Implemented simultaneous processing of multiple measurements (averaging, (d14a3970) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+396 −244

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/CalibrationHardwareInterface.java

+47 −12

Original line number	Diff line number	Diff line
		@@ -47,6 +47,7 @@ import java.util.ArrayList;
		import java.util.Iterator;
		import java.util.Properties;
		import java.util.Set;
		import java.util.concurrent.TimeUnit;
		import java.util.concurrent.atomic.AtomicInteger;

		import javax.xml.parsers.DocumentBuilder;
		@@ -1800,14 +1801,18 @@ public class CalibrationHardwareInterface {
		}

		public static class PowerControl{
		public boolean [] states={false,false,false};
		public String [] groups={"heater","fan","light"};
		public int debugLevel=1;
		private String powerIP="192.168.0.80";
		private double lightsDelay=5.0;
		private final String urlFormat="http://%s/insteon/index.php?cmd=%s&group=%s";
		private final String rootElement="Document";
		public boolean powerConrtolEnabled=false;
		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"powerIP",this.powerIP+"");
		properties.setProperty(prefix+"powerConrtolEnabled",this.powerConrtolEnabled+"");
		properties.setProperty(prefix+"lightsDelay",this.lightsDelay+"");
		}
		//Integer.decode(string)
		public void getProperties(String prefix,Properties properties){
		@@ -1815,6 +1820,8 @@ public class CalibrationHardwareInterface {
		this.powerIP=properties.getProperty(prefix+"powerIP");
		if (properties.getProperty(prefix+"powerConrtolEnabled")!=null)
		this.powerConrtolEnabled=Boolean.parseBoolean(properties.getProperty(prefix+"powerConrtolEnabled"));
		if (properties.getProperty(prefix+"lightsDelay")!=null)
		this.lightsDelay=Double.parseDouble(properties.getProperty(prefix+"lightsDelay"));
		}

		public boolean setPower (String group, String state){
		@@ -1822,6 +1829,7 @@ public class CalibrationHardwareInterface {
		System.out.println("=== Power control is disabled ===");
		return false;
		}
		System.out.println("=== Power control: "+group+":"+state+" ===");
		String url=String.format(urlFormat,this.powerIP,state,group);
		if (this.debugLevel>2) System.out.println("setPower: "+url);
		Document dom=null;
		@@ -1856,16 +1864,22 @@ public class CalibrationHardwareInterface {
		se.printStackTrace();
		return false;
		}
		for (int i=0;i<this.groups.length;i++) if (this.groups[i].equals(group)){
		this.states[i]=state.equals("on");
		}
		return true;
		}
		public boolean showDialog(String title, boolean control) {
		GenericDialog gd = new GenericDialog(title);
		boolean heaterOn=false, fanOn=false;
		gd.addCheckbox("Enable power control (heater, fan) ", this.powerConrtolEnabled);
		boolean heaterOn=false, fanOn=false, lightOn=false;
		gd.addCheckbox("Enable power control (heater, fan, lights) ", this.powerConrtolEnabled);
		gd.addStringField("IP address of the power control",this.powerIP,15);
		gd.addNumericField("Delay after lights on", this.lightsDelay, 1,4,"sec");

		if (control){
		gd.addCheckbox("Heater On", heaterOn);
		gd.addCheckbox("Fan On", fanOn);
		gd.addCheckbox("Lights On", lightOn);
		}
		WindowTools.addScrollBars(gd);
		if (control) gd.enableYesNoCancel("OK", "Control Power");
		@@ -1873,16 +1887,33 @@ public class CalibrationHardwareInterface {
		if (gd.wasCanceled()) return false;
		this.powerConrtolEnabled=gd.getNextBoolean();
		this.powerIP=gd.getNextString();
		this.lightsDelay=gd.getNextNumber();
		if (control){
		heaterOn=gd.getNextBoolean();
		fanOn=gd.getNextBoolean();
		lightOn=gd.getNextBoolean();
		if (!gd.wasOKed()) {
		setPower("heater",heaterOn?"on":"off");
		setPower("fan",fanOn?"on":"off");
		setPower("light",lightOn?"on":"off");
		}
		}
		return true;
		}
		public void lightsOnWithDelay(){
		if (this.states[2] \|\| !this.powerConrtolEnabled) return; // already on
		setPower("light","on");
		System.out.print("Sleeping "+this.lightsDelay+" seconds to let lights stibilize on...");
		try {
		TimeUnit.MILLISECONDS.sleep((long) (1000*this.lightsDelay));
		} catch (InterruptedException e) {
		System.out.println("Sleep was interrupted");
		// TODO Auto-generated catch block
		}
		System.out.println(" Done");

		}

		public boolean isPowerControlEnabled(){
		return this.powerConrtolEnabled;
		}
		@@ -5218,22 +5249,26 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		}

		public double [] temperatureLinearApproximation(
		double [][] ZTM, // Z, tXx, tY, m1,m2,m3 found with LMA
		double [][] ZTT, // Z, tXx, tY, m1,m2,m3 found with LMA - may contain NaN
		int numSamples // number of last samples from history to use, 0 - use all
		){
		if (numSamples<=0) numSamples=this.history.size();
		if (numSamples>this.history.size()) numSamples=this.history.size();
		int firstSample=this.history.size()-numSamples;
		// if (numSamples<=0) this.history.size();
		// if (numSamples>this.history.size()) numSamples=this.history.size();
		// int firstSample=this.history.size()-numSamples;

		if (numSamples<=0) numSamples=ZTT.length;
		if (numSamples>ZTT.length) numSamples=ZTT.length;
		int firstSample=ZTT.length-numSamples;
		int numGoodSamples=0;
		for (int nSample=0;nSample<numSamples;nSample++){
		if (ZTM[firstSample+nSample]!=null) numGoodSamples++;
		if (ZTT[firstSample+nSample]!=null) numGoodSamples++;
		}
		double [][] data =new double [numGoodSamples][2]; // no weights
		int index=0;
		for (int nSample=0;nSample<numSamples;nSample++) if (ZTM[firstSample+nSample]!=null) {
		data[index][0]=this.history.get(firstSample+nSample).getTemperature();
		data[index++][1]=ZTM[firstSample+nSample][0]; // Z
		for (int nSample=0;nSample<numSamples;nSample++) if (ZTT[firstSample+nSample]!=null) {
		// data[index][0]=this.history.get(firstSample+nSample).getTemperature();
		data[index][0]=ZTT[firstSample+nSample][3];
		data[index++][1]=ZTT[firstSample+nSample][0]; // Z
		}
		PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
		double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear

src/main/java/FocusingField.java

+1259 −243

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/LensAdjustment.java

+22 −5

Original line number	Diff line number	Diff line
		@@ -226,13 +226,14 @@ public class LensAdjustment {
		public int lensSerialLength=4;
		public String lensSerial=""; // Lens serial number
		public boolean askLensSerial=true; // Ask lens serial on camera power cycle
		public double reportTemperature=50; // temperature to report focal length

		public boolean includeLensSerial=true; // add lens serial to config filename
		public double centerDeltaX=0.0; // required X-difference between lens center and sensor center
		public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center
		// with the seam in the middle - make even # of samples horizontally
		public Rectangle margins=new Rectangle (100,100,2392,1736) ; // maximal height 1816 (1936-120)
		public int [] numSamples={4,3}; // number of samples in x and y directions
		public int [] numSamples={8,5}; // number of samples in x and y directions
		public int sampleSize=256;// 512; // size of square (2^n), in sensor pixels (twice FFT size)
		public int numInCenter=(numSamples[0]-2)*(numSamples[1]-2);// 2 - number of "center" samples
		public boolean centerSamples=true; // Select samples in the WOI symmetrical around the lens center
		@@ -583,7 +584,8 @@ public class LensAdjustment {
		int numIterations, // maximal number of iterations
		boolean cameraIsConfigured,
		int [] motorPos,
		double [] ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored)
		double [] ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
		double reportTemperature // temperature to report focal length
		){
		this.gridGeometryFile=gridGeometryFile;
		this.initialCalibrationFile=initialCalibrationFile;
		@@ -734,7 +736,7 @@ public class LensAdjustment {
		this.cameraIsConfigured=cameraIsConfigured;
		this.motorPos=motorPos;
		this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored)

		this.reportTemperature=reportTemperature;

		}
		public FocusMeasurementParameters clone(){
		@@ -887,7 +889,8 @@ public class LensAdjustment {
		this.numIterations,
		this.cameraIsConfigured,
		this.motorPos,
		this.ampsSeconds // cumulative Amps*seconds (read only, but will be saved/restored)
		this.ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
		this.reportTemperature
		);
		}
		public void setProperties(String prefix,Properties properties){
		@@ -1049,6 +1052,7 @@ public class LensAdjustment {
		properties.setProperty(prefix+"numIterations",this.numIterations+"");
		for (int i=0;i<this.ampsSeconds.length;i++)
		properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+"");
		properties.setProperty(prefix+"reportTemperature",this.reportTemperature+"");
		}
		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"gridGeometryFile")!=null)
		@@ -1368,9 +1372,10 @@ public class LensAdjustment {
		this.thresholdFinish=Double.parseDouble(properties.getProperty(prefix+"thresholdFinish"));
		if (properties.getProperty(prefix+"numIterations")!=null)
		this.numIterations=Integer.parseInt(properties.getProperty(prefix+"numIterations"));

		for (int i=0;i<this.ampsSeconds.length;i++) if (properties.getProperty(prefix+"ampsSeconds_"+i)!=null)
		this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i));
		if (properties.getProperty(prefix+"reportTemperature")!=null)
		this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature"));
		}
		public boolean getLensSerial(){
		while (true) { // loop until OK-ed
		@@ -1628,13 +1633,23 @@ public class LensAdjustment {
		gd.addNumericField("Expand during extrapolation (relative to the average grid period)", this.flatFieldExpand, 3);
		gd.addNumericField("Threshold RMS to exit LMA", this.thresholdFinish, 7,9,"pix");
		gd.addNumericField("Maximal number of LMA iterations per series",this.numIterations, 0);
		gd.addMessage("-----");
		gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");

		if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C");

		if (!Double.isNaN(this.result_lastKT)) gd.addMessage("Temperature focal distance coefficient measured in last run is "+this.result_lastKT+"microns/C");
		if (!Double.isNaN(this.result_lastFD20)) gd.addMessage("Focal distance @20C measured at last run is "+this.result_lastFD20+" microns");
		if (!Double.isNaN(this.result_lastKT) && !Double.isNaN(this.result_lastFD20)){
		gd.addMessage("Focal distance @"+this.reportTemperature+"C measured at last run is "+
		(this.result_lastFD20+(this.reportTemperature-20.0)*this.result_lastKT)+" microns");
		}
		if (!Double.isNaN(this.result_allHistoryKT)) gd.addMessage("Temperature focal distance coefficient calculated from all measurements is "+this.result_allHistoryKT+" microns");
		if (!Double.isNaN(this.result_allHistoryFD20)) gd.addMessage("Focal distance @20C calculated from all measurements is "+this.result_allHistoryFD20+" microns");
		if (!Double.isNaN(this.result_allHistoryKT) && !Double.isNaN(this.result_allHistoryFD20)){
		gd.addMessage("Focal distance @"+this.reportTemperature+"C calculated from all measurements is "+
		(this.result_allHistoryFD20+(this.reportTemperature-20.0)*this.result_allHistoryKT)+" microns");
		}
		if (!Double.isNaN(this.result_fDistance)) gd.addMessage("Focal distance is "+this.result_fDistance+" microns");
		if (!Double.isNaN(this.result_tiltX)) gd.addMessage("Horizontal angular/tangential asymmetry "+this.result_tiltX);
		if (!Double.isNaN(this.result_tiltY)) gd.addMessage("Vertical angular/tangential asymmetry "+this.result_tiltY);
		@@ -1650,6 +1665,7 @@ public class LensAdjustment {
		if (!Double.isNaN(this.result_FocalLength)) gd.addMessage("Lens focal length "+this.result_FocalLength+" mm");
		gd.addMessage("Cumulative currents that ran through UV LEDs:");
		for (int i=0;i<this.ampsSeconds.length;i++) gd.addMessage("UV LED "+(i+1)+":"+IJ.d2s(this.ampsSeconds[i],3)+" coulombs (amp-seconds)");

		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		@@ -1803,6 +1819,7 @@ public class LensAdjustment {
		this.flatFieldExpand= gd.getNextNumber();
		this.thresholdFinish= gd.getNextNumber();
		this.numIterations= (int) gd.getNextNumber();
		this.reportTemperature= gd.getNextNumber();
		return true;
		}
		/* ======================================================================== */

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