DISTORTION, //
	@@ -3577,7 +3579,7 @@ if (MORE_BUTTONS) {
	// reset matchSimulatedPattern, so it will start from scratch		// reset matchSimulatedPattern, so it will start from scratch
	matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // new instance, all reset		matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // new instance, all reset
	// next 2 lines are not needed for the new instance, but can be used alternatively if keeipg it		// next 2 lines are not needed for the new instance, but can be used alternatively if keeipg it
	matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Filed calibration - different image.		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
	matchSimulatedPattern.invalidateFocusMask();		matchSimulatedPattern.invalidateFocusMask();


	@@ -4252,6 +4254,90 @@ if (MORE_BUTTONS) {
	);		);
	return;		return;
	}		}
			/* ======================================================================== */
			if (label.equals("Save History")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			double pX0=FOCUS_MEASUREMENT_PARAMETERS.result_PX0;
			double pY0=FOCUS_MEASUREMENT_PARAMETERS.result_PY0;
			double [][][] sampleCoord=FOCUS_MEASUREMENT_PARAMETERS.sampleCoordinates( //{x,y,r}
			pX0, // lens center on the sensor
			pY0);
			// set file path
			String path=null;
			String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);
			File dFile=new File(dir);
			if (!dFile.isDirectory() && !dFile.mkdirs()) {
			String msg="Failed to create directory "+dir;
			IJ.showMessage(msg);
			throw new IllegalArgumentException (msg);
			}

			String lensPrefix="";
			if (FOCUS_MEASUREMENT_PARAMETERS.includeLensSerial && (FOCUS_MEASUREMENT_PARAMETERS.lensSerial.length()>0)){
			lensPrefix=String.format("LENS%S-S%02d-",FOCUS_MEASUREMENT_PARAMETERS.lensSerial,FOCUS_MEASUREMENT_PARAMETERS.manufacturingState);
			}
			path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml";
			FOCUSING_FIELD= new FocusingField(
			FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
			FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
			FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
			pX0,
			pY0,
			sampleCoord,
			this.SYNC_COMMAND.stopRequested);

			System.out.println("Saving measurement history to "+path);
			MOTORS.addCurrentHistoryToFocusingField(FOCUSING_FIELD);
			FOCUSING_FIELD.saveXML(path);
			return;
			}
			/* ======================================================================== */
			if (label.equals("Restore History")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			FOCUSING_FIELD=new FocusingField(
			true, // boolean smart, // do not open dialog if default matches
			"",//); //String defaultPath); // AtomicInteger stopRequested
			this.SYNC_COMMAND.stopRequested);
			System.out.println("Loaded FocusingField");
			FOCUSING_FIELD.configureDataVector("Configure curvature",true);
			FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector());
			double []focusing_fx=FOCUSING_FIELD.createFXandJacobian(true);
			double rms= FOCUSING_FIELD.getRMS(focusing_fx);
			System.out.println("rms="+rms);
			return;
			}
			/* ======================================================================== */
			if (label.equals("Modify LMA")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if (FOCUSING_FIELD==null) return;
			FOCUSING_FIELD.configureDataVector("Re-configure curvature parameters",false);
			FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector());
			return;
			}
			/* ======================================================================== */
			if (label.equals("LMA History")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if (FOCUSING_FIELD==null) return;
			FOCUSING_FIELD.LevenbergMarquardt(true, DEBUG_LEVEL); //boolean openDialog, int debugLevel){
			return;
			}
			/* ======================================================================== */
			if (label.equals("List curv pars")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if (FOCUSING_FIELD==null) return;
			FOCUSING_FIELD.listParameters("Field curvature measurement parameters",null); // to screen
			return;
			}
			/* ======================================================================== */
			if (label.equals("List curv data")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if (FOCUSING_FIELD==null) return;
			FOCUSING_FIELD.listData("Field curvature measurement data",null); // to screen
			return;
			}

			//"LMA History"

	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("Show PSF")) {		if (label.equals("Show PSF")) {

	@@ -8010,7 +8096,7 @@ if (MORE_BUTTONS) {
	LENS_DISTORTIONS.debugLevel=DEBUG_LEVEL;		LENS_DISTORTIONS.debugLevel=DEBUG_LEVEL;


	GenericDialog gd=new GenericDialog("Pattern Flat Filed parameters");		GenericDialog gd=new GenericDialog("Pattern Flat Field parameters");
	gd.addNumericField("Fitting series number (to select images), negative - use all enabled images", -1,0);		gd.addNumericField("Fitting series number (to select images), negative - use all enabled images", -1,0);
	gd.addNumericField("Reference station number (unity target brightness)", 0,0);		gd.addNumericField("Reference station number (unity target brightness)", 0,0);
	gd.addNumericField("Shrink sensor mask", 100.0, 1,6,"sensor pix");		gd.addNumericField("Shrink sensor mask", 100.0, 1,6,"sensor pix");
	@@ -10100,7 +10186,7 @@ if (MORE_BUTTONS) {
	for (int jj=0;jj<sampleCoord[0].length;jj++){		for (int jj=0;jj<sampleCoord[0].length;jj++){
	int index=ii*sampleCoord[0].length+jj;		int index=ii*sampleCoord[0].length+jj;
	imp_psf.setProperty("pX_"+index, ""+sampleCoord[ii][jj][0]);		imp_psf.setProperty("pX_"+index, ""+sampleCoord[ii][jj][0]);
	imp_psf.setProperty("pX_"+index, ""+sampleCoord[ii][jj][0]);		imp_psf.setProperty("pY_"+index, ""+sampleCoord[ii][jj][1]);
	if (fullResults[ii][jj]!=null){		if (fullResults[ii][jj]!=null){
	for (int cc=0;cc<fullResults[ii][jj].length;cc++) if (fullResults[ii][jj][cc]!=null){		for (int cc=0;cc<fullResults[ii][jj].length;cc++) if (fullResults[ii][jj][cc]!=null){
	imp_psf.setProperty("R50_"+cc+"_"+index, ""+fullResults[ii][jj][cc][0]);		imp_psf.setProperty("R50_"+cc+"_"+index, ""+fullResults[ii][jj][cc][0]);
	@@ -10196,6 +10282,11 @@ if (MORE_BUTTONS) {
	double r=Math.sqrt(xx+yy);		double r=Math.sqrt(xx+yy);
	double ca=(sampleCoord[i][j][0]-x0)/r;		double ca=(sampleCoord[i][j][0]-x0)/r;
	double sa=(sampleCoord[i][j][1]-y0)/r;		double sa=(sampleCoord[i][j][1]-y0)/r;
			// System.out.println("extractPSFMetrics.. color="+color+" i="+i+" j="+j+" cos="+ca+" sin="+sa+
			// " psf_cutoffEnergy="+focusMeasurementParameters.psf_cutoffEnergy+
			// " psf_cutoffLevel="+focusMeasurementParameters.psf_cutoffLevel+
			// " psf_minArea="+focusMeasurementParameters.psf_minArea+
			// " psf_blurSigma="+focusMeasurementParameters.psf_blurSigma);
	double [] tanRad= matchSimulatedPattern.tangetRadialSizes(		double [] tanRad= matchSimulatedPattern.tangetRadialSizes(
	ca, // cosine of the center to sample vector		ca, // cosine of the center to sample vector
	sa, // sine of the center to sample vector		sa, // sine of the center to sample vector
	@@ -11739,7 +11830,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	}		}
	// images cap[ture in portrait mode, opened in landscape mode (rotated CCW90 from original)		// images cap[ture in portrait mode, opened in landscape mode (rotated CCW90 from original)
	// returns valid images for sub-bands: top, middle and bottom: mask bits 1- top (left) valid, 2 - middle valid, 4 - bottom (right) vlaid		// returns valid images for sub-bands: top, middle and bottom: mask bits 1- top (left) valid, 2 - middle valid, 4 - bottom (right) vlaid
	private int calcValidFlatFiledMask(FlatFieldParameters flatFieldParameters, int [] ranges, ImagePlus imp){		private int calcValidFlatFieldMask(FlatFieldParameters flatFieldParameters, int [] ranges, ImagePlus imp){
	int mask=0, maskO=0, maskU=0;		int mask=0, maskO=0, maskU=0;
	int [] mranges=ranges.clone();		int [] mranges=ranges.clone();
	mranges[0]=flatFieldParameters.margins[0];		mranges[0]=flatFieldParameters.margins[0];
	@@ -11864,7 +11955,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	ip=imp_single.getChannelProcessor();		ip=imp_single.getChannelProcessor();
	// currently all images in all channels should be the same width		// currently all images in all channels should be the same width
	if (weightMasks[0]==null)initFlatFieldArrays (imp_single.getWidth(), weightMasks, ranges, weights);		if (weightMasks[0]==null)initFlatFieldArrays (imp_single.getWidth(), weightMasks, ranges, weights);
	int diagMask= calcValidFlatFiledMask(flatFieldParameters, ranges, imp_single);		int diagMask= calcValidFlatFieldMask(flatFieldParameters, ranges, imp_single);
	int validBandsMask = diagMask & 7;		int validBandsMask = diagMask & 7;
	String imageExpStatus="";		String imageExpStatus="";
	for (int n=0;n<3;n++) {		for (int n=0;n<3;n++) {

