Adding support for a dual-quad camera for CNN ground truth

src/main/java/CorrectionColorProc.java

@@ -521,6 +521,7 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 
 
     public static class ColorGainsParameters {
+    	public static final String AUX_PREFIX = "AUX-";
     	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,
@@ -548,7 +549,7 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
     			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) {
         		int numChannels=Integer.parseInt(properties.getProperty(prefix+"channels"));
         		this.gain=       new double[numChannels];
@@ -559,7 +560,9 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
         			this.balanceRed[i]= Double.parseDouble(properties.getProperty(prefix+"balanceRed_"+i));
         			this.balanceBlue[i]=Double.parseDouble(properties.getProperty(prefix+"balanceBlue_"+i));
         		}
+        		return true;
     		}
+    		return false;
     	}
 
     	public void modifyNumChannels(int numChannels){
@@ -599,6 +602,43 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
     		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/EyesisCorrections.java

@@ -25,6 +25,11 @@
 **
 */
 
+import java.io.IOException;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import javax.swing.SwingUtilities;
+
 import ij.CompositeImage;
 import ij.IJ;
 import ij.ImagePlus;
@@ -35,12 +40,6 @@ import ij.io.FileSaver;
 import ij.process.ColorProcessor;
 import ij.process.FloatProcessor;
 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.ServiceException;
 import loci.formats.FormatException;
@@ -84,14 +83,43 @@ public class EyesisCorrections {
 	}
 
 	public int getNumChannels(){return (this.usedChannels!=null)?this.usedChannels.length:0;}
+
+
 	// TODO: preserve some data when re-running with new source files
+	// FIXME: Make forgiving alien files
 	public void initSensorFiles(int debugLevel){
+		initSensorFiles(debugLevel, false);
+	}
+	public void initSensorFiles(int debugLevel, boolean missing_ok){
 		this.sharpKernelPaths=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);
 		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
 		this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());
-// TODO: Combine with additional channel map to be able to select single image (of all 3) 		
+		// 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);
 		}
@@ -108,8 +136,8 @@ public class EyesisCorrections {
 		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 			testFF(correctionsParameters.sourcePaths[0]);
 		}
-		
 	}
+
 	public double [] calcReferenceExposures(int debugLevel){
 		String [] paths=this.correctionsParameters.getSourcePaths();
 		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.imageNoiseGains[chn]==null) ||
-						(!this.sharpKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||
-						(!this.smoothKernelPaths[chn].equals((String) this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){
+						(!this.sharpKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("sharpKernelPath"))) ||
+						(!this.smoothKernelPaths[chn].equals(this.imageNoiseGains[chn].getProperty("smoothKernelPath")))){
 
 					ImagePlus imp_kernel_sharp=new ImagePlus(this.sharpKernelPaths[chn]);
 					  if (imp_kernel_sharp.getStackSize()<3) {
@@ -486,6 +514,10 @@ public class EyesisCorrections {
 	}
 
 	boolean [] usedChannels(String [] paths){
+		return usedChannels(paths, false);
+	}
+
+	boolean [] usedChannels(String [] paths, boolean missing_ok){
 		if (paths==null) paths=new String[0];
 		int numChannels=this.pixelMapping.getNumChannels();
 		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;
 			} else {
 				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;
 			}
 		}
@@ -1795,6 +1829,7 @@ public class EyesisCorrections {
 //			  System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");
 			  for (int ithread = 0; ithread < threads.length; ithread++) {
 				  threads[ithread] = new Thread() {
+					  @Override
 					public void run() {
 						  float [] pixels=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();
 							  if (numFinished % (numberOfKernels/100+1) == 0) {
 								  SwingUtilities.invokeLater(new Runnable() {
+									  @Override
 									public void run() {
 										  IJ.showProgress(numFinished,numberOfKernels);
 									  }
@@ -2210,6 +2246,7 @@ public class EyesisCorrections {
 		  final long startTime = System.nanoTime();
 		  for (int ithread = 0; ithread < threads.length; ithread++) {
 			  threads[ithread] = new Thread() {
+				  @Override
 				public void run() {
 					  DoubleGaussianBlur gb=null;
 					  if (blurSigma>0)	 gb=new DoubleGaussianBlur();

src/main/java/PixelMapping.java

@@ -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
     //removeUnusedSensorData xshould be off!
     public int [] channelsForSubCamera(int subCamera){
+    	if (subCamera < 0) {
+    		return null;
+    	}
 		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);
 //    	ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>();
     	ArrayList<Point> cam_port = new ArrayList<Point>();
@@ -172,11 +175,11 @@ public class PixelMapping {
 			}
 		});
 		// 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) {
-			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;
 		}
+		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;
     	int numChannels=0;
     	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {