Adding support for a dual-quad camera for CNN ground truth (f19a4557) · Commits · Elphel / imagej-elphel

src/main/java/CorrectionColorProc.java

+41 −1

Original line number	Original line	Diff line number	Diff line
	@@ -521,6 +521,7 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg


	public static class ColorGainsParameters {		public static class ColorGainsParameters {
			public static final String AUX_PREFIX = "AUX-";
	public double[] gain={		public double[] gain={
	1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,		1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
	1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,		1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
	@@ -548,7 +549,7 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
	properties.setProperty(prefix+"balanceBlue_"+i,this.balanceBlue[i]+"");		properties.setProperty(prefix+"balanceBlue_"+i,this.balanceBlue[i]+"");
	}		}
	}		}
	public void getProperties(String prefix,Properties properties){		public boolean getProperties(String prefix,Properties properties){
	if (properties.getProperty(prefix+"channels")!=null) {		if (properties.getProperty(prefix+"channels")!=null) {
	int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));		int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));
	this.gain= new double[numChannels];		this.gain= new double[numChannels];
	@@ -559,7 +560,9 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
	this.balanceRed[i]= Double.parseDouble(properties.getProperty(prefix+"balanceRed_"+i));		this.balanceRed[i]= Double.parseDouble(properties.getProperty(prefix+"balanceRed_"+i));
	this.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));		this.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));
	}		}
			return true;
	}		}
			return false;
	}		}

	public void modifyNumChannels(int numChannels){		public void modifyNumChannels(int numChannels){
	@@ -599,6 +602,43 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
	return true;		return true;
	}		}

			public boolean showDialog(ColorGainsParameters aux) {

			GenericJTabbedDialog gd = new GenericJTabbedDialog("Individual channels colors/gains", 600,1000);
			if (aux != null) gd.addTab("Main camera");
			for (int i =0; i<this.gain.length;i++){
			gd.addMessage(String.format("=== CHANNEL %02d ===",i));
			gd.addNumericField(String.format("%02d: Gain (brightness)",i), this.gain[i], 3);
			gd.addNumericField(String.format("%02d: Balance Red/Green",i), this.balanceRed[i], 3);
			gd.addNumericField(String.format("%02d: Balance Blue/Green",i), this.balanceBlue[i], 3);
			}
			if (aux != null) {
			gd.addTab("Auxiliary camera");
			for (int i =0; i<this.gain.length;i++){
			gd.addMessage(String.format("=== CHANNEL %02d ===",i));
			gd.addNumericField(String.format("%02d: Gain (brightness)",i), aux.gain[i], 3);
			gd.addNumericField(String.format("%02d: Balance Red/Green",i), aux.balanceRed[i], 3);
			gd.addNumericField(String.format("%02d: Balance Blue/Green",i), aux.balanceBlue[i], 3);
			}

			}
			gd.showDialog();
			if (gd.wasCanceled()) return false;
			for (int i =0; i<this.gain.length;i++){
			this.gain[i]= gd.getNextNumber();
			this.balanceRed[i]= gd.getNextNumber();
			this.balanceBlue[i]=gd.getNextNumber();
			}
			if (aux != null) {
			for (int i =0; i<this.gain.length;i++){
			aux.gain[i]= gd.getNextNumber();
			aux.balanceRed[i]= gd.getNextNumber();
			aux.balanceBlue[i]=gd.getNextNumber();
			}
			}
			return true;
			}