src/main/java/CalibrationHardwareInterface.java

+126 −6

Original line number	Original line	Diff line number	Diff line
	@@ -31,9 +31,12 @@ import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;		import ij.process.ImageProcessor;
	import ij.text.TextWindow;		import ij.text.TextWindow;

			import java.io.BufferedWriter;
			import java.io.File;
	import java.io.FileInputStream;		import java.io.FileInputStream;
	import java.io.FileNotFoundException;		import java.io.FileNotFoundException;
	import java.io.FileOutputStream;		import java.io.FileOutputStream;
			import java.io.FileWriter;
	import java.io.IOException;		import java.io.IOException;
	import java.io.InputStream;		import java.io.InputStream;
	import java.io.OutputStream;		import java.io.OutputStream;
	@@ -50,6 +53,8 @@ import javax.xml.parsers.DocumentBuilder;
	import javax.xml.parsers.DocumentBuilderFactory;		import javax.xml.parsers.DocumentBuilderFactory;
	import javax.xml.parsers.ParserConfigurationException;		import javax.xml.parsers.ParserConfigurationException;

			import org.apache.commons.configuration.ConfigurationException;
			import org.apache.commons.configuration.XMLConfiguration;
	import org.w3c.dom.Document;		import org.w3c.dom.Document;
	import org.w3c.dom.Node;		import org.w3c.dom.Node;
	import org.xml.sax.SAXException;		import org.xml.sax.SAXException;
	@@ -2513,7 +2518,7 @@ public class CalibrationHardwareInterface {
	public FocusingSharpness focusingSharpness=new FocusingSharpness(1000);		public FocusingSharpness focusingSharpness=new FocusingSharpness(1000);
	public int debugLevel=1;		public int debugLevel=1;
	public String motorsStatePath="lensAdjustmentMotorPosition.xml"; // will be saved in ~/.imagej/		public String motorsStatePath="lensAdjustmentMotorPosition.xml"; // will be saved in ~/.imagej/
	public String prefsDirectory=Prefs.getPrefsDir()+Prefs.getFileSeparator(); // "~/.imagej/"		public String prefsDirectory=null; // prefs.getPrefsDir()+Prefs.getFileSeparator(); // "~/.imagej/" - too early !!!
	private Properties motorProperties=new Properties();		private Properties motorProperties=new Properties();
	public boolean interactiveRestore=true; // ask for confirmation to restore motor position		public boolean interactiveRestore=true; // ask for confirmation to restore motor position
	public boolean stateValid=false;		public boolean stateValid=false;
	@@ -2528,6 +2533,12 @@ public class CalibrationHardwareInterface {
	public double getMicronsPerStep(){return 1000.0this.threadPitchthis.linearReductionRatio/stepsPerRevolution;}		public double getMicronsPerStep(){return 1000.0this.threadPitchthis.linearReductionRatio/stepsPerRevolution;}
	public void setLinearReductionRatio(double lrr){this.linearReductionRatio=lrr;}		public void setLinearReductionRatio(double lrr){this.linearReductionRatio=lrr;}

			public String getPrefsDir(){
			if (prefsDirectory==null) prefsDirectory=Prefs.getPrefsDir();
			if (prefsDirectory!=null) prefsDirectory+=Prefs.getFileSeparator(); // "~/.imagej/"
			return prefsDirectory;
			}

	public boolean isInitialized(){		public boolean isInitialized(){
	return this.stateValid;		return this.stateValid;
	}		}
	@@ -2568,7 +2579,7 @@ public class CalibrationHardwareInterface {
	public void saveMotorState() throws IOException{		public void saveMotorState() throws IOException{
	if (!this.stateValid) return; // do not save until allowed		if (!this.stateValid) return; // do not save until allowed
	for (int i=0;i<curpos.length;i++) this.motorProperties.setProperty("motor"+(i+1),this.curpos[i]+"");		for (int i=0;i<curpos.length;i++) this.motorProperties.setProperty("motor"+(i+1),this.curpos[i]+"");
	String path=this.prefsDirectory+this.motorsStatePath;		String path=this.getPrefsDir()+this.motorsStatePath;
	OutputStream os;		OutputStream os;
	try {		try {
	os = new FileOutputStream(path);		os = new FileOutputStream(path);
	@@ -2600,7 +2611,7 @@ public class CalibrationHardwareInterface {
	}		}

	public int [] loadMotorState() throws IOException{		public int [] loadMotorState() throws IOException{
	String path=this.prefsDirectory+this.motorsStatePath;		String path=this.getPrefsDir()+this.motorsStatePath;
	InputStream is;		InputStream is;
	try {		try {
	is = new FileInputStream(path);		is = new FileInputStream(path);
	@@ -2756,7 +2767,7 @@ public class CalibrationHardwareInterface {
	if (this.debugLevel>2) System.out.println("--savedPosition="+((savedPosition==null)?"null":("{"+savedPosition[0]+","+savedPosition[1]+","+savedPosition[2]+"}")));		if (this.debugLevel>2) System.out.println("--savedPosition="+((savedPosition==null)?"null":("{"+savedPosition[0]+","+savedPosition[1]+","+savedPosition[2]+"}")));
	if (this.interactiveRestore){		if (this.interactiveRestore){
	gd = new GenericDialog("Missing motor position file");		gd = new GenericDialog("Missing motor position file");
	gd.addMessage("No motor position file ("+this.prefsDirectory+this.motorsStatePath+") found.");		gd.addMessage("No motor position file ("+this.getPrefsDir()+this.motorsStatePath+") found.");
	gd.addMessage("If you run the program for the first time it is normal, you may click \"OK\" and the new file will be created");		gd.addMessage("If you run the program for the first time it is normal, you may click \"OK\" and the new file will be created");
	gd.addMessage("If you select \"Cancel\" the current command will be aborted, you may check the file and restart the program.");		gd.addMessage("If you select \"Cancel\" the current command will be aborted, you may check the file and restart the program.");
	gd.showDialog();		gd.showDialog();
	@@ -3056,6 +3067,28 @@ public class CalibrationHardwareInterface {
	result_lastKT,		result_lastKT,
	result_allHistoryKT);		result_allHistoryKT);
	}		}
			public void saveHistoryXML(
			String path,
			String serialNumber,
			String lensSerial, // if null - do not add average
			String comment,
			double pX0,
			double pY0,
			double [][][] sampleCoord){ // x,y,r
			this.focusingHistory.saveXML(
			path,
			serialNumber,
			lensSerial, // if null - do not add average
			comment,
			pX0,
			pY0,
			sampleCoord);
			}