	}		}

src/main/java/EyesisCorrectionParameters.java

+286 −286

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/EyesisCorrections.java

+197 −160

Original line number	Original line	Diff line number	Diff line
	@@ -25,6 +25,11 @@
	**		**
	*/		*/

			import java.io.IOException;
			import java.util.concurrent.atomic.AtomicInteger;

			import javax.swing.SwingUtilities;

	import ij.CompositeImage;		import ij.CompositeImage;
	import ij.IJ;		import ij.IJ;
	import ij.ImagePlus;		import ij.ImagePlus;
	@@ -35,12 +40,6 @@ import ij.io.FileSaver;
	import ij.process.ColorProcessor;		import ij.process.ColorProcessor;
	import ij.process.FloatProcessor;		import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;		import ij.process.ImageProcessor;

	import java.io.IOException;
	import java.util.concurrent.atomic.AtomicInteger;

	import javax.swing.SwingUtilities;

	import loci.common.services.DependencyException;		import loci.common.services.DependencyException;
	import loci.common.services.ServiceException;		import loci.common.services.ServiceException;
	import loci.formats.FormatException;		import loci.formats.FormatException;
	@@ -84,10 +83,39 @@ public class EyesisCorrections {
	}		}

	public int getNumChannels(){return (this.usedChannels!=null)?this.usedChannels.length:0;}		public int getNumChannels(){return (this.usedChannels!=null)?this.usedChannels.length:0;}


	// TODO: preserve some data when re-running with new source files		// TODO: preserve some data when re-running with new source files
			// FIXME: Make forgiving alien files
	public void initSensorFiles(int debugLevel){		public void initSensorFiles(int debugLevel){
			initSensorFiles(debugLevel, false);
			}
			public void initSensorFiles(int debugLevel, boolean missing_ok){
	this.sharpKernelPaths=null;		this.sharpKernelPaths=null;
	this.smoothKernelPaths=null;		this.smoothKernelPaths=null;
			String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
			this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
			this.usedChannels= usedChannels(correctionsParameters.getSourcePaths(),missing_ok);
			// TODO: Combine with additional channel map to be able to select single image (of all 3)
			if (correctionsParameters.removeUnusedSensorData){
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
			}
			int numUsedChannels=0;
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) numUsedChannels++;
			if (this.debugLevel>0) {
			String sChannels="";
			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) sChannels+=" "+nChn;
			System.out.println ("Number of used channels: "+numUsedChannels+" ("+sChannels+" )");
			}
			createChannelVignetting();
			if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
			testFF(correctionsParameters.sourcePaths[0]);
			}
			}

			public void initSensorFilesAux(int debugLevel){
			// this.sharpKernelPaths=null;
			// this.smoothKernelPaths=null;
	String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
	this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
	this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());		this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());
	@@ -108,8 +136,8 @@ public class EyesisCorrections {
	if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
	testFF(correctionsParameters.sourcePaths[0]);		testFF(correctionsParameters.sourcePaths[0]);
	}		}

	}		}

	public double [] calcReferenceExposures(int debugLevel){		public double [] calcReferenceExposures(int debugLevel){
	String [] paths=this.correctionsParameters.getSourcePaths();		String [] paths=this.correctionsParameters.getSourcePaths();
	double [] exposures=new double [paths.length];		double [] exposures=new double [paths.length];
	@@ -329,8 +357,8 @@ public class EyesisCorrections {
	if (this.usedChannels[chn] && (this.sharpKernelPaths[chn]!=null) && (!nonlinParameters.useDiffNoiseGains \|\|(this.smoothKernelPaths[chn]!=null))){		if (this.usedChannels[chn] && (this.sharpKernelPaths[chn]!=null) && (!nonlinParameters.useDiffNoiseGains \|\|(this.smoothKernelPaths[chn]!=null))){
	if (		if (
	(this.imageNoiseGains[chn]==null) \|\|		(this.imageNoiseGains[chn]==null) \|\|
	(!this.sharpKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) \|\|		(!this.sharpKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) \|\|
	(!this.smoothKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){		(!this.smoothKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){

	ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);		ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);
	if (imp_kernel_sharp.getStackSize()<3) {		if (imp_kernel_sharp.getStackSize()<3) {
	@@ -486,6 +514,10 @@ public class EyesisCorrections {
	}		}

	boolean [] usedChannels(String [] paths){		boolean [] usedChannels(String [] paths){
			return usedChannels(paths, false);
			}

			boolean [] usedChannels(String [] paths, boolean missing_ok){
	if (paths==null) paths=new String[0];		if (paths==null) paths=new String[0];
	int numChannels=this.pixelMapping.getNumChannels();		int numChannels=this.pixelMapping.getNumChannels();
	boolean [] usedChannels=new boolean[numChannels];		boolean [] usedChannels=new boolean[numChannels];
	@@ -498,7 +530,9 @@ public class EyesisCorrections {
	if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;		if (channels!=null) for (int j=0;j<channels.length;j++) usedChannels[channels[j]]=true;
	} else {		} else {
	if (!this.pixelMapping.isChannelAvailable(srcChannel)){		if (!this.pixelMapping.isChannelAvailable(srcChannel)){
	if (debugLevel>0) System.out.println("No sensor data for channel "+srcChannel+", needed for source file "+paths[i]);		if ((debugLevel>0) && !missing_ok) {
			System.out.println("No sensor data for channel "+srcChannel+", needed for source file "+paths[i]);
			}
	} else usedChannels[srcChannel] = true;		} else usedChannels[srcChannel] = true;
	}		}
	}		}
	@@ -1795,6 +1829,7 @@ public class EyesisCorrections {
	// System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");		// System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	float [] pixels=null; // will be initialized at first use		float [] pixels=null; // will be initialized at first use
	float [] kernelPixels=null; // will be initialized at first use		float [] kernelPixels=null; // will be initialized at first use
	@@ -1880,6 +1915,7 @@ public class EyesisCorrections {
	final int numFinished=tilesFinishedAtomic.getAndIncrement();		final int numFinished=tilesFinishedAtomic.getAndIncrement();
	if (numFinished % (numberOfKernels/100+1) == 0) {		if (numFinished % (numberOfKernels/100+1) == 0) {
	SwingUtilities.invokeLater(new Runnable() {		SwingUtilities.invokeLater(new Runnable() {
			@Override
	public void run() {		public void run() {
	IJ.showProgress(numFinished,numberOfKernels);		IJ.showProgress(numFinished,numberOfKernels);
	}		}
	@@ -2210,6 +2246,7 @@ public class EyesisCorrections {
	final long startTime = System.nanoTime();		final long startTime = System.nanoTime();
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	DoubleGaussianBlur gb=null;		DoubleGaussianBlur gb=null;
	if (blurSigma>0) gb=new DoubleGaussianBlur();		if (blurSigma>0) gb=new DoubleGaussianBlur();

src/main/java/Eyesis_Correction.java

+1079 −1127

File changed.

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src/main/java/PixelMapping.java

+5 −2

Original line number	Original line	Diff line number	Diff line
	@@ -154,6 +154,9 @@ public class PixelMapping {
	// as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations		// as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations
	//removeUnusedSensorData xshould be off!		//removeUnusedSensorData xshould be off!
	public int [] channelsForSubCamera(int subCamera){		public int [] channelsForSubCamera(int subCamera){
			if (subCamera < 0) {
			return null;
			}
	System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);
	// ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();		// ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();
	ArrayList<Point> cam_port = new ArrayList<Point>();		ArrayList<Point> cam_port = new ArrayList<Point>();
	@@ -172,11 +175,11 @@ public class PixelMapping {
	}		}
	});		});
	// debugging:		// debugging:
	System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
	if (subCamera >= cam_port_arr.length) {		if (subCamera >= cam_port_arr.length) {
	System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);		System.out.println("Error: Subcamera "+subCamera+" > that total number of sensor ports in the system = "+cam_port_arr.length);
	return null;		return null;
	}		}
			System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
	if (this.sensors == null) return null;		if (this.sensors == null) return null;
	int numChannels=0;		int numChannels=0;
	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {		for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {

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