			public void addCurrentHistoryToFocusingField(FocusingField focusingField){
			this.focusingHistory.addCurrentHistory(focusingField);
			}

	public int historySize(){		public int historySize(){
	return this.focusingHistory.history.size();		return this.focusingHistory.history.size();
	}		}
	@@ -5437,7 +5470,94 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
	Double.NaN);		Double.NaN);
	}		}

			public void addCurrentHistory(
			FocusingField focusingField)
			{
			for (int i=0;i<this.history.size();i++){
			FocusingState focusingState=this.history.get(i);
			focusingField.addSample(
			focusingState.getTimestamp(),
			focusingState.getTemperature(),
			focusingState.motorsPos,
			focusingState.getSamples());
			}

			}

			public void saveXML(
			String path,
			String serialNumber,
			String lensSerial, // if null - do not add average
			String comment,
			double pX0,
			double pY0,
			double [][][] sampleCoord){ // x,y,r
			String sep=" "; //",";
			ArrayList<String> nodeList=new ArrayList<String>();
			XMLConfiguration hConfig=new XMLConfiguration();
			hConfig.setRootElementName("focusingHistory");
			if (comment!=null) hConfig.addProperty("comment",comment);
			if (serialNumber!=null) hConfig.addProperty("serialNumber",serialNumber);
			if (lensSerial!=null) hConfig.addProperty("lensSerial",lensSerial);
			hConfig.addProperty("lens_center_x",pX0);
			hConfig.addProperty("lens_center_y",pY0);
			if ((sampleCoord!=null) && (sampleCoord.length>0) && (sampleCoord[0] != null) && (sampleCoord[0].length>0)){
			hConfig.addProperty("samples_x",sampleCoord[0].length);
			hConfig.addProperty("samples_y",sampleCoord.length);
			for (int i=0;i<sampleCoord.length;i++)
			for (int j=0;j<sampleCoord[i].length;j++){
			// double coord[] = {sampleCoord[i][j][0],sampleCoord[i][j][1]};
			hConfig.addProperty("sample_"+i+"_"+j,sampleCoord[i][j][0]+sep+sampleCoord[i][j][1]);
			}
			}
			hConfig.addProperty("measurements",this.history.size());
			for (int i=0;i<this.history.size();i++){
			FocusingState focusingState=this.history.get(i);
			String prefix="measurement_"+i+".";
			if (focusingState.getTimestamp()!=null)
			hConfig.addProperty(prefix+"timestamp",focusingState.getTimestamp());
			hConfig.addProperty(prefix+"temperature",focusingState.getTemperature());
			hConfig.addProperty(prefix+"motors",focusingState.motorsPos[0]+sep+focusingState.motorsPos[1]+sep+focusingState.motorsPos[2]); // array of 3
			double [][][][] samples=focusingState.getSamples();
			nodeList.clear();
			if ((samples!=null) && (samples.length>0) && (samples[0]!=null) && (samples[0].length>0)){
			for (int ii=0;ii<samples.length;ii++) for (int jj=0;jj<samples[ii].length;jj++){
			if ((samples[ii][jj]!=null) && (samples[ii][jj].length>0)) {
			String sdata=ii+sep+jj;
			for (int cc=0;cc<samples[ii][jj].length;cc++) {
			double rt=samples[ii][jj][cc][0]/Math.sqrt((1+samples[ii][jj][cc][1]*samples[ii][jj][cc][1])/2.0); // tangential;
			double rs=rt*samples[ii][jj][cc][1]; // saggital
			sdata += sep+rs+ // saggital
			sep+rt; // tangential
			// double [] samples_st={
			// samples[ii][jj][cc][0], // saggital
			// samples[ii][jj][cc][0]/samples[ii][jj][cc][1] // tangential (was ratio)
			// };
			if ((samples[ii][jj]!=null) && (samples[ii][jj][cc]!=null)) {
			// hConfig.addProperty(prefix+"y"+ii+".x"+jj+".c"+cc,samples_st); // array of 2
			// nodeList.add(sdata);
			}
			}
			nodeList.add(sdata);
			}
			}
			hConfig.addProperty(prefix+"sample",nodeList);
			}
			}
			File file=new File (path);
			BufferedWriter writer;
			try {
			writer = new BufferedWriter(new FileWriter(file));
			hConfig.save(writer);
			} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			} catch (ConfigurationException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			}

			}
	public void list(		public void list(
	String path,		String path,
	String serialNumber,		String serialNumber,

src/main/java/FocusingField.java

0 → 100644

+2210 −0

File added.

Preview size limit exceeded, changes collapsed.

src/main/java/MatchSimulatedPattern.java

+4 −1

Original line number	Original line	Diff line number	Diff line
	@@ -5332,6 +5332,7 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
	if (mask[i]<maskCutOff) mask[i]=0.0;		if (mask[i]<maskCutOff) mask[i]=0.0;
	int size = (int) Math.sqrt(psf.length);		int size = (int) Math.sqrt(psf.length);
	int hsize=size/2;		int hsize=size/2;
			// int nn=0;
	double S0=0.0, SR=0.0, ST=0.0,SR2=0.0,ST2=0.0; //,SRT=0.0;		double S0=0.0, SR=0.0, ST=0.0,SR2=0.0,ST2=0.0; //,SRT=0.0;
	for (int i=0;i<mask.length;i++) if (mask[i]>0.0) {		for (int i=0;i<mask.length;i++) if (mask[i]>0.0) {
	double x=(i % size) - hsize;		double x=(i % size) - hsize;
	@@ -5344,10 +5345,12 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
	ST+=d*tc;		ST+=d*tc;
	SR2+=drcrc;		SR2+=drcrc;
	ST2+=dtctc;		ST2+=dtctc;
	// SRT+=drctc;		// nn++;
	}		}
	if (S0==0.0) return null; // make sure it is OK		if (S0==0.0) return null; // make sure it is OK
	double [] result={ Math.sqrt(ST2S0 - STST)/S0, Math.sqrt(SR2S0 - SRSR)/S0};		double [] result={ Math.sqrt(ST2S0 - STST)/S0, Math.sqrt(SR2S0 - SRSR)/S0};
			// System.out.println(" mask.length="+mask.length+" nn="+nn+" S0="+S0+" SR="+SR+" ST="+ST+" SR2="+SR2+" ST2="+ST2+
			// " result={"+result[0]+","+result[1]+"}");
	return result;		return result;
	}		}

src/main/resources/plugins.config

+5 −5

Original line number	Original line	Diff line number	Diff line
	@@ -8,9 +8,9 @@
	#		#
	# If something like ("<arg>") is appended to the class name, the setup() method		# If something like ("<arg>") is appended to the class name, the setup() method
	# will get that as arg parameter; otherwise arg is simply the empty string.		# will get that as arg parameter; otherwise arg is simply the empty string.
	Process, "Process Pixels", Process_Pixels		#Process, "Process Pixels", Process_Pixels
	Process, "Aberration Calibration", Aberration_Calibration		Process, "Aberration Calibration", Aberration_Calibration
	#Plugins, "Aberration Calibration", Aberration_Calibration		Plugins, "Aberration Calibration", Aberration_Calibration
	#Process, "Aberration Correction", Aberration_Correction		Process, "Aberration Correction", Aberration_Correction
	#Process, "Eyesis Correction", Eyesis_Correction		Process, "Eyesis Correction", Eyesis_Correction
	#Process, "JP46 Reader camera", JP46_Reader_camera		Process, "JP46 Reader camera", JP46_Reader_camera

